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changes to Packages and Speed doc files

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Steven J. Plimpton 2018-07-30 12:31:12 -06:00
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commit d9c328932f
166 changed files with 1618 additions and 1637 deletions
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6
doc/src/Errors_messages.txt
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@ -21,9 +21,9 @@ means that line #78 in the file src/velocity.cpp generated the error.
Looking in the source code may help you figure out what went wrong.
Note that error messages from "user-contributed
packages"_Section_package.html#table_user are not listed here. If
such an error occurs and is not self-explanatory, you'll need to look
in the source code or contact the author of the package.
packages"_Packages_user.html are not listed here. If such an error
occurs and is not self-explanatory, you'll need to look in the source
code or contact the author of the package.
Doc page with "WARNING messages"_Errors_warnings.html

6
doc/src/Errors_warnings.txt
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@ -21,9 +21,9 @@ means that line #187 in the file src/domain.cpp generated the error.
Looking in the source code may help you figure out what went wrong.
Note that warning messages from "user-contributed
packages"_Section_start.html#table_user are not listed here. If such
a warning occurs and is not self-explanatory, you'll need to look in
the source code or contact the author of the package.
packages"_Packages_user.html are not listed here. If such a warning
occurs and is not self-explanatory, you'll need to look in the source
code or contact the author of the package.
Doc page with "ERROR messages"_Errors_messages.html

2
doc/src/Examples.txt
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@ -143,5 +143,5 @@ The USER directory has a large number of sub-directories which
correspond by name to a USER package. They contain scripts that
illustrate how to use the command(s) provided in that package. Many
of the sub-directories have their own README files which give further
instructions. See the "Section 4"_Section_packages.html doc
instructions. See the "Packages_details"_Packages_details.html doc
page for more info on specific USER packages.

29
doc/src/Manual.txt
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@ -111,11 +111,10 @@ it gives quick access to documentation for all LAMMPS commands.
Section_intro
Section_start
Section_commands
Section_packages
Section_accelerate
Packages
Speed
Section_howto
Examples
Section_perf
Tools
Modify
Python
@ -167,19 +166,8 @@ END_RST -->
3.3 "Input script structure"_cmd_3 :b
3.4 "Commands listed by category"_cmd_4 :b
3.5 "Commands listed alphabetically"_cmd_5 :ule,b
"Packages"_Section_packages.html :l
4.1 "Standard packages"_pkg_1 :ulb,b
4.2 "User packages"_pkg_2 :ule,b
"Accelerating LAMMPS performance"_Section_accelerate.html :l
5.1 "Measuring performance"_acc_1 :ulb,b
5.2 "Algorithms and code options to boost performace"_acc_2 :b
5.3 "Accelerator packages with optimized styles"_acc_3 :b
5.3.1 "GPU package"_accelerate_gpu.html :b
5.3.2 "USER-INTEL package"_accelerate_intel.html :b
5.3.3 "KOKKOS package"_accelerate_kokkos.html :b
5.3.4 "USER-OMP package"_accelerate_omp.html :b
5.3.5 "OPT package"_accelerate_opt.html :b
5.4 "Comparison of various accelerator packages"_acc_4 :ule,b
"Optional packages"_Packages.html :l
"Accelerate performance"_Speed.html :l
"How-to discussions"_Section_howto.html :l
6.1 "Restarting a simulation"_howto_1 :ulb,b
6.2 "2d simulations"_howto_2 :b
@ -209,7 +197,6 @@ END_RST -->
6.26 "Adiabatic core/shell model"_howto_26 :b
6.27 "Drude induced dipoles"_howto_27 :ule,b
"Example scripts"_Examples.html :l
"Performance & scalability"_Section_perf.html :l
"Auxiliary tools"_Tools.html :l
"Modify & extend LAMMPS"_Modify.html :l
"Use Python with LAMMPS"_Python.html :l
@ -240,14 +227,6 @@ END_RST -->
:link(cmd_4,Section_commands.html#cmd_4)
:link(cmd_5,Section_commands.html#cmd_5)
:link(pkg_1,Section_packages.html#pkg_1)
:link(pkg_2,Section_packages.html#pkg_2)
:link(acc_1,Section_accelerate.html#acc_1)
:link(acc_2,Section_accelerate.html#acc_2)
:link(acc_3,Section_accelerate.html#acc_3)
:link(acc_4,Section_accelerate.html#acc_4)
:link(howto_1,Section_howto.html#howto_1)
:link(howto_2,Section_howto.html#howto_2)
:link(howto_3,Section_howto.html#howto_3)

39
doc/src/Packages.txt Normal file
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@ -0,0 +1,39 @@
"Previous Section"_Section_commands.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Speed.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Optional packages :h2
This section gives an overview of the optional packages that extend
LAMMPS functionality. Packages are groups of files that enable a
specific set of features. For example, force fields for molecular
systems or rigid-body constraint are in packages. You can see the
list of all packages and "make" commands to manage them by typing
"make package" from within the src directory of the LAMMPS
distribution. "Section 2.3"_Section_start.html#start_3 gives general
info on how to install and un-install packages as part of the LAMMPS
build process.
<!-- RST
.. toctree::
Packages_standard
Packages_user
Packages_details
END_RST -->
<!-- HTML_ONLY -->
"Standard packages"_Packages_standard.html
"User packages"_Packages_user.html
"Details on each package"_Packages_details.html :ul
<!-- END_HTML_ONLY -->

330
doc/src/Section_packages.txt → doc/src/Packages_details.txt
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@ -1,6 +1,5 @@
"Previous Section"_Section_commands.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_accelerate.html :c
"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@ -8,152 +7,89 @@ Section"_Section_accelerate.html :c
:line
4. Packages :h2
Package details :h3
This section gives an overview of the optional packages that extend
LAMMPS functionality with instructions on how to build LAMMPS with
each of them. Packages are groups of files that enable a specific set
of features. For example, force fields for molecular systems or
granular systems are in packages. You can see the list of all
packages and "make" commands to manage them by typing "make package"
from within the src directory of the LAMMPS distribution. "Section
2.3"_Section_start.html#start_3 gives general info on how to install
and un-install packages as part of the LAMMPS build process.
There are two kinds of packages in LAMMPS, standard and user packages:
"Table of standard packages"_#table_standard
"Table of user packages"_#table_user :ul
Either of these kinds of packages may work as is, may require some
additional code compiled located in the lib folder, or may require
an external library to be downloaded, compiled, installed, and LAMMPS
configured to know about its location and additional compiler flags.
You can often do the build of the internal or external libraries
in one step by typing "make lib-name args='...'" from the src dir,
with appropriate arguments included in args='...'. If you just type
"make lib-name" you should see a help message about supported flags
and some examples. For more details about this, please study the
tables below and the sections about the individual packages.
Standard packages are supported by the LAMMPS developers and are
written in a syntax and style consistent with the rest of LAMMPS.
This means the developers will answer questions about them, debug and
fix them if necessary, and keep them compatible with future changes to
LAMMPS.
User packages have been contributed by users, and begin with the
"user" prefix. If they are a single command (single file), they are
typically in the user-misc package. User packages don't necessarily
meet the requirements of the standard packages. This means the
developers will try to keep things working and usually can answer
technical questions about compiling the package. If you have problems
using a feature provided in a user package, you may need to contact
the contributor directly to get help. Information on how to submit
additions you make to LAMMPS as single files or as a standard or user
package are given in the "Modify contribute"_Modify.html doc page.
Following the next two tables is a sub-section for each package. It
lists authors (if applicable) and summarizes the package contents. It
has specific instructions on how to install the package, including (if
necessary) downloading or building any extra library it requires. It
also gives links to documentation, example scripts, and
pictures/movies (if available) that illustrate use of the package.
Here is a brief description of all the standard and user packages in
LAMMPS. It lists authors (if applicable) and summarizes the package
contents. It has specific instructions on how to install the package,
including, if necessary, info on how to download or build any extra
library it requires. It also gives links to documentation, example
scripts, and pictures/movies (if available) that illustrate use of the
package.
NOTE: To see the complete list of commands a package adds to LAMMPS,
just look at the files in its src directory, e.g. "ls src/GRANULAR".
Files with names that start with fix, compute, atom, pair, bond,
angle, etc correspond to commands with the same style names.
you can examine the files in its src directory, e.g. "ls
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.
In these two tables, the "Example" column is a sub-directory in the
examples directory of the distribution which has an input script that
uses the package. E.g. "peptide" refers to the examples/peptide
directory; USER/atc refers to the examples/USER/atc directory. The
"Library" column indicates whether an extra library is needed to build
and use the package:
"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"_#REPLICA,
"RIGID"_#RIGID,
"SHOCK"_#SHOCK,
"SNAP"_#SNAP,
"SRD"_#SRD,
"VORONOI"_#VORONOI :tb(c=6,ea=c)
dash = no library
sys = system library: you likely have it on your machine
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
:line
:line
[Standard packages] :link(table_standard),p
Package, Description, Doc page, Example, Library
"ASPHERE"_#ASPHERE, aspherical particle models, "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, "atom_style colloid"_atom_style.html, colloid, -
"COMPRESS"_#COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys
"CORESHELL"_#CORESHELL, adiabatic core/shell model, "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, "Section 5.3.1"_accelerate_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int
"GRANULAR"_#GRANULAR, granular systems, "Section 6.6.6"_Section_howto.html#howto_6, pour, -
"KIM"_#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
"KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
"KSPACE"_#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
"LATTE"_#LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
"MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
"MC"_#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
"MEAM"_#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
"MISC"_#MISC, miscellanous single-file commands, -, -, -
"MOLECULE"_#MOLECULE, molecular system force fields, "Section 6.6.3"_Section_howto.html#howto_3, peptide, -
"MPIIO"_#MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, -
"MSCG"_#MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext
"OPT"_#OPT, optimized pair styles, "Section 5.3.5"_accelerate_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
"PERI"_#PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, -
"POEMS"_#POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
"PYTHON"_#PYTHON, embed Python code in an input script, "python"_python.html, python, sys
"QEQ"_#QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, -
"REAX"_#REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
"REPLICA"_#REPLICA, multi-replica methods, "Section 6.6.5"_Section_howto.html#howto_5, tad, -
"RIGID"_#RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, -
"SHOCK"_#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
"SNAP"_#SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, -
"SPIN"_#SPIN, magnetic atomic spin dynamics, "Section 6.6.28"_Section_howto.html#howto_28, SPIN, -
"SRD"_#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
"VORONOI"_#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)
[USER packages] :link(table_user),p
Package, Description, Doc page, Example, Library
"USER-ATC"_#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
"USER-AWPMD"_#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
"USER-BOCS"_#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
"USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
"USER-COLVARS"_#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
"USER-DIFFRACTION"_#USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, -
"USER-DPD"_#USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, -
"USER-DRUDE"_#USER-DRUDE, Drude oscillators, "tutorial"_tutorial_drude.html, USER/drude, -
"USER-EFF"_#USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, -
"USER-FEP"_#USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, -
"USER-H5MD"_#USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext
"USER-INTEL"_#USER-INTEL, optimized Intel CPU and KNL styles,"Section 5.3.2"_accelerate_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
"USER-LB"_#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, -
"USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
"USER-MEAMC"_#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, -
"USER-MESO"_#USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, -
"USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -
"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
"USER-MOFFF"_#USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, -
"USER-MOLFILE"_#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
"USER-NETCDF"_#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
"USER-OMP"_#USER-OMP, OpenMP-enabled styles,"Section 5.3.4"_accelerate_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
"USER-PHONON"_#USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, -
"USER-QMMM"_#USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
"USER-QTB"_#USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -
"USER-QUIP"_#USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
"USER-REAXC"_#USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, -
"USER-SMD"_#USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
"USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
"USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
"USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
"USER-UEF"_#USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, -
"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)
"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)
:line
:line
@ -380,14 +316,14 @@ GPU package :link(GPU),h4
[Contents:]
Dozens of pair styles and a version of the PPPM long-range Coulombic
solver optimized for GPUs. All such styles have a "gpu" as a
suffix in their style name. The GPU code can be compiled with either
CUDA or OpenCL, however the OpenCL variants are no longer actively
maintained and only the CUDA versions are regularly tested.
"Section 5.3.1"_accelerate_gpu.html 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
solver optimized for GPUs. All such styles have a "gpu" as a suffix
in their style name. The GPU code can be compiled with either CUDA or
OpenCL, however the OpenCL variants are no longer actively maintained
and only the CUDA versions are regularly tested. The "Speed
gpu"_Speed_gpu.html doc page gives details of what hardware and GPU
software is required on your system, and details on how to build and
use this package. Its styles can be invoked at run time via the "-sf
gpu" or "-suffix gpu" "command-line
switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS
package, which has GPU-enabled styles.
@ -453,8 +389,8 @@ GPU library.
src/GPU: filenames -> commands
src/GPU/README
lib/gpu/README
"Section 5.3"_Section_accelerate.html#acc_3
"Section 5.3.1"_accelerate_gpu.html
"Speed packages"_Speed_packages.html
"Speed gpu"_Speed_gpu.html.html
"Section 2.6 -sf gpu"_Section_start.html#start_6
"Section 2.6 -pk gpu"_Section_start.html#start_6
"package gpu"_package.html
@ -579,10 +515,10 @@ Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute
styles adapted to compile using the Kokkos library which can convert
them to OpenMP or CUDA code so that they run efficiently on multicore
CPUs, KNLs, or GPUs. All the styles have a "kk" as a suffix in their
style name. "Section 5.3.3"_accelerate_kokkos.html 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
style name. The "Speed kokkos"_Speed_kokkos.html doc page gives
details of what hardware and software is required on your system, and
how to build and use this package. Its styles can be invoked at run
time via the "-sf kk" or "-suffix kk" "command-line
switches"_Section_start.html#start_6. Also see the "GPU"_#GPU,
"OPT"_#OPT, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP
packages, which have styles optimized for CPUs, KNLs, and GPUs.
@ -649,8 +585,8 @@ make machine :pre
src/KOKKOS: filenames -> commands
src/KOKKOS/README
lib/kokkos/README
"Section 5.3"_Section_accelerate.html#acc_3
"Section 5.3.3"_accelerate_kokkos.html
"Speed packages"_Speed_packages.html
"Speed kokkos"_Speed_kokkos.html
"Section 2.6 -k on ..."_Section_start.html#start_6
"Section 2.6 -sf kk"_Section_start.html#start_6
"Section 2.6 -pk kokkos"_Section_start.html#start_6
@ -1048,9 +984,9 @@ OPT package :link(OPT),h4
A handful of pair styles which are optimized for improved CPU
performance on single or multiple cores. These include EAM, LJ,
CHARMM, and Morse potentials. The styles have an "opt" suffix in
their style name. "Section 5.3.5"_accelerate_opt.html 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
their style name. The "Speed opt"_Speed_opt.html doc page gives
details of how to build and use this package. Its styles can be
invoked at run time via the "-sf opt" or "-suffix opt" "command-line
switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS,
"USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which
have styles optimized for CPU performance.
@ -1076,8 +1012,8 @@ CCFLAGS: add -restrict for Intel compilers :ul
[Supporting info:]
src/OPT: filenames -> commands
"Section 5.3"_Section_accelerate.html#acc_3
"Section 5.3.5"_accelerate_opt.html
"Speed packages"_Speed_packages.html
"Speed opt"_Speed_opt.html
"Section 2.6 -sf opt"_Section_start.html#start_6
Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (t)
"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@ -1178,10 +1114,10 @@ PYTHON package :link(PYTHON),h4
A "python"_python.html command which allow you to execute Python code
from a LAMMPS input script. The code can be in a separate file or
embedded in the input script itself. See the "Python
call"_Python_call.html doc page for an overview of using Python from
LAMMPS in this manner and the "Python"_Python.html doc page for other
ways to use LAMMPS and Python together.
embedded in the input script itself. See "Section
11.2"_Section_python.html#py_2 for an overview of using Python from
LAMMPS in this manner and the entire section for other ways to use
LAMMPS and Python together.
[Install or un-install:]
@ -1202,7 +1138,7 @@ to Makefile.lammps) if the LAMMPS build fails.
[Supporting info:]
src/PYTHON: filenames -> commands
"Python call"_Python_call.html
"Section 11"_Section_python.html
lib/python/README
examples/python :ul
@ -1415,38 +1351,6 @@ examples/snap :ul
:line
SPIN package :link(SPIN),h4
[Contents:]
Model atomic magnetic spins classically, coupled to atoms moving in
the usual manner via MD. Various pair, fix, and compute styles.
[Author:] Julian Tranchida (Sandia).
[Install or un-install:]
make yes-spin
make machine :pre
make no-spin
make machine :pre
[Supporting info:]
src/SPIN: filenames -> commands
"Section 6.28"_Section_howto.html#howto_28
"pair_style spin/dmi"_pair_spin_dmi.html
"pair_style spin/exchange"_pair_spin_exchange.html
"pair_style spin/magelec"_pair_spin_magelec.html
"pair_style spin/neel"_pair_spin_neel.html
"fix nve/spin"_fix_nve_spin.html
"fix precession/spin"_fix_precession_spin.html
"compute spin"_compute_spin.html
examples/SPIN :ul
:line
SRD package :link(SRD),h4
[Contents:]
@ -2065,8 +1969,8 @@ USER-INTEL package :link(USER-INTEL),h4
Dozens of pair, fix, bond, angle, dihedral, improper, and kspace
styles which are optimized for Intel CPUs and KNLs (Knights Landing).
All of them have an "intel" in their style name. "Section
5.3.2"_accelerate_intel.html gives details of what hardware and
All of them have an "intel" in their style name. The "Speed
intel"_Speed_intel.html doc page gives details of what hardware and
compilers are required on your system, and how to build and use this
package. Its styles can be invoked at run time via the "-sf intel" or
"-suffix intel" "command-line switches"_Section_start.html#start_6.
@ -2116,7 +2020,7 @@ hardware target, to produce a separate executable.
You should also typically install the USER-OMP package, as it can be
used in tandem with the USER-INTEL package to good effect, as
explained in "Section 5.3.2"_accelerate_intel.html.
explained on the "Speed intel"_Speed_intel.html doc page.
make yes-user-intel yes-user-omp
make machine :pre
@ -2128,8 +2032,8 @@ make machine :pre
src/USER-INTEL: filenames -> commands
src/USER-INTEL/README
"Section 5.3"_Section_accelerate.html#acc_3
"Section 5.3.2"_accelerate_gpu.html
"Speed packages"_Speed_packages.html
"Speed intel"_Speed_intel.html
"Section 2.6 -sf intel"_Section_start.html#start_6
"Section 2.6 -pk intel"_Section_start.html#start_6
"package intel"_package.html
@ -2475,10 +2379,10 @@ USER-OMP package :link(USER-OMP),h4
Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and
kspace styles which are altered to enable threading on many-core CPUs
via OpenMP directives. All of them have an "omp" in their style name.
"Section 5.3.4"_accelerate_omp.html gives details of what hardware and
compilers are required on your system, and how to build and use this
package. Its styles can be invoked at run time via the "-sf omp" or
"-suffix omp" "command-line switches"_Section_start.html#start_6.
The "Speed omp"_Speed_omp.html doc page gives details of what hardware
and compilers are required on your system, and how to build and use
this package. Its styles can be invoked at run time via the "-sf omp"
or "-suffix omp" "command-line switches"_Section_start.html#start_6.
Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and
"USER-INTEL"_#USER-INTEL packages, which have styles optimized for
CPUs.
@ -2513,8 +2417,8 @@ LINKFLAGS: add -fopenmp :ul
src/USER-OMP: filenames -> commands
src/USER-OMP/README
"Section 5.3"_Section_accelerate.html#acc_3
"Section 5.3.4"_accelerate_omp.html
"Speed packages"_Speed_packages.html
"Speed omp"_Speed_omp.html
"Section 2.6 -sf omp"_Section_start.html#start_6
"Section 2.6 -pk omp"_Section_start.html#start_6
"package omp"_package.html

65
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@ -0,0 +1,65 @@
"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Standard packages :h3
This is the list of standard packages in LAMMPS. The link for each
package name gives more details.
Standard packages are supported by the LAMMPS developers and are
written in a syntax and style consistent with the rest of LAMMPS.
This means the developers will answer questions about them, debug and
fix them if necessary, and keep them compatible with future changes to
LAMMPS.
The "Example" column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. "peptide" refers to the examples/peptide directory; USER/atc
refers to the examples/USER/atc directory. The "Library" column
indicates whether an extra library is needed to build and use the
package:
dash = no library
sys = system library: you likely have it on your machine
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, "Section 6.6.14"_Section_howto.html#howto_14, ellipse, -
"BODY"_Packages_details.html#BODY, body-style particles, "body"_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, "Section 6.6.25"_Section_howto.html#howto_25, 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, "Section 6.6.6"_Section_howto.html#howto_6, 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, "Section 6.6.3"_Section_howto.html#howto_3, 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#REPLICA, multi-replica methods, "Section 6.6.5"_Section_howto.html#howto_5, 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, -
"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)

74
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@ -0,0 +1,74 @@
"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
User packages :h3
This is a list of user packages in LAMMPS. The link for each package
name gives more details.
User packages have been contributed by users, and begin with the
"user" prefix. If a contribution is a single command (single file),
it is typically in the user-misc package. User packages don't
necessarily meet the requirements of the "standard
packages"_Packages_standard.html. This means the developers will try
to keep things working and usually can answer technical questions
about compiling the package. If you have problems using a specific
feature provided in a user package, you may need to contact the
contributor directly to get help. Information on how to submit
additions you make to LAMMPS as single files or as a standard or user
package is explained on the "Modify contribute"_Modify_contribute.html
doc page.
The "Example" column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. "peptide" refers to the examples/peptide directory; USER/atc
refers to the examples/USER/atc directory. The "Library" column
indicates whether an extra library is needed to build and use the
package:
dash = no library
sys = system library: you likely have it on your machine
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, "tutorial"_tutorial_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)

391
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@ -1,391 +0,0 @@
"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_howto.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
5. Accelerating LAMMPS performance :h2
This section describes various methods for improving LAMMPS
performance for different classes of problems running on different
kinds of machines.
There are two thrusts to the discussion that follows. The
first is using code options that implement alternate algorithms
that can speed-up a simulation. The second is to use one
of the several accelerator packages provided with LAMMPS that
contain code optimized for certain kinds of hardware, including
multi-core CPUs, GPUs, and Intel Xeon Phi coprocessors.
5.1 "Measuring performance"_#acc_1 :ulb,l
5.2 "Algorithms and code options to boost performace"_#acc_2 :l
5.3 "Accelerator packages with optimized styles"_#acc_3 :l
5.3.1 "GPU package"_accelerate_gpu.html :l
5.3.2 "USER-INTEL package"_accelerate_intel.html :l
5.3.3 "KOKKOS package"_accelerate_kokkos.html :l
5.3.4 "USER-OMP package"_accelerate_omp.html :l
5.3.5 "OPT package"_accelerate_opt.html :l
5.4 "Comparison of various accelerator packages"_#acc_4 :l
:ule
The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS
web site gives performance results for the various accelerator
packages discussed in Section 5.2, for several of the standard LAMMPS
benchmark problems, as a function of problem size and number of
compute nodes, on different hardware platforms.
:line
:line
5.1 Measuring performance :h3,link(acc_1)
Before trying to make your simulation run faster, you should
understand how it currently performs and where the bottlenecks are.
The best way to do this is run the your system (actual number of
atoms) for a modest number of timesteps (say 100 steps) on several
different processor counts, including a single processor if possible.
Do this for an equilibrium version of your system, so that the
100-step timings are representative of a much longer run. There is
typically no need to run for 1000s of timesteps to get accurate
timings; you can simply extrapolate from short runs.
For the set of runs, look at the timing data printed to the screen and
log file at the end of each LAMMPS run. "This
section"_Section_start.html#start_7 of the manual has an overview.
Running on one (or a few processors) should give a good estimate of
the serial performance and what portions of the timestep are taking
the most time. Running the same problem on a few different processor
counts should give an estimate of parallel scalability. I.e. if the
simulation runs 16x faster on 16 processors, its 100% parallel
efficient; if it runs 8x faster on 16 processors, it's 50% efficient.
The most important data to look at in the timing info is the timing
breakdown and relative percentages. For example, trying different
options for speeding up the long-range solvers will have little impact
if they only consume 10% of the run time. If the pairwise time is
dominating, you may want to look at GPU or OMP versions of the pair
style, as discussed below. Comparing how the percentages change as
you increase the processor count gives you a sense of how different
operations within the timestep are scaling. Note that if you are
running with a Kspace solver, there is additional output on the
breakdown of the Kspace time. For PPPM, this includes the fraction
spent on FFTs, which can be communication intensive.
Another important detail in the timing info are the histograms of
atoms counts and neighbor counts. If these vary widely across
processors, you have a load-imbalance issue. This often results in
inaccurate relative timing data, because processors have to wait when
communication occurs for other processors to catch up. Thus the
reported times for "Communication" or "Other" may be higher than they
really are, due to load-imbalance. If this is an issue, you can
uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile
LAMMPS, to obtain synchronized timings.
:line
5.2 General strategies :h3,link(acc_2)
NOTE: this section 5.2 is still a work in progress
Here is a list of general ideas for improving simulation performance.
Most of them are only applicable to certain models and certain
bottlenecks in the current performance, so let the timing data you
generate be your guide. It is hard, if not impossible, to predict how
much difference these options will make, since it is a function of
problem size, number of processors used, and your machine. There is
no substitute for identifying performance bottlenecks, and trying out
various options.
rRESPA
2-FFT PPPM
Staggered PPPM
single vs double PPPM
partial charge PPPM
verlet/split run style
processor command for proc layout and numa layout
load-balancing: balance and fix balance :ul
2-FFT PPPM, also called {analytic differentiation} or {ad} PPPM, uses
2 FFTs instead of the 4 FFTs used by the default {ik differentiation}
PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to
achieve the same accuracy as 4-FFT PPPM. For problems where the FFT
cost is the performance bottleneck (typically large problems running
on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM.
Staggered PPPM performs calculations using two different meshes, one
shifted slightly with respect to the other. This can reduce force
aliasing errors and increase the accuracy of the method, but also
doubles the amount of work required. For high relative accuracy, using
staggered PPPM allows one to half the mesh size in each dimension as
compared to regular PPPM, which can give around a 4x speedup in the
kspace time. However, for low relative accuracy, using staggered PPPM
gives little benefit and can be up to 2x slower in the kspace
time. For example, the rhodopsin benchmark was run on a single
processor, and results for kspace time vs. relative accuracy for the
different methods are shown in the figure below. For this system,
staggered PPPM (using ik differentiation) becomes useful when using a
relative accuracy of slightly greater than 1e-5 and above.
:c,image(JPG/rhodo_staggered.jpg)
NOTE: Using staggered PPPM may not give the same increase in accuracy
of energy and pressure as it does in forces, so some caution must be
used if energy and/or pressure are quantities of interest, such as
when using a barostat.
:line
5.3 Packages with optimized styles :h3,link(acc_3)
Accelerated versions of various "pair_style"_pair_style.html,
"fixes"_fix.html, "computes"_compute.html, and other commands have
been added to LAMMPS, which will typically run faster than the
standard non-accelerated versions. Some require appropriate hardware
to be present on your system, e.g. GPUs or Intel Xeon Phi
coprocessors.
All of these commands are in packages provided with LAMMPS. An
overview of packages is give in "Section
packages"_Section_packages.html.
These are the accelerator packages
currently in LAMMPS, either as standard or user packages:
"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:
Many-core CPUs : "USER-INTEL"_accelerate_intel.html, "KOKKOS"_accelerate_kokkos.html, "USER-OMP"_accelerate_omp.html, "OPT"_accelerate_opt.html packages
NVIDIA GPUs : "GPU"_accelerate_gpu.html, "KOKKOS"_accelerate_kokkos.html packages
Intel Phi : "USER-INTEL"_accelerate_intel.html, "KOKKOS"_accelerate_kokkos.html packages :tb(s=:)
Which package is fastest for your hardware may depend on the size
problem you are running and what commands (accelerated and
non-accelerated) are invoked by your input script. While these doc
pages include performance guidelines, there is no substitute for
trying out the different packages appropriate to your hardware.
Any accelerated style has the same name as the corresponding standard
style, except that a suffix is appended. Otherwise, the syntax for
the command that uses the style is identical, their functionality is
the same, and the numerical results it produces should also be the
same, except for precision and round-off effects.
For example, all of these styles are accelerated variants of the
Lennard-Jones "pair_style lj/cut"_pair_lj.html:
"pair_style lj/cut/gpu"_pair_lj.html
"pair_style lj/cut/intel"_pair_lj.html
"pair_style lj/cut/kk"_pair_lj.html
"pair_style lj/cut/omp"_pair_lj.html
"pair_style lj/cut/opt"_pair_lj.html :ul
To see what accelerate styles are currently available, see
"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.
To use an accelerator package in LAMMPS, and one or more of the styles
it provides, follow these general steps. Details vary from package to
package and are explained in the individual accelerator doc pages,
listed above:
build the accelerator library |
only for GPU package |
install the accelerator package |
make yes-opt, make yes-user-intel, etc |
add compile/link flags to Makefile.machine in src/MAKE |
only for USER-INTEL, KOKKOS, USER-OMP, OPT packages |
re-build LAMMPS |
make machine |
prepare and test a regular LAMMPS simulation |
lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script |
enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_6, |
only needed for KOKKOS package |
set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_6 or "package"_package.html command, |
only if defaults need to be changed |
use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
:tb(c=2,s=|)
Note that the first 4 steps can be done as a single command with
suitable make command invocations. This is discussed in "Section
4"_Section_packages.html of the manual, and its use is
illustrated in the individual accelerator sections. Typically these
steps only need to be done once, to create an executable that uses one
or more accelerator packages.
The last 4 steps can all be done from the command-line when LAMMPS is
launched, without changing your input script, as illustrated in the
individual accelerator sections. Or you can add
"package"_package.html and "suffix"_suffix.html commands to your input
script.
NOTE: With a few exceptions, you can build a single LAMMPS executable
with all its accelerator packages installed. Note however that the
USER-INTEL and KOKKOS packages require you to choose one of their
hardware options when building for a specific platform. I.e. CPU or
Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi
option for the KOKKOS package.
These are the exceptions. You cannot build a single executable with:
both the USER-INTEL Phi and KOKKOS Phi options
the USER-INTEL Phi or Kokkos Phi option, and the GPU package :ul
See the examples/accelerate/README and make.list files for sample
Make.py commands that build LAMMPS with any or all of the accelerator
packages. As an example, here is a command that builds with all the
GPU related packages installed (GPU, KOKKOS with Cuda), including
settings to build the needed auxiliary GPU libraries for Kepler GPUs:
Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi \
-gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi :pre
The examples/accelerate directory also has input scripts that can be
used with all of the accelerator packages. See its README file for
details.
Likewise, the bench directory has FERMI and KEPLER and PHI
sub-directories with Make.py commands and input scripts for using all
the accelerator packages on various machines. See the README files in
those dirs.
As mentioned above, the "Benchmark
page"_http://lammps.sandia.gov/bench.html of the LAMMPS web site gives
performance results for the various accelerator packages for several
of the standard LAMMPS benchmark problems, as a function of problem
size and number of compute nodes, on different hardware platforms.
Here is a brief summary of what the various packages provide. Details
are in the individual accelerator sections.
Styles with a "gpu" suffix are part of the GPU package, and can be run
on NVIDIA GPUs. The speed-up on a GPU depends on a variety of
factors, discussed in the accelerator sections. :ulb,l
Styles with an "intel" suffix are part of the USER-INTEL
package. These styles support vectorized single and mixed precision
calculations, in addition to full double precision. In extreme cases,
this can provide speedups over 3.5x on CPUs. The package also
supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM)
coprocessors. This can result in additional speedup over 2x depending
on the hardware configuration. :l
Styles with a "kk" suffix are part of the KOKKOS package, and can be
run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel
Xeon Phi in "native" mode. The speed-up depends on a variety of
factors, as discussed on the KOKKOS accelerator page. :l
Styles with an "omp" suffix are part of the USER-OMP package and allow
a pair-style to be run in multi-threaded mode using OpenMP. This can
be useful on nodes with high-core counts when using less MPI processes
than cores is advantageous, e.g. when running with PPPM so that FFTs
are run on fewer MPI processors or when the many MPI tasks would
overload the available bandwidth for communication. :l
Styles with an "opt" suffix are part of the OPT package and typically
speed-up the pairwise calculations of your simulation by 5-25% on a
CPU. :l
:ule
The individual accelerator package doc pages explain:
what hardware and software the accelerated package requires
how to build LAMMPS with the accelerated package
how to run with the accelerated package either via command-line switches or modifying the input script
speed-ups to expect
guidelines for best performance
restrictions :ul
:line
5.4 Comparison of various accelerator packages :h3,link(acc_4)
NOTE: this section still needs to be re-worked with additional KOKKOS
and USER-INTEL information.
The next section compares and contrasts the various accelerator
options, since there are multiple ways to perform OpenMP threading,
run on GPUs, and run on Intel Xeon Phi coprocessors.
All 3 of these packages accelerate a LAMMPS calculation using NVIDIA
hardware, but they do it in different ways.
As a consequence, for a particular simulation on specific hardware,
one package may be faster than the other. We give guidelines below,
but the best way to determine which package is faster for your input
script is to try both of them on your machine. See the benchmarking
section below for examples where this has been done.
[Guidelines for using each package optimally:]
The GPU package allows you to assign multiple CPUs (cores) to a single
GPU (a common configuration for "hybrid" nodes that contain multicore
CPU(s) and GPU(s)) and works effectively in this mode. :ulb,l
The GPU package moves per-atom data (coordinates, forces)
back-and-forth between the CPU and GPU every timestep. The
KOKKOS/CUDA package only does this on timesteps when a CPU calculation
is required (e.g. to invoke a fix or compute that is non-GPU-ized).
Hence, if you can formulate your input script to only use GPU-ized
fixes and computes, and avoid doing I/O too often (thermo output, dump
file snapshots, restart files), then the data transfer cost of the
KOKKOS/CUDA package can be very low, causing it to run faster than the
GPU package. :l
The GPU package is often faster than the KOKKOS/CUDA package, if the
number of atoms per GPU is smaller. The crossover point, in terms of
atoms/GPU at which the KOKKOS/CUDA package becomes faster depends
strongly on the pair style. For example, for a simple Lennard Jones
system the crossover (in single precision) is often about 50K-100K
atoms per GPU. When performing double precision calculations the
crossover point can be significantly smaller. :l
Both packages compute bonded interactions (bonds, angles, etc) on the
CPU. If the GPU package is running with several MPI processes
assigned to one GPU, the cost of computing the bonded interactions is
spread across more CPUs and hence the GPU package can run faster. :l
When using the GPU package with multiple CPUs assigned to one GPU, its
performance depends to some extent on high bandwidth between the CPUs
and the GPU. Hence its performance is affected if full 16 PCIe lanes
are not available for each GPU. In HPC environments this can be the
case if S2050/70 servers are used, where two devices generally share
one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide
full 16 lanes to each of the PCIe 2.0 16x slots. :l
:ule
[Differences between the two packages:]
The GPU package accelerates only pair force, neighbor list, and PPPM
calculations. :ulb,l
The GPU package requires neighbor lists to be built on the CPU when using
exclusion lists, hybrid pair styles, or a triclinic simulation box. :l
:ule

44
doc/src/Section_commands.txt
View File

@ -1,4 +1,4 @@
"Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_packages.html :c
"Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Packages.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@ -554,8 +554,8 @@ Fix styles :h3
See the "fix"_fix.html command for one-line descriptions of each style
or click on the style itself for a full description. Some of the
styles have accelerated versions, which can be used if LAMMPS is built
with the "appropriate accelerated package"_Section_accelerate.html.
This is indicated by additional letters in parenthesis: g = GPU, i =
with the "appropriate accelerated package"_Speed_packages.html. This
is indicated by additional letters in parenthesis: g = GPU, i =
USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"adapt"_fix_adapt.html,
@ -775,9 +775,9 @@ See the "compute"_compute.html command for one-line descriptions of
each style or click on the style itself for a full description. Some
of the styles have accelerated versions, which can be used if LAMMPS
is built with the "appropriate accelerated
package"_Section_accelerate.html. This is indicated by additional
letters in parenthesis: g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
package"_Speed_packages.html. This is indicated by additional letters
in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
"aggregate/atom"_compute_cluster_atom.html,
"angle"_compute_angle.html,
@ -920,9 +920,9 @@ See the "pair_style"_pair_style.html command for an overview of pair
potentials. Click on the style itself for a full description. Many
of the styles have accelerated versions, which can be used if LAMMPS
is built with the "appropriate accelerated
package"_Section_accelerate.html. This is indicated by additional
letters in parenthesis: g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
package"_Speed_packages.html. This is indicated by additional letters
in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
"none"_pair_none.html,
"zero"_pair_zero.html,
@ -1142,9 +1142,9 @@ See the "bond_style"_bond_style.html command for an overview of bond
potentials. Click on the style itself for a full description. Some
of the styles have accelerated versions, which can be used if LAMMPS
is built with the "appropriate accelerated
package"_Section_accelerate.html. This is indicated by additional
letters in parenthesis: g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
package"_Speed_packages.html. This is indicated by additional letters
in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
"none"_bond_none.html,
"zero"_bond_zero.html,
@ -1176,9 +1176,9 @@ See the "angle_style"_angle_style.html command for an overview of
angle potentials. Click on the style itself for a full description.
Some of the styles have accelerated versions, which can be used if
LAMMPS is built with the "appropriate accelerated
package"_Section_accelerate.html. This is indicated by additional
letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o =
USER-OMP, t = OPT.
package"_Speed_packages.html. This is indicated by additional letters
in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
"none"_angle_none.html,
"zero"_angle_zero.html,
@ -1212,7 +1212,7 @@ See the "dihedral_style"_dihedral_style.html command for an overview
of dihedral potentials. Click on the style itself for a full
description. Some of the styles have accelerated versions, which can
be used if LAMMPS is built with the "appropriate accelerated
package"_Section_accelerate.html. This is indicated by additional
package"_Speed_packages.html. This is indicated by additional
letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o =
USER-OMP, t = OPT.
@ -1247,9 +1247,9 @@ See the "improper_style"_improper_style.html command for an overview
of improper potentials. Click on the style itself for a full
description. Some of the styles have accelerated versions, which can
be used if LAMMPS is built with the "appropriate accelerated
package"_Section_accelerate.html. This is indicated by additional
letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o =
USER-OMP, t = OPT.
package"_Speed_packages.html. This is indicated by additional letters
in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
"none"_improper_none.html,
"zero"_improper_zero.html,
@ -1276,9 +1276,9 @@ See the "kspace_style"_kspace_style.html command for an overview of
Kspace solvers. Click on the style itself for a full description.
Some of the styles have accelerated versions, which can be used if
LAMMPS is built with the "appropriate accelerated
package"_Section_accelerate.html. This is indicated by additional
letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o =
USER-OMP, t = OPT.
package"_Speed_packages.html. This is indicated by additional letters
in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
"ewald (o)"_kspace_style.html,
"ewald/disp"_kspace_style.html,

2
doc/src/Section_intro.txt
View File

@ -253,7 +253,7 @@ Specialized features :h4
LAMMPS can be built with optional packages which implement a variety
of additional capabilities. An overview of all the packages is "given
here"_Section_packages.html.
here"_Packages.html.
These are some LAMMPS capabilities which you may not think of as
typical classical molecular dynamics options:

100
doc/src/Section_start.txt
View File

@ -119,10 +119,11 @@ lower-case name of the package, e.g. replica or user-misc.
If you want to do one of the following:
use a LAMMPS command that requires an extra library (e.g. "dump image"_dump_image.html)
build with a package that requires an extra library
build with an accelerator package that requires special compiler/linker settings
run on a machine that has its own compilers, settings, or libraries :ul
use a LAMMPS command that requires an extra library (e.g. "dump
image"_dump_image.html) build with a package that requires an extra
library build with an accelerator package that requires special
compiler/linker settings run on a machine that has its own compilers,
settings, or libraries :ul
then building LAMMPS is more complicated. You may need to find where
extra libraries exist on your machine or install them if they don't.
@ -697,8 +698,8 @@ are always included, plus optional packages. Packages are groups of
files that enable a specific set of features. For example, force
fields for molecular systems or granular systems are in packages.
"Section 4"_Section_packages.html in the manual has details about all
the packages, which come in two flavors: [standard] and [user]
The "Packages"_Packages.html doc pages has details about all the
packages, which come in two flavors: [standard] and [user]
packages. It also has specific instructions for building LAMMPS with
any package which requires an extra library. General instructions are
below.
@ -828,45 +829,47 @@ options.
Packages that require extra libraries :h4,link(start_3_3)
A few of the standard and user packages require extra libraries. See
"Section 4"_Section_packages.html for two tables of packages which
indicate which ones require libraries. For each such package, the
Section 4 doc page gives details on how to build the extra library,
including how to download it if necessary. The basic ideas are
summarized here.
the "Packages"_Packages.html doc pages for two tables of packages
which indicate which ones require libraries. For each such package,
the Section 4 doc page gives details on how to build the extra
library, including how to download it if necessary. The basic ideas
are summarized here.
[System libraries:]
Packages in the tables "Section 4"_Section_packages.html with a "sys"
in the last column link to system libraries that typically already
exist on your machine. E.g. the python package links to a system
Python library. If your machine does not have the required library,
you will have to download and install it on your machine, in either
the system or user space.
Packages in the standard and user tables of the
"Packages"_Packages.html doc pages with a "sys" in the last column
link to system libraries that typically already exist on your machine.
E.g. the python package links to a system Python library. If your
machine does not have the required library, you will have to download
and install it on your machine, in either the system or user space.
[Internal libraries:]
Packages in the tables "Section 4"_Section_packages.html with an "int"
in the last column link to internal libraries whose source code is
included with LAMMPS, in the lib/name directory where name is the
package name. You must first build the library in that directory
before building LAMMPS with that package installed. E.g. the gpu
package links to a library you build in the lib/gpu dir. You can
often do the build in one step by typing "make lib-name args=..."
from the src dir, with appropriate arguments. You can leave off the
args to see a help message. See "Section 4"_Section_packages.html for
details for each package.
Packages in the standard and user tables of the
"Packages"_Packages.html doc pages with an "int" in the last column
link to internal libraries whose source code is included with LAMMPS,
in the lib/name directory where name is the package name. You must
first build the library in that directory before building LAMMPS with
that package installed. E.g. the gpu package links to a library you
build in the lib/gpu dir. You can often do the build in one step by
typing "make lib-name args=..." from the src dir, with appropriate
arguments. You can leave off the args to see a help message. See the
"Packages details"_Packages_details.html doc page for details for each
package.
[External libraries:]
Packages in the tables "Section 4"_Section_packages.html with an "ext"
in the last column link to external libraries whose source code is not
included with LAMMPS. You must first download and install the library
before building LAMMPS with that package installed. E.g. the voronoi
package links to the freely available "Voro++ library"_voro_home2. You
can often do the download/build in one step by typing "make lib-name
Packages in the standard and user tables of the
"Packages"_Packages.html doc pages with an "ext" in the last column
link to external libraries whose source code is not included with
LAMMPS. You must first download and install the library before
building LAMMPS with that package installed. E.g. the voronoi package
links to the freely available "Voro++ library"_voro_home2. You can
often do the download/build in one step by typing "make lib-name
args=..." from the src dir, with appropriate arguments. You can leave
off the args to see a help message. See "Section
4"_Section_packages.html for details for each package.
off the args to see a help message. See the "Packages
details"_Packages_details.html doc page for details for each package.
:link(voro_home2,http://math.lbl.gov/voro++)
@ -888,9 +891,9 @@ copied from a lib/name/Makefile.lammps.* file when the library is
built. If those settings are not correct for your machine you will
need to edit or create an appropriate Makefile.lammps file.
Package-specific details for these steps are given in "Section
4"_Section_packages.html an in README files in the lib/name
directories.
Package-specific details for these steps are given on the "Packages
details"_Packages_details.html doc page and in README files in the
lib/name directories.
[Compiler options needed for accelerator packages:]
@ -901,14 +904,14 @@ these accelerator packages for optimal performance requires specific
settings in the Makefile.machine file you use.
A summary of the Makefile.machine settings needed for each of these
packages is given in "Section 4"_Section_packages.html. More info is
given on the doc pages that describe each package in detail:
packages is given on the "Packages"_Packages.html doc pages. More
info is given on the doc pages that describe each package in detail:
5.3.1 "USER-INTEL package"_accelerate_intel.html
5.3.2 "GPU package"_accelerate_intel.html
5.3.3 "KOKKOS package"_accelerate_kokkos.html
5.3.4 "USER-OMP package"_accelerate_omp.html
5.3.5 "OPT package"_accelerate_opt.html :all(b)
"USER-INTEL package"_Speed_intel.html
"GPU package"_Speed_gpu.html
"KOKKOS package"_Speed_kokkos.html
"USER-OMP package"_Speed_omp.html
"OPT package"_Speed_opt.html :all(b)
You can also use or examine the following machine Makefiles in
src/MAKE/OPTIONS, which include the settings. Note that the
@ -1276,8 +1279,8 @@ Either the full word or an abbreviation can be used for the keywords.
Note that the keywords do not use a leading minus sign. I.e. the
keyword is "t", not "-t". Also note that each of the keywords has a
default setting. Example of when to use these options and what
settings to use on different platforms is given in "Section
5.3"_Section_accelerate.html#acc_3.
settings to use on different platforms is given on the "Speed
kokkos"_Speed_kokkos.html doc page.
d or device
g or gpus
@ -1461,8 +1464,7 @@ 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 5"_Section_accelerate.html doc pages for
more details.
See the "Speed tips"_Speed_tips.html doc page for more details.
If the keyword {nth} is used with a setting {N}, then it means every
Nth processor will be moved to the end of the ranking. This is useful

69
doc/src/Speed.txt Normal file
View File

@ -0,0 +1,69 @@
"Previous Section"_Package.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_howto.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Accelerate performance :h2
This section describes various methods for improving LAMMPS
performance for different classes of problems running on different
kinds of machines.
There are two thrusts to the discussion that follows. The first is
using code options that implement alternate algorithms that can
speed-up a simulation. The second is to use one of the several
accelerator packages provided with LAMMPS that contain code optimized
for certain kinds of hardware, including multi-core CPUs, GPUs, and
Intel Xeon Phi coprocessors.
The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS
web site gives performance results for the various accelerator
packages discussed on the "Speed packages"_Speed_packages.html doc
page, for several of the standard LAMMPS benchmark problems, as a
function of problem size and number of compute nodes, on different
hardware platforms.
<!-- RST
.. toctree::
Speed_bench
Speed_measure
.. toctree::
Speed_tips
.. toctree::
Speed_packages
Speed_gpu
Speed_intel
Speed_kokkos
Speed_omp
Speed_opt
Speed_compare
END_RST -->
<!-- HTML_ONLY -->
"Benchmarks"_Speed_bench.html
"Measuring performance"_Speed_measure.html :all(b)
"General tips"_Speed_tips.html :all(b)
"Accelerator packages"_Speed_packages.html
"GPU package"_Speed_gpu.html
"USER-INTEL package"_Speed_intel.html
"KOKKOS package"_Speed_kokkos.html
"USER-OMP package"_Speed_omp.html
"OPT package"_Speed_opt.html
"Comparison of accelerator packages"_Speed_compare.html :all(b)
<!-- END_HTML_ONLY -->

19
doc/src/Section_perf.txt → doc/src/Speed_bench.txt
View File

@ -1,6 +1,5 @@
"Previous Section"_Examples.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Tools.html
:c
"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@ -8,12 +7,12 @@ Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Tools.html
:line
8. Performance & scalability :h2
Benchmarks :h3
Current LAMMPS performance is discussed on the Benchmarks page of the
"LAMMPS WWW Site"_lws where CPU timings and parallel efficiencies are
listed. The page has several sections, which are briefly described
below:
Current LAMMPS performance is discussed on the "Benchmarks
page"_http://lammps.sandia.gov/bench.html of the "LAMMPS website"_lws
where timings and parallel efficiencies are listed. The page has
several sections, which are briefly described below:
CPU performance on 5 standard problems, strong and weak scaling
GPU and Xeon Phi performance on same and related problems
@ -53,8 +52,8 @@ of these 5 problems on 1 or 4 cores of Linux desktop. The bench/FERMI
and bench/KEPLER dirs have input files and scripts and instructions
for running the same (or similar) problems using OpenMP or GPU or Xeon
Phi acceleration options. See the README files in those dirs and the
"Section 5.3"_Section_accelerate.html#acc_3 doc pages for
instructions on how to build LAMMPS and run on that kind of hardware.
"Speed packages"_Speed_packages.html doc pages for instructions on how
to build LAMMPS and run on that kind of hardware.
The bench/POTENTIALS directory has input files which correspond to the
table of results on the

73
doc/src/Speed_compare.txt Normal file
View File

@ -0,0 +1,73 @@
"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Comparison of various accelerator packages :h3
NOTE: this section still needs to be re-worked with additional KOKKOS
and USER-INTEL information.
The next section compares and contrasts the various accelerator
options, since there are multiple ways to perform OpenMP threading,
run on GPUs, and run on Intel Xeon Phi coprocessors.
All 3 of these packages accelerate a LAMMPS calculation using NVIDIA
hardware, but they do it in different ways.
As a consequence, for a particular simulation on specific hardware,
one package may be faster than the other. We give guidelines below,
but the best way to determine which package is faster for your input
script is to try both of them on your machine. See the benchmarking
section below for examples where this has been done.
[Guidelines for using each package optimally:]
The GPU package allows you to assign multiple CPUs (cores) to a single
GPU (a common configuration for "hybrid" nodes that contain multicore
CPU(s) and GPU(s)) and works effectively in this mode. :ulb,l
The GPU package moves per-atom data (coordinates, forces)
back-and-forth between the CPU and GPU every timestep. The
KOKKOS/CUDA package only does this on timesteps when a CPU calculation
is required (e.g. to invoke a fix or compute that is non-GPU-ized).
Hence, if you can formulate your input script to only use GPU-ized
fixes and computes, and avoid doing I/O too often (thermo output, dump
file snapshots, restart files), then the data transfer cost of the
KOKKOS/CUDA package can be very low, causing it to run faster than the
GPU package. :l
The GPU package is often faster than the KOKKOS/CUDA package, if the
number of atoms per GPU is smaller. The crossover point, in terms of
atoms/GPU at which the KOKKOS/CUDA package becomes faster depends
strongly on the pair style. For example, for a simple Lennard Jones
system the crossover (in single precision) is often about 50K-100K
atoms per GPU. When performing double precision calculations the
crossover point can be significantly smaller. :l
Both packages compute bonded interactions (bonds, angles, etc) on the
CPU. If the GPU package is running with several MPI processes
assigned to one GPU, the cost of computing the bonded interactions is
spread across more CPUs and hence the GPU package can run faster. :l
When using the GPU package with multiple CPUs assigned to one GPU, its
performance depends to some extent on high bandwidth between the CPUs
and the GPU. Hence its performance is affected if full 16 PCIe lanes
are not available for each GPU. In HPC environments this can be the
case if S2050/70 servers are used, where two devices generally share
one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide
full 16 lanes to each of the PCIe 2.0 16x slots. :l
:ule
[Differences between the two packages:]
The GPU package accelerates only pair force, neighbor list, and PPPM
calculations. :ulb,l
The GPU package requires neighbor lists to be built on the CPU when using
exclusion lists, hybrid pair styles, or a triclinic simulation box. :l
:ule

15
doc/src/accelerate_gpu.txt → doc/src/Speed_gpu.txt
View File

@ -1,5 +1,5 @@
"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@ -7,9 +7,7 @@
:line
"Return to Section accelerate overview"_Section_accelerate.html
5.3.1 GPU package :h5
GPU package :h3
The GPU package was developed by Mike Brown at ORNL and his
collaborators, particularly Trung Nguyen (ORNL). It provides GPU
@ -72,10 +70,9 @@ Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) t
[Building LAMMPS with the GPU package:]
This requires two steps (a,b): build the GPU library, then build
LAMMPS with the GPU package.
You can do both these steps in one line as described in
"Section 4"_Section_packages.html of the manual.
LAMMPS with the GPU package. You can do both these steps in one line
as described on the "Packages details"_Packages_details.html#GPU doc
page.
Or you can follow these two (a,b) steps:

14
doc/src/accelerate_intel.txt → doc/src/Speed_intel.txt
View File

@ -1,5 +1,5 @@
"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@ -7,9 +7,7 @@
:line
"Return to Section accelerate overview"_Section_accelerate.html
5.3.2 USER-INTEL package :h5
USER-INTEL package :h3
The USER-INTEL package is maintained by Mike Brown at Intel
Corporation. It provides two methods for accelerating simulations,
@ -233,9 +231,9 @@ source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
# or psxevars.csh for C-shell
make intel_cpu_intelmpi :pre
Alternatively this can be done as a single command with
suitable make command invocations. This is discussed in "Section
4"_Section_packages.html of the manual.
Alternatively this can be done as a single command with suitable make
command invocations, as described on the "Packages
details"_Packages_details.html#USER-INTEL doc page.
Note that if you build with support for a Phi coprocessor, the same
binary can be used on nodes with or without coprocessors installed.

20
doc/src/accelerate_kokkos.txt → doc/src/Speed_kokkos.txt
View File

@ -1,5 +1,5 @@
"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@ -7,9 +7,7 @@
:line
"Return to Section accelerate overview"_Section_accelerate.html
5.3.3 KOKKOS package :h5
KOKKOS package :h3
Kokkos is a templated C++ library that provides abstractions to allow
a single implementation of an application kernel (e.g. a pair style) to run efficiently on
@ -85,10 +83,10 @@ make kokkos_phi :pre
[Compile for CPUs and GPUs (with OpenMPI or MPICH):]
NOTE: To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA software
version 7.5 or later must be installed on your system. See the
discussion for the "GPU"_accelerate_gpu.html package for details of
how to check and do this.
NOTE: To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA
software version 7.5 or later must be installed on your system. See
the discussion for the "GPU package"_Speed_gpu.html for details of how
to check and do this.
use a C++11 compatible compiler and set KOKKOS_ARCH variable in
/src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi for both GPU and CPU as described
@ -434,8 +432,8 @@ migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be
used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not
necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP
provides alternative methods via environment variables for binding
threads to hardware cores. More info on binding threads to cores is
given in "Section 5.3"_Section_accelerate.html#acc_3.
threads to hardware cores. More info on binding threads to cores is
given on the "Speed omp"_Speed_omp.html doc page.
KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism
on most Unix platforms. This library is not available on all

55
doc/src/Speed_measure.txt Normal file
View File

@ -0,0 +1,55 @@
"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Measuring performance :h3
Before trying to make your simulation run faster, you should
understand how it currently performs and where the bottlenecks are.
The best way to do this is run the your system (actual number of
atoms) for a modest number of timesteps (say 100 steps) on several
different processor counts, including a single processor if possible.
Do this for an equilibrium version of your system, so that the
100-step timings are representative of a much longer run. There is
typically no need to run for 1000s of timesteps to get accurate
timings; you can simply extrapolate from short runs.
For the set of runs, look at the timing data printed to the screen and
log file at the end of each LAMMPS run. "This
section"_Section_start.html#start_7 of the manual has an overview.
Running on one (or a few processors) should give a good estimate of
the serial performance and what portions of the timestep are taking
the most time. Running the same problem on a few different processor
counts should give an estimate of parallel scalability. I.e. if the
simulation runs 16x faster on 16 processors, its 100% parallel
efficient; if it runs 8x faster on 16 processors, it's 50% efficient.
The most important data to look at in the timing info is the timing
breakdown and relative percentages. For example, trying different
options for speeding up the long-range solvers will have little impact
if they only consume 10% of the run time. If the pairwise time is
dominating, you may want to look at GPU or OMP versions of the pair
style, as discussed below. Comparing how the percentages change as
you increase the processor count gives you a sense of how different
operations within the timestep are scaling. Note that if you are
running with a Kspace solver, there is additional output on the
breakdown of the Kspace time. For PPPM, this includes the fraction
spent on FFTs, which can be communication intensive.
Another important detail in the timing info are the histograms of
atoms counts and neighbor counts. If these vary widely across
processors, you have a load-imbalance issue. This often results in
inaccurate relative timing data, because processors have to wait when
communication occurs for other processors to catch up. Thus the
reported times for "Communication" or "Other" may be higher than they
really are, due to load-imbalance. If this is an issue, you can
uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile
LAMMPS, to obtain synchronized timings.

11
doc/src/accelerate_omp.txt → doc/src/Speed_omp.txt
View File

@ -1,5 +1,5 @@
"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@ -7,9 +7,7 @@
:line
"Return to Section 5 overview"_Section_accelerate.html
5.3.4 USER-OMP package :h5
USER-OMP package :h3
The USER-OMP package was developed by Axel Kohlmeyer at Temple
University. It provides multi-threaded versions of most pair styles,
@ -39,7 +37,8 @@ each MPI task running on a CPU.
The lines above illustrate how to include/build with the USER-OMP
package in two steps, using the "make" command. Or how to do it with
one command as described in "Section 4"_Section_packages.html of the manual.
one command as described on the "Packages
details"_Packages_details.html#USER-OMP doc page.
Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
include "-fopenmp". Likewise, if you use an Intel compiler, the

11
doc/src/accelerate_opt.txt → doc/src/Speed_opt.txt
View File

@ -1,5 +1,5 @@
"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@ -7,9 +7,7 @@
:line
"Return to Section accelerate overview"_Section_accelerate.html
5.3.5 OPT package :h5
OPT package :h3
The OPT package was developed by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
@ -34,7 +32,8 @@ None.
The lines above illustrate how to build LAMMPS with the OPT package in
two steps, using the "make" command. Or how to do it with one command
as described in "Section 4"_Section_packages.html of the manual.
as described on the "Packages details"_Packages_details.html#OPT doc
page.
Note that if you use an Intel compiler to build with the OPT package,
the CCFLAGS setting in your Makefile.machine must include "-restrict".

191
doc/src/Speed_packages.txt Normal file
View File

@ -0,0 +1,191 @@
"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
Accelerator packages :h3
Accelerated versions of various "pair_style"_pair_style.html,
"fixes"_fix.html, "computes"_compute.html, and other commands have
been added to LAMMPS, which will typically run faster than the
standard non-accelerated versions. Some require appropriate hardware
to be present on your system, e.g. GPUs or Intel Xeon Phi
coprocessors.
All of these commands are in packages provided with LAMMPS. An
overview of packages is give on the "Packages"_Packages.html doc
pages.
These are the accelerator packages currently in LAMMPS, either as
standard or user packages:
"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:
Many-core CPUs : "USER-INTEL"_accelerate_intel.html, "KOKKOS"_accelerate_kokkos.html, "USER-OMP"_accelerate_omp.html, "OPT"_accelerate_opt.html packages
NVIDIA GPUs : "GPU"_accelerate_gpu.html, "KOKKOS"_accelerate_kokkos.html packages
Intel Phi : "USER-INTEL"_accelerate_intel.html, "KOKKOS"_accelerate_kokkos.html packages :tb(s=:)
Which package is fastest for your hardware may depend on the size
problem you are running and what commands (accelerated and
non-accelerated) are invoked by your input script. While these doc
pages include performance guidelines, there is no substitute for
trying out the different packages appropriate to your hardware.
Any accelerated style has the same name as the corresponding standard
style, except that a suffix is appended. Otherwise, the syntax for
the command that uses the style is identical, their functionality is
the same, and the numerical results it produces should also be the
same, except for precision and round-off effects.
For example, all of these styles are accelerated variants of the
Lennard-Jones "pair_style lj/cut"_pair_lj.html:
"pair_style lj/cut/gpu"_pair_lj.html
"pair_style lj/cut/intel"_pair_lj.html
"pair_style lj/cut/kk"_pair_lj.html
"pair_style lj/cut/omp"_pair_lj.html
"pair_style lj/cut/opt"_pair_lj.html :ul
To see what accelerate styles are currently available, see
"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.
To use an accelerator package in LAMMPS, and one or more of the styles
it provides, follow these general steps. Details vary from package to
package and are explained in the individual accelerator doc pages,
listed above:
build the accelerator library |
only for GPU package |
install the accelerator package |
make yes-opt, make yes-user-intel, etc |
add compile/link flags to Makefile.machine in src/MAKE |
only for USER-INTEL, KOKKOS, USER-OMP, OPT packages |
re-build LAMMPS |
make machine |
prepare and test a regular LAMMPS simulation |
lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script |
enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_6, |
only needed for KOKKOS package |
set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_6 or "package"_package.html command, |
only if defaults need to be changed |
use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
:tb(c=2,s=|)
Note that the first 4 steps can be done as a single command with
suitable make command invocations. This is discussed on the
"Packages"_Packages.html doc pages, and its use is illustrated in the
individual accelerator sections. Typically these steps only need to
be done once, to create an executable that uses one or more
accelerator packages.
The last 4 steps can all be done from the command-line when LAMMPS is
launched, without changing your input script, as illustrated in the
individual accelerator sections. Or you can add
"package"_package.html and "suffix"_suffix.html commands to your input
script.
NOTE: With a few exceptions, you can build a single LAMMPS executable
with all its accelerator packages installed. Note however that the
USER-INTEL and KOKKOS packages require you to choose one of their
hardware options when building for a specific platform. I.e. CPU or
Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi
option for the KOKKOS package.
These are the exceptions. You cannot build a single executable with:
both the USER-INTEL Phi and KOKKOS Phi options
the USER-INTEL Phi or Kokkos Phi option, and the GPU package :ul
See the examples/accelerate/README and make.list files for sample
Make.py commands that build LAMMPS with any or all of the accelerator
packages. As an example, here is a command that builds with all the
GPU related packages installed (GPU, KOKKOS with Cuda), including
settings to build the needed auxiliary GPU libraries for Kepler GPUs:
Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi \
-gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi :pre
The examples/accelerate directory also has input scripts that can be
used with all of the accelerator packages. See its README file for
details.
Likewise, the bench directory has FERMI and KEPLER and PHI
sub-directories with Make.py commands and input scripts for using all
the accelerator packages on various machines. See the README files in
those dirs.
As mentioned above, the "Benchmark
page"_http://lammps.sandia.gov/bench.html of the LAMMPS web site gives
performance results for the various accelerator packages for several
of the standard LAMMPS benchmark problems, as a function of problem
size and number of compute nodes, on different hardware platforms.
Here is a brief summary of what the various packages provide. Details
are in the individual accelerator sections.
Styles with a "gpu" suffix are part of the GPU package, and can be run
on NVIDIA GPUs. The speed-up on a GPU depends on a variety of
factors, discussed in the accelerator sections. :ulb,l
Styles with an "intel" suffix are part of the USER-INTEL
package. These styles support vectorized single and mixed precision
calculations, in addition to full double precision. In extreme cases,
this can provide speedups over 3.5x on CPUs. The package also
supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM)
coprocessors. This can result in additional speedup over 2x depending
on the hardware configuration. :l
Styles with a "kk" suffix are part of the KOKKOS package, and can be
run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel
Xeon Phi in "native" mode. The speed-up depends on a variety of
factors, as discussed on the KOKKOS accelerator page. :l
Styles with an "omp" suffix are part of the USER-OMP package and allow
a pair-style to be run in multi-threaded mode using OpenMP. This can
be useful on nodes with high-core counts when using less MPI processes
than cores is advantageous, e.g. when running with PPPM so that FFTs
are run on fewer MPI processors or when the many MPI tasks would
overload the available bandwidth for communication. :l
Styles with an "opt" suffix are part of the OPT package and typically
speed-up the pairwise calculations of your simulation by 5-25% on a
CPU. :l
:ule
The individual accelerator package doc pages explain:
what hardware and software the accelerated package requires
how to build LAMMPS with the accelerated package
how to run with the accelerated package either via command-line switches or modifying the input script
speed-ups to expect
guidelines for best performance
restrictions :ul

63
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View File

@ -0,0 +1,63 @@
"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
General tips :h3
NOTE: this section 5.2 is still a work in progress
Here is a list of general ideas for improving simulation performance.
Most of them are only applicable to certain models and certain
bottlenecks in the current performance, so let the timing data you
generate be your guide. It is hard, if not impossible, to predict how
much difference these options will make, since it is a function of
problem size, number of processors used, and your machine. There is
no substitute for identifying performance bottlenecks, and trying out
various options.
make individual pages for these, or one for PPPM
one for timestepping, etc
one for balancing
or proc layout
rRESPA
2-FFT PPPM
Staggered PPPM
single vs double PPPM
partial charge PPPM
verlet/split run style
processor command for proc layout and numa layout
load-balancing: balance and fix balance :ul
2-FFT PPPM, also called {analytic differentiation} or {ad} PPPM, uses
2 FFTs instead of the 4 FFTs used by the default {ik differentiation}
PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to
achieve the same accuracy as 4-FFT PPPM. For problems where the FFT
cost is the performance bottleneck (typically large problems running
on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM.
Staggered PPPM performs calculations using two different meshes, one
shifted slightly with respect to the other. This can reduce force
aliasing errors and increase the accuracy of the method, but also
doubles the amount of work required. For high relative accuracy, using
staggered PPPM allows one to half the mesh size in each dimension as
compared to regular PPPM, which can give around a 4x speedup in the
kspace time. However, for low relative accuracy, using staggered PPPM
gives little benefit and can be up to 2x slower in the kspace
time. For example, the rhodopsin benchmark was run on a single
processor, and results for kspace time vs. relative accuracy for the
different methods are shown in the figure below. For this system,
staggered PPPM (using ik differentiation) becomes useful when using a
relative accuracy of slightly greater than 1e-5 and above.
:c,image(JPG/rhodo_staggered.jpg)
NOTE: Using staggered PPPM may not give the same increase in accuracy
of energy and pressure as it does in forces, so some caution must be
used if energy and/or pressure are quantities of interest, such as
when using a barostat.

11
doc/src/angle_charmm.txt
View File

@ -51,10 +51,9 @@ 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 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.
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
@ -66,8 +65,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/angle_class2.txt
View File

@ -83,10 +83,9 @@ 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 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.
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
@ -98,8 +97,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/angle_cosine.txt
View File

@ -38,10 +38,9 @@ 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 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.
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
@ -53,8 +52,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/angle_cosine_delta.txt
View File

@ -43,10 +43,9 @@ 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 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.
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
@ -58,8 +57,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/angle_cosine_periodic.txt
View File

@ -51,10 +51,9 @@ 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 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.
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
@ -66,8 +65,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/angle_cosine_shift.txt
View File

@ -41,10 +41,9 @@ 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 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.
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
@ -56,8 +55,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/angle_cosine_shift_exp.txt
View File

@ -53,10 +53,9 @@ 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 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.
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
@ -68,8 +67,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/angle_cosine_squared.txt
View File

@ -43,10 +43,9 @@ 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 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.
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
@ -58,8 +57,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/angle_dipole.txt
View File

@ -71,10 +71,9 @@ 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 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.
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
@ -86,8 +85,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
[Restrictions:]

11
doc/src/angle_fourier.txt
View File

@ -39,10 +39,9 @@ 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 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.
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
@ -54,8 +53,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/angle_fourier_simple.txt
View File

@ -38,10 +38,9 @@ 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 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.
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
@ -53,8 +52,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/angle_harmonic.txt
View File

@ -45,10 +45,9 @@ 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 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.
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
@ -60,8 +59,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/angle_quartic.txt
View File

@ -45,10 +45,9 @@ 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 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.
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
@ -60,8 +59,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/angle_table.txt
View File

@ -124,10 +124,9 @@ 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 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.
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
@ -139,8 +138,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

12
doc/src/atom_style.txt
View File

@ -261,10 +261,10 @@ styles; see the "Modify"_Modify.html doc page.
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 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.
run faster, depending on your available hardware, as discussed in 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.
Note that other acceleration packages in LAMMPS, specifically the GPU,
USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom
@ -279,8 +279,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
[Restrictions:]

11
doc/src/bond_class2.txt
View File

@ -44,10 +44,9 @@ 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 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.
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
@ -59,8 +58,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/bond_fene.txt
View File

@ -47,10 +47,9 @@ 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 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.
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
@ -62,8 +61,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/bond_fene_expand.txt
View File

@ -50,10 +50,9 @@ 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 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.
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
@ -65,8 +64,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/bond_gromos.txt
View File

@ -40,10 +40,9 @@ 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 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.
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
@ -55,8 +54,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/bond_harmonic.txt
View File

@ -42,10 +42,9 @@ 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 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.
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
@ -57,8 +56,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/bond_harmonic_shift.txt
View File

@ -43,10 +43,9 @@ 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 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.
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
@ -58,8 +57,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/bond_harmonic_shift_cut.txt
View File

@ -43,10 +43,9 @@ 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 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.
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
@ -58,8 +57,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/bond_morse.txt
View File

@ -41,10 +41,9 @@ 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 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.
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
@ -56,8 +55,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/bond_nonlinear.txt
View File

@ -41,10 +41,9 @@ 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 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.
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
@ -56,8 +55,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/bond_quartic.txt
View File

@ -76,10 +76,9 @@ 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 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.
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
@ -91,8 +90,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/bond_table.txt
View File

@ -121,10 +121,9 @@ 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 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.
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
@ -136,8 +135,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/compute_pressure.txt
View File

@ -105,10 +105,9 @@ 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 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.
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
@ -120,8 +119,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/compute_temp.txt
View File

@ -67,10 +67,9 @@ 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 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.
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
@ -82,8 +81,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/compute_temp_partial.txt
View File

@ -74,10 +74,9 @@ 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 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.
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
@ -89,8 +88,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/dihedral_charmm.txt
View File

@ -116,10 +116,9 @@ computed.
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 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.
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
@ -131,8 +130,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/dihedral_class2.txt
View File

@ -141,10 +141,9 @@ r3 (distance) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section 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.
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
@ -156,8 +155,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/dihedral_cosine_shift_exp.txt
View File

@ -52,10 +52,9 @@ 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 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.
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
@ -67,8 +66,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/dihedral_fourier.txt
View File

@ -44,10 +44,9 @@ dm (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 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.
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
@ -59,8 +58,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/dihedral_harmonic.txt
View File

@ -53,10 +53,9 @@ Some force fields let {n} be positive or negative which corresponds to
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section 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.
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
@ -68,8 +67,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/dihedral_helix.txt
View File

@ -46,10 +46,9 @@ C (energy) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section 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.
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
@ -61,8 +60,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/dihedral_multi_harmonic.txt
View File

@ -40,10 +40,9 @@ A5 (energy) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section 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.
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
@ -55,8 +54,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/dihedral_nharmonic.txt
View File

@ -40,10 +40,9 @@ An (energy) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section 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.
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
@ -55,8 +54,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/dihedral_opls.txt
View File

@ -48,10 +48,9 @@ K4 (energy) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section 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.
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
@ -63,8 +62,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/dihedral_quadratic.txt
View File

@ -41,10 +41,9 @@ phi0 (degrees) :ul
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section 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.
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
@ -56,8 +55,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/dihedral_table.txt
View File

@ -174,10 +174,9 @@ 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 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.
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
@ -189,8 +188,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
[Restrictions:]

16
doc/src/fix_addforce.txt
View File

@ -103,12 +103,12 @@ converge properly.
:line
Styles with a suffix are functionally the same as the corresponding
style without the suffix. They have been optimized to run faster,
depending on your available hardware, as discussed in
"Section 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.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@ -120,8 +120,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

16
doc/src/fix_aveforce.txt
View File

@ -63,12 +63,12 @@ to it.
:line
Styles with a suffix are functionally the same as the corresponding
style without the suffix. They have been optimized to run faster,
depending on your available hardware, as discussed in
"Section 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.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@ -80,8 +80,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

13
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"_Section_packages.html#USER-UEF and its "fix
package"_Packages_details.html#USER-UEF and its "fix
commands"_fix_nh_uef.html.
For the {x}, {y}, {z} parameters, the associated dimension cannot be
@ -550,10 +550,9 @@ command if you want to include lattice spacings in a variable formula.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section 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.
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
@ -565,8 +564,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]

11
doc/src/fix_dpd_energy.txt
View File

@ -50,10 +50,9 @@ examples/USER/dpd directory.
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 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.
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
@ -65,8 +64,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/fix_enforce2d.txt
View File

@ -31,10 +31,9 @@ not move from their initial z coordinate.
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 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.
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
@ -46,8 +45,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/fix_eos_table_rx.txt
View File

@ -156,10 +156,9 @@ no 0.93 0.00 0.000 -1.76 :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 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.
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
@ -171,8 +170,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

16
doc/src/fix_freeze.txt
View File

@ -31,12 +31,12 @@ using "fix setforce"_fix_setforce.html.
:line
Styles with a suffix are functionally the same as the corresponding
style without the suffix. They have been optimized to run faster,
depending on your available hardware, as discussed in
"Section 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.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@ -48,8 +48,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/fix_gravity.txt
View File

@ -90,10 +90,9 @@ field.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section 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.
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
@ -105,8 +104,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/fix_langevin.txt
View File

@ -264,10 +264,9 @@ generates an average temperature of 220 K, instead of 300 K.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section 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.
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
@ -279,8 +278,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/fix_momentum.txt
View File

@ -61,10 +61,9 @@ initial velocities with zero aggregate linear and/or angular momentum.
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 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.
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
@ -76,8 +75,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]

11
doc/src/fix_nh.txt
View File

@ -484,10 +484,9 @@ the various ways to do this.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section 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.
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
@ -499,8 +498,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/fix_nph_asphere.txt
View File

@ -81,10 +81,9 @@ It also means that changing attributes of {thermo_temp} or
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section 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.
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
@ -96,8 +95,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]

11
doc/src/fix_nph_body.txt
View File

@ -80,10 +80,9 @@ It also means that changing attributes of {thermo_temp} or
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section 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.
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
@ -95,8 +94,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]

11
doc/src/fix_nph_sphere.txt
View File

@ -90,10 +90,9 @@ It also means that changing attributes of {thermo_temp} or
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section 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.
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
@ -105,8 +104,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]

11
doc/src/fix_nphug.txt
View File

@ -140,10 +140,9 @@ It also means that changing attributes of {thermo_temp} or
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section 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.
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
@ -155,8 +154,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/fix_npt_asphere.txt
View File

@ -105,10 +105,9 @@ thermal degrees of freedom, and the bias is added back in.
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 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.
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
@ -120,8 +119,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]

11
doc/src/fix_npt_body.txt
View File

@ -104,10 +104,9 @@ thermal degrees of freedom, and the bias is added back in.
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 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.
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
@ -119,8 +118,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]

11
doc/src/fix_npt_sphere.txt
View File

@ -115,10 +115,9 @@ thermal degrees of freedom, and the bias is added back in.
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 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.
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
@ -130,8 +129,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]

11
doc/src/fix_nve.txt
View File

@ -34,10 +34,9 @@ ensemble.
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 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.
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
@ -49,8 +48,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/fix_nve_asphere.txt
View File

@ -45,10 +45,9 @@ This fix is not invoked during "energy minimization"_minimize.html.
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 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.
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
@ -60,8 +59,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/fix_nve_sphere.txt
View File

@ -65,10 +65,9 @@ moment of inertia, as used in the time integration.
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 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.
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
@ -80,8 +79,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/fix_nvt_asphere.txt
View File

@ -86,10 +86,9 @@ thermal degrees of freedom, and the bias is added back in.
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 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.
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
@ -101,8 +100,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]

11
doc/src/fix_nvt_body.txt
View File

@ -85,10 +85,9 @@ thermal degrees of freedom, and the bias is added back in.
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 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.
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
@ -100,8 +99,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]

11
doc/src/fix_nvt_sllod.txt
View File

@ -109,10 +109,9 @@ thermal degrees of freedom, and the bias is added back in.
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 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.
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
@ -124,8 +123,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]

11
doc/src/fix_nvt_sphere.txt
View File

@ -96,10 +96,9 @@ thermal degrees of freedom, and the bias is added back in.
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 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.
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
@ -111,8 +110,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
[Restart, fix_modify, output, run start/stop, minimize info:]

11
doc/src/fix_qeq_comb.txt
View File

@ -62,10 +62,9 @@ equilibration calculation is written to the specified file.
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 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.
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
@ -77,8 +76,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/fix_qeq_reax.txt
View File

@ -80,10 +80,9 @@ This fix is invoked during "energy minimization"_minimize.html.
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 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.
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
@ -95,8 +94,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/fix_rigid.txt
View File

@ -690,10 +690,9 @@ rigid/nvt.
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 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.
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
@ -705,8 +704,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/fix_rx.txt
View File

@ -186,10 +186,9 @@ read_data data.dpd fix foo_SPECIES NULL Species
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 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.
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
@ -201,8 +200,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

16
doc/src/fix_setforce.txt
View File

@ -65,12 +65,12 @@ to it.
:line
Styles with a r {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 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.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
The region keyword is also supported by Kokkos, but a Kokkos-enabled
region must be used. See the region "region"_region.html command for
@ -85,8 +85,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

16
doc/src/fix_shake.txt
View File

@ -145,12 +145,12 @@ info of atoms in the molecule.
:line
Styles with a suffix are functionally the same as the corresponding
style without the suffix. They have been optimized to run faster,
depending on your available hardware, as discussed in
"Section 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.
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
@ -162,8 +162,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/fix_shardlow.txt
View File

@ -56,10 +56,9 @@ examples/USER/dpd directory.
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 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.
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
@ -71,8 +70,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/fix_wall.txt
View File

@ -288,10 +288,9 @@ option for this fix.
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 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.
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
@ -303,8 +302,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/fix_wall_reflect.txt
View File

@ -130,10 +130,9 @@ position = c0 + A (1 - cos(omega*delta)) :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 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.
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
@ -145,8 +144,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/improper_class2.txt
View File

@ -87,10 +87,9 @@ radians internally; hence the units of M 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 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.
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
@ -102,8 +101,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/improper_cossq.txt
View File

@ -53,10 +53,9 @@ X0 (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 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.
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
@ -68,8 +67,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

11
doc/src/improper_cvff.txt
View File

@ -54,10 +54,9 @@ n (0,1,2,3,4,6) :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 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.
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
@ -69,8 +68,8 @@ 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 5"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line

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