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correct section link descriptions

This commit is contained in:
Axel Kohlmeyer 2016-09-10 21:03:38 -04:00
parent 4d298ccf2f
commit f8d5488409
190 changed files with 400 additions and 388 deletions
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12
doc/src/Section_accelerate.txt
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@ -157,11 +157,11 @@ packages"_Section_packages.html.
These are the accelerator packages
currently in LAMMPS, either as standard or user packages:
"GPU"_accelerate_gpu.html : for NVIDIA GPUs as well as OpenCL support
"USER-INTEL"_accelerate_intel.html : for Intel CPUs and Intel Xeon Phi
"KOKKOS"_accelerate_kokkos.html : for GPUs, Intel Xeon Phi, and OpenMP threading
"USER-OMP"_accelerate_omp.html : for OpenMP threading
"OPT"_accelerate_opt.html : generic CPU optimizations :tb(s=:)
"GPU Package"_accelerate_gpu.html with CUDA and OpenCL support for Nvidia GPUs and others :h5
"USER-INTEL Package"_accelerate_intel.html for Intel CPUs and Intel Xeon Phi :h5
"KOKKOS Package"_accelerate_kokkos.html for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading :h5
"USER-OMP Package "_accelerate_omp.html for OpenMP threading and generic CPU optimizations :h5
"OPT Package"_accelerate_opt.html generic CPU optimizations :h5
Inverting this list, LAMMPS currently has acceleration support for
three kinds of hardware, via the listed packages:
@ -192,7 +192,7 @@ Lennard-Jones "pair_style lj/cut"_pair_lj.html:
"pair_style lj/cut/opt"_pair_lj.html :ul
To see what accelerate styles are currently available, see
"Section_commands 5"_Section_commands.html#cmd_5 of the manual. The
"Section 3.5"_Section_commands.html#cmd_5 of the manual. The
doc pages for individual commands (e.g. "pair lj/cut"_pair_lj.html or
"fix nve"_fix_nve.html) also list any accelerated variants available
for that style.

2
doc/src/Section_commands.txt
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@ -195,7 +195,7 @@ allowed, but that should be sufficient for most use cases.
This section describes the structure of a typical LAMMPS input script.
The "examples" directory in the LAMMPS distribution contains many
sample input scripts; the corresponding problems are discussed in
"Section_example"_Section_example.html, and animated on the "LAMMPS
"Section 7"_Section_example.html, and animated on the "LAMMPS
WWW Site"_lws.
A LAMMPS input script typically has 4 parts:

2
doc/src/Section_errors.txt
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@ -11579,7 +11579,7 @@ This may not be what you intended. :dd
If there are other fixes that act immediately after the intitial stage
of time integration within a timestep (i.e. after atoms move), then
the command that sets up the dynamic group should appear after those
fixes. This will insure that dynamic group assignements are made
fixes. This will insure that dynamic group assignments are made
after all atoms have moved. :dd
{One or more respa levels compute no forces} :dt

28
doc/src/Section_history.txt
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@ -22,15 +22,27 @@ dynamics codes our group has distributed.
13.1 Coming attractions :h4,link(hist_1)
The "Wish list link"_http://lammps.sandia.gov/future.html on the
LAMMPS WWW page gives a list of features we are hoping to add to
LAMMPS in the future, including contact names of individuals you can
email if you are interested in contributing to the developement or
would be a future user of that feature.
As of summer 2016 we are using the "LAMMPS project issue tracker
on GitHub"_https://github.com/lammps/lammps/issues for keeping
track of suggested, planned or pending new features. This includes
discussions of how to best implement them, or why they would be
useful. Especially if a planned or proposed feature is non-trivial
to add, e.g. because it requires changes to some of the core
classes of LAMMPS, people planning to contribute a new feature to
LAMMS are encouraged to submit an issue about their planned
implementation this way in order to receive feedback from the
LAMMPS core developers. They will provide suggestions about
the validity of the proposed approach and possible improvements,
pitfalls or alternatives.
You can also send "email to the
developers"_http://lammps.sandia.gov/authors.html if you want to add
your wish to the list.
Please see some of the closed issues for examples of how to
suggest code enhancements, submit proposed changes, or report
elated issues and how they are resoved.
As an alternative to using GitHub, you may e-mail the
"core developers"_http://lammps.sandia.gov/authors.html or send
an e-mail to the "LAMMPS Mail list"_http://lammps.sandia.gov/mail.html
if you want to have your suggestion added to the list.
:line

16
doc/src/Section_howto.txt
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@ -39,7 +39,7 @@ This section describes how to perform common tasks using LAMMPS.
6.27 "Drude induced dipoles"_#howto_27 :all(b)
The example input scripts included in the LAMMPS distribution and
highlighted in "Section_example"_Section_example.html also show how to
highlighted in "Section 7"_Section_example.html also show how to
setup and run various kinds of simulations.
:line
@ -180,7 +180,7 @@ used in the CHARMM, AMBER, and DREIDING force fields. Setting
coefficients is done in the input data file via the
"read_data"_read_data.html command or in the input script with
commands like "pair_coeff"_pair_coeff.html or
"bond_coeff"_bond_coeff.html. See "Section_tools"_Section_tools.html
"bond_coeff"_bond_coeff.html. See "Section 9"_Section_tools.html
for additional tools that can use CHARMM or AMBER to assign force
field coefficients and convert their output into LAMMPS input.
@ -673,7 +673,7 @@ processors to start up another program). In the latter case the
stand-alone code could communicate with LAMMPS thru files that the
command writes and reads.
See "Section_modify"_Section_modify.html of the documentation for how
See "Section 10"_Section_modify.html of the documentation for how
to add a new command to LAMMPS.
(3) Use LAMMPS as a library called by another code. In this case the
@ -709,12 +709,12 @@ 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
"Section_python"_Section_python.html of the manual for a description
"Section 11"_Section_python.html of the manual 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 "Section_howto 19"_Section_howto.html#howto_19 of the
to LAMMPS. See "Section 6.19"_Section_howto.html#howto_19 of the
manual for a description of the interface and how to extend it for
your needs.
@ -746,7 +746,7 @@ and atom trajectories.
Several programs included with LAMMPS as auxiliary tools can convert
native LAMMPS dump files to other formats. See the
"Section_tools"_Section_tools.html doc page for details. The first is
"Section 9"_Section_tools.html doc page for details. The first is
the "ch2lmp tool"_Section_tools.html#charmm, which contains a
lammps2pdb Perl script which converts LAMMPS dump files into PDB
files. The second is the "lmp2arc tool"_Section_tools.html#arc which
@ -1840,7 +1840,7 @@ converge and requires careful post-processing "(Shinoda)"_#Shinoda
6.19 Library interface to LAMMPS :link(howto_19),h4
As described in "Section_start 5"_Section_start.html#start_5, LAMMPS
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"_Section_howto.html#howto_10 with other
codes, or driven through a "Python interface"_Section_python.html.
@ -2212,7 +2212,7 @@ Note that this compute allows the per-atom output of other
"variables"_variable.html to be used to define chunk IDs for each
atom. This means you can write your own compute or fix to output a
per-atom quantity to use as chunk ID. See
"Section_modify"_Section_modify.html of the documentation for how to
"Section 10"_Section_modify.html of the documentation for how to
do this. You can also define a "per-atom variable"_variable.html in
the input script that uses a formula to generate a chunk ID for each
atom.

18
doc/src/Section_intro.txt
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@ -41,7 +41,7 @@ parallel machines and Beowulf-style clusters.
:link(mpi,http://www-unix.mcs.anl.gov/mpi)
LAMMPS can model systems with only a few particles up to millions or
billions. See "Section_perf"_Section_perf.html for information on
billions. See "Section 8"_Section_perf.html for information on
LAMMPS performance and scalability, or the Benchmarks section of the
"LAMMPS WWW Site"_lws.
@ -54,12 +54,12 @@ brief discussion of the open-source philosophy.
LAMMPS is designed to be easy to modify or extend with new
capabilities, such as new force fields, atom types, boundary
conditions, or diagnostics. See "Section_modify"_Section_modify.html
conditions, or diagnostics. See "Section 10"_Section_modify.html
for more details.
The current version of LAMMPS is written in C++. Earlier versions
were written in F77 and F90. See
"Section_history"_Section_history.html for more information on
"Section 13"_Section_history.html for more information on
different versions. All versions can be downloaded from the "LAMMPS
WWW Site"_lws.
@ -94,7 +94,7 @@ LAMMPS are listed in "this section"_#intro_5.
This section highlights LAMMPS features, with pointers to specific
commands which give more details. If LAMMPS doesn't have your
favorite interatomic potential, boundary condition, or atom type, see
"Section_modify"_Section_modify.html, which describes how you can add
"Section 10"_Section_modify.html, which describes how you can add
it to LAMMPS.
General features :h5
@ -330,7 +330,7 @@ Similarly, LAMMPS creates output files in a simple format. Most users
post-process these files with their own analysis tools or re-format
them for input into other programs, including visualization packages.
If you are convinced you need to compute something on-the-fly as
LAMMPS runs, see "Section_modify"_Section_modify.html for a discussion
LAMMPS runs, see "Section 10"_Section_modify.html for a discussion
of how you can use the "dump"_dump.html and "compute"_compute.html and
"fix"_fix.html commands to print out data of your choosing. Keep in
mind that complicated computations can slow down the molecular
@ -352,7 +352,7 @@ following packages:
"RasMol"_http://www.openrasmol.org :ul
Other features that LAMMPS does not yet (and may never) support are
discussed in "Section_history"_Section_history.html.
discussed in "Section 13"_Section_history.html.
Finally, these are freely-available molecular dynamics codes, most of
them parallel, which may be well-suited to the problems you want to
@ -427,7 +427,7 @@ Site"_lws, or have a suggestion for something to clarify or include,
send an email to the
"developers"_http://lammps.sandia.gov/authors.html. :l
If you find a bug, "Section_errors 2"_Section_errors.html#err_2
If you find a bug, "Section 12.2"_Section_errors.html#err_2
describes how to report it. :l
If you publish a paper using LAMMPS results, send the citation (and
@ -440,7 +440,7 @@ directory. :l
The tools sub-directory of the LAMMPS distribution has various
stand-alone codes for pre- and post-processing of LAMMPS data. More
details are given in "Section_tools"_Section_tools.html. If you write
details are given in "Section 9"_Section_tools.html. If you write
a new tool that users will find useful, it can be added to the LAMMPS
distribution. :l
@ -531,7 +531,7 @@ Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for gran
Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SPH package :ul
As discussed in "Section_history"_Section_history.html, LAMMPS
As discussed in "Section 13"_Section_history.html, LAMMPS
originated as a cooperative project between DOE labs and industrial
partners. Folks involved in the design and testing of the original
version of LAMMPS were the following:

2
doc/src/Section_modify.txt
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@ -528,7 +528,7 @@ Body particles can represent complex entities, such as surface meshes
of discrete points, collections of sub-particles, deformable objects,
etc.
See "Section_howto 14"_Section_howto.html#howto_14 of the manual for
See "Section 6.14"_Section_howto.html#howto_14 of the manual for
an overview of using body particles and the "body"_body.html doc page
for details on the various body styles LAMMPS supports. New styles
can be created to add new kinds of body particles to LAMMPS.

24
doc/src/Section_packages.txt
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@ -23,7 +23,7 @@ packages.
4.1 "Standard packages"_#pkg_1
4.2 "User packages"_#pkg_2 :all(b)
"Section_start 3"_Section_start.html#start_3 of the manual describes
"Section 2.3"_Section_start.html#start_3 of the manual describes
the difference between standard packages and user packages. It also
has general details on how to include/exclude specific packages as
part of the LAMMPS build process, and on how to build auxiliary
@ -64,28 +64,28 @@ The current list of standard packages is as follows. Each package
name links to a sub-section below with more details.
Package, Description, Author(s), Doc page, Example, Library
"ASPHERE"_#ASPHERE, aspherical particles, -, "Section_howto 6.14"_Section_howto.html#howto_14, ellipse, -
"ASPHERE"_#ASPHERE, aspherical particles, -, "Section 6.6.14"_Section_howto.html#howto_14, ellipse, -
"BODY"_#BODY, body-style particles, -, "body"_body.html, body, -
"CLASS2"_#CLASS2, class 2 force fields, -, "pair_style lj/class2"_pair_class2.html, -, -
"COLLOID"_#COLLOID, colloidal particles, Kumar (1), "atom_style colloid"_atom_style.html, colloid, -
"COMPRESS"_#COMPRESS, I/O compression, Axel Kohlmeyer (Temple U), "dump */gz"_dump.html, -, -
"CORESHELL"_#CORESHELL, adiabatic core/shell model, Hendrik Heenen (Technical U of Munich), "Section_howto 6.25"_Section_howto.html#howto_25, coreshell, -
"CORESHELL"_#CORESHELL, adiabatic core/shell model, Hendrik Heenen (Technical U of Munich), "Section 6.6.25"_Section_howto.html#howto_25, coreshell, -
"DIPOLE"_#DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dipole, -
"GPU"_#GPU, GPU-enabled styles, Mike Brown (ORNL), "Section accelerate"_accelerate_gpu.html, gpu, lib/gpu
"GRANULAR"_#GRANULAR, granular systems, -, "Section_howto 6.6"_Section_howto.html#howto_6, pour, -
"GRANULAR"_#GRANULAR, granular systems, -, "Section 6.6.6"_Section_howto.html#howto_6, pour, -
"KIM"_#KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, KIM
"KOKKOS"_#KOKKOS, Kokkos-enabled styles, Trott & Moore (4), "Section_accelerate"_accelerate_kokkos.html, kokkos, lib/kokkos
"KOKKOS"_#KOKKOS, Kokkos-enabled styles, Trott & Moore (4), "Section 5"_accelerate_kokkos.html, kokkos, lib/kokkos
"KSPACE"_#KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -
"MANYBODY"_#MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -
"MEAM"_#MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam
"MC"_#MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, -
"MOLECULE"_#MOLECULE, molecular system force fields, -, "Section_howto 6.3"_Section_howto.html#howto_3, peptide, -
"MOLECULE"_#MOLECULE, molecular system force fields, -, "Section 6.6.3"_Section_howto.html#howto_3, peptide, -
"OPT"_#OPT, optimized pair styles, Fischer & Richie & Natoli (2), "Section accelerate"_accelerate_opt.html, -, -
"PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
"POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
"PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python
"REAX"_#REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax, lib/reax
"REPLICA"_#REPLICA, multi-replica methods, -, "Section_howto 6.5"_Section_howto.html#howto_5, tad, -
"REPLICA"_#REPLICA, multi-replica methods, -, "Section 6.6.5"_Section_howto.html#howto_5, tad, -
"RIGID"_#RIGID, rigid bodies, -, "fix rigid"_fix_rigid.html, rigid, -
"SHOCK"_#SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
"SNAP"_#SNAP, quantum-fit potential, Aidan Thompson (Sandia), "pair snap"_pair_snap.html, snap, -
@ -112,7 +112,7 @@ Stan Moore (Sandia). It uses the Kokkos library which was developed
by Carter Edwards, Christian Trott, and others at Sandia.
The "Doc page" column links to either a sub-section of the
"Section_howto"_Section_howto.html of the manual, or an input script
"Section 6"_Section_howto.html of the manual, or an input script
command implemented as part of the package, or to additional
documentation provided within the package.
@ -1198,7 +1198,7 @@ Mattox (Engility), and John Brennan (ARL).
Daniel Queteschiner (DCS Computing).
The "Doc page" column links to either a sub-section of the
"Section_howto"_Section_howto.html of the manual, or an input script
"Section 6"_Section_howto.html of the manual, or an input script
command implemented as part of the package, or to additional
documentation provided within the package.
@ -1440,7 +1440,7 @@ Phi-enabled styles.
Supporting info: examples/accelerate, src/USER-INTEL/TEST
"Section_accelerate"_Section_accelerate.html#acc_3
"Section 5"_Section_accelerate.html#acc_3
Author: Mike Brown at Intel (michael.w.brown at intel.com). Contact
him directly if you have questions.
@ -1532,7 +1532,7 @@ More information about each feature can be found by reading its doc
page in the LAMMPS doc directory. The doc page which lists all LAMMPS
input script commands is as follows:
"Section_commands"_Section_commands.html#cmd_5
"Section 3"_Section_commands.html#cmd_5
User-contributed features are listed at the bottom of the fix,
compute, pair, etc sections.
@ -1609,7 +1609,7 @@ styles, and fix styles.
See this section of the manual to get started:
"Section_accelerate"_Section_accelerate.html#acc_3
"Section 5"_Section_accelerate.html#acc_3
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.

12
doc/src/Section_python.txt
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@ -42,7 +42,7 @@ pieces of software together, such as a simulation package plus a
visualization package, or to run a coupled multiscale or multiphysics
model.
See "Section_howto 10"_Section_howto.html#howto_10 of the manual and
See "Section 6.10"_Section_howto.html#howto_10 of the manual and
the couple directory of the distribution for more ideas about coupling
LAMMPS to other codes. See "Section_howto
19"_Section_howto.html#howto_19 for a description of the LAMMPS
@ -179,7 +179,7 @@ file and the shared library.
11.3 Building LAMMPS as a shared library :link(py_3),h4
Instructions on how to build LAMMPS as a shared library are given in
"Section_start 5"_Section_start.html#start_5. A shared library is one
"Section 2.5"_Section_start.html#start_5. 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".
@ -198,7 +198,7 @@ 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_start 5"_Section_start.html#start_5 for more details.
"Section 2.5"_Section_start.html#start_5 for more details.
:line
@ -419,8 +419,8 @@ 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_start
5"_Section_start.html#start_5 and above about building a shared
If an error occurs, carefully go thru the steps in "Section
2.5"_Section_start.html#start_5 and above about building a shared
library and about insuring Python can find the necessary two files
it needs.
@ -656,7 +656,7 @@ subscripting. The one exception is that for a fix that calculates a
global vector or array, a single double value from the vector or array
is returned, indexed by I (vector) or I and J (array). I,J are
zero-based indices. The I,J arguments can be left out if not needed.
See "Section_howto 15"_Section_howto.html#howto_15 of the manual for a
See "Section 6.15"_Section_howto.html#howto_15 of the manual for a
discussion of global, per-atom, and local data, and of scalar, vector,
and array data types. See the doc pages for individual
"computes"_compute.html and "fixes"_fix.html for a description of what

18
doc/src/Section_start.txt
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@ -690,7 +690,7 @@ commands known to your executable, and immediately exit.
There are two kinds of packages in LAMMPS, standard and user packages.
More information about the contents of standard and user packages is
given in "Section_packages"_Section_packages.html of the manual. The
given in "Section 4"_Section_packages.html of the manual. The
difference between standard and user packages is as follows:
Standard packages, such as molecule or kspace, are supported by the
@ -795,7 +795,7 @@ libraries. Many of them are provided with LAMMPS, in which case they
must be compiled first, before LAMMPS is built, if you wish to include
that package. If you get a LAMMPS build error about a missing
library, this is likely the reason. See the
"Section_packages"_Section_packages.html doc page for a list of
"Section 4"_Section_packages.html doc page for a list of
packages that have these kinds of auxiliary libraries.
The lib directory in the distribution has sub-directories with package
@ -1055,7 +1055,7 @@ dynamically loaded, e.g. from Python, type
make foo mode=shlib :pre
where foo is the machine name. This kind of library is required when
wrapping LAMMPS with Python; see "Section_python"_Section_python.html
wrapping LAMMPS with Python; see "Section 11"_Section_python.html
for details. This will use the SHFLAGS and SHLIBFLAGS settings in
src/MAKE/Makefile.foo and perform the build in the directory
Obj_shared_foo. This is so that each file can be compiled with the
@ -1135,8 +1135,8 @@ src/library.cpp and src/library.h.
See the sample codes in examples/COUPLE/simple for examples of C++ and
C and Fortran codes that invoke LAMMPS thru its library interface.
There are other examples as well in the COUPLE directory which are
discussed in "Section_howto 10"_Section_howto.html#howto_10 of the
manual. See "Section_python"_Section_python.html of the manual for a
discussed in "Section 6.10"_Section_howto.html#howto_10 of the
manual. See "Section 11"_Section_python.html of the manual for a
description of the Python wrapper provided with LAMMPS that operates
through the LAMMPS library interface.
@ -1257,7 +1257,7 @@ than your working directory, which is probably not what you want.
If LAMMPS encounters errors in the input script or while running a
simulation it will print an ERROR message and stop or a WARNING
message and continue. See "Section_errors"_Section_errors.html for a
message and continue. See "Section 12"_Section_errors.html for a
discussion of the various kinds of errors LAMMPS can or can't detect,
a list of all ERROR and WARNING messages, and what to do about them.
@ -1473,7 +1473,7 @@ installed on a machine (e.g. your desktop), you can run on more
(virtual) processors than you have physical processors.
To run multiple independent simulatoins from one input script, using
multiple partitions, see "Section_howto 4"_Section_howto.html#howto_4
multiple partitions, see "Section 6.4"_Section_howto.html#howto_4
of the manual. World- and universe-style "variables"_variable.html
are useful in this context.
@ -1539,7 +1539,7 @@ cores within each node are ranked in a desired order. Or when using
the "run_style verlet/split"_run_style.html command with 2 partitions
to insure that a specific Kspace processor (in the 2nd partition) is
matched up with a specific set of processors in the 1st partition.
See the "Section_accelerate"_Section_accelerate.html doc pages for
See the "Section 5"_Section_accelerate.html doc pages for
more details.
If the keyword {nth} is used with a setting {N}, then it means every
@ -1863,7 +1863,7 @@ communication, roughly 75% in the example above.
The current C++ began with a complete rewrite of LAMMPS 2001, which
was written in F90. Features of earlier versions of LAMMPS are listed
in "Section_history"_Section_history.html. The F90 and F77 versions
in "Section 13"_Section_history.html. The F90 and F77 versions
(2001 and 99) are also freely distributed as open-source codes; check
the "LAMMPS WWW Site"_lws for distribution information if you prefer
those versions. The 99 and 2001 versions are no longer under active

4
doc/src/accelerate_gpu.txt
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@ -9,7 +9,7 @@
"Return to Section accelerate overview"_Section_accelerate.html
5.3.1 GPU package :h4
5.3.1 GPU package :h5
The GPU package was developed by Mike Brown at ORNL and his
collaborators, particularly Trung Nguyen (ORNL). It provides GPU
@ -26,7 +26,7 @@ between the CPU(s) and GPU every timestep. :l
Neighbor lists can be built on the CPU or on the GPU :l
The charge assignement and force interpolation portions of PPPM can be
The charge assignment and force interpolation portions of PPPM can be
run on the GPU. The FFT portion, which requires MPI communication
between processors, runs on the CPU. :l

2
doc/src/accelerate_intel.txt
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@ -9,7 +9,7 @@
"Return to Section accelerate overview"_Section_accelerate.html
5.3.2 USER-INTEL package :h4
5.3.2 USER-INTEL package :h5
The USER-INTEL package is maintained by Mike Brown at Intel
Corporation. It provides two methods for accelerating simulations,

2
doc/src/accelerate_kokkos.txt
View File

@ -9,7 +9,7 @@
"Return to Section accelerate overview"_Section_accelerate.html
5.3.3 KOKKOS package :h4
5.3.3 KOKKOS package :h5
The KOKKOS package was developed primarily by Christian Trott (Sandia)
with contributions of various styles by others, including Sikandar

2
doc/src/accelerate_omp.txt
View File

@ -9,7 +9,7 @@
"Return to Section accelerate overview"_Section_accelerate.html
5.3.4 USER-OMP package :h4
5.3.4 USER-OMP package :h5
The USER-OMP package was developed by Axel Kohlmeyer at Temple
University. It provides multi-threaded versions of most pair styles,

2
doc/src/accelerate_opt.txt
View File

@ -9,7 +9,7 @@
"Return to Section accelerate overview"_Section_accelerate.html
5.3.5 OPT package :h4
5.3.5 OPT package :h5
The OPT package was developed by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge

4
doc/src/angle_charmm.txt
View File

@ -51,7 +51,7 @@ internally; hence the units of K are in energy/radian^2.
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -66,7 +66,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/angle_class2.txt
View File

@ -81,7 +81,7 @@ same value from the Ea formula.
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -96,7 +96,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/angle_cosine.txt
View File

@ -38,7 +38,7 @@ K (energy) :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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -53,7 +53,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/angle_cosine_delta.txt
View File

@ -43,7 +43,7 @@ internally.
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -58,7 +58,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/angle_cosine_periodic.txt
View File

@ -51,7 +51,7 @@ geometry.
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -66,7 +66,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/angle_cosine_shift.txt
View File

@ -41,7 +41,7 @@ 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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -56,7 +56,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/angle_cosine_shift_exp.txt
View File

@ -53,7 +53,7 @@ A (real number) :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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -68,7 +68,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/angle_cosine_squared.txt
View File

@ -43,7 +43,7 @@ internally.
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -58,7 +58,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/angle_dipole.txt
View File

@ -71,7 +71,7 @@ gamma0 (degrees) :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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -86,7 +86,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
[Restrictions:]

4
doc/src/angle_fourier.txt
View File

@ -39,7 +39,7 @@ C2 (real) :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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -54,7 +54,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/angle_fourier_simple.txt
View File

@ -38,7 +38,7 @@ n (real) :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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -53,7 +53,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/angle_harmonic.txt
View File

@ -45,7 +45,7 @@ internally; hence the units of K are in energy/radian^2.
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -60,7 +60,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/angle_quartic.txt
View File

@ -45,7 +45,7 @@ internally; hence the units of K are in energy/radian^2.
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -60,7 +60,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/angle_table.txt
View File

@ -124,7 +124,7 @@ one that matches the specified keyword.
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -139,7 +139,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/atom_style.txt
View File

@ -233,7 +233,7 @@ styles; see "this section"_Section_modify.html.
Styles with a {kk} 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 in
"Section_accelerate"_Section_accelerate.html of the manual. The
"Section 5"_Section_accelerate.html of the manual. The
accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.
@ -250,7 +250,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
[Restrictions:]

10
doc/src/body.txt
View File

@ -17,9 +17,9 @@ surface meshes of discrete points, collections of sub-particles,
deformable objects, etc. Note that other kinds of finite-size
spherical and aspherical particles are also supported by LAMMPS, such
as spheres, ellipsoids, line segments, and triangles, but they are
simpler entities that body particles. See "Section_howto
14"_Section_howto.html#howto_14 for a general overview of all these
particle types.
simpler entities that body particles. See "Section
6.14"_Section_howto.html#howto_14 for a general overview of all
these particle types.
Body particles are used via the "atom_style body"_atom_style.html
command. It takes a body style as an argument. The current body
@ -38,8 +38,8 @@ style are described below.
NOTE: The rounded/polygon style listed in the table above and
described below has not yet been relesed in LAMMPS. It will be soon.
We hope to add more styles in the future. See "Section_modify
12"_Section_modify.html#mod_12 for details on how to add a new body
We hope to add more styles in the future. See "Section
10.12"_Section_modify.html#mod_12 for details on how to add a new body
style to the code.
:line

4
doc/src/bond_class2.txt
View File

@ -43,7 +43,7 @@ K4 (energy/distance^4) :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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -58,7 +58,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/bond_fene.txt
View File

@ -47,7 +47,7 @@ sigma (distance) :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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -62,7 +62,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/bond_fene_expand.txt
View File

@ -50,7 +50,7 @@ delta (distance) :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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -65,7 +65,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/bond_harmonic.txt
View File

@ -42,7 +42,7 @@ r0 (distance) :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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -57,7 +57,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/bond_harmonic_shift.txt
View File

@ -43,7 +43,7 @@ rc (distance) :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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -58,7 +58,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/bond_harmonic_shift_cut.txt
View File

@ -43,7 +43,7 @@ rc (distance) :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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -58,7 +58,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/bond_morse.txt
View File

@ -41,7 +41,7 @@ r0 (distance) :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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -56,7 +56,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/bond_nonlinear.txt
View File

@ -41,7 +41,7 @@ lamda (distance) :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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -56,7 +56,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/bond_quartic.txt
View File

@ -76,7 +76,7 @@ delete_bonds all bond 0 remove :pre
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -91,7 +91,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/bond_table.txt
View File

@ -121,7 +121,7 @@ one that matches the specified keyword.
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -136,7 +136,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

2
doc/src/boundary.txt
View File

@ -74,7 +74,7 @@ and xhi faces of the box are planes tilting in the +y direction as y
increases. These tilted planes are shrink-wrapped around the atoms to
determine the x extent of the box.
See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages
See "Section 6.12"_Section_howto.html#howto_12 of the doc pages
for a geometric description of triclinic boxes, as defined by LAMMPS,
and how to transform these parameters to and from other commonly used
triclinic representations.

2
doc/src/change_box.txt
View File

@ -75,7 +75,7 @@ The "create_box"_create_box.html, "read data"_read_data.html, and
simulation box is orthogonal or triclinic and their doc pages explain
the meaning of the xy,xz,yz tilt factors.
See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages
See "Section 6.12"_Section_howto.html#howto_12 of the doc pages
for a geometric description of triclinic boxes, as defined by LAMMPS,
and how to transform these parameters to and from other commonly used
triclinic representations.

2
doc/src/compute_ackland_atom.txt
View File

@ -50,7 +50,7 @@ which computes this quantity.-
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
"Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
[Restrictions:]

2
doc/src/compute_body_local.txt
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@ -32,7 +32,7 @@ Define a computation that calculates properties of individual body
sub-particles. The number of datums generated, aggregated across all
processors, equals the number of body sub-particles plus the number of
non-body particles in the system, modified by the group parameter as
explained below. See "Section_howto 14"_Section_howto.html#howto_14
explained below. See "Section 6.14"_Section_howto.html#howto_14
of the manual and the "body"_body.html doc page for more details on
using body particles.

4
doc/src/compute_chunk_atom.txt
View File

@ -104,7 +104,7 @@ can simply be accessed by any command that uses per-atom values from a
compute as input, as discussed in "Section_howto
15"_Section_howto.html#howto_15.
See "Section_howto 23"_Section_howto.html#howto_23 for an overview of
See "Section 6.23"_Section_howto.html#howto_23 for an overview of
how this compute can be used with a variety of other commands to
tabulate properties of a simulation. The howto section gives several
examples of input script commands that can be used to calculate
@ -624,7 +624,7 @@ cylinder, x for a y-axis cylinder, and x for a z-axis cylinder.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
"Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values are unitless chunk IDs, ranging from 1 to

2
doc/src/compute_cluster_atom.txt
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@ -59,7 +59,7 @@ the neighbor list.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
"Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values will be an ID > 0, as explained above.

2
doc/src/compute_cna_atom.txt
View File

@ -74,7 +74,7 @@ too frequently or to have multiple compute/dump commands, each with a
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
"Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values will be a number from 0 to 5, as explained

2
doc/src/compute_contact_atom.txt
View File

@ -36,7 +36,7 @@ specified compute group.
This compute calculates a per-atom vector, whose values can be
accessed by any command that uses per-atom values from a compute as
input. See "Section_howto 15"_Section_howto.html#howto_15 for an
input. See "Section 6.15"_Section_howto.html#howto_15 for an
overview of LAMMPS output options.
The per-atom vector values will be a number >= 0.0, as explained

2
doc/src/compute_damage_atom.txt
View File

@ -44,7 +44,7 @@ group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
"Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values are unitlesss numbers (damage) >= 0.0.

2
doc/src/compute_erotate_asphere.txt
View File

@ -40,7 +40,7 @@ will be the same as in 3d.
This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See "Section_howto 15"_Section_howto.html#howto_15 for an
input. See "Section 6.15"_Section_howto.html#howto_15 for an
overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The

2
doc/src/compute_erotate_rigid.txt
View File

@ -42,7 +42,7 @@ calculation.
This compute calculates a global scalar (the summed rotational energy
of all the rigid bodies). This value can be used by any command that
uses a global scalar value from a compute as input. See
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
"Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The scalar value calculated by this compute is "extensive". The

2
doc/src/compute_erotate_sphere.txt
View File

@ -35,7 +35,7 @@ as in 3d.
This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See "Section_howto 15"_Section_howto.html#howto_15 for an
input. See "Section 6.15"_Section_howto.html#howto_15 for an
overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The

2
doc/src/compute_erotate_sphere_atom.txt
View File

@ -39,7 +39,7 @@ in the specified compute group or for point particles with a radius =
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
"Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values will be in energy "units"_units.html.

2
doc/src/compute_event_displace.txt
View File

@ -43,7 +43,7 @@ local atom displacements and may generate "false postives."
This compute calculates a global scalar (the flag). This value can be
used by any command that uses a global scalar value from a compute as
input. See "Section_howto 15"_Section_howto.html#howto_15 for an
input. See "Section 6.15"_Section_howto.html#howto_15 for an
overview of LAMMPS output options.
The scalar value calculated by this compute is "intensive". The

2
doc/src/compute_ke.txt
View File

@ -44,7 +44,7 @@ include different degrees of freedom (translational, rotational, etc).
This compute calculates a global scalar (the summed KE). This value
can be used by any command that uses a global scalar value from a
compute as input. See "Section_howto 15"_Section_howto.html#howto_15
compute as input. See "Section 6.15"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The

2
doc/src/compute_ke_atom.txt
View File

@ -34,7 +34,7 @@ specified compute group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
"Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values will be in energy "units"_units.html.

2
doc/src/compute_ke_atom_eff.txt
View File

@ -58,7 +58,7 @@ electrons) not in the specified compute group.
This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom computes as input. See
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
"Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values will be in energy "units"_units.html.

2
doc/src/compute_ke_eff.txt
View File

@ -61,7 +61,7 @@ See "compute temp/eff"_compute_temp_eff.html.
This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See "Section_howto 15"_Section_howto.html#howto_15 for an
input. See "Section 6.15"_Section_howto.html#howto_15 for an
overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The

2
doc/src/compute_meso_e_atom.txt
View File

@ -38,7 +38,7 @@ specified compute group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
"Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values will be in energy "units"_units.html.

2
doc/src/compute_meso_rho_atom.txt
View File

@ -38,7 +38,7 @@ specified compute group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
"Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values will be in mass/volume "units"_units.html.

2
doc/src/compute_meso_t_atom.txt
View File

@ -40,7 +40,7 @@ specified compute group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
"Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values will be in temperature "units"_units.html.

2
doc/src/compute_pe_atom.txt
View File

@ -80,7 +80,7 @@ those are global contributions to the system energy.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
"Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values will be in energy "units"_units.html.

4
doc/src/compute_pressure.txt
View File

@ -98,7 +98,7 @@ where "thermo_temp" is the ID of a similarly defined compute of style
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -113,7 +113,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

2
doc/src/compute_rdf.txt
View File

@ -121,7 +121,7 @@ coordinate (center of the bin), Each successive set of 2 columns has
the g(r) and coord(r) values for a specific set of {itypeN} versus
{jtypeN} interactions, as described above. These values can be used
by any command that uses a global values from a compute as input. See
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
"Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The array values calculated by this compute are all "intensive".

2
doc/src/compute_reduce.txt
View File

@ -192,7 +192,7 @@ This compute calculates a global scalar if a single input value is
specified or a global vector of length N where N is the number of
inputs, and which can be accessed by indices 1 to N. These values can
be used by any command that uses global scalar or vector values from a
compute as input. See "Section_howto 15"_Section_howto.html#howto_15
compute as input. See "Section 6.15"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
All the scalar or vector values calculated by this compute are

2
doc/src/compute_smd_contact_radius.txt
View File

@ -37,7 +37,7 @@ specified compute group.
This compute calculates a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input. See
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
"Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-particle vector values will be in distance "units"_units.html.

2
doc/src/compute_smd_ulsph_num_neighs.txt
View File

@ -32,7 +32,7 @@ Mach Dynamics in LAMMPS.
This compute returns a per-particle vector, which can be accessed by
any command that uses per-particle values from a compute as input.
See "Section_howto 15"_Section_howto.html#howto_15 for an overview of
See "Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-particle values will be given dimentionless, see "units"_units.html.

2
doc/src/compute_smd_ulsph_strain.txt
View File

@ -31,7 +31,7 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle tensor, which can be accessed
by any command that uses per-particle values from a compute as input.
See "Section_howto 15"_Section_howto.html#howto_15 for an overview of
See "Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-particle vector has 6 entries, corresponding to the xx, yy,

4
doc/src/compute_temp.txt
View File

@ -67,7 +67,7 @@ thermostatting.
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -82,7 +82,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

2
doc/src/compute_temp_cs.txt
View File

@ -28,7 +28,7 @@ Define a computation that calculates the temperature of a system based
on the center-of-mass velocity of atom pairs that are bonded to each
other. This compute is designed to be used with the adiabatic
core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham. See
"Section_howto 25"_Section_howto.html#howto_25 of the manual for an
"Section 6.25"_Section_howto.html#howto_25 of the manual for an
overview of the model as implemented in LAMMPS. Specifically, this
compute enables correct temperature calculation and thermostatting of
core/shell pairs where it is desirable for the internal degrees of

4
doc/src/compute_temp_partial.txt
View File

@ -74,7 +74,7 @@ thermostatting.
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -89,7 +89,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

2
doc/src/compute_torque_chunk.txt
View File

@ -72,7 +72,7 @@ number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
3 for the 3 xyz components of the torque for each chunk. These values
can be accessed by any command that uses global array values from a
compute as input. See "Section_howto 15"_Section_howto.html#howto_15
compute as input. See "Section 6.15"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
The array values are "intensive". The array values will be in

2
doc/src/create_box.txt
View File

@ -73,7 +73,7 @@ factors that exceed these limits, you can use the "box tilt"_box.html
command, with a setting of {large}; a setting of {small} is the
default.
See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages
See "Section 6.12"_Section_howto.html#howto_12 of the doc pages
for a geometric description of triclinic boxes, as defined by LAMMPS,
and how to transform these parameters to and from other commonly used
triclinic representations.

4
doc/src/dihedral_charmm.txt
View File

@ -86,7 +86,7 @@ non-bonded interactions.
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -101,7 +101,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/dihedral_class2.txt
View File

@ -140,7 +140,7 @@ r3 (distance) :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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -155,7 +155,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/dihedral_cosine_shift_exp.txt
View File

@ -52,7 +52,7 @@ A (real number) :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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -67,7 +67,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/dihedral_harmonic.txt
View File

@ -53,7 +53,7 @@ Some force fields let {n} be positive or negative which corresponds to
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -68,7 +68,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/dihedral_helix.txt
View File

@ -46,7 +46,7 @@ C (energy) :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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -61,7 +61,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/dihedral_multi_harmonic.txt
View File

@ -40,7 +40,7 @@ A5 (energy) :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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -55,7 +55,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/dihedral_nharmonic.txt
View File

@ -40,7 +40,7 @@ An (energy) :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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -55,7 +55,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/dihedral_opls.txt
View File

@ -48,7 +48,7 @@ K4 (energy) :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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -63,7 +63,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/dihedral_quadratic.txt
View File

@ -41,7 +41,7 @@ phi0 (degrees) :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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -56,7 +56,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/dihedral_table.txt
View File

@ -174,7 +174,7 @@ that matches the specified keyword.
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -189,7 +189,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
[Restrictions:]

2
doc/src/dimension.txt
View File

@ -26,7 +26,7 @@ prior to setting up a simulation box via the
"create_box"_create_box.html or "read_data"_read_data.html commands.
Restart files also store this setting.
See the discussion in "Section_howto"_Section_howto.html for
See the discussion in "Section 6"_Section_howto.html for
additional instructions on how to run 2d simulations.
NOTE: Some models in LAMMPS treat particles as finite-size spheres or

2
doc/src/dump.txt
View File

@ -626,7 +626,7 @@ The {d_name} and {i_name} attributes allow to output custom per atom
floating point or integer properties that are managed by
"fix property/atom"_fix_property_atom.html.
See "Section_modify"_Section_modify.html of the manual for information
See "Section 10"_Section_modify.html of the manual for information
on how to add new compute and fix styles to LAMMPS to calculate
per-atom quantities which could then be output into dump files.

2
doc/src/dump_custom_vtk.txt
View File

@ -306,7 +306,7 @@ invoke other computes, fixes, or variables when they are evaluated, so
this is a very general means of creating quantities to output to a
dump file.
See "Section_modify"_Section_modify.html of the manual for information
See "Section 10"_Section_modify.html of the manual for information
on how to add new compute and fix styles to LAMMPS to calculate
per-atom quantities which could then be output into dump files.

2
doc/src/dump_image.txt
View File

@ -606,7 +606,7 @@ supported. :l
:line
See "Section_modify"_Section_modify.html of the manual for information
See "Section 10"_Section_modify.html of the manual for information
on how to add new compute and fix styles to LAMMPS to calculate
per-atom quantities which could then be output into dump files.

4
doc/src/fix_addforce.txt
View File

@ -106,7 +106,7 @@ converge properly.
Styles with a 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 in
"Section_accelerate"_Section_accelerate.html of the manual. The
"Section 5"_Section_accelerate.html of the manual. The
accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.
@ -120,7 +120,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/fix_aveforce.txt
View File

@ -66,7 +66,7 @@ to it.
Styles with a 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 in
"Section_accelerate"_Section_accelerate.html of the manual. The
"Section 5"_Section_accelerate.html of the manual. The
accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.
@ -80,7 +80,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/fix_deform.txt
View File

@ -545,7 +545,7 @@ command if you want to include lattice spacings in a variable formula.
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -560,7 +560,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]

4
doc/src/fix_enforce2d.txt
View File

@ -30,7 +30,7 @@ not move from their initial z coordinate.
Styles with a 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 in
"Section_accelerate"_Section_accelerate.html of the manual. The
"Section 5"_Section_accelerate.html of the manual. The
accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.
@ -44,7 +44,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/fix_freeze.txt
View File

@ -34,7 +34,7 @@ using "fix setforce"_fix_setforce.html.
Styles with a 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 in
"Section_accelerate"_Section_accelerate.html of the manual. The
"Section 5"_Section_accelerate.html of the manual. The
accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.
@ -48,7 +48,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/fix_gravity.txt
View File

@ -90,7 +90,7 @@ field.
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -105,7 +105,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/fix_langevin.txt
View File

@ -264,7 +264,7 @@ generates an average temperature of 220 K, instead of 300 K.
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -279,7 +279,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

2
doc/src/fix_neb.txt
View File

@ -26,7 +26,7 @@ Add inter-replica forces to atoms in the group for a multi-replica
simulation run via the "neb"_neb.html command to perform a nudged
elastic band (NEB) calculation for transition state finding. Hi-level
explanations of NEB are given with the "neb"_neb.html command and in
"Section_howto 5"_Section_howto.html#howto_5 of the manual. The fix
"Section 6.5"_Section_howto.html#howto_5 of the manual. The fix
neb command must be used with the "neb" command to define how
inter-replica forces are computed.

4
doc/src/fix_nh.txt
View File

@ -490,7 +490,7 @@ the various ways to do this.
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -505,7 +505,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line

4
doc/src/fix_nph_asphere.txt
View File

@ -81,7 +81,7 @@ It also means that changing attributes of {thermo_temp} or
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -96,7 +96,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]

4
doc/src/fix_nph_body.txt
View File

@ -80,7 +80,7 @@ It also means that changing attributes of {thermo_temp} or
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -95,7 +95,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]

4
doc/src/fix_nph_sphere.txt
View File

@ -81,7 +81,7 @@ It also means that changing attributes of {thermo_temp} or
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 in "Section_accelerate"_Section_accelerate.html
hardware, as discussed in "Section 5"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
@ -96,7 +96,7 @@ 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.
See "Section_accelerate"_Section_accelerate.html of the manual for
See "Section 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]

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