tx258/lammps-gran-kokkos
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

fix a bunch more broken, duplicate links and misformatted text

Browse Source
This commit is contained in:
Axel Kohlmeyer
2018-08-09 19:46:25 +02:00
parent 108f2d0ed7
commit a5170e93ec
13 changed files with 237 additions and 236 deletions
Download Patch File Download Diff File Expand all files Collapse all files

12
doc/src/Build_extras.txt
View File

@ -58,7 +58,7 @@ available on your system.
If CMake cannot find the library, you can set these variables:
-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file
-D ZLIB_LIBRARIES=path # path to libzlib.a (.so) file
-D ZLIB_LIBRARIES=path # path to libzlib.a (.so) file :pre
[Traditional make]:
@ -82,11 +82,11 @@ to build the library in lib/gpu first.
-D OCL_TUNE=value # hardware choice for GPU_API=opencl
# generic (default) or intel (Intel CPU) or phi (Intel Xeon Phi) or fermi (NVIDIA) or kepler (NVIDIA) or cypress (NVIDIA)
-D GPU_ARCH=value # hardware choice for GPU_API=cuda
# value = sm20 (Fermi) or sm30 (Kepler) or sm50 (Maxwell) or sm60 (Pascal) or sm70 (Volta)
# value = sm20 (Fermi) or sm30 or sm (Kepler) or sm50 (Maxwell) or sm60 (Pascal) or sm70 (Volta)
# default is Cuda-compiler dependent, but typically Fermi
-D CUDPP_OPT=value # optimization setting for GPU_API=cudea
# enables CUDA Performance Primitives Optimizations
# on (default) or off
# enables CUDA Performance Primitives Optimizations
# on (default) or off :pre
[Traditional make]:
@ -191,13 +191,13 @@ traditional make settings
[Traditional make]:
how to choose these 3 things: mode archgpu=N archcpu=SNB
how to choose these 3 things: mode archgpu=N archcpu=SNB
mode = omp or cuda or phi (def = KOKKOS_DEVICES setting in Makefile )
archgpu = number like 35 (Kepler) or 21 (Fermi) (def = none)
sets KOKKOS_ARCH for GPU to appropriate value
archcpu = SNB or HSW or BGQ or Power7 or Power8 (def = none)
for CPU = SandyBridge, Haswell, BGQ, Power7, Power8
sets KOKKOS_ARCH for GPU to appropriate value
sets KOKKOS_ARCH for GPU to appropriate value :pre
For the KOKKOS package, you have 3 choices when building. You can
build with either CPU or KNL or GPU support. Each choice requires

2
doc/src/Build_settings.txt
View File

@ -252,7 +252,7 @@ gzip compression by several LAMMPS commands, including
-D LAMMPS_GZIP=value # yes or no
# default is yes if CMake can find gzip, else no
-D GZIP_EXECUTABLE=path # path to gzip executable if CMake cannot find it
-D GZIP_EXECUTABLE=path # path to gzip executable if CMake cannot find it :pre
[Makefile.machine setting]:

2
doc/src/Errors_common.txt
View File

@ -60,7 +60,7 @@ package which was not compiled into your executable. The list of
available styles in your executable can be listed by using "the -h
command-line swith"_Run_options.html. The installation and
compilation of optional packages is explained on the "Build
packages"_Build_packages.html doc page.
packages"_Build_package.html doc page.
For a given command, LAMMPS expects certain arguments in a specified
order. If you mess this up, LAMMPS will often flag the error, but it

10
doc/src/Install_git.txt
View File

@ -62,9 +62,9 @@ Or they can be generated from the content provided in doc/src by
typing "make html" from the the doc directory.
After initial cloning, as bug fixes and new features are added to
LAMMPS, as listed on "this page"_bug.html, you can stay up-to-date by
typing the following Git commands from within the "mylammps"
directory:
LAMMPS, as listed on "this page"_Errors_bugs.html, you can stay
up-to-date by typing the following Git commands from within the
"mylammps" directory:
git checkout unstable # not needed if you always stay in this branch
git checkout stable # use one of the 3 checkout commands
@ -86,8 +86,8 @@ this is as follows.
git checkout tagID :pre
Stable versions and what tagID to use for a particular stable version
are discussed on "this page"_bug.html. Note that this command will
print some warnings, because in order to get back to the latest
are discussed on "this page"_Errors_bugs.html. Note that this command
will print some warnings, because in order to get back to the latest
revision and to be able to update with "git pull" again, you first
will need to first type "git checkout unstable" (or check out any
other desired branch).

2
doc/src/Install_linux.txt
View File

@ -12,7 +12,7 @@ Download an executable for Linux :h3
Binaries are available for many different versions of Linux:
"Pre-built binary RPMs for Fedora/RedHat/CentOS/openSUSE"_#rpm
"Pre-built Ubuntu Linux executables"_#unbuntu
"Pre-built Ubuntu Linux executables"_#ubuntu
"Pre-built Gentoo Linux executable"_#gentoo :all(b)
:line

6
doc/src/Install_svn.txt
View File

@ -50,9 +50,9 @@ Or they can be generated from the content provided in doc/src by
typing "make html" from the the doc directory.
After initial checkout, as bug fixes and new features are added to
LAMMPS, as listed on "this page"_bug.html, you can stay up-to-date by
typing the following SVN commands from within the "mylammps"
directory:
LAMMPS, as listed on "this page"_Errors_bugs.html, you can stay
up-to-date by typing the following SVN commands from within the
"mylammps" directory:
svn update :pre

292
doc/src/Packages_details.txt
View File

@ -30,79 +30,79 @@ src/GRANULAR". Files with names that start with fix, compute, atom,
pair, bond, angle, etc correspond to commands with the same style name
as contained in the file name.
"ASPHERE"_#ASPHERE,
"BODY"_#BODY,
"CLASS2"_#CLASS2,
"COLLOID"_#COLLOID,
"COMPRESS"_#COMPRESS,
"CORESHELL"_#CORESHELL,
"DIPOLE"_#DIPOLE,
"GPU"_#GPU,
"GRANULAR"_#GRANULAR,
"KIM"_#KIM,
"KOKKOS"_#KOKKOS,
"KSPACE"_#KSPACE,
"LATTE"_#LATTE,
"MANYBODY"_#MANYBODY,
"MC"_#MC,
"MEAM"_#MEAM,
"MISC"_#MISC,
"MOLECULE"_#MOLECULE,
"MPIIO"_#MPIIO,
"MSCG"_#MSCG,
"OPT"_#OPT,
"PERI"_#PERI,
"POEMS"_#POEMS,
"PYTHON"_#PYTHON,
"QEQ"_#QEQ,
"REAX"_#REAX,
"REPLICA"_#REPLICA2,
"RIGID"_#RIGID,
"SHOCK"_#SHOCK,
"SNAP"_#SNAP,
"SPIN"_#SPIN,
"SRD"_#SRD,
"VORONOI"_#VORONOI :tb(c=6,ea=c)
"ASPHERE"_#PKG-ASPHERE,
"BODY"_#PKG-BODY,
"CLASS2"_#PKG-CLASS2,
"COLLOID"_#PKG-COLLOID,
"COMPRESS"_#PKG-COMPRESS,
"CORESHELL"_#PKG-CORESHELL,
"DIPOLE"_#PKG-DIPOLE,
"GPU"_#PKG-GPU,
"GRANULAR"_#PKG-GRANULAR,
"KIM"_#PKG-KIM,
"KOKKOS"_#PKG-KOKKOS,
"KSPACE"_#PKG-KSPACE,
"LATTE"_#PKG-LATTE,
"MANYBODY"_#PKG-MANYBODY,
"MC"_#PKG-MC,
"MEAM"_#PKG-MEAM,
"MISC"_#PKG-MISC,
"MOLECULE"_#PKG-MOLECULE,
"MPIIO"_#PKG-MPIIO,
"MSCG"_#PKG-MSCG,
"OPT"_#PKG-OPT,
"PERI"_#PKG-PERI,
"POEMS"_#PKG-POEMS,
"PYTHON"_#PKG-PYTHON,
"QEQ"_#PKG-QEQ,
"REAX"_#PKG-REAX,
"REPLICA"_#PKG-REPLICA2,
"RIGID"_#PKG-RIGID,
"SHOCK"_#PKG-SHOCK,
"SNAP"_#PKG-SNAP,
"SPIN"_#PKG-SPIN,
"SRD"_#PKG-SRD,
"VORONOI"_#PKG-VORONOI :tb(c=6,ea=c)
"USER-ATC"_#USER-ATC,
"USER-AWPMD"_#USER-AWPMD,
"USER-BOCS"_#USER-BOCS,
"USER-CGDNA"_#USER-CGDNA,
"USER-CGSDK"_#USER-CGSDK,
"USER-COLVARS"_#USER-COLVARS,
"USER-DIFFRACTION"_#USER-DIFFRACTION,
"USER-DPD"_#USER-DPD,
"USER-DRUDE"_#USER-DRUDE,
"USER-EFF"_#USER-EFF,
"USER-FEP"_#USER-FEP,
"USER-H5MD"_#USER-H5MD,
"USER-INTEL"_#USER-INTEL,
"USER-LB"_#USER-LB,
"USER-MANIFOLD"_#USER-MANIFOLD,
"USER-MEAMC"_#USER-MEAMC,
"USER-MESO"_#USER-MESO,
"USER-MGPT"_#USER-MGPT,
"USER-MISC"_#USER-MISC,
"USER-MOFFF"_#USER-MOFFF,
"USER-MOLFILE"_#USER-MOLFILE,
"USER-NETCDF"_#USER-NETCDF,
"USER-OMP"_#USER-OMP,
"USER-PHONON"_#USER-PHONON,
"USER-QMMM"_#USER-QMMM,
"USER-QTB"_#USER-QTB,
"USER-QUIP"_#USER-QUIP,
"USER-REAXC"_#USER-REAXC,
"USER-SMD"_#USER-SMD,
"USER-SMTBQ"_#USER-SMTBQ,
"USER-SPH"_#USER-SPH,
"USER-TALLY"_#USER-TALLY,
"USER-UEF"_#USER-UEF,
"USER-VTK"_#USER-VTK :tb(c=6,ea=c)
"USER-ATC"_#PKG-USER-ATC,
"USER-AWPMD"_#PKG-USER-AWPMD,
"USER-BOCS"_#PKG-USER-BOCS,
"USER-CGDNA"_#PKG-USER-CGDNA,
"USER-CGSDK"_#PKG-USER-CGSDK,
"USER-COLVARS"_#PKG-USER-COLVARS,
"USER-DIFFRACTION"_#PKG-USER-DIFFRACTION,
"USER-DPD"_#PKG-USER-DPD,
"USER-DRUDE"_#PKG-USER-DRUDE,
"USER-EFF"_#PKG-USER-EFF,
"USER-FEP"_#PKG-USER-FEP,
"USER-H5MD"_#PKG-USER-H5MD,
"USER-INTEL"_#PKG-USER-INTEL,
"USER-LB"_#PKG-USER-LB,
"USER-MANIFOLD"_#PKG-USER-MANIFOLD,
"USER-MEAMC"_#PKG-USER-MEAMC,
"USER-MESO"_#PKG-USER-MESO,
"USER-MGPT"_#PKG-USER-MGPT,
"USER-MISC"_#PKG-USER-MISC,
"USER-MOFFF"_#PKG-USER-MOFFF,
"USER-MOLFILE"_#PKG-USER-MOLFILE,
"USER-NETCDF"_#PKG-USER-NETCDF,
"USER-OMP"_#PKG-USER-OMP,
"USER-PHONON"_#PKG-USER-PHONON,
"USER-QMMM"_#PKG-USER-QMMM,
"USER-QTB"_#PKG-USER-QTB,
"USER-QUIP"_#PKG-USER-QUIP,
"USER-REAXC"_#PKG-USER-REAXC,
"USER-SMD"_#PKG-USER-SMD,
"USER-SMTBQ"_#PKG-USER-SMTBQ,
"USER-SPH"_#PKG-USER-SPH,
"USER-TALLY"_#PKG-USER-TALLY,
"USER-UEF"_#PKG-USER-UEF,
"USER-VTK"_#PKG-USER-VTK :tb(c=6,ea=c)
:line
:line
ASPHERE package :link(ASPHERE),h4
ASPHERE package :link(PKG-ASPHERE),h4
[Contents:]
@ -124,7 +124,7 @@ http://lammps.sandia.gov/movies.html#tri :ul
:line
BODY package :link(BODY),h4
BODY package :link(PKG-BODY),h4
[Contents:]
@ -144,7 +144,7 @@ examples/body :ul
:line
CLASS2 package :link(CLASS2),h4
CLASS2 package :link(PKG-CLASS2),h4
[Contents:]
@ -162,7 +162,7 @@ src/CLASS2: filenames -> commands
:line
COLLOID package :link(COLLOID),h4
COLLOID package :link(PKG-COLLOID),h4
[Contents:]
@ -189,7 +189,7 @@ examples/srd :ul
:line
COMPRESS package :link(COMPRESS),h4
COMPRESS package :link(PKG-COMPRESS),h4
[Contents:]
@ -219,7 +219,7 @@ lib/compress/README
:line
CORESHELL package :link(CORESHELL),h4
CORESHELL package :link(PKG-CORESHELL),h4
[Contents:]
@ -246,7 +246,7 @@ examples/coreshell :ul
:line
DIPOLE package :link(DIPOLE),h4
DIPOLE package :link(PKG-DIPOLE),h4
[Contents:]
@ -264,7 +264,7 @@ examples/dipole :ul
:line
GPU package :link(GPU),h4
GPU package :link(PKG-GPU),h4
[Contents:]
@ -277,7 +277,7 @@ gpu"_Speed_gpu.html doc page gives details of what hardware and GPU
software is required on your system, and details on how to build and
use this package. Its styles can be invoked at run time via the "-sf
gpu" or "-suffix gpu" "command-line switches"_Run_options.html. See
also the "KOKKOS"_#KOKKOS package, which has GPU-enabled styles.
also the "KOKKOS"_#PKG-KOKKOS package, which has GPU-enabled styles.
[Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
(Northwestern U) while at ORNL.
@ -303,7 +303,7 @@ lib/gpu/README
:line
GRANULAR package :link(GRANULAR),h4
GRANULAR package :link(PKG-GRANULAR),h4
[Contents:]
@ -330,7 +330,7 @@ http://lammps.sandia.gov/movies.html#granregion :ul
:line
KIM package :link(KIM),h4
KIM package :link(PKG-KIM),h4
[Contents:]
@ -366,7 +366,7 @@ examples/kim :ul
:line
KOKKOS package :link(KOKKOS),h4
KOKKOS package :link(PKG-KOKKOS),h4
[Contents:]
@ -378,8 +378,8 @@ style name. The "Speed kokkos"_Speed_kokkos.html doc page gives
details of what hardware and software is required on your system, and
how to build and use this package. Its styles can be invoked at run
time via the "-sf kk" or "-suffix kk" "command-line
switches"_Run_options.html. Also see the "GPU"_#GPU, "OPT"_#OPT,
"USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which
switches"_Run_options.html. Also see the "GPU"_#PKG-GPU, "OPT"_#PKG-OPT,
"USER-INTEL"_#PKG-USER-INTEL, and "USER-OMP"_#PKG-USER-OMP packages, which
have styles optimized for CPUs, KNLs, and GPUs.
You must have a C++11 compatible compiler to use this package.
@ -413,7 +413,7 @@ lib/kokkos/README
:line
KSPACE package :link(KSPACE),h4
KSPACE package :link(PKG-KSPACE),h4
[Contents:]
@ -446,7 +446,7 @@ bench/in.rhodo :ul
:line
LATTE package :link(LATTE),h4
LATTE package :link(PKG-LATTE),h4
[Contents:]
@ -481,7 +481,7 @@ examples/latte
:line
MANYBODY package :link(MANYBODY),h4
MANYBODY package :link(PKG-MANYBODY),h4
[Contents:]
@ -502,7 +502,7 @@ bench/in.eam :ul
:line
MC package :link(MC),h4
MC package :link(PKG-MC),h4
[Contents:]
@ -524,14 +524,14 @@ http://lammps.sandia.gov/movies.html#gcmc :ul
:line
MEAM package :link(MEAM),h4
MEAM package :link(PKG-MEAM),h4
[Contents:]
A pair style for the modified embedded atom (MEAM) potential.
Please note that the MEAM package has been superseded by the
"USER-MEAMC"_#USER-MEAMC package, which is a direct translation
"USER-MEAMC"_#PKG-USER-MEAMC package, which is a direct translation
of the MEAM package to C++. USER-MEAMC contains additional
optimizations making it run faster than MEAM on most machines,
while providing the identical features and USER interface.
@ -558,7 +558,7 @@ examples/meam :ul
:line
MISC package :link(MISC),h4
MISC package :link(PKG-MISC),h4
[Contents:]
@ -585,7 +585,7 @@ http://lammps.sandia.gov/movies.html#evaporation :ul
:line
MOLECULE package :link(MOLECULE),h4
MOLECULE package :link(PKG-MOLECULE),h4
[Contents:]
@ -614,7 +614,7 @@ bench/in.rhodo :ul
:line
MPIIO package :link(MPIIO),h4
MPIIO package :link(PKG-MPIIO),h4
[Contents:]
@ -633,7 +633,7 @@ src/MPIIO: filenames -> commands
:line
MSCG package :link(mscg),h4
MSCG package :link(PKG-mscg),h4
[Contents:]
@ -665,7 +665,7 @@ examples/mscg :ul
:line
OPT package :link(OPT),h4
OPT package :link(PKG-OPT),h4
[Contents:]
@ -675,8 +675,8 @@ CHARMM, and Morse potentials. The styles have an "opt" suffix in
their style name. The "Speed opt"_Speed_opt.html doc page gives
details of how to build and use this package. Its styles can be
invoked at run time via the "-sf opt" or "-suffix opt" "command-line
switches"_Run_options.html. See also the "KOKKOS"_#KOKKOS,
"USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which
switches"_Run_options.html. See also the "KOKKOS"_#PKG-KOKKOS,
"USER-INTEL"_#PKG-USER-INTEL, and "USER-OMP"_#PKG-USER-OMP packages, which
have styles optimized for CPU performance.
[Authors:] James Fischer (High Performance Technologies), David Richie,
@ -699,7 +699,7 @@ src/OPT: filenames -> commands
:line
PERI package :link(PERI),h4
PERI package :link(PKG-PERI),h4
[Contents:]
@ -727,7 +727,7 @@ http://lammps.sandia.gov/movies.html#peri :ul
:line
POEMS package :link(POEMS),h4
POEMS package :link(PKG-POEMS),h4
[Contents:]
@ -755,7 +755,7 @@ examples/rigid :ul
:line
PYTHON package :link(PYTHON),h4
PYTHON package :link(PKG-PYTHON),h4
[Contents:]
@ -786,7 +786,7 @@ examples/python :ul
:line
QEQ package :link(QEQ),h4
QEQ package :link(PKG-QEQ),h4
[Contents:]
@ -803,13 +803,13 @@ examples/streitz :ul
:line
REAX package :link(REAX),h4
REAX package :link(PKG-REAX),h4
[Contents:]
A pair style which wraps a Fortran library which implements the ReaxFF
potential, which is a universal reactive force field. See the
"USER-REAXC package"_#USER-REAXC for an alternate implementation in
"USER-REAXC package"_#PKG-USER-REAXC for an alternate implementation in
C/C++. Also a "fix reax/bonds"_fix_reax_bonds.html command for
monitoring molecules as bonds are created and destroyed.
@ -831,7 +831,7 @@ examples/reax :ul
:line
REPLICA package :link(REPLICA2),h4
REPLICA package :link(PKG-REPLICA2),h4
[Contents:]
@ -860,7 +860,7 @@ examples/tad :ul
:line
RIGID package :link(RIGID),h4
RIGID package :link(PKG-RIGID),h4
[Contents:]
@ -884,7 +884,7 @@ http://lammps.sandia.gov/movies.html#star :ul
:line
SHOCK package :link(SHOCK),h4
SHOCK package :link(PKG-SHOCK),h4
[Contents:]
@ -903,7 +903,7 @@ examples/msst :ul
:line
SNAP package :link(SNAP),h4
SNAP package :link(PKG-SNAP),h4
[Contents:]
@ -925,7 +925,7 @@ examples/snap :ul
:line
SPIN package :link(SPIN),h4
SPIN package :link(PKG-SPIN),h4
[Contents:]
@ -949,7 +949,7 @@ examples/SPIN :ul
:line
SRD package :link(SRD),h4
SRD package :link(PKG-SRD),h4
[Contents:]
@ -970,7 +970,7 @@ http://lammps.sandia.gov/movies.html#poly :ul
:line
VORONOI package :link(VORONOI),h4
VORONOI package :link(PKG-VORONOI),h4
[Contents:]
@ -1005,7 +1005,7 @@ examples/voronoi :ul
:line
:line
USER-ATC package :link(USER-ATC),h4
USER-ATC package :link(PKG-USER-ATC),h4
[Contents:]
@ -1032,7 +1032,7 @@ http://lammps.sandia.gov/pictures.html#atc :ul
:line
USER-AWPMD package :link(USER-AWPMD),h4
USER-AWPMD package :link(PKG-USER-AWPMD),h4
[Contents:]
@ -1058,7 +1058,7 @@ examples/USER/awpmd :ul
:line
USER-BOCS package :link(USER-BOCS),h4
USER-BOCS package :link(PKG-USER-BOCS),h4
[Contents:]
@ -1088,7 +1088,7 @@ Example inputs are in the examples/USER/bocs folder.
:line
USER-CGDNA package :link(USER-CGDNA),h4
USER-CGDNA package :link(PKG-USER-CGDNA),h4
[Contents:]
@ -1112,7 +1112,7 @@ src/USER-CGDNA: filenames -> commands
:line
USER-CGSDK package :link(USER-CGSDK),h4
USER-CGSDK package :link(PKG-USER-CGSDK),h4
[Contents:]
@ -1134,7 +1134,7 @@ http://lammps.sandia.gov/pictures.html#cg :ul
:line
USER-COLVARS package :link(USER-COLVARS),h4
USER-COLVARS package :link(PKG-USER-COLVARS),h4
[Contents:]
@ -1168,7 +1168,7 @@ examples/USER/colvars :ul
:line
USER-DIFFRACTION package :link(USER-DIFFRACTION),h4
USER-DIFFRACTION package :link(PKG-USER-DIFFRACTION),h4
[Contents:]
@ -1187,7 +1187,7 @@ examples/USER/diffraction :ul
:line
USER-DPD package :link(USER-DPD),h4
USER-DPD package :link(PKG-USER-DPD),h4
[Contents:]
@ -1225,7 +1225,7 @@ examples/USER/dpd :ul
:line
USER-DRUDE package :link(USER-DRUDE),h4
USER-DRUDE package :link(PKG-USER-DRUDE),h4
[Contents:]
@ -1255,7 +1255,7 @@ tools/drude :ul
:line
USER-EFF package :link(USER-EFF),h4
USER-EFF package :link(PKG-USER-EFF),h4
[Contents:]
@ -1288,7 +1288,7 @@ http://lammps.sandia.gov/movies.html#eff :ul
:line
USER-FEP package :link(USER-FEP),h4
USER-FEP package :link(PKG-USER-FEP),h4
[Contents:]
@ -1313,7 +1313,7 @@ tools/fep :ul
:line
USER-H5MD package :link(USER-H5MD),h4
USER-H5MD package :link(PKG-USER-H5MD),h4
[Contents:]
@ -1346,7 +1346,7 @@ lib/h5md/README
:line
USER-INTEL package :link(USER-INTEL),h4
USER-INTEL package :link(PKG-USER-INTEL),h4
[Contents:]
@ -1357,7 +1357,7 @@ intel"_Speed_intel.html doc page gives details of what hardware and
compilers are required on your system, and how to build and use this
package. Its styles can be invoked at run time via the "-sf intel" or
"-suffix intel" "command-line switches"_Run_options.html. Also see
the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-OMP"_#USER-OMP packages,
the "KOKKOS"_#PKG-KOKKOS, "OPT"_#PKG-OPT, and "USER-OMP"_#PKG-USER-OMP packages,
which have styles optimized for CPUs and KNLs.
You need to have an Intel compiler, version 14 or higher to take full
@ -1390,7 +1390,7 @@ src/USER-INTEL/TEST
:line
USER-LB package :link(USER-LB),h4
USER-LB package :link(PKG-USER-LB),h4
[Contents:]
@ -1411,7 +1411,7 @@ examples/USER/lb :ul
:line
USER-MGPT package :link(USER-MGPT),h4
USER-MGPT package :link(PKG-USER-MGPT),h4
[Contents:]
@ -1435,7 +1435,7 @@ examples/USER/mgpt :ul
:line
USER-MISC package :link(USER-MISC),h4
USER-MISC package :link(PKG-USER-MISC),h4
[Contents:]
@ -1455,7 +1455,7 @@ examples/USER/misc :ul
:line
USER-MANIFOLD package :link(USER-MANIFOLD),h4
USER-MANIFOLD package :link(PKG-USER-MANIFOLD),h4
[Contents:]
@ -1483,7 +1483,7 @@ http://lammps.sandia.gov/movies.html#manifold :ul
:line
USER-MEAMC package :link(USER-MEAMC),h4
USER-MEAMC package :link(PKG-USER-MEAMC),h4
[Contents:]
@ -1506,7 +1506,7 @@ examples/meam :ul
:line
USER-MESO package :link(USER-MESO),h4
USER-MESO package :link(PKG-USER-MESO),h4
[Contents:]
@ -1534,7 +1534,7 @@ http://lammps.sandia.gov/movies.html#mesodpd :ul
:line
USER-MOFFF package :link(USER-MOFFF),h4
USER-MOFFF package :link(PKG-USER-MOFFF),h4
[Contents:]
@ -1564,7 +1564,7 @@ examples/USER/mofff :ul
:line
USER-MOLFILE package :link(USER-MOLFILE),h4
USER-MOLFILE package :link(PKG-USER-MOLFILE),h4
[Contents:]
@ -1607,7 +1607,7 @@ lib/molfile/README
:line
USER-NETCDF package :link(USER-NETCDF),h4
USER-NETCDF package :link(PKG-USER-NETCDF),h4
[Contents:]
@ -1646,7 +1646,7 @@ lib/netcdf/README
:line
USER-OMP package :link(USER-OMP),h4
USER-OMP package :link(PKG-USER-OMP),h4
[Contents:]
@ -1657,7 +1657,7 @@ The "Speed omp"_Speed_omp.html doc page gives details of what hardware
and compilers are required on your system, and how to build and use
this package. Its styles can be invoked at run time via the "-sf omp"
or "-suffix omp" "command-line switches"_Run_options.html. Also see
the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-INTEL"_#USER-INTEL
the "KOKKOS"_#PKG-KOKKOS, "OPT"_#PKG-OPT, and "USER-INTEL"_#PKG-USER-INTEL
packages, which have styles optimized for CPUs.
[Author:] Axel Kohlmeyer (Temple U).
@ -1695,7 +1695,7 @@ src/USER-OMP/README
:line
USER-PHONON package :link(USER-PHONON),h4
USER-PHONON package :link(PKG-USER-PHONON),h4
[Contents:]
@ -1714,7 +1714,7 @@ examples/USER/phonon :ul
:line
USER-QMMM package :link(USER-QMMM),h4
USER-QMMM package :link(PKG-USER-QMMM),h4
[Contents:]
@ -1752,7 +1752,7 @@ lib/qmmm/example-mc/README :ul
:line
USER-QTB package :link(USER-QTB),h4
USER-QTB package :link(PKG-USER-QTB),h4
[Contents:]
@ -1777,7 +1777,7 @@ examples/USER/qtb :ul
:line
USER-QUIP package :link(USER-QUIP),h4
USER-QUIP package :link(PKG-USER-QUIP),h4
[Contents:]
@ -1808,12 +1808,12 @@ examples/USER/quip :ul
:line
USER-REAXC package :link(USER-REAXC),h4
USER-REAXC package :link(PKG-USER-REAXC),h4
[Contents:]
A pair style which implements the ReaxFF potential in C/C++ (in
contrast to the "REAX package"_#REAX and its Fortran library). ReaxFF
contrast to the "REAX package"_#PKG-REAX and its Fortran library). ReaxFF
is universal reactive force field. See the src/USER-REAXC/README file
for more info on differences between the two packages. Also two fixes
for monitoring molecules as bonds are created and destroyed.
@ -1831,14 +1831,14 @@ examples/reax :ul
:line
USER-SMD package :link(USER-SMD),h4
USER-SMD package :link(PKG-USER-SMD),h4
[Contents:]
An atom style, fixes, computes, and several pair styles which
implements smoothed Mach dynamics (SMD) for solids, which is a model
related to smoothed particle hydrodynamics (SPH) for liquids (see the
"USER-SPH package"_#USER-SPH).
"USER-SPH package"_#PKG-USER-SPH).
This package solves solids mechanics problems via a state of the art
stabilized meshless method with hourglass control. It can specify
@ -1868,7 +1868,7 @@ http://lammps.sandia.gov/movies.html#smd :ul
:line
USER-SMTBQ package :link(USER-SMTBQ),h4
USER-SMTBQ package :link(PKG-USER-SMTBQ),h4
[Contents:]
@ -1888,13 +1888,13 @@ examples/USER/smtbq :ul
:line
USER-SPH package :link(USER-SPH),h4
USER-SPH package :link(PKG-USER-SPH),h4
[Contents:]
An atom style, fixes, computes, and several pair styles which
implements smoothed particle hydrodynamics (SPH) for liquids. See the
related "USER-SMD package"_#USER-SMD package for smooth Mach dynamics
related "USER-SMD package"_#PKG-USER-SMD package for smooth Mach dynamics
(SMD) for solids.
This package contains ideal gas, Lennard-Jones equation of states,
@ -1920,7 +1920,7 @@ http://lammps.sandia.gov/movies.html#sph :ul
:line
USER-TALLY package :link(USER-TALLY),h4
USER-TALLY package :link(PKG-USER-TALLY),h4
[Contents:]
@ -1939,7 +1939,7 @@ examples/USER/tally :ul
:line
USER-UEF package :link(USER-UEF),h4
USER-UEF package :link(PKG-USER-UEF),h4
[Contents:]
@ -1962,7 +1962,7 @@ examples/uef :ul
:line
USER-VTK package :link(USER-VTK),h4
USER-VTK package :link(PKG-USER-VTK),h4
[Contents:]

65
doc/src/Packages_standard.txt
View File

@ -31,35 +31,36 @@ int = internal library: provided with LAMMPS, but you may need to build it
ext = external library: you will need to download and install it on your machine :ul
Package, Description, Doc page, Example, Library
"ASPHERE"_Packages_details.html#ASPHERE, aspherical particle models, "Howto spherical"_Howto_spherical.html, ellipse, -
"BODY"_Packages_details.html#BODY, body-style particles, "Howto body"_Howto_body.html, body, -
"CLASS2"_Packages_details.html#CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, -, -
"COLLOID"_Packages_details.html#COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, -
"COMPRESS"_Packages_details.html#COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys
"CORESHELL"_Packages_details.html#CORESHELL, adiabatic core/shell model, "Howto coreshell"_Howto_coreshell.html, coreshell, -
"DIPOLE"_Packages_details.html#DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, -
"GPU"_Packages_details.html#GPU, GPU-enabled styles, "Section gpu"_Speed_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int
"GRANULAR"_Packages_details.html#GRANULAR, granular systems, "Howto granular"_Howto_granular.html, pour, -
"KIM"_Packages_details.html#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
"KOKKOS"_Packages_details.html#KOKKOS, Kokkos-enabled styles, "Speed kokkos"_Speed_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
"KSPACE"_Packages_details.html#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
"LATTE"_Packages_details.html#LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
"MANYBODY"_Packages_details.html#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
"MC"_Packages_details.html#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
"MEAM"_Packages_details.html#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
"MISC"_Packages_details.html#MISC, miscellanous single-file commands, -, -, -
"MOLECULE"_Packages_details.html#MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, -
"MPIIO"_Packages_details.html#MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, -
"MSCG"_Packages_details.html#MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext
"OPT"_Packages_details.html#OPT, optimized pair styles, "Speed opt"_Speed_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
"PERI"_Packages_details.html#PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, -
"POEMS"_Packages_details.html#POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
"PYTHON"_Packages_details.html#PYTHON, embed Python code in an input script, "python"_python.html, python, sys
"QEQ"_Packages_details.html#QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, -
"REAX"_Packages_details.html#REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
"REPLICA"_Packages_details.html#REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, -
"RIGID"_Packages_details.html#RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, -
"SHOCK"_Packages_details.html#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
"SNAP"_Packages_details.html#SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, -
"SPIN"_#SPIN, magnetic atomic spin dynamics, "Howto spins"_Howto_spins.html, SPIN, -"SRD"_Packages_details.html#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
"VORONOI"_Packages_details.html#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)
"ASPHERE"_Packages_details.html#PKG-ASPHERE, aspherical particle models, "Howto spherical"_Howto_spherical.html, ellipse, -
"BODY"_Packages_details.html#PKG-BODY, body-style particles, "Howto body"_Howto_body.html, body, -
"CLASS2"_Packages_details.html#PKG-CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, -, -
"COLLOID"_Packages_details.html#PKG-COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, -
"COMPRESS"_Packages_details.html#PKG-COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys
"CORESHELL"_Packages_details.html#PKG-CORESHELL, adiabatic core/shell model, "Howto coreshell"_Howto_coreshell.html, coreshell, -
"DIPOLE"_Packages_details.html#PKG-DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, -
"GPU"_Packages_details.html#PKG-GPU, GPU-enabled styles, "Section gpu"_Speed_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int
"GRANULAR"_Packages_details.html#PKG-GRANULAR, granular systems, "Howto granular"_Howto_granular.html, pour, -
"KIM"_Packages_details.html#PKG-KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
"KOKKOS"_Packages_details.html#PKG-KOKKOS, Kokkos-enabled styles, "Speed kokkos"_Speed_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
"KSPACE"_Packages_details.html#PKG-KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
"LATTE"_Packages_details.html#PKG-LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
"MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
"MISC"_Packages_details.html#PKG-MISC, miscellanous single-file commands, -, -, -
"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, -
"MPIIO"_Packages_details.html#PKG-MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, -
"MSCG"_Packages_details.html#PKG-MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext
"OPT"_Packages_details.html#PKG-OPT, optimized pair styles, "Speed opt"_Speed_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
"PERI"_Packages_details.html#PKG-PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, -
"POEMS"_Packages_details.html#PKG-POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
"PYTHON"_Packages_details.html#PKG-PYTHON, embed Python code in an input script, "python"_python.html, python, sys
"QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, -
"REAX"_Packages_details.html#PKG-REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
"REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, -
"RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, -
"SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
"SNAP"_Packages_details.html#PKG-SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, -
"SPIN"_Packages_details.html#PKG-SPIN, magnetic atomic spin dynamics, "Howto spins"_Howto_spins.html, SPIN, -
"SRD"_Packages_details.html#PKG-SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
"VORONOI"_Packages_details.html#PKG-VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)

68
doc/src/Packages_user.txt
View File

@ -38,37 +38,37 @@ int = internal library: provided with LAMMPS, but you may need to build it
ext = external library: you will need to download and install it on your machine :ul
Package, Description, Doc page, Example, Library
"USER-ATC"_Packages_details.html#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
"USER-AWPMD"_Packages_details.html#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
"USER-BOCS"_Packages_details.html#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
"USER-CGDNA"_Packages_details.html#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
"USER-CGSDK"_Packages_details.html#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
"USER-COLVARS"_Packages_details.html#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
"USER-DIFFRACTION"_Packages_details.html#USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, -
"USER-DPD"_Packages_details.html#USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, -
"USER-DRUDE"_Packages_details.html#USER-DRUDE, Drude oscillators, "Howto drude"_Howto_drude.html, USER/drude, -
"USER-EFF"_Packages_details.html#USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, -
"USER-FEP"_Packages_details.html#USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, -
"USER-H5MD"_Packages_details.html#USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext
"USER-INTEL"_Packages_details.html#USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
"USER-LB"_Packages_details.html#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, -
"USER-MANIFOLD"_Packages_details.html#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
"USER-MEAMC"_Packages_details.html#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, -
"USER-MESO"_Packages_details.html#USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, -
"USER-MGPT"_Packages_details.html#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -
"USER-MISC"_Packages_details.html#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
"USER-MOFFF"_Packages_details.html#USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, -
"USER-MOLFILE"_Packages_details.html#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
"USER-NETCDF"_Packages_details.html#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
"USER-OMP"_Packages_details.html#USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
"USER-PHONON"_Packages_details.html#USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, -
"USER-QMMM"_Packages_details.html#USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
"USER-QTB"_Packages_details.html#USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -
"USER-QUIP"_Packages_details.html#USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
"USER-REAXC"_Packages_details.html#USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, -
"USER-SMD"_Packages_details.html#USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
"USER-SMTBQ"_Packages_details.html#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
"USER-SPH"_Packages_details.html#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
"USER-TALLY"_Packages_details.html#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
"USER-UEF"_Packages_details.html#USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, -
"USER-VTK"_Packages_details.html#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)
"USER-ATC"_Packages_details.html#PKG-USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
"USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
"USER-CGDNA"_Packages_details.html#PKG-USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
"USER-CGSDK"_Packages_details.html#PKG-USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
"USER-COLVARS"_Packages_details.html#PKG-USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
"USER-DIFFRACTION"_Packages_details.html#PKG-USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, -
"USER-DPD"_Packages_details.html#PKG-USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, -
"USER-DRUDE"_Packages_details.html#PKG-USER-DRUDE, Drude oscillators, "Howto drude"_Howto_drude.html, USER/drude, -
"USER-EFF"_Packages_details.html#PKG-USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, -
"USER-FEP"_Packages_details.html#PKG-USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, -
"USER-H5MD"_Packages_details.html#PKG-USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext
"USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
"USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, -
"USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, -
"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, -
"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -
"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
"USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, -
"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
"USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
"USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, -
"USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
"USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -
"USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
"USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, -
"USER-SMD"_Packages_details.html#PKG-USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
"USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
"USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
"USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
"USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, -
"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)

8
doc/src/angle_cosine_shift.txt
View File

@ -40,10 +40,10 @@ 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"_Build_package.html doc page kages"_Speed_packages.html doc page.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if

2
doc/src/fix_deform.txt
View File

@ -94,7 +94,7 @@ nvt/sllod"_fix_nvt_sllod.html and "compute
temp/deform"_compute_temp_deform.html commands for more details. Note
that simulation of a continuously extended system (extensional flow)
can be modeled using the "USER-UEF
package"_Packages_details.html#USER-UEF and its "fix
package"_Packages_details.html#PKG-USER-UEF and its "fix
commands"_fix_nh_uef.html.
For the {x}, {y}, {z} parameters, the associated dimension cannot be

2
doc/src/fix_nve_dot.txt
View File

@ -44,7 +44,7 @@ A technical report with more information on this integrator can be found
[Restrictions:]
These pair styles can only be used if LAMMPS was built with the
"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package.
"USER-CGDNA"_Package_details.html#PKG-USER-CGDNA package and the MOLECULE and ASPHERE package.
See the "Build package"_Build_package.html doc page for more info.
[Related commands:]

2
doc/src/fix_nve_dotc_langevin.txt
View File

@ -122,7 +122,7 @@ A technical report with more information on this integrator can be found
[Restrictions:]
These pair styles can only be used if LAMMPS was built with the
"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package.
"USER-CGDNA"_Package_details.html#USER-CGDNA package and the MOLECULE and ASPHERE package.
See the "Build package"_Build_package.html doc page for more info.
[Related commands:]