From d9c328932fac636d6d0d187bde2fdeb9ea3884e7 Mon Sep 17 00:00:00 2001
From: "Steven J. Plimpton" <sjplimp@singsing.sandia.gov>
Date: Mon, 30 Jul 2018 12:31:12 -0600
Subject: [PATCH] changes to Packages and Speed doc files
---
doc/src/Errors_messages.txt | 6 +-
doc/src/Errors_warnings.txt | 6 +-
doc/src/Examples.txt | 2 +-
doc/src/Manual.txt | 29 +-
doc/src/Packages.txt | 39 ++
...tion_packages.txt => Packages_details.txt} | 336 ++++++---------
doc/src/Packages_standard.txt | 65 +++
doc/src/Packages_user.txt | 74 ++++
doc/src/Section_accelerate.txt | 391 ------------------
doc/src/Section_commands.txt | 44 +-
doc/src/Section_intro.txt | 2 +-
doc/src/Section_start.txt | 100 ++---
doc/src/Speed.txt | 69 ++++
doc/src/{Section_perf.txt => Speed_bench.txt} | 19 +-
doc/src/Speed_compare.txt | 73 ++++
doc/src/{accelerate_gpu.txt => Speed_gpu.txt} | 15 +-
.../{accelerate_intel.txt => Speed_intel.txt} | 14 +-
...accelerate_kokkos.txt => Speed_kokkos.txt} | 20 +-
doc/src/Speed_measure.txt | 55 +++
doc/src/{accelerate_omp.txt => Speed_omp.txt} | 11 +-
doc/src/{accelerate_opt.txt => Speed_opt.txt} | 11 +-
doc/src/Speed_packages.txt | 191 +++++++++
doc/src/Speed_tips.txt | 63 +++
doc/src/angle_charmm.txt | 11 +-
doc/src/angle_class2.txt | 11 +-
doc/src/angle_cosine.txt | 11 +-
doc/src/angle_cosine_delta.txt | 11 +-
doc/src/angle_cosine_periodic.txt | 11 +-
doc/src/angle_cosine_shift.txt | 11 +-
doc/src/angle_cosine_shift_exp.txt | 11 +-
doc/src/angle_cosine_squared.txt | 11 +-
doc/src/angle_dipole.txt | 11 +-
doc/src/angle_fourier.txt | 11 +-
doc/src/angle_fourier_simple.txt | 11 +-
doc/src/angle_harmonic.txt | 11 +-
doc/src/angle_quartic.txt | 11 +-
doc/src/angle_table.txt | 11 +-
doc/src/atom_style.txt | 12 +-
doc/src/bond_class2.txt | 11 +-
doc/src/bond_fene.txt | 11 +-
doc/src/bond_fene_expand.txt | 11 +-
doc/src/bond_gromos.txt | 11 +-
doc/src/bond_harmonic.txt | 11 +-
doc/src/bond_harmonic_shift.txt | 11 +-
doc/src/bond_harmonic_shift_cut.txt | 11 +-
doc/src/bond_morse.txt | 11 +-
doc/src/bond_nonlinear.txt | 11 +-
doc/src/bond_quartic.txt | 11 +-
doc/src/bond_table.txt | 11 +-
doc/src/compute_pressure.txt | 11 +-
doc/src/compute_temp.txt | 11 +-
doc/src/compute_temp_partial.txt | 11 +-
doc/src/dihedral_charmm.txt | 11 +-
doc/src/dihedral_class2.txt | 11 +-
doc/src/dihedral_cosine_shift_exp.txt | 11 +-
doc/src/dihedral_fourier.txt | 11 +-
doc/src/dihedral_harmonic.txt | 11 +-
doc/src/dihedral_helix.txt | 11 +-
doc/src/dihedral_multi_harmonic.txt | 11 +-
doc/src/dihedral_nharmonic.txt | 11 +-
doc/src/dihedral_opls.txt | 11 +-
doc/src/dihedral_quadratic.txt | 11 +-
doc/src/dihedral_table.txt | 11 +-
doc/src/fix_addforce.txt | 16 +-
doc/src/fix_aveforce.txt | 16 +-
doc/src/fix_deform.txt | 13 +-
doc/src/fix_dpd_energy.txt | 11 +-
doc/src/fix_enforce2d.txt | 11 +-
doc/src/fix_eos_table_rx.txt | 11 +-
doc/src/fix_freeze.txt | 16 +-
doc/src/fix_gravity.txt | 11 +-
doc/src/fix_langevin.txt | 11 +-
doc/src/fix_momentum.txt | 11 +-
doc/src/fix_nh.txt | 11 +-
doc/src/fix_nph_asphere.txt | 11 +-
doc/src/fix_nph_body.txt | 11 +-
doc/src/fix_nph_sphere.txt | 11 +-
doc/src/fix_nphug.txt | 11 +-
doc/src/fix_npt_asphere.txt | 11 +-
doc/src/fix_npt_body.txt | 11 +-
doc/src/fix_npt_sphere.txt | 11 +-
doc/src/fix_nve.txt | 11 +-
doc/src/fix_nve_asphere.txt | 11 +-
doc/src/fix_nve_sphere.txt | 11 +-
doc/src/fix_nvt_asphere.txt | 11 +-
doc/src/fix_nvt_body.txt | 11 +-
doc/src/fix_nvt_sllod.txt | 11 +-
doc/src/fix_nvt_sphere.txt | 11 +-
doc/src/fix_qeq_comb.txt | 11 +-
doc/src/fix_qeq_reax.txt | 11 +-
doc/src/fix_rigid.txt | 11 +-
doc/src/fix_rx.txt | 11 +-
doc/src/fix_setforce.txt | 16 +-
doc/src/fix_shake.txt | 16 +-
doc/src/fix_shardlow.txt | 11 +-
doc/src/fix_wall.txt | 11 +-
doc/src/fix_wall_reflect.txt | 11 +-
doc/src/improper_class2.txt | 11 +-
doc/src/improper_cossq.txt | 11 +-
doc/src/improper_cvff.txt | 11 +-
doc/src/improper_fourier.txt | 11 +-
doc/src/improper_harmonic.txt | 11 +-
doc/src/improper_ring.txt | 11 +-
doc/src/improper_umbrella.txt | 11 +-
doc/src/kspace_style.txt | 15 +-
doc/src/lammps.book | 12 +-
doc/src/package.txt | 6 +-
doc/src/pair_adp.txt | 11 +-
doc/src/pair_agni.txt | 14 +-
doc/src/pair_airebo.txt | 11 +-
doc/src/pair_beck.txt | 11 +-
doc/src/pair_born.txt | 11 +-
doc/src/pair_buck.txt | 11 +-
doc/src/pair_buck_long.txt | 11 +-
doc/src/pair_charmm.txt | 11 +-
doc/src/pair_class2.txt | 11 +-
doc/src/pair_colloid.txt | 11 +-
doc/src/pair_comb.txt | 11 +-
doc/src/pair_coul.txt | 11 +-
doc/src/pair_dipole.txt | 11 +-
doc/src/pair_dpd.txt | 11 +-
doc/src/pair_dpd_fdt.txt | 11 +-
doc/src/pair_eam.txt | 9 +-
doc/src/pair_edip.txt | 11 +-
doc/src/pair_eim.txt | 11 +-
doc/src/pair_exp6_rx.txt | 11 +-
doc/src/pair_gauss.txt | 11 +-
doc/src/pair_gayberne.txt | 11 +-
doc/src/pair_gran.txt | 11 +-
doc/src/pair_gromacs.txt | 11 +-
doc/src/pair_hbond_dreiding.txt | 11 +-
doc/src/pair_hybrid.txt | 8 +-
doc/src/pair_kim.txt | 4 +-
doc/src/pair_lj.txt | 11 +-
doc/src/pair_lj96.txt | 11 +-
doc/src/pair_lj_cubic.txt | 11 +-
doc/src/pair_lj_expand.txt | 11 +-
doc/src/pair_lj_long.txt | 11 +-
doc/src/pair_lj_smooth.txt | 11 +-
doc/src/pair_lj_smooth_linear.txt | 11 +-
doc/src/pair_lj_soft.txt | 11 +-
doc/src/pair_meam_spline.txt | 11 +-
doc/src/pair_morse.txt | 11 +-
doc/src/pair_multi_lucy_rx.txt | 11 +-
doc/src/pair_nb3b_harmonic.txt | 11 +-
doc/src/pair_nm.txt | 11 +-
doc/src/pair_peri.txt | 11 +-
doc/src/pair_reaxc.txt | 21 +-
doc/src/pair_resquared.txt | 11 +-
doc/src/pair_sdk.txt | 11 +-
doc/src/pair_snap.txt | 11 +-
doc/src/pair_soft.txt | 11 +-
doc/src/pair_sw.txt | 11 +-
doc/src/pair_table.txt | 11 +-
doc/src/pair_table_rx.txt | 11 +-
doc/src/pair_tersoff.txt | 11 +-
doc/src/pair_tersoff_mod.txt | 11 +-
doc/src/pair_tersoff_zbl.txt | 11 +-
doc/src/pair_thole.txt | 11 +-
doc/src/pair_ufm.txt | 11 +-
doc/src/pair_vashishta.txt | 11 +-
doc/src/pair_yukawa.txt | 11 +-
doc/src/pair_yukawa_colloid.txt | 11 +-
doc/src/pair_zbl.txt | 11 +-
doc/src/region.txt | 16 +-
doc/src/run_style.txt | 30 +-
166 files changed, 1621 insertions(+), 1640 deletions(-)
create mode 100644 doc/src/Packages.txt
rename doc/src/{Section_packages.txt => Packages_details.txt} (86%)
create mode 100644 doc/src/Packages_standard.txt
create mode 100644 doc/src/Packages_user.txt
delete mode 100644 doc/src/Section_accelerate.txt
create mode 100644 doc/src/Speed.txt
rename doc/src/{Section_perf.txt => Speed_bench.txt} (86%)
create mode 100644 doc/src/Speed_compare.txt
rename doc/src/{accelerate_gpu.txt => Speed_gpu.txt} (96%)
rename doc/src/{accelerate_intel.txt => Speed_intel.txt} (98%)
rename doc/src/{accelerate_kokkos.txt => Speed_kokkos.txt} (97%)
create mode 100644 doc/src/Speed_measure.txt
rename doc/src/{accelerate_omp.txt => Speed_omp.txt} (96%)
rename doc/src/{accelerate_opt.txt => Speed_opt.txt} (86%)
create mode 100644 doc/src/Speed_packages.txt
create mode 100644 doc/src/Speed_tips.txt
diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt
index 1563e02901..39eabbd232 100644
--- a/doc/src/Errors_messages.txt
+++ b/doc/src/Errors_messages.txt
@@ -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
diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt
index 0324f563b6..1da777043c 100644
--- a/doc/src/Errors_warnings.txt
+++ b/doc/src/Errors_warnings.txt
@@ -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
diff --git a/doc/src/Examples.txt b/doc/src/Examples.txt
index 08afca8b20..467ddcc959 100644
--- a/doc/src/Examples.txt
+++ b/doc/src/Examples.txt
@@ -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.
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index 4481c911a0..31b8a6a1d4 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -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)
diff --git a/doc/src/Packages.txt b/doc/src/Packages.txt
new file mode 100644
index 0000000000..6498d03063
--- /dev/null
+++ b/doc/src/Packages.txt
@@ -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 -->
diff --git a/doc/src/Section_packages.txt b/doc/src/Packages_details.txt
similarity index 86%
rename from doc/src/Section_packages.txt
rename to doc/src/Packages_details.txt
index 340a77310d..af18d097d9 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Packages_details.txt
@@ -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
-
-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.
+Package details :h3
+
+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.
-
-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:
-
-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)
+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.
+
+"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)
+
+"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
diff --git a/doc/src/Packages_standard.txt b/doc/src/Packages_standard.txt
new file mode 100644
index 0000000000..095bf699a6
--- /dev/null
+++ b/doc/src/Packages_standard.txt
@@ -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)
diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt
new file mode 100644
index 0000000000..73c7fdb65d
--- /dev/null
+++ b/doc/src/Packages_user.txt
@@ -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)
diff --git a/doc/src/Section_accelerate.txt b/doc/src/Section_accelerate.txt
deleted file mode 100644
index d5cbf77a84..0000000000
--- a/doc/src/Section_accelerate.txt
+++ /dev/null
@@ -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
diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
index 7b9349a233..7948e0de32 100644
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@@ -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,
diff --git a/doc/src/Section_intro.txt b/doc/src/Section_intro.txt
index c7cf5bf8d2..36a1181ca7 100644
--- a/doc/src/Section_intro.txt
+++ b/doc/src/Section_intro.txt
@@ -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:
diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt
index d8f340b179..cd445b3e14 100644
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@@ -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
diff --git a/doc/src/Speed.txt b/doc/src/Speed.txt
new file mode 100644
index 0000000000..2339a11c06
--- /dev/null
+++ b/doc/src/Speed.txt
@@ -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 -->
diff --git a/doc/src/Section_perf.txt b/doc/src/Speed_bench.txt
similarity index 86%
rename from doc/src/Section_perf.txt
rename to doc/src/Speed_bench.txt
index f320780129..dc76588c11 100644
--- a/doc/src/Section_perf.txt
+++ b/doc/src/Speed_bench.txt
@@ -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
diff --git a/doc/src/Speed_compare.txt b/doc/src/Speed_compare.txt
new file mode 100644
index 0000000000..6c947b9662
--- /dev/null
+++ b/doc/src/Speed_compare.txt
@@ -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
diff --git a/doc/src/accelerate_gpu.txt b/doc/src/Speed_gpu.txt
similarity index 96%
rename from doc/src/accelerate_gpu.txt
rename to doc/src/Speed_gpu.txt
index 816a31c788..d6ebbf8069 100644
--- a/doc/src/accelerate_gpu.txt
+++ b/doc/src/Speed_gpu.txt
@@ -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:
diff --git a/doc/src/accelerate_intel.txt b/doc/src/Speed_intel.txt
similarity index 98%
rename from doc/src/accelerate_intel.txt
rename to doc/src/Speed_intel.txt
index 71f5185b15..acf5c3f2f9 100644
--- a/doc/src/accelerate_intel.txt
+++ b/doc/src/Speed_intel.txt
@@ -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.
diff --git a/doc/src/accelerate_kokkos.txt b/doc/src/Speed_kokkos.txt
similarity index 97%
rename from doc/src/accelerate_kokkos.txt
rename to doc/src/Speed_kokkos.txt
index 0c9178d6e4..8e01db7bdc 100644
--- a/doc/src/accelerate_kokkos.txt
+++ b/doc/src/Speed_kokkos.txt
@@ -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
diff --git a/doc/src/Speed_measure.txt b/doc/src/Speed_measure.txt
new file mode 100644
index 0000000000..03c0345c20
--- /dev/null
+++ b/doc/src/Speed_measure.txt
@@ -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.
+
diff --git a/doc/src/accelerate_omp.txt b/doc/src/Speed_omp.txt
similarity index 96%
rename from doc/src/accelerate_omp.txt
rename to doc/src/Speed_omp.txt
index fa7bef1a52..3700580225 100644
--- a/doc/src/accelerate_omp.txt
+++ b/doc/src/Speed_omp.txt
@@ -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
diff --git a/doc/src/accelerate_opt.txt b/doc/src/Speed_opt.txt
similarity index 86%
rename from doc/src/accelerate_opt.txt
rename to doc/src/Speed_opt.txt
index 845264b522..7d0d7169f0 100644
--- a/doc/src/accelerate_opt.txt
+++ b/doc/src/Speed_opt.txt
@@ -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".
diff --git a/doc/src/Speed_packages.txt b/doc/src/Speed_packages.txt
new file mode 100644
index 0000000000..18850d52e0
--- /dev/null
+++ b/doc/src/Speed_packages.txt
@@ -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
+
diff --git a/doc/src/Speed_tips.txt b/doc/src/Speed_tips.txt
new file mode 100644
index 0000000000..c0d360cd8e
--- /dev/null
+++ b/doc/src/Speed_tips.txt
@@ -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.
diff --git a/doc/src/angle_charmm.txt b/doc/src/angle_charmm.txt
index 7ff7ef8fd4..fe109d24fb 100644
--- a/doc/src/angle_charmm.txt
+++ b/doc/src/angle_charmm.txt
@@ -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
diff --git a/doc/src/angle_class2.txt b/doc/src/angle_class2.txt
index d4330139c9..c13a64afb6 100644
--- a/doc/src/angle_class2.txt
+++ b/doc/src/angle_class2.txt
@@ -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
diff --git a/doc/src/angle_cosine.txt b/doc/src/angle_cosine.txt
index c0ce3c9301..99264b02a6 100644
--- a/doc/src/angle_cosine.txt
+++ b/doc/src/angle_cosine.txt
@@ -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
diff --git a/doc/src/angle_cosine_delta.txt b/doc/src/angle_cosine_delta.txt
index 830fd6db58..052300412f 100644
--- a/doc/src/angle_cosine_delta.txt
+++ b/doc/src/angle_cosine_delta.txt
@@ -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
diff --git a/doc/src/angle_cosine_periodic.txt b/doc/src/angle_cosine_periodic.txt
index b5c53b1b0f..4bedae3246 100644
--- a/doc/src/angle_cosine_periodic.txt
+++ b/doc/src/angle_cosine_periodic.txt
@@ -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
diff --git a/doc/src/angle_cosine_shift.txt b/doc/src/angle_cosine_shift.txt
index 6ed9fe2150..185b9f5309 100644
--- a/doc/src/angle_cosine_shift.txt
+++ b/doc/src/angle_cosine_shift.txt
@@ -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
diff --git a/doc/src/angle_cosine_shift_exp.txt b/doc/src/angle_cosine_shift_exp.txt
index 44a68c1087..e5c7fdd709 100644
--- a/doc/src/angle_cosine_shift_exp.txt
+++ b/doc/src/angle_cosine_shift_exp.txt
@@ -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
diff --git a/doc/src/angle_cosine_squared.txt b/doc/src/angle_cosine_squared.txt
index 065cdad542..e85c514d1e 100644
--- a/doc/src/angle_cosine_squared.txt
+++ b/doc/src/angle_cosine_squared.txt
@@ -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
diff --git a/doc/src/angle_dipole.txt b/doc/src/angle_dipole.txt
index 34cc8c153c..31ae2e9464 100644
--- a/doc/src/angle_dipole.txt
+++ b/doc/src/angle_dipole.txt
@@ -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:]
diff --git a/doc/src/angle_fourier.txt b/doc/src/angle_fourier.txt
index da39e7cf32..18eb56b478 100644
--- a/doc/src/angle_fourier.txt
+++ b/doc/src/angle_fourier.txt
@@ -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
diff --git a/doc/src/angle_fourier_simple.txt b/doc/src/angle_fourier_simple.txt
index 5adda6cb32..6faff5f10d 100644
--- a/doc/src/angle_fourier_simple.txt
+++ b/doc/src/angle_fourier_simple.txt
@@ -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
diff --git a/doc/src/angle_harmonic.txt b/doc/src/angle_harmonic.txt
index 4c74763964..fe803be623 100644
--- a/doc/src/angle_harmonic.txt
+++ b/doc/src/angle_harmonic.txt
@@ -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
diff --git a/doc/src/angle_quartic.txt b/doc/src/angle_quartic.txt
index f7640bdfbc..a31214f435 100644
--- a/doc/src/angle_quartic.txt
+++ b/doc/src/angle_quartic.txt
@@ -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
diff --git a/doc/src/angle_table.txt b/doc/src/angle_table.txt
index bd6e167bd8..29b56875e7 100644
--- a/doc/src/angle_table.txt
+++ b/doc/src/angle_table.txt
@@ -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
diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt
index 442bb5ac70..0e6aa8a033 100644
--- a/doc/src/atom_style.txt
+++ b/doc/src/atom_style.txt
@@ -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:]
diff --git a/doc/src/bond_class2.txt b/doc/src/bond_class2.txt
index 9687a63168..049482c973 100644
--- a/doc/src/bond_class2.txt
+++ b/doc/src/bond_class2.txt
@@ -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
diff --git a/doc/src/bond_fene.txt b/doc/src/bond_fene.txt
index 9050c3bf5c..be154a53b1 100644
--- a/doc/src/bond_fene.txt
+++ b/doc/src/bond_fene.txt
@@ -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
diff --git a/doc/src/bond_fene_expand.txt b/doc/src/bond_fene_expand.txt
index ff687444a9..77ebd977c8 100644
--- a/doc/src/bond_fene_expand.txt
+++ b/doc/src/bond_fene_expand.txt
@@ -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
diff --git a/doc/src/bond_gromos.txt b/doc/src/bond_gromos.txt
index cc3ff75878..7a56cb3afa 100644
--- a/doc/src/bond_gromos.txt
+++ b/doc/src/bond_gromos.txt
@@ -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
diff --git a/doc/src/bond_harmonic.txt b/doc/src/bond_harmonic.txt
index c18a7e0fd4..54e89fcc72 100644
--- a/doc/src/bond_harmonic.txt
+++ b/doc/src/bond_harmonic.txt
@@ -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
diff --git a/doc/src/bond_harmonic_shift.txt b/doc/src/bond_harmonic_shift.txt
index bf3b3c115a..0213b5cc6f 100644
--- a/doc/src/bond_harmonic_shift.txt
+++ b/doc/src/bond_harmonic_shift.txt
@@ -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
diff --git a/doc/src/bond_harmonic_shift_cut.txt b/doc/src/bond_harmonic_shift_cut.txt
index 1918ce00b6..d907bf4a62 100644
--- a/doc/src/bond_harmonic_shift_cut.txt
+++ b/doc/src/bond_harmonic_shift_cut.txt
@@ -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
diff --git a/doc/src/bond_morse.txt b/doc/src/bond_morse.txt
index 4f6a32e341..66f2d08cab 100644
--- a/doc/src/bond_morse.txt
+++ b/doc/src/bond_morse.txt
@@ -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
diff --git a/doc/src/bond_nonlinear.txt b/doc/src/bond_nonlinear.txt
index 434af62506..e0aa5629b3 100644
--- a/doc/src/bond_nonlinear.txt
+++ b/doc/src/bond_nonlinear.txt
@@ -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
diff --git a/doc/src/bond_quartic.txt b/doc/src/bond_quartic.txt
index 4dc7ad4a36..760a5d7f07 100644
--- a/doc/src/bond_quartic.txt
+++ b/doc/src/bond_quartic.txt
@@ -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
diff --git a/doc/src/bond_table.txt b/doc/src/bond_table.txt
index 906d3e5d76..fe0b3ce22b 100644
--- a/doc/src/bond_table.txt
+++ b/doc/src/bond_table.txt
@@ -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
diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt
index f0691ad207..8b7491da49 100644
--- a/doc/src/compute_pressure.txt
+++ b/doc/src/compute_pressure.txt
@@ -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
diff --git a/doc/src/compute_temp.txt b/doc/src/compute_temp.txt
index b88be79e20..f9fa56c882 100644
--- a/doc/src/compute_temp.txt
+++ b/doc/src/compute_temp.txt
@@ -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
diff --git a/doc/src/compute_temp_partial.txt b/doc/src/compute_temp_partial.txt
index fe2420b4e4..59ec8cf20b 100644
--- a/doc/src/compute_temp_partial.txt
+++ b/doc/src/compute_temp_partial.txt
@@ -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
diff --git a/doc/src/dihedral_charmm.txt b/doc/src/dihedral_charmm.txt
index 06abe054e4..f808649a44 100644
--- a/doc/src/dihedral_charmm.txt
+++ b/doc/src/dihedral_charmm.txt
@@ -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
diff --git a/doc/src/dihedral_class2.txt b/doc/src/dihedral_class2.txt
index cb9fc72c22..41282b22a3 100644
--- a/doc/src/dihedral_class2.txt
+++ b/doc/src/dihedral_class2.txt
@@ -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
diff --git a/doc/src/dihedral_cosine_shift_exp.txt b/doc/src/dihedral_cosine_shift_exp.txt
index 715682affc..483745be41 100644
--- a/doc/src/dihedral_cosine_shift_exp.txt
+++ b/doc/src/dihedral_cosine_shift_exp.txt
@@ -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
diff --git a/doc/src/dihedral_fourier.txt b/doc/src/dihedral_fourier.txt
index 0accbb22bf..0270139f68 100644
--- a/doc/src/dihedral_fourier.txt
+++ b/doc/src/dihedral_fourier.txt
@@ -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
diff --git a/doc/src/dihedral_harmonic.txt b/doc/src/dihedral_harmonic.txt
index d9a48ff384..a25a7969fe 100644
--- a/doc/src/dihedral_harmonic.txt
+++ b/doc/src/dihedral_harmonic.txt
@@ -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
diff --git a/doc/src/dihedral_helix.txt b/doc/src/dihedral_helix.txt
index 1e907557b2..814962a472 100644
--- a/doc/src/dihedral_helix.txt
+++ b/doc/src/dihedral_helix.txt
@@ -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
diff --git a/doc/src/dihedral_multi_harmonic.txt b/doc/src/dihedral_multi_harmonic.txt
index 7d3c2ea083..62cad4141a 100644
--- a/doc/src/dihedral_multi_harmonic.txt
+++ b/doc/src/dihedral_multi_harmonic.txt
@@ -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
diff --git a/doc/src/dihedral_nharmonic.txt b/doc/src/dihedral_nharmonic.txt
index 8392d83899..a49979fa66 100644
--- a/doc/src/dihedral_nharmonic.txt
+++ b/doc/src/dihedral_nharmonic.txt
@@ -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
diff --git a/doc/src/dihedral_opls.txt b/doc/src/dihedral_opls.txt
index d1a6ba3ff2..9b33173da4 100644
--- a/doc/src/dihedral_opls.txt
+++ b/doc/src/dihedral_opls.txt
@@ -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
diff --git a/doc/src/dihedral_quadratic.txt b/doc/src/dihedral_quadratic.txt
index ca2f5aed40..f90c4b79f1 100644
--- a/doc/src/dihedral_quadratic.txt
+++ b/doc/src/dihedral_quadratic.txt
@@ -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
diff --git a/doc/src/dihedral_table.txt b/doc/src/dihedral_table.txt
index 0b88f26a61..6a480fec93 100644
--- a/doc/src/dihedral_table.txt
+++ b/doc/src/dihedral_table.txt
@@ -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:]
diff --git a/doc/src/fix_addforce.txt b/doc/src/fix_addforce.txt
index b2ac95eabb..5bba9acb3f 100644
--- a/doc/src/fix_addforce.txt
+++ b/doc/src/fix_addforce.txt
@@ -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
diff --git a/doc/src/fix_aveforce.txt b/doc/src/fix_aveforce.txt
index 5d7dec3e6a..4944996695 100644
--- a/doc/src/fix_aveforce.txt
+++ b/doc/src/fix_aveforce.txt
@@ -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
diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt
index c870c73bdc..681986561a 100644
--- a/doc/src/fix_deform.txt
+++ b/doc/src/fix_deform.txt
@@ -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:]
diff --git a/doc/src/fix_dpd_energy.txt b/doc/src/fix_dpd_energy.txt
index 1c10d954d6..4f2b5d573f 100644
--- a/doc/src/fix_dpd_energy.txt
+++ b/doc/src/fix_dpd_energy.txt
@@ -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
diff --git a/doc/src/fix_enforce2d.txt b/doc/src/fix_enforce2d.txt
index 4bbf41d25d..67b351e4b8 100644
--- a/doc/src/fix_enforce2d.txt
+++ b/doc/src/fix_enforce2d.txt
@@ -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
diff --git a/doc/src/fix_eos_table_rx.txt b/doc/src/fix_eos_table_rx.txt
index 0c87874347..f74a838c47 100644
--- a/doc/src/fix_eos_table_rx.txt
+++ b/doc/src/fix_eos_table_rx.txt
@@ -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
diff --git a/doc/src/fix_freeze.txt b/doc/src/fix_freeze.txt
index a63ee4cb32..9619f4120b 100644
--- a/doc/src/fix_freeze.txt
+++ b/doc/src/fix_freeze.txt
@@ -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
diff --git a/doc/src/fix_gravity.txt b/doc/src/fix_gravity.txt
index dae8ac5ed0..f39955d4f8 100644
--- a/doc/src/fix_gravity.txt
+++ b/doc/src/fix_gravity.txt
@@ -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
diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt
index 93c73f5a5d..6ab236e572 100644
--- a/doc/src/fix_langevin.txt
+++ b/doc/src/fix_langevin.txt
@@ -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
diff --git a/doc/src/fix_momentum.txt b/doc/src/fix_momentum.txt
index bcf4465fb8..aa5199ac14 100644
--- a/doc/src/fix_momentum.txt
+++ b/doc/src/fix_momentum.txt
@@ -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:]
diff --git a/doc/src/fix_nh.txt b/doc/src/fix_nh.txt
index 41d0e6438f..e3a39c6bc6 100644
--- a/doc/src/fix_nh.txt
+++ b/doc/src/fix_nh.txt
@@ -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
diff --git a/doc/src/fix_nph_asphere.txt b/doc/src/fix_nph_asphere.txt
index 8c35b6a1a7..ff8c300c47 100644
--- a/doc/src/fix_nph_asphere.txt
+++ b/doc/src/fix_nph_asphere.txt
@@ -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:]
diff --git a/doc/src/fix_nph_body.txt b/doc/src/fix_nph_body.txt
index 1e590f1cb3..9263470e9e 100644
--- a/doc/src/fix_nph_body.txt
+++ b/doc/src/fix_nph_body.txt
@@ -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:]
diff --git a/doc/src/fix_nph_sphere.txt b/doc/src/fix_nph_sphere.txt
index 62b45edfd7..ba3b2f6c06 100644
--- a/doc/src/fix_nph_sphere.txt
+++ b/doc/src/fix_nph_sphere.txt
@@ -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:]
diff --git a/doc/src/fix_nphug.txt b/doc/src/fix_nphug.txt
index 292e46f94a..4f696e9590 100644
--- a/doc/src/fix_nphug.txt
+++ b/doc/src/fix_nphug.txt
@@ -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
diff --git a/doc/src/fix_npt_asphere.txt b/doc/src/fix_npt_asphere.txt
index 5f3979e36e..a21caa1042 100644
--- a/doc/src/fix_npt_asphere.txt
+++ b/doc/src/fix_npt_asphere.txt
@@ -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:]
diff --git a/doc/src/fix_npt_body.txt b/doc/src/fix_npt_body.txt
index d89bf19db2..0f678a1b7d 100644
--- a/doc/src/fix_npt_body.txt
+++ b/doc/src/fix_npt_body.txt
@@ -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:]
diff --git a/doc/src/fix_npt_sphere.txt b/doc/src/fix_npt_sphere.txt
index c4cf2cb08d..862f95603f 100644
--- a/doc/src/fix_npt_sphere.txt
+++ b/doc/src/fix_npt_sphere.txt
@@ -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:]
diff --git a/doc/src/fix_nve.txt b/doc/src/fix_nve.txt
index c04c17858e..ac9cb53b50 100644
--- a/doc/src/fix_nve.txt
+++ b/doc/src/fix_nve.txt
@@ -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
diff --git a/doc/src/fix_nve_asphere.txt b/doc/src/fix_nve_asphere.txt
index 1f31fb9679..5be7a7aa68 100644
--- a/doc/src/fix_nve_asphere.txt
+++ b/doc/src/fix_nve_asphere.txt
@@ -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
diff --git a/doc/src/fix_nve_sphere.txt b/doc/src/fix_nve_sphere.txt
index 21dc6cba8a..cfe73a854d 100644
--- a/doc/src/fix_nve_sphere.txt
+++ b/doc/src/fix_nve_sphere.txt
@@ -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
diff --git a/doc/src/fix_nvt_asphere.txt b/doc/src/fix_nvt_asphere.txt
index 21b900f16a..031c60e4be 100644
--- a/doc/src/fix_nvt_asphere.txt
+++ b/doc/src/fix_nvt_asphere.txt
@@ -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:]
diff --git a/doc/src/fix_nvt_body.txt b/doc/src/fix_nvt_body.txt
index 6a5e09ba7f..80de7fd7c3 100644
--- a/doc/src/fix_nvt_body.txt
+++ b/doc/src/fix_nvt_body.txt
@@ -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:]
diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt
index 392dbc281c..bb3c092939 100644
--- a/doc/src/fix_nvt_sllod.txt
+++ b/doc/src/fix_nvt_sllod.txt
@@ -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:]
diff --git a/doc/src/fix_nvt_sphere.txt b/doc/src/fix_nvt_sphere.txt
index ecf0922b79..897d5606d7 100644
--- a/doc/src/fix_nvt_sphere.txt
+++ b/doc/src/fix_nvt_sphere.txt
@@ -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:]
diff --git a/doc/src/fix_qeq_comb.txt b/doc/src/fix_qeq_comb.txt
index 7f82404127..783dc3133c 100644
--- a/doc/src/fix_qeq_comb.txt
+++ b/doc/src/fix_qeq_comb.txt
@@ -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
diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt
index 18450c7cd5..a534a66c09 100644
--- a/doc/src/fix_qeq_reax.txt
+++ b/doc/src/fix_qeq_reax.txt
@@ -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
diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt
index 8d803ac6da..f3dd20daa3 100644
--- a/doc/src/fix_rigid.txt
+++ b/doc/src/fix_rigid.txt
@@ -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
diff --git a/doc/src/fix_rx.txt b/doc/src/fix_rx.txt
index 0810a34740..aff3303f43 100644
--- a/doc/src/fix_rx.txt
+++ b/doc/src/fix_rx.txt
@@ -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
diff --git a/doc/src/fix_setforce.txt b/doc/src/fix_setforce.txt
index f5be0f93a5..0af1c92922 100644
--- a/doc/src/fix_setforce.txt
+++ b/doc/src/fix_setforce.txt
@@ -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
diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt
index 46452a1f7e..7428b30a14 100644
--- a/doc/src/fix_shake.txt
+++ b/doc/src/fix_shake.txt
@@ -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
diff --git a/doc/src/fix_shardlow.txt b/doc/src/fix_shardlow.txt
index 24726d8610..6d14346334 100644
--- a/doc/src/fix_shardlow.txt
+++ b/doc/src/fix_shardlow.txt
@@ -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
diff --git a/doc/src/fix_wall.txt b/doc/src/fix_wall.txt
index e814c89a07..959a103f02 100644
--- a/doc/src/fix_wall.txt
+++ b/doc/src/fix_wall.txt
@@ -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
diff --git a/doc/src/fix_wall_reflect.txt b/doc/src/fix_wall_reflect.txt
index 954ec65bf6..5380bdf738 100644
--- a/doc/src/fix_wall_reflect.txt
+++ b/doc/src/fix_wall_reflect.txt
@@ -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
diff --git a/doc/src/improper_class2.txt b/doc/src/improper_class2.txt
index 14ec6258de..ef2abf5091 100644
--- a/doc/src/improper_class2.txt
+++ b/doc/src/improper_class2.txt
@@ -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
diff --git a/doc/src/improper_cossq.txt b/doc/src/improper_cossq.txt
index 138a6a1650..22ba990ba4 100644
--- a/doc/src/improper_cossq.txt
+++ b/doc/src/improper_cossq.txt
@@ -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
diff --git a/doc/src/improper_cvff.txt b/doc/src/improper_cvff.txt
index 5f69eccc60..1662d93b14 100644
--- a/doc/src/improper_cvff.txt
+++ b/doc/src/improper_cvff.txt
@@ -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
diff --git a/doc/src/improper_fourier.txt b/doc/src/improper_fourier.txt
index f9062da207..99132b8931 100644
--- a/doc/src/improper_fourier.txt
+++ b/doc/src/improper_fourier.txt
@@ -48,10 +48,9 @@ all (integer >= 0) :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
diff --git a/doc/src/improper_harmonic.txt b/doc/src/improper_harmonic.txt
index bb17e5a641..f37338e468 100644
--- a/doc/src/improper_harmonic.txt
+++ b/doc/src/improper_harmonic.txt
@@ -58,10 +58,9 @@ 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
@@ -73,8 +72,8 @@ 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
diff --git a/doc/src/improper_ring.txt b/doc/src/improper_ring.txt
index c02d392474..84c35f9f5c 100644
--- a/doc/src/improper_ring.txt
+++ b/doc/src/improper_ring.txt
@@ -57,10 +57,9 @@ theta0 (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
@@ -72,8 +71,8 @@ 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
diff --git a/doc/src/improper_umbrella.txt b/doc/src/improper_umbrella.txt
index d6df9ee6cc..e72cc7f0ad 100644
--- a/doc/src/improper_umbrella.txt
+++ b/doc/src/improper_umbrella.txt
@@ -51,10 +51,9 @@ omega0 (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
@@ -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
diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt
index 4f27c9aa78..8dbb3dde49 100644
--- a/doc/src/kspace_style.txt
+++ b/doc/src/kspace_style.txt
@@ -145,8 +145,8 @@ speedup in the KSpace time (8x less mesh points, 2x more expensive).
However, for low relative accuracy, the staggered PPPM mesh size may
be essentially the same as for regular PPPM, which means the method
will be up to 2x slower in the KSpace time (simply 2x more expensive).
-For more details and timings, see
-"Section 5"_Section_accelerate.html.
+For more details and timings, see the "Speed tips"_Speed_tips.html doc
+page.
NOTE: Using {pppm/stagger} may not give the same increase in the
accuracy of energy and pressure as it does in forces, so some caution
@@ -267,10 +267,9 @@ relative RMS error.
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.
More specifically, the {pppm/gpu} style performs charge assignment and
force interpolation calculations on the GPU. These processes are
@@ -291,8 +290,8 @@ KOKKOS, USER-OMP, and OPT packages respectively. They are only
enabled if LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
-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
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 4274ef48b3..f96960ff39 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -4,13 +4,11 @@ Manual.html
Section_intro.html
Section_start.html
Section_commands.html
-Section_packages.html
-Section_accelerate.html
-accelerate_gpu.html
-accelerate_intel.html
-accelerate_kokkos.html
-accelerate_omp.html
-accelerate_opt.html
+Packages.html
+Packages_standard.html
+Packages_user.html
+Packages_details.html
+Speed.html
Section_howto.html
Examples.html
Section_perf.html
diff --git a/doc/src/package.txt b/doc/src/package.txt
index 5fd42f67d3..81e1db9bd8 100644
--- a/doc/src/package.txt
+++ b/doc/src/package.txt
@@ -149,9 +149,9 @@ the style options are set, either to default values or to specified
settings. I.e. settings from previous invocations do not persist
across multiple invocations.
-See the "Section 5.3"_Section_accelerate.html#acc_3 section of the
-manual for more details about using the various accelerator packages
-for speeding up LAMMPS simulations.
+See the "Speed packages"_Speed_packages.html doc page for more details
+about using the various accelerator packages for speeding up LAMMPS
+simulations.
:line
diff --git a/doc/src/pair_adp.txt b/doc/src/pair_adp.txt
index 9d2a48dcbc..1ba59b7732 100644
--- a/doc/src/pair_adp.txt
+++ b/doc/src/pair_adp.txt
@@ -125,10 +125,9 @@ array tabulated with a scaling by r.
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
@@ -140,8 +139,8 @@ 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
diff --git a/doc/src/pair_agni.txt b/doc/src/pair_agni.txt
index 402e537dad..352e00249a 100644
--- a/doc/src/pair_agni.txt
+++ b/doc/src/pair_agni.txt
@@ -58,11 +58,11 @@ and input files are provided in the examples/USER/misc/agni directory.
:line
Styles with {omp} suffix is 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 style takes the same arguments and
-should produce the same results, except for round-off and precision
-issues.
+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 style takes
+the same arguments and should produce the same results, except for
+round-off and precision issues.
The accelerated style is part of the USER-OMP. They are only enabled if
LAMMPS was built with those packages. See the "Making
@@ -73,8 +73,8 @@ 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
diff --git a/doc/src/pair_airebo.txt b/doc/src/pair_airebo.txt
index 1aa017f278..b5add21f24 100644
--- a/doc/src/pair_airebo.txt
+++ b/doc/src/pair_airebo.txt
@@ -176,10 +176,9 @@ thermo_style custom step temp epair v_REBO v_LJ v_TORSION :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
@@ -191,8 +190,8 @@ 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
diff --git a/doc/src/pair_beck.txt b/doc/src/pair_beck.txt
index e160f09b3d..1aca4b4f9a 100644
--- a/doc/src/pair_beck.txt
+++ b/doc/src/pair_beck.txt
@@ -51,10 +51,9 @@ Rc is used.
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
diff --git a/doc/src/pair_born.txt b/doc/src/pair_born.txt
index f867107426..2504fb7e25 100644
--- a/doc/src/pair_born.txt
+++ b/doc/src/pair_born.txt
@@ -145,10 +145,9 @@ pair_style command.
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
@@ -160,8 +159,8 @@ 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
diff --git a/doc/src/pair_buck.txt b/doc/src/pair_buck.txt
index d18b39d5d9..de247b9c01 100644
--- a/doc/src/pair_buck.txt
+++ b/doc/src/pair_buck.txt
@@ -140,10 +140,9 @@ pair_style command.
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
diff --git a/doc/src/pair_buck_long.txt b/doc/src/pair_buck_long.txt
index 05e760e1b2..94bf6a2d7c 100644
--- a/doc/src/pair_buck_long.txt
+++ b/doc/src/pair_buck_long.txt
@@ -102,10 +102,9 @@ global Coulombic cutoff is allowed.
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
@@ -117,8 +116,8 @@ 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
diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt
index 75a8e4bff9..af20661bbd 100644
--- a/doc/src/pair_charmm.txt
+++ b/doc/src/pair_charmm.txt
@@ -184,10 +184,9 @@ the pair_style command.
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
@@ -199,8 +198,8 @@ 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
diff --git a/doc/src/pair_class2.txt b/doc/src/pair_class2.txt
index 36fae5068b..e62971a645 100644
--- a/doc/src/pair_class2.txt
+++ b/doc/src/pair_class2.txt
@@ -102,10 +102,9 @@ cutoff distance.
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
@@ -117,8 +116,8 @@ 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
diff --git a/doc/src/pair_colloid.txt b/doc/src/pair_colloid.txt
index 83b15b358b..a7bb0db08a 100644
--- a/doc/src/pair_colloid.txt
+++ b/doc/src/pair_colloid.txt
@@ -127,10 +127,9 @@ commands for efficiency: "neighbor multi"_neighbor.html and
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
@@ -142,8 +141,8 @@ 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
diff --git a/doc/src/pair_comb.txt b/doc/src/pair_comb.txt
index f5461b1cbc..6949ca50c2 100644
--- a/doc/src/pair_comb.txt
+++ b/doc/src/pair_comb.txt
@@ -112,10 +112,9 @@ nor file {ffield.comb3} with style {comb}.
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
@@ -127,8 +126,8 @@ 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
diff --git a/doc/src/pair_coul.txt b/doc/src/pair_coul.txt
index aa3a008bd3..650575d055 100644
--- a/doc/src/pair_coul.txt
+++ b/doc/src/pair_coul.txt
@@ -268,10 +268,9 @@ command.
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
@@ -283,8 +282,8 @@ 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
diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt
index 2516e5eae4..e7d196d599 100644
--- a/doc/src/pair_dipole.txt
+++ b/doc/src/pair_dipole.txt
@@ -186,10 +186,9 @@ type pair.
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
diff --git a/doc/src/pair_dpd.txt b/doc/src/pair_dpd.txt
index 9e29e93430..a36029ea63 100644
--- a/doc/src/pair_dpd.txt
+++ b/doc/src/pair_dpd.txt
@@ -110,10 +110,9 @@ random force.
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
@@ -125,8 +124,8 @@ 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
diff --git a/doc/src/pair_dpd_fdt.txt b/doc/src/pair_dpd_fdt.txt
index 867f3f2315..129d3c84af 100644
--- a/doc/src/pair_dpd_fdt.txt
+++ b/doc/src/pair_dpd_fdt.txt
@@ -129,10 +129,9 @@ significantly larger timesteps to be taken.
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
@@ -144,8 +143,8 @@ 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
diff --git a/doc/src/pair_eam.txt b/doc/src/pair_eam.txt
index 03e77f53ab..8d4d11341c 100644
--- a/doc/src/pair_eam.txt
+++ b/doc/src/pair_eam.txt
@@ -371,10 +371,9 @@ are listed.
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
@@ -386,7 +385,7 @@ by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-See "Section 5"_Section_accelerate.html of the manual for more
+See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt
index e5b1420b59..f0d1927812 100644
--- a/doc/src/pair_edip.txt
+++ b/doc/src/pair_edip.txt
@@ -109,10 +109,9 @@ the EDIP package.
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.
:line
diff --git a/doc/src/pair_eim.txt b/doc/src/pair_eim.txt
index 75ad2d4683..7f94d919f2 100644
--- a/doc/src/pair_eim.txt
+++ b/doc/src/pair_eim.txt
@@ -136,10 +136,9 @@ needs.
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
@@ -151,8 +150,8 @@ 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
diff --git a/doc/src/pair_exp6_rx.txt b/doc/src/pair_exp6_rx.txt
index 7eafa23543..dec660fd1d 100644
--- a/doc/src/pair_exp6_rx.txt
+++ b/doc/src/pair_exp6_rx.txt
@@ -153,10 +153,9 @@ pair interaction.
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
@@ -168,8 +167,8 @@ 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
diff --git a/doc/src/pair_gauss.txt b/doc/src/pair_gauss.txt
index f6f46a2de8..7716f89f17 100644
--- a/doc/src/pair_gauss.txt
+++ b/doc/src/pair_gauss.txt
@@ -84,10 +84,9 @@ is used.
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
@@ -99,8 +98,8 @@ by including their suffix, or you can use the "-suffix command-line
switch7_Section_start.html#start_6 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
-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
diff --git a/doc/src/pair_gayberne.txt b/doc/src/pair_gayberne.txt
index c923578586..e9a98a0b84 100644
--- a/doc/src/pair_gayberne.txt
+++ b/doc/src/pair_gayberne.txt
@@ -133,10 +133,9 @@ pair_coeff sigma to 1.0 as well.
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
@@ -148,8 +147,8 @@ 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
diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt
index d7e87af013..86b04f96de 100644
--- a/doc/src/pair_gran.txt
+++ b/doc/src/pair_gran.txt
@@ -179,10 +179,9 @@ potential.
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
@@ -194,8 +193,8 @@ 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
diff --git a/doc/src/pair_gromacs.txt b/doc/src/pair_gromacs.txt
index ec84a2d57a..7daf805e2b 100644
--- a/doc/src/pair_gromacs.txt
+++ b/doc/src/pair_gromacs.txt
@@ -91,10 +91,9 @@ cutoff(s) specified in the pair_style command.
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
@@ -106,8 +105,8 @@ 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
diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/src/pair_hbond_dreiding.txt
index d3cf90ec14..45f852c254 100644
--- a/doc/src/pair_hbond_dreiding.txt
+++ b/doc/src/pair_hbond_dreiding.txt
@@ -166,10 +166,9 @@ optional parameters.
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
@@ -181,8 +180,8 @@ 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
diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt
index d37dedc709..9503256d26 100644
--- a/doc/src/pair_hybrid.txt
+++ b/doc/src/pair_hybrid.txt
@@ -315,8 +315,8 @@ off C/C interaction, i.e. by setting the appropriate coefficients 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.
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page.
Since the {hybrid} and {hybrid/overlay} styles delegate computation to
the individual sub-styles, the suffix versions of the {hybrid} and
@@ -334,8 +334,8 @@ 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
diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt
index c5d910e27c..fc2c1405af 100644
--- a/doc/src/pair_kim.txt
+++ b/doc/src/pair_kim.txt
@@ -46,8 +46,8 @@ are included in the KIM library by default, in the "What is in the KIM
API source package?" section.
To use this pair style, you must first download and install the KIM
-API library from the "OpenKIM website"_https://openkim.org. The "KIM
-section of Section packages"_Section_packages.html#KIM has
+API library from the "OpenKIM website"_https://openkim.org. The KIM
+section of the "Packages details"_Packages_details.html doc page has
instructions on how to do this with a simple make command, when
building LAMMPS.
diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt
index e297d479bc..c2968ffdf3 100644
--- a/doc/src/pair_lj.txt
+++ b/doc/src/pair_lj.txt
@@ -269,10 +269,9 @@ pair_style command.
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
@@ -284,8 +283,8 @@ 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
diff --git a/doc/src/pair_lj96.txt b/doc/src/pair_lj96.txt
index 83f6ec063d..a0a9971474 100644
--- a/doc/src/pair_lj96.txt
+++ b/doc/src/pair_lj96.txt
@@ -49,10 +49,9 @@ cutoff specified in the pair_style command is used.
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
@@ -64,8 +63,8 @@ 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
diff --git a/doc/src/pair_lj_cubic.txt b/doc/src/pair_lj_cubic.txt
index 4ca8c3c141..c4e2af5062 100644
--- a/doc/src/pair_lj_cubic.txt
+++ b/doc/src/pair_lj_cubic.txt
@@ -63,10 +63,9 @@ located at rmin = 2^(1/6)*sigma. In the above example, sigma =
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
@@ -78,8 +77,8 @@ 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
diff --git a/doc/src/pair_lj_expand.txt b/doc/src/pair_lj_expand.txt
index e0838426f6..c156fefef2 100644
--- a/doc/src/pair_lj_expand.txt
+++ b/doc/src/pair_lj_expand.txt
@@ -53,10 +53,9 @@ optional. If not specified, the global LJ cutoff is used.
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
diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt
index 6be4562d18..bc851adb74 100644
--- a/doc/src/pair_lj_long.txt
+++ b/doc/src/pair_lj_long.txt
@@ -156,10 +156,9 @@ specified in the pair_style command.
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
diff --git a/doc/src/pair_lj_smooth.txt b/doc/src/pair_lj_smooth.txt
index b1678cad58..653520966b 100644
--- a/doc/src/pair_lj_smooth.txt
+++ b/doc/src/pair_lj_smooth.txt
@@ -62,10 +62,9 @@ specified, the global values for Rin and Rc are used.
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
diff --git a/doc/src/pair_lj_smooth_linear.txt b/doc/src/pair_lj_smooth_linear.txt
index 5f7c226cee..aebde2e653 100644
--- a/doc/src/pair_lj_smooth_linear.txt
+++ b/doc/src/pair_lj_smooth_linear.txt
@@ -49,10 +49,9 @@ LJ cutoff specified in the pair_style command is used.
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
@@ -64,8 +63,8 @@ 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
diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_lj_soft.txt
index 2ef133da55..7add9f623d 100644
--- a/doc/src/pair_lj_soft.txt
+++ b/doc/src/pair_lj_soft.txt
@@ -207,10 +207,9 @@ directory tree, under examples/USER/fep.
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
@@ -222,8 +221,8 @@ 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
diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt
index 6653b397a0..74242e32b9 100644
--- a/doc/src/pair_meam_spline.txt
+++ b/doc/src/pair_meam_spline.txt
@@ -106,10 +106,9 @@ MEAM files.
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
@@ -121,8 +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
diff --git a/doc/src/pair_morse.txt b/doc/src/pair_morse.txt
index 3eb5ac5afe..34876011a1 100644
--- a/doc/src/pair_morse.txt
+++ b/doc/src/pair_morse.txt
@@ -101,10 +101,9 @@ cutoff is used.
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
@@ -116,8 +115,8 @@ 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
diff --git a/doc/src/pair_multi_lucy_rx.txt b/doc/src/pair_multi_lucy_rx.txt
index 57abcf4a4c..b043030907 100644
--- a/doc/src/pair_multi_lucy_rx.txt
+++ b/doc/src/pair_multi_lucy_rx.txt
@@ -204,10 +204,9 @@ This pair style can only be used via the {pair} keyword of the
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
@@ -219,8 +218,8 @@ 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
diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/src/pair_nb3b_harmonic.txt
index 2395707fb4..e6e103f517 100644
--- a/doc/src/pair_nb3b_harmonic.txt
+++ b/doc/src/pair_nb3b_harmonic.txt
@@ -92,10 +92,9 @@ a particular simulation; LAMMPS ignores those entries.
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
@@ -107,8 +106,8 @@ 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
diff --git a/doc/src/pair_nm.txt b/doc/src/pair_nm.txt
index 81cea1a38d..08c3393993 100644
--- a/doc/src/pair_nm.txt
+++ b/doc/src/pair_nm.txt
@@ -133,10 +133,9 @@ the "run_style respa"_run_style.html command. They do not support the
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
@@ -148,8 +147,8 @@ 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:]
diff --git a/doc/src/pair_peri.txt b/doc/src/pair_peri.txt
index deca093e3b..4327003057 100644
--- a/doc/src/pair_peri.txt
+++ b/doc/src/pair_peri.txt
@@ -139,10 +139,9 @@ details please see the description in "(Mtchell2011a)".
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
@@ -154,8 +153,8 @@ 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
diff --git a/doc/src/pair_reaxc.txt b/doc/src/pair_reaxc.txt
index 39759b3111..8d8c7e84e7 100644
--- a/doc/src/pair_reaxc.txt
+++ b/doc/src/pair_reaxc.txt
@@ -50,11 +50,11 @@ as a package.
The {reax/c/kk} style is a Kokkos version of the ReaxFF potential that
is derived from the {reax/c} style. The Kokkos version can run on GPUs
and can also use OpenMP multithreading. For more information about the
-Kokkos package, see "Section 4"_Section_packages.html#kokkos and
-"Section 5.3.3"_accelerate_kokkos.html. One important consideration
-when using the {reax/c/kk} style is the choice of either half or full
-neighbor lists. This setting can be changed using the Kokkos
-"package"_package.html command.
+Kokkos package, see "Packages details"_Packages_details.html and
+"Speed kokkos"_Speed_kokkos.html doc pages. One important
+consideration when using the {reax/c/kk} style is the choice of either
+half or full neighbor lists. This setting can be changed using the
+Kokkos "package"_package.html command.
The {reax/c} style differs from the "pair_style reax"_pair_reax.html
command in the lo-level implementation details. The {reax} style is a
@@ -303,10 +303,9 @@ This pair style can only be used via the {pair} keyword of the
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
@@ -318,8 +317,8 @@ 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
diff --git a/doc/src/pair_resquared.txt b/doc/src/pair_resquared.txt
index 9ad95eb5fc..6ea5c73c0d 100644
--- a/doc/src/pair_resquared.txt
+++ b/doc/src/pair_resquared.txt
@@ -145,10 +145,9 @@ specified in the pair_style command is used.
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
@@ -160,8 +159,8 @@ 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
diff --git a/doc/src/pair_sdk.txt b/doc/src/pair_sdk.txt
index 360136a4ea..4cd56bc43d 100644
--- a/doc/src/pair_sdk.txt
+++ b/doc/src/pair_sdk.txt
@@ -85,10 +85,9 @@ pair_style command.
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.
:line
diff --git a/doc/src/pair_snap.txt b/doc/src/pair_snap.txt
index 27dcf6082b..c3d6e67e82 100644
--- a/doc/src/pair_snap.txt
+++ b/doc/src/pair_snap.txt
@@ -175,10 +175,9 @@ This pair style can only be used via the {pair} keyword of the
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
@@ -190,8 +189,8 @@ 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
diff --git a/doc/src/pair_soft.txt b/doc/src/pair_soft.txt
index 08fa88c477..adbfa596c9 100644
--- a/doc/src/pair_soft.txt
+++ b/doc/src/pair_soft.txt
@@ -82,10 +82,9 @@ variables.
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
@@ -97,8 +96,8 @@ 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
diff --git a/doc/src/pair_sw.txt b/doc/src/pair_sw.txt
index 4932fe55d3..7c9ce4a4f9 100644
--- a/doc/src/pair_sw.txt
+++ b/doc/src/pair_sw.txt
@@ -144,10 +144,9 @@ taken from the ij and ik pairs (sigma, a, gamma)
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
@@ -164,8 +163,8 @@ additional 5 to 10 percent performance improvement when the
Stillinger-Weber parameters p and q are set to 4 and 0 respectively.
These parameters are common for modeling silicon and water.
-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
diff --git a/doc/src/pair_table.txt b/doc/src/pair_table.txt
index b99491b477..f5e69a6d54 100644
--- a/doc/src/pair_table.txt
+++ b/doc/src/pair_table.txt
@@ -217,10 +217,9 @@ 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
@@ -232,8 +231,8 @@ 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
diff --git a/doc/src/pair_table_rx.txt b/doc/src/pair_table_rx.txt
index cd3a7ef31b..52760c396b 100644
--- a/doc/src/pair_table_rx.txt
+++ b/doc/src/pair_table_rx.txt
@@ -227,10 +227,9 @@ This pair style can only be used via the {pair} keyword of the
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
@@ -242,8 +241,8 @@ 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
diff --git a/doc/src/pair_tersoff.txt b/doc/src/pair_tersoff.txt
index 918e889924..70fe207f0a 100644
--- a/doc/src/pair_tersoff.txt
+++ b/doc/src/pair_tersoff.txt
@@ -179,10 +179,9 @@ defined in various papers.
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
@@ -194,8 +193,8 @@ 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
diff --git a/doc/src/pair_tersoff_mod.txt b/doc/src/pair_tersoff_mod.txt
index e0c2b5a5cb..aced6d40d6 100644
--- a/doc/src/pair_tersoff_mod.txt
+++ b/doc/src/pair_tersoff_mod.txt
@@ -131,10 +131,9 @@ for SiSiSi means Si bonded to a Si with another Si atom influencing the bond.
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
@@ -146,8 +145,8 @@ 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
diff --git a/doc/src/pair_tersoff_zbl.txt b/doc/src/pair_tersoff_zbl.txt
index 21d57e4e88..838c2f39cf 100644
--- a/doc/src/pair_tersoff_zbl.txt
+++ b/doc/src/pair_tersoff_zbl.txt
@@ -189,10 +189,9 @@ providing the base ZBL implementation.
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
@@ -204,8 +203,8 @@ 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
diff --git a/doc/src/pair_thole.txt b/doc/src/pair_thole.txt
index 41a4059cee..11d4b85cff 100644
--- a/doc/src/pair_thole.txt
+++ b/doc/src/pair_thole.txt
@@ -130,10 +130,9 @@ the {pair_style} command line.
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.
[Mixing]:
diff --git a/doc/src/pair_ufm.txt b/doc/src/pair_ufm.txt
index 88a22864cc..5af8741502 100644
--- a/doc/src/pair_ufm.txt
+++ b/doc/src/pair_ufm.txt
@@ -69,10 +69,9 @@ NOTE: The thermodynamic integration procedure can be performed with this potenti
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
@@ -84,8 +83,8 @@ 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
diff --git a/doc/src/pair_vashishta.txt b/doc/src/pair_vashishta.txt
index d9c66d45c0..e90a9d8f50 100644
--- a/doc/src/pair_vashishta.txt
+++ b/doc/src/pair_vashishta.txt
@@ -171,10 +171,9 @@ two-body parameters from the CCC and CSiSi entries.
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
@@ -186,8 +185,8 @@ 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
diff --git a/doc/src/pair_yukawa.txt b/doc/src/pair_yukawa.txt
index e7c063ded9..979165dda0 100644
--- a/doc/src/pair_yukawa.txt
+++ b/doc/src/pair_yukawa.txt
@@ -49,10 +49,9 @@ cutoff is used.
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
@@ -64,8 +63,8 @@ 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
diff --git a/doc/src/pair_yukawa_colloid.txt b/doc/src/pair_yukawa_colloid.txt
index 2037a9451f..a1752c261e 100644
--- a/doc/src/pair_yukawa_colloid.txt
+++ b/doc/src/pair_yukawa_colloid.txt
@@ -80,10 +80,9 @@ yukawa/colloid cutoff is used.
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
diff --git a/doc/src/pair_zbl.txt b/doc/src/pair_zbl.txt
index 1984cd831f..0507083295 100644
--- a/doc/src/pair_zbl.txt
+++ b/doc/src/pair_zbl.txt
@@ -71,10 +71,9 @@ copper.
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.
:line
diff --git a/doc/src/region.txt b/doc/src/region.txt
index 5039e4a516..1ac3861e67 100644
--- a/doc/src/region.txt
+++ b/doc/src/region.txt
@@ -358,12 +358,12 @@ sub-regions can be defined with the {open} keyword.
:line
-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.
+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 code using the region (such as a fix or compute) must also be supported
by Kokkos or no acceleration will occur. Currently, only {block} style
@@ -378,8 +378,8 @@ 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
diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt
index 7717ede86f..a896a648af 100644
--- a/doc/src/run_style.txt
+++ b/doc/src/run_style.txt
@@ -119,13 +119,13 @@ switches"_Section_start.html#start_6 to change this. The log and
screen file for the 2nd partition will not contain thermodynamic
output beyond the 1st timestep of the run.
-See "Section 5"_Section_accelerate.html of the manual for
-performance details of the speed-up offered by the {verlet/split}
-style. One important performance consideration is the assignment of
-logical processors in the 2 partitions to the physical cores of a
-parallel machine. The "processors"_processors.html command has
-options to support this, and strategies are discussed in
-"Section 5"_Section_accelerate.html of the manual.
+See the "Speed packages"_Speed_packages.html doc page for performance
+details of the speed-up offered by the {verlet/split} style. One
+important performance consideration is the assignment of logical
+processors in the 2 partitions to the physical cores of a parallel
+machine. The "processors"_processors.html command has options to
+support this, and strategies are discussed in "Section
+5"_Section_accelerate.html of the manual.
:line
@@ -274,21 +274,21 @@ run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3 :pre
:line
-The {respa/omp} styles is a variant of {respa} adapted for use with
+The {respa/omp} style is a variant of {respa} adapted for use with
pair, bond, angle, dihedral, improper, or kspace styles with an {omp}
-suffix. It is functionally equivalent to {respa} but performs additional
-operations required for managing {omp} styles. For more on {omp} styles
-see the "Section 5"_Section_accelerate.html of the manual.
-Accelerated styles take the same arguments and should produce the same
-results, except for round-off and precision issues.
+suffix. It is functionally equivalent to {respa} but performs
+additional operations required for managing {omp} styles. For more on
+{omp} styles see the "Speed omp"_Speed_omp.html doc page. Accelerated
+styles take the same arguments and should produce the same results,
+except for round-off and precision issues.
You can specify {respa/omp} explicitly in your input script, or
you can use the "-suffix command-line switch"_Section_start.html#start_6
when you invoke LAMMPS, or you can use the "suffix"_suffix.html
command in your input script.
-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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