diff --git a/doc/src/Errors_common.txt b/doc/src/Errors_common.txt
index 43d1a85a7bd0ff2772c5dfeb690073d93d50bb10..8f26b22b3a8a8f9b47ea2df5e6b650a318fc795f 100644
--- a/doc/src/Errors_common.txt
+++ b/doc/src/Errors_common.txt
@@ -58,9 +58,9 @@ style", with ... being fix, compute, pair, etc, it means that you
mistyped the style name or that the command is part of an optional
package which was not compiled into your executable. The list of
available styles in your executable can be listed by using "the -h
-command-line argument"_Section_start.html#start_6. The installation
-and compilation of optional packages is explained in the "installation
-instructions"_Section_start.html#start_3.
+command-line swith"_Run_options.html. The installation and
+compilation of optional packages is explained on the "Build
+packages"_Build_packages.html doc page.
For a given command, LAMMPS expects certain arguments in a specified
order. If you mess this up, LAMMPS will often flag the error, but it
diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt
index 03fc25b5618c3b6803c719cdbb5473edad5cbf6a..d279b5e9758c0366169abb962e3d27b9fddaa56e 100644
--- a/doc/src/Errors_messages.txt
+++ b/doc/src/Errors_messages.txt
@@ -7911,8 +7911,8 @@ Atom IDs must be positive integers. :dd
{One or more atom IDs is too big} :dt
The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL
-setting in your Makefile. See Section_start 2.2 of the manual for
-more details. :dd
+setting in your LAMMPS build. See the "Build
+settings"_Build_settings.html doc page for more info. :dd
{One or more atom IDs is zero} :dt
diff --git a/doc/src/Examples.txt b/doc/src/Examples.txt
index 5bd8da2409185873b745cc87b1ae95b5a0b6ac1b..4b6db8a047f64b5ab204750c8bf0a88da9d45140 100644
--- a/doc/src/Examples.txt
+++ b/doc/src/Examples.txt
@@ -112,10 +112,10 @@ web site.
If you uncomment the "dump image"_dump_image.html line(s) in the input
script a series of JPG images will be produced by the run (assuming
-you built LAMMPS with JPG support; see "Section
-2.2"_Section_start.html#start_2 for details). These can be viewed
-individually or turned into a movie or animated by tools like
-ImageMagick or QuickTime or various Windows-based tools. See the
+you built LAMMPS with JPG support; see the
+"Build_settings"_Build_settings.html doc page for details). These can
+be viewed individually or turned into a movie or animated by tools
+like ImageMagick or QuickTime or various Windows-based tools. See the
"dump image"_dump_image.html doc page for more details. E.g. this
Imagemagick command would create a GIF file suitable for viewing in a
browser.
diff --git a/doc/src/Howto.txt b/doc/src/Howto.txt
index d9a60d1ef4b8e8365683794e5bfc96d5fc325b32..6e434552e7ef4a13d9a34dc9d24a7f592f1b7a3b 100644
--- a/doc/src/Howto.txt
+++ b/doc/src/Howto.txt
@@ -84,7 +84,7 @@ END_RST -->
"Using GitHub with LAMMPS"_Howto_github.html
"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html
-"Using LAMMPS with bash on Windows"_Howto_bash.html
+"Using LAMMPS with bash on Windows"_Howto_bash.html :all(b)
"Restart a simulation"_Howto_restart.html
"Visualize LAMMPS snapshots"_Howto_viz.html
@@ -121,8 +121,8 @@ END_RST -->
"Polarizable models"_Howto_polarizable.html
"Adiabatic core/shell model"_Howto_coreshell.html
"Drude induced dipoles"_Howto_drude.html
-"Drude induced dipoles (extended)"_Howto_drude2.html :all(b)
+"Drude induced dipoles (extended)"_Howto_drude2.html
"Manifolds (surfaces)"_Howto_manifold.html
-"Magnetic spins"_Howto_spins.html
+"Magnetic spins"_Howto_spins.html :all(b)
<!-- END_HTML_ONLY -->
diff --git a/doc/src/Howto_couple.txt b/doc/src/Howto_couple.txt
index 38595a9d1641ddb869cf5606ce003c2189690813..4c0f72a806e5982759b4f0909f93e22adb2b825f 100644
--- a/doc/src/Howto_couple.txt
+++ b/doc/src/Howto_couple.txt
@@ -77,17 +77,16 @@ strain induced across grain boundaries :l
:link(quest,http://dft.sandia.gov/Quest)
:link(spparks,http://www.sandia.gov/~sjplimp/spparks.html)
-"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
-example, from C++ you could create one (or more) "instances" of
-LAMMPS, pass it an input script to process, or execute individual
-commands, all by invoking the correct class methods in LAMMPS. From C
-or Fortran you can make function calls to do the same things. See the
-"Python"_Python.html doc pages for a description of the Python wrapper
-provided with LAMMPS that operates through the LAMMPS library
-interface.
+The "Build basics"_Build_basics.html doc page 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 example, from C++ you could
+create one (or more) "instances" of LAMMPS, pass it an input script to
+process, or execute individual commands, all by invoking the correct
+class methods in LAMMPS. From C or Fortran you can make function
+calls to do the same things. See the "Python"_Python.html doc pages
+for a description of the Python wrapper provided with LAMMPS that
+operates through the LAMMPS library interface.
The files src/library.cpp and library.h contain the C-style interface
to LAMMPS. See the "Howto library"_Howto_library.html doc page for a
diff --git a/doc/src/Howto_library.txt b/doc/src/Howto_library.txt
index 0d4852fbf247adee92be56045d7b98af7e5a3542..8e99182f872cc15f0a6f99957dff10f9063dc286 100644
--- a/doc/src/Howto_library.txt
+++ b/doc/src/Howto_library.txt
@@ -9,10 +9,10 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Library interface to LAMMPS :h3
-As described in "Section 2.5"_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"_Howto_couple.html with other codes, or driven
-through a "Python interface"_Python.html.
+As described on the "Build basics"_Build_basics.html doc page, LAMMPS
+can be built as a library, so that it can be called by another code,
+used in a "coupled manner"_Howto_couple.html with other codes, or
+driven through a "Python interface"_Python.html.
All of these methodologies use a C-style interface to LAMMPS that is
provided in the files src/library.cpp and src/library.h. The
@@ -51,12 +51,11 @@ void lammps_free(void *) :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
-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
-lammps_open() function can be called multiple times, to create
-multiple instances of LAMMPS.
+arguments"_Run_options.html 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 lammps_open() function can be
+called multiple times, to create multiple instances of LAMMPS.
LAMMPS will run on the set of processors in the communicator. This
means the calling code can run LAMMPS on all or a subset of
diff --git a/doc/src/Howto_multiple.txt b/doc/src/Howto_multiple.txt
index edcb8196cf015543db85b6ab83411d4d13373758..9ad872fedc1890c9fc166b884a3585f56dd3a329 100644
--- a/doc/src/Howto_multiple.txt
+++ b/doc/src/Howto_multiple.txt
@@ -80,8 +80,7 @@ jump in.polymer :pre
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.
+the "-partition command-line switch"_Run_options.html.
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
diff --git a/doc/src/Howto_replica.txt b/doc/src/Howto_replica.txt
index 1b44fe53748d4dc1adf35aebe333b97bea4c33ac..2135e52e0e360c7b62f052b58763262d6d0d651e 100644
--- a/doc/src/Howto_replica.txt
+++ b/doc/src/Howto_replica.txt
@@ -29,29 +29,28 @@ runs different replicas at a series of temperature to facilitate
rare-event sampling.
These commands can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc page for more
+info.
PIMD runs different replicas whose individual particles are coupled
together by springs to model a system or ring-polymers.
This commands can only be used if LAMMPS was built with the USER-MISC
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc page for more
+info.
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
-partitions, which in this context are the same as replicas. E.g.
-these commands:
+switch"_Run_options.html to launch LAMMPS on multiple partitions,
+which in this context are the same as replicas. E.g. these commands:
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
-the input script which is required when running in multi-replica mode.
+of the "-in command-line switch"_Run_options.html 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),
you can run on more (virtual) processors than you have physical
diff --git a/doc/src/Howto_restart.txt b/doc/src/Howto_restart.txt
index b211775479bfc367301a408ef15e45f8bd46cca0..bc67daa78e3b9a3c2e866b8d9a748753300e6ffe 100644
--- a/doc/src/Howto_restart.txt
+++ b/doc/src/Howto_restart.txt
@@ -16,8 +16,8 @@ restart files can be saved to disk using the "restart"_restart.html
command. At a later time, these binary files can be read via a
"read_restart"_read_restart.html command in a new script. Or they can
be converted to text data files using the "-r command-line
-switch"_Section_start.html#start_6 and read by a
-"read_data"_read_data.html command in a new script.
+switch"_Run_options.html and read by a "read_data"_read_data.html
+command in a new script.
Here we give examples of 2 scripts that read either a binary restart
file or a converted data file and then issue a new run command to
diff --git a/doc/src/Howto_temperature.txt b/doc/src/Howto_temperature.txt
index 7a318250cffa956692693e601638e749cc4d6df4..8a9e262da1b071abde5ab8b6957addba8444b718 100644
--- a/doc/src/Howto_temperature.txt
+++ b/doc/src/Howto_temperature.txt
@@ -17,7 +17,10 @@ aggregate motion of particles) and its thermal velocity. The sum of
the two is the particle's total velocity, but the latter is often what
is wanted to compute a temperature.
-LAMMPS has several options for computing temperatures, any of which can be used in "thermostatting"_Howto_thermostat.html and "barostatting"_Howto_barostat.html. These "compute commands"_compute.html calculate temperature:
+LAMMPS has several options for computing temperatures, any of which
+can be used in "thermostatting"_Howto_thermostat.html and
+"barostatting"_Howto_barostat.html. These "compute
+commands"_compute.html calculate temperature:
"compute temp"_compute_temp.html
"compute temp/sphere"_compute_temp_sphere.html
@@ -35,6 +38,6 @@ velocities) that are removed when computing the thermal temperature.
temp/asphere"_compute_temp_asphere.html compute kinetic energy for
finite-size particles that includes rotational degrees of freedom.
They both allow for velocity biases indirectly, via an optional extra
-argument which is another temperature compute that subtracts a velocity bias.
-This allows the translational velocity of spherical or aspherical
-particles to be adjusted in prescribed ways.
+argument which is another temperature compute that subtracts a
+velocity bias. This allows the translational velocity of spherical or
+aspherical particles to be adjusted in prescribed ways.
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index a5e8b63640be29f7212d66e1d6b42ceb66747a41..a3747465cd6b391bb7fb996bd9393a71aa826b4a 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -72,7 +72,9 @@ every LAMMPS command.
:includehidden:
Intro
- Section_start
+ Install
+ Build
+ Run
Commands
Packages
Speed
@@ -107,15 +109,9 @@ END_RST -->
<!-- HTML_ONLY -->
"Introduction"_Intro.html :olb,l
-"Getting started"_Section_start.html :l
- 2.1 "What's in the LAMMPS distribution"_start_1 :ulb,b
- 2.2 "Making LAMMPS"_start_2 :b
- 2.3 "Making LAMMPS with optional packages"_start_3 :b
- 2.4 "Building LAMMPS as a library"_start_4 :b
- 2.5 "Running LAMMPS"_start_5 :b
- 2.6 "Command-line options"_start_6 :b
- 2.7 "Screen output"_start_7 :b
- 2.8 "Tips for users of previous versions"_start_8 :ule,b
+"Install LAMMPS"_Install.html :l
+"Build LAMMPS"_Build.html :l
+"Run LAMMPS"_Run.html :l
"Commands"_Commands.html :l
"Optional packages"_Packages.html :l
"Accelerate performance"_Speed.html :l
@@ -127,15 +123,6 @@ END_RST -->
"Errors"_Errors.html :l
:ole
-:link(start_1,Section_start.html#start_1)
-:link(start_2,Section_start.html#start_2)
-:link(start_3,Section_start.html#start_3)
-:link(start_4,Section_start.html#start_4)
-:link(start_5,Section_start.html#start_5)
-:link(start_6,Section_start.html#start_6)
-:link(start_7,Section_start.html#start_7)
-:link(start_8,Section_start.html#start_8)
-
<!-- END_HTML_ONLY -->
</BODY>
diff --git a/doc/src/Modify_contribute.txt b/doc/src/Modify_contribute.txt
index ef9fe6a7174eed7d41a74908b49b21e8ecfa6f6d..8cbea8bb317f912a500857886b50a6f8a42e3c4d 100644
--- a/doc/src/Modify_contribute.txt
+++ b/doc/src/Modify_contribute.txt
@@ -44,13 +44,14 @@ compression, as this works well on all platforms.
If the new features/files are broadly useful we may add them as core
files to LAMMPS or as part of a "standard
-package"_Section_start.html#start_3. Else we will add them as a
-user-contributed file or package. Examples of user packages are in
-src sub-directories that start with USER. The USER-MISC package is
-simply a collection of (mostly) unrelated single files, which is the
-simplest way to have your contribution quickly added to the LAMMPS
-distribution. You can see a list of the both standard and user
-packages by typing "make package" in the LAMMPS src directory.
+package"_Packages_standard.html. Else we will add them as a
+user-contributed file or "user package"_Packages_user.html. Examples
+of user packages are in src sub-directories that start with USER. The
+USER-MISC package is simply a collection of (mostly) unrelated single
+files, which is the simplest way to have your contribution quickly
+added to the LAMMPS distribution. All the standard and user packages
+are listed and described on the "Packages
+details"_Packages_details.html doc page.
Note that by providing us files to release, you are agreeing to make
them open-source, i.e. we can release them under the terms of the GPL,
diff --git a/doc/src/Packages.txt b/doc/src/Packages.txt
index a7f45a99b7fa8f3d33e3c8d2e771f069139a0249..e48c947be3c5c4d436f250fb4106cbc1c26953a3 100644
--- a/doc/src/Packages.txt
+++ b/doc/src/Packages.txt
@@ -13,12 +13,12 @@ Optional packages :h2
This section gives an overview of the optional packages that extend
LAMMPS functionality. Packages are groups of files that enable a
specific set of features. For example, force fields for molecular
-systems or rigid-body constraint are in packages. You can see the
+systems or rigid-body constraints are in packages. You can see the
list of all packages and "make" commands to manage them by typing
"make package" from within the src directory of the LAMMPS
-distribution. "Section 2.3"_Section_start.html#start_3 gives general
-info on how to install and un-install packages as part of the LAMMPS
-build process.
+distribution. The "Build package"_Build_package.html doc page gives
+general info on how to install and un-install packages as part of the
+LAMMPS build process.
<!-- RST
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index eb92fe4dc4c27506cf41b250f7a3dce49e159941..1dbde273b46bdc8ca8ba28a966af7c3a1613c612 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -17,6 +17,13 @@ library it requires. It also gives links to documentation, example
scripts, and pictures/movies (if available) that illustrate use of the
package.
+The majority of packages can be included in a LAMMPS build with a
+single setting (-D PGK_NAME for CMake) or command ("make yes-name" for
+make). See the "Build package"_Build_package.html doc page for more
+info. A few packages may require additional steps; this is indicated
+in the descriptions below. The "Build extras"_Build_extras.html doc
+page gives those details.
+
NOTE: To see the complete list of commands a package adds to LAMMPS,
you can examine the files in its src directory, e.g. "ls
src/GRANULAR". Files with names that start with fix, compute, atom,
@@ -102,14 +109,6 @@ ASPHERE package :link(ASPHERE),h4
Computes, time-integration fixes, and pair styles for aspherical
particle models including ellipsoids, 2d lines, and 3d triangles.
-[Install or un-install:]
-
-make yes-asphere
-make machine :pre
-
-make no-asphere
-make machine :pre
-
[Supporting info:]
src/ASPHERE: filenames -> commands
@@ -134,14 +133,6 @@ time-integration fixes, pair styles, as well as the body styles
themselves. See the "Howto body"_Howto_body.html doc page for an
overview.
-[Install or un-install:]
-
-make yes-body
-make machine :pre
-
-make no-body
-make machine :pre
-
[Supporting info:]
src/BODY filenames -> commands
@@ -160,14 +151,6 @@ CLASS2 package :link(CLASS2),h4
Bond, angle, dihedral, improper, and pair styles for the COMPASS
CLASS2 molecular force field.
-[Install or un-install:]
-
-make yes-class2
-make machine :pre
-
-make no-class2
-make machine :pre
-
[Supporting info:]
src/CLASS2: filenames -> commands
@@ -192,14 +175,6 @@ simplified approximation to Stokesian dynamics.
which were created by Amit Kumar and Michael Bybee from Jonathan
Higdon's group at UIUC.
-[Install or un-install:]
-
-make yes-colloid
-make machine :pre
-
-make no-colloid
-make machine :pre
-
[Supporting info:]
src/COLLOID: filenames -> commands
@@ -226,19 +201,11 @@ available on your system.
[Author:] Axel Kohlmeyer (Temple U).
-[Install or un-install:]
-
-Note that building with this package assumes you have the zlib
-compression library available on your system. The LAMMPS build uses
-the settings in the lib/compress/Makefile.lammps file in the
-compile/link process. You should only need to edit this file if the
-LAMMPS build fails on your system.
+[Install:]
-make yes-compress
-make machine :pre
-
-make no-compress
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -266,14 +233,6 @@ this package.
[Author:] Hendrik Heenen (Technical U of Munich).
-[Install or un-install:]
-
-make yes-coreshell
-make machine :pre
-
-make no-coreshell
-make machine :pre
-
[Supporting info:]
src/CORESHELL: filenames -> commands
@@ -294,14 +253,6 @@ DIPOLE package :link(DIPOLE),h4
An atom style and several pair styles for point dipole models with
short-range or long-range interactions.
-[Install or un-install:]
-
-make yes-dipole
-make machine :pre
-
-make no-dipole
-make machine :pre
-
[Supporting info:]
src/DIPOLE: filenames -> commands
@@ -325,66 +276,17 @@ and only the CUDA versions are regularly tested. The "Speed
gpu"_Speed_gpu.html doc page gives details of what hardware and GPU
software is required on your system, and details on how to build and
use this package. Its styles can be invoked at run time via the "-sf
-gpu" or "-suffix gpu" "command-line
-switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS
-package, which has GPU-enabled styles.
+gpu" or "-suffix gpu" "command-line switches"_Run_options.html. See
+also the "KOKKOS"_#KOKKOS package, which has GPU-enabled styles.
[Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
(Northwestern U) while at ORNL.
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first build the GPU
-library in lib/gpu from a set of provided C and CUDA files. You can
-do this manually if you prefer; follow the instructions in
-lib/gpu/README. Please note, that the GPU library uses MPI calls, so
-you have to make certain to use the same MPI library (or the STUBS
-library) settings as the main LAMMPS code. That same applies to the
--DLAMMPS_BIGBIG, -DLAMMPS_SMALLBIG, or -DLAMMPS_SMALLSMALL define.
-
-You can also do it in one step from the lammps/src
-dir, using a command like these, which simply invoke the
-lib/gpu/Install.py script with the specified args:
-
-make lib-gpu # print help message
-make lib-gpu args="-b" # build GPU library with default Makefile.linux
-make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision
-make lib-gpu args="-m mpi -p mixed -b" # build GPU library with mixed precision using settings in Makefile.mpi :pre
+[Install:]
-Note that this procedure through the '-m machine' flag starts with one of
-the existing Makefile.machine files in lib/gpu. For your convenience,
-machine makefiles for "mpi" and "serial" are provided, which have the
-same settings as the corresponding machine makefiles in the main LAMMPS
-source folder. In addition you can alter 4 important settings in that
-Makefile, via the -h, -a, -p, -e switches, and also save a copy of the
-new Makefile, if desired:
-
-CUDA_HOME = where NVIDIA CUDA software is installed on your system
-CUDA_ARCH = what GPU hardware you have (see help message for details)
-CUDA_PRECISION = precision (double, mixed, single)
-EXTRAMAKE = which Makefile.lammps.* file to copy to Makefile.lammps :ul
-
-If the library build is successful, at least 3 files should be created:
-lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, and lib/gpu/Makefile.lammps.
-The latter has settings that enable LAMMPS to link with CUDA libraries.
-If the settings in Makefile.lammps for your machine are not correct,
-the LAMMPS build will fail, and lib/gpu/Makefile.lammps may need to
-be edited.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-gpu
-make machine :pre
-
-make no-gpu
-make machine :pre
-
-NOTE: If you re-build the GPU library in lib/gpu, you should always
-un-install the GPU package, then re-install it and re-build LAMMPS.
-This is because the compilation of files in the GPU package use the
-library settings from the lib/gpu/Makefile.machine used to build the
-GPU library.
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -393,8 +295,8 @@ src/GPU/README
lib/gpu/README
"Speed packages"_Speed_packages.html
"Speed gpu"_Speed_gpu.html.html
-"Section 2.6 -sf gpu"_Section_start.html#start_6
-"Section 2.6 -pk gpu"_Section_start.html#start_6
+"Section 2.6 -sf gpu"_Run_options.html
+"Section 2.6 -pk gpu"_Run_options.html
"package gpu"_package.html
"Commands all"_Commands_all.html pages (pair,kspace) for styles followed by (g)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@@ -409,14 +311,6 @@ Pair styles and fixes for finite-size granular particles, which
interact with each other and boundaries via frictional and dissipative
potentials.
-[Install or un-install:]
-
-make yes-granular
-make machine :pre
-
-make no-granular
-make machine :pre
-
[Supporting info:]
src/GRANULAR: filenames -> commands
@@ -456,48 +350,11 @@ API which the "pair_style kim"_pair_kim.html command uses. He
developed the pair style in collaboration with Valeriu Smirichinski (U
Minnesota).
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first download and
-build the KIM library and include the KIM models that you want to
-use. You can do this manually if you prefer; follow the instructions
-in lib/kim/README. You can also do it in one step from the lammps/src
-dir, using a command like these, which simply invoke the
-lib/kim/Install.py script with the specified args.
-
-make lib-kim # print help message
-make lib-kim args="-b " # (re-)install KIM API lib with only example models
-make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model
-make lib-kim args="-b -a everything" # install KIM API lib with all models
-make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver
-make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location
-make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
-
-Note that in LAMMPS lingo, a KIM model driver is a pair style
-(e.g. EAM or Tersoff). A KIM model is a pair style for a particular
-element or alloy and set of parameters, e.g. EAM for Cu with a
-specific EAM potential file. Also note that installing the KIM API
-library with all its models, may take around 30 min to build. Of
-course you only need to do that once.
-
-See the list of KIM model drivers here:
-https://openkim.org/kim-items/model-drivers/alphabetical
-
-See the list of all KIM models here:
-https://openkim.org/kim-items/models/by-model-drivers
-
-See the list of example KIM models included by default here:
-https://openkim.org/kim-api on the "What is in the KIM API source
-package?" page.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
+[Install:]
-make yes-kim
-make machine :pre
-
-make no-kim
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -521,9 +378,9 @@ style name. The "Speed kokkos"_Speed_kokkos.html doc page gives
details of what hardware and software is required on your system, and
how to build and use this package. Its styles can be invoked at run
time via the "-sf kk" or "-suffix kk" "command-line
-switches"_Section_start.html#start_6. Also see the "GPU"_#GPU,
-"OPT"_#OPT, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP
-packages, which have styles optimized for CPUs, KNLs, and GPUs.
+switches"_Run_options.html. Also see the "GPU"_#GPU, "OPT"_#OPT,
+"USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which
+have styles optimized for CPUs, KNLs, and GPUs.
You must have a C++11 compatible compiler to use this package.
@@ -534,53 +391,11 @@ which was developed by Carter Edwards, Christian Trott, and others at
Sandia, and which is included in the LAMMPS distribution in
lib/kokkos.
-[Install or un-install:]
-
-For the KOKKOS package, you have 3 choices when building. You can
-build with either CPU or KNL or GPU support. Each choice requires
-additional settings in your Makefile.machine for the KOKKOS_DEVICES
-and KOKKOS_ARCH settings. See the src/MAKE/OPTIONS/Makefile.kokkos*
-files for examples.
-
-For multicore CPUs using OpenMP:
-
-KOKKOS_DEVICES = OpenMP
-KOKKOS_ARCH = HSW # HSW = Haswell, SNB = SandyBridge, BDW = Broadwell, etc :pre
-
-For Intel KNLs using OpenMP:
-
-KOKKOS_DEVICES = OpenMP
-KOKKOS_ARCH = KNL :pre
-
-For NVIDIA GPUs using CUDA:
+[Install:]
-KOKKOS_DEVICES = Cuda
-KOKKOS_ARCH = Pascal60,Power8 # P100 hosted by an IBM Power8, etc
-KOKKOS_ARCH = Kepler37,Power8 # K80 hosted by an IBM Power8, etc :pre
-
-For GPUs, you also need these 2 lines in your Makefile.machine before
-the CC line is defined, in this case for use with OpenMPI mpicxx. The
-2 lines define a nvcc wrapper compiler, which will use nvcc for
-compiling CUDA files or use a C++ compiler for non-Kokkos, non-CUDA
-files.
-
-KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
-export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
-CC = mpicxx :pre
-
-Once you have an appropriate Makefile.machine, you can
-install/un-install the package and build LAMMPS in the usual manner.
-Note that you cannot build one executable to run on multiple hardware
-targets (CPU or KNL or GPU). You need to build LAMMPS once for each
-hardware target, to produce a separate executable. Also note that we
-do not recommend building with other acceleration packages installed
-(GPU, OPT, USER-INTEL, USER-OMP) when also building with KOKKOS.
-
-make yes-kokkos
-make machine :pre
-
-make no-kokkos
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -589,9 +404,9 @@ src/KOKKOS/README
lib/kokkos/README
"Speed packages"_Speed_packages.html
"Speed kokkos"_Speed_kokkos.html
-"Section 2.6 -k on ..."_Section_start.html#start_6
-"Section 2.6 -sf kk"_Section_start.html#start_6
-"Section 2.6 -pk kokkos"_Section_start.html#start_6
+"Section 2.6 -k on ..."_Run_options.html
+"Section 2.6 -sf kk"_Run_options.html
+"Section 2.6 -pk kokkos"_Run_options.html
"package kokkos"_package.html
"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (k)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@@ -607,20 +422,14 @@ which compute the corresponding short-range pairwise Coulombic
interactions. These include Ewald, particle-particle particle-mesh
(PPPM), and multilevel summation method (MSM) solvers.
-[Install or un-install:]
+[Install:]
Building with this package requires a 1d FFT library be present on
your system for use by the PPPM solvers. This can be the KISS FFT
library provided with LAMMPS, 3rd party libraries like FFTW, or a
-vendor-supplied FFT library. See step 6 of "Section
-2.2.2"_Section_start.html#start_2_2 of the manual for details on how
-to select different FFT options in your machine Makefile.
-
-make yes-kspace
-make machine :pre
-
-make no-kspace
-make machine :pre
+vendor-supplied FFT library. See the "Build
+settings"_Build_settings.html doc page for details on how to select
+different FFT options for your LAMPMS build.
[Supporting info:]
@@ -655,36 +464,11 @@ description is given with the "fix latte"_fix_latte.html command.
itself is developed at Los Alamos National Laboratory by Marc
Cawkwell, Anders Niklasson, and Christian Negre.
-[Install or un-install:]
+[Install:]
-Before building LAMMPS with this package, you must first download and
-build the LATTE library. You can do this manually if you prefer;
-follow the instructions in lib/latte/README. You can also do it in
-one step from the lammps/src dir, using a command like these, which
-simply invokes the lib/latte/Install.py script with the specified
-args:
-
-make lib-latte # print help message
-make lib-latte args="-b" # download and build in lib/latte/LATTE-master
-make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
-make lib-latte args="-b -m gfortran" # download and build in lib/latte and
- # copy Makefile.lammps.gfortran to Makefile.lammps
-:pre
-
-Note that 3 symbolic (soft) links, "includelink" and "liblink" and
-"filelink.o", are created in lib/latte to point into the LATTE home dir.
-When LAMMPS builds in src it will use these links. You should
-also check that the Makefile.lammps file you create is appropriate
-for the compiler you use on your system to build LATTE.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-latte
-make machine :pre
-
-make no-latte
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -704,14 +488,6 @@ MANYBODY package :link(MANYBODY),h4
A variety of manybody and bond-order potentials. These include
(AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials.
-[Install or un-install:]
-
-make yes-manybody
-make machine :pre
-
-make no-manybody
-make machine :pre
-
[Supporting info:]
src/MANYBODY: filenames -> commands
@@ -735,14 +511,6 @@ attributes. These include fixes for creating, breaking, and swapping
bonds, for performing atomic swaps, and performing grand-canonical MC
(GCMC) in conjuction with dynamics.
-[Install or un-install:]
-
-make yes-mc
-make machine :pre
-
-make no-mc
-make machine :pre
-
[Supporting info:]
src/MC: filenames -> commands
@@ -770,37 +538,11 @@ while providing the identical features and USER interface.
[Author:] Greg Wagner (Northwestern U) while at Sandia.
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first build the
-MEAM library in lib/meam. You can do this manually if you prefer;
-follow the instructions in lib/meam/README. You can also do it in one
-step from the lammps/src dir, using a command like these, which simply
-invoke the lib/meam/Install.py script with the specified args:
-
-make lib-meam # print help message
-make lib-meam args="-m mpi" # build with default Fortran compiler compatible with your MPI library
-make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran)
-make lib-meam args="-m ifort" # build with Intel Fortran compiler using Makefile.ifort :pre
-
-The build should produce two files: lib/meam/libmeam.a and
-lib/meam/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
-Fortran (MEAM library). Typically the two compilers used for LAMMPS
-and the MEAM library need to be consistent (e.g. both Intel or both
-GNU compilers). If necessary, you can edit/create a new
-lib/meam/Makefile.machine file for your system, which should define an
-EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
-file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-meam
-make machine :pre
+[Install:]
-make no-meam
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
NOTE: You should test building the MEAM library with both the Intel
and GNU compilers to see if a simulation runs faster with one versus
@@ -827,14 +569,6 @@ listing, "ls src/MISC", to see the list of commands.
NOTE: the MISC package contains styles that require using the
-restrict flag, when compiling with Intel compilers.
-[Install or un-install:]
-
-make yes-misc
-make machine :pre
-
-make no-misc
-make machine :pre
-
[Supporting info:]
src/MISC: filenames -> commands
@@ -860,14 +594,6 @@ that are used to model molecular systems with fixed covalent bonds.
The pair styles include the Dreiding (hydrogen-bonding) and CHARMM
force fields, and a TIP4P water model.
-[Install or un-install:]
-
-make yes-molecule
-make machine :pre
-
-make no-molecule
-make machine :pre
-
[Supporting info:]
src/MOLECULE: filenames -> commands
@@ -897,18 +623,6 @@ MPIIO library. It adds "dump styles"_dump.html with a "mpiio" in
their style name. Restart files with an ".mpiio" suffix are also
written and read in parallel.
-[Install or un-install:]
-
-Note that MPIIO is part of the standard message-passing interface
-(MPI) library, so you should not need any additional compiler or link
-settings, beyond what LAMMPS normally uses for MPI on your system.
-
-make yes-mpiio
-make machine :pre
-
-make no-mpiio
-make machine :pre
-
[Supporting info:]
src/MPIIO: filenames -> commands
@@ -936,39 +650,11 @@ system.
library was developed by Jacob Wagner in Greg Voth's group at the
University of Chicago.
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first download and
-build the MS-CG library. Building the MS-CG library and using it from
-LAMMPS requires a C++11 compatible compiler and that the GSL
-(GNU Scientific Library) headers and libraries are installed on your
-machine. See the lib/mscg/README and MSCG/Install files for more details.
-
-Assuming these libraries are in place, you can do the download and
-build of MS-CG manually if you prefer; follow the instructions in
-lib/mscg/README. You can also do it in one step from the lammps/src
-dir, using a command like these, which simply invoke the
-lib/mscg/Install.py script with the specified args:
-
-make lib-mscg # print help message
-make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master
- # with the settings compatible with "make serial"
-make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master
- # with the settings compatible with "make mpi"
-make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release :pre
-
-Note that 2 symbolic (soft) links, "includelink" and "liblink", will be created in lib/mscg
-to point to the MS-CG src/installation dir. When LAMMPS is built in src it will use these links.
-You should not need to edit the lib/mscg/Makefile.lammps file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-mscg
-make machine :pre
+[Install:]
-make no-mscg
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -989,34 +675,25 @@ CHARMM, and Morse potentials. The styles have an "opt" suffix in
their style name. The "Speed opt"_Speed_opt.html doc page gives
details of how to build and use this package. Its styles can be
invoked at run time via the "-sf opt" or "-suffix opt" "command-line
-switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS,
+switches"_Run_options.html. See also the "KOKKOS"_#KOKKOS,
"USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which
have styles optimized for CPU performance.
[Authors:] James Fischer (High Performance Technologies), David Richie,
and Vincent Natoli (Stone Ridge Technolgy).
-[Install or un-install:]
+[Install:]
-make yes-opt
-make machine :pre
-
-make no-opt
-make machine :pre
-
-NOTE: The compile flag "-restrict" must be used to build LAMMPS with
-the OPT package when using Intel compilers. It should be added to
-the CCFLAGS line of your Makefile.machine. See Makefile.opt in
-src/MAKE/OPTIONS for an example.
-
-CCFLAGS: add -restrict for Intel compilers :ul
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
src/OPT: filenames -> commands
"Speed packages"_Speed_packages.html
"Speed opt"_Speed_opt.html
-"Section 2.6 -sf opt"_Section_start.html#start_6
+"Section 2.6 -sf opt"_Run_options.html
"Commands pair"_Commands_pair.html for styles followed by (t)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@@ -1035,14 +712,6 @@ model.
Additional Peridynamics models were added by Rezwanur Rahman and John
Foster (UTSA).
-[Install or un-install:]
-
-make yes-peri
-make machine :pre
-
-make no-peri
-make machine :pre
-
[Supporting info:]
src/PERI: filenames -> commands
@@ -1070,35 +739,11 @@ connections at hinge points.
[Author:] Rudra Mukherjee (JPL) while at RPI.
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first build the
-POEMS library in lib/poems. You can do this manually if you prefer;
-follow the instructions in lib/poems/README. You can also do it in
-one step from the lammps/src dir, using a command like these, which
-simply invoke the lib/poems/Install.py script with the specified args:
-
-make lib-poems # print help message
-make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
-make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi")
-make lib-poems args="-m icc" # build with Intel icc compiler :pre
+[Install:]
-The build should produce two files: lib/poems/libpoems.a and
-lib/poems/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to build LAMMPS with the
-POEMS library (though typically the settings are just blank). If
-necessary, you can edit/create a new lib/poems/Makefile.machine file
-for your system, which should define an EXTRAMAKE variable to specify
-a corresponding Makefile.lammps.machine file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-poems
-make machine :pre
-
-make no-meam
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1121,21 +766,16 @@ call"_Python_call.html doc page for an overview of using Python from
LAMMPS in this manner and all the "Python"_Python.html doc pages for
other ways to use LAMMPS and Python together.
-[Install or un-install:]
-
-make yes-python
-make machine :pre
-
-make no-python
-make machine :pre
-
NOTE: Building with the PYTHON package assumes you have a Python
shared library available on your system, which needs to be a Python 2
version, 2.6 or later. Python 3 is not yet supported. See the
-lib/python/README for more details. Note that the build uses the
-lib/python/Makefile.lammps file in the compile/link process. You
-should only need to create a new Makefile.lammps.* file (and copy it
-to Makefile.lammps) if the LAMMPS build fails.
+lib/python/README for more details.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1154,14 +794,6 @@ Several fixes for performing charge equilibration (QEq) via different
algorithms. These can be used with pair styles that perform QEq as
part of their formulation.
-[Install or un-install:]
-
-make yes-qeq
-make machine :pre
-
-make no-qeq
-make machine :pre
-
[Supporting info:]
src/QEQ: filenames -> commands
@@ -1183,37 +815,11 @@ monitoring molecules as bonds are created and destroyed.
[Author:] Aidan Thompson (Sandia).
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first build the
-REAX library in lib/reax. You can do this manually if you prefer;
-follow the instructions in lib/reax/README. You can also do it in one
-step from the lammps/src dir, using a command like these, which simply
-invoke the lib/reax/Install.py script with the specified args:
-
-make lib-reax # print help message
-make lib-reax args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
-make lib-reax args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
-make lib-reax args="-m ifort" # build with Intel ifort compiler :pre
-
-The build should produce two files: lib/reax/libreax.a and
-lib/reax/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
-Fortran (REAX library). Typically the two compilers used for LAMMPS
-and the REAX library need to be consistent (e.g. both Intel or both
-GNU compilers). If necessary, you can edit/create a new
-lib/reax/Makefile.machine file for your system, which should define an
-EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
-file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-reax
-make machine :pre
+[Install:]
-make no-reax
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1239,14 +845,6 @@ verlet/split algorithm for performing long-range Coulombics on one set
of processors, and the remainder of the force field calcalation on
another set.
-[Install or un-install:]
-
-make yes-replica
-make machine :pre
-
-make no-replica
-make machine :pre
-
[Supporting info:]
src/REPLICA: filenames -> commands
@@ -1271,16 +869,6 @@ particles. This includes SHAKE and RATTLE, as well as varous
rigid-body integrators for a few large bodies or many small bodies.
Also several computes which calculate properties of rigid bodies.
-To install/build:
-
-make yes-rigid
-make machine :pre
-
-To un-install/re-build:
-
-make no-rigid
-make machine :pre
-
[Supporting info:]
src/RIGID: filenames -> commands
@@ -1303,14 +891,6 @@ SHOCK package :link(SHOCK),h4
Fixes for running impact simulations where a shock-wave passes through
a material.
-[Install or un-install:]
-
-make yes-shock
-make machine :pre
-
-make no-shock
-make machine :pre
-
[Supporting info:]
src/SHOCK: filenames -> commands
@@ -1334,14 +914,6 @@ computes which analyze attributes of the potential.
[Author:] Aidan Thompson (Sandia).
-[Install or un-install:]
-
-make yes-snap
-make machine :pre
-
-make no-snap
-make machine :pre
-
[Supporting info:]
src/SNAP: filenames -> commands
@@ -1362,14 +934,6 @@ the usual manner via MD. Various pair, fix, and compute styles.
[Author:] Julian Tranchida (Sandia).
-[Install or un-install:]
-
-make yes-spin
-make machine :pre
-
-make no-spin
-make machine :pre
-
[Supporting info:]
src/SPIN: filenames -> commands
@@ -1393,16 +957,6 @@ A pair of fixes which implement the Stochastic Rotation Dynamics (SRD)
method for coarse-graining of a solvent, typically around large
colloidal particles.
-To install/build:
-
-make yes-srd
-make machine :pre
-
-To un-install/re-build:
-
-make no-srd
-make machine :pre
-
[Supporting info:]
src/SRD: filenames -> commands
@@ -1434,33 +988,11 @@ system.
library was written by Chris Rycroft (Harvard U) while at UC Berkeley
and LBNL.
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first download and
-build the Voro++ library. You can do this manually if you prefer;
-follow the instructions in lib/voronoi/README. You can also do it in
-one step from the lammps/src dir, using a command like these, which
-simply invoke the lib/voronoi/Install.py script with the specified
-args:
-
-make lib-voronoi # print help message
-make lib-voronoi args="-b" # download and build the default version in lib/voronoi/voro++-<version>
-make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++
-make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6 :pre
-
-Note that 2 symbolic (soft) links, "includelink" and "liblink", are
-created in lib/voronoi to point to the Voro++ src dir. When LAMMPS
-builds in src it will use these links. You should not need to edit
-the lib/voronoi/Makefile.lammps file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
+[Install:]
-make yes-voronoi
-make machine :pre
-
-make no-voronoi
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1484,46 +1016,11 @@ atomic information to continuum fields.
[Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first build the ATC
-library in lib/atc. You can do this manually if you prefer; follow
-the instructions in lib/atc/README. You can also do it in one step
-from the lammps/src dir, using a command like these, which simply
-invoke the lib/atc/Install.py script with the specified args:
-
-make lib-atc # print help message
-make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
-make lib-atc args="-m icc" # build with Intel icc compiler :pre
-
-The build should produce two files: lib/atc/libatc.a and
-lib/atc/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to build LAMMPS with the ATC
-library. If necessary, you can edit/create a new
-lib/atc/Makefile.machine file for your system, which should define an
-EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
-file.
-
-Note that the Makefile.lammps file has settings for the BLAS and
-LAPACK linear algebra libraries. As explained in lib/atc/README these
-can either exist on your system, or you can use the files provided in
-lib/linalg. In the latter case you also need to build the library
-in lib/linalg with a command like these:
-
-make lib-linalg # print help message
-make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
-make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
-make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-atc
-make machine :pre
+[Install:]
-make no-user-atc
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1546,46 +1043,11 @@ model.
[Author:] Ilya Valuev (JIHT, Russia).
-[Install or un-install:]
+[Install:]
-Before building LAMMPS with this package, you must first build the
-AWPMD library in lib/awpmd. You can do this manually if you prefer;
-follow the instructions in lib/awpmd/README. You can also do it in
-one step from the lammps/src dir, using a command like these, which
-simply invoke the lib/awpmd/Install.py script with the specified args:
-
-make lib-awpmd # print help message
-make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
-make lib-awpmd args="-m icc" # build with Intel icc compiler :pre
-
-The build should produce two files: lib/awpmd/libawpmd.a and
-lib/awpmd/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to build LAMMPS with the
-AWPMD library. If necessary, you can edit/create a new
-lib/awpmd/Makefile.machine file for your system, which should define
-an EXTRAMAKE variable to specify a corresponding
-Makefile.lammps.machine file.
-
-Note that the Makefile.lammps file has settings for the BLAS and
-LAPACK linear algebra libraries. As explained in lib/awpmd/README
-these can either exist on your system, or you can use the files
-provided in lib/linalg. In the latter case you also need to build the
-library in lib/linalg with a command like these:
-
-make lib-linalg # print help message
-make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
-make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
-make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-awpmd
-make machine :pre
-
-make no-user-awpmd
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1608,15 +1070,8 @@ N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
accurately describe the structure, pressure, and compressibility of
molecular liquids," J. Chem. Phys. 143, 243148 (2015).
-[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University)
-
-[Install or un-install:]
-
-make yes-user-bocs
-make machine :pre
-
-make no-user-bocs
-make machine :pre
+[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The
+Pennsylvania State University)
[Supporting info:]
@@ -1645,14 +1100,6 @@ stability.
[Author:] Oliver Henrich (University of Strathclyde, Glasgow).
-[Install or un-install:]
-
-make yes-user-cgdna
-make machine :pre
-
-make no-user-cgdna
-make machine :pre
-
[Supporting info:]
src/USER-CGDNA: filenames -> commands
@@ -1676,14 +1123,6 @@ acids.
[Author:] Axel Kohlmeyer (Temple U).
-[Install or un-install:]
-
-make yes-user-cgsdk
-make machine :pre
-
-make no-user-cgsdk
-make machine :pre
-
[Supporting info:]
src/USER-CGSDK: filenames -> commands
@@ -1712,36 +1151,11 @@ and Jerome Henin (LISM, CNRS, Marseille, France), originally for
the NAMD MD code, but with portability in mind. Axel Kohlmeyer
(Temple U) provided the interface to LAMMPS.
-[Install or un-install:]
+[Install:]
-Before building LAMMPS with this package, you must first build the
-COLVARS library in lib/colvars. You can do this manually if you
-prefer; follow the instructions in lib/colvars/README. You can also
-do it in one step from the lammps/src dir, using a command like these,
-which simply invoke the lib/colvars/Install.py script with the
-specified args:
-
-make lib-colvars # print help message
-make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial")
-make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi")
-make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled :pre
-
-The build should produce two files: lib/colvars/libcolvars.a and
-lib/colvars/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to build LAMMPS with the
-COLVARS library (though typically the settings are just blank). If
-necessary, you can edit/create a new lib/colvars/Makefile.machine file
-for your system, which should define an EXTRAMAKE variable to specify
-a corresponding Makefile.lammps.machine file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-colvars
-make machine :pre
-
-make no-user-colvars
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -1763,14 +1177,6 @@ intensities based on kinematic diffraction theory.
[Author:] Shawn Coleman while at the U Arkansas.
-[Install or un-install:]
-
-make yes-user-diffraction
-make machine :pre
-
-make no-user-diffraction
-make machine :pre
-
[Supporting info:]
src/USER-DIFFRACTION: filenames -> commands
@@ -1798,14 +1204,6 @@ algorithm.
[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and and John
Brennan (ARL).
-[Install or un-install:]
-
-make yes-user-dpd
-make machine :pre
-
-make no-user-dpd
-make machine :pre
-
[Supporting info:]
src/USER-DPD: filenames -> commands
@@ -1840,14 +1238,6 @@ for using this package in tools/drude.
[Authors:] Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien
Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
-[Install or un-install:]
-
-make yes-user-drude
-make machine :pre
-
-make no-user-drude
-make machine :pre
-
[Supporting info:]
src/USER-DRUDE: filenames -> commands
@@ -1879,14 +1269,6 @@ tools/eff; see its README file.
[Author:] Andres Jaramillo-Botero (CalTech).
-[Install or un-install:]
-
-make yes-user-eff
-make machine :pre
-
-make no-user-eff
-make machine :pre
-
[Supporting info:]
src/USER-EFF: filenames -> commands
@@ -1918,14 +1300,6 @@ for using this package in tools/fep; see its README file.
[Author:] Agilio Padua (Universite Blaise Pascal Clermont-Ferrand)
-[Install or un-install:]
-
-make yes-user-fep
-make machine :pre
-
-make no-user-fep
-make machine :pre
-
[Supporting info:]
src/USER-FEP: filenames -> commands
@@ -1957,37 +1331,11 @@ system.
[Author:] Pierre de Buyl (KU Leuven) created both the package and the
H5MD format.
-[Install or un-install:]
-
-Note that to follow these steps to compile and link to the CH5MD
-library, you need the standard HDF5 software package installed on your
-system, which should include the h5cc compiler and the HDF5 library.
-
-Before building LAMMPS with this package, you must first build the
-CH5MD library in lib/h5md. You can do this manually if you prefer;
-follow the instructions in lib/h5md/README. You can also do it in one
-step from the lammps/src dir, using a command like these, which simply
-invoke the lib/h5md/Install.py script with the specified args:
-
-make lib-h5md # print help message
-make lib-hm5d args="-m h5cc" # build with h5cc compiler :pre
-
-The build should produce two files: lib/h5md/libch5md.a and
-lib/h5md/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to build LAMMPS with the
-system HDF5 library. If necessary, you can edit/create a new
-lib/h5md/Makefile.machine file for your system, which should define an
-EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
-file.
+[Install:]
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-h5md
-make machine :pre
-
-make no-user-h5md
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2008,9 +1356,9 @@ All of them have an "intel" in their style name. The "Speed
intel"_Speed_intel.html doc page gives details of what hardware and
compilers are required on your system, and how to build and use this
package. Its styles can be invoked at run time via the "-sf intel" or
-"-suffix intel" "command-line switches"_Section_start.html#start_6.
-Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-OMP"_#USER-OMP
-packages, which have styles optimized for CPUs and KNLs.
+"-suffix intel" "command-line switches"_Run_options.html. Also see
+the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-OMP"_#USER-OMP packages,
+which have styles optimized for CPUs and KNLs.
You need to have an Intel compiler, version 14 or higher to take full
advantage of this package. While compilation with GNU compilers is
@@ -2019,49 +1367,13 @@ supported, performance will be suboptimal.
NOTE: the USER-INTEL package contains styles that require using the
-restrict flag, when compiling with Intel compilers.
-
[Author:] Mike Brown (Intel).
-[Install or un-install:]
-
-For the USER-INTEL package, you have 2 choices when building. You can
-build with either CPU or KNL support. Each choice requires additional
-settings in your Makefile.machine for CCFLAGS and LINKFLAGS and
-optimized malloc libraries. See the
-src/MAKE/OPTIONS/Makefile.intel_cpu and src/MAKE/OPTIONS/Makefile.knl
-files for examples.
+[Install:]
-For CPUs:
-
-OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
-CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
--fno-alias -ansi-alias -restrict $(OPTFLAGS)
-LINKFLAGS = -g -qopenmp $(OPTFLAGS)
-LIB = -ltbbmalloc -ltbbmalloc_proxy :pre
-
-For KNLs:
-
-OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
-CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
--fno-alias -ansi-alias -restrict $(OPTFLAGS)
-LINKFLAGS = -g -qopenmp $(OPTFLAGS)
-LIB = -ltbbmalloc :pre
-
-Once you have an appropriate Makefile.machine, you can
-install/un-install the package and build LAMMPS in the usual manner.
-Note that you cannot build one executable to run on multiple hardware
-targets (Intel CPUs or KNL). You need to build LAMMPS once for each
-hardware target, to produce a separate executable.
-
-You should also typically install the USER-OMP package, as it can be
-used in tandem with the USER-INTEL package to good effect, as
-explained on the "Speed intel"_Speed_intel.html doc page.
-
-make yes-user-intel yes-user-omp
-make machine :pre
-
-make no-user-intel no-user-omp
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2069,8 +1381,8 @@ src/USER-INTEL: filenames -> commands
src/USER-INTEL/README
"Speed packages"_Speed_packages.html
"Speed intel"_Speed_intel.html
-"Section 2.6 -sf intel"_Section_start.html#start_6
-"Section 2.6 -pk intel"_Section_start.html#start_6
+"Section 2.6 -sf intel"_Run_options.html
+"Section 2.6 -pk intel"_Run_options.html
"package intel"_package.html
"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (i)
src/USER-INTEL/TEST
@@ -2088,14 +1400,6 @@ can be used to model MD particles influenced by hydrodynamic forces.
[Authors:] Frances Mackay and Colin Denniston (University of Western
Ontario).
-[Install or un-install:]
-
-make yes-user-lb
-make machine :pre
-
-make no-user-lb
-make machine :pre
-
[Supporting info:]
src/USER-LB: filenames -> commands
@@ -2122,14 +1426,6 @@ matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
[Authors:] Tomas Oppelstrup and John Moriarty (LLNL).
-[Install or un-install:]
-
-make yes-user-mgpt
-make machine :pre
-
-make no-user-mgpt
-make machine :pre
-
[Supporting info:]
src/USER-MGPT: filenames -> commands
@@ -2150,14 +1446,6 @@ dihedral, improper, or command style.
[Authors:] The author for each style in the package is listed in the
src/USER-MISC/README file.
-[Install or un-install:]
-
-make yes-user-misc
-make machine :pre
-
-make no-user-misc
-make machine :pre
-
[Supporting info:]
src/USER-MISC: filenames -> commands
@@ -2178,16 +1466,9 @@ algorithm to formulate single-particle constraint functions
g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold)
n = grad(g).
-[Author:] Stefan Paquay (until 2017: Eindhoven University of Technology (TU/e), The
-Netherlands; since 2017: Brandeis University, Waltham, MA, USA)
-
-[Install or un-install:]
-
-make yes-user-manifold
-make machine :pre
-
-make no-user-manifold
-make machine :pre
+[Author:] Stefan Paquay (until 2017: Eindhoven University of
+Technology (TU/e), The Netherlands; since 2017: Brandeis University,
+Waltham, MA, USA)
[Supporting info:]
@@ -2216,14 +1497,6 @@ multiple times.
based on the Fortran version of Greg Wagner (Northwestern U) while at
Sandia.
-[Install or un-install:]
-
-make yes-user-meamc
-make machine :pre
-
-make no-user-meamc
-make machine :pre
-
[Supporting info:]
src/USER-MEAMC: filenames -> commands
@@ -2247,14 +1520,6 @@ algorithm.
[Author:] Zhen Li (Division of Applied Mathematics, Brown University)
-[Install or un-install:]
-
-make yes-user-meso
-make machine :pre
-
-make no-user-meso
-make machine :pre
-
[Supporting info:]
src/USER-MESO: filenames -> commands
@@ -2287,14 +1552,6 @@ well as the "MOF+"_MOFplus website.
[Author:] Hendrik Heenen (Technical U of Munich),
Rochus Schmid (Ruhr-University Bochum).
-[Install or un-install:]
-
-make yes-user-mofff
-make machine :pre
-
-make no-user-mofff
-make machine :pre
-
[Supporting info:]
src/USER-MOFFF: filenames -> commands
@@ -2335,20 +1592,11 @@ at
[Author:] Axel Kohlmeyer (Temple U).
-[Install or un-install:]
-
-Note that the lib/molfile/Makefile.lammps file has a setting for a
-dynamic loading library libdl.a that should is typically present on
-all systems, which is required for LAMMPS to link with this package.
-If the setting is not valid for your system, you will need to edit the
-Makefile.lammps file. See lib/molfile/README and
-lib/molfile/Makefile.lammps for details.
+[Install:]
-make yes-user-molfile
-make machine :pre
-
-make no-user-molfile
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2383,20 +1631,11 @@ tools:
[Author:] Lars Pastewka (Karlsruhe Institute of Technology).
-[Install or un-install:]
-
-Note that to follow these steps, you need the standard NetCDF software
-package installed on your system. The lib/netcdf/Makefile.lammps file
-has settings for NetCDF include and library files that LAMMPS needs to
-compile and linkk with this package. If the settings are not valid
-for your system, you will need to edit the Makefile.lammps file. See
-lib/netcdf/README for details.
+[Install:]
-make yes-user-netcdf
-make machine :pre
-
-make no-user-netcdf
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2417,10 +1656,9 @@ via OpenMP directives. All of them have an "omp" in their style name.
The "Speed omp"_Speed_omp.html doc page gives details of what hardware
and compilers are required on your system, and how to build and use
this package. Its styles can be invoked at run time via the "-sf omp"
-or "-suffix omp" "command-line switches"_Section_start.html#start_6.
-Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and
-"USER-INTEL"_#USER-INTEL packages, which have styles optimized for
-CPUs.
+or "-suffix omp" "command-line switches"_Run_options.html. Also see
+the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-INTEL"_#USER-INTEL
+packages, which have styles optimized for CPUs.
[Author:] Axel Kohlmeyer (Temple U).
@@ -2437,16 +1675,11 @@ See src/MAKE/OPTIONS/Makefile.omp for an example.
Once you have an appropriate Makefile.machine, you can
install/un-install the package and build LAMMPS in the usual manner:
-[Install or un-install:]
-
-make yes-user-omp
-make machine :pre
+[Install:]
-make no-user-omp
-make machine :pre
-
-CCFLAGS: add -fopenmp (and -restrict when using Intel compilers)
-LINKFLAGS: add -fopenmp :ul
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2454,8 +1687,8 @@ src/USER-OMP: filenames -> commands
src/USER-OMP/README
"Speed packages"_Speed_packages.html
"Speed omp"_Speed_omp.html
-"Section 2.6 -sf omp"_Section_start.html#start_6
-"Section 2.6 -pk omp"_Section_start.html#start_6
+"Section 2.6 -sf omp"_Run_options.html
+"Section 2.6 -pk omp"_Run_options.html
"package omp"_package.html
"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (o)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@@ -2472,14 +1705,6 @@ relations, directly from molecular dynamics simulations.
[Author:] Ling-Ti Kong (Shanghai Jiao Tong University).
-[Install or un-install:]
-
-make yes-user-phonon
-make machine :pre
-
-make no-user-phonon
-make machine :pre
-
[Supporting info:]
src/USER-PHONON: filenames -> commands
@@ -2510,42 +1735,11 @@ without changes to LAMMPS itself.
[Author:] Axel Kohlmeyer (Temple U).
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first build the
-QMMM library in lib/qmmm. You can do this manually if you prefer;
-follow the first two steps explained in lib/qmmm/README. You can
-also do it in one step from the lammps/src dir, using a command like
-these, which simply invoke the lib/qmmm/Install.py script with the
-specified args:
-
-make lib-qmmm # print help message
-make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial")
-make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi")
-make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler :pre
-
-The build should produce two files: lib/qmmm/libqmmm.a and
-lib/qmmm/Makefile.lammps. The latter is copied from an existing
-Makefile.lammps.* and has settings needed to build LAMMPS with the
-QMMM library (though typically the settings are just blank). If
-necessary, you can edit/create a new lib/qmmm/Makefile.machine file
-for your system, which should define an EXTRAMAKE variable to specify
-a corresponding Makefile.lammps.machine file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
+[Install:]
-make yes-user-qmmm
-make machine :pre
-
-make no-user-qmmm
-make machine :pre
-
-NOTE: The LAMMPS executable these steps produce is not yet functional
-for a QM/MM simulation. You must also build Quantum ESPRESSO and
-create a new executable which links LAMMPS and Quantum ESPRESSO
-together. These are steps 3 and 4 described in the lib/qmmm/README
-file.
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2573,14 +1767,6 @@ simulation.
[Author:] Yuan Shen (Stanford U).
-[Install or un-install:]
-
-make yes-user-qtb
-make machine :pre
-
-make no-user-qtb
-make machine :pre
-
[Supporting info:]
src/USER-QTB: filenames -> commands
@@ -2607,26 +1793,11 @@ on your system.
[Author:] Albert Bartok (Cambridge University)
-[Install or un-install:]
-
-Note that to follow these steps to compile and link to the QUIP
-library, you must first download and build QUIP on your systems. It
-can be obtained from GitHub. See step 1 and step 1.1 in the
-lib/quip/README file for details on how to do this. Note that it
-requires setting two environment variables, QUIP_ROOT and QUIP_ARCH,
-which will be accessed by the lib/quip/Makefile.lammps file which is
-used when you compile and link LAMMPS with this package. You should
-only need to edit this file if the LAMMPS build can not use its
-settings to successfully build on your system.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-quip
-make machine :pre
+[Install:]
-make no-user-quip
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2649,14 +1820,6 @@ for monitoring molecules as bonds are created and destroyed.
[Author:] Hasan Metin Aktulga (MSU) while at Purdue University.
-[Install or un-install:]
-
-make yes-user-reaxc
-make machine :pre
-
-make no-user-reaxc
-make machine :pre
-
[Supporting info:]
src/USER-REAXC: filenames -> commands
@@ -2689,31 +1852,11 @@ specified as surface geometries from *.STL files.
[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
Dynamics, Ernst Mach Institute, Germany).
-[Install or un-install:]
-
-Before building LAMMPS with this package, you must first download the
-Eigen library. Eigen is a template library, so you do not need to
-build it, just download it. You can do this manually if you prefer;
-follow the instructions in lib/smd/README. You can also do it in one
-step from the lammps/src dir, using a command like these, which simply
-invoke the lib/smd/Install.py script with the specified args:
-
-make lib-smd # print help message
-make lib-smd args="-b" # download and build in default lib/smd/eigen-eigen-...
-make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3 :pre
-
-Note that a symbolic (soft) link named "includelink" is created in
-lib/smd to point to the Eigen dir. When LAMMPS builds it will use
-this link. You should not need to edit the lib/smd/Makefile.lammps file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-smd
-make machine :pre
+[Install:]
-make no-user-smd
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
@@ -2736,14 +1879,6 @@ ionocovalent bonds in oxides.
[Authors:] Nicolas Salles, Emile Maras, Olivier Politano, and Robert
Tetot (LAAS-CNRS, France).
-[Install or un-install:]
-
-make yes-user-smtbq
-make machine :pre
-
-make no-user-smtbq
-make machine :pre
-
[Supporting info:]
src/USER-SMTBQ: filenames -> commands
@@ -2775,14 +1910,6 @@ property/atom"_compute_property_atom.html command.
[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
Dynamics, Ernst Mach Institute, Germany).
-[Install or un-install:]
-
-make yes-user-sph
-make machine :pre
-
-make no-user-sph
-make machine :pre
-
[Supporting info:]
src/USER-SPH: filenames -> commands
@@ -2803,14 +1930,6 @@ stress, etc) about individual interactions.
[Author:] Axel Kohlmeyer (Temple U).
-[Install or un-install:]
-
-make yes-user-tally
-make machine :pre
-
-make no-user-tally
-make machine :pre
-
[Supporting info:]
src/USER-TALLY: filenames -> commands
@@ -2830,14 +1949,6 @@ supporting compute styles and an output option.
[Author:] David Nicholson (MIT).
-[Install or un-install:]
-
-make yes-user-uef
-make machine :pre
-
-make no-user-uef
-make machine :pre
-
[Supporting info:]
src/USER-UEF: filenames -> commands
@@ -2867,23 +1978,11 @@ system.
[Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
-[Install or un-install:]
-
-The lib/vtk/Makefile.lammps file has settings for accessing VTK files
-and its library, which are required for LAMMPS to build and link with
-this package. If the settings are not valid for your system, check if
-one of the other lib/vtk/Makefile.lammps.* files is compatible and
-copy it to Makefile.lammps. If none of the provided files work, you
-will need to edit the Makefile.lammps file.
-
-You can then install/un-install the package and build LAMMPS in the
-usual manner:
-
-make yes-user-vtk
-make machine :pre
+[Install:]
-make no-user-vtk
-make machine :pre
+This package has "specific installation
+instructions"_Build_extras.html#gpu on the "Build
+extras"_Build_extras.html doc page.
[Supporting info:]
diff --git a/doc/src/Python_shlib.txt b/doc/src/Python_shlib.txt
index 1a921e4025cde5cc1376c603a4beb2cf5c4c58fb..18775cd2fd4ada808d0951cc241866765d598f10 100644
--- a/doc/src/Python_shlib.txt
+++ b/doc/src/Python_shlib.txt
@@ -9,10 +9,11 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Build LAMMPS as a shared library :h3
-Instructions on how to build LAMMPS as a shared library are given in
-"Section 2.4"_Section_start.html#start_4. A shared library is one
-that is dynamically loadable, which is what Python requires to wrap
-LAMMPS. On Linux this is a library file that ends in ".so", not ".a".
+Instructions on how to build LAMMPS as a shared library are given on
+the "Build_basics"_Build_basics.html doc page. A shared library is
+one that is dynamically loadable, which is what Python requires to
+wrap LAMMPS. On Linux this is a library file that ends in ".so", not
+".a".
From the src directory, type
@@ -29,6 +30,6 @@ NOTE: If you are building LAMMPS with an MPI or FFT library or other
auxiliary libraries (used by various packages), then all of these
extra libraries must also be shared libraries. If the LAMMPS
shared-library build fails with an error complaining about this, see
-"Section 2.4"_Section_start.html#start_4 for more details.
+the "Build_basics"_Build_basics.html doc page.
-Also include CMake info on this
+TODO: Also include CMake info on this
diff --git a/doc/src/Python_test.txt b/doc/src/Python_test.txt
index 4a05d5c4680df053cd563f5e09d017e64fe4bb1f..3d52485aa8726fe4eddae6ee1a5420315d584eeb 100644
--- a/doc/src/Python_test.txt
+++ b/doc/src/Python_test.txt
@@ -32,10 +32,10 @@ first importing from the lammps.py file:
>>> from ctypes import CDLL
>>> CDLL("liblammps.so") :pre
-If an error occurs, carefully go thru the steps in "Section
-2.4"_Section_start.html#start_4 and above about building a shared
-library and about insuring Python can find the necessary two files
-it needs.
+If an error occurs, carefully go thru the steps on the
+"Build_basics"_Build_basics.html doc page about building a shared
+library and the "Python_install"_Python_install.html doc page about
+insuring Python can find the necessary two files it needs.
[Test LAMMPS and Python in serial:] :h4
diff --git a/doc/src/Speed_gpu.txt b/doc/src/Speed_gpu.txt
index ab8ec7e9d164b64c269e729e77936cd92fd6dfc0..cd81c03ba09136bb520ebd5f4084e77212f170cf 100644
--- a/doc/src/Speed_gpu.txt
+++ b/doc/src/Speed_gpu.txt
@@ -52,9 +52,9 @@ specify the # of GPUs per node
use GPU styles in your input script :ul
The latter two steps can be done using the "-pk gpu" and "-sf gpu"
-"command-line switches"_Section_start.html#start_6 respectively. Or
-the effect of the "-pk" or "-sf" switches can be duplicated by adding
-the "package gpu"_package.html or "suffix gpu"_suffix.html commands
+"command-line switches"_Run_options.html respectively. Or the effect
+of the "-pk" or "-sf" switches can be duplicated by adding the
+"package gpu"_package.html or "suffix gpu"_suffix.html commands
respectively to your input script.
[Required hardware/software:]
@@ -143,10 +143,10 @@ automatically if you create more MPI tasks/node than there are
GPUs/mode. E.g. with 8 MPI tasks/node and 2 GPUs, each GPU will be
shared by 4 MPI tasks.
-Use the "-sf gpu" "command-line switch"_Section_start.html#start_6,
-which will automatically append "gpu" to styles that support it. Use
-the "-pk gpu Ng" "command-line switch"_Section_start.html#start_6 to
-set Ng = # of GPUs/node to use.
+Use the "-sf gpu" "command-line switch"_Run_options.html, which will
+automatically append "gpu" to styles that support it. Use the "-pk
+gpu Ng" "command-line switch"_Run_options.html to set Ng = # of
+GPUs/node to use.
lmp_machine -sf gpu -pk gpu 1 -in in.script # 1 MPI task uses 1 GPU
mpirun -np 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node
@@ -180,8 +180,8 @@ pair_style lj/cut/gpu 2.5 :pre
You must also use the "package gpu"_package.html command to enable the
GPU package, unless the "-sf gpu" or "-pk gpu" "command-line
-switches"_Section_start.html#start_6 were used. It specifies the
-number of GPUs/node to use, as well as other options.
+switches"_Run_options.html were used. It specifies the number of
+GPUs/node to use, as well as other options.
[Speed-ups to expect:]
diff --git a/doc/src/Speed_intel.txt b/doc/src/Speed_intel.txt
index 20f49672e02849e2f0b544604bc6a88049eb0f05..2b29ec3b0f58e20c9315172f962337b60c29d48f 100644
--- a/doc/src/Speed_intel.txt
+++ b/doc/src/Speed_intel.txt
@@ -306,31 +306,31 @@ Hyper-Threading technology disabled.
[Run with the USER-INTEL package from the command line:]
To enable USER-INTEL optimizations for all available styles used in
-the input script, the "-sf intel"
-"command-line switch"_Section_start.html#start_6 can be used without
-any requirement for editing the input script. This switch will
-automatically append "intel" to styles that support it. It also
-invokes a default command: "package intel 1"_package.html. This
-package command is used to set options for the USER-INTEL package.
-The default package command will specify that USER-INTEL calculations
-are performed in mixed precision, that the number of OpenMP threads
-is specified by the OMP_NUM_THREADS environment variable, and that
-if coprocessors are present and the binary was built with offload
-support, that 1 coprocessor per node will be used with automatic
-balancing of work between the CPU and the coprocessor.
+the input script, the "-sf intel" "command-line
+switch"_Run_options.html can be used without any requirement for
+editing the input script. This switch will automatically append
+"intel" to styles that support it. It also invokes a default command:
+"package intel 1"_package.html. This package command is used to set
+options for the USER-INTEL package. The default package command will
+specify that USER-INTEL calculations are performed in mixed precision,
+that the number of OpenMP threads is specified by the OMP_NUM_THREADS
+environment variable, and that if coprocessors are present and the
+binary was built with offload support, that 1 coprocessor per node
+will be used with automatic balancing of work between the CPU and the
+coprocessor.
You can specify different options for the USER-INTEL package by using
-the "-pk intel Nphi" "command-line switch"_Section_start.html#start_6
-with keyword/value pairs as specified in the documentation. Here,
-Nphi = # of Xeon Phi coprocessors/node (ignored without offload
+the "-pk intel Nphi" "command-line switch"_Run_options.html with
+keyword/value pairs as specified in the documentation. Here, Nphi = #
+of Xeon Phi coprocessors/node (ignored without offload
support). Common options to the USER-INTEL package include {omp} to
override any OMP_NUM_THREADS setting and specify the number of OpenMP
-threads, {mode} to set the floating-point precision mode, and
-{lrt} to enable Long-Range Thread mode as described below. See the
-"package intel"_package.html command for details, including the
-default values used for all its options if not specified, and how to
-set the number of OpenMP threads via the OMP_NUM_THREADS environment
-variable if desired.
+threads, {mode} to set the floating-point precision mode, and {lrt} to
+enable Long-Range Thread mode as described below. See the "package
+intel"_package.html command for details, including the default values
+used for all its options if not specified, and how to set the number
+of OpenMP threads via the OMP_NUM_THREADS environment variable if
+desired.
Examples (see documentation for your MPI/Machine for differences in
launching MPI applications):
@@ -390,19 +390,18 @@ lj/cut or when using LRT mode on processors supporting AVX-512.
Not all styles are supported in the USER-INTEL package. You can mix
the USER-INTEL package with styles from the "OPT"_Speed_opt.html
-package or the "USER-OMP package"_Speed_omp.html. Of course,
-this requires that these packages were installed at build time. This
-can performed automatically by using "-sf hybrid intel opt" or
-"-sf hybrid intel omp" command-line options. Alternatively, the "opt"
-and "omp" suffixes can be appended manually in the input script. For
-the latter, the "package omp"_package.html command must be in the
-input script or the "-pk omp Nt" "command-line
-switch"_Section_start.html#start_6 must be used where Nt is the
-number of OpenMP threads. The number of OpenMP threads should not be
-set differently for the different packages. Note that the "suffix
-hybrid intel omp"_suffix.html command can also be used within the
-input script to automatically append the "omp" suffix to styles when
-USER-INTEL styles are not available.
+package or the "USER-OMP package"_Speed_omp.html. Of course, this
+requires that these packages were installed at build time. This can
+performed automatically by using "-sf hybrid intel opt" or "-sf hybrid
+intel omp" command-line options. Alternatively, the "opt" and "omp"
+suffixes can be appended manually in the input script. For the latter,
+the "package omp"_package.html command must be in the input script or
+the "-pk omp Nt" "command-line switch"_Run_options.html must be used
+where Nt is the number of OpenMP threads. The number of OpenMP threads
+should not be set differently for the different packages. Note that
+the "suffix hybrid intel omp"_suffix.html command can also be used
+within the input script to automatically append the "omp" suffix to
+styles when USER-INTEL styles are not available.
NOTE: For simulations on higher node counts, add "processors * * *
grid numa"_processors.html" to the beginning of the input script for
@@ -496,8 +495,8 @@ sorting"_atom_modify.html is changed to 1 so that the per-atom data is
effectively sorted at every rebuild of the neighbor lists. All the
available coprocessor threads on each Phi will be divided among MPI
tasks, unless the {tptask} option of the "-pk intel" "command-line
-switch"_Section_start.html#start_6 is used to limit the coprocessor
-threads per MPI task.
+switch"_Run_options.html is used to limit the coprocessor threads per
+MPI task.
[Restrictions:]
diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt
index 14f4103aed8d6df6e782eba0e63c196c2daf380d..f26b2df7e1032326f4fedee73b562c4bf7d6f520 100644
--- a/doc/src/Speed_kokkos.txt
+++ b/doc/src/Speed_kokkos.txt
@@ -142,12 +142,11 @@ mpirun -np 2 lmp_kokkos_omp -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI
mpirun -np 32 -ppn 4 lmp_kokkos_omp -k on t 4 -sf kk -in in.lj # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre
To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk
-kokkos" "command-line switches"_Section_start.html#start_7 in your
-mpirun command. You must use the "-k on" "command-line
-switch"_Section_start.html#start_7 to enable the KOKKOS package. It
-takes additional arguments for hardware settings appropriate to your
-system. Those arguments are "documented
-here"_Section_start.html#start_7. For OpenMP use:
+kokkos" "command-line switches"_Run_options.html in your mpirun
+command. You must use the "-k on" "command-line
+switch"_Run_options.html to enable the KOKKOS package. It takes
+additional arguments for hardware settings appropriate to your system.
+For OpenMP use:
-k on t Nt :pre
@@ -162,11 +161,11 @@ command (with no additional arguments) which sets various KOKKOS
options to default values, as discussed on the "package"_package.html
command doc page.
-The "-sf kk" "command-line switch"_Section_start.html#start_7 will
-automatically append the "/kk" suffix to styles that support it. In
-this manner no modification to the input script is
-needed. Alternatively, one can run with the KOKKOS package by editing
-the input script as described below.
+The "-sf kk" "command-line switch"_Run_options.html will automatically
+append the "/kk" suffix to styles that support it. In this manner no
+modification to the input script is needed. Alternatively, one can run
+with the KOKKOS package by editing the input script as described
+below.
NOTE: The default for the "package kokkos"_package.html command is to
use "full" neighbor lists and set the Newton flag to "off" for both
@@ -174,10 +173,10 @@ pairwise and bonded interactions. However, when running on CPUs, it
will typically be faster to use "half" neighbor lists and set the
Newton flag to "on", just as is the case for non-accelerated pair
styles. It can also be faster to use non-threaded communication. Use
-the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
-change the default "package kokkos"_package.html options. See its doc
-page for details and default settings. Experimenting with its options
-can provide a speed-up for specific calculations. For example:
+the "-pk kokkos" "command-line switch"_Run_options.html to change the
+default "package kokkos"_package.html options. See its doc page for
+details and default settings. Experimenting with its options can
+provide a speed-up for specific calculations. For example:
mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj # Newton on, Half neighbor list, non-threaded comm :pre
@@ -237,10 +236,10 @@ pairwise and bonded interactions. When running on KNL, this will
typically be best for pair-wise potentials. For manybody potentials,
using "half" neighbor lists and setting the Newton flag to "on" may be
faster. It can also be faster to use non-threaded communication. Use
-the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
-change the default "package kokkos"_package.html options. See its doc
-page for details and default settings. Experimenting with its options
-can provide a speed-up for specific calculations. For example:
+the "-pk kokkos" "command-line switch"_Run_options.html to change the
+default "package kokkos"_package.html options. See its doc page for
+details and default settings. Experimenting with its options can
+provide a speed-up for specific calculations. For example:
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm no -in in.lj # Newton off, full neighbor list, non-threaded comm
mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton on neigh half comm no -in in.reax # Newton on, half neighbor list, non-threaded comm :pre
@@ -255,16 +254,15 @@ supports.
[Running on GPUs:]
-Use the "-k" "command-line switch"_Section_start.html#start_7 to
-specify the number of GPUs per node. Typically the -np setting of the
-mpirun command should set the number of MPI tasks/node to be equal to
-the # of physical GPUs on the node. You can assign multiple MPI tasks
-to the same GPU with the KOKKOS package, but this is usually only
-faster if significant portions of the input script have not been
-ported to use Kokkos. Using CUDA MPS is recommended in this
-scenario. As above for multi-core CPUs (and no GPU), if N is the
-number of physical cores/node, then the number of MPI tasks/node
-should not exceed N.
+Use the "-k" "command-line switch"_Run_options.html to specify the
+number of GPUs per node. Typically the -np setting of the mpirun
+command should set the number of MPI tasks/node to be equal to the #
+of physical GPUs on the node. You can assign multiple MPI tasks to
+the same GPU with the KOKKOS package, but this is usually only faster
+if significant portions of the input script have not been ported to
+use Kokkos. Using CUDA MPS is recommended in this scenario. As above
+for multi-core CPUs (and no GPU), if N is the number of physical
+cores/node, then the number of MPI tasks/node should not exceed N.
-k on g Ng :pre
@@ -281,10 +279,10 @@ When running on Maxwell or Kepler GPUs, this will typically be
best. For Pascal GPUs, using "half" neighbor lists and setting the
Newton flag to "on" may be faster. For many pair styles, setting the
neighbor binsize equal to the ghost atom cutoff will give speedup.
-Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7
-to change the default "package kokkos"_package.html options. See its
-doc page for details and default settings. Experimenting with its
-options can provide a speed-up for specific calculations. For example:
+Use the "-pk kokkos" "command-line switch"_Run_options.html to change
+the default "package kokkos"_package.html options. See its doc page
+for details and default settings. Experimenting with its options can
+provide a speed-up for specific calculations. For example:
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos binsize 2.8 -in in.lj # Set binsize = neighbor ghost cutoff
mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighborlist, set binsize = neighbor ghost cutoff :pre
@@ -315,10 +313,9 @@ kk"_suffix.html commands to your input script.
The discussion above for building LAMMPS with the KOKKOS package, the
mpirun/mpiexec command, and setting appropriate thread are the same.
-You must still use the "-k on" "command-line
-switch"_Section_start.html#start_7 to enable the KOKKOS package, and
-specify its additional arguments for hardware options appropriate to
-your system, as documented above.
+You must still use the "-k on" "command-line switch"_Run_options.html
+to enable the KOKKOS package, and specify its additional arguments for
+hardware options appropriate to your system, as documented above.
You can use the "suffix kk"_suffix.html command, or you can explicitly add a
"kk" suffix to individual styles in your input script, e.g.
@@ -327,7 +324,7 @@ pair_style lj/cut/kk 2.5 :pre
You only need to use the "package kokkos"_package.html command if you
wish to change any of its option defaults, as set by the "-k on"
-"command-line switch"_Section_start.html#start_7.
+"command-line switch"_Run_options.html.
[Using OpenMP threading and CUDA together (experimental):]
diff --git a/doc/src/Speed_measure.txt b/doc/src/Speed_measure.txt
index 78dc220088d3873b241aae6237b84b8426f03776..647ff71e36593f9a642c22360e74c36752e43e7d 100644
--- a/doc/src/Speed_measure.txt
+++ b/doc/src/Speed_measure.txt
@@ -21,8 +21,8 @@ typically no need to run for 1000s of timesteps to get accurate
timings; you can simply extrapolate from short runs.
For the set of runs, look at the timing data printed to the screen and
-log file at the end of each LAMMPS run. "This
-section"_Section_start.html#start_7 of the manual has an overview.
+log file at the end of each LAMMPS run. The
+"Run_output"_Run_output.html doc page gives an overview.
Running on one (or a few processors) should give a good estimate of
the serial performance and what portions of the timestep are taking
diff --git a/doc/src/Speed_omp.txt b/doc/src/Speed_omp.txt
index bcfc406902d0947e2c6d9e0426b2fe8d7406dda3..e788d3300c25317322f6da0635c6c2eac109c608 100644
--- a/doc/src/Speed_omp.txt
+++ b/doc/src/Speed_omp.txt
@@ -57,19 +57,18 @@ threads/task should not exceed the physical number of cores (on a
node), otherwise performance will suffer.
As in the lines above, use the "-sf omp" "command-line
-switch"_Section_start.html#start_6, which will automatically append
-"omp" to styles that support it. The "-sf omp" switch also issues a
-default "package omp 0"_package.html command, which will set the
-number of threads per MPI task via the OMP_NUM_THREADS environment
-variable.
+switch"_Run_options.html, which will automatically append "omp" to
+styles that support it. The "-sf omp" switch also issues a default
+"package omp 0"_package.html command, which will set the number of
+threads per MPI task via the OMP_NUM_THREADS environment variable.
You can also use the "-pk omp Nt" "command-line
-switch"_Section_start.html#start_6, to explicitly set Nt = # of OpenMP
-threads per MPI task to use, as well as additional options. Its
-syntax is the same as the "package omp"_package.html command whose doc
-page gives details, including the default values used if it is not
-specified. It also gives more details on how to set the number of
-threads via the OMP_NUM_THREADS environment variable.
+switch"_Run_options.html, to explicitly set Nt = # of OpenMP threads
+per MPI task to use, as well as additional options. Its syntax is the
+same as the "package omp"_package.html command whose doc page gives
+details, including the default values used if it is not specified. It
+also gives more details on how to set the number of threads via the
+OMP_NUM_THREADS environment variable.
[Or run with the USER-OMP package by editing an input script:]
diff --git a/doc/src/Speed_opt.txt b/doc/src/Speed_opt.txt
index 676a5d84182e90ea4f832c3938bab51e5a3011dc..bb0bcd255cbdc4b0fb7df2a7b2dfce142b97475b 100644
--- a/doc/src/Speed_opt.txt
+++ b/doc/src/Speed_opt.txt
@@ -41,8 +41,8 @@ the CCFLAGS setting in your Makefile.machine must include "-restrict".
[Run with the OPT package from the command line:]
As in the lines above, use the "-sf opt" "command-line
-switch"_Section_start.html#start_6, which will automatically append
-"opt" to styles that support it.
+switch"_Run_options.html, which will automatically append "opt" to
+styles that support it.
[Or run with the OPT package by editing an input script:]
diff --git a/doc/src/Speed_packages.txt b/doc/src/Speed_packages.txt
index f463ed91b85d28cf495db638a401f7c52a5326fe..6c837885cd4dd5272e9b7925d84aa01ee8f9ab79 100644
--- a/doc/src/Speed_packages.txt
+++ b/doc/src/Speed_packages.txt
@@ -93,11 +93,11 @@ re-build LAMMPS |
make machine |
prepare and test a regular LAMMPS simulation |
lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script |
-enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_6, |
+enable specific accelerator support via '-k on' "command-line switch"_Run_options.html, |
only needed for KOKKOS package |
-set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_6 or "package"_package.html command, |
+set any needed options for the package via "-pk" "command-line switch"_Run_options.html or "package"_package.html command, |
only if defaults need to be changed |
-use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
+use accelerated styles in your input via "-sf" "command-line switch"_Run_options.html or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
:tb(c=2,s=|)
Note that the first 4 steps can be done as a single command with
diff --git a/doc/src/angle_charmm.txt b/doc/src/angle_charmm.txt
index f72f0862348328bbd5c62a11d42274bb4f4c14d3..8b0e298a43cccc82433505de4646f0cd254ffcb0 100644
--- a/doc/src/angle_charmm.txt
+++ b/doc/src/angle_charmm.txt
@@ -57,13 +57,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -73,8 +73,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/angle_class2.txt b/doc/src/angle_class2.txt
index 3e5445d3a3c17200bd5e548791bdbfbb31f4dcbe..fa5e29582cf4762e2851ba82c69624076a09e705 100644
--- a/doc/src/angle_class2.txt
+++ b/doc/src/angle_class2.txt
@@ -89,13 +89,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -123,8 +123,8 @@ The bond-bond and bond-angle terms remain unchanged.
This angle style can only be used if LAMMPS was built with the CLASS2
package. For the {class2/p6} style LAMMPS needs to be built with the
-USER-MOFFF package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MOFFF package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_cosine.txt b/doc/src/angle_cosine.txt
index 5a1fe91c834271bfe883e1b2d5a410f3bb148a23..80cf8ae8f13ecee4bde4faf93ab923a153e61118 100644
--- a/doc/src/angle_cosine.txt
+++ b/doc/src/angle_cosine.txt
@@ -44,13 +44,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -60,8 +60,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/angle_cosine_buck6d.txt b/doc/src/angle_cosine_buck6d.txt
index 63a451b7631456aa21b870eadf5808e92b052ec9..54709c1370f65d740f134a4e8d9bc80b8e106ca3 100644
--- a/doc/src/angle_cosine_buck6d.txt
+++ b/doc/src/angle_cosine_buck6d.txt
@@ -55,8 +55,8 @@ the "special_bonds"_special_bonds.html 1-3 interactions to be weighted
"special_bonds"_special_bonds.html 0.0 weighting of 1-3 interactions.
This angle style can only be used if LAMMPS was built with the
-USER-MOFFF package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-MOFFF package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_cosine_delta.txt b/doc/src/angle_cosine_delta.txt
index b6ac0ed8181ad55b183ab59962e9502c2cd5ab93..1532e39b31007e149d964912a1fbde27fe4fe253 100644
--- a/doc/src/angle_cosine_delta.txt
+++ b/doc/src/angle_cosine_delta.txt
@@ -49,13 +49,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -65,8 +65,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/angle_cosine_periodic.txt b/doc/src/angle_cosine_periodic.txt
index c5b184e0b46b1e5b14efb8b1dd0477740c59ae19..039144797ff75badb1771d220720db471aebf6e6 100644
--- a/doc/src/angle_cosine_periodic.txt
+++ b/doc/src/angle_cosine_periodic.txt
@@ -57,13 +57,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -73,8 +73,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/angle_cosine_shift.txt b/doc/src/angle_cosine_shift.txt
index 90ac61fe23c9d45f595c579e937d55bdea284909..8e23e1b49fe35d9bef211537616894f89721d0f4 100644
--- a/doc/src/angle_cosine_shift.txt
+++ b/doc/src/angle_cosine_shift.txt
@@ -40,20 +40,20 @@ theta (angle) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page. The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
+They have been optimized to run faster, depending on
+your"_Build_package.html doc page kages"_Speed_packages.html doc page.
+The accelerated styles take the same arguments and should produce the
+same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -63,8 +63,7 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package.
[Related commands:]
diff --git a/doc/src/angle_cosine_shift_exp.txt b/doc/src/angle_cosine_shift_exp.txt
index f1c4c93c425e0ce8f51d12e39dd34c9493bf0426..3091e838850742d8f1efdae6b1b921aa4afd6afd 100644
--- a/doc/src/angle_cosine_shift_exp.txt
+++ b/doc/src/angle_cosine_shift_exp.txt
@@ -59,13 +59,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -75,8 +75,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_cosine_squared.txt b/doc/src/angle_cosine_squared.txt
index ba5fd9d4139a4f1142c287e121d3e3e7f002a6d4..07fcb1ceb4cb731c89f1dc7eae7452fafe266c86 100644
--- a/doc/src/angle_cosine_squared.txt
+++ b/doc/src/angle_cosine_squared.txt
@@ -49,13 +49,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -65,8 +65,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/angle_dipole.txt b/doc/src/angle_dipole.txt
index c001d9d9206c743222357f1cdcb345934f9a9ead..cdb11972ecb01dc7d6c602c8444495fef8d46dba 100644
--- a/doc/src/angle_dipole.txt
+++ b/doc/src/angle_dipole.txt
@@ -77,13 +77,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -91,8 +91,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_2_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
NOTE: In the "Angles" section of the data file, the atom ID 'j'
defining the direction of the dipole vector to restrain must come
diff --git a/doc/src/angle_fourier.txt b/doc/src/angle_fourier.txt
index e0e32c1eed001fa0d6ecb70f2f2c69542d39d6c0..7dc9975793353787e56cd677c25459744c0f2d87 100644
--- a/doc/src/angle_fourier.txt
+++ b/doc/src/angle_fourier.txt
@@ -45,13 +45,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -61,8 +61,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_fourier_simple.txt b/doc/src/angle_fourier_simple.txt
index 3c50536a2cbc0720ec69c4a4b02cdefa15bd48ff..ae5d30835387a071bf801c7f30af3b0f2cad6ce6 100644
--- a/doc/src/angle_fourier_simple.txt
+++ b/doc/src/angle_fourier_simple.txt
@@ -44,13 +44,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -60,8 +60,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_harmonic.txt b/doc/src/angle_harmonic.txt
index 76c7a491e8943aa7cdd720750394818fc7460b9e..b632f684786bc8c465bf350b270cd91388b4ef66 100644
--- a/doc/src/angle_harmonic.txt
+++ b/doc/src/angle_harmonic.txt
@@ -51,13 +51,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -67,8 +67,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_hybrid.txt b/doc/src/angle_hybrid.txt
index 26469034212fe359d66a965e216543404b2d1020..0046c161be6a30ea500e8b1a26b61b3145166f6a 100644
--- a/doc/src/angle_hybrid.txt
+++ b/doc/src/angle_hybrid.txt
@@ -76,8 +76,8 @@ for specific angle types.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
Unlike other angle styles, the hybrid angle style does not store angle
coefficient info for individual sub-styles in a "binary restart
diff --git a/doc/src/angle_quartic.txt b/doc/src/angle_quartic.txt
index 294be330b1faab22d868d16b1a78edb048be928c..b20a06eb8d681fd0f7987e9f686e4e247699ffa0 100644
--- a/doc/src/angle_quartic.txt
+++ b/doc/src/angle_quartic.txt
@@ -51,13 +51,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -67,8 +67,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_sdk.txt b/doc/src/angle_sdk.txt
index 9c5630ef3adf62b7688dbbd021555283536b2cff..4de1a6755d9eebf47045996fdad8b711367d9f6d 100644
--- a/doc/src/angle_sdk.txt
+++ b/doc/src/angle_sdk.txt
@@ -46,8 +46,8 @@ from the pair_style.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER-CGSDK package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-CGSDK package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/angle_style.txt b/doc/src/angle_style.txt
index 63295faf264d8fee8b2a75fb32143ae710d02586..756cfc0c6038d3d3a0e9dd7a12b229e2f8f11c09 100644
--- a/doc/src/angle_style.txt
+++ b/doc/src/angle_style.txt
@@ -83,10 +83,9 @@ Angle styles can only be set for atom_styles that allow angles to be
defined.
Most angle styles are part of the MOLECULE package. They are only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
-The doc pages for individual bond potentials tell if it is part of a
-package.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. The doc pages for
+individual bond potentials tell if it is part of a package.
[Related commands:]
diff --git a/doc/src/angle_table.txt b/doc/src/angle_table.txt
index 31ab532be17c95598c2b54f3a34becbf3c966120..6b9187e512a355649ef7fffdaa87c3747d9a3010 100644
--- a/doc/src/angle_table.txt
+++ b/doc/src/angle_table.txt
@@ -130,13 +130,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -146,8 +146,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/atom_modify.txt b/doc/src/atom_modify.txt
index c882d1b0ba0f43a916ee3a954a4b85e41d6c2007..4b4ac3862d102b54ed08cb0b2d8b63f84ec32f89 100644
--- a/doc/src/atom_modify.txt
+++ b/doc/src/atom_modify.txt
@@ -58,9 +58,9 @@ simulation so large that IDs cannot be uniquely assigned. For a
default LAMMPS build this limit is 2^31 or about 2 billion atoms.
However, even in this case, you can use 64-bit atom IDs, allowing 2^63
or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG
-switch. This is described in "Section 2.2"_Section_start.html#start_2
-of the manual. If atom IDs are not used, they must be specified as 0
-for all atoms, e.g. in a data or restart file.
+switch. This is described on the "Build_settings"_Build_settings.html
+doc page. If atom IDs are not used, they must be specified as 0 for
+all atoms, e.g. in a data or restart file.
The {map} keyword determines how atoms with specific IDs are found
when required. An example are the bond (angle, etc) methods which
diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt
index abf05885a3ee3d96846af804d6ef1caaf42643c6..db2e285dc48fefb79709933d1230ed4a750f084d 100644
--- a/doc/src/atom_style.txt
+++ b/doc/src/atom_style.txt
@@ -272,13 +272,13 @@ USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom
styles.
The accelerated styles are part of the KOKKOS package. They are only
-enabled if LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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_7 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -289,8 +289,8 @@ This command cannot be used after the simulation box is defined by a
"read_data"_read_data.html or "create_box"_create_box.html command.
Many of the styles listed above are only enabled if LAMMPS was built
-with a specific package, as listed below. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+with a specific package, as listed below. See the "Build
+package"_Build_package.html doc page for more info.
The {angle}, {bond}, {full}, {molecular}, and {template} styles are
part of the MOLECULE package.
diff --git a/doc/src/balance.txt b/doc/src/balance.txt
index 06c4eca491d1bd6cdb3c68a5caa2381718159ea7..26e146d89b3222fabdfdabe9daf4e6720d5f6750 100644
--- a/doc/src/balance.txt
+++ b/doc/src/balance.txt
@@ -394,11 +394,11 @@ weights. It assigns the same weight to each particle owned by a
processor based on the total computational time spent by that
processor. See details below on what time window is used. It uses
the same timing information as is used for the "MPI task timing
-breakdown"_Section_start.html#start_7, namely, for sections {Pair},
-{Bond}, {Kspace}, and {Neigh}. The time spent in those portions of
-the timestep are measured for each MPI rank, summed, then divided by
-the number of particles owned by that processor. I.e. the weight is
-an effective CPU time/particle averaged over the particles on that
+breakdown"_Run_output.html, namely, for sections {Pair}, {Bond},
+{Kspace}, and {Neigh}. The time spent in those portions of the
+timestep are measured for each MPI rank, summed, then divided by the
+number of particles owned by that processor. I.e. the weight is an
+effective CPU time/particle averaged over the particles on that
processor.
The {factor} setting is applied as an overall scale factor to the
diff --git a/doc/src/bond_class2.txt b/doc/src/bond_class2.txt
index 3d8d5007bad145439de155227c8873fcfce616a9..4390e3613c001741ecc9a2203e6c3899402a8356 100644
--- a/doc/src/bond_class2.txt
+++ b/doc/src/bond_class2.txt
@@ -50,13 +50,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -66,8 +66,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This bond style can only be used if LAMMPS was built with the CLASS2
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/bond_fene.txt b/doc/src/bond_fene.txt
index e16307a71076c6c2c2b6aecd5c660eb4acda8f2a..9ec4017d000a865108d08a209226283918b57c17 100644
--- a/doc/src/bond_fene.txt
+++ b/doc/src/bond_fene.txt
@@ -53,13 +53,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -68,9 +68,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
You typically should specify "special_bonds fene"_special_bonds.html
or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
diff --git a/doc/src/bond_fene_expand.txt b/doc/src/bond_fene_expand.txt
index 8edd325885e457e039765074ce14be6fe5fe2764..4d7d2d54382e3afbfa74a4f25924052ed544b16a 100644
--- a/doc/src/bond_fene_expand.txt
+++ b/doc/src/bond_fene_expand.txt
@@ -56,13 +56,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -71,9 +71,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
You typically should specify "special_bonds fene"_special_bonds.html
or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
diff --git a/doc/src/bond_gromos.txt b/doc/src/bond_gromos.txt
index 275036a421f618085eb25625f87a716cb28876c5..e039e6c4117ccbdabc132f24b723d4e5f2c8d1e2 100644
--- a/doc/src/bond_gromos.txt
+++ b/doc/src/bond_gromos.txt
@@ -46,13 +46,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -61,9 +61,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/bond_harmonic.txt b/doc/src/bond_harmonic.txt
index e4b2015fed2987dfe52a06e22021fff70bbb6ce6..3afdf4ceba020fdd4f5e31d3a075da2b79b8712e 100644
--- a/doc/src/bond_harmonic.txt
+++ b/doc/src/bond_harmonic.txt
@@ -48,13 +48,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -63,9 +63,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/bond_harmonic_shift.txt b/doc/src/bond_harmonic_shift.txt
index b6dc18a5fd69453806968cebd189c4ca7c0d5dd3..23d3dcb5d509337005b973fd7610e59ab0ae81a1 100644
--- a/doc/src/bond_harmonic_shift.txt
+++ b/doc/src/bond_harmonic_shift.txt
@@ -49,13 +49,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -65,8 +65,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/bond_harmonic_shift_cut.txt b/doc/src/bond_harmonic_shift_cut.txt
index b3054437d8e8b4a4bda593bb756e7721ff7ebe26..13ccb5843b44b132789305b9779bccac6d08ed72 100644
--- a/doc/src/bond_harmonic_shift_cut.txt
+++ b/doc/src/bond_harmonic_shift_cut.txt
@@ -49,13 +49,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -65,8 +65,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/bond_hybrid.txt b/doc/src/bond_hybrid.txt
index 140fb723785476a1a09c67360b6865a898f8d1f5..0996f72ce3a4cbbf8f25869363f2b5072d790996 100644
--- a/doc/src/bond_hybrid.txt
+++ b/doc/src/bond_hybrid.txt
@@ -58,9 +58,9 @@ bond types.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
Unlike other bond styles, the hybrid bond style does not store bond
coefficient info for individual sub-styles in a "binary restart
diff --git a/doc/src/bond_morse.txt b/doc/src/bond_morse.txt
index 9b64e8c5c1d2da41936def16578ba299160121a9..60fd16e17a0894ef131bc9794354d645c067ac33 100644
--- a/doc/src/bond_morse.txt
+++ b/doc/src/bond_morse.txt
@@ -47,13 +47,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -62,9 +62,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/bond_nonlinear.txt b/doc/src/bond_nonlinear.txt
index 08109bc699dfed95d7ad70cff09dbded043627f5..af51383213998faa6427bcb8b078b5c400127b6b 100644
--- a/doc/src/bond_nonlinear.txt
+++ b/doc/src/bond_nonlinear.txt
@@ -47,13 +47,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -62,9 +62,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/bond_oxdna.txt b/doc/src/bond_oxdna.txt
index a0e14a123abed8da2728ed13d3ad3b836fc3414b..1944f7027a6573de91d6b490482931af332e0ed5 100644
--- a/doc/src/bond_oxdna.txt
+++ b/doc/src/bond_oxdna.txt
@@ -62,8 +62,8 @@ The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-CGDNA package and the MOLECULE and ASPHERE package. See the
+"Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/bond_quartic.txt b/doc/src/bond_quartic.txt
index 87a21eff02ef4577638e44a5a6932ab181ec5a71..b7b1ee4ce61aac52c01b80a98acb9cd889e359bd 100644
--- a/doc/src/bond_quartic.txt
+++ b/doc/src/bond_quartic.txt
@@ -82,13 +82,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -97,9 +97,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
The {quartic} style requires that "special_bonds"_special_bonds.html
parameters be set to 1,1,1. Three- and four-body interactions (angle,
diff --git a/doc/src/bond_style.txt b/doc/src/bond_style.txt
index 41fa1cabb213847c51aef2b7acef0b1bb6bee00e..22fae3e34698a7da47dd8d171fd2d996a682a01f 100644
--- a/doc/src/bond_style.txt
+++ b/doc/src/bond_style.txt
@@ -90,10 +90,9 @@ Bond styles can only be set for atom styles that allow bonds to be
defined.
Most bond styles are part of the MOLECULE package. They are only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
-The doc pages for individual bond potentials tell if it is part of a
-package.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. The doc pages for
+individual bond potentials tell if it is part of a package.
[Related commands:]
diff --git a/doc/src/bond_table.txt b/doc/src/bond_table.txt
index e53cbdfa9f626c0c36377d9ac56a8bea016f958b..fbf6eb5815cc48661804af29a4e0e49543c75e70 100644
--- a/doc/src/bond_table.txt
+++ b/doc/src/bond_table.txt
@@ -127,13 +127,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -142,9 +142,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This bond style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+This bond style can only be used if LAMMPS was built with the MOLECULE
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/compute_ackland_atom.txt b/doc/src/compute_ackland_atom.txt
index 485c191313209e46eb2ac979d004f23314678190..cda4a36b34d01c83a4977440adc94e747ea090df 100644
--- a/doc/src/compute_ackland_atom.txt
+++ b/doc/src/compute_ackland_atom.txt
@@ -66,8 +66,8 @@ LAMMPS output options.
[Restrictions:]
This compute is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The per-atom vector values will be unitless since they are the
integers defined above.
diff --git a/doc/src/compute_basal_atom.txt b/doc/src/compute_basal_atom.txt
index 067a020c35ebec8da9acda96b21abb8c68724a30..5c28b8e378d6c3a0f6b3cc4d99b3f8b66b0572c7 100644
--- a/doc/src/compute_basal_atom.txt
+++ b/doc/src/compute_basal_atom.txt
@@ -55,8 +55,8 @@ components of a unit vector.
[Restrictions:]
This compute is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The output of this compute will be meaningless unless the atoms are on
(or near) hcp lattice sites, since the calculation assumes a
diff --git a/doc/src/compute_cnp_atom.txt b/doc/src/compute_cnp_atom.txt
index 44a77d23ca0fedade05df5f523302bcdaaa6215a..95dd59089f60fb4fcccc1d4e79f1f0cb1e840639 100644
--- a/doc/src/compute_cnp_atom.txt
+++ b/doc/src/compute_cnp_atom.txt
@@ -95,8 +95,8 @@ FCC dislocation core ~ 11 :pre
[Restrictions:]
This compute is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_damage_atom.txt b/doc/src/compute_damage_atom.txt
index 74939e22806077fe5fb274cd17a7630954db9017..2594dfe3561e02bdcbbdbbfa0651d1f0db668d88 100644
--- a/doc/src/compute_damage_atom.txt
+++ b/doc/src/compute_damage_atom.txt
@@ -52,8 +52,8 @@ The per-atom vector values are unitless numbers (damage) >= 0.0.
[Restrictions:]
This compute is part of the PERI package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_dilatation_atom.txt b/doc/src/compute_dilatation_atom.txt
index 498110cf99338e56fb24a2b9a362438f03f5f9f3..292638bdf5e57f4fbe9cfc1079bb3ae64dec20fa 100644
--- a/doc/src/compute_dilatation_atom.txt
+++ b/doc/src/compute_dilatation_atom.txt
@@ -56,8 +56,8 @@ The per-atom vector values are unitless numbers (theta) >= 0.0.
[Restrictions:]
This compute is part of the PERI package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_dpd.txt b/doc/src/compute_dpd.txt
index 1721456e35ab0da5a82d3965f676f35a3d4baa3b..eccffee9b8fe85d02321ba85167a9b090c2b7972 100644
--- a/doc/src/compute_dpd.txt
+++ b/doc/src/compute_dpd.txt
@@ -49,8 +49,8 @@ The vector values will be in energy and temperature "units"_units.html.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command also requires use of the "atom_style dpd"_atom_style.html
command.
diff --git a/doc/src/compute_dpd_atom.txt b/doc/src/compute_dpd_atom.txt
index 8e502d4a6060f297da9132013adf5e19d40b565a..2f9b4098cff988047b9a39f2926b3320b85e3aa3 100644
--- a/doc/src/compute_dpd_atom.txt
+++ b/doc/src/compute_dpd_atom.txt
@@ -45,8 +45,8 @@ and temperature (dpdTheta) "units"_units.html.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command also requires use of the "atom_style dpd"_atom_style.html
command.
diff --git a/doc/src/compute_edpd_temp_atom.txt b/doc/src/compute_edpd_temp_atom.txt
index f33398e03d68995dc18da4d73fd9537f5e75656d..f3c1418d44c52c1d6678e32b568c3df389118fc0 100644
--- a/doc/src/compute_edpd_temp_atom.txt
+++ b/doc/src/compute_edpd_temp_atom.txt
@@ -41,8 +41,8 @@ The per-atom vector values will be in temperature "units"_units.html.
[Restrictions:]
This compute is part of the USER-MESO package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_entropy_atom.txt b/doc/src/compute_entropy_atom.txt
index 9c45fd287099ea6150621a177f55837bbc5855fb..b3891841b8ce04185b3f0705e877b8c34f87b34f 100644
--- a/doc/src/compute_entropy_atom.txt
+++ b/doc/src/compute_entropy_atom.txt
@@ -109,8 +109,8 @@ ordered environments.
[Restrictions:]
This compute is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_erotate_rigid.txt b/doc/src/compute_erotate_rigid.txt
index 5b9077870e1d25440827b5a6006b5c6e3233d830..fa433c1c97699957320110651323240b2cced994 100644
--- a/doc/src/compute_erotate_rigid.txt
+++ b/doc/src/compute_erotate_rigid.txt
@@ -51,8 +51,8 @@ scalar value will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the RIGID package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_event_displace.txt b/doc/src/compute_event_displace.txt
index 561ded35c052ef3e99e53ea8cb0533e00d3f99e3..a36cf2c9c49440c6428908915caa2f16ca58dab5 100644
--- a/doc/src/compute_event_displace.txt
+++ b/doc/src/compute_event_displace.txt
@@ -52,8 +52,8 @@ scalar value will be a 0 or 1 as explained above.
[Restrictions:]
This command can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/compute_fep.txt b/doc/src/compute_fep.txt
index 8b4a92e16ea3a0486ca2c7113bf0b1ac87a47399..5b3a6915dd4a6c3c442be5034caa03b7fb709602 100644
--- a/doc/src/compute_fep.txt
+++ b/doc/src/compute_fep.txt
@@ -230,8 +230,8 @@ The values calculated by this compute are "extensive".
[Restrictions:]
This compute is distributed as the USER-FEP package. It is only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_ke_atom_eff.txt b/doc/src/compute_ke_atom_eff.txt
index f665f35055f36be914f26aa5c032b2b76233ccf2..29905f81d6b624f119cfb05a8daebfb959971492 100644
--- a/doc/src/compute_ke_atom_eff.txt
+++ b/doc/src/compute_ke_atom_eff.txt
@@ -66,8 +66,8 @@ The per-atom vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the USER-EFF package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_ke_eff.txt b/doc/src/compute_ke_eff.txt
index d6d7fdb10f5f3667a8443047505e80a775c3b1b6..fa2c51a032607c696bbb61c23abe489b189a3975 100644
--- a/doc/src/compute_ke_eff.txt
+++ b/doc/src/compute_ke_eff.txt
@@ -70,8 +70,8 @@ scalar value will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the USER-EFF package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:] none
diff --git a/doc/src/compute_ke_rigid.txt b/doc/src/compute_ke_rigid.txt
index 45ba2673b0283a8106d55ee621103a7f8eb3a7fa..ad6baf567fa87e8e4be7e67d65f9fe5a7333ba40 100644
--- a/doc/src/compute_ke_rigid.txt
+++ b/doc/src/compute_ke_rigid.txt
@@ -50,8 +50,8 @@ scalar value will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the RIGID package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_meso_e_atom.txt b/doc/src/compute_meso_e_atom.txt
index 9a9c7fae118d4b6a84636b94a9f83d582c6331c8..0f0cfda2d1c8a9c01d367608e5e36d27f01de416 100644
--- a/doc/src/compute_meso_e_atom.txt
+++ b/doc/src/compute_meso_e_atom.txt
@@ -46,8 +46,8 @@ The per-atom vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the USER-SPH package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_meso_rho_atom.txt b/doc/src/compute_meso_rho_atom.txt
index 30b1142b6cdfef0afb329f7d3be5a360d9487465..5127ad2c48f7a3f033957e800a7ba8303dfa0fe7 100644
--- a/doc/src/compute_meso_rho_atom.txt
+++ b/doc/src/compute_meso_rho_atom.txt
@@ -46,8 +46,8 @@ The per-atom vector values will be in mass/volume "units"_units.html.
[Restrictions:]
This compute is part of the USER-SPH package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_meso_t_atom.txt b/doc/src/compute_meso_t_atom.txt
index ab92f05018a15b6f45edf30d4844b82b2c237493..f4ab869ec27bd943dffcfe5b4df1dce358efa5cf 100644
--- a/doc/src/compute_meso_t_atom.txt
+++ b/doc/src/compute_meso_t_atom.txt
@@ -48,8 +48,8 @@ The per-atom vector values will be in temperature "units"_units.html.
[Restrictions:]
This compute is part of the USER-SPH package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_msd_nongauss.txt b/doc/src/compute_msd_nongauss.txt
index 814159121d11781bf29850db7c8787ab5644b807..c6e89a10615a191d4df77fd3e4d207d07ecb69a4 100644
--- a/doc/src/compute_msd_nongauss.txt
+++ b/doc/src/compute_msd_nongauss.txt
@@ -66,9 +66,9 @@ the 3rd is dimensionless.
[Restrictions:]
-This compute is part of the MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+This compute is part of the MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_plasticity_atom.txt b/doc/src/compute_plasticity_atom.txt
index 50a51d99377899c3ed62a81059351ab494968567..b82179712abcd146420f0ac7b538f2c49b01f855 100644
--- a/doc/src/compute_plasticity_atom.txt
+++ b/doc/src/compute_plasticity_atom.txt
@@ -50,8 +50,8 @@ The per-atom vector values are unitless numbers (lambda) >= 0.0.
[Restrictions:]
This compute is part of the PERI package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt
index dea0a7f05b7f03d209077628f19a07172eb93e0f..6acbaf7d3d5619c4c08001bf712a606b911e280e 100644
--- a/doc/src/compute_pressure.txt
+++ b/doc/src/compute_pressure.txt
@@ -111,13 +111,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/compute_pressure_uef.txt b/doc/src/compute_pressure_uef.txt
index 61cc85ad8097b3b43ac740cf186b7456f02db707..c4c0fc405ff563273c1d9b1ff72c51a638eedf02 100644
--- a/doc/src/compute_pressure_uef.txt
+++ b/doc/src/compute_pressure_uef.txt
@@ -38,9 +38,9 @@ The keywords and output information are documented in
[Restrictions:]
-This fix is part of the USER-UEF package. It is only enabled if
-LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+This fix is part of the USER-UEF package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command can only be used when "fix nvt/uef"_fix_nh_uef.html
or "fix npt/uef"_fix_nh_uef.html is active.
diff --git a/doc/src/compute_rigid_local.txt b/doc/src/compute_rigid_local.txt
index b5e6954ab99943f090a3153829ca08a6daa8f0b7..9b829a70fcb82a1de7defbafbce6b949ca833f20 100644
--- a/doc/src/compute_rigid_local.txt
+++ b/doc/src/compute_rigid_local.txt
@@ -175,8 +175,8 @@ inertiax,inertiay,inertiaz = mass*distance^2 units :ul
[Restrictions:]
This compute is part of the RIGID package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_saed.txt b/doc/src/compute_saed.txt
index 8c17a30fcaf1acb403a936d4a15938206e89ad4d..b27c36e318757159978998b723d2e3bc5b5c3924 100644
--- a/doc/src/compute_saed.txt
+++ b/doc/src/compute_saed.txt
@@ -152,8 +152,8 @@ All array values calculated by this compute are "intensive".
[Restrictions:]
This compute is part of the USER-DIFFRACTION package. It is only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The compute_saed command does not work for triclinic cells.
diff --git a/doc/src/compute_smd_contact_radius.txt b/doc/src/compute_smd_contact_radius.txt
index cd1381604788bfcd42f00653d2c5e9b46f98d25f..4ab03e3738c4fcc60378ab988a60c33b1260ad41 100644
--- a/doc/src/compute_smd_contact_radius.txt
+++ b/doc/src/compute_smd_contact_radius.txt
@@ -45,8 +45,8 @@ The per-particle vector values will be in distance "units"_units.html.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_smd_damage.txt b/doc/src/compute_smd_damage.txt
index afabe23d7cc1407496463c926ba8adcb9ddc7ff0..139fb3ec7bfb48e56b56e23af5cce1176f45cdbe 100644
--- a/doc/src/compute_smd_damage.txt
+++ b/doc/src/compute_smd_damage.txt
@@ -38,8 +38,8 @@ The per-particle values are dimensionless an in the range of zero to one.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+LAMMPS was built with that package. See the "Build
+
[Related commands:]
diff --git a/doc/src/compute_smd_hourglass_error.txt b/doc/src/compute_smd_hourglass_error.txt
index 13fd20a5891cab8bdeeabb570d8343c063a705af..5bc3e3a2decbefdcd3e026e12e1aae6ccf535758 100644
--- a/doc/src/compute_smd_hourglass_error.txt
+++ b/doc/src/compute_smd_hourglass_error.txt
@@ -48,8 +48,8 @@ The per-particle vector values will are dimensionless. See
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This quantity will be computed only for particles which interact with
tlsph pair style.
diff --git a/doc/src/compute_smd_internal_energy.txt b/doc/src/compute_smd_internal_energy.txt
index 6585c3429f27a9c97d17c66a15dff959ebbbe5be..b9d18ce933966e161c26a1ecc783e8a2bbc76abe 100644
--- a/doc/src/compute_smd_internal_energy.txt
+++ b/doc/src/compute_smd_internal_energy.txt
@@ -39,10 +39,10 @@ The per-particle vector values will be given in "units"_units.html of energy.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. This compute
-can only be used for particles which interact via the updated
-Lagrangian or total Lagrangian SPH pair styles.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. This compute can
+only be used for particles which interact via the updated Lagrangian
+or total Lagrangian SPH pair styles.
[Related Commands:]
diff --git a/doc/src/compute_smd_plastic_strain.txt b/doc/src/compute_smd_plastic_strain.txt
index fb3c5c9138cb5ae444320a5ff9f4a73878780a67..d12be7222a23744d489b6a1153bae16fb91f6753 100644
--- a/doc/src/compute_smd_plastic_strain.txt
+++ b/doc/src/compute_smd_plastic_strain.txt
@@ -40,10 +40,10 @@ The per-particle values will be given dimensionless. See "units"_units.html.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. This compute
-can only be used for particles which interact via the updated
-Lagrangian or total Lagrangian SPH pair styles.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. This compute can
+only be used for particles which interact via the updated Lagrangian
+or total Lagrangian SPH pair styles.
[Related commands:]
diff --git a/doc/src/compute_smd_plastic_strain_rate.txt b/doc/src/compute_smd_plastic_strain_rate.txt
index b913ae90976009a7caf916352cbfe9475577d9db..ffc009b2a70978a272f9184b71ca6b1828dc768a 100644
--- a/doc/src/compute_smd_plastic_strain_rate.txt
+++ b/doc/src/compute_smd_plastic_strain_rate.txt
@@ -40,10 +40,10 @@ The per-particle values will be given in "units"_units.html of one over time.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. This compute
-can only be used for particles which interact via the updated
-Lagrangian or total Lagrangian SPH pair styles.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. This compute can
+only be used for particles which interact via the updated Lagrangian
+or total Lagrangian SPH pair styles.
[Related commands:]
diff --git a/doc/src/compute_smd_rho.txt b/doc/src/compute_smd_rho.txt
index a1ee1d9c5b95a2971e64a52ad4416e74e54fc226..31d7351c92e2aaeb55f53c71bd7fe75be82df9bc 100644
--- a/doc/src/compute_smd_rho.txt
+++ b/doc/src/compute_smd_rho.txt
@@ -41,8 +41,8 @@ The per-particle values will be in "units"_units.html of mass over volume.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_smd_tlsph_defgrad.txt b/doc/src/compute_smd_tlsph_defgrad.txt
index 1663c84f65fd3b3c59daf427d4b15fe6a5d27ea9..a733a3d6a75f1394889be1c13eb402b146a1edc5 100644
--- a/doc/src/compute_smd_tlsph_defgrad.txt
+++ b/doc/src/compute_smd_tlsph_defgrad.txt
@@ -44,10 +44,10 @@ entry is the determinant of the deformation gradient.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. TThis
-compute can only be used for particles which interact via the total
-Lagrangian SPH pair style.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. TThis compute can
+only be used for particles which interact via the total Lagrangian SPH
+pair style.
[Related commands:]
diff --git a/doc/src/compute_smd_tlsph_dt.txt b/doc/src/compute_smd_tlsph_dt.txt
index c714f3266bceaf96ea1b86d487cf653cdeeeb47e..92f5923de05f735931aae9908844b197ad127fe3 100644
--- a/doc/src/compute_smd_tlsph_dt.txt
+++ b/doc/src/compute_smd_tlsph_dt.txt
@@ -45,8 +45,8 @@ The per-particle values will be given in "units"_units.html of time.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This compute can only be used for particles interacting with the
Total-Lagrangian SPH pair style.
diff --git a/doc/src/compute_smd_tlsph_num_neighs.txt b/doc/src/compute_smd_tlsph_num_neighs.txt
index af5b0741db6c0c964ab4a73b21bdb928b663fe42..db977fe676b5185f39088c96e2a5157dda30a30f 100644
--- a/doc/src/compute_smd_tlsph_num_neighs.txt
+++ b/doc/src/compute_smd_tlsph_num_neighs.txt
@@ -40,8 +40,8 @@ The per-particle values are dimensionless. See "units"_units.html.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This quantity will be computed only for particles which interact with
the Total-Lagrangian pair style.
diff --git a/doc/src/compute_smd_tlsph_shape.txt b/doc/src/compute_smd_tlsph_shape.txt
index 927cd7c7aecaa51cc45c095066586899bd37aefb..9c17194ec18ed8c40fc775b4d68aa9ef54bf9e69 100644
--- a/doc/src/compute_smd_tlsph_shape.txt
+++ b/doc/src/compute_smd_tlsph_shape.txt
@@ -47,8 +47,8 @@ particle relative to its initial state.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This quantity will be computed only for particles which interact with
the Total-Lagrangian SPH pair style.
diff --git a/doc/src/compute_smd_tlsph_strain.txt b/doc/src/compute_smd_tlsph_strain.txt
index 4536f26c8ea364d40d306f1ac863f3fc4a278dff..70f996e2064f0dc530844b825e8116f10b04b94b 100644
--- a/doc/src/compute_smd_tlsph_strain.txt
+++ b/doc/src/compute_smd_tlsph_strain.txt
@@ -43,8 +43,8 @@ zz, xy, xz, yz components of the symmetric strain tensor.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This quantity will be computed only for particles which interact with
the Total-Lagrangian SPH pair style.
diff --git a/doc/src/compute_smd_tlsph_strain_rate.txt b/doc/src/compute_smd_tlsph_strain_rate.txt
index ae2883e4bbedb0e698cac841601984de90af2031..e6d968c523d62ce483b05a5a4522959bf4f6e2cb 100644
--- a/doc/src/compute_smd_tlsph_strain_rate.txt
+++ b/doc/src/compute_smd_tlsph_strain_rate.txt
@@ -42,8 +42,8 @@ zz, xy, xz, yz components of the symmetric strain rate tensor.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This quantity will be computed only for particles which interact with
Total-Lagrangian SPH pair style.
diff --git a/doc/src/compute_smd_tlsph_stress.txt b/doc/src/compute_smd_tlsph_stress.txt
index 50d6b7f4344ffb585cc27a00d644e803904e5fad..8340e885363c43c931f6734ffdbd2a415d74f74b 100644
--- a/doc/src/compute_smd_tlsph_stress.txt
+++ b/doc/src/compute_smd_tlsph_stress.txt
@@ -44,8 +44,8 @@ invariant of the stress tensor, i.e., the von Mises equivalent stress.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This quantity will be computed only for particles which interact with
the Total-Lagrangian SPH pair style.
diff --git a/doc/src/compute_smd_triangle_mesh_vertices.txt b/doc/src/compute_smd_triangle_mesh_vertices.txt
index 9e167924d1401fea40a6ac9b0d9bcc7d257d4355..cd1f8fdd9b29b007ae0f3f0a28a491b7dee2fd7e 100644
--- a/doc/src/compute_smd_triangle_mesh_vertices.txt
+++ b/doc/src/compute_smd_triangle_mesh_vertices.txt
@@ -51,8 +51,8 @@ The values will be given in "units"_units.html of distance.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_smd_ulsph_num_neighs.txt b/doc/src/compute_smd_ulsph_num_neighs.txt
index 202b8f15e1d95ec3441e272a23b618a0f57f443a..5157f17e578e80ec2a8799b63ea894c5ffc60ac5 100644
--- a/doc/src/compute_smd_ulsph_num_neighs.txt
+++ b/doc/src/compute_smd_ulsph_num_neighs.txt
@@ -40,10 +40,10 @@ The per-particle values will be given dimensionless, see "units"_units.html.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_2 section for more info. This compute
-can only be used for particles which interact with the updated
-Lagrangian SPH pair style.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. This compute can
+only be used for particles which interact with the updated Lagrangian
+SPH pair style.
[Related commands:]
diff --git a/doc/src/compute_smd_ulsph_strain.txt b/doc/src/compute_smd_ulsph_strain.txt
index 76c47162a5c85e0def8c8231224ccda416ea6360..3dc6bd5249439a82cc76d12bd519f3f1803bbd27 100644
--- a/doc/src/compute_smd_ulsph_strain.txt
+++ b/doc/src/compute_smd_ulsph_strain.txt
@@ -43,10 +43,10 @@ The per-particle tensor values will be given dimensionless, see
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. This compute
-can only be used for particles which interact with the updated
-Lagrangian SPH pair style.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. This compute can
+only be used for particles which interact with the updated Lagrangian
+SPH pair style.
[Related commands:]
diff --git a/doc/src/compute_smd_ulsph_strain_rate.txt b/doc/src/compute_smd_ulsph_strain_rate.txt
index c851e767b34a418a614cfeb537638ec294ae489f..1ade5ac2d5a8b77c950d4dfab582ad95aafa52e4 100644
--- a/doc/src/compute_smd_ulsph_strain_rate.txt
+++ b/doc/src/compute_smd_ulsph_strain_rate.txt
@@ -43,10 +43,11 @@ zz, xy, xz, yz components of the symmetric strain rate tensor.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_2 section for more info. This compute
-can only be used for particles which interact with the updated
-Lagrangian SPH pair style.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+This compute can only be used for particles which interact with the
+updated Lagrangian SPH pair style.
[Related commands:]
diff --git a/doc/src/compute_smd_ulsph_stress.txt b/doc/src/compute_smd_ulsph_stress.txt
index a5692b2412ce589165a29514c6b199b7d0dd802d..ff53e777c50615386d28db11a07a46ec682c0563 100644
--- a/doc/src/compute_smd_ulsph_stress.txt
+++ b/doc/src/compute_smd_ulsph_stress.txt
@@ -43,10 +43,10 @@ stress tensor, i.e., the von Mises equivalent stress.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. This compute
-can only be used for particles which interact with the updated
-Lagrangian SPH pair style.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. This compute can
+only be used for particles which interact with the updated Lagrangian
+SPH pair style.
[Related commands:]
diff --git a/doc/src/compute_smd_vol.txt b/doc/src/compute_smd_vol.txt
index fc4871d6f301157c45fcaf88e99301f20cdff31c..0edd61f624228972e7090aa15549b2361b24d0c8 100644
--- a/doc/src/compute_smd_vol.txt
+++ b/doc/src/compute_smd_vol.txt
@@ -43,8 +43,8 @@ per-particle volumes of the group for which the fix is defined.
[Restrictions:]
This compute is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt
index 3b302a0a71c65de87fee8ae571e866b3cc19653c..95d183937f8db2d79e202af0796c814b000b0ca2 100644
--- a/doc/src/compute_sna_atom.txt
+++ b/doc/src/compute_sna_atom.txt
@@ -250,8 +250,8 @@ page for an overview of LAMMPS output options.
[Restrictions:]
These computes are part of the SNAP package. They are only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_spin.txt b/doc/src/compute_spin.txt
index 792706ecdfae311acd293546d899b51b2bf28d73..787ff8cdcfa822ba37c896d464e6c9655d5e543a 100644
--- a/doc/src/compute_spin.txt
+++ b/doc/src/compute_spin.txt
@@ -61,10 +61,10 @@ metal units ("units"_units.html).
[Restrictions:]
-The {spin} compute is part of the SPIN package.
-This compute is only enabled if LAMMPS was built with this package.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
-The atom_style has to be "spin" for this compute to be valid.
+The {spin} compute is part of the SPIN package. This compute is only
+enabled if LAMMPS was built with this package. See the "Build
+package"_Build_package.html doc page for more info. The atom_style
+has to be "spin" for this compute to be valid.
[Related commands:] none
diff --git a/doc/src/compute_tally.txt b/doc/src/compute_tally.txt
index 23fac4309384bac044259f51d128726725fcd3f7..a4a8441f9ec4e7555f977b454a56f3f8ffb137b0 100644
--- a/doc/src/compute_tally.txt
+++ b/doc/src/compute_tally.txt
@@ -76,9 +76,9 @@ Both the scalar and vector values calculated by this compute are
[Restrictions:]
-This compute is part of the USER-TALLY package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+This compute is part of the USER-TALLY package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Not all pair styles can be evaluated in a pairwise mode as required by
this compute. For example, 3-body and other many-body potentials,
diff --git a/doc/src/compute_tdpd_cc_atom.txt b/doc/src/compute_tdpd_cc_atom.txt
index 9ee4d3da3462fbed0bc3be6b66212d6988fd938d..a385bef10b612c9e5a4a485570c82e406f83ff16 100644
--- a/doc/src/compute_tdpd_cc_atom.txt
+++ b/doc/src/compute_tdpd_cc_atom.txt
@@ -43,8 +43,8 @@ per unit mass.
[Restrictions:]
This compute is part of the USER-MESO package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_temp.txt b/doc/src/compute_temp.txt
index 9f3a1ca9061feeaab02ac197f5ab15c1844a709a..757e00c4d2f3e57ba70ccd180acc69099ee0e325 100644
--- a/doc/src/compute_temp.txt
+++ b/doc/src/compute_temp.txt
@@ -73,13 +73,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/compute_temp_asphere.txt b/doc/src/compute_temp_asphere.txt
index 6766729ae0c463ce51c6470de27d6966102a0cff..eb73891e82572001a3834f292a373772edf9b396 100644
--- a/doc/src/compute_temp_asphere.txt
+++ b/doc/src/compute_temp_asphere.txt
@@ -135,8 +135,8 @@ vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the ASPHERE package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This compute requires that atoms store angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
diff --git a/doc/src/compute_temp_body.txt b/doc/src/compute_temp_body.txt
index 4e3ce3e77f86db797f0222b62d403df6ef82c827..341d6d7f792c7815c540b03c25c480b212df9deb 100644
--- a/doc/src/compute_temp_body.txt
+++ b/doc/src/compute_temp_body.txt
@@ -117,8 +117,8 @@ vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the BODY package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This compute requires that atoms store angular momentum and a
quaternion as defined by the "atom_style body"_atom_style.html
diff --git a/doc/src/compute_temp_deform_eff.txt b/doc/src/compute_temp_deform_eff.txt
index 876d492f3446f7294ed295974e20c0f28a2369bd..4af61dc91867890533ea9a4f20606275bf4e3d07 100644
--- a/doc/src/compute_temp_deform_eff.txt
+++ b/doc/src/compute_temp_deform_eff.txt
@@ -61,8 +61,8 @@ vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the USER-EFF package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_temp_eff.txt b/doc/src/compute_temp_eff.txt
index 35ddb75b12c30ffac0d1d5fc249f9abe33617a0a..415cb775956ec3e759e0dfa6c2209c9e4b68520d 100644
--- a/doc/src/compute_temp_eff.txt
+++ b/doc/src/compute_temp_eff.txt
@@ -83,8 +83,8 @@ the simulation.
[Restrictions:]
This compute is part of the USER-EFF package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_temp_partial.txt b/doc/src/compute_temp_partial.txt
index 2769246532fd55f8cf36df3c076d6d822609d765..14294842a15b11c11461618224b663840b1dce0c 100644
--- a/doc/src/compute_temp_partial.txt
+++ b/doc/src/compute_temp_partial.txt
@@ -80,13 +80,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/compute_temp_region_eff.txt b/doc/src/compute_temp_region_eff.txt
index 95892eb25778eac67c1042de5acf2ed97494c4f1..f15f3155b08c51880ae3ae8fc9f6b255ff9b78fe 100644
--- a/doc/src/compute_temp_region_eff.txt
+++ b/doc/src/compute_temp_region_eff.txt
@@ -52,8 +52,8 @@ vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the USER-EFF package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_temp_rotate.txt b/doc/src/compute_temp_rotate.txt
index 189246d3e47e734b00a63da770e83a0333c9c85e..8dac0405b402efa55594068b1e7c57775ee47359 100644
--- a/doc/src/compute_temp_rotate.txt
+++ b/doc/src/compute_temp_rotate.txt
@@ -86,8 +86,8 @@ vector values will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_temp_uef.txt b/doc/src/compute_temp_uef.txt
index a94d5db8ed767604c3dd6edac9bf81723d02da1b..9a509da4503db6cb3a9e03b0314de6300e28d36b 100644
--- a/doc/src/compute_temp_uef.txt
+++ b/doc/src/compute_temp_uef.txt
@@ -35,9 +35,9 @@ documentation for "compute temp"_compute_temp.html.
[Restrictions:]
-This fix is part of the USER-UEF package. It is only enabled if
-LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+This fix is part of the USER-UEF package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command can only be used when "fix nvt/uef"_fix_nh_uef.html
or "fix npt/uef"_fix_nh_uef.html is active.
diff --git a/doc/src/compute_ti.txt b/doc/src/compute_ti.txt
index e79b594e3f32a252a1ea352a1b3fc113324ebb3d..9057cab4769c5e201d1a30a7b47b8d1f6645d324 100644
--- a/doc/src/compute_ti.txt
+++ b/doc/src/compute_ti.txt
@@ -121,8 +121,8 @@ The scalar value will be in energy "units"_units.html.
[Restrictions:]
This compute is part of the MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/compute_voronoi_atom.txt b/doc/src/compute_voronoi_atom.txt
index a8ce77882ad42069d32d51864cb06ce3566c8bba..d01f4df71217920649b688cb20562dab8396ac82 100644
--- a/doc/src/compute_voronoi_atom.txt
+++ b/doc/src/compute_voronoi_atom.txt
@@ -212,8 +212,8 @@ The Voronoi face area will be in distance "units"_units.html squared.
[Restrictions:]
This compute is part of the VORONOI package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
It also requires you have a copy of the Voro++ library built and
installed on your system. See instructions on obtaining and
diff --git a/doc/src/compute_xrd.txt b/doc/src/compute_xrd.txt
index 609fde3582d9efd03bd9c0ae6fbb63ac3d54db20..41523f25afa828f214491d7d3bdae2cf87172905 100644
--- a/doc/src/compute_xrd.txt
+++ b/doc/src/compute_xrd.txt
@@ -170,8 +170,8 @@ All array values calculated by this compute are "intensive".
[Restrictions:]
This compute is part of the USER-DIFFRACTION package. It is only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The compute_xrd command does not work for triclinic cells.
diff --git a/doc/src/dihedral_charmm.txt b/doc/src/dihedral_charmm.txt
index 8adef6cf4b5ed1ee5f25ab1d72c7fc12f43078fc..637a10102dc1f79c65995c9361731b00777bd1c9 100644
--- a/doc/src/dihedral_charmm.txt
+++ b/doc/src/dihedral_charmm.txt
@@ -122,13 +122,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -146,8 +146,8 @@ Otherwise non-bonded contributions for these 1-4 pairs will be
computed multiple times.
These dihedral styles can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/dihedral_class2.txt b/doc/src/dihedral_class2.txt
index 1a2f37abbbd0352fd04bc6e958912c0b17966627..9936f3768df703d8b2e63072499c3d0c96d2c3f8 100644
--- a/doc/src/dihedral_class2.txt
+++ b/doc/src/dihedral_class2.txt
@@ -147,13 +147,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -163,8 +163,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-CLASS2 package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+CLASS2 package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dihedral_cosine_shift_exp.txt b/doc/src/dihedral_cosine_shift_exp.txt
index 7ef27e6bc966b129156159c9714e27a2cc050853..e2a46d28d8ad9f686f6221e2594a7f3b7a4392d3 100644
--- a/doc/src/dihedral_cosine_shift_exp.txt
+++ b/doc/src/dihedral_cosine_shift_exp.txt
@@ -58,13 +58,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -74,8 +74,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dihedral_fourier.txt b/doc/src/dihedral_fourier.txt
index f51cbc9c8cd8e1aeed0248730d7b633a3d636f74..3045f6824b1b27d393a720578193cca47627b160 100644
--- a/doc/src/dihedral_fourier.txt
+++ b/doc/src/dihedral_fourier.txt
@@ -50,13 +50,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -66,8 +66,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dihedral_harmonic.txt b/doc/src/dihedral_harmonic.txt
index 1eda0c5d02b8f1a7bbba646ad26d684cff7e7806..27bc04f9df6d05cf8774270a2900a5fb96cf1d4c 100644
--- a/doc/src/dihedral_harmonic.txt
+++ b/doc/src/dihedral_harmonic.txt
@@ -59,13 +59,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -75,8 +75,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/dihedral_helix.txt b/doc/src/dihedral_helix.txt
index 3af4b410bcd24e4469ccdc50e9576fb81cc9539c..3b3607337b91bb056d3ea7f4227cc3cabb07c3d7 100644
--- a/doc/src/dihedral_helix.txt
+++ b/doc/src/dihedral_helix.txt
@@ -52,13 +52,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -68,8 +68,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/dihedral_hybrid.txt b/doc/src/dihedral_hybrid.txt
index c9ca86680c175aca2188891523265ca4d2203f81..a4a2a2808eb1ca170a315708fa92c23326840aae 100644
--- a/doc/src/dihedral_hybrid.txt
+++ b/doc/src/dihedral_hybrid.txt
@@ -77,8 +77,8 @@ for specific dihedral types.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
Unlike other dihedral styles, the hybrid dihedral style does not store
dihedral coefficient info for individual sub-styles in a "binary
diff --git a/doc/src/dihedral_multi_harmonic.txt b/doc/src/dihedral_multi_harmonic.txt
index 7c22391923b37a065369b53c0871d20cd90710fe..74f1f6abc69cc1e1dfbe009a5ef096de88a0110a 100644
--- a/doc/src/dihedral_multi_harmonic.txt
+++ b/doc/src/dihedral_multi_harmonic.txt
@@ -46,13 +46,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -62,8 +62,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/dihedral_nharmonic.txt b/doc/src/dihedral_nharmonic.txt
index aa8f1e0d7fdc646fa6c06009909b750294e06613..7a8bf6cdb7c6ce73c0593896ace978cac62e044a 100644
--- a/doc/src/dihedral_nharmonic.txt
+++ b/doc/src/dihedral_nharmonic.txt
@@ -46,13 +46,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -62,8 +62,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dihedral_opls.txt b/doc/src/dihedral_opls.txt
index f0cf91f30ad67fe914b376aef1c0c94ef5145955..7fa5d81a14a778baf76815ad2cc8cede3a5ae4ce 100644
--- a/doc/src/dihedral_opls.txt
+++ b/doc/src/dihedral_opls.txt
@@ -54,13 +54,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -70,8 +70,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/dihedral_quadratic.txt b/doc/src/dihedral_quadratic.txt
index e65cf2dee86a2b108513f1d83a5cbfe29c8a0034..dc951e4269fdbf3752dd7f36aa366b81a06389fd 100644
--- a/doc/src/dihedral_quadratic.txt
+++ b/doc/src/dihedral_quadratic.txt
@@ -47,13 +47,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -63,8 +63,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dihedral_spherical.txt b/doc/src/dihedral_spherical.txt
index 10a757e8986d6d9c5f450a84bfffc6be81221078..61949174df8d052740a1f0676a8c68e8b00606dd 100644
--- a/doc/src/dihedral_spherical.txt
+++ b/doc/src/dihedral_spherical.txt
@@ -78,8 +78,8 @@ wn (typically 0.0 or 1.0) :ul
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dihedral_style.txt b/doc/src/dihedral_style.txt
index 6aff3f0994777390eba737e8273524f770fd5e8e..749f74e399559570fc52f0c8fa65be30a9557a1d 100644
--- a/doc/src/dihedral_style.txt
+++ b/doc/src/dihedral_style.txt
@@ -104,10 +104,9 @@ Dihedral styles can only be set for atom styles that allow dihedrals
to be defined.
Most dihedral styles are part of the MOLECULE package. They are only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
-The doc pages for individual dihedral potentials tell if it is part of
-a package.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. The doc pages for
+individual dihedral potentials tell if it is part of a package.
[Related commands:]
diff --git a/doc/src/dihedral_table.txt b/doc/src/dihedral_table.txt
index d722ef7c82a76c67ac0353a02b1656b8a8de73c0..3f679f57093c95954927fddbe73a3aa9beeb94bd 100644
--- a/doc/src/dihedral_table.txt
+++ b/doc/src/dihedral_table.txt
@@ -180,13 +180,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -194,8 +194,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dihedral_table_cut.txt b/doc/src/dihedral_table_cut.txt
index cc7df8cdf9de397a6a91d9ec89bef542f5b5002a..b8e0ec64c8863ac4b87db5b7433c84c3c4dbff55 100644
--- a/doc/src/dihedral_table_cut.txt
+++ b/doc/src/dihedral_table_cut.txt
@@ -192,8 +192,8 @@ that matches the specified keyword.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/dump.txt b/doc/src/dump.txt
index 5b478b7301960bd536ef29158086c0c8b0f34023..8b630cc7069ccc949579c5cda38cc1834a4c0d54 100644
--- a/doc/src/dump.txt
+++ b/doc/src/dump.txt
@@ -634,23 +634,22 @@ which could then be output into dump files.
[Restrictions:]
To write gzipped dump files, you must either compile LAMMPS with the
--DLAMMPS_GZIP option or use the styles from the COMPRESS package
-- see the "Making LAMMPS"_Section_start.html#start_2 section of
-the documentation.
+-DLAMMPS_GZIP option or use the styles from the COMPRESS package.
+See the "Build settings"_Build_settings.html doc page for details.
-The {atom/gz}, {cfg/gz}, {custom/gz}, and {xyz/gz} styles are part
-of the COMPRESS package. They are only enabled if LAMMPS was built
-with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+The {atom/gz}, {cfg/gz}, {custom/gz}, and {xyz/gz} styles are part of
+the COMPRESS package. They are only enabled if LAMMPS was built with
+that package. See the "Build package"_Build_package.html doc page for
+more info.
The {atom/mpiio}, {cfg/mpiio}, {custom/mpiio}, and {xyz/mpiio} styles
are part of the MPIIO package. They are only enabled if LAMMPS was
-built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
The {xtc} style is part of the MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/dump_cfg_uef.txt b/doc/src/dump_cfg_uef.txt
index 665be14be1330e0b902c73686d430f3ce904a315..16e4aba4c04fd6db18adfb622e670ba8448ddc10 100644
--- a/doc/src/dump_cfg_uef.txt
+++ b/doc/src/dump_cfg_uef.txt
@@ -38,9 +38,9 @@ reference frame as the atomic positions.
[Restrictions:]
-This fix is part of the USER-UEF package. It is only enabled if
-LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+This fix is part of the USER-UEF package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command can only be used when "fix nvt/uef"_fix_nh_uef.html
or "fix npt/uef"_fix_nh_uef.html is active.
diff --git a/doc/src/dump_h5md.txt b/doc/src/dump_h5md.txt
index fbd682dad9cac9c112fc10ee30c31c922e00f4a0..9065e8a648b4ae8f600e680bac713298d2043f37 100644
--- a/doc/src/dump_h5md.txt
+++ b/doc/src/dump_h5md.txt
@@ -98,13 +98,13 @@ note above). Only orthogonal domains are currently supported. This is
a limitation of the present dump h5md command and not of H5MD itself.
The {h5md} dump style is part of the USER-H5MD package. It is only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. It also
-requires (i) building the ch5md library provided with LAMMPS (See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.) and
-(ii) having the "HDF5"_HDF5_ws library installed (C bindings are
-sufficient) on your system. The library ch5md is compiled with the
-h5cc wrapper provided by the HDF5 library.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. It also requires
+(i) building the ch5md library provided with LAMMPS (See the "Build
+package"_Build_package.html doc page for more info.) and (ii) having
+the "HDF5"_HDF5_ws library installed (C bindings are sufficient) on
+your system. The library ch5md is compiled with the h5cc wrapper
+provided by the HDF5 library.
:link(HDF5_ws,http://www.hdfgroup.org/HDF5/)
diff --git a/doc/src/dump_image.txt b/doc/src/dump_image.txt
index 06332b5dcf92a593ba084c50f9daaacfd7fb4ae3..9b56dd95a6006878dc9e865be9c148093e3f52a5 100644
--- a/doc/src/dump_image.txt
+++ b/doc/src/dump_image.txt
@@ -142,8 +142,8 @@ framerate can be set using the "dump_modify"_dump_modify.html command.
To write out JPEG and PNG format files, you must build LAMMPS with
support for the corresponding JPEG or PNG library. To convert images
into movies, LAMMPS has to be compiled with the -DLAMMPS_FFMPEG
-flag. See "this section"_Section_start.html#start_2_4 of the manual
-for instructions on how to do this.
+flag. See the "Build settings"_Build_settings.html doc page for
+details.
NOTE: Because periodic boundary conditions are enforced only on
timesteps when neighbor lists are rebuilt, the coordinates of an atom
@@ -624,8 +624,7 @@ building LAMMPS and have the FFmpeg executable available on the
machine where LAMMPS is being run. Typically it's name is lowercase,
i.e. ffmpeg.
-See the "Making LAMMPS"_Section_start.html#start_2_4 section of the
-documentation for details on how to compile with optional switches.
+See the "Build settings"_Build_settings.html doc page for details.
Note that since FFmpeg is run as an external program via a pipe,
LAMMPS has limited control over its execution and no knowledge about
diff --git a/doc/src/dump_molfile.txt b/doc/src/dump_molfile.txt
index 9fa04bd1aeed0de92d8fac59dfe3e8e0d83bee3e..dd2b212f0baafc6efd4200c42eb4439e1d6715e3 100644
--- a/doc/src/dump_molfile.txt
+++ b/doc/src/dump_molfile.txt
@@ -90,8 +90,8 @@ determine the sequence of timesteps on which dump files are written.
[Restrictions:]
The {molfile} dump style is part of the USER-MOLFILE package. It is
-only enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Molfile plugins provide a consistent programming interface to read and
write file formats commonly used in molecular simulations. The
diff --git a/doc/src/dump_netcdf.txt b/doc/src/dump_netcdf.txt
index b1c63736514d00e4c35e1056aebab49d18f1cc54..52d757eac562083eff17a2dc5ffebfc741b5b2f5 100644
--- a/doc/src/dump_netcdf.txt
+++ b/doc/src/dump_netcdf.txt
@@ -66,8 +66,8 @@ by "thermo_style"_thermo_style.html.
The {netcdf} and {netcdf/mpiio} dump styles are part of the
USER-NETCDF package. They are only enabled if LAMMPS was built with
-that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+that package. See the "Build package"_Build_package.html doc page for
+more info.
:line
diff --git a/doc/src/dump_vtk.txt b/doc/src/dump_vtk.txt
index afc6099534eb5c80ffb18461f0f8426ea50bcc67..7eaa59a79505a18318633a031cf4a64e8a3d4b43 100644
--- a/doc/src/dump_vtk.txt
+++ b/doc/src/dump_vtk.txt
@@ -156,9 +156,9 @@ write out much faster.
The {vtk} style does not support writing of gzipped dump files.
-The {vtk} dump style is part of the USER-VTK package. It is
-only enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+The {vtk} dump style is part of the USER-VTK package. It is only
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
To use this dump style, you also must link to the VTK library. See
the info in lib/vtk/README and insure the Makefile.lammps file in that
diff --git a/doc/src/echo.txt b/doc/src/echo.txt
index dc6918dc8981af7b971e3e3cd406d29c6aa2e8b7..3436737faaa6f364c520b62c713647a96e63d7d7 100644
--- a/doc/src/echo.txt
+++ b/doc/src/echo.txt
@@ -26,8 +26,8 @@ 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_6 -echo can be used
-in place of this command.
+The "command-line switch"_Run_options.html -echo can be used in place
+of this command.
[Restrictions:] none
diff --git a/doc/src/fix.txt b/doc/src/fix.txt
index fd966b5bd9916407648f6db1ea7f01d293faef10..9c3a1d0349fd097eb9f5572b943872bce1254a4e 100644
--- a/doc/src/fix.txt
+++ b/doc/src/fix.txt
@@ -309,9 +309,9 @@ accerlerated styles exist.
[Restrictions:]
Some fix styles are part of specific packages. They are only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
-The doc pages for individual fixes tell if it is part of a package.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. The doc pages for
+individual fixes tell if it is part of a package.
[Related commands:]
diff --git a/doc/src/fix_addforce.txt b/doc/src/fix_addforce.txt
index 51be39fdb2b72156560b0d85c56b6fc1a517056f..4fdf9a41ddefb31f80e5d391aee7b2adc60c5a35 100644
--- a/doc/src/fix_addforce.txt
+++ b/doc/src/fix_addforce.txt
@@ -112,13 +112,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_addtorque.txt b/doc/src/fix_addtorque.txt
index c80fad26da1c5e40d8a96f42c034f2f8b18cdb86..0963915e7a38aabb9db22c12a7fcac6b918c35a9 100644
--- a/doc/src/fix_addtorque.txt
+++ b/doc/src/fix_addtorque.txt
@@ -88,8 +88,8 @@ the iteration count during the minimization.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_append_atoms.txt b/doc/src/fix_append_atoms.txt
index c6af361afcfe24a5da8cc97c4e917238fe981ab0..d83f265982cdaadc3303c751779e1d7cf9112b18 100644
--- a/doc/src/fix_append_atoms.txt
+++ b/doc/src/fix_append_atoms.txt
@@ -95,8 +95,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix style is part of the SHOCK package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The boundary on which atoms are added with append/atoms must be
shrink/minimum. The opposite boundary may be any boundary type other
diff --git a/doc/src/fix_atom_swap.txt b/doc/src/fix_atom_swap.txt
index c1d84dade1954b2a8d1ec15bb699cb99a5d1e1ae..22091eca005540b5316aee0bccd2c3d4e77aa2ba 100644
--- a/doc/src/fix_atom_swap.txt
+++ b/doc/src/fix_atom_swap.txt
@@ -165,8 +165,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MC package. It is only enabled if LAMMPS was
-built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_ave_correlate_long.txt b/doc/src/fix_ave_correlate_long.txt
index ac0ef873aac6ae3cd90fca5077a3cc86e3160645..d94bf8af7b08daf2767255ddeaaed993c2e1691a 100644
--- a/doc/src/fix_ave_correlate_long.txt
+++ b/doc/src/fix_ave_correlate_long.txt
@@ -120,8 +120,8 @@ the run command. This fix is not invoked during energy minimization.
[Restrictions:]
This compute is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_aveforce.txt b/doc/src/fix_aveforce.txt
index 1fc7e4a18dd8f5efd1b84a21c0a785797be692a1..8c759864c67eb60bf8583d3654c4f4d51a55fca1 100644
--- a/doc/src/fix_aveforce.txt
+++ b/doc/src/fix_aveforce.txt
@@ -72,13 +72,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_bocs.txt b/doc/src/fix_bocs.txt
index f5bbc8a2519dcef980bdce8e3d08eb22a8789867..7acc22d702e4b7cfd496df2865fdbdc0844bd276 100644
--- a/doc/src/fix_bocs.txt
+++ b/doc/src/fix_bocs.txt
@@ -85,8 +85,8 @@ XXXX_press, where XXXX is the ID given to the fix bocs command (in the
example, the ID of the fix bocs command is 1 ).
This fix is part of the USER-BOCS package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related:]
diff --git a/doc/src/fix_bond_break.txt b/doc/src/fix_bond_break.txt
index bdb2f2a8624869a8552992b246a111cb3396e7c5..59fea8f45b846b3ad94f4d9b29f8617025d1bb4d 100644
--- a/doc/src/fix_bond_break.txt
+++ b/doc/src/fix_bond_break.txt
@@ -131,8 +131,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MC package. It is only enabled if LAMMPS was
-built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_bond_create.txt b/doc/src/fix_bond_create.txt
index ab34433cecf631fbb8b9cff9fb87d43b87d7c07d..02655577fdb2f9c6d712638ef4ed781ae0b1b6dc 100644
--- a/doc/src/fix_bond_create.txt
+++ b/doc/src/fix_bond_create.txt
@@ -226,8 +226,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MC package. It is only enabled if LAMMPS was
-built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt
index 883968e012557e2ee8d13eddef15b8bc1f6873ef..7317dd26bb3b9d4b563b0266364490fafc39d37c 100644
--- a/doc/src/fix_bond_react.txt
+++ b/doc/src/fix_bond_react.txt
@@ -312,8 +312,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_bond_swap.txt b/doc/src/fix_bond_swap.txt
index a829171f333aa3aa850fbc04c659eae6ac61ad40..3c90bb53f6d57606bf1f82870477de9055ff15db 100644
--- a/doc/src/fix_bond_swap.txt
+++ b/doc/src/fix_bond_swap.txt
@@ -165,8 +165,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MC package. It is only enabled if LAMMPS was
-built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
The settings of the "special_bond" command must be 0,1,1 in order to
use this fix, which is typical of bead-spring chains with FENE or
diff --git a/doc/src/fix_cmap.txt b/doc/src/fix_cmap.txt
index 6f3769fafe6a634770dcdedb8908540972ee5d70..ef48e8b51c6c445f3ff1d0e365ec054392ee956f 100644
--- a/doc/src/fix_cmap.txt
+++ b/doc/src/fix_cmap.txt
@@ -125,8 +125,8 @@ To function as expected this fix command must be issued {before} a
"read_restart"_read_restart.html command.
This fix can only be used if LAMMPS was built with the MOLECULE
-package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/fix_colvars.txt b/doc/src/fix_colvars.txt
index 4a1d84de64a458dbc56999885ca8246a03ba21ed..3a64840bdcc10620033873ce65a42900a7e1a866 100644
--- a/doc/src/fix_colvars.txt
+++ b/doc/src/fix_colvars.txt
@@ -106,8 +106,8 @@ fix is "extensive".
[Restrictions:]
This fix is part of the USER-COLVARS package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
There can only be one colvars fix active at a time. Since the interface
communicates only the minimum amount of information and colvars module
diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt
index e92d1e6b19c5943d4de785c916738fdd10dc8ef0..6ba713e662b50798cf0d654cd29e62f2a94c46f0 100644
--- a/doc/src/fix_deform.txt
+++ b/doc/src/fix_deform.txt
@@ -556,13 +556,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_deposit.txt b/doc/src/fix_deposit.txt
index 277ca8777ad7409e586eb16344df34168786c165..265f43bd4be218146ce5384c59b7d57b74ca3bda 100644
--- a/doc/src/fix_deposit.txt
+++ b/doc/src/fix_deposit.txt
@@ -271,8 +271,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The specified insertion region cannot be a "dynamic" region, as
defined by the "region"_region.html command.
diff --git a/doc/src/fix_dpd_energy.txt b/doc/src/fix_dpd_energy.txt
index f539bc534e76b7e667938ce4dcd78a2f9501ed4e..5e8e295de915c91c4df76d59815f2f919f0f0190 100644
--- a/doc/src/fix_dpd_energy.txt
+++ b/doc/src/fix_dpd_energy.txt
@@ -56,13 +56,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -72,8 +72,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix must be used with an additional fix that specifies time
integration, e.g. "fix nve"_fix_nve.html.
diff --git a/doc/src/fix_dpd_source.txt b/doc/src/fix_dpd_source.txt
index 04af9a28a184676e1ebc51f67dc13eb5340787a0..691cfe86f15c1840f9fd0b6c2ef1baefa7bf54bb 100644
--- a/doc/src/fix_dpd_source.txt
+++ b/doc/src/fix_dpd_source.txt
@@ -71,8 +71,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MESO package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Fix {edpd/source} must be used with the "pair_style
edpd"_pair_meso.html command. Fix {tdpd/source} must be used with the
diff --git a/doc/src/fix_efield.txt b/doc/src/fix_efield.txt
index b5a43f68aa76b5a205f50df3e6ff9325099711bb..cecfb6e6a3ce804b958fd36b89b476e6d466cd2d 100644
--- a/doc/src/fix_efield.txt
+++ b/doc/src/fix_efield.txt
@@ -156,8 +156,8 @@ system (the quantity being minimized), you MUST enable the
[Restrictions:]
This fix is part of the MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_ehex.txt b/doc/src/fix_ehex.txt
index cfcc917d012ba1dca5ff08afd75fb718bb101f82..75651e21a4c5812593699735b9eaf1bc2a549bc7 100644
--- a/doc/src/fix_ehex.txt
+++ b/doc/src/fix_ehex.txt
@@ -156,8 +156,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the RIGID package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_enforce2d.txt b/doc/src/fix_enforce2d.txt
index 2925e44bda17ef8cf023a9e41c0513694d4c50fa..17ac8146fd3242d531df02ba409dba553d946b9f 100644
--- a/doc/src/fix_enforce2d.txt
+++ b/doc/src/fix_enforce2d.txt
@@ -37,13 +37,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_eos_cv.txt b/doc/src/fix_eos_cv.txt
index b94e2c64a97ebd8373b3a3dafcee2ab9ecad6ed5..b2ac0eb6b932396ab229d8a14292d65cb1d99b39 100644
--- a/doc/src/fix_eos_cv.txt
+++ b/doc/src/fix_eos_cv.txt
@@ -39,8 +39,8 @@ possible.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command also requires use of the "atom_style dpd"_atom_style.html
command.
diff --git a/doc/src/fix_eos_table.txt b/doc/src/fix_eos_table.txt
index 743c51f4157cfeffc8c59840f9f95ab3132a3d74..53b32043728d9213e15b2ff86d5b301e0dabf2c5 100644
--- a/doc/src/fix_eos_table.txt
+++ b/doc/src/fix_eos_table.txt
@@ -99,8 +99,8 @@ one that matches the specified keyword.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command also requires use of the "atom_style dpd"_atom_style.html
command.
diff --git a/doc/src/fix_eos_table_rx.txt b/doc/src/fix_eos_table_rx.txt
index f9deab61c8acebfb5ffe69966b1880e7cacff369..1a2daa0bc646f19bec6032c43a2adfb28e4d5c36 100644
--- a/doc/src/fix_eos_table_rx.txt
+++ b/doc/src/fix_eos_table_rx.txt
@@ -162,13 +162,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -178,8 +178,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command also requires use of the "atom_style dpd"_atom_style.html
command.
diff --git a/doc/src/fix_evaporate.txt b/doc/src/fix_evaporate.txt
index 6237a137fd0aa8c719d5f96f7791ebb176b669da..59dab43d9a200465ba18e883cdb2e3a4dd80b23b 100644
--- a/doc/src/fix_evaporate.txt
+++ b/doc/src/fix_evaporate.txt
@@ -84,8 +84,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_filter_corotate.txt b/doc/src/fix_filter_corotate.txt
index d1e5e12f3ef1b764d4d2d9cc35a5d8f504c27a4e..b30966c2f941de518e42f4c90463f543a21fdad5 100644
--- a/doc/src/fix_filter_corotate.txt
+++ b/doc/src/fix_filter_corotate.txt
@@ -70,8 +70,8 @@ fixes are not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Currently, it does not support "molecule templates"_molecule.html.
diff --git a/doc/src/fix_flow_gauss.txt b/doc/src/fix_flow_gauss.txt
index 843c2a66a5505d5b3c7051fd9d84897a99ea4138..46a9477aa2184e4bb7699f8462db78aaf8316bbf 100644
--- a/doc/src/fix_flow_gauss.txt
+++ b/doc/src/fix_flow_gauss.txt
@@ -111,8 +111,8 @@ flow/gauss fixes, one that specifies {fix_modify respa 3} and one with
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
No information about this fix is written to "binary restart
files"_restart.html.
diff --git a/doc/src/fix_freeze.txt b/doc/src/fix_freeze.txt
index 76a9fd3b1a2d3f3ffc8372a2cebac2ac85f9fb6f..89f2dd8179f9f6ab02cf054c24f790e9c10e7662 100644
--- a/doc/src/fix_freeze.txt
+++ b/doc/src/fix_freeze.txt
@@ -40,13 +40,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -72,8 +72,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the GRANULAR package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
There can only be a single freeze fix defined. This is because other
the "granular pair styles"_pair_gran.html treat frozen particles
diff --git a/doc/src/fix_gcmc.txt b/doc/src/fix_gcmc.txt
index 394690ea5d173b898b51acc6ee9b2094aa5d26b1..6b9a02eecada3fa7f2e8f2886b8ff6b88a106d7c 100644
--- a/doc/src/fix_gcmc.txt
+++ b/doc/src/fix_gcmc.txt
@@ -403,8 +403,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MC package. It is only enabled if LAMMPS was
-built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
Do not set "neigh_modify once yes" or else this fix will never be
called. Reneighboring is required.
diff --git a/doc/src/fix_gld.txt b/doc/src/fix_gld.txt
index 1c5db6157ddaca593ffc5fc70ebc59613038ae88..97c3d0e408e9ea2d4eb675a994cb7c96a579b0e6 100644
--- a/doc/src/fix_gld.txt
+++ b/doc/src/fix_gld.txt
@@ -137,8 +137,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_gle.txt b/doc/src/fix_gle.txt
index 9fdc72bf9f206f9b5a6e55267638af159810beeb..70a8e7f34246b446d4b40456945c784b11c54665 100644
--- a/doc/src/fix_gle.txt
+++ b/doc/src/fix_gle.txt
@@ -132,9 +132,9 @@ In order to perform constant-pressure simulations please use
"fix npt"_fix_nh.html, to avoid duplicate integration of the
equations of motion.
-This fix is part of the USER-MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_gravity.txt b/doc/src/fix_gravity.txt
index 832c677f81559e3893e643dc32330d0e9699a1f7..ea596c866867e89f3c4b6b8a598ead8662976e57 100644
--- a/doc/src/fix_gravity.txt
+++ b/doc/src/fix_gravity.txt
@@ -96,13 +96,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_grem.txt b/doc/src/fix_grem.txt
index 506e266505a54248fee381d4135802122fd86aba..e096d4bd3cbe8ee0d461444985ac932f38bab787 100644
--- a/doc/src/fix_grem.txt
+++ b/doc/src/fix_grem.txt
@@ -91,8 +91,8 @@ by this fix to add the rescaled kinetic pressure as part of
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_imd.txt b/doc/src/fix_imd.txt
index 8e21a1619b8647b0ba6c497540ac2b7c4973b36a..a58cfdb3d396d7bec9ad67324bec3ba0bbe60fb1 100644
--- a/doc/src/fix_imd.txt
+++ b/doc/src/fix_imd.txt
@@ -143,8 +143,8 @@ fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
When used in combination with VMD, a topology or coordinate file has
to be loaded, which matches (in number and ordering of atoms) the
diff --git a/doc/src/fix_ipi.txt b/doc/src/fix_ipi.txt
index eba30ef08821d7c55ab06270d18a4300da293de5..b115aba7dfa38d5a85a0aee82000d2e8bf568fcd 100644
--- a/doc/src/fix_ipi.txt
+++ b/doc/src/fix_ipi.txt
@@ -81,9 +81,9 @@ define an external potential acting on the atoms that are moved by
i-PI.
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. Because of
-the use of UNIX domain sockets, this fix will only work in a UNIX
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. Because of the
+use of UNIX domain sockets, this fix will only work in a UNIX
environment.
[Related commands:]
diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt
index 4d7728cdba4b918d1cc8926f2aaef266bc20a42b..e97c7c3c3785011551f6c7b476c709acc2ec1925 100644
--- a/doc/src/fix_langevin.txt
+++ b/doc/src/fix_langevin.txt
@@ -270,13 +270,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_langevin_eff.txt b/doc/src/fix_langevin_eff.txt
index cf42f9c036b2dc4da5a9f2afb98296d8a78862d4..e55e40c6c80ea7e822222ffc84eedbbf9841d9e3 100644
--- a/doc/src/fix_langevin_eff.txt
+++ b/doc/src/fix_langevin_eff.txt
@@ -93,8 +93,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] none
This fix is part of the USER-EFF package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_langevin_spin.txt b/doc/src/fix_langevin_spin.txt
index 1b1936376de0fe29450cf9b4c2db7e298e6d64ab..7bb25e0a687af2c0af3f14a1ccd9d0c9a73e7257 100644
--- a/doc/src/fix_langevin_spin.txt
+++ b/doc/src/fix_langevin_spin.txt
@@ -76,9 +76,9 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
-The {langevin/spin} fix is part of the SPIN package.
-This style is only enabled if LAMMPS was built with this package.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+The {langevin/spin} fix is part of the SPIN package. This style is
+only enabled if LAMMPS was built with this package. See the "Build
+package"_Build_package.html doc page for more info.
The numerical integration has to be performed with {fix nve/spin}
when {fix langevin/spin} is enabled.
diff --git a/doc/src/fix_latte.txt b/doc/src/fix_latte.txt
index 9bc589520bc3689a4ad4370f99e92b9977bb209c..17beb6720689aea51030ba28698ad41138191977 100644
--- a/doc/src/fix_latte.txt
+++ b/doc/src/fix_latte.txt
@@ -136,8 +136,8 @@ quantity being minimized), you MUST enable the
[Restrictions:]
This fix is part of the LATTE package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
You must use metal units, as set by the "units"_units command to use
this fix.
@@ -154,8 +154,8 @@ doing 99% or more of the work to compute quantum-accurate forces.
NOTE: NEB calculations can be done using this fix using multiple
replicas and running LAMMPS in parallel. However, each replica must
be run on a single MPI task. For details, see the "neb"_neb.html
-command and -partition command-line explained in "Section
-2.6"_Section_start.html#start_6 of the manual.
+command doc page and the "-partition command-line
+switch"_Run_options.html
[Related commands:] none
diff --git a/doc/src/fix_lb_fluid.txt b/doc/src/fix_lb_fluid.txt
index 5347f0147f4be26b5e3b61877084925003c4fbf4..1a5239782268f34870cd3ec3faac1b560f7c451a 100644
--- a/doc/src/fix_lb_fluid.txt
+++ b/doc/src/fix_lb_fluid.txt
@@ -307,8 +307,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-LB package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix can only be used with an orthogonal simulation domain.
diff --git a/doc/src/fix_lb_momentum.txt b/doc/src/fix_lb_momentum.txt
index a58c5d257eabeb012284a3fd2dd3e2eecd20c1d7..408978f64c40cb1eff59995ed62481c1200b4960 100644
--- a/doc/src/fix_lb_momentum.txt
+++ b/doc/src/fix_lb_momentum.txt
@@ -61,8 +61,8 @@ Can only be used if a lattice-Boltzmann fluid has been created via the
command.
This fix is part of the USER-LB package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_lb_pc.txt b/doc/src/fix_lb_pc.txt
index bd121b7813253cb3b9e547235db88cdc85e5e472..05b5eb20a21ce268024eda47782fae035496efb2 100644
--- a/doc/src/fix_lb_pc.txt
+++ b/doc/src/fix_lb_pc.txt
@@ -42,8 +42,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-LB package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Can only be used if a lattice-Boltzmann fluid has been created via the
"fix lb/fluid"_fix_lb_fluid.html command, and must come after this
diff --git a/doc/src/fix_lb_rigid_pc_sphere.txt b/doc/src/fix_lb_rigid_pc_sphere.txt
index bc8fa2ea257212f588dabe01b824d98ff4289a1b..ddaa552ecc15165daa71f813b532e3737f5f6e80 100644
--- a/doc/src/fix_lb_rigid_pc_sphere.txt
+++ b/doc/src/fix_lb_rigid_pc_sphere.txt
@@ -122,8 +122,8 @@ of the "run"_run.html command. These fixes are not invoked during
[Restrictions:]
This fix is part of the USER-LB package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Can only be used if a lattice-Boltzmann fluid has been created via the
"fix lb/fluid"_fix_lb_fluid.html command, and must come after this
diff --git a/doc/src/fix_lb_viscous.txt b/doc/src/fix_lb_viscous.txt
index 7bbdd204e34d1a4fae91fcf2f4bb2aa4c32fefbf..ba91a2cd541984096f79925097f2c38d9db17eee 100644
--- a/doc/src/fix_lb_viscous.txt
+++ b/doc/src/fix_lb_viscous.txt
@@ -70,8 +70,8 @@ for details."
[Restrictions:]
This fix is part of the USER-LB package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Can only be used if a lattice-Boltzmann fluid has been created via the
"fix lb/fluid"_fix_lb_fluid.html command, and must come after this
diff --git a/doc/src/fix_manifoldforce.txt b/doc/src/fix_manifoldforce.txt
index aa32a875bfe2f77de00cdbee7f87085af8443a94..8dd992170b1b73a77fe09d865bc83f844f302a85 100644
--- a/doc/src/fix_manifoldforce.txt
+++ b/doc/src/fix_manifoldforce.txt
@@ -24,10 +24,14 @@ fix constrain all manifoldforce sphere 5.0
[Description:]
-This fix subtracts each time step from the force the component along the normal of the specified "manifold"_manifolds.html.
-This can be used in combination with "minimize"_minimize.html to remove overlap between particles while
-keeping them (roughly) constrained to the given manifold, e.g. to set up a run with "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html.
-I have found that only {hftn} and {quickmin} with a very small time step perform adequately though.
+This fix subtracts each time step from the force the component along
+the normal of the specified "manifold"_manifolds.html. This can be
+used in combination with "minimize"_minimize.html to remove overlap
+between particles while keeping them (roughly) constrained to the
+given manifold, e.g. to set up a run with "fix
+nve/manifold/rattle"_fix_nve_manifold_rattle.html. I have found that
+only {hftn} and {quickmin} with a very small time step perform
+adequately though.
:line
@@ -45,17 +49,18 @@ minimization"_minimize.html.
[Restrictions:]
-This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
-was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+This fix is part of the USER-MANIFOLD package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
-Only use this with {min_style hftn} or {min_style quickmin}. If not, the constraints
-will not be satisfied very well at all. A warning is generated if the {min_style} is
-incompatible but no error.
+Only use this with {min_style hftn} or {min_style quickmin}. If not,
+the constraints will not be satisfied very well at all. A warning is
+generated if the {min_style} is incompatible but no error.
:line
[Related commands:]
-"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html, "fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html
+"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html, "fix
+nvt/manifold/rattle"_fix_nvt_manifold_rattle.html
diff --git a/doc/src/fix_meso.txt b/doc/src/fix_meso.txt
index 8f5ad29929313fc6d1b31169b140b5dad0d46959..8c0ce5a9b7b729b42ce2f13a3c612c1ea46cd096 100644
--- a/doc/src/fix_meso.txt
+++ b/doc/src/fix_meso.txt
@@ -42,8 +42,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-SPH package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_meso_stationary.txt b/doc/src/fix_meso_stationary.txt
index 38d26b34d67ad7d0a38eec70c7f28583394778eb..1a546efec06e64e6f125b53e006f78db7e2f5d69 100644
--- a/doc/src/fix_meso_stationary.txt
+++ b/doc/src/fix_meso_stationary.txt
@@ -43,8 +43,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-SPH package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_momentum.txt b/doc/src/fix_momentum.txt
index f7fe35be2a9fd3825b82db9a0cd3d3cca76dfb56..aeedad07197163423a2a3db32025095294fbf676 100644
--- a/doc/src/fix_momentum.txt
+++ b/doc/src/fix_momentum.txt
@@ -67,13 +67,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_mscg.txt b/doc/src/fix_mscg.txt
index aadc3caf5aa909c8ff32f23d51bcac2d3f0919ab..1ad780412756a117c28e8ac193295206e153c811 100644
--- a/doc/src/fix_mscg.txt
+++ b/doc/src/fix_mscg.txt
@@ -103,8 +103,8 @@ dihedrals a bead can have in the coarse-grained model.
[Restrictions:]
This fix is part of the MSCG package. It is only enabled if LAMMPS was
-built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
The MS-CG library uses C++11, which may not be supported by older
compilers. The MS-CG library also has some additional numeric library
diff --git a/doc/src/fix_msst.txt b/doc/src/fix_msst.txt
index 91ffbbb0fa147ea6e520ac75658d114198654da6..e31f61e5f7c815c8a0253b3db69b6f8c8fcb6a35 100644
--- a/doc/src/fix_msst.txt
+++ b/doc/src/fix_msst.txt
@@ -162,8 +162,8 @@ are "extensive"; the vector values are "intensive".
[Restrictions:]
This fix style is part of the SHOCK package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
All cell dimensions must be periodic. This fix can not be used with a
triclinic cell. The MSST fix has been tested only for the group-ID
diff --git a/doc/src/fix_mvv_dpd.txt b/doc/src/fix_mvv_dpd.txt
index 1e9bf631fde813d95546bcc6638b3c24172a0e79..507f271469df32842ba0dbd29630c513d79c8c3c 100644
--- a/doc/src/fix_mvv_dpd.txt
+++ b/doc/src/fix_mvv_dpd.txt
@@ -77,8 +77,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MESO package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_neb.txt b/doc/src/fix_neb.txt
index 5341d6999c4e6b0f5220af5d5d77ebd331176fbb..d331d9ad75fbf7c2a203bfe68bb1035abcfd410a 100644
--- a/doc/src/fix_neb.txt
+++ b/doc/src/fix_neb.txt
@@ -203,8 +203,8 @@ as invoked by the "minimize"_minimize.html command via the
[Restrictions:]
This command can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/fix_nh.txt b/doc/src/fix_nh.txt
index f6b155e2db2c66bad86e479a8d1ee67d86fd51a7..644ced4bdc6c0aaba54d27dc59004aebb0f16022 100644
--- a/doc/src/fix_nh.txt
+++ b/doc/src/fix_nh.txt
@@ -491,13 +491,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_nh_eff.txt b/doc/src/fix_nh_eff.txt
index afb319bfa51f6c518b213f63f75cbab14741e0bc..d7c045770860e1792dacb682170f6e64034282e6 100644
--- a/doc/src/fix_nh_eff.txt
+++ b/doc/src/fix_nh_eff.txt
@@ -101,8 +101,8 @@ for details.
[Restrictions:]
This fix is part of the USER-EFF package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Other restriction discussed on the doc page for the "fix nvt, npt, and
nph"_fix_nh.html commands also apply.
diff --git a/doc/src/fix_nh_uef.txt b/doc/src/fix_nh_uef.txt
index 0e73c57e089b44643834f1b78fad2c1f046281f4..ae403cafd1d8ff7c5ee8f6e7fcc0589dd9437cb6 100644
--- a/doc/src/fix_nh_uef.txt
+++ b/doc/src/fix_nh_uef.txt
@@ -182,8 +182,8 @@ The fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-UEF package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Due to requirements of the boundary conditions, when the {strain}
keyword is set to zero (or unset), the initial simulation box must be
diff --git a/doc/src/fix_nph_asphere.txt b/doc/src/fix_nph_asphere.txt
index 6bfd9d3fe26085cff9f1d3c5c0b32fbbd5c5948a..5cabf930e73b00b9eb2e46701c026b1f37397985 100644
--- a/doc/src/fix_nph_asphere.txt
+++ b/doc/src/fix_nph_asphere.txt
@@ -87,13 +87,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -132,8 +132,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the ASPHERE package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
diff --git a/doc/src/fix_nph_body.txt b/doc/src/fix_nph_body.txt
index 377e1980eb3cf8c9c46b41baa6a14b2e379c7816..e04c240de951965f94124617a1e88e658f5b8402 100644
--- a/doc/src/fix_nph_body.txt
+++ b/doc/src/fix_nph_body.txt
@@ -86,13 +86,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -131,8 +131,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the BODY package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style body"_atom_style.html
diff --git a/doc/src/fix_nph_sphere.txt b/doc/src/fix_nph_sphere.txt
index 8b7639c4c6a7467e9107db127699efabea8a8993..f94c057c93f300a911b5f524087187038f58fc48 100644
--- a/doc/src/fix_nph_sphere.txt
+++ b/doc/src/fix_nph_sphere.txt
@@ -96,13 +96,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_nphug.txt b/doc/src/fix_nphug.txt
index 0bd5153152b4afdcd8a0048b0472df81ad63ed08..855a4c9ae49fb49cf7929b59f796a8dc6dc89a30 100644
--- a/doc/src/fix_nphug.txt
+++ b/doc/src/fix_nphug.txt
@@ -146,13 +146,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -208,8 +208,8 @@ shock calculated from the RH conditions. They have units of distance/time.
[Restrictions:]
This fix style is part of the SHOCK package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
All the usual restrictions for "fix npt"_fix_nh.html apply,
plus the additional ones mentioned above.
diff --git a/doc/src/fix_npt_asphere.txt b/doc/src/fix_npt_asphere.txt
index 9c95a80d3310a08e3e8ddecd12af471419340773..194f4ff499ea8763112456accddb26f308fb738e 100644
--- a/doc/src/fix_npt_asphere.txt
+++ b/doc/src/fix_npt_asphere.txt
@@ -111,13 +111,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -157,8 +157,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the ASPHERE package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
diff --git a/doc/src/fix_npt_body.txt b/doc/src/fix_npt_body.txt
index 0d2b797299dd4d3c803e96cbfb1f4030ac13c032..1d608137b619e5b989c212a8aad83d92753c0570 100644
--- a/doc/src/fix_npt_body.txt
+++ b/doc/src/fix_npt_body.txt
@@ -110,13 +110,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -156,8 +156,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the BODY package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style body"_atom_style.html
diff --git a/doc/src/fix_npt_sphere.txt b/doc/src/fix_npt_sphere.txt
index dcb25d1c737b39f3a2bcea9a4e01eb1a011fbb60..6ebb68e176311fe1eda0c1d71a2c84a6861a8366 100644
--- a/doc/src/fix_npt_sphere.txt
+++ b/doc/src/fix_npt_sphere.txt
@@ -121,13 +121,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_nve.txt b/doc/src/fix_nve.txt
index e446b273977b4dd05865de697b3d10af144bb149..2347f957aef8636dc1e8ab2261cee737c93de8e5 100644
--- a/doc/src/fix_nve.txt
+++ b/doc/src/fix_nve.txt
@@ -40,13 +40,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_nve_asphere.txt b/doc/src/fix_nve_asphere.txt
index b7fb3e922ce418d666b0cfe9b87170daa7c195ed..bd9e4ae8731b35fdc140063e6f76c80dea58ef61 100644
--- a/doc/src/fix_nve_asphere.txt
+++ b/doc/src/fix_nve_asphere.txt
@@ -51,13 +51,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -67,8 +67,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This fix is part of the ASPHERE package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
diff --git a/doc/src/fix_nve_asphere_noforce.txt b/doc/src/fix_nve_asphere_noforce.txt
index e57417bda5e1657ca69a621840ea82f2199b14b1..94b627bf1be5c1cfa813613af4dc0b4b7fba7fae 100644
--- a/doc/src/fix_nve_asphere_noforce.txt
+++ b/doc/src/fix_nve_asphere_noforce.txt
@@ -46,8 +46,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the ASPHERE package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
diff --git a/doc/src/fix_nve_body.txt b/doc/src/fix_nve_body.txt
index d072bfa1611770921b5e97f7f1fb2bce2128c748..1a9efb5e139f99efd1ed8008b6e4fdcb10c6b84e 100644
--- a/doc/src/fix_nve_body.txt
+++ b/doc/src/fix_nve_body.txt
@@ -44,8 +44,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the BODY package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style body"_atom_style.html
diff --git a/doc/src/fix_nve_dot.txt b/doc/src/fix_nve_dot.txt
index 1041a248d8784a0cfae575f1d5a515a4e2c76e35..54b199c1df3de390dedebab8a54c880f386e5102 100644
--- a/doc/src/fix_nve_dot.txt
+++ b/doc/src/fix_nve_dot.txt
@@ -44,8 +44,8 @@ A technical report with more information on this integrator can be found
[Restrictions:]
These pair styles can only be used if LAMMPS was built with the
-"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package.
+See the "Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_nve_dotc_langevin.txt b/doc/src/fix_nve_dotc_langevin.txt
index 68c1b4232830fe1a2eaaadaf8ce832474a394f13..c6148a71656bcff2eac8d10ea3b355172756acd5 100644
--- a/doc/src/fix_nve_dotc_langevin.txt
+++ b/doc/src/fix_nve_dotc_langevin.txt
@@ -122,8 +122,8 @@ A technical report with more information on this integrator can be found
[Restrictions:]
These pair styles can only be used if LAMMPS was built with the
-"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package.
+See the "Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_nve_eff.txt b/doc/src/fix_nve_eff.txt
index 7343ddc4292df0f02e7eadef7829ec8041ccae5b..556b95deba6d5400466d088c8b34c9bdf1d24e56 100644
--- a/doc/src/fix_nve_eff.txt
+++ b/doc/src/fix_nve_eff.txt
@@ -43,8 +43,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-EFF package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_nve_line.txt b/doc/src/fix_nve_line.txt
index dd5101489b00d27a707ac4c044bed5f4a84be643..896e3b810d83049198c1e0f7f630d545836698c7 100644
--- a/doc/src/fix_nve_line.txt
+++ b/doc/src/fix_nve_line.txt
@@ -44,8 +44,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the ASPHERE package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that particles be line segments as defined by the
"atom_style line"_atom_style.html command.
diff --git a/doc/src/fix_nve_manifold_rattle.txt b/doc/src/fix_nve_manifold_rattle.txt
index b333d093fb8eec0ce08d16c8affb3a2cf481c802..5301ea603ce65747344f68fe42bf93233ecccac7 100644
--- a/doc/src/fix_nve_manifold_rattle.txt
+++ b/doc/src/fix_nve_manifold_rattle.txt
@@ -78,8 +78,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MANIFOLD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
:line
diff --git a/doc/src/fix_nve_sphere.txt b/doc/src/fix_nve_sphere.txt
index 6e259bdb8e7803482ee894d68d2a354dcefc0e6f..818940a9bd1ebda7b50c44120a209aaa4ef4e270 100644
--- a/doc/src/fix_nve_sphere.txt
+++ b/doc/src/fix_nve_sphere.txt
@@ -71,13 +71,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_nve_spin.txt b/doc/src/fix_nve_spin.txt
index e31185bc889e785030dbef61a36019a7ba086af0..08f0eab61dcfd4f505d1c840f0a0fb434c336c18 100644
--- a/doc/src/fix_nve_spin.txt
+++ b/doc/src/fix_nve_spin.txt
@@ -47,9 +47,9 @@ in "(Tranchida)"_#Tranchida1.
[Restrictions:]
-This fix style can only be used if LAMMPS was built with the
-SPIN package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+This fix style can only be used if LAMMPS was built with the SPIN
+package. See the "Build package"_Build_package.html doc page for more
+info.
To use the spin algorithm, it is necessary to define a map with
the atom_modify command. Typically, by adding the command:
diff --git a/doc/src/fix_nve_tri.txt b/doc/src/fix_nve_tri.txt
index ebdda19e36428828bdbeb6558b3202cc00982a80..c14907ca02596e448a3ee9004574f93bd3fd2e35 100644
--- a/doc/src/fix_nve_tri.txt
+++ b/doc/src/fix_nve_tri.txt
@@ -44,8 +44,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the ASPHERE package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that particles be triangles as defined by the
"atom_style tri"_atom_style.html command.
diff --git a/doc/src/fix_nvk.txt b/doc/src/fix_nvk.txt
index e3189f8e8a3981b76f848f64080b6baa50500738..98f63487b73144d9cc155ffd937147d0358d618b 100644
--- a/doc/src/fix_nvk.txt
+++ b/doc/src/fix_nvk.txt
@@ -54,9 +54,9 @@ the simulation box. Therefore, the group must be set to all.
This fix has not yet been implemented to work with the RESPA integrator.
-This fix is part of the USER-MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:] none
diff --git a/doc/src/fix_nvt_asphere.txt b/doc/src/fix_nvt_asphere.txt
index 7b9763717574062e64b9e812bd201d8174cb4880..a2187f8495f63ddec697337b417a16f53348da5f 100644
--- a/doc/src/fix_nvt_asphere.txt
+++ b/doc/src/fix_nvt_asphere.txt
@@ -92,13 +92,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -133,8 +133,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the ASPHERE package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
diff --git a/doc/src/fix_nvt_body.txt b/doc/src/fix_nvt_body.txt
index 4493a892777221ee5c4375769438f8c02cfaf570..62c7cfecf822973c40c343c17eb2c3e54e3a6d74 100644
--- a/doc/src/fix_nvt_body.txt
+++ b/doc/src/fix_nvt_body.txt
@@ -91,13 +91,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -132,8 +132,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the BODY package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion as defined by the "atom_style body"_atom_style.html
diff --git a/doc/src/fix_nvt_manifold_rattle.txt b/doc/src/fix_nvt_manifold_rattle.txt
index 1b4ad7916626ea3550b69c4aef84514318acb30e..0c4b81aa32d83fa348ec660116a0ce8b53b56a34 100644
--- a/doc/src/fix_nvt_manifold_rattle.txt
+++ b/doc/src/fix_nvt_manifold_rattle.txt
@@ -27,8 +27,6 @@ keyword = {temp} or {tchain} or {every}
N = length of thermostat chain (1 = single thermostat)
{every} value = N
N = print info about iteration every N steps. N = 0 means no output :pre
-
-
:ule
[Examples:]
@@ -59,20 +57,18 @@ minimization"_minimize.html.
:line
-
[Restrictions:]
-This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
-was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+This fix is part of the USER-MANIFOLD package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
:line
-
[Related commands:]
-"fix nve/manifold/rattle"_fix_nvt_manifold_rattle.html, "fix manifoldforce"_fix_manifoldforce.html
-[Default:] every = 0
+"fix nve/manifold/rattle"_fix_nvt_manifold_rattle.html, "fix
+manifoldforce"_fix_manifoldforce.html [Default:] every = 0
:line
diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt
index 9eb506536910f574867121e26d6dee23ff8071a0..97a864a231d32cbc503031840d17384fcfa8e44f 100644
--- a/doc/src/fix_nvt_sllod.txt
+++ b/doc/src/fix_nvt_sllod.txt
@@ -115,13 +115,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_nvt_sllod_eff.txt b/doc/src/fix_nvt_sllod_eff.txt
index 0200d5cb002312980fb21344687676dd06d74fee..5cba15c8cf3f3af230263ba9215efca001144726 100644
--- a/doc/src/fix_nvt_sllod_eff.txt
+++ b/doc/src/fix_nvt_sllod_eff.txt
@@ -69,8 +69,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-EFF package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix works best without Nose-Hoover chain thermostats, i.e. using
tchain = 1. Setting tchain to larger values can result in poor
diff --git a/doc/src/fix_nvt_sphere.txt b/doc/src/fix_nvt_sphere.txt
index a87e4abe677ed4c44d6b54470e5d2ee9539d8f7c..75222e0de81d09462d5b1465c3f232f2a4903c44 100644
--- a/doc/src/fix_nvt_sphere.txt
+++ b/doc/src/fix_nvt_sphere.txt
@@ -102,13 +102,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_orient.txt b/doc/src/fix_orient.txt
index 7552bea8c5bcfb73867322c90f502887276aacf9..9d8e4e86282727eaa85292803f1095e2224596f8 100644
--- a/doc/src/fix_orient.txt
+++ b/doc/src/fix_orient.txt
@@ -151,8 +151,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix should only be used with fcc or bcc lattices.
diff --git a/doc/src/fix_phonon.txt b/doc/src/fix_phonon.txt
index 30e5864e3d16af76cdc86ea021c0cf80fda6b2ff..0c449899df2a15965649820af6202e7f06bd702f 100644
--- a/doc/src/fix_phonon.txt
+++ b/doc/src/fix_phonon.txt
@@ -171,11 +171,11 @@ temperature of the system should not exceed the melting temperature to
keep the system in its solid state.
This fix is part of the USER-PHONON package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
-This fix requires LAMMPS be built with an FFT library. See the
-"Making LAMMPS"_Section_start.html#start_2 section for more info.
+This fix requires LAMMPS be built with an FFT library. See the "Build
+settings"_Build_settings.html doc page for details.
[Related commands:]
diff --git a/doc/src/fix_pimd.txt b/doc/src/fix_pimd.txt
index b61b3f3065a7c0c57f5994a2a2a23d6ed8778407..a82624497308567c3528413e6c052a63c693605c 100644
--- a/doc/src/fix_pimd.txt
+++ b/doc/src/fix_pimd.txt
@@ -136,8 +136,8 @@ read_restart system_$\{ibead\}.restart2 :pre
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
A PIMD simulation can be initialized with a single data file read via
the "read_data"_read_data.html command. However, this means all
diff --git a/doc/src/fix_poems.txt b/doc/src/fix_poems.txt
index 1a79c2a048fb75dc04935e978fdc50ae84ab9e69..52ab0ca44d7a740113441c0dd9d9e9a55f9b84a3 100644
--- a/doc/src/fix_poems.txt
+++ b/doc/src/fix_poems.txt
@@ -123,8 +123,8 @@ minimization"_minimize.html.
This fix is part of the POEMS package. It is only enabled if LAMMPS
was built with that package, which also requires the POEMS library be
-built and linked with LAMMPS. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built and linked with LAMMPS. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_pour.txt b/doc/src/fix_pour.txt
index e58d8ebc3ad90069a45cfd92ae504ce4656305dc..65f01c00fb85d7335afa734263a4c7da0a71255a 100644
--- a/doc/src/fix_pour.txt
+++ b/doc/src/fix_pour.txt
@@ -245,8 +245,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the GRANULAR package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
For 3d simulations, a gravity fix in the -z direction must be defined
for use in conjunction with this fix. For 2d simulations, gravity
diff --git a/doc/src/fix_precession_spin.txt b/doc/src/fix_precession_spin.txt
index fafe78448be133680f5b22711403262f1f28086b..d58cd622b0913de70a3674396bc856771c1c9212 100644
--- a/doc/src/fix_precession_spin.txt
+++ b/doc/src/fix_precession_spin.txt
@@ -75,10 +75,10 @@ files"_restart.html.
[Restrictions:]
-The {precession/spin} style is part of the SPIN package.
-This style is only enabled if LAMMPS was built with this package, and
-if the atom_style "spin" was declared.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+The {precession/spin} style is part of the SPIN package. This style
+is only enabled if LAMMPS was built with this package, and if the
+atom_style "spin" was declared. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_python_invoke.txt b/doc/src/fix_python_invoke.txt
index 5e0c0369a54b62f81c5c14c6360d182c1f655df0..2a0124e6bfc0dd01d65f3b47d76df3a7de1bebc4 100644
--- a/doc/src/fix_python_invoke.txt
+++ b/doc/src/fix_python_invoke.txt
@@ -62,9 +62,9 @@ case not work or in the worst case result in undefined behavior.
[Restrictions:]
-This fix is part of the PYTHON package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+This fix is part of the PYTHON package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Building LAMMPS with the PYTHON package will link LAMMPS with the
Python library on your system. Settings to enable this are in the
diff --git a/doc/src/fix_python_move.txt b/doc/src/fix_python_move.txt
index a4e0eb39376ea0945bd667ce6625c406b697534a..c64ee788af9354955eb9fd2b63d07f8dcf773945 100644
--- a/doc/src/fix_python_move.txt
+++ b/doc/src/fix_python_move.txt
@@ -91,8 +91,8 @@ minimization"_minimize.html.
[Restrictions:]
This pair style is part of the PYTHON package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_qbmsst.txt b/doc/src/fix_qbmsst.txt
index e96bd97f4587cfa7446b5adc5606a6f4e13df09d..546d8c0813235c18868dfc47ad07b60d799e4d1d 100644
--- a/doc/src/fix_qbmsst.txt
+++ b/doc/src/fix_qbmsst.txt
@@ -189,8 +189,8 @@ in the command "fix qtb"_fix_qtb.html.
[Restrictions:]
This fix style is part of the USER-QTB package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
All cell dimensions must be periodic. This fix can not be used with a
triclinic cell. The QBMSST fix has been tested only for the group-ID
diff --git a/doc/src/fix_qeq.txt b/doc/src/fix_qeq.txt
index 27fb613ef957fc91f280f5eccf7328afcc1cdb35..46d2dd918cfc9f260a5307bdbd7657c8a671fa56 100644
--- a/doc/src/fix_qeq.txt
+++ b/doc/src/fix_qeq.txt
@@ -187,8 +187,8 @@ Thexe fixes are invoked during "energy minimization"_minimize.html.
[Restrictions:]
These fixes are part of the QEQ package. They are only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_qeq_comb.txt b/doc/src/fix_qeq_comb.txt
index 99e86df030fb80215b1dfceab6d521fd8f4167f8..714d03f6020f398d04fb3ee67d8f395c3f9a9a21 100644
--- a/doc/src/fix_qeq_comb.txt
+++ b/doc/src/fix_qeq_comb.txt
@@ -68,13 +68,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt
index cf16daf84731096ec617c9abce809de80764ee73..b62d46d9de3a21e76a4f9405cc8acabaaa7009a0 100644
--- a/doc/src/fix_qeq_reax.txt
+++ b/doc/src/fix_qeq_reax.txt
@@ -86,13 +86,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -102,8 +102,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This fix is part of the USER-REAXC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix does not correctly handle interactions
involving multiple periodic images of the same atom. Hence, it should not
diff --git a/doc/src/fix_qmmm.txt b/doc/src/fix_qmmm.txt
index 657ee841810a25338390cb7c14d6218691dfd6c1..2dbf935f93d3e82d7db6cbf8488da63e9d57812d 100644
--- a/doc/src/fix_qmmm.txt
+++ b/doc/src/fix_qmmm.txt
@@ -54,8 +54,8 @@ fix is not invoked during "energy minimization"_minimize.html.
This fix is part of the USER-QMMM package. It is only enabled if
LAMMPS was built with that package. It also requires building a
-library provided with LAMMPS. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+library provided with LAMMPS. See the "Build
+package"_Build_package.html doc page for more info.
The fix is only functional when LAMMPS is built as a library and
linked with a compatible QM program and a QM/MM frontend into a QM/MM
diff --git a/doc/src/fix_qtb.txt b/doc/src/fix_qtb.txt
index 5b212934a94780b1d6e34c8c90873519b1bcc543..c412146604d49dd4bded74ee6e97b4e885256405 100644
--- a/doc/src/fix_qtb.txt
+++ b/doc/src/fix_qtb.txt
@@ -155,8 +155,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix style is part of the USER-QTB package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
:line
diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reax_bonds.txt
index 49d61f4db80d45f1993bec664a07bc249f259ca1..06d30d871adbc423057799f1469aba3d50c505ff 100644
--- a/doc/src/fix_reax_bonds.txt
+++ b/doc/src/fix_reax_bonds.txt
@@ -79,13 +79,13 @@ issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See "Speed"_Speed.html of the manual for
more instructions on how to use the accelerated styles effectively.
@@ -101,8 +101,8 @@ which also requires the REAX library be built and linked with LAMMPS.
The fix reax/c/bonds command requires that the "pair_style
reax/c"_pair_reaxc.html be invoked. This fix is part of the
USER-REAXC package. It is only enabled if LAMMPS was built with that
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
+package. See the "Build package"_Build_package.html doc page for more
+info.
To write gzipped bond files, you must compile LAMMPS with the
-DLAMMPS_GZIP option.
diff --git a/doc/src/fix_reaxc_species.txt b/doc/src/fix_reaxc_species.txt
index 5be1c46230b477e62f07ff70c9dcf02c03ef7da3..980384ff34c778e6ee3246c91762faff19b9e37e 100644
--- a/doc/src/fix_reaxc_species.txt
+++ b/doc/src/fix_reaxc_species.txt
@@ -146,13 +146,13 @@ issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See "Speed"_Speed.html of the manual for
more instructions on how to use the accelerated styles effectively.
@@ -161,12 +161,12 @@ more instructions on how to use the accelerated styles effectively.
[Restrictions:]
-The fix species currently only works with
-"pair_style reax/c"_pair_reaxc.html and it requires that the "pair_style
+The fix species currently only works with "pair_style
+reax/c"_pair_reaxc.html and it requires that the "pair_style
reax/c"_pair_reaxc.html be invoked. This fix is part of the
USER-REAXC package. It is only enabled if LAMMPS was built with that
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
+package. See the "Build package"_Build_package.html doc page for more
+info.
To write gzipped species files, you must compile LAMMPS with the
-DLAMMPS_GZIP option.
diff --git a/doc/src/fix_rhok.txt b/doc/src/fix_rhok.txt
index 68cce694e9b46eb71275eb61b5af3ad877eb1fa5..a3d1ab702ebd6b28c55215a80d40d548017cc863 100644
--- a/doc/src/fix_rhok.txt
+++ b/doc/src/fix_rhok.txt
@@ -40,8 +40,8 @@ An example of using the interface pinning method is located in the
[Restrictions:]
This fix is part of the MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt
index d5e3b0166810dd39613d4a9105d9ac0ed43e86b9..af4b51948ecf3dd085fe7f873f4b37b93c536fe9 100644
--- a/doc/src/fix_rigid.txt
+++ b/doc/src/fix_rigid.txt
@@ -696,13 +696,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -806,8 +806,8 @@ of the "run"_run.html command. These fixes are not invoked during
[Restrictions:]
These fixes are all part of the RIGID package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Assigning a temperature via the "velocity create"_velocity.html
command to a system with "rigid bodies"_fix_rigid.html may not have
diff --git a/doc/src/fix_rx.txt b/doc/src/fix_rx.txt
index d39e41e922d16158b2f643e4b0d4eb60e900493a..ad42c577aaf279c007a3aa6a55cceea0b382ed05 100644
--- a/doc/src/fix_rx.txt
+++ b/doc/src/fix_rx.txt
@@ -192,13 +192,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -208,8 +208,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This command also requires use of the "atom_style dpd"_atom_style.html
command.
diff --git a/doc/src/fix_setforce.txt b/doc/src/fix_setforce.txt
index 14fceb7b49e87a01596f1e8f131c4aecd84d26de..4b9abba52ffee7bba246501c3fc77a8d5f495616 100644
--- a/doc/src/fix_setforce.txt
+++ b/doc/src/fix_setforce.txt
@@ -77,13 +77,13 @@ region must be used. See the region "region"_region.html command for
more information.
These accelerated styles are part of the r Kokkos package. They are
-only enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt
index ea38de41cd1ba8b0ad9f2c759db429666798f524..77bb5794f6d8e91852c1eb1857357e25e13337a9 100644
--- a/doc/src/fix_shake.txt
+++ b/doc/src/fix_shake.txt
@@ -154,13 +154,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -202,8 +202,8 @@ fixes are not invoked during "energy minimization"_minimize.html.
[Restrictions:]
These fixes are part of the RIGID package. They are only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
For computational efficiency, there can only be one shake or rattle
fix defined in a simulation.
diff --git a/doc/src/fix_shardlow.txt b/doc/src/fix_shardlow.txt
index 33db2bf7cc9e25d81e6b842e6b8282d6ed5feb07..c1be146fa6f7ed71dd7114b46f5f77d954f5b5e0 100644
--- a/doc/src/fix_shardlow.txt
+++ b/doc/src/fix_shardlow.txt
@@ -62,13 +62,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -78,8 +78,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix is currently limited to orthogonal simulation cell
geometries.
diff --git a/doc/src/fix_smd.txt b/doc/src/fix_smd.txt
index 2f083dafc337f887ab75da54c4859dd901701844..644c04eadb9efe7e64d6f51f68893e8d9e59a1e7 100644
--- a/doc/src/fix_smd.txt
+++ b/doc/src/fix_smd.txt
@@ -130,8 +130,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_smd_adjust_dt.txt b/doc/src/fix_smd_adjust_dt.txt
index 740b10559d8aced34b4c1428bb355b20c144f325..3535ddfcc22edee05efdaf4d2c6ab932d683ef5d 100644
--- a/doc/src/fix_smd_adjust_dt.txt
+++ b/doc/src/fix_smd_adjust_dt.txt
@@ -25,18 +25,23 @@ fix 1 all smd/adjust_dt 0.1 :pre
[Description:]
-The fix calculates a new stable time increment for use with the SMD time integrators.
+The fix calculates a new stable time increment for use with the SMD
+time integrators.
-The stable time increment is based on multiple conditions. For the SPH pair styles, a
-CFL criterion (Courant, Friedrichs & Lewy, 1928) is evaluated, which determines the speed of
-sound cannot propagate further than a typical spacing between particles within a single time step to ensure
-no information is lost. For the contact pair styles, a linear analysis of the pair potential determines a
-stable maximum time step.
+The stable time increment is based on multiple conditions. For the SPH
+pair styles, a CFL criterion (Courant, Friedrichs & Lewy, 1928) is
+evaluated, which determines the speed of sound cannot propagate
+further than a typical spacing between particles within a single time
+step to ensure no information is lost. For the contact pair styles, a
+linear analysis of the pair potential determines a stable maximum time
+step.
-This fix inquires the minimum stable time increment across all particles contained in the group for which this
-fix is defined. An additional safety factor {s_fact} is applied to the time increment.
+This fix inquires the minimum stable time increment across all
+particles contained in the group for which this fix is defined. An
+additional safety factor {s_fact} is applied to the time increment.
-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach
+Dynamics in LAMMPS.
[Restart, fix_modify, output, run start/stop, minimize info:]
@@ -45,8 +50,8 @@ Currently, no part of USER-SMD supports restarting nor minimization.
[Restrictions:]
This fix is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_smd_integrate_tlsph.txt b/doc/src/fix_smd_integrate_tlsph.txt
index cd676a51ce3cdc3eb1978e8d8d29ff7f3acc7832..029605ff7f7b5143e1ad99d5f6161fd4718a0764 100644
--- a/doc/src/fix_smd_integrate_tlsph.txt
+++ b/doc/src/fix_smd_integrate_tlsph.txt
@@ -27,22 +27,26 @@ fix 1 all smd/integrate_tlsph limit_velocity 1000 :pre
[Description:]
-The fix performs explicit time integration for particles which interact according with the Total-Lagrangian SPH pair style.
+The fix performs explicit time integration for particles which
+interact according with the Total-Lagrangian SPH pair style.
-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach
+Dynamics in LAMMPS.
-The {limit_velocity} keyword will control the velocity, scaling the norm of
-the velocity vector to max_vel in case it exceeds this velocity limit.
+The {limit_velocity} keyword will control the velocity, scaling the
+norm of the velocity vector to max_vel in case it exceeds this
+velocity limit.
[Restart, fix_modify, output, run start/stop, minimize info:]
-Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
+Currently, no part of USER-SMD supports restarting nor
+minimization. This fix has no outputs.
[Restrictions:]
This fix is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_smd_integrate_ulsph.txt b/doc/src/fix_smd_integrate_ulsph.txt
index 7f16b4b7ceabf7288252e5be36e84bda4c949465..a99574cc85d75427a5507cc90d3c69e8aece085e 100644
--- a/doc/src/fix_smd_integrate_ulsph.txt
+++ b/doc/src/fix_smd_integrate_ulsph.txt
@@ -24,7 +24,6 @@ adjust_radius values = adjust_radius_factor min_nn max_nn
limit_velocity values = max_velocity
max_velocity = maximum allowed velocity.
-
[Examples:]
fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50
@@ -32,28 +31,33 @@ fix 1 all smd/integrate_ulsph limit_velocity 1000 :pre
[Description:]
-The fix performs explicit time integration for particles which interact with the updated Lagrangian SPH pair style.
-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
+The fix performs explicit time integration for particles which
+interact with the updated Lagrangian SPH pair style.
+
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach
+Dynamics in LAMMPS.
-The {adjust_radius} keyword activates dynamic adjustment of the per-particle SPH smoothing kernel radius such that the number of neighbors per particles remains
-within the interval {min_nn} to {max_nn}. The parameter {adjust_radius_factor} determines the amount of adjustment per timestep. Typical values are
-{adjust_radius_factor} =1.02, {min_nn} =15, and {max_nn} =20.
+The {adjust_radius} keyword activates dynamic adjustment of the
+per-particle SPH smoothing kernel radius such that the number of
+neighbors per particles remains within the interval {min_nn} to
+{max_nn}. The parameter {adjust_radius_factor} determines the amount
+of adjustment per timestep. Typical values are {adjust_radius_factor}
+=1.02, {min_nn} =15, and {max_nn} =20.
The {limit_velocity} keyword will control the velocity, scaling the norm of
the velocity vector to max_vel in case it exceeds this velocity limit.
[Restart, fix_modify, output, run start/stop, minimize info:]
-Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
+Currently, no part of USER-SMD supports restarting nor
+minimization. This fix has no outputs.
[Restrictions:]
This fix is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
-
-[Related commands:]
-
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+[Related commands:] none
[Default:] none
diff --git a/doc/src/fix_smd_move_triangulated_surface.txt b/doc/src/fix_smd_move_triangulated_surface.txt
index aeabf187686e105a9af292b6e5fd93ab01216095..2a998ba8c6128b86ebd42c9e9f80ad03d07caf50 100644
--- a/doc/src/fix_smd_move_triangulated_surface.txt
+++ b/doc/src/fix_smd_move_triangulated_surface.txt
@@ -25,7 +25,6 @@ keyword = {*LINEAR} or {*WIGGLE} or {*ROTATE} :l
Px,Py,Pz = origin point of axis of rotation (distance units)
Rx,Ry,Rz = axis of rotation vector
period = period of rotation (time units) :pre
-
:ule
[Examples:]
@@ -36,9 +35,11 @@ fix 2 tool smd/move_tri_surf *ROTATE 0 0 0 5 2 1 :pre
[Description:]
-This fix applies only to rigid surfaces read from .STL files via fix "smd/wall_surface"_fix_smd_wall_surface.html .
-It updates position and velocity for the particles in the group each timestep without regard to forces on the particles.
-The rigid surfaces can thus be moved along simple trajectories during the simulation.
+This fix applies only to rigid surfaces read from .STL files via fix
+"smd/wall_surface"_fix_smd_wall_surface.html . It updates position
+and velocity for the particles in the group each timestep without
+regard to forces on the particles. The rigid surfaces can thus be
+moved along simple trajectories during the simulation.
The {*LINEAR} style moves particles with the specified constant velocity
vector V = (Vx,Vy,Vz). This style also sets the velocity of each particle
@@ -49,27 +50,30 @@ Particles are moved along (vx, vy, vz) with constant velocity until a
displacement of max_travel is reached. Then, the velocity vector is
reversed. This process is repeated.
-The {*ROTATE} style rotates particles around a rotation axis R = (Rx,Ry,Rz) that
-goes through a point P = (Px,Py,Pz). The period of the rotation is also
-specified. This style also sets the velocity of each particle to (omega cross
-Rperp) where omega is its angular velocity around the rotation axis and
-Rperp is a perpendicular vector from the rotation axis to the particle.
+The {*ROTATE} style rotates particles around a rotation axis R =
+(Rx,Ry,Rz) that goes through a point P = (Px,Py,Pz). The period of the
+rotation is also specified. This style also sets the velocity of each
+particle to (omega cross Rperp) where omega is its angular velocity
+around the rotation axis and Rperp is a perpendicular vector from the
+rotation axis to the particle.
-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach
+Dynamics in LAMMPS.
[Restart, fix_modify, output, run start/stop, minimize info:]
-Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
+Currently, no part of USER-SMD supports restarting nor
+minimization. This fix has no outputs.
[Restrictions:]
This fix is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
-
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
-"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html, "smd/wall_surface"_fix_smd_wall_surface.html
+"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html,
+"smd/wall_surface"_fix_smd_wall_surface.html
[Default:] none
diff --git a/doc/src/fix_smd_setvel.txt b/doc/src/fix_smd_setvel.txt
index 6634751d6ad9e1ef17333982a7826b1c1e7d724b..b170eff8608c4465c77d02a4ff5a0d726c8e110b 100644
--- a/doc/src/fix_smd_setvel.txt
+++ b/doc/src/fix_smd_setvel.txt
@@ -76,8 +76,8 @@ the "run"_run.html command.
[Restrictions:]
This fix is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:] none
diff --git a/doc/src/fix_smd_wall_surface.txt b/doc/src/fix_smd_wall_surface.txt
index a19b2c4cfb7eb2478ca21f684589491127b71eab..dc3625e95ed18df89d863785613a5241d80ece76 100644
--- a/doc/src/fix_smd_wall_surface.txt
+++ b/doc/src/fix_smd_wall_surface.txt
@@ -17,9 +17,7 @@ smd/wall_surface = style name of this fix command :l
arg = {file} :l
{file} = file name of a triangular mesh in stl format :pre
type = particle type to be given to the new particles created by this fix :l
-mol-ID = molecule-ID to be given to the new particles created by this fix (must be >= 65535) :l
-
-:ule
+mol-ID = molecule-ID to be given to the new particles created by this fix (must be >= 65535) :l,ule
[Examples:]
@@ -27,32 +25,47 @@ fix stl_surf all smd/wall_surface tool.stl 2 65535 :pre
[Description:]
-This fix creates reads a triangulated surface from a file in .STL format.
-For each triangle, a new particle is created which stores the barycenter of the triangle and the vertex positions.
-The radius of the new particle is that of the minimum circle which encompasses the triangle vertices.
+This fix creates reads a triangulated surface from a file in .STL
+format. For each triangle, a new particle is created which stores the
+barycenter of the triangle and the vertex positions. The radius of
+the new particle is that of the minimum circle which encompasses the
+triangle vertices.
-The triangulated surface can be used as a complex rigid wall via the "smd/tri_surface"_pair_smd_triangulated_surface.html pair style.
-It is possible to move the triangulated surface via the "smd/move_tri_surf"_fix_smd_move_triangulated_surface.html fix style.
+The triangulated surface can be used as a complex rigid wall via the
+"smd/tri_surface"_pair_smd_triangulated_surface.html pair style. It
+is possible to move the triangulated surface via the
+"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html fix style.
-Immediately after a .STL file has been read, the simulation needs to be run for 0 timesteps in order to properly register the new particles
-in the system. See the "funnel_flow" example in the USER-SMD examples directory.
+Immediately after a .STL file has been read, the simulation needs to
+be run for 0 timesteps in order to properly register the new particles
+in the system. See the "funnel_flow" example in the USER-SMD examples
+directory.
-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach
+Dynamics in LAMMPS.
[Restart, fix_modify, output, run start/stop, minimize info:]
-Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
+Currently, no part of USER-SMD supports restarting nor
+minimization. This fix has no outputs.
[Restrictions:]
This fix is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info. The molecule ID given to the particles created by this fix have to be equal to or larger than 65535.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+The molecule ID given to the particles created by this fix have to be
+equal to or larger than 65535.
-Within each .STL file, only a single triangulated object must be present, even though the STL format allows for the possibility of multiple objects in one file.
+Within each .STL file, only a single triangulated object must be
+present, even though the STL format allows for the possibility of
+multiple objects in one file.
[Related commands:]
-"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html, "smd/move_tri_surf"_fix_smd_move_triangulated_surface.html, "smd/tri_surface"_pair_smd_triangulated_surface.html
+"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html,
+"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html,
+"smd/tri_surface"_pair_smd_triangulated_surface.html
[Default:] none
diff --git a/doc/src/fix_srd.txt b/doc/src/fix_srd.txt
index 893557b9acad71bd2f1be0690a3b0694b68022f6..557eee1cfc65738f56609a576882bd06c8b7224f 100644
--- a/doc/src/fix_srd.txt
+++ b/doc/src/fix_srd.txt
@@ -371,8 +371,8 @@ minimization"_minimize.html.
[Restrictions:]
This command can only be used if LAMMPS was built with the SRD
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/fix_temp_rescale_eff.txt b/doc/src/fix_temp_rescale_eff.txt
index 0e08e4f1e81c9451e7c50742263f0b0b7b6988b9..83b360df858d61f1769e1f8f3e56fde72985b7ec 100644
--- a/doc/src/fix_temp_rescale_eff.txt
+++ b/doc/src/fix_temp_rescale_eff.txt
@@ -64,8 +64,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the USER-EFF package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_tfmc.txt b/doc/src/fix_tfmc.txt
index ddfa46261929de1fc4e1ab0c411537e6df97744d..2d4f00360761be172621dd3a2ca20566778dbf48 100644
--- a/doc/src/fix_tfmc.txt
+++ b/doc/src/fix_tfmc.txt
@@ -125,8 +125,8 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix is part of the MC package. It is only enabled if LAMMPS was
-built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
This fix is not compatible with "fix shake"_fix_shake.html.
diff --git a/doc/src/fix_thermal_conductivity.txt b/doc/src/fix_thermal_conductivity.txt
index 86fc6f2c72feba87286126f2b48dacf0983bce69..2ab32b25f071545cde44fc1afd97e3f2032a6486 100644
--- a/doc/src/fix_thermal_conductivity.txt
+++ b/doc/src/fix_thermal_conductivity.txt
@@ -123,8 +123,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Swaps conserve both momentum and kinetic energy, even if the masses of
the swapped atoms are not equal. Thus you should not need to
diff --git a/doc/src/fix_ti_spring.txt b/doc/src/fix_ti_spring.txt
index afe5373220095b949e9429f41e800f4e2fa6ad79..290ee95b9aef0f7fefb60ad34d13519450dcf659 100644
--- a/doc/src/fix_ti_spring.txt
+++ b/doc/src/fix_ti_spring.txt
@@ -146,8 +146,8 @@ this fix.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Default:]
diff --git a/doc/src/fix_tmd.txt b/doc/src/fix_tmd.txt
index c2541692f5f4cb2667084e11c5f375132e99abf3..73e95ba9fe58783c8b25df7d8081ca2e8c3980f1 100644
--- a/doc/src/fix_tmd.txt
+++ b/doc/src/fix_tmd.txt
@@ -110,8 +110,8 @@ are not multiple competing holonomic constraints applied to the same
atoms.
To read gzipped target files, you must compile LAMMPS with the
--DLAMMPS_GZIP option - see the "Making
-LAMMPS"_Section_start.html#start_2 section of the documentation.
+-DLAMMPS_GZIP option. See the "Build settings"_Build_settings.html
+doc page for details.
[Related commands:] none
diff --git a/doc/src/fix_ttm.txt b/doc/src/fix_ttm.txt
index 6001def5817736192fd0f7ac357a63ce148ca3c1..85407f2466cb9aaaae417174361fbd237d7481bf 100644
--- a/doc/src/fix_ttm.txt
+++ b/doc/src/fix_ttm.txt
@@ -295,8 +295,7 @@ of the "run"_run.html command. The fixes are not invoked during
Fix {ttm} is part of the MISC package. It is only enabled if LAMMPS
was built with that package. Fix {ttm/mod} is part of the USER-MISC
package. It is only enabled if LAMMPS was built with that package.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more
-info.
+See the "Build package"_Build_package.html doc page for more info.
These fixes can only be used for 3d simulations and orthogonal
simulation boxes. You must also use periodic
diff --git a/doc/src/fix_tune_kspace.txt b/doc/src/fix_tune_kspace.txt
index b4e8472591dee2164ddb4ef2550431ce0b575e4e..147bb1eb3dc71792c23078312db4f00eb3c3e412 100644
--- a/doc/src/fix_tune_kspace.txt
+++ b/doc/src/fix_tune_kspace.txt
@@ -79,9 +79,9 @@ minimization"_minimize.html.
[Restrictions:]
-This fix is part of the KSPACE package. It is only enabled if LAMMPS was
-built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+This fix is part of the KSPACE package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Do not set "neigh_modify once yes" or else this fix will never be
called. Reneighboring is required.
diff --git a/doc/src/fix_viscosity.txt b/doc/src/fix_viscosity.txt
index 934da3efdd7820fff834d01e1daf8354e14c39c2..d86b13d0557f52e79685a06e3196333ae7147802 100644
--- a/doc/src/fix_viscosity.txt
+++ b/doc/src/fix_viscosity.txt
@@ -129,8 +129,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the MISC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Swaps conserve both momentum and kinetic energy, even if the masses of
the swapped atoms are not equal. Thus you should not need to
diff --git a/doc/src/fix_wall.txt b/doc/src/fix_wall.txt
index 2ac59d9588155915370d834c1eb2b0e7727602ca..162e32c68c8e84d0613f47312185fe58a13ec60c 100644
--- a/doc/src/fix_wall.txt
+++ b/doc/src/fix_wall.txt
@@ -294,13 +294,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/fix_wall_body_polygon.txt b/doc/src/fix_wall_body_polygon.txt
index 0946a85131ae6c003daa63e7af939f9adf442227..45cbb2841db4e4bb8d74c24e1aa704b1a3f3da2a 100644
--- a/doc/src/fix_wall_body_polygon.txt
+++ b/doc/src/fix_wall_body_polygon.txt
@@ -91,8 +91,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the BODY package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Any dimension (xy) that has a wall must be non-periodic.
diff --git a/doc/src/fix_wall_body_polyhedron.txt b/doc/src/fix_wall_body_polyhedron.txt
index 407cf9fb339047e9b881c0e4df9b950280d5cbed..231ab1f0fe7763ddbe0fa3339cc5c0e5de3813ab 100644
--- a/doc/src/fix_wall_body_polyhedron.txt
+++ b/doc/src/fix_wall_body_polyhedron.txt
@@ -89,9 +89,9 @@ minimization"_minimize.html.
[Restrictions:]
-This fix is part of the BODY package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+This fix is part of the BODY package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Any dimension (xyz) that has a wall must be non-periodic.
diff --git a/doc/src/fix_wall_ees.txt b/doc/src/fix_wall_ees.txt
index ae16ca40d2ab731af1a4b77ac474d3dd8b00f841..4cc91f52227ba759280c9a7db34ef706d0c45fbd 100644
--- a/doc/src/fix_wall_ees.txt
+++ b/doc/src/fix_wall_ees.txt
@@ -97,8 +97,8 @@ of using this fix in the examples/USER/misc/ees/ directory.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This fix requires that atoms be ellipsoids as defined by the
"atom_style ellipsoid"_atom_style.html command.
diff --git a/doc/src/fix_wall_gran.txt b/doc/src/fix_wall_gran.txt
index 6c2769fc12840c85fdd60248009a45a851d8174a..0ea5b194ebefe000653562444ba455793b0a5da4 100644
--- a/doc/src/fix_wall_gran.txt
+++ b/doc/src/fix_wall_gran.txt
@@ -156,8 +156,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the GRANULAR package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Any dimension (xyz) that has a granular wall must be non-periodic.
diff --git a/doc/src/fix_wall_gran_region.txt b/doc/src/fix_wall_gran_region.txt
index 187214c1a36ca27c304d291150d16f56d440d204..50d744b305040799044fc85f033e10078150b0f7 100644
--- a/doc/src/fix_wall_gran_region.txt
+++ b/doc/src/fix_wall_gran_region.txt
@@ -188,8 +188,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix is part of the GRANULAR package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/fix_wall_piston.txt b/doc/src/fix_wall_piston.txt
index eecf69ebf2b80164672bb2b21cdb48f3ce855a0d..b1968e0d490c1840005bae18e77f2589799adf4b 100644
--- a/doc/src/fix_wall_piston.txt
+++ b/doc/src/fix_wall_piston.txt
@@ -99,8 +99,8 @@ minimization"_minimize.html.
[Restrictions:]
This fix style is part of the SHOCK package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The face that has the wall/piston must be boundary type 's'
(shrink-wrapped). The opposing face can be
diff --git a/doc/src/fix_wall_reflect.txt b/doc/src/fix_wall_reflect.txt
index 78be84eb638224ec631841fabc022bf0700a5162..e4dd7e2fb9a5ab32c31d702023c43ee79efd88a9 100644
--- a/doc/src/fix_wall_reflect.txt
+++ b/doc/src/fix_wall_reflect.txt
@@ -136,13 +136,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/group2ndx.txt b/doc/src/group2ndx.txt
index 242d6a69a4092798fb073f2f89a4c44957b46061..ed9bcb003a6ec590c14b70eed2bc51073b16855d 100644
--- a/doc/src/group2ndx.txt
+++ b/doc/src/group2ndx.txt
@@ -54,8 +54,8 @@ This command requires that atoms have atom IDs, since this is the
information that is written to the index file.
These commands are part of the USER-COLVARS package. They are only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/improper_class2.txt b/doc/src/improper_class2.txt
index c38f73c64dc017d58ce25e86cb431d5c068e9b1e..704944920eceaf00f67138723c017991e2fdd10d 100644
--- a/doc/src/improper_class2.txt
+++ b/doc/src/improper_class2.txt
@@ -93,13 +93,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -109,8 +109,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-CLASS2 package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+CLASS2 package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/improper_cossq.txt b/doc/src/improper_cossq.txt
index 04aa45255cb2faf860dcd0493b53e301c6a65bde..8bd02afb84b4e27dbb31f4e3f9318c83dd6cf9d4 100644
--- a/doc/src/improper_cossq.txt
+++ b/doc/src/improper_cossq.txt
@@ -59,13 +59,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -75,8 +75,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/improper_cvff.txt b/doc/src/improper_cvff.txt
index d01faf288554e0281f1841e45c9f0c415083c547..d57fddc5122c737c2c0835919b3d9dc67b147c3e 100644
--- a/doc/src/improper_cvff.txt
+++ b/doc/src/improper_cvff.txt
@@ -60,13 +60,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -76,8 +76,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/improper_distance.txt b/doc/src/improper_distance.txt
index 93235fe60197f01fc50297ec4f8d0504c16c6b9a..bfd92f57ec9261b94c5b23c045fb726139efdafa 100644
--- a/doc/src/improper_distance.txt
+++ b/doc/src/improper_distance.txt
@@ -48,8 +48,8 @@ K_4 (energy/distance^4) :ul
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/improper_fourier.txt b/doc/src/improper_fourier.txt
index 78cc1b3f760fe81de8682983f11bc0f90615f9d4..8b2021dccd5ff156aaaaf671cf77b12af9f1d105 100644
--- a/doc/src/improper_fourier.txt
+++ b/doc/src/improper_fourier.txt
@@ -54,13 +54,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -70,8 +70,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This angle style can only be used if LAMMPS was built with the
-USER_MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER_MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/improper_harmonic.txt b/doc/src/improper_harmonic.txt
index f398dc425f935f605c3446075783df2b91d49c00..1e9e7172f9ca5be5bdc0f83758b364997a370835 100644
--- a/doc/src/improper_harmonic.txt
+++ b/doc/src/improper_harmonic.txt
@@ -64,13 +64,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -80,8 +80,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/improper_hybrid.txt b/doc/src/improper_hybrid.txt
index 42afbe8577dc30163dcc8e5053de9cc05022b6a2..929eec43e16e0f6fd1d4f3cb4f24097a4d672f6f 100644
--- a/doc/src/improper_hybrid.txt
+++ b/doc/src/improper_hybrid.txt
@@ -55,8 +55,8 @@ types.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
Unlike other improper styles, the hybrid improper style does not store
improper coefficient info for individual sub-styles in a "binary
diff --git a/doc/src/improper_inversion_harmonic.txt b/doc/src/improper_inversion_harmonic.txt
index 2c0f2f0af84e1275c8511fc3d65f2508163a89cd..43ffdeb8e9fae741bfd2825e1a620b079c6fc39e 100644
--- a/doc/src/improper_inversion_harmonic.txt
+++ b/doc/src/improper_inversion_harmonic.txt
@@ -52,8 +52,8 @@ in between.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-USER-MOFFF package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-MOFFF package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/improper_ring.txt b/doc/src/improper_ring.txt
index 60bbca170a9a3d06cc3d819d847fdf37370691d9..8a2ee29e17a9c6a694d8a8f6497e93f2a5f161c0 100644
--- a/doc/src/improper_ring.txt
+++ b/doc/src/improper_ring.txt
@@ -63,13 +63,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -79,8 +79,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/improper_style.txt b/doc/src/improper_style.txt
index 3d29b28ec4a69b2200db24e2fb742fdf1c7fabd4..ef0c524d14086488d8f360b505bf640d09e9f3ff 100644
--- a/doc/src/improper_style.txt
+++ b/doc/src/improper_style.txt
@@ -81,10 +81,9 @@ Improper styles can only be set for atom_style choices that allow
impropers to be defined.
Most improper styles are part of the MOLECULE package. They are only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
-The doc pages for individual improper potentials tell if it is part of
-a package.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. The doc pages for
+individual improper potentials tell if it is part of a package.
[Related commands:]
diff --git a/doc/src/improper_umbrella.txt b/doc/src/improper_umbrella.txt
index b05cf4b181bfceaed1160cebb650d99922af039a..6c29ec7ac5d879befb81202bbb6883b49c0b6599 100644
--- a/doc/src/improper_umbrella.txt
+++ b/doc/src/improper_umbrella.txt
@@ -57,13 +57,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -73,8 +73,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This improper style can only be used if LAMMPS was built with the
-MOLECULE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package. See the "Build package"_Build_package.html doc page
+for more info.
[Related commands:]
diff --git a/doc/src/jump.txt b/doc/src/jump.txt
index b5afeb6559f4c80629947cf9376ae455fdde1a63..2e26d32c4047537c6ca208456636277612bed612 100644
--- a/doc/src/jump.txt
+++ b/doc/src/jump.txt
@@ -40,15 +40,14 @@ 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 or by some MPI
implementations. This can be worked around by using the "-in
-command-line argument"_Section_start.html#start_6, e.g.
+command-line switch"_Run_options.html, e.g.
lmp_g++ -in in.script :pre
-or by using the "-var command-line
-argument"_Section_start.html#start_6 to pass the script name as a
-variable to the input script. In the latter case, a
-"variable"_variable.html called "fname" could be used in place of
-SELF, e.g.
+or by using the "-var command-line switch"_Run_options.html to pass
+the script name as a variable to the input script. In the latter
+case, a "variable"_variable.html called "fname" could be used in place
+of SELF, e.g.
lmp_g++ -var fname in.script < in.script :pre
diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt
index 55ad4ab6107b828fd74e5daa91025063d29c5115..7e479c76a64e69a1e8116712457779c0f67b43b6 100644
--- a/doc/src/kspace_style.txt
+++ b/doc/src/kspace_style.txt
@@ -180,9 +180,9 @@ lo-level Makefile. This setting also changes some of the PPPM
operations (e.g. mapping charge to mesh and interpolating electric
fields to particles) to be performed in single precision. This option
can speed-up long-range calculations, particularly in parallel or on
-GPUs. The use of the -DFFT_SINGLE flag is discussed in "this
-section"_Section_start.html#start_2_4 of the manual. MSM does not
-currently support the -DFFT_SINGLE compiler switch.
+GPUs. The use of the -DFFT_SINGLE flag is discussed on the "Build
+settings"_Build_settings.html doc page. MSM does not currently support
+the -DFFT_SINGLE compiler switch.
:line
@@ -286,10 +286,10 @@ The {pppm/kk} style also performs charge assignment and force
interpolation calculations on the GPU while the FFTs themselves are
calculated on the CPU in non-threaded mode.
-These accelerated styles are part of the GPU, USER-INTEL,
-KOKKOS, USER-OMP, and OPT packages respectively. They are only
-enabled if LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP, and OPT packages respectively. They are only enabled if
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -308,9 +308,9 @@ triclinic simulation cells may not yet be supported by suffix versions
of these styles.
All of the kspace styles are part of the KSPACE package. They are
-only enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. Note that
-the KSPACE package is installed by default.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. Note that the
+KSPACE package is installed by default.
For MSM, a simulation must be 3d and one can use any combination of
periodic, non-periodic, or shrink-wrapped boundaries (specified using
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index c0ca357f211aa973f0c80f28155b2cc9b6e0ebcd..88ef6d77cb69255671b9b35017b82f8c7b8ce34b 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -8,7 +8,27 @@ Intro_nonfeatures.html
Intro_opensource.html
Intro_authors.html
Intro_website.html
-Section_start.html
+Install.html
+Install_linux.html
+Install_mac.html
+Install_windows.html
+Install_tarball.html
+Install_git.html
+Install_svn.html
+Install_patch.html
+Build.html
+Build_cmake.html
+Build_make.html
+Build_link.html
+Build_basics.html
+Build_settings.html
+Build_package.html
+Build_extras.html
+Run.html
+Run_basics.html
+Run_options.html
+Run_output.html
+Run_windows.html
Commands.html
Commands_input.html
Commands_parse.html
diff --git a/doc/src/log.txt b/doc/src/log.txt
index 76037685194b5ba9b324b02d35ffd0ed34ea26d3..d526158a3c6a59919fe5a6fdfcba5e5adf3e3889 100644
--- a/doc/src/log.txt
+++ b/doc/src/log.txt
@@ -33,9 +33,8 @@ be a variable, so that different processors do not attempt to write to
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 2.6"_Section_start.html#start_6 for
-details.
+name of the initial log file can also be set by the "-log command-line
+switch"_Run_options.html.
[Restrictions:] none
diff --git a/doc/src/neb.txt b/doc/src/neb.txt
index fbd77ee32903f1d99f4f63232538e0fd88cdde7d..57e122fdcd53cec635f42746fd23c475f8fca7fc 100644
--- a/doc/src/neb.txt
+++ b/doc/src/neb.txt
@@ -50,14 +50,14 @@ follows the discussion in these 4 papers: "(HenkelmanA)"_#HenkelmanA,
"(HenkelmanB)"_#HenkelmanB, "(Nakano)"_#Nakano3 and "(Maras)"_#Maras2.
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 2.6"_Section_start.html#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 just one or two
-processors. You will simply not get the performance speed-up you
-would see with one or more physical processors per replica. See the
-"Howto replica"_Howto_replica.html doc page for further discussion.
+partitions are defined at run-time using the "-partition command-line
+switch"_Run_options.html. 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 just one or two processors. You will simply not get the
+performance speed-up you would see with one or more physical
+processors per replica. See the "Howto replica"_Howto_replica.html
+doc page for further discussion.
NOTE: As explained below, a NEB calculation perfoms a damped dynamics
minimization across all the replicas. The minimizer uses whatever
@@ -395,8 +395,8 @@ image.
[Restrictions:]
This command can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
:line
diff --git a/doc/src/neighbor.txt b/doc/src/neighbor.txt
index 7c7e7b05e5229b3d1144f251543d5b8ded341c60..3e590eaff109e524fc08986bd5275ff858a651e1 100644
--- a/doc/src/neighbor.txt
+++ b/doc/src/neighbor.txt
@@ -65,8 +65,8 @@ 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.
+are printed to the screen and log file. See the "Run
+output"_Run_output.html doc page for details.
[Restrictions:] none
diff --git a/doc/src/next.txt b/doc/src/next.txt
index 5a0b30b2a7fe6ff0d824a066376404808702958f..aefb2ca5949f16001a1016ac94aa07984082c491 100644
--- a/doc/src/next.txt
+++ b/doc/src/next.txt
@@ -70,11 +70,11 @@ incrementing is done, using a single lock file for all variables. The
next value (for each variable) is assigned to whichever processor
partition executes the command first. All processors in the partition
are assigned the same value(s). 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 {uloop}-style variables are incremented using the files
-"tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will
-see in your directory during and after such a LAMMPS run.
+of processors via the "-partition command-line
+switch"_Run_options.html. {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
+and after such a LAMMPS run.
Here is an example of running a series of simulations using the next
command with an {index}-style variable. If this input script is named
diff --git a/doc/src/package.txt b/doc/src/package.txt
index c2e7345bb74c4e25a5dc4861194c704d3017232d..76246c22f6266308e4f7e799a5298399a374d618 100644
--- a/doc/src/package.txt
+++ b/doc/src/package.txt
@@ -121,8 +121,8 @@ their initialization, before a simulation is defined.
This command can also be specified from the command-line when
launching LAMMPS, using the "-pk" "command-line
-switch"_Section_start.html#start_6. The syntax is exactly the same as
-when used in an input script.
+switch"_Run_options.html. The syntax is exactly the same as when used
+in an input script.
Note that all of the accelerator packages require the package command
to be specified (except the OPT package), if the package is to be used
@@ -132,22 +132,21 @@ a default version of the command is typically invoked by other
accelerator settings.
The KOKKOS package requires a "-k on" "command-line
-switch"_Section_start.html#start_6 respectively, which invokes a
-"package kokkos" command with default settings.
+switch"_Run_options.html respectively, which invokes a "package
+kokkos" command with default settings.
For the GPU, USER-INTEL, and USER-OMP packages, if a "-sf gpu" or "-sf
-intel" or "-sf omp" "command-line switch"_Section_start.html#start_6
-is used to auto-append accelerator suffixes to various styles in the
-input script, then those switches also invoke a "package gpu",
-"package intel", or "package omp" command with default settings.
+intel" or "-sf omp" "command-line switch"_Run_options.html is used to
+auto-append accelerator suffixes to various styles in the input
+script, then those switches also invoke a "package gpu", "package
+intel", or "package omp" command with default settings.
NOTE: A package command for a particular style can be invoked multiple
-times when a simulation is setup, e.g. by the "-c on", "-k on", "-sf",
-and "-pk" "command-line switches"_Section_start.html#start_6, and by
-using this command in an input script. Each time it is used all of
-the style options are set, either to default values or to specified
-settings. I.e. settings from previous invocations do not persist
-across multiple invocations.
+times when a simulation is setup, e.g. by the "-c on, -k on, -sf, and
+-pk command-line switches"_Run_options.html, and by using this command
+in an input script. Each time it is used all of the style options are
+set, either to default values or to specified settings. I.e. settings
+from previous invocations do not persist across multiple invocations.
See the "Speed packages"_Speed_packages.html doc page for more details
about using the various accelerator packages for speeding up LAMMPS
@@ -338,10 +337,10 @@ value via their package commands, but there is only a single global
{Nthreads} value used by OpenMP. Thus if both package commands are
invoked, you should insure the two values are consistent. If they are
not, the last one invoked will take precedence, for both packages.
-Also note that if the "-sf hybrid intel omp" "command-line
-switch"_"_Section_start.html#start_6 is used, it invokes a "package
-intel" command, followed by a "package omp" command, both with a
-setting of {Nthreads} = 0.
+Also note that if the "-sf hybrid intel omp command-line
+switch"_Run_options.html is used, it invokes a "package intel"
+command, followed by a "package omp" command, both with a setting of
+{Nthreads} = 0.
The {mode} keyword determines the precision mode to use for
computing pair style forces, either on the CPU or on the coprocessor,
@@ -568,58 +567,56 @@ This command cannot be used after the simulation box is defined by a
"read_data"_read_data.html or "create_box"_create_box.html command.
The gpu style of this command can only be invoked if LAMMPS was built
-with the GPU package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+with the GPU package. See the "Build package"_Build_package.html doc
+page for more info.
The intel style of this command can only be invoked if LAMMPS was
-built with the USER-INTEL package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with the USER-INTEL package. See the "Build
+package"_Build_package.html doc page for more info.
The kk style of this command can only be invoked if LAMMPS was built
-with the KOKKOS package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+with the KOKKOS package. See the "Build package"_Build_package.html
+doc page for more info.
The omp style of this command can only be invoked if LAMMPS was built
-with the USER-OMP package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+with the USER-OMP package. See the "Build package"_Build_package.html
+doc page for more info.
[Related commands:]
-"suffix"_suffix.html, "-pk" "command-line
-setting"_Section_start.html#start_6
+"suffix"_suffix.html, "-pk command-line switch"_Run_options.html
[Default:]
For the GPU package, the default is Ngpu = 1 and the option defaults
are neigh = yes, newton = off, binsize = 0.0, split = 1.0, gpuID = 0
to Ngpu-1, tpa = 1, and device = not used. These settings are made
-automatically if the "-sf gpu" "command-line
-switch"_Section_start.html#start_6 is used. If it is not used, you
-must invoke the package gpu command in your input script or via the
-"-pk gpu" "command-line switch"_Section_start.html#start_6.
+automatically if the "-sf gpu" "command-line switch"_Run_options.html
+is used. If it is not used, you must invoke the package gpu command
+in your input script or via the "-pk gpu" "command-line
+switch"_Run_options.html.
For the USER-INTEL package, the default is Nphi = 1 and the option
defaults are omp = 0, mode = mixed, lrt = no, balance = -1, tpc = 4,
tptask = 240. The default ghost option is determined by the pair
style being used. This value is output to the screen in the offload
report at the end of each run. Note that all of these settings,
-except "omp" and "mode", are ignored if LAMMPS was not built with
-Xeon Phi coprocessor support. These settings are made automatically
-if the "-sf intel" "command-line switch"_Section_start.html#start_6
-is used. If it is not used, you must invoke the package intel
-command in your input script or or via the "-pk intel" "command-line
-switch"_Section_start.html#start_6.
-
-For the KOKKOS package, the option defaults neigh = full,
-neigh/qeq = full, newton = off, binsize = 0.0, and comm = device.
-These settings are made automatically by the required "-k on" "command-line
-switch"_Section_start.html#start_6. You can change them bu using the
-package kokkos command in your input script or via the "-pk kokkos"
-"command-line switch"_Section_start.html#start_6.
+except "omp" and "mode", are ignored if LAMMPS was not built with Xeon
+Phi coprocessor support. These settings are made automatically if the
+"-sf intel" "command-line switch"_Run_options.html is used. If it is
+not used, you must invoke the package intel command in your input
+script or or via the "-pk intel" "command-line
+switch"_Run_options.html.
+
+For the KOKKOS package, the option defaults neigh = full, neigh/qeq =
+full, newton = off, binsize = 0.0, and comm = device. These settings
+are made automatically by the required "-k on" "command-line
+switch"_Run_options.html. You can change them bu using the package
+kokkos command in your input script or via the "-pk kokkos"
+"command-line switch"_Run_options.html.
For the OMP package, the default is Nthreads = 0 and the option
defaults are neigh = yes. These settings are made automatically if
-the "-sf omp" "command-line switch"_Section_start.html#start_6 is
-used. If it is not used, you must invoke the package omp command in
-your input script or via the "-pk omp" "command-line
-switch"_Section_start.html#start_6.
+the "-sf omp" "command-line switch"_Run_options.html is used. If it
+is not used, you must invoke the package omp command in your input
+script or via the "-pk omp" "command-line switch"_Run_options.html.
diff --git a/doc/src/pair_adp.txt b/doc/src/pair_adp.txt
index 382a97eceaf93bf844915871d3210a4bca0e7666..fc888ffbffa7b38779ddaa9730316c787445d3cc 100644
--- a/doc/src/pair_adp.txt
+++ b/doc/src/pair_adp.txt
@@ -131,13 +131,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_agni.txt b/doc/src/pair_agni.txt
index 34f99001390ca24026f0ea3218316ab465d68ac0..74aef4125575d02b79436b7e8c79b6c468757f0e 100644
--- a/doc/src/pair_agni.txt
+++ b/doc/src/pair_agni.txt
@@ -64,14 +64,14 @@ packages"_Speed_packages.html doc page. The accelerated style takes
the same arguments and should produce the same results, except for
round-off and precision issues.
-The accelerated style is part of the USER-OMP. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+The accelerated style is part of the USER-OMP. They are only enabled
+if LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page for more info.
You can specify the accelerated style 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -96,13 +96,14 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
-Currently, only elemental systems are implemented. Also, the method only
-provides access to the forces and not energies or stresses. However, one
-can access the energy via thermodynamic integration of the forces as
-discussed in "(Botu3)"_#Botu2016construct. This pair style is part
-of the USER-MISC package. It is only enabled if LAMMPS was built with
-that package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
+Currently, only elemental systems are implemented. Also, the method
+only provides access to the forces and not energies or
+stresses. However, one can access the energy via thermodynamic
+integration of the forces as discussed in
+"(Botu3)"_#Botu2016construct. This pair style is part of the
+USER-MISC package. It is only enabled if LAMMPS was built with that
+package. See the "Build package"_Build_package.html doc page for more
+info.
The AGNI force field files provided with LAMMPS (see the
potentials directory) are parameterized for metal "units"_units.html.
diff --git a/doc/src/pair_airebo.txt b/doc/src/pair_airebo.txt
index 94a692226d608687a094d48455070c1084eed3f4..c090a39af756189a63728c59b4c58e369c847111 100644
--- a/doc/src/pair_airebo.txt
+++ b/doc/src/pair_airebo.txt
@@ -182,13 +182,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -212,8 +212,8 @@ These pair styles can only be used via the {pair} keyword of the
[Restrictions:]
These pair styles are part of the MANYBODY package. They are only
-enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
These pair potentials require the "newton"_newton.html setting to be
"on" for pair interactions.
diff --git a/doc/src/pair_beck.txt b/doc/src/pair_beck.txt
index ca4186e27b102d8199327d87a3ca0cd9da09f92f..af60041ff98b6a14e0bc84117a14082691a071b0 100644
--- a/doc/src/pair_beck.txt
+++ b/doc/src/pair_beck.txt
@@ -57,13 +57,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_body_nparticle.txt b/doc/src/pair_body_nparticle.txt
index 9fb88102eb0aece7ace62e32360614fa3bdef106..158eb68ca8f4c8357167534d0e936db7c4de2cff 100644
--- a/doc/src/pair_body_nparticle.txt
+++ b/doc/src/pair_body_nparticle.txt
@@ -103,8 +103,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This style is part of the BODY package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_2_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Defining particles to be bodies so they participate in body/body or
body/particle interactions requires the use of the "atom_style
diff --git a/doc/src/pair_body_rounded_polygon.txt b/doc/src/pair_body_rounded_polygon.txt
index e724874032afffe0d59f1f6fe2622a1669797b35..fc07d8faddc61a91dcba3cbcf32eb36211df8cff 100644
--- a/doc/src/pair_body_rounded_polygon.txt
+++ b/doc/src/pair_body_rounded_polygon.txt
@@ -116,8 +116,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
These pair styles are part of the BODY package. They are only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_body_rounded_polyhedron.txt b/doc/src/pair_body_rounded_polyhedron.txt
index 0f8548d98eab86a6d5e3647f46119162764409cb..e650e5138ac456a405448f1476e29ec5cf7e754a 100644
--- a/doc/src/pair_body_rounded_polyhedron.txt
+++ b/doc/src/pair_body_rounded_polyhedron.txt
@@ -111,8 +111,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
These pair styles are part of the BODY package. They are only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_bop.txt b/doc/src/pair_bop.txt
index 654a7eb0b332dd5efdd4a9ca41410fbf6bd131df..f9b4262f0c5f9717854e7c0bfeedefe831eeed46 100644
--- a/doc/src/pair_bop.txt
+++ b/doc/src/pair_bop.txt
@@ -382,9 +382,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
These pair styles are part of the MANYBODY package. They are only
-enabled if LAMMPS was built with that package.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more
-info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
These pair potentials require the "newtion"_newton.html setting to be
"on" for pair interactions.
diff --git a/doc/src/pair_born.txt b/doc/src/pair_born.txt
index c408de6db6f23b579f2800d7865fdcd35649f9e6..195d3e666961c321638fe03c1cfc0c67cb2c6c96 100644
--- a/doc/src/pair_born.txt
+++ b/doc/src/pair_born.txt
@@ -151,13 +151,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -193,8 +193,8 @@ respa"_run_style.html command. They do not support the {inner},
[Restrictions:]
The {born/coul/long} style is part of the KSPACE package. It is only
-enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_brownian.txt b/doc/src/pair_brownian.txt
index eaff85cbbca374db982add0557f03b57dedceaaf..52720daa23f4c67a88e7ce88b43fb23524a4eac5 100644
--- a/doc/src/pair_brownian.txt
+++ b/doc/src/pair_brownian.txt
@@ -80,13 +80,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See "this section"_Speed.html of the manual for more
instructions on how to use the accelerated styles effectively.
@@ -122,8 +122,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
These styles are part of the COLLOID package. They are only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Only spherical monodisperse particles are allowed for pair_style
brownian.
diff --git a/doc/src/pair_buck.txt b/doc/src/pair_buck.txt
index cc782c11cf3f551930264316b838c488de4ddb6e..5b1688e8687345464fb832161360f15700608320 100644
--- a/doc/src/pair_buck.txt
+++ b/doc/src/pair_buck.txt
@@ -145,13 +145,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -186,8 +186,8 @@ respa"_run_style.html command. They do not support the {inner},
The {buck/coul/long} style is part of the KSPACE package. The
{buck/coul/long/cs} style is part of the CORESHELL package. They are
-only enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_buck6d_coul_gauss.txt b/doc/src/pair_buck6d_coul_gauss.txt
index 485c35c6b2fffb04c14fa04469bd33a6400c65d5..4c43978fe5a44eae7d15fc21aecf5e2d2c8f780c 100644
--- a/doc/src/pair_buck6d_coul_gauss.txt
+++ b/doc/src/pair_buck6d_coul_gauss.txt
@@ -122,9 +122,9 @@ to be specified in an input script that reads a restart file.
[Restrictions:]
-These styles are part of the USER-MOFFF package. They are only enabled
-if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+These styles are part of the USER-MOFFF package. They are only
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_buck_long.txt b/doc/src/pair_buck_long.txt
index 551204f1a7fe97ea559e98c7cfd1ddd92370d328..7f3a959ad620a39db19c466ad7012b6412740cc6 100644
--- a/doc/src/pair_buck_long.txt
+++ b/doc/src/pair_buck_long.txt
@@ -108,13 +108,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -153,9 +153,9 @@ details.
[Restrictions:]
This style is part of the KSPACE package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. Note that
-the KSPACE package is installed by default.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. Note that the
+KSPACE package is installed by default.
[Related commands:]
diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt
index 39c6f29b047fdbf02017352a1e787cc60c79cb78..dfc87e1bcebf2c650867f24436da365ce516a40a 100644
--- a/doc/src/pair_charmm.txt
+++ b/doc/src/pair_charmm.txt
@@ -190,13 +190,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -245,9 +245,9 @@ details.
All the styles with {coul/charmm} or {coul/charmmfsh} styles are part
of the MOLECULE package. All the styles with {coul/long} style are
part of the KSPACE package. They are only enabled if LAMMPS was built
-with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. Note that
-the MOLECULE and KSPACE packages are installed by default.
+with those packages. See the "Build package"_Build_package.html doc
+page for more info. Note that the MOLECULE and KSPACE packages are
+installed by default.
[Related commands:]
diff --git a/doc/src/pair_class2.txt b/doc/src/pair_class2.txt
index 104c51474c25764c20a7b064dad9722e548e0809..5fc42e78f9f9b4a34d854e30d9bd96999177252b 100644
--- a/doc/src/pair_class2.txt
+++ b/doc/src/pair_class2.txt
@@ -108,13 +108,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -154,8 +154,8 @@ support the {inner}, {middle}, {outer} keywords.
[Restrictions:]
These styles are part of the CLASS2 package. They are only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_colloid.txt b/doc/src/pair_colloid.txt
index 08540cfee082c761259d3d8e3772015557c21210..e8a44e1cba7ec053e09831ee1201d074f62db215 100644
--- a/doc/src/pair_colloid.txt
+++ b/doc/src/pair_colloid.txt
@@ -133,13 +133,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -177,8 +177,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This style is part of the COLLOID package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Normally, this pair style should be used with finite-size particles
which have a diameter, e.g. see the "atom_style
diff --git a/doc/src/pair_comb.txt b/doc/src/pair_comb.txt
index fc4cddbbae1fefa91ce37e930e2a589279f42566..45ce3a3b7611d0847ef3aa05886d0a6dd6fb20b4 100644
--- a/doc/src/pair_comb.txt
+++ b/doc/src/pair_comb.txt
@@ -118,13 +118,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -154,9 +154,9 @@ These pair styles can only be used via the {pair} keyword of the
[Restrictions:]
-These pair styles are part of the MANYBODY package. It is only enabled
-if LAMMPS was built with that package. See
-the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+These pair styles are part of the MANYBODY package. It is only
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
These pair styles requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_coul.txt b/doc/src/pair_coul.txt
index 2fd9445785e26a44a3b1f7b070caa7531e61003d..bc0d76a071829dba2182fede5e1aadcc725a5759 100644
--- a/doc/src/pair_coul.txt
+++ b/doc/src/pair_coul.txt
@@ -274,13 +274,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -319,7 +319,7 @@ This pair style can only be used via the {pair} keyword of the
The {coul/long}, {coul/msm} and {tip4p/long} styles are part of the
KSPACE package. The {coul/long/cs} style is part of the CORESHELL
package. They are only enabled if LAMMPS was built with that package.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+See the "Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_coul_diel.txt b/doc/src/pair_coul_diel.txt
index 14932c4835043aa7e93cf7b900672def64f10323..7708287db9e476c18c13932906ba885aa2e94fa9 100644
--- a/doc/src/pair_coul_diel.txt
+++ b/doc/src/pair_coul_diel.txt
@@ -67,7 +67,8 @@ The global cutoff (r_c) specified in the pair_style command is used.
[Mixing, shift, table, tail correction, restart, rRESPA info]:
-This pair style does not support parameter mixing. Coefficients must be given explicitly for each type of particle pairs.
+This pair style does not support parameter mixing. Coefficients must
+be given explicitly for each type of particle pairs.
This pair style supports the "pair_modify"_pair_modify.html shift
option for the energy of the Gauss-potential portion of the pair
@@ -86,9 +87,9 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
-This style is part of the "user-misc" package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_2_3 section for more info.
+This style is part of the "USER-MISC" package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_coul_shield.txt b/doc/src/pair_coul_shield.txt
index 029e6e5b3b3458ce3fdbab9daaecdad467061dce..62ac157e76cf4b78797dfc2a073d9007c7eee270 100644
--- a/doc/src/pair_coul_shield.txt
+++ b/doc/src/pair_coul_shield.txt
@@ -69,9 +69,9 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
-This style is part of the USER-MISC package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_2_3 section for more info.
+This style is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_cs.txt b/doc/src/pair_cs.txt
index 6540c4b8f0d4dd72b704854146d50b4f74815720..8bd4abed68bb8bac94116d77c575453eb0c6d717 100644
--- a/doc/src/pair_cs.txt
+++ b/doc/src/pair_cs.txt
@@ -100,8 +100,8 @@ core/shell pair.
[Restrictions:]
These pair styles are part of the CORESHELL package. They are only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt
index 1d8abc4521d2b26d2152d2157081a9d718bc3b47..dcb2448949699655f3021a860ca3112ae398d542 100644
--- a/doc/src/pair_dipole.txt
+++ b/doc/src/pair_dipole.txt
@@ -192,13 +192,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -240,12 +240,12 @@ This pair style can only be used via the {pair} keyword of the
The {lj/cut/dipole/cut}, {lj/cut/dipole/long}, and
{lj/long/dipole/long} styles are part of the DIPOLE package. They are
-only enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The {lj/sf/dipole/sf} style is part of the USER-MISC package. It is
-only enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Using dipole pair styles with {electron} "units"_units.html is not
currently supported.
diff --git a/doc/src/pair_dpd.txt b/doc/src/pair_dpd.txt
index 1b636795d962254fed114fd7cad91b2b53fb8bac..55ae2986824e0c8baf92c5bf8cd4ba555837fdb9 100644
--- a/doc/src/pair_dpd.txt
+++ b/doc/src/pair_dpd.txt
@@ -116,13 +116,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_dpd_fdt.txt b/doc/src/pair_dpd_fdt.txt
index 0d180ba068ffdec47eb78bc7fc7fcdb458aab766..4f2459588a9b317d3f92b3bc732536d10ec2dbc4 100644
--- a/doc/src/pair_dpd_fdt.txt
+++ b/doc/src/pair_dpd_fdt.txt
@@ -135,13 +135,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -151,8 +151,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
These commands are part of the USER-DPD package. They are only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Pair styles {dpd/fdt} and {dpd/fdt/energy} require use of the
"comm_modify vel yes"_comm_modify.html option so that velocites are
diff --git a/doc/src/pair_dsmc.txt b/doc/src/pair_dsmc.txt
index 2478a96d5ff183f52d21f817a1205eee6ce99855..adaeeb8390e07f080259009962109f909857f56b 100644
--- a/doc/src/pair_dsmc.txt
+++ b/doc/src/pair_dsmc.txt
@@ -130,8 +130,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This style is part of the MC package. It is only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_eam.txt b/doc/src/pair_eam.txt
index 361dacb703d41a95c365abd2ce5101e915fe11d3..6c3793cb61bc2ad74102e02f1f9b73c9dcf2be74 100644
--- a/doc/src/pair_eam.txt
+++ b/doc/src/pair_eam.txt
@@ -377,13 +377,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -414,8 +414,8 @@ The eam pair styles can only be used via the {pair} keyword of the
[Restrictions:]
All of these styles are part of the MANYBODY package. They are only
-enabled if LAMMPS was built with that package.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt
index cce564856e6c2c420771e4c070b23605e0cdafe8..053d43b2baeed3cd87cfb17e57aabb60335ca7d8 100644
--- a/doc/src/pair_edip.txt
+++ b/doc/src/pair_edip.txt
@@ -115,13 +115,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -147,8 +147,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_eff.txt b/doc/src/pair_eff.txt
index a55860297e609eb106b63cda6655babf3f696966..a665654af090af278e348dbd35e763df430cf547 100644
--- a/doc/src/pair_eff.txt
+++ b/doc/src/pair_eff.txt
@@ -280,8 +280,8 @@ These pair styles can only be used via the {pair} keyword of the
These pair styles will only be enabled if LAMMPS is built with the
USER-EFF package. It will only be enabled if LAMMPS was built with
-that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+that package. See the "Build package"_Build_package.html doc page for
+more info.
These pair styles require that particles store electron attributes
such as radius, radial velocity, and radial force, as defined by the
diff --git a/doc/src/pair_eim.txt b/doc/src/pair_eim.txt
index 6490a859c16b361e217faaa3eb04e52386b87143..5f9dcd4c5c349b5123a1539a8ee60db1a09d77b9 100644
--- a/doc/src/pair_eim.txt
+++ b/doc/src/pair_eim.txt
@@ -142,13 +142,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_exp6_rx.txt b/doc/src/pair_exp6_rx.txt
index 08ab1cf3c9b64a40fe70b251500fcecfcd2994f6..790674644d8223230329ce8c2387c9879e7670eb 100644
--- a/doc/src/pair_exp6_rx.txt
+++ b/doc/src/pair_exp6_rx.txt
@@ -159,13 +159,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -175,8 +175,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_gauss.txt b/doc/src/pair_gauss.txt
index 9662a4f29c743fefb3bddc480b6f70f75045ff88..ef924b1ef07bffe80ba266df8b111fe8395ddb97 100644
--- a/doc/src/pair_gauss.txt
+++ b/doc/src/pair_gauss.txt
@@ -90,13 +90,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-switch7_Section_start.html#start_6 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -167,8 +167,8 @@ thermo_style custom step temp epair v_occ :pre
[Restrictions:]
The {gauss/cut} style is part of the "user-misc" package. It is only
-enabled if LAMMPS is build with that package. See the "Making of
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS is build with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_gayberne.txt b/doc/src/pair_gayberne.txt
index af41f6879e80ed299050eb6822553e819e22607f..426352dc4cebe292b969fbdd5a2b119827fd8f3c 100644
--- a/doc/src/pair_gayberne.txt
+++ b/doc/src/pair_gayberne.txt
@@ -139,13 +139,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -184,8 +184,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
The {gayberne} style is part of the ASPHERE package. It is only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
These pair style require that atoms store torque and a quaternion to
represent their orientation, as defined by the
diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt
index 55b00a172f56c4063a20298509cc54856d9b276a..e06d4100849b339d78999bf3ae54c02cbe73ffd3 100644
--- a/doc/src/pair_gran.txt
+++ b/doc/src/pair_gran.txt
@@ -185,13 +185,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -232,8 +232,8 @@ pair/local"_compute_pair_local.html command, as {p1}, {p2}, ...,
[Restrictions:]
All the granular pair styles are part of the GRANULAR package. It is
-only enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
These pair styles require that atoms store torque and angular velocity
(omega) as defined by the "atom_style"_atom_style.html. They also
diff --git a/doc/src/pair_gromacs.txt b/doc/src/pair_gromacs.txt
index 9f34ac8c43da024cd0123454dfdc2666116379f3..6a36a036c93b2a8af88ebb62bdfac7f53dc243aa 100644
--- a/doc/src/pair_gromacs.txt
+++ b/doc/src/pair_gromacs.txt
@@ -97,13 +97,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_gw.txt b/doc/src/pair_gw.txt
index 809ff008bc86dbaa33e6f899c354957e09a65fef..ff85955dc006e05da8cf6fb22a8ebe8859979c09 100644
--- a/doc/src/pair_gw.txt
+++ b/doc/src/pair_gw.txt
@@ -96,8 +96,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the MANYBODY package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/src/pair_hbond_dreiding.txt
index 60b0b021743374cc08cfdd5cdc58a8605f02c9b0..d4bdcd9258750593512a9acf727f476d7e0321de 100644
--- a/doc/src/pair_hbond_dreiding.txt
+++ b/doc/src/pair_hbond_dreiding.txt
@@ -172,13 +172,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt
index 9b36109c279e7381ba5a73aea7adad55dee2f3c7..6e68e820a883184ac4c1927fd232a3ce05c048a4 100644
--- a/doc/src/pair_hybrid.txt
+++ b/doc/src/pair_hybrid.txt
@@ -324,15 +324,15 @@ the individual sub-styles, the suffix versions of the {hybrid} and
to all sub-styles, if those versions exist. Otherwise the
non-accelerated version will be used.
-The individual accelerated sub-styles are part of the GPU,
-USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+The individual accelerated sub-styles are part of the GPU, USER-OMP
+and OPT packages, respectively. They are only enabled if LAMMPS was
+built with those packages. See the "Build package"_Build_package.html
+doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt
index 9c9304c4a73ba02e35d575331f135ad32187a81e..02d0db7af25e6c86f6ece52e56623bf71825173a 100644
--- a/doc/src/pair_ilp_graphene_hbn.txt
+++ b/doc/src/pair_ilp_graphene_hbn.txt
@@ -87,8 +87,8 @@ that reads a restart file.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair potential requires the newton setting to be {on} for pair
interactions.
diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt
index 889c1e892fe69202a92ca98b02650b982c68c849..e1bde4f10e1b445e978185286c1fc7d0a906542d 100644
--- a/doc/src/pair_kim.txt
+++ b/doc/src/pair_kim.txt
@@ -126,8 +126,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the KIM package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This current version of pair_style kim is compatible with the
kim-api package version 1.6.0 and higher.
diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt
index 8fc6bbff4996ecaefa81e0257048a14c702a7e5d..358d2168df277c2ce74e00992dfb87fe403817e5 100644
--- a/doc/src/pair_kolmogorov_crespi_full.txt
+++ b/doc/src/pair_kolmogorov_crespi_full.txt
@@ -78,8 +78,8 @@ that reads a restart file.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair potential requires the newton setting to be {on} for pair
interactions.
diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt
index 7dad2e3701b852d41a2856e785d80be041f2f5c6..f557e6c731db499de0820bbb39ef9aab1aa0f46a 100644
--- a/doc/src/pair_kolmogorov_crespi_z.txt
+++ b/doc/src/pair_kolmogorov_crespi_z.txt
@@ -51,8 +51,8 @@ Other interactions can be set to zero using pair_style {none}.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_lcbop.txt b/doc/src/pair_lcbop.txt
index ddf8551d560ff042b8c3d64331db263e5c3d5289..21c809bf6a2f3a5b853b2dcbbde5296ca81008e1 100644
--- a/doc/src/pair_lcbop.txt
+++ b/doc/src/pair_lcbop.txt
@@ -72,8 +72,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair styles is part of the MANYBODY package. It is only enabled
-if LAMMPS was built with that package. See
-the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair potential requires the "newton"_newton.html setting to be
"on" for pair interactions.
diff --git a/doc/src/pair_line_lj.txt b/doc/src/pair_line_lj.txt
index c2c6beb97f5490ce4cc11ab6cb3c0634375afc0f..ca5ececa5697f6cd6d90bda77e9aa62497f90f0b 100644
--- a/doc/src/pair_line_lj.txt
+++ b/doc/src/pair_line_lj.txt
@@ -130,8 +130,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This style is part of the ASPHERE package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Defining particles to be line segments so they participate in
line/line or line/particle interactions requires the use the
diff --git a/doc/src/pair_list.txt b/doc/src/pair_list.txt
index 023cc0be4f1c52404fe1f875bdfd86cf03b68e7d..9500a4c508ad061b585dd695b3fe02b7ad4324cb 100644
--- a/doc/src/pair_list.txt
+++ b/doc/src/pair_list.txt
@@ -130,8 +130,8 @@ atom J (assuming the images are within the cutoff distance), but only
with the nearest image.
This style is part of the USER-MISC package. It is only enabled if
-LAMMPS is build with that package. See the "Making of
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS is build with that package. See the "Build
+package"_Build_package.html doc page on for more info.
[Related commands:]
diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt
index a55cb348d7568f14dd25c715adf8a7fe382f3a23..b5a572618228d0b8e514e8157ad0347fc2690481 100644
--- a/doc/src/pair_lj.txt
+++ b/doc/src/pair_lj.txt
@@ -275,13 +275,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -326,9 +326,9 @@ See the "run_style"_run_style.html command for details.
The {lj/cut/coul/long} and {lj/cut/tip4p/long} styles are part of the
KSPACE package. The {lj/cut/tip4p/cut} style is part of the MOLECULE
package. These styles are only enabled if LAMMPS was built with those
-packages. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info. Note that the KSPACE and MOLECULE packages are
-installed by default.
+packages. See the "Build package"_Build_package.html doc page for
+more info. Note that the KSPACE and MOLECULE packages are installed
+by default.
[Related commands:]
diff --git a/doc/src/pair_lj96.txt b/doc/src/pair_lj96.txt
index 7c68e26acef1c9cf8d21b47fc70ba1109296e502..19369adc66d1074ce4b5410f8c634cee68860ea6 100644
--- a/doc/src/pair_lj96.txt
+++ b/doc/src/pair_lj96.txt
@@ -55,13 +55,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_lj_cubic.txt b/doc/src/pair_lj_cubic.txt
index d04a3d8b9d1b6e021ea2df92d2ee16a74ba5e45d..0a56672d2861ff2d7b8555a684141d58149524b6 100644
--- a/doc/src/pair_lj_cubic.txt
+++ b/doc/src/pair_lj_cubic.txt
@@ -69,13 +69,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_lj_expand.txt b/doc/src/pair_lj_expand.txt
index 3e9996da4d5507158a37cca38cf1db68597dcfdb..d26c88e4f76f50db857c8510be9e6c23fdd77beb 100644
--- a/doc/src/pair_lj_expand.txt
+++ b/doc/src/pair_lj_expand.txt
@@ -59,13 +59,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt
index 1ba3610f8621801864930acf73a20b4d16bd5a04..2bc2b656ac7b95832c60e7304b5ccd254e04953c 100644
--- a/doc/src/pair_lj_long.txt
+++ b/doc/src/pair_lj_long.txt
@@ -162,13 +162,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -209,9 +209,9 @@ different levels of the rRESPA hierarchy. See the
[Restrictions:]
These styles are part of the KSPACE package. They are only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info. Note that
-the KSPACE package is installed by default.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. Note that the
+KSPACE package is installed by default.
[Related commands:]
diff --git a/doc/src/pair_lj_smooth.txt b/doc/src/pair_lj_smooth.txt
index 575c023579b4cf5b91927dd241c65d3ee9365c83..0c66dd0f669f199f06bcb1d9878120bc1b44a070 100644
--- a/doc/src/pair_lj_smooth.txt
+++ b/doc/src/pair_lj_smooth.txt
@@ -68,13 +68,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_lj_smooth_linear.txt b/doc/src/pair_lj_smooth_linear.txt
index 0fab768b8fbd9eecc9c80d0760262f9d9ea6111b..9c509515c0d71d1f1788e49a24f9176340ff254c 100644
--- a/doc/src/pair_lj_smooth_linear.txt
+++ b/doc/src/pair_lj_smooth_linear.txt
@@ -55,13 +55,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_lj_soft.txt
index d10fcd0472d24ebd91510e0c4793597292e31127..9bcc83fa66fcdf39c81a0375bce48aa69bcf89d3 100644
--- a/doc/src/pair_lj_soft.txt
+++ b/doc/src/pair_lj_soft.txt
@@ -213,13 +213,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -261,7 +261,7 @@ similar substyle can be used via the
All of the plain {soft} pair styles are part of the USER-FEP package.
The {long} styles also requires the KSPACE package to be installed.
They are only enabled if LAMMPS was built with those packages. See
-the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+the "Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_lubricate.txt b/doc/src/pair_lubricate.txt
index e9a0a0d2910e5a6036f4993c23e59b0849b88d78..83a67d03006390b7031a73d03d4c35d03adc8e1d 100644
--- a/doc/src/pair_lubricate.txt
+++ b/doc/src/pair_lubricate.txt
@@ -149,13 +149,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See "this section"_Speed.html of the manual for more
instructions on how to use the accelerated styles effectively.
@@ -191,8 +191,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
These styles are part of the COLLOID package. They are only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_2_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Only spherical monodisperse particles are allowed for pair_style
lubricate.
diff --git a/doc/src/pair_lubricateU.txt b/doc/src/pair_lubricateU.txt
index 6b74c208bf2c211ec71b9efff608c2345626505e..bfc7c36013d2c7060686a20ee99440712e66fca0 100644
--- a/doc/src/pair_lubricateU.txt
+++ b/doc/src/pair_lubricateU.txt
@@ -179,8 +179,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
These styles are part of the COLLOID package. They are only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_2_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Currently, these pair styles assume that all other types of
forces/torques on the particles have been already been computed when
diff --git a/doc/src/pair_mdf.txt b/doc/src/pair_mdf.txt
index e5a8cac845effe56f019729b2660ad001226923d..8a1551ddedf3b3ba964691798e7844693cc719ba 100644
--- a/doc/src/pair_mdf.txt
+++ b/doc/src/pair_mdf.txt
@@ -148,8 +148,8 @@ See the "run_style"_run_style.html command for details.
[Restrictions:]
These pair styles can only be used if LAMMPS was built with the
-USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/pair_meam.txt b/doc/src/pair_meam.txt
index 45f88f0bbec33570565284ab50945076acb85906..0b1c1ac767eb987adbc0af82adbf67633f4dfef7 100644
--- a/doc/src/pair_meam.txt
+++ b/doc/src/pair_meam.txt
@@ -352,14 +352,14 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
-The {meam} style is part of the MEAM package. It is only enabled if LAMMPS
-was built with that package, which also requires the MEAM library be
-built and linked with LAMMPS.
-The {meam/c} style is provided in the USER-MEAMC package. It is only enabled
-if LAMMPS was built with that package. In contrast to the {meam} style,
-{meam/c} does not require a separate library to be compiled and it can be
+The {meam} style is part of the MEAM package. It is only enabled if
+LAMMPS was built with that package, which also requires the MEAM
+library be built and linked with LAMMPS. The {meam/c} style is
+provided in the USER-MEAMC package. It is only enabled if LAMMPS was
+built with that package. In contrast to the {meam} style, {meam/c}
+does not require a separate library to be compiled and it can be
instantiated multiple times in a "hybrid"_pair_hybrid.html pair style.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+See the "Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt
index 96155120419297e54de85192f772f8fcb05216d5..df5db812648a9c4ff87e1e723578118d3b5075db 100644
--- a/doc/src/pair_meam_spline.txt
+++ b/doc/src/pair_meam_spline.txt
@@ -112,13 +112,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -147,8 +147,8 @@ This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
This pair style is only enabled if LAMMPS was built with the USER-MISC
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/pair_meam_sw_spline.txt b/doc/src/pair_meam_sw_spline.txt
index ba0953a17c3957825fac150f3b373c92a5df44b9..2e8c26658aea1de5840ba254fbeb7029640f194a 100644
--- a/doc/src/pair_meam_sw_spline.txt
+++ b/doc/src/pair_meam_sw_spline.txt
@@ -111,8 +111,9 @@ support the {inner}, {middle}, {outer} keywords.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
-This pair style is only enabled if LAMMPS was built with the USER-MISC package.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+This pair style is only enabled if LAMMPS was built with the USER-MISC
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/pair_meso.txt b/doc/src/pair_meso.txt
index ad3880e642411c30179bb8a1e9d3b8451cc9c227..005498d8bfdd1f1080f1bc297d4b1b3f1513ba5c 100644
--- a/doc/src/pair_meso.txt
+++ b/doc/src/pair_meso.txt
@@ -245,8 +245,8 @@ that reads a restart file.
The pair styles {edpd}, {mdpd}, {mdpd/rhosum} and {tdpd} are part of
the USER-MESO package. It is only enabled if LAMMPS was built with
-that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+that package. See the "Build package"_Build_package.html doc page for
+more info.
[Related commands:]
diff --git a/doc/src/pair_mgpt.txt b/doc/src/pair_mgpt.txt
index 09fe61168698455d05fef6b67ed6a80b1b43a962..bd55d529b8177f52e0589fbf0fafc19b0b82a72d 100644
--- a/doc/src/pair_mgpt.txt
+++ b/doc/src/pair_mgpt.txt
@@ -159,8 +159,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the USER-MGPT package and is only enabled
-if LAMMPS is built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS is built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The MGPT potentials require the "newtion"_newton.html setting to be
"on" for pair style interactions.
diff --git a/doc/src/pair_momb.txt b/doc/src/pair_momb.txt
index 545b650f75176e7a32d83ce85312e29720731f0c..f1989f56f49a39d66bf8242522cc07987984c9ce 100644
--- a/doc/src/pair_momb.txt
+++ b/doc/src/pair_momb.txt
@@ -50,8 +50,8 @@ Rr (distance units, typically sum of atomic vdW radii) :ul
[Restrictions:]
This style is part of the USER-MISC package. It is only enabled if
-LAMMPS is built with that package. See the "Making of
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS is built with that package. See the "Build
+package"_Build_package.html doc page on for more info.
[Related commands:]
diff --git a/doc/src/pair_morse.txt b/doc/src/pair_morse.txt
index 85a42986ec87ed45e30fe3fc3120587b4d345492..68894f691384d7445196aa4783dbb882964d6b3f 100644
--- a/doc/src/pair_morse.txt
+++ b/doc/src/pair_morse.txt
@@ -107,13 +107,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -148,12 +148,12 @@ These pair styles can only be used via the {pair} keyword of the
[Restrictions:]
The {morse/smooth/linear} pair style is only enabled if LAMMPS was
-built with the USER-MISC package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+built with the USER-MISC package. See the "Build
+package"_Build_package.html doc page for more info.
The {morse/soft} pair style is only enabled if LAMMPS was built with
-the USER-FEP package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+the USER-FEP package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/pair_multi_lucy.txt b/doc/src/pair_multi_lucy.txt
index 31d52a58c89386b5cca80afcd4b585c4e314fc15..0b3a430417370765db40d4ef682f70040ddb1863 100644
--- a/doc/src/pair_multi_lucy.txt
+++ b/doc/src/pair_multi_lucy.txt
@@ -177,8 +177,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_multi_lucy_rx.txt b/doc/src/pair_multi_lucy_rx.txt
index e09dde3f8051128f22a0817f847b3238061f9ad6..819a15b6244bb557c3d1b2f43f19aac2d8c8ec51 100644
--- a/doc/src/pair_multi_lucy_rx.txt
+++ b/doc/src/pair_multi_lucy_rx.txt
@@ -210,13 +210,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -226,8 +226,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/src/pair_nb3b_harmonic.txt
index 720b9ea2a1f903f42b54525f4481e63f071aa389..6a119d74e160da95d9a61e522e6c87d75ad1627d 100644
--- a/doc/src/pair_nb3b_harmonic.txt
+++ b/doc/src/pair_nb3b_harmonic.txt
@@ -98,13 +98,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -114,8 +114,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This pair style can only be used if LAMMPS was built with the MANYBODY
-package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+package. See the "Build package"_Build_package.html doc page for more
+info.
[Related commands:]
diff --git a/doc/src/pair_nm.txt b/doc/src/pair_nm.txt
index 355bfd5573e951c2f28effcc2e4e0aee5c351917..a42dfa3c98a632e2decfc4564940501957be9cf5 100644
--- a/doc/src/pair_nm.txt
+++ b/doc/src/pair_nm.txt
@@ -139,13 +139,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -153,8 +153,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
These pair styles are part of the MISC package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt
index 5ec99152978f42f5f603a1c87329ad005093583f..b24e3c07dfad96f51a4d74dccf885b525f502427 100644
--- a/doc/src/pair_oxdna.txt
+++ b/doc/src/pair_oxdna.txt
@@ -82,8 +82,8 @@ The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
[Restrictions:]
These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-CGDNA package and the MOLECULE and ASPHERE package. See the
+"Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt
index a1d2cfdb7c862f96affbd60ec4d216baef0795bc..c5662abdeb9dbfc49959af673d3f54992c1d9b67 100644
--- a/doc/src/pair_oxdna2.txt
+++ b/doc/src/pair_oxdna2.txt
@@ -88,8 +88,8 @@ The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
[Restrictions:]
These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+USER-CGDNA package and the MOLECULE and ASPHERE package. See the
+"Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_peri.txt b/doc/src/pair_peri.txt
index 14abd4541e4b3f33d1dac80119d894f8b758608e..b6baa4edc5790ef45d0f56264b1d2d240b8c2b2a 100644
--- a/doc/src/pair_peri.txt
+++ b/doc/src/pair_peri.txt
@@ -145,13 +145,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -182,8 +182,8 @@ These pair styles can only be used via the {pair} keyword of the
[Restrictions:]
All of these styles are part of the PERI package. They are only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_polymorphic.txt b/doc/src/pair_polymorphic.txt
index eb0c30f249cff1b58a11e21dcb2ff5df14a599fb..7460044043754ae55519a714cbb91396b1fbabc9 100644
--- a/doc/src/pair_polymorphic.txt
+++ b/doc/src/pair_polymorphic.txt
@@ -191,8 +191,8 @@ input script. If using read_data, atomic masses must be defined in the
atomic structure data file.
This pair style is part of the MANYBODY package. It is only enabled if
-LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair potential requires the "newtion"_newton.html setting to be
"on" for pair interactions.
diff --git a/doc/src/pair_python.txt b/doc/src/pair_python.txt
index 1433557e0388e581c94b2668ecc2721fdeea1928..23da86fc495a6daabdee6048cc4d8dcb72525b6b 100644
--- a/doc/src/pair_python.txt
+++ b/doc/src/pair_python.txt
@@ -204,8 +204,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the PYTHON package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_quip.txt b/doc/src/pair_quip.txt
index 3570a52801852be5207d72ef27a45438518ef6bb..1f794d0c84b87d72dbbcbed8603cdeca00c9e526 100644
--- a/doc/src/pair_quip.txt
+++ b/doc/src/pair_quip.txt
@@ -74,8 +74,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the USER-QUIP package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
QUIP potentials are parametrized in electron-volts and Angstroms and
therefore should be used with LAMMPS metal "units"_units.html.
diff --git a/doc/src/pair_reaxc.txt b/doc/src/pair_reaxc.txt
index ec575486404904c6b92dd165e4d6ae490e8a7303..e63f4a90eef6a957787fabcfa43084c00d090ff7 100644
--- a/doc/src/pair_reaxc.txt
+++ b/doc/src/pair_reaxc.txt
@@ -309,13 +309,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -325,8 +325,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This pair style is part of the USER-REAXC package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
The ReaxFF potential files provided with LAMMPS in the potentials
directory are parameterized for real "units"_units.html. You can use
diff --git a/doc/src/pair_resquared.txt b/doc/src/pair_resquared.txt
index 6e72408ebc1a7243f3d01aadaa79dd02afd66553..5e760be495e0a52e9b7294ed73b1e756a403e2c9 100644
--- a/doc/src/pair_resquared.txt
+++ b/doc/src/pair_resquared.txt
@@ -151,13 +151,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -203,8 +203,8 @@ command"_run_style.html.
[Restrictions:]
This style is part of the ASPHERE package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires that atoms be ellipsoids as defined by the
"atom_style ellipsoid"_atom_style.html command.
diff --git a/doc/src/pair_sdk.txt b/doc/src/pair_sdk.txt
index ccf704b6f7f85b163fdcdd375b8821146ee37c37..b977aefe889c25f066e509efacba760ac71842a4 100644
--- a/doc/src/pair_sdk.txt
+++ b/doc/src/pair_sdk.txt
@@ -91,13 +91,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP, and OPT packages respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -133,11 +133,11 @@ respa"_run_style.html command.
[Restrictions:]
-All of the lj/sdk pair styles are part of the USER-CGSDK package.
-The {lj/sdk/coul/long} style also requires the KSPACE package to be
-built (which is enabled by default). They are only enabled if LAMMPS
-was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+All of the lj/sdk pair styles are part of the USER-CGSDK package. The
+{lj/sdk/coul/long} style also requires the KSPACE package to be built
+(which is enabled by default). They are only enabled if LAMMPS was
+built with that package. See the "Build package"_Build_package.html
+doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_smd_hertz.txt b/doc/src/pair_smd_hertz.txt
index f2d633903ab99a90ac5485e1f871c994b872f69a..2581c84dc97d647ec69c67c6590c52a5b8cc6740 100644
--- a/doc/src/pair_smd_hertz.txt
+++ b/doc/src/pair_smd_hertz.txt
@@ -19,32 +19,36 @@ pair_coeff 1 1 <contact_stiffness>
[Description:]
-The {smd/hertz} style calculates contact forces between SPH particles belonging to different physical bodies.
+The {smd/hertz} style calculates contact forces between SPH particles
+belonging to different physical bodies.
-The contact forces are calculated using a Hertz potential, which evaluates the overlap between two particles
-(whose spatial extents are defined via its contact radius).
-The effect is that a particles cannot penetrate into each other.
-The parameter <contact_stiffness> has units of pressure and should equal roughly one half
-of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particles.
+The contact forces are calculated using a Hertz potential, which
+evaluates the overlap between two particles (whose spatial extents are
+defined via its contact radius). The effect is that a particles
+cannot penetrate into each other. The parameter <contact_stiffness>
+has units of pressure and should equal roughly one half of the Young's
+modulus (or bulk modulus in the case of fluids) of the material model
+associated with the SPH particles.
-The parameter {scale_factor} can be used to scale the particles' contact radii. This can be useful to control how close
-particles can approach each other. Usually, {scale_factor} =1.0.
+The parameter {scale_factor} can be used to scale the particles'
+contact radii. This can be useful to control how close particles can
+approach each other. Usually, {scale_factor} =1.0.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
-No mixing is performed automatically.
-Currently, no part of USER-SMD supports restarting nor minimization.
-rRESPA does not apply to this pair style.
+No mixing is performed automatically. Currently, no part of USER-SMD
+supports restarting nor minimization. rRESPA does not apply to this
+pair style.
:line
[Restrictions:]
This fix is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_smd_tlsph.txt b/doc/src/pair_smd_tlsph.txt
index 3aeaa3155382ee4b0b0b34c0bc8beaa381c68bac..44b0c6cae81961bf6f08abf04815937ff694e78e 100644
--- a/doc/src/pair_smd_tlsph.txt
+++ b/doc/src/pair_smd_tlsph.txt
@@ -16,10 +16,11 @@ pair_style smd/tlsph args :pre
pair_style smd/tlsph
-
[Description:]
-The {smd/tlsph} style computes particle interactions according to continuum mechanics constitutive laws and a Total-Lagrangian Smooth-Particle Hydrodynamics algorithm.
+The {smd/tlsph} style computes particle interactions according to
+continuum mechanics constitutive laws and a Total-Lagrangian
+Smooth-Particle Hydrodynamics algorithm.
This pair style is invoked with the following command:
@@ -27,35 +28,40 @@ pair_style smd/tlsph
pair_coeff i j *COMMON rho0 E nu Q1 Q2 hg Cp &
*END :pre
-Here, {i} and {j} denote the {LAMMPS} particle types for which this pair style is
-defined. Note that {i} and {j} must be equal, i.e., no {tlsph} cross interactions
-between different particle types are allowed.
-In contrast to the usual {LAMMPS} {pair coeff} definitions, which are given solely a
-number of floats and integers, the {tlsph} {pair coeff} definition is organised using
-keywords. These keywords mark the beginning of different sets of parameters for particle properties,
-material constitutive models, and damage models. The {pair coeff} line must be terminated with
-the {*END} keyword. The use the line continuation operator {&} is recommended. A typical
-invocation of the {tlsph} for a solid body would consist of an equation of state for computing
-the pressure (the diagonal components of the stress tensor), and a material model to compute shear
-stresses (the off-diagonal components of the stress tensor). Damage and failure models can also be added.
-
-Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a complete listing of the possible keywords and material models.
+Here, {i} and {j} denote the {LAMMPS} particle types for which this
+pair style is defined. Note that {i} and {j} must be equal, i.e., no
+{tlsph} cross interactions between different particle types are
+allowed. In contrast to the usual {LAMMPS} {pair coeff} definitions,
+which are given solely a number of floats and integers, the {tlsph}
+{pair coeff} definition is organised using keywords. These keywords
+mark the beginning of different sets of parameters for particle
+properties, material constitutive models, and damage models. The {pair
+coeff} line must be terminated with the {*END} keyword. The use the
+line continuation operator {&} is recommended. A typical invocation of
+the {tlsph} for a solid body would consist of an equation of state for
+computing the pressure (the diagonal components of the stress tensor),
+and a material model to compute shear stresses (the off-diagonal
+components of the stress tensor). Damage and failure models can also
+be added.
+
+Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a
+complete listing of the possible keywords and material models.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
-No mixing is performed automatically.
-Currently, no part of USER-SMD supports restarting nor minimization.
-rRESPA does not apply to this pair style.
+No mixing is performed automatically. Currently, no part of USER-SMD
+supports restarting nor minimization. rRESPA does not apply to this
+pair style.
:line
[Restrictions:]
This fix is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_smd_triangulated_surface.txt b/doc/src/pair_smd_triangulated_surface.txt
index 65526cfba8cc15a6be2d8dd22510106b5d6a40cf..9eb5e311b8e20dec7a7f51756b02454260d7879e 100644
--- a/doc/src/pair_smd_triangulated_surface.txt
+++ b/doc/src/pair_smd_triangulated_surface.txt
@@ -19,17 +19,21 @@ pair_coeff 1 1 <contact_stiffness>
[Description:]
-The {smd/tri_surface} style calculates contact forces between SPH particles and a rigid wall boundary defined via the
+The {smd/tri_surface} style calculates contact forces between SPH
+particles and a rigid wall boundary defined via the
"smd/wall_surface"_fix_smd_wall_surface.html fix.
-The contact forces are calculated using a Hertz potential, which evaluates the overlap between a particle
-(whose spatial extents are defined via its contact radius) and the triangle.
-The effect is that a particle cannot penetrate into the triangular surface.
-The parameter <contact_stiffness> has units of pressure and should equal roughly one half
-of the Young's modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particle
+The contact forces are calculated using a Hertz potential, which
+evaluates the overlap between a particle (whose spatial extents are
+defined via its contact radius) and the triangle. The effect is that
+a particle cannot penetrate into the triangular surface. The
+parameter <contact_stiffness> has units of pressure and should equal
+roughly one half of the Young's modulus (or bulk modulus in the case
+of fluids) of the material model associated with the SPH particle
-The parameter {scale_factor} can be used to scale the particles' contact radii. This can be useful to control how close
-particles can approach the triangulated surface. Usually, {scale_factor} =1.0.
+The parameter {scale_factor} can be used to scale the particles'
+contact radii. This can be useful to control how close particles can
+approach the triangulated surface. Usually, {scale_factor} =1.0.
:line
@@ -44,8 +48,8 @@ rRESPA does not apply to this pair style.
[Restrictions:]
This fix is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_smd_ulsph.txt b/doc/src/pair_smd_ulsph.txt
index a5bda54d5f0c46d792fc23bdbdba13f6168bbeee..f28dd9043cec1e504df6c89a28c1f2fd4dcbb4d6 100644
--- a/doc/src/pair_smd_ulsph.txt
+++ b/doc/src/pair_smd_ulsph.txt
@@ -17,11 +17,13 @@ keyword = {*DENSITY_SUMMATION} or {*DENSITY_CONTINUITY} and {*VELOCITY_GRADIENT}
[Examples:]
-pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION
+pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION :pre
[Description:]
-The {smd/ulsph} style computes particle interactions according to continuum mechanics constitutive laws and an updated Lagrangian Smooth-Particle Hydrodynamics algorithm.
+The {smd/ulsph} style computes particle interactions according to
+continuum mechanics constitutive laws and an updated Lagrangian
+Smooth-Particle Hydrodynamics algorithm.
This pair style is invoked similar to the following command:
@@ -29,37 +31,45 @@ pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECT
pair_coeff i j *COMMON rho0 c0 Q1 Cp hg &
*END :pre
-Here, {i} and {j} denote the {LAMMPS} particle types for which this pair style is
-defined. Note that {i} and {j} can be different, i.e., {ulsph} cross interactions
-between different particle types are allowed. However, {i}--{i} respectively {j}--{j} pair_coeff lines have to precede a cross interaction.
-In contrast to the usual {LAMMPS} {pair coeff} definitions, which are given solely a
-number of floats and integers, the {ulsph} {pair coeff} definition is organised using
-keywords. These keywords mark the beginning of different sets of parameters for particle properties,
-material constitutive models, and damage models. The {pair coeff} line must be terminated with
-the {*END} keyword. The use the line continuation operator {&} is recommended. A typical
-invocation of the {ulsph} for a solid body would consist of an equation of state for computing
-the pressure (the diagonal components of the stress tensor), and a material model to compute shear
-stresses (the off-diagonal components of the stress tensor).
-
-Note that the use of *GRADIENT_CORRECTION can lead to severe numerical instabilities. For a general fluid simulation, *NO_GRADIENT_CORRECTION is recommended.
-
-Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a complete listing of the possible keywords and material models.
+Here, {i} and {j} denote the {LAMMPS} particle types for which this
+pair style is defined. Note that {i} and {j} can be different, i.e.,
+{ulsph} cross interactions between different particle types are
+allowed. However, {i}--{i} respectively {j}--{j} pair_coeff lines have
+to precede a cross interaction. In contrast to the usual {LAMMPS}
+{pair coeff} definitions, which are given solely a number of floats
+and integers, the {ulsph} {pair coeff} definition is organised using
+keywords. These keywords mark the beginning of different sets of
+parameters for particle properties, material constitutive models, and
+damage models. The {pair coeff} line must be terminated with the
+{*END} keyword. The use the line continuation operator {&} is
+recommended. A typical invocation of the {ulsph} for a solid body
+would consist of an equation of state for computing the pressure (the
+diagonal components of the stress tensor), and a material model to
+compute shear stresses (the off-diagonal components of the stress
+tensor).
+
+Note that the use of *GRADIENT_CORRECTION can lead to severe numerical
+instabilities. For a general fluid simulation, *NO_GRADIENT_CORRECTION
+is recommended.
+
+Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a
+complete listing of the possible keywords and material models.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
-No mixing is performed automatically.
-Currently, no part of USER-SMD supports restarting nor minimization.
-rRESPA does not apply to this pair style.
+No mixing is performed automatically. Currently, no part of USER-SMD
+supports restarting nor minimization. rRESPA does not apply to this
+pair style.
:line
[Restrictions:]
This fix is part of the USER-SMD package. It is only enabled if
-LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_smtbq.txt b/doc/src/pair_smtbq.txt
index c70202c2e13f536307ad84c1f50133490e8bff72..e81411678a71e9347811d0a3990b442db26d1fe8 100644
--- a/doc/src/pair_smtbq.txt
+++ b/doc/src/pair_smtbq.txt
@@ -219,8 +219,8 @@ This pair style can only be used via the {pair} keyword of the
[Restriction:]
This pair style is part of the USER-SMTBQ package and is only enabled
-if LAMMPS is built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS is built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This potential requires using atom type 1 for oxygen and atom type
higher than 1 for metal atoms.
diff --git a/doc/src/pair_snap.txt b/doc/src/pair_snap.txt
index f9bd8910e49ddfe37a044cf9e801f937a1b0cd7e..6f8cc3d8a8b9998f28775ad20fcbe920efdc5e52 100644
--- a/doc/src/pair_snap.txt
+++ b/doc/src/pair_snap.txt
@@ -181,13 +181,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -196,9 +196,9 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
-This style is part of the SNAP package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+This style is part of the SNAP package. It is only enabled if LAMMPS
+was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_soft.txt b/doc/src/pair_soft.txt
index 374711825b5d4bbf656d15fab9a3753c6f2239ce..ca0266f34a7842c8f273a076f087ce442a6b92d0 100644
--- a/doc/src/pair_soft.txt
+++ b/doc/src/pair_soft.txt
@@ -88,13 +88,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_sph_heatconduction.txt b/doc/src/pair_sph_heatconduction.txt
index d19c28a3cb5a0fec2f893d69fc23715abed8ae64..78a9cf2b63bc7906d737f0c81f78759082c0bea2 100644
--- a/doc/src/pair_sph_heatconduction.txt
+++ b/doc/src/pair_sph_heatconduction.txt
@@ -53,8 +53,8 @@ respa"_run_style.html command. It does not support the {inner},
[Restrictions:]
This pair style is part of the USER-SPH package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_sph_idealgas.txt b/doc/src/pair_sph_idealgas.txt
index a670949a892025d8d30ca9a5d63134020483ddc3..59513e7a7370845c3e3dd43f81cd4b90d5627a7d 100644
--- a/doc/src/pair_sph_idealgas.txt
+++ b/doc/src/pair_sph_idealgas.txt
@@ -60,8 +60,8 @@ respa"_run_style.html command. It does not support the {inner},
[Restrictions:]
This pair style is part of the USER-SPH package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_sph_lj.txt b/doc/src/pair_sph_lj.txt
index 152e6cf8a292cd5b03f895ff84282b9ac6652d63..43e77f1aae2d8cfbecd4539ce1b0b7ce35183937 100644
--- a/doc/src/pair_sph_lj.txt
+++ b/doc/src/pair_sph_lj.txt
@@ -60,8 +60,8 @@ As noted above, the Lennard-Jones parameters epsilon and sigma are set
to unity.
This pair style is part of the USER-SPH package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_sph_rhosum.txt b/doc/src/pair_sph_rhosum.txt
index 3cd1c5abb2577e0d7c155d7d5cedd9ae1b768307..9069176f29388ea1a0a1f2e3b24283d183f91214 100644
--- a/doc/src/pair_sph_rhosum.txt
+++ b/doc/src/pair_sph_rhosum.txt
@@ -54,8 +54,8 @@ respa"_run_style.html command. It does not support the {inner},
[Restrictions:]
This pair style is part of the USER-SPH package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_sph_taitwater.txt b/doc/src/pair_sph_taitwater.txt
index 7b9a8188f28b36d30e7a71d64d8b49024ffadd1e..dcb9e39603ff0440d2beb97dafb847f4320df47f 100644
--- a/doc/src/pair_sph_taitwater.txt
+++ b/doc/src/pair_sph_taitwater.txt
@@ -63,8 +63,8 @@ respa"_run_style.html command. It does not support the {inner},
[Restrictions:]
This pair style is part of the USER-SPH package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_sph_taitwater_morris.txt b/doc/src/pair_sph_taitwater_morris.txt
index 02f16d8982f5af327d25e4ce43fbeb9fa877015b..b88707d1afa1e43a3fc2885993db6d544b86391b 100644
--- a/doc/src/pair_sph_taitwater_morris.txt
+++ b/doc/src/pair_sph_taitwater_morris.txt
@@ -62,8 +62,8 @@ respa"_run_style.html command. It does not support the {inner},
[Restrictions:]
This pair style is part of the USER-SPH package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_spin_dmi.txt b/doc/src/pair_spin_dmi.txt
index 375e59fe89486ebec90679a9a4c08b20f9655bb4..bd605bd064637191044f1cfbba122632d5cbb98a 100644
--- a/doc/src/pair_spin_dmi.txt
+++ b/doc/src/pair_spin_dmi.txt
@@ -69,10 +69,10 @@ pair style cannot be used.
[Restrictions:]
-All the {pair/spin} styles are part of the SPIN package.
-These styles are only enabled if LAMMPS was built with this package, and
-if the atom_style "spin" was declared.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+All the {pair/spin} styles are part of the SPIN package. These styles
+are only enabled if LAMMPS was built with this package, and if the
+atom_style "spin" was declared. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_spin_exchange.txt b/doc/src/pair_spin_exchange.txt
index 24eb635b819cd1982c5bc4a37d3e48950e13c28c..2f158704a98007ba083e4b3e90cf67dbb4c5e5bc 100644
--- a/doc/src/pair_spin_exchange.txt
+++ b/doc/src/pair_spin_exchange.txt
@@ -79,10 +79,10 @@ None of those coefficients is optional. If not specified, the
[Restrictions:]
-All the {pair/spin} styles are part of the SPIN package.
-These styles are only enabled if LAMMPS was built with this package, and
-if the atom_style "spin" was declared.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+All the {pair/spin} styles are part of the SPIN package. These styles
+are only enabled if LAMMPS was built with this package, and if the
+atom_style "spin" was declared. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_spin_magelec.txt b/doc/src/pair_spin_magelec.txt
index b338fae5dcdc3597e16dda8df691a012025114c1..f552c56a4bd34b93f68beb5b95f0146785908e3b 100644
--- a/doc/src/pair_spin_magelec.txt
+++ b/doc/src/pair_spin_magelec.txt
@@ -51,10 +51,10 @@ More details about the derivation of these torques/forces are reported in
[Restrictions:]
-All the {pair/spin} styles are part of the SPIN package.
-These styles are only enabled if LAMMPS was built with this package, and
-if the atom_style "spin" was declared.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+All the {pair/spin} styles are part of the SPIN package. These styles
+are only enabled if LAMMPS was built with this package, and if the
+atom_style "spin" was declared. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_spin_neel.txt b/doc/src/pair_spin_neel.txt
index 0967632ed2037ccac12228f089b56c31c8272ad1..fe3bb1ad14ea69240f6bd71b4f9bf06fd63278ef 100644
--- a/doc/src/pair_spin_neel.txt
+++ b/doc/src/pair_spin_neel.txt
@@ -62,10 +62,10 @@ More details about the derivation of these torques/forces are reported in
[Restrictions:]
-All the {pair/spin} styles are part of the SPIN package.
-These styles are only enabled if LAMMPS was built with this package, and
-if the atom_style "spin" was declared.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+All the {pair/spin} styles are part of the SPIN package. These styles
+are only enabled if LAMMPS was built with this package, and if the
+atom_style "spin" was declared. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt
index cd395133293545306ceb7824e6158b47b5a211fb..b33897c5aa506cd6be92ef275194ec2ceb83ce44 100644
--- a/doc/src/pair_style.txt
+++ b/doc/src/pair_style.txt
@@ -218,10 +218,9 @@ This command must be used before any coefficients are set by the
"read_restart"_read_restart.html commands.
Some pair styles are part of specific packages. They are only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
-The doc pages for individual pair potentials tell if it is part of a
-package.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info. The doc pages for
+individual pair potentials tell if it is part of a package.
[Related commands:]
diff --git a/doc/src/pair_sw.txt b/doc/src/pair_sw.txt
index e6741791dfe8d103ded1dbcfc27a9bcaf70e9527..ff83316419081f1e25b0778a66aaa00b78535819 100644
--- a/doc/src/pair_sw.txt
+++ b/doc/src/pair_sw.txt
@@ -150,13 +150,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
When using the USER-INTEL package with this style, there is an
additional 5 to 10 percent performance improvement when the
@@ -191,8 +191,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the MANYBODY package. It is only enabled
-if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_table.txt b/doc/src/pair_table.txt
index 5e3c1f5ff6f2e1bf58c27589afc653c71c569d18..22c63a1f32b2d347884218f4cb449f95beb7e219 100644
--- a/doc/src/pair_table.txt
+++ b/doc/src/pair_table.txt
@@ -223,13 +223,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_table_rx.txt b/doc/src/pair_table_rx.txt
index 41be067bacfcc6eb60286b7f259926c2729e832b..9b9a6abff861daab0e499ee53e7276e138631e0e 100644
--- a/doc/src/pair_table_rx.txt
+++ b/doc/src/pair_table_rx.txt
@@ -233,13 +233,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -249,8 +249,8 @@ instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command is part of the USER-DPD package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/pair_tersoff.txt b/doc/src/pair_tersoff.txt
index 821c38f3e4174310f43c6ee504ede9b194ebdab8..20744bc2a9ae3928a98f3d7dc23e361067d35b73 100644
--- a/doc/src/pair_tersoff.txt
+++ b/doc/src/pair_tersoff.txt
@@ -185,13 +185,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -221,8 +221,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the MANYBODY package. It is only enabled
-if LAMMPS was built with that package. See
-the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_tersoff_mod.txt b/doc/src/pair_tersoff_mod.txt
index ac1f79a80b772f602f951ed34e373eb3b8bb0f0b..2df23045a397b16e56409ec506d8bfeeae85a1a1 100644
--- a/doc/src/pair_tersoff_mod.txt
+++ b/doc/src/pair_tersoff_mod.txt
@@ -137,13 +137,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -169,8 +169,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the MANYBODY package. It is only enabled
-if LAMMPS was built with that package. See
-the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_tersoff_zbl.txt b/doc/src/pair_tersoff_zbl.txt
index a89d4e3ea1fbce4376fa787123d1a98bf25dbbb2..5f03ffd94eca4028b40283b554815d7e67c9198c 100644
--- a/doc/src/pair_tersoff_zbl.txt
+++ b/doc/src/pair_tersoff_zbl.txt
@@ -195,13 +195,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -231,8 +231,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the MANYBODY package. It is only enabled
-if LAMMPS was built with that package. See
-the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_thole.txt b/doc/src/pair_thole.txt
index 7ce8b7cf4bed33dc699d8c08197b01392d1d6ac3..c7a304ca41689df96344438eb094796a0108657c 100644
--- a/doc/src/pair_thole.txt
+++ b/doc/src/pair_thole.txt
@@ -136,13 +136,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -161,8 +161,8 @@ are defined using
[Restrictions:]
These pair styles are part of the USER-DRUDE package. They are only
-enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair_style should currently not be used with the "charmm dihedral
style"_dihedral_charmm.html if the latter has non-zero 1-4 weighting
diff --git a/doc/src/pair_tri_lj.txt b/doc/src/pair_tri_lj.txt
index 3915ffc2383c79220f2b403f7e2d43dc0041ab1e..98bb4e284efcad05315c08b7a0d542febf3e5d2d 100644
--- a/doc/src/pair_tri_lj.txt
+++ b/doc/src/pair_tri_lj.txt
@@ -101,8 +101,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This style is part of the ASPHERE package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Defining particles to be triangles so they participate in tri/tri or
tri/particle interactions requires the use the "atom_style
diff --git a/doc/src/pair_ufm.txt b/doc/src/pair_ufm.txt
index dbc6fd0664b99572fd39dcab68c60003ceef722f..787c60a1bd8a8565f880863178d2d959528bf5e5 100644
--- a/doc/src/pair_ufm.txt
+++ b/doc/src/pair_ufm.txt
@@ -75,13 +75,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_vashishta.txt b/doc/src/pair_vashishta.txt
index 2e404e8befcba50b462a0efbb61b48f0ba8cc82e..01d089b4de9b0727103d4b1fd653b2684cf711a5 100644
--- a/doc/src/pair_vashishta.txt
+++ b/doc/src/pair_vashishta.txt
@@ -177,13 +177,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -213,8 +213,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
These pair style are part of the MANYBODY package. They is only
-enabled if LAMMPS was built with that package. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
These pair styles requires the "newton"_newton.html setting to be "on"
for pair interactions.
diff --git a/doc/src/pair_yukawa.txt b/doc/src/pair_yukawa.txt
index 5a8363260a5e31f507d279500ea9eb2c78199758..154fd3e8367620af646bd283270f4d71ffafe507 100644
--- a/doc/src/pair_yukawa.txt
+++ b/doc/src/pair_yukawa.txt
@@ -55,13 +55,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/pair_yukawa_colloid.txt b/doc/src/pair_yukawa_colloid.txt
index 515062d9eb679cefc969f91e41c376b265541bd4..b36c4c235c6cefef90ade34eaabf4b3fe7b08b36 100644
--- a/doc/src/pair_yukawa_colloid.txt
+++ b/doc/src/pair_yukawa_colloid.txt
@@ -86,13 +86,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -129,8 +129,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This style is part of the COLLOID package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
This pair style requires that atoms be finite-size spheres with a
diameter, as defined by the "atom_style sphere"_atom_style.html
diff --git a/doc/src/pair_zbl.txt b/doc/src/pair_zbl.txt
index 1472c7b6726d970179eeacd97915edabdfcdd55c..4c8dfb545526e07e11979d911856b1c3becdf341 100644
--- a/doc/src/pair_zbl.txt
+++ b/doc/src/pair_zbl.txt
@@ -77,13 +77,13 @@ produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
-LAMMPS was built with those packages. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with those packages. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/partition.txt b/doc/src/partition.txt
index d4fe06c098fd2de94520c38b96346407a0cbf3b9..86673c226bd5ef463e1723fb9f0fcdc023f4a678 100644
--- a/doc/src/partition.txt
+++ b/doc/src/partition.txt
@@ -26,9 +26,8 @@ partition yes 6* fix all nvt temp 1.0 1.0 0.1 :pre
[Description:]
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 2.6"_Section_start.html#start_6
-for an explanation of the switch.
+partitions of processors you have defined via the "-partition
+command-line switch"_Run_options.html.
Normally, every input script command in your script is invoked by
every partition. This behavior can be modified by defining world- or
@@ -49,7 +48,7 @@ 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"_Run_options.html.
{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/src/prd.txt b/doc/src/prd.txt
index b2145ebad1a43ac0037f484f030a945479dd0ecb..f71f285336ff716db8af3da6f05b232932629ae2 100644
--- a/doc/src/prd.txt
+++ b/doc/src/prd.txt
@@ -62,15 +62,15 @@ timescale spanned by the multiple simulations, while waiting for an
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 2.6"_Section_start.html#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 two
-processors. However for PRD, this makes little sense, since running a
-replica on virtual instead of physical processors,offers no effective
-parallel speed-up in searching for infrequent events. See the "Howto
-replica"_Howto_replica.html doc page for further discussion.
+partitions are defined at run-time using the "-partition command-line
+switch"_Run_options.html. 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 two processors. However for PRD, this makes
+little sense, since running a replica on virtual instead of physical
+processors,offers no effective parallel speed-up in searching for
+infrequent events. See the "Howto replica"_Howto_replica.html doc
+page for further discussion.
When a PRD simulation is performed, it is assumed that each replica is
running the same model, though LAMMPS does not check for this.
@@ -285,8 +285,8 @@ value for the first event in the new run will be slightly off.
[Restrictions:]
This command can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
The {N} and {t_correlate} settings must be integer multiples of
{t_event}.
diff --git a/doc/src/processors.txt b/doc/src/processors.txt
index df13ae1f617fd9507bdbf7192b52d668c3ca44df..b9bd927f9688efbde7448eaa025bd111335eca4b 100644
--- a/doc/src/processors.txt
+++ b/doc/src/processors.txt
@@ -81,11 +81,11 @@ 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
-section"_Section_start.html#start_6 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.
+number of processors in this partition; see the "-partition
+command-line switch"_Run_options.html doc page for details. 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.
You can use the "partition"_partition.html command to specify
different processor grids for different partitions, e.g.
@@ -249,7 +249,7 @@ 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"_Run_options.html.
A "dependency" means that the sending partition will create its
regular 3d grid as Px by Py by Pz and after it has done this, it will
@@ -286,8 +286,8 @@ 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
-use of MPI-specific launch options such as a config file.
+"-reorder command-line switch"_Run_options.html 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
to a different file, e.g. using a "world-style variable"_variable.html
@@ -300,11 +300,11 @@ 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.
-The universe and original IDs will only be different if you used the
-"-reorder command-line switch"_Section_start.html#start_6 to reorder
-the processors differently than their rank in the original
-communicator LAMMPS was instantiated with.
+see the "-partition command-line switch"_Run_options.html. The
+universe and original IDs will only be different if you used the
+"-reorder command-line switch"_Run_options.html to reorder the
+processors differently than their rank in the original communicator
+LAMMPS was instantiated with.
I,J,K are the indices of the processor in the regular 3d grid, each
from 1 to Nd, where Nd is the number of processors in that dimension
@@ -332,7 +332,8 @@ 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
+"partition"_partition.html, "-reorder command-line
+switch"_Run_options.html
[Default:]
diff --git a/doc/src/python.txt b/doc/src/python.txt
index 4f4faca8f43c5fc6ca5db28f748238798405b862..0c0a203ccdbf479cc68d77c94a2740a1a51f0169 100644
--- a/doc/src/python.txt
+++ b/doc/src/python.txt
@@ -469,8 +469,8 @@ sys.exit() in the except clause).
[Restrictions:]
This command is part of the PYTHON package. It is only enabled if
-LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
Building LAMMPS with the PYTHON package will link LAMMPS with the
Python library on your system. Settings to enable this are in the
diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt
index ded51a4d99855abfd9abc4361c1f0f2b052729dd..ef899a15b44b153621cc194d317c3a313bd9afac 100644
--- a/doc/src/read_data.txt
+++ b/doc/src/read_data.txt
@@ -63,8 +63,8 @@ simulation. The file can be ASCII text or a gzipped text file
atom coordinates; see the "read_restart"_read_restart.html and
"create_atoms"_create_atoms.html commands for alternative methods.
Also see the explanation of the "-restart command-line
-switch"_Section_start.html#start_6 which can convert a restart file to
-a data file.
+switch"_Run_options.html which can convert a restart file to a data
+file.
This command can be used multiple times to add new atoms and their
properties to an existing system by using the {add}, {offset}, and
@@ -1153,8 +1153,8 @@ Translational velocities can also be set by the
[Restrictions:]
To read gzipped data files, you must compile LAMMPS with the
--DLAMMPS_GZIP option - see the "Making
-LAMMPS"_Section_start.html#start_2 section of the documentation.
+-DLAMMPS_GZIP option. See the "Build settings"_Build_settings.html
+doc page for details.
[Related commands:]
diff --git a/doc/src/read_dump.txt b/doc/src/read_dump.txt
index a3c0733e07369da85b63f222069ce12b224a3f13..db9cfca825b10f19a55292b8e78da88ce8a15950 100644
--- a/doc/src/read_dump.txt
+++ b/doc/src/read_dump.txt
@@ -311,12 +311,12 @@ needed to generate absolute, unscaled coordinates.
[Restrictions:]
To read gzipped dump files, you must compile LAMMPS with the
--DLAMMPS_GZIP option - see the "Making
-LAMMPS"_Section_start.html#start_2 section of the documentation.
+-DLAMMPS_GZIP option. See the "Build settings"_Build_settings.html
+doc page for details.
The {molfile} dump file formats are part of the USER-MOLFILE package.
They are only enabled if LAMMPS was built with that packages. See the
-"Making LAMMPS"_Section_start.html#start_3 section for more info.
+"Build package"_Build_package.html doc page for more info.
[Related commands:]
diff --git a/doc/src/read_restart.txt b/doc/src/read_restart.txt
index 488c36f02081d5be3c3a9a9067ed2638e4738c63..08cb6a2e6cc459351e5b7598c95bcbabe939e2b1 100644
--- a/doc/src/read_restart.txt
+++ b/doc/src/read_restart.txt
@@ -80,8 +80,7 @@ produced the restart file, it could be a LAMMPS bug, so consider
Because restart files are binary, they may not be portable to other
machines. In this case, you can use the "-restart command-line
-switch"_Section_start.html#start_6 to convert a restart file to a data
-file.
+switch"_Run_options.html to convert a restart file to a data file.
Similar to how restart files are written (see the
"write_restart"_write_restart.html and "restart"_restart.html
diff --git a/doc/src/region.txt b/doc/src/region.txt
index 21396ae1fd2b6652fc6928d24f685cfc39bc7031..acc85dcebbd89986d59da3f09a59ea45bf35ee29 100644
--- a/doc/src/region.txt
+++ b/doc/src/region.txt
@@ -370,13 +370,13 @@ by Kokkos or no acceleration will occur. Currently, only {block} style
regions are supported by Kokkos.
These accelerated styles are part of the Kokkos package. They are
-only enabled if LAMMPS was built with that package. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+only enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page 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
-use the "suffix"_suffix.html command in your input script.
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
diff --git a/doc/src/rerun.txt b/doc/src/rerun.txt
index 8eb3ebd5a19458aec21e3c799ef80cacf936e998..71ad464bb0015a109bca2f812ac8fe289d99c1b2 100644
--- a/doc/src/rerun.txt
+++ b/doc/src/rerun.txt
@@ -189,8 +189,8 @@ every 1000 steps, then you will only see thermodynamic output every
[Restrictions:]
To read gzipped dump files, you must compile LAMMPS with the
--DLAMMPS_GZIP option - see the "Making
-LAMMPS"_Section_start.html#start_2 section of the documentation.
+-DLAMMPS_GZIP option. See the "Build settings"_Build_settings.html
+doc page for details.
[Related commands:]
diff --git a/doc/src/restart.txt b/doc/src/restart.txt
index 6f2dc5ca467c354a9c576d467af4c5d49c1e9301..7c034f36e0c6d002739c35362afca8440f9358a5 100644
--- a/doc/src/restart.txt
+++ b/doc/src/restart.txt
@@ -125,8 +125,7 @@ Restart files can be read by a "read_restart"_read_restart.html
command to restart a simulation from a particular state. Because the
file is binary (to enable exact restarts), it may not be readable on
another machine. In this case, you can use the "-r command-line
-switch"_Section_start.html#start_6 to convert a restart file to a data
-file.
+switch"_Run_options.html to convert a restart file to a data file.
NOTE: Although the purpose of restart files is to enable restarting a
simulation from where it left off, not all information about a
diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt
index deee51cfd3d6fc0857ea99b5b169d323cbc323c7..6dd9b56908960bbbe820bcd7f2667a3faf158a73 100644
--- a/doc/src/run_style.txt
+++ b/doc/src/run_style.txt
@@ -69,8 +69,8 @@ The {verlet} style is a standard velocity-Verlet integrator.
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 2.6"_Section_start.html#start_6 for an
-explanation of the -partition command-line switch.
+processors. See the "-partition command-line switch"_Run_options.html
+for info on how to run LAMMPS with multiple partitions.
Specifically, this style performs all computation except the
"kspace_style"_kspace_style.html portion of the force field on the 1st
@@ -115,9 +115,9 @@ When you run in 2-partition mode with the {verlet/split} style, the
thermodynamic 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
-screen file for the 2nd partition will not contain thermodynamic
-output beyond the 1st timestep of the run.
+switches"_Run_options.html to change this. The log and screen file
+for the 2nd partition will not contain thermodynamic output beyond the
+1st timestep of the run.
See the "Speed packages"_Speed_packages.html doc page for performance
details of the speed-up offered by the {verlet/split} style. One
@@ -282,10 +282,10 @@ additional operations required for managing {omp} styles. For more on
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
-You can specify {respa/omp} explicitly in your input script, or
-you can use the "-suffix command-line switch"_Section_start.html#start_6
-when you invoke LAMMPS, or you can use the "suffix"_suffix.html
-command in your input script.
+You can specify {respa/omp} explicitly in your input script, or you
+can use the "-suffix command-line switch"_Run_options.html when you
+invoke LAMMPS, or you can use the "suffix"_suffix.html command in your
+input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
@@ -296,8 +296,8 @@ instructions on how to use the accelerated styles effectively.
The {verlet/split} style can only be used if LAMMPS was built with the
REPLICA package. Correspondingly the {respa/omp} style is available
-only if the USER-OMP package was included. See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+only if the USER-OMP package was included. See the "Build
+package"_Build_package.html doc page for more info.
Whenever using rRESPA, the user should experiment with trade-offs in
speed and accuracy for their system, and verify that they are
diff --git a/doc/src/suffix.txt b/doc/src/suffix.txt
index bb0619f1e04af5ab1bafc7772c2e40f09e1f3767..62e41ed29a10a1a7d077cbbbef7074fdb45412c5 100644
--- a/doc/src/suffix.txt
+++ b/doc/src/suffix.txt
@@ -28,16 +28,16 @@ suffix kk :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
-to turn off or back on any suffix setting made via the command line.
+command-line switch"_Run_options.html. It also has options to turn
+off or back on any suffix setting made via the command line.
The specified style can be {gpu}, {intel}, {kk}, {omp}, {opt} or
{hybrid}. These refer to optional packages that LAMMPS can be built
-with, as described in "this section of the
-manual"_Section_start.html#start_3. The "gpu" style corresponds to
-the GPU package, the "intel" style to the USER-INTEL package, the "kk"
-style to the KOKKOS package, the "omp" style to the USER-OMP package,
-and the "opt" style to the OPT package.
+with, as described on the "Build package"_Build_package.html doc page.
+The "gpu" style corresponds to the GPU package, the "intel" style to
+the USER-INTEL package, the "kk" style to the KOKKOS package, the
+"omp" style to the USER-OMP package, and the "opt" style to the OPT
+package.
These are the variants these packages provide:
@@ -105,6 +105,6 @@ input script.
[Related commands:]
-"Command-line switch -suffix"_Section_start.html#start_6
+"-suffix command-line switch"_Run_options.html
[Default:] none
diff --git a/doc/src/tad.txt b/doc/src/tad.txt
index a26ff79318ceed4f91cd402bb095a08c546baea5..9b34a68636c1eaa0b37ddbc9dce9ca6a5f61bd27 100644
--- a/doc/src/tad.txt
+++ b/doc/src/tad.txt
@@ -271,8 +271,8 @@ are always monotonically increasing.
[Restrictions:]
This command can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
{N} setting must be integer multiple of {t_event}.
diff --git a/doc/src/temper.txt b/doc/src/temper.txt
index c7b482acc6467948a15321a363e138f5fb1962ae..edd578fbc93449e4d3eb3e0c4fb15dad6bad507f 100644
--- a/doc/src/temper.txt
+++ b/doc/src/temper.txt
@@ -31,14 +31,14 @@ Run a parallel tempering or replica exchange simulation using multiple
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 2.6"_Section_start.html#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 two
-processors. You will simply not get the performance speed-up you
-would see with one or more physical processors per replica. See the
-"Howto replica"_Howto_replica.html doc page for further discussion.
+partitions are defined at run-time using the "-partition command-line
+switch"_Run_options.html. 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 two processors. You will simply not get the
+performance speed-up you would see with one or more physical
+processors per replica. See the "Howto replica"_Howto_replica.html
+doc page for further discussion.
Each replica's temperature is controlled at a different value by a fix
with {fix-ID} that controls temperature. Most thermostat fix styles
@@ -68,9 +68,8 @@ 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
-switches"_Section_start.html#start_6 for info on how to change these
-names.
+with N = # of replicas. See the "-log and -screen command-line
+swiches"_Run_options.html for info on how to change these names.
The main screen and log file (log.lammps) will list information about
which temperature is assigned to each replica at each thermodynamic
@@ -138,8 +137,8 @@ example above with $w as the last argument.
[Restrictions:]
This command can only be used if LAMMPS was built with the REPLICA
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
[Related commands:]
diff --git a/doc/src/temper_grem.txt b/doc/src/temper_grem.txt
index 9cb1bab78465c890c0f6377d9c5fb45d0803b145..7d22e464032dc8dbf93580eb33779f16b068c37e 100644
--- a/doc/src/temper_grem.txt
+++ b/doc/src/temper_grem.txt
@@ -94,8 +94,8 @@ identical to "temper"_temper.html.
[Restrictions:]
This command can only be used if LAMMPS was built with the USER-MISC
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc
+page for more info.
This command must be used with "fix grem"_fix_grem.html.
diff --git a/doc/src/temper_npt.txt b/doc/src/temper_npt.txt
index 4eee225de73cfd0e3ea3b4354a293d902fa8250c..50ac5615f69ad6ca5282fa959db24ad231612274 100644
--- a/doc/src/temper_npt.txt
+++ b/doc/src/temper_npt.txt
@@ -48,8 +48,8 @@ on how the parallel tempering is handled in general.
[Restrictions:]
This command can only be used if LAMMPS was built with the USER-MISC
-package. See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package. See the "Build package"_Build_package.html doc page for more
+info.
This command should be used with a fix that maintains the
isothermal-isobaric (NPT) ensemble.
diff --git a/doc/src/thermo_style.txt b/doc/src/thermo_style.txt
index cbc2612f28c69a49bcd4dcb28b3b1c7a132fd85c..4d294c1df7b4c6d6a364448304c535ba7d44b950 100644
--- a/doc/src/thermo_style.txt
+++ b/doc/src/thermo_style.txt
@@ -253,9 +253,9 @@ proceed for the maximum number of allowed iterations.
The {part} keyword is useful for multi-replica or multi-partition
simulations to indicate which partition this output and this file
corresponds to, or for use in a "variable"_variable.html to append to
-a filename for output specific to this partition. See "Section
-2.6"_Section_start.html#start_6 of the manual for details on running
-in multi-partition mode.
+a filename for output specific to this partition. See discussion of
+the "-partition command-line switch"_Run_options.html for details on
+running in multi-partition mode.
The {timeremain} keyword returns the remaining seconds when a
timeout has been configured via the "timer timeout"_timer.html command.
diff --git a/doc/src/timer.txt b/doc/src/timer.txt
index 10737dbda0cebfea9b99582c28327168aa55faa6..4025af9ea623a0de7e9a13b5b7994387e76fb58d 100644
--- a/doc/src/timer.txt
+++ b/doc/src/timer.txt
@@ -39,8 +39,8 @@ During a simulation run LAMMPS collects information about how much
time is spent in different sections of the code and thus can provide
information for determining performance and load imbalance problems.
This can be done at different levels of detail and accuracy. For more
-information about the timing output, see this "discussion of screen
-output in Section 2.7"_Section_start.html#start_7.
+information about the timing output, see the "Run
+output"_Run_output.html doc page.
The {off} setting will turn all time measurements off. The {loop}
setting will only measure the total time for a run and not collect any
diff --git a/doc/src/variable.txt b/doc/src/variable.txt
index c6598ccb514d2855259038e99d1560488f7cdff9..a8d50503ac96bb6ea49041c6469449ae9438ee05 100644
--- a/doc/src/variable.txt
+++ b/doc/src/variable.txt
@@ -178,9 +178,8 @@ This means variables can NOT be re-defined in an input script (with
two 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 -var
-will override a corresponding index variable setting in the input
-script.
+that using the "command-line switch"_Run_options.html -var will
+override a corresponding index variable setting in the input script.
There are two exceptions to this rule. First, variables of style
{string}, {getenv}, {internal}, {equal}, {vector}, {atom}, and
@@ -247,8 +246,7 @@ 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
-section"_Section_start.html#start_6 for details.
+using the "command-line switch -var"_Run_options.html.
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
@@ -263,32 +261,31 @@ inclusive, and the string N1 is initially assigned to the variable.
N1 <= N2 and N2 >= 0 is required.
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
-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
-next command cannot be used with {equal} style variables, since there
-is only one value per world. This style of variable is useful when
-you wish to run different simulations on different partitions, or when
-performing a parallel tempering simulation (see the
+be one string for each processor partition or "world". LAMMPS can be
+run with multiple partitions via the "-partition command-line
+switch"_Run_options.html. This variable command assigns one string to
+each world. All processors in the world are assigned the same string.
+The next command cannot be used with {equal} style variables, since
+there is only one value per world. This style of variable is useful
+when you wish to run different simulations on different partitions, or
+when performing a parallel tempering simulation (see the
"temper"_temper.html command), to assign different temperatures to
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
-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
-using this variable, the first processor partition to encounter it, is
-assigned the next available string. This continues until all the
-variable strings are consumed. Thus, this command can be used to run
-50 simulations on 8 processor partitions. The simulations will be run
-one after the other on whatever partition becomes available, until
-they are all finished. {Universe} 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.
+"worlds". LAMMPS can be run with multiple partitions via the
+"-partition command-line switch"_Run_options.html. This variable
+command initially assigns one string to each world. When a
+"next"_next.html command is encountered using this variable, the first
+processor partition to encounter it, is assigned the next available
+string. This continues until all the variable strings are consumed.
+Thus, this command can be used to run 50 simulations on 8 processor
+partitions. The simulations will be run one after the other on
+whatever partition becomes available, until they are all finished.
+{Universe} 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.
The {uloop} style is identical to the {universe} style except that the
strings are the integers from 1 to N. This allows generation of long
diff --git a/doc/src/write_data.txt b/doc/src/write_data.txt
index d8a33f457f2ab15cb38d6922ec54c5b5b8d5d202..b6002b52529a14621623a490316d751c0ad421bc 100644
--- a/doc/src/write_data.txt
+++ b/doc/src/write_data.txt
@@ -60,7 +60,7 @@ If you want to do more exact restarts, using binary files, see the
"restart"_restart.html, "write_restart"_write_restart.html, and
"read_restart"_read_restart.html commands. You can also convert
binary restart files to text data files, after a simulation has run,
-using the "-r command-line switch"_Section_start.html#start_6.
+using the "-r command-line switch"_Run_options.html.
NOTE: Only limited information about a simulation is stored in a data
file. For example, no information about atom "groups"_group.html and
diff --git a/doc/src/write_restart.txt b/doc/src/write_restart.txt
index 3935a5d5387bfd6118134c605058a146fbc81a43..c393c7f735ece6718966ad7bf37fd31194b0408c 100644
--- a/doc/src/write_restart.txt
+++ b/doc/src/write_restart.txt
@@ -66,8 +66,7 @@ Restart files can be read by a "read_restart"_read_restart.html
command to restart a simulation from a particular state. Because the
file is binary (to enable exact restarts), it may not be readable on
another machine. In this case, you can use the "-r command-line
-switch"_Section_start.html#start_6 to convert a restart file to a data
-file.
+switch"_Run_options.html to convert a restart file to a data file.
NOTE: Although the purpose of restart files is to enable restarting a
simulation from where it left off, not all information about a