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24
doc/src/Manual.txt
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@ -69,7 +69,7 @@ Labs and Temple University:
Aidan Thompson, athomps at sandia.gov :l
Stan Moore, stamoore at sandia.gov :l
"Axel Kohlmeyer"_ako, akohlmey at gmail.com :l
:ulb
:ule
Past core developers include Paul Crozier, Ray Shan and Mark Stevens,
all at Sandia. The [LAMMPS home page] at
@ -77,6 +77,11 @@ all at Sandia. The [LAMMPS home page] at
about the code and its uses. Interaction with external LAMMPS developers,
bug reports and feature requests are mainly coordinated through the
"LAMMPS project on GitHub."_https://github.com/lammps/lammps
The lammps.org domain, currently hosting "public continuous integration
testing"_https://ci.lammps.org/job/lammps/ and "precompiled Linux
RPM and Windows installer packages"_http://rpm.lammps.org is located
at Temple University and managed by Richard Berger,
richard.berger at temple.edu.
:link(bug,http://lammps.sandia.gov/bug.html)
:link(sjp,http://www.sandia.gov/~sjplimp)
@ -101,6 +106,9 @@ it gives quick access to documentation for all LAMMPS commands.
.. toctree::
:maxdepth: 2
:numbered:
:caption: User Documentation
:name: userdoc
:includehidden:
Section_intro
Section_start
@ -116,6 +124,20 @@ it gives quick access to documentation for all LAMMPS commands.
Section_errors
Section_history
.. toctree::
:caption: Index
:name: index
:hidden:
tutorials
commands
fixes
computes
pairs
bonds
angles
dihedrals
impropers
Indices and tables
==================

26
doc/src/Section_accelerate.txt
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@ -157,11 +157,25 @@ 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 : for NVIDIA GPUs as well as OpenCL support
"USER-INTEL Package"_accelerate_intel.html : for Intel CPUs and Intel Xeon Phi
"KOKKOS Package"_accelerate_kokkos.html : for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading
"USER-OMP Package"_accelerate_omp.html : for OpenMP threading and generic CPU optimizations
"OPT Package"_accelerate_opt.html : generic CPU optimizations :tb(s=:)
<!-- RST
.. toctree::
:maxdepth: 1
:hidden:
accelerate_gpu
accelerate_intel
accelerate_kokkos
accelerate_omp
accelerate_opt
END_RST -->
Inverting this list, LAMMPS currently has acceleration support for
three kinds of hardware, via the listed packages:
@ -192,7 +206,7 @@ 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.

3
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:
@ -660,7 +660,6 @@ package"_Section_start.html#start_3.
"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html,
"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html,
"smd/setvel"_fix_smd_setvel.html,
"smd/tlsph/reference/configuration"_fix_smd_tlsph_reference_configuration.html,
"smd/wall/surface"_fix_smd_wall_surface.html,
"temp/rescale/eff"_fix_temp_rescale_eff.html,
"ti/rs"_fix_ti_rs.html,

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.

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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
@ -347,12 +347,12 @@ following packages:
"VMD"_http://www.ks.uiuc.edu/Research/vmd
"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A
"PyMol"_http://pymol.sourceforge.net
"PyMol"_http://www.pymol.org
"Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html
"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.

20
doc/src/Section_python.txt
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@ -42,10 +42,10 @@ 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
LAMMPS to other codes. See "Section
6.19"_Section_howto.html#howto_19 for a description of the LAMMPS
library interface provided in src/library.cpp and src/library.h, and
how to extend it for your needs. As described below, that interface
is what is exposed to Python either when calling LAMMPS from Python or
@ -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
@ -790,13 +790,13 @@ capability needed by these Python scripts.
Note that for PyMol, you need to have built and installed the
open-source version of PyMol in your Python, so that you can import it
from a Python script. See the PyMol WWW pages "here"_pymol or
from a Python script. See the PyMol WWW pages "here"_pymolhome or
"here"_pymolopen for more details:
http://www.pymol.org
http://sourceforge.net/scm/?type=svn&group_id=4546 :pre
:link(pymol,http://www.pymol.org)
:link(pymolhome,http://www.pymol.org)
:link(pymolopen,http://sourceforge.net/scm/?type=svn&group_id=4546)
The latter link is to the open-source version.

194
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@ -30,8 +30,7 @@ When you download a LAMMPS tarball you will need to unzip and untar
the downloaded file with the following commands, after placing the
tarball in an appropriate directory.
gunzip lammps*.tar.gz
tar xvf lammps*.tar :pre
tar -xzvf lammps*.tar.gz :pre
This will create a LAMMPS directory containing two files and several
sub-directories:
@ -46,16 +45,17 @@ src: source files
tools: pre- and post-processing tools :tb(s=:)
Note that the "download page"_download also has links to download
Windows exectubles and installers, as well as pre-built executables
for a few specific Linux distributions. It also has instructions for
how to download/install LAMMPS for Macs (via Homebrew), and to
pre-build Windows installers, as well as pre-built packages for
several widely used Linux distributions. It also has instructions
for how to download/install LAMMPS for Macs (via Homebrew), and to
download and update LAMMPS from SVN and Git repositories, which gives
you the same files that are in the download tarball.
you access to the up-to-date sources that are used by the LAMMPS
core developers.
:link(download,http://lammps.sandia.gov/download.html)
The Windows and Linux executables for serial or parallel only include
certain packages and bug-fixes/upgrades listed on "this
The Windows and Linux packages for serial or parallel include
only selected packages and bug-fixes/upgrades listed on "this
page"_http://lammps.sandia.gov/bug.html up to a certain date, as
stated on the download page. If you want an executable with
non-included packages or that is more current, then you'll need to
@ -79,7 +79,7 @@ This section has the following sub-sections:
:line
[{Read this first:}] :link(start_2_1)
Read this first :h5,link(start_2_1)
If you want to avoid building LAMMPS yourself, read the preceeding
section about options available for downloading and installing
@ -148,9 +148,9 @@ include it in the LAMMPS distribution.
:line
[{Steps to build a LAMMPS executable:}] :link(start_2_2)
Steps to build a LAMMPS executable :h5,link(start_2_2)
[Step 0]
Step 0 :h6
The src directory contains the C++ source and header files for LAMMPS.
It also contains a top-level Makefile and a MAKE sub-directory with
@ -172,10 +172,12 @@ a list of available choices from src/MAKE and all of its
sub-directories. If one of those has the options you want or is the
machine you want, you can type a command like:
make mpi
make mpi :pre
or
make serial_icc
make serial :pre
or
gmake mac :pre
Note that the corresponding Makefile.machine can exist in src/MAKE or
@ -189,14 +191,14 @@ Note that on a multi-processor or multi-core platform you can launch a
parallel make, by using the "-j" switch with the make command, which
will build LAMMPS more quickly.
If you get no errors and an executable like lmp_mpi or lmp_g++_serial
or lmp_mac is produced, then you're done; it's your lucky day.
If you get no errors and an executable like [lmp_mpi] or [lmp_serial]
or [lmp_mac] is produced, then you're done; it's your lucky day.
Note that by default only a few of LAMMPS optional packages are
installed. To build LAMMPS with optional packages, see "this
section"_#start_3 below.
[Step 1]
Step 1 :h6
If Step 0 did not work, you will need to create a low-level Makefile
for your machine, like Makefile.foo. You should make a copy of an
@ -207,13 +209,13 @@ the first line, the "compiler/linker settings" section, and the
file in src/MAKE/MINE and it will not be altered by any future LAMMPS
updates.
[Step 2]
Step 2 :h6
Change the first line of Makefile.foo to list the word "foo" after the
"#", and whatever other options it will set. This is the line you
will see if you just type "make".
[Step 3]
Step 3 :h6
The "compiler/linker settings" section lists compiler and linker
settings for your C++ compiler, including optimization flags. You can
@ -242,7 +244,7 @@ first time on a new platform, a long list of *.d files will be printed
out rapidly. This is not an error; it is the Makefile doing its
normal creation of dependencies.
[Step 4]
Step 4 :h6
The "system-specific settings" section has several parts. Note that
if you change any -D setting in this section, you should do a full
@ -349,7 +351,7 @@ platforms. The -DPACK_ARRAY setting is the default. See the
"kspace_style"_kspace_style.html command for info about PPPM. See
Step 6 below for info about building LAMMPS with an FFT library.
[Step 5]
Step 5 :h6
The 3 MPI variables are used to specify an MPI library to build LAMMPS
with. Note that you do not need to set these if you use the MPI
@ -405,7 +407,7 @@ Note that the ANSI-standard function clock() rolls over after an hour
or so, and is therefore insufficient for timing long LAMMPS
simulations.
[Step 6]
Step 6 :h6
The 3 FFT variables allow you to specify an FFT library which LAMMPS
uses (for performing 1d FFTs) when running the particle-particle
@ -458,7 +460,7 @@ accuracy for reduced memory use and parallel communication costs for
transposing 3d FFT data. Note that single precision FFTs have only
been tested with the FFTW3, FFTW2, MKL, and KISS FFT options.
[Step 7]
Step 7 :h6
The 3 JPG variables allow you to specify a JPEG and/or PNG library
which LAMMPS uses when writing out JPEG or PNG files via the "dump
@ -481,13 +483,13 @@ find it.
As before, if these header and library files are in the usual place on
your machine, you may not need to set these variables.
[Step 8]
Step 8 :h6
Note that by default only a few of LAMMPS optional packages are
installed. To build LAMMPS with optional packages, see "this
section"_#start_3 below, before proceeding to Step 9.
[Step 9]
Step 9 :h6
That's it. Once you have a correct Makefile.foo, and you have
pre-built any other needed libraries (e.g. MPI, FFT, etc) all you need
@ -506,7 +508,7 @@ You should get the executable lmp_foo when the build is complete.
:line
[{Errors that can occur when making LAMMPS:}] :link(start_2_3)
Errors that can occur when making LAMMPS: h5 :link(start_2_3)
NOTE: If an error occurs when building LAMMPS, the compiler or linker
will state very explicitly what the problem is. The error message
@ -543,22 +545,22 @@ above in Step 4.
:line
[{Additional build tips:}] :link(start_2_4)
Additional build tips :h5,link(start_2_4)
(1) Building LAMMPS for multiple platforms.
Building LAMMPS for multiple platforms. :h6
You can make LAMMPS for multiple platforms from the same src
directory. Each target creates its own object sub-directory called
Obj_target where it stores the system-specific *.o files.
(2) Cleaning up.
Cleaning up. :h6
Typing "make clean-all" or "make clean-machine" will delete *.o object
files created when LAMMPS is built, for either all builds or for a
particular machine.
(3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
-DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
-DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
As explained above, any of these 3 settings can be specified on the
LMP_INC line in your low-level src/MAKE/Makefile.foo.
@ -608,39 +610,43 @@ neighbor lists and would run very slowly in terms of CPU secs/timestep.
:line
[{Building for a Mac:}] :link(start_2_5)
Building for a Mac :h5,link(start_2_5)
OS X is BSD Unix, so it should just work. See the
src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.
:line
[{Building for Windows:}] :link(start_2_6)
Building for Windows :h5,link(start_2_6)
The LAMMPS download page has an option to download both a serial and
parallel pre-built Windows executable. See the "Running
LAMMPS"_#start_6 section for instructions on running these executables
on a Windows box.
If you want to build a Windows version of LAMMPS, you can build it
yourself, but it may require some effort. LAMMPS expects a Unix-like
build environment for the default build procedure. This can be done
using either Cygwin or MinGW; the latter also exists as a ready-to-use
Linux-to-Windows cross-compiler in several Linux distributions. In
these cases, you can do the installation after installing several
unix-style commands like make, grep, sed and bash with some shell
utilities.
The pre-built executables hosted on the "LAMMPS download
page"_http://lammps.sandia.gov/download.html are built with a subset
of the available packages; see the download page for the list. These
are single executable files. No examples or documentation in
included. You will need to download the full source code package to
obtain those.
For Cygwin and the MinGW cross-compilers, suitable makefiles are
provided in src/MAKE/MACHINES. When using other compilers, like
Visual C++ or Intel compilers for Windows, you may have to implement
your own build system. Since none of the current LAMMPS core developers
has significant experience building executables on Windows, we are
happy to distribute contributed instructions and modifications, but
we cannot provide support for those.
With the so-called "Anniversary Update" to Windows 10, there is a
Ubuntu subsystem available for Windows, that can be installed and
then it can be used to compile/install LAMMPS as if you are running
on a Ubuntu Linux system.
As an alternative, you can download "daily builds" (and some older
versions) of the installer packages from
"rpm.lammps.org/windows.html"_http://rpm.lammps.org/windows.html.
These executables are built with most optional packages and the
download includes documentation, some tools and most examples.
If you want a Windows version with specific packages included and
excluded, you can build it yourself.
One way to do this is install and use cygwin to build LAMMPS with a
standard unix style make program, just as you would on a Linux box;
see src/MAKE/MACHINES/Makefile.cygwin.
download includes documentation, potential files, some tools and
many examples, but no source code.
:line
@ -660,7 +666,7 @@ Makefile.machine to add settings needed by some packages.
:line
[{Package basics:}] :link(start_3_1)
Package basics: :h5,link(start_3_1)
The source code for LAMMPS is structured as a set of core files which
are always included, plus optional packages. Packages are groups of
@ -690,7 +696,7 @@ 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
@ -714,7 +720,7 @@ files or either a standard or user-contributed package are given in
:line
[{Including/excluding packages:}] :link(start_3_2)
Including/excluding packages :h5,link(start_3_2)
To use (or not use) a package you must include it (or exclude it)
before building LAMMPS. From the src directory, this is typically as
@ -788,14 +794,14 @@ package-related make options.
:line
[{Packages that require extra libraries:}] :link(start_3_3)
Packages that require extra libraries :h5,link(start_3_3)
A few of the standard and user packages require additional auxiliary
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
@ -873,7 +879,7 @@ the LAMMPS build will typically fail.
:line
[{Packages that require Makefile.machine settings}] :link(start_3_4)
Packages that require Makefile.machine settings :h5,link(start_3_4)
A few packages require specific settings in Makefile.machine, to
either build or use the package effectively. These are the
@ -1033,7 +1039,7 @@ then be called from another application or a scripting language. See
LAMMPS to other codes. See "this section"_Section_python.html for
more info on wrapping and running LAMMPS from Python.
[Static library:] :h5
Static library :h5
To build LAMMPS as a static library (*.a file on Linux), type
@ -1047,7 +1053,7 @@ will create the file liblammps_foo.a which another application can
link to. It will also create a soft link liblammps.a, which will
point to the most recently built static library.
[Shared library:] :h5
Shared library :h5
To build LAMMPS as a shared library (*.so file on Linux), which can be
dynamically loaded, e.g. from Python, type
@ -1055,7 +1061,7 @@ 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
@ -1119,7 +1125,7 @@ For the csh or tcsh shells, you would add something like this to your
setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre
[Calling the LAMMPS library:] :h5
Calling the LAMMPS library :h5
Either flavor of library (static or shared) allows one or more LAMMPS
objects to be instantiated from the calling program.
@ -1135,14 +1141,14 @@ 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.
The files src/library.cpp and library.h define the C-style API for
using LAMMPS as a library. See "Section_howto
19"_Section_howto.html#howto_19 of the manual for a description of the
using LAMMPS as a library. 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.
:line
@ -1191,23 +1197,17 @@ LAMMPS to be built with one or more of its optional packages.
:line
On a Windows box, you can skip making LAMMPS and simply download an
executable, as described above, though the pre-packaged executables
include only certain packages.
installer package from "here"_http://rpm.lammps.org/windows.html
To run a LAMMPS executable on a Windows machine, first decide whether
you want to download the non-MPI (serial) or the MPI (parallel)
version of the executable. Download and save the version you have
chosen.
For the non-MPI version, follow these steps:
For running the non-MPI executable, follow these steps:
Get a command prompt by going to Start->Run... ,
then typing "cmd". :ulb,l
Move to the directory where you have saved lmp_win_no-mpi.exe
(e.g. by typing: cd "Documents"). :l
Move to the directory where you have your input, e.g. a copy of
the [in.lj] input from the bench folder. (e.g. by typing: cd "Documents"). :l
At the command prompt, type "lmp_win_no-mpi -in in.lj", replacing in.lj
At the command prompt, type "lmp_serial -in in.lj", replacing [in.lj]
with the name of your LAMMPS input script. :l
:ule
@ -1218,27 +1218,39 @@ Download and install
"MPICH2"_http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloads
for Windows. :ulb,l
You'll need to use the mpiexec.exe and smpd.exe files from the MPICH2
package. Put them in same directory (or path) as the LAMMPS Windows
executable. :l
The LAMMPS Windows installer packages will automatically adjust your
path for the default location of this MPI package. After the installation
of the MPICH software, it needs to be integrated into the system.
For this you need to start a Command Prompt in {Administrator Mode}
(right click on the icon and select it). Change into the MPICH2
installation directory, then into the subdirectory [bin] and execute
[smpd.exe -install]. Exit the command window.
Get a command prompt by going to Start->Run... ,
Get a new, regular command prompt by going to Start->Run... ,
then typing "cmd". :l
Move to the directory where you have saved lmp_win_mpi.exe
Move to the directory where you have your input file
(e.g. by typing: cd "Documents"). :l
Then type something like this: "mpiexec -localonly 4 lmp_win_mpi -in
in.lj", replacing in.lj with the name of your LAMMPS input script. :l
Then type something like this:
Note that you may need to provide smpd with a passphrase (it doesn't
matter what you type). :l
mpiexec -localonly 4 lmp_mpi -in in.lj :pre
or
mpiexec -np 4 lmp_mpi -in in.lj :pre
replacing in.lj with the name of your LAMMPS input script. For the latter
case, you may be prompted to enter your password. :l
In this mode, output may not immediately show up on the screen, so if
your input script takes a long time to execute, you may need to be
patient before the output shows up. :l Alternatively, you can still
use this executable to run on a single processor by typing something
like: "lmp_win_mpi -in in.lj". :l
patient before the output shows up. :l
The parallel executable can also run on a single processor by typing
something like:
lmp_mpi -in in.lj :pre
:ule
:line
@ -1257,7 +1269,7 @@ 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 +1485,7 @@ 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 +1551,7 @@ 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 +1875,7 @@ 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

9
doc/src/Section_tools.txt
View File

@ -330,7 +330,7 @@ Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.
matlab tool :h4,link(matlab)
The matlab sub-directory contains several "MATLAB"_matlab scripts for
The matlab sub-directory contains several "MATLAB"_matlabhome scripts for
post-processing LAMMPS output. The scripts include readers for log
and dump files, a reader for EAM potential files, and a converter that
reads LAMMPS dump files and produces CFG files that can be visualized
@ -342,7 +342,7 @@ See the README.pdf file for more information.
These scripts were written by Arun Subramaniyan at Purdue Univ
(asubrama at purdue.edu).
:link(matlab,http://www.mathworks.com)
:link(matlabhome,http://www.mathworks.com)
:line
@ -427,9 +427,10 @@ pymol_asphere tool :h4,link(pymol)
The pymol_asphere sub-directory contains a tool for converting a
LAMMPS dump file that contains orientation info for ellipsoidal
particles into an input file for the "PyMol visualization
package"_pymol.
package"_pymolhome or its "open source variant"_pymolopen.
:link(pymol,http://pymol.sourceforge.net)
:link(pymolhome,http://www.pymol.org)
:link(pymolopen,http://sourceforge.net/scm/?type=svn&group_id=4546)
Specifically, the tool triangulates the ellipsoids so they can be
viewed as true ellipsoidal particles within PyMol. See the README and

4
doc/src/accelerate_gpu.txt
View File

@ -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
View File

@ -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

27
doc/src/angles.txt Normal file
View File

@ -0,0 +1,27 @@
Angle Styles :h1
<!-- RST
.. toctree::
:maxdepth: 1
angle_charmm
angle_class2
angle_cosine
angle_cosine_delta
angle_cosine_periodic
angle_cosine_shift
angle_cosine_shift_exp
angle_cosine_squared
angle_dipole
angle_fourier
angle_fourier_simple
angle_harmonic
angle_hybrid
angle_none
angle_quartic
angle_sdk
angle_table
angle_zero
END_RST -->

8
doc/src/atom_style.txt
View File

@ -98,8 +98,8 @@ output the custom values.
All of the above styles define point particles, except the {sphere},
{ellipsoid}, {electron}, {peri}, {wavepacket}, {line}, {tri}, and
{body} styles, which define finite-size particles. See "Section_howto
14"_Section_howto.html#howto_14 for an overview of using finite-size
{body} styles, which define finite-size particles. See "Section
6.14"_Section_howto.html#howto_14 for an overview of using finite-size
particle models with LAMMPS.
All of the point-particle styles assign mass to particles on a
@ -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:]

3
doc/src/balance.txt
View File

@ -140,7 +140,8 @@ partitioning of the simulation box across processors (one sub-box for
each of 16 processors); the middle diagram is after a "grid" method
has been applied.
:c,image(JPG/balance_uniform_small.jpg,JPG/balance_uniform.jpg),image(JPG/balance_nonuniform_small.jpg,JPG/balance_nonuniform.jpg),image(JPG/balance_rcb_small.jpg,JPG/balance_rcb.jpg)
:image(JPG/balance_uniform_small.jpg,JPG/balance_uniform.jpg),image(JPG/balance_nonuniform_small.jpg,JPG/balance_nonuniform.jpg),image(JPG/balance_rcb_small.jpg,JPG/balance_rcb.jpg)
:c
The {rcb} style is a "tiling" method which does not produce a logical
3d grid of processors. Rather it tiles the simulation domain with

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

22
doc/src/bonds.txt Normal file
View File

@ -0,0 +1,22 @@
Bond Styles :h1
<!-- RST
.. toctree::
:maxdepth: 1
bond_class2
bond_fene
bond_fene_expand
bond_harmonic
bond_harmonic_shift
bond_harmonic_shift_cut
bond_hybrid
bond_morse
bond_none
bond_nonlinear
bond_quartic
bond_table
bond_zero
END_RST -->

2
doc/src/boundary.txt
View File

@ -82,7 +82,7 @@ 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.

109
doc/src/commands.txt Normal file
View File

@ -0,0 +1,109 @@
Commands :h1
<!-- RST
.. toctree::
:maxdepth: 1
angle_coeff
angle_style
atom_modify
atom_style
balance
bond_coeff
bond_style
bond_write
boundary
box
change_box
clear
comm_modify
comm_style
compute
compute_modify
create_atoms
create_bonds
create_box
delete_atoms
delete_bonds
dielectric
dihedral_coeff
dihedral_style
dimension
displace_atoms
dump
dump_custom_vtk
dump_h5md
dump_image
dump_modify
dump_molfile
echo
fix
fix_modify
group
group2ndx
if
improper_coeff
improper_style
include
info
jump
kspace_modify
kspace_style
label
lattice
log
mass
min_modify
min_style
minimize
molecule
neb
neigh_modify
neighbor
newton
next
package
pair_coeff
pair_modify
pair_style
pair_write
partition
prd
print
processors
python
quit
read_data
read_dump
read_restart
region
replicate
rerun
reset_timestep
restart
run
run_style
set
shell
special_bonds
suffix
tad
temper
thermo
thermo_modify
thermo_style
timer
timestep
uncompute
undump
unfix
units
variable
velocity
write_coeff
write_data
write_dump
write_restart
END_RST -->

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:]

8
doc/src/compute_angmom_chunk.txt
View File

@ -30,8 +30,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto
23"_Section_howto.html#howto_23 for details of how chunks can be
chunk/atom"_compute_chunk_atom.html doc page and "Section
6.23"_Section_howto.html#howto_23 for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.
@ -73,8 +73,8 @@ 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 angular momentum 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 for an overview of LAMMPS output
values from a 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

4
doc/src/compute_basal_atom.txt
View File

@ -46,8 +46,8 @@ in examples/USER/misc/basal.
This compute calculates a per-atom array with 3 columns, which can be
accessed by indices 1-3 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 LAMMPS output
a compute as input. See "Section
6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The per-atom vector values are unitless since the 3 columns represent

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_centro_atom.txt
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@ -97,8 +97,8 @@ too frequently or to have multiple compute/dump commands, each with a
By default, this compute calculates the centrosymmetry value for each
atom as 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 LAMMPS output
uses per-atom values from a compute as input. See "Section
6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
If the {axes} keyword setting is {yes}, then a per-atom array is

8
doc/src/compute_chunk_atom.txt
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@ -101,10 +101,10 @@ msd/chunk"_compute_msd_chunk.html. Or they can be used by the "fix
ave/chunk"_fix_ave_chunk.html command to sum and time average a
variety of per-atom properties over the atoms in each chunk. Or they
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.
compute as input, as discussed in "Section
6.15"_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
View File

@ -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

8
doc/src/compute_com_chunk.txt
View File

@ -30,8 +30,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto
23"_Section_howto.html#howto_23 for details of how chunks can be
chunk/atom"_compute_chunk_atom.html doc page and "Section
6.23"_Section_howto.html#howto_23 for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.
@ -71,8 +71,8 @@ number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
3 for the x,y,z center-of-mass coordinates of 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 for an overview of LAMMPS output
from a 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/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

4
doc/src/compute_coord_atom.txt
View File

@ -76,8 +76,8 @@ If single {type1} keyword is specified (or if none are specified),
this compute calculates a per-atom vector. If multiple {typeN}
keywords are specified, this compute calculates a per-atom array, with
N columns. These 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 overview of LAMMPS output
per-atom values from a compute as input. See "Section
6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The per-atom vector or array values will be a number >= 0.0, as

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.

8
doc/src/compute_dipole_chunk.txt
View File

@ -32,8 +32,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto
23"_Section_howto.html#howto_23 for details of how chunks can be
chunk/atom"_compute_chunk_atom.html doc page and "Section
6.23"_Section_howto.html#howto_23 for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.
@ -76,8 +76,8 @@ number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
4 for the x,y,z dipole vector components and the total dipole of 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 for an overview of LAMMPS output
array values from a 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

4
doc/src/compute_displace_atom.txt
View File

@ -53,8 +53,8 @@ correctly with time=0 atom coordinates from the restart file.
This compute calculates a per-atom array with 4 columns, which can be
accessed by indices 1-4 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 LAMMPS output
a compute as input. See "Section
6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The per-atom array values will be in distance "units"_units.html.

2
doc/src/compute_dpd_atom.txt
View File

@ -36,7 +36,7 @@ particles.
This compute calculates a per-particle array with 4 columns (u_cond,
u_mech, u_chem, dpdTheta), which can be accessed by indices 1-4 by any command
that uses per-particle values from a compute as input. See
"Section_howto15"_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 array values will be in energy (u_cond, u_mech, u_chem)

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

4
doc/src/compute_fep.txt
View File

@ -219,8 +219,8 @@ unperturbed parameters. The energies include kspace terms if these
are used in the simulation.
These output results can be used by any command that uses a global
scalar or vector from a compute as input. See "Section_howto
15"_Section_howto.html#howto_15 for an overview of LAMMPS output
scalar or vector from a compute as input. See "Section
6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
options. For example, the computed values can be averaged using "fix
ave/time"_fix_ave_time.html.

4
doc/src/compute_gyration.txt
View File

@ -55,8 +55,8 @@ using the "set image"_set.html command.
This compute calculates a global scalar (Rg) and a global vector of
length 6 (Rg^2 tensor), which can be accessed by indices 1-6. These
values can be used by any command that uses a global scalar value or
vector values from a compute as input. See "Section_howto
15"_Section_howto.html#howto_15 for an overview of LAMMPS output
vector values from a compute as input. See "Section
6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The scalar and vector values calculated by this compute are

4
doc/src/compute_gyration_chunk.txt
View File

@ -35,8 +35,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto
23"_Section_howto.html#howto_23 for details of how chunks can be
chunk/atom"_compute_chunk_atom.html doc page and "Section
6.23"_Section_howto.html#howto_23 for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.

4
doc/src/compute_hexorder_atom.txt
View File

@ -96,8 +96,8 @@ real and imaginary parts {qn}, a complex number restricted to the
unit disk of the complex plane i.e. Re({qn})^2 + Im({qn})^2 <= 1 .
These 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 overview of LAMMPS output
per-atom values from a compute as input. See "Section
6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
[Restrictions:] none

8
doc/src/compute_inertia_chunk.txt
View File

@ -30,8 +30,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto
23"_Section_howto.html#howto_23 for details of how chunks can be
chunk/atom"_compute_chunk_atom.html doc page and "Section
6.23"_Section_howto.html#howto_23 for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.
@ -72,8 +72,8 @@ number of chunks {Nchunk} as calculated by the specified "compute
chunk/atom"_compute_chunk_atom.html command. The number of columns =
6 for the 6 components of the inertia tensor for each chunk, ordered
as listed above. 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 for an overview of LAMMPS output
uses global array values from a 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/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

4
doc/src/compute_ke_rigid.txt
View File

@ -40,8 +40,8 @@ calculation.
This compute calculates a global scalar (the summed KE 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 LAMMPS output
global scalar value from a 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_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.

4
doc/src/compute_msd_chunk.txt
View File

@ -30,8 +30,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto
23"_Section_howto.html#howto_23 for details of how chunks can be
chunk/atom"_compute_chunk_atom.html doc page and "Section
6.23"_Section_howto.html#howto_23 for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.

8
doc/src/compute_omega_chunk.txt
View File

@ -30,8 +30,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto
23"_Section_howto.html#howto_23 for details of how chunks can be
chunk/atom"_compute_chunk_atom.html doc page and "Section
6.23"_Section_howto.html#howto_23 for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.
@ -73,8 +73,8 @@ 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 angular velocity 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 for an overview of LAMMPS output
values from a 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

4
doc/src/compute_orientorder_atom.txt
View File

@ -99,8 +99,8 @@ This compute calculates a per-atom array with {nlvalues} columns, giving the
{Ql} values for each atom, which are real numbers on the range 0 <= {Ql} <= 1.
These 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 overview of LAMMPS output
per-atom values from a compute as input. See "Section
6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
[Restrictions:] none

4
doc/src/compute_pe.txt
View File

@ -64,8 +64,8 @@ See the "thermo_style" command for more details.
This compute calculates a global scalar (the potential energy). 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 LAMMPS output
a 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_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

4
doc/src/compute_property_chunk.txt
View File

@ -36,8 +36,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the "compute
chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto
23"_Section_howto.html#howto_23 for details of how chunks can be
chunk/atom"_compute_chunk_atom.html doc page and "Section
6.23"_Section_howto.html#howto_23 for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.

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.

12
doc/src/compute_smd_triangle_mesh_vertices.txt
View File

@ -4,8 +4,6 @@
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:link(ls,fix_smd_wall_surface.html)
:line
compute smd/triangle/mesh/vertices :h3
@ -25,7 +23,7 @@ compute 1 all smd/triangle/mesh/vertices :pre
Define a computation that returns the coordinates of the vertices
corresponding to the triangle-elements of a mesh created by the "fix
smd/wall_surface"_ls.
smd/wall_surface"_fix_smd_wall_surface.html.
See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
Mach Dynamics in LAMMPS.
@ -42,10 +40,10 @@ The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and
each triangle.
It is only meaningful to use this compute for a group of particles
which is created via the "fix smd/wall_surface"_ls command.
which is created via the "fix smd/wall_surface"_fix_smd_wall_surface.html command.
The output of this compute can be used with the dump2vtk_tris tool to
generate a VTK representation of the smd/wall_surace mesh for
generate a VTK representation of the smd/wall_surface mesh for
visualization purposes.
The values will be given in "units"_units.html of distance.
@ -58,7 +56,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"compute smd/move/tri/surf"_fix_smd_move_triangulated_surface.html,
"compute smd/wall/surface"_ls
"fix smd/move/tri/surf"_fix_smd_move_triangulated_surface.html,
"fix smd/wall_surface"_fix_smd_wall_surface.html
[Default:] none

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_smd_ulsph_strain_rate.txt
View File

@ -32,8 +32,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector of vectors (tensors),
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 LAMMPS output
from a compute as input. See "Section
6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The values will be given in "units"_units.html of one over time.

4
doc/src/compute_smd_ulsph_stress.txt
View File

@ -30,8 +30,8 @@ Mach Dynamics in LAMMPS.
This compute calculates a per-particle vector of vectors (tensors),
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 LAMMPS output
from a compute as input. See "Section
6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The values will be given in "units"_units.html of pressure.

4
doc/src/compute_sna_atom.txt
View File

@ -205,8 +205,8 @@ notation. Each of these sub-blocks contains one column for each
bispectrum component, the same as for compute {sna/atom}
These 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 overview of LAMMPS output
from a compute as input. See "Section
6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
[Restrictions:]

4
doc/src/compute_stress_atom.txt
View File

@ -137,8 +137,8 @@ thermo_style custom step temp etotal press v_press :pre
This compute calculates a per-atom array with 6 columns, which can be
accessed by indices 1-6 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 LAMMPS output
a compute as input. See "Section
6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The per-atom array values will be in pressure*volume

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

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