From 5e6dff36e4e12ff93228009abba034607a6d4734 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Sep 2016 02:01:47 -0400 Subject: [PATCH 01/18] add new commands to lammps.book --- doc/lammps.book | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/lammps.book b/doc/lammps.book index f768cdc7d3..f28bb48b56 100644 --- a/doc/lammps.book +++ b/doc/lammps.book @@ -148,6 +148,7 @@ fix_bond_create.html fix_bond_swap.html fix_box_relax.html fix_colvars.html +fix_controller.html fix_deform.html fix_deposit.html fix_drag.html @@ -162,6 +163,7 @@ fix_eos_table.html fix_eos_table_rx.html fix_evaporate.html fix_external.html +fix_flow_gauss.html fix_freeze.html fix_gcmc.html fix_gld.html From fc093a0aab1760e1edf30c968516f9b95f6720d6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Sep 2016 02:07:16 -0400 Subject: [PATCH 02/18] replace :ule,l and :ole,l with :l
:ule and :l
:ole --- doc/src/Manual.txt | 3 ++- doc/src/Section_accelerate.txt | 5 +++-- doc/src/Section_intro.txt | 3 ++- doc/src/Section_perf.txt | 3 ++- doc/src/dihedral_harmonic.txt | 3 ++- doc/src/dump_image.txt | 3 ++- doc/src/suffix.txt | 3 ++- doc/src/tutorial_drude.txt | 6 ++++-- 8 files changed, 19 insertions(+), 10 deletions(-) diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index adf6b5c47e..f4ff4542aa 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -47,7 +47,8 @@ it to be part of every patch. :l There is also a "Developer.pdf"_Developer.pdf file in the doc directory, which describes the internal structure and algorithms of -LAMMPS. :ule,l +LAMMPS. :l +:ule LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. diff --git a/doc/src/Section_accelerate.txt b/doc/src/Section_accelerate.txt index 9977853b43..e002cbb5f9 100644 --- a/doc/src/Section_accelerate.txt +++ b/doc/src/Section_accelerate.txt @@ -28,8 +28,9 @@ multi-core CPUs, GPUs, and Intel Xeon Phi coprocessors. 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,ule -5.4 "Comparison of various accelerator packages"_#acc_4 :l,ule + 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 diff --git a/doc/src/Section_intro.txt b/doc/src/Section_intro.txt index 99751a13ff..089921d45d 100644 --- a/doc/src/Section_intro.txt +++ b/doc/src/Section_intro.txt @@ -460,7 +460,8 @@ Site"_lws. It might be added to the page. No promises. :l Cash. Small denominations, unmarked bills preferred. Paper sack OK. Leave on desk. VISA also accepted. Chocolate chip cookies -encouraged. :ule,l +encouraged. :l +:ule :line diff --git a/doc/src/Section_perf.txt b/doc/src/Section_perf.txt index d1cafa0bda..fc59dbe1dc 100644 --- a/doc/src/Section_perf.txt +++ b/doc/src/Section_perf.txt @@ -36,7 +36,8 @@ sigma cutoff (7 neighbors per atom), NVE integration :l Rhodo = rhodopsin protein in solvated lipid bilayer, CHARMM force field with a 10 Angstrom LJ cutoff (440 neighbors per atom), particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT -integration :ole,l +integration :l +:ole Input files for these 5 problems are provided in the bench directory of the LAMMPS distribution. Each has 32,000 atoms and runs for 100 diff --git a/doc/src/dihedral_harmonic.txt b/doc/src/dihedral_harmonic.txt index ac124ffd48..1de4370a46 100644 --- a/doc/src/dihedral_harmonic.txt +++ b/doc/src/dihedral_harmonic.txt @@ -45,7 +45,8 @@ in some force fields trans = 0 degrees. :ulb,l Some force fields reverse the sign convention on {d}. :l Some force fields let {n} be positive or negative which corresponds to -{d} = 1 or -1 for the harmonic style. :ule,l +{d} = 1 or -1 for the harmonic style. :l +:ule :line diff --git a/doc/src/dump_image.txt b/doc/src/dump_image.txt index 826c3f992b..2f2ca4809b 100644 --- a/doc/src/dump_image.txt +++ b/doc/src/dump_image.txt @@ -598,7 +598,8 @@ obviously play movie files directly. Similarly for corresponding tools bundled with Linux desktop environments. However, due to licensing issues with some file formats, the formats may require installing additional libraries, purchasing a license, or may not be -supported. :ule,l +supported. :l +:ule :line diff --git a/doc/src/suffix.txt b/doc/src/suffix.txt index 51aead3f37..7450d27baf 100644 --- a/doc/src/suffix.txt +++ b/doc/src/suffix.txt @@ -59,7 +59,8 @@ multi-threading :l OPT = a handful of pair styles, cache-optimized for faster CPU performance :l -HYBRID = a combination of two packages can be specified (see below) :ule,l +HYBRID = a combination of two packages can be specified (see below) :l +:ule As an example, all of the packages provide a "pair_style lj/cut"_pair_lj.html variant, with style names lj/cut/opt, lj/cut/omp, diff --git a/doc/src/tutorial_drude.txt b/doc/src/tutorial_drude.txt index 3ab8afcae3..a6080fef27 100644 --- a/doc/src/tutorial_drude.txt +++ b/doc/src/tutorial_drude.txt @@ -67,7 +67,8 @@ for all Drude particles, and to calculate the force constant for each \ type of core-Drude bond from equation (1). The timesteps used by these \ authors are between 0.5 and 2 fs, with the degrees of freedom of the \ Drude oscillators kept cold at 1 K. :l -In both these force fields hydrogen atoms are treated as non-polarizable. :ule,l +In both these force fields hydrogen atoms are treated as non-polarizable. :l +:ule The motion of of the Drude particles can be calculated by minimizing @@ -104,7 +105,8 @@ due to the short distances, so an atom may capture the Drude particle \ (shell) of a neighbor, or the induced dipoles within the same molecule \ may align too much. To avoid this, damping at short of the \ interactions between the point charges composing the induced dipole \ -can be done by "Thole"_#Thole functions. :ole,l +can be done by "Thole"_#Thole functions. :l +:ole :line From ab84acc2cdfc77a9018014d22eb7a632d1afa7f2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Sep 2016 02:26:49 -0400 Subject: [PATCH 03/18] synchronize LAMMPS developer list with webpage and move ray to "past" --- doc/html/Manual.html | 15 ++++++++++----- doc/src/Manual.txt | 17 ++++++++++++----- 2 files changed, 22 insertions(+), 10 deletions(-) diff --git a/doc/html/Manual.html b/doc/html/Manual.html index 5c7ec2f31d..7c9ef3678f 100644 --- a/doc/html/Manual.html +++ b/doc/html/Manual.html @@ -166,11 +166,16 @@ run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL).

-

The primary developers of LAMMPS are Steve Plimpton, Aidan -Thompson, and Paul Crozier who can be contacted at -sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at -http://lammps.sandia.gov has more information about the code and its -uses.

+

The core group of LAMMPS developers is at Sandia National Labs and Temple University:

+
    +
  • Steve Plimpton, sjplimp at sandia.gov
    • +
  • Aidan Thompson, athomps at sandia.gov
    • +
  • Stan Moore, stamoore at sandia.gov
    • +
  • Axel Kohlmeyer, akohlmey at gmail.com
    • +
+

Past core developers include Paul Crozier, Ray Shan and Mark Stevens, all at Sandia. +The LAMMPS WWW Site at “http://lammps.sandia.gov:_http://lammps.sandia.gov +has more information about the code and its uses.

The LAMMPS documentation is organized into the following sections. If you find errors or omissions in this manual or have suggestions for diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index f4ff4542aa..6b6760c3dc 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -59,14 +59,21 @@ National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL). -The primary developers of LAMMPS are "Steve Plimpton"_sjp, Aidan -Thompson, and Paul Crozier who can be contacted at -sjplimp,athomps,pscrozi at sandia.gov. The "LAMMPS WWW Site"_lws at -http://lammps.sandia.gov has more information about the code and its -uses. +The core group of LAMMPS developers is at Sandia National Labs and Temple University: + +"Steve Plimpton"_sjp, sjplimp at sandia.gov :ulb,l +Aidan Thompson, athomps at sandia.gov :l +Stan Moore, stamoore at sandia.gov :l +"Axel Kohlmeyer"_ako, akohlmey at gmail.com :l +:ulb + +Past core developers include Paul Crozier, Ray Shan and Mark Stevens, all at Sandia. +The "LAMMPS WWW Site"_lws at "http://lammps.sandia.gov:_http://lammps.sandia.gov +has more information about the code and its uses. :link(bug,http://lammps.sandia.gov/bug.html) :link(sjp,http://www.sandia.gov/~sjplimp) +:link(ako,http://goo.gl/1wk0) :line From 431d1a6dae03584491ae2194717492400d57f185 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 1 Sep 2016 02:37:55 -0400 Subject: [PATCH 04/18] mention stable releases --- doc/html/Manual.html | 6 ++++-- doc/src/Manual.txt | 7 +++++-- 2 files changed, 9 insertions(+), 4 deletions(-) diff --git a/doc/html/Manual.html b/doc/html/Manual.html index 7c9ef3678f..bcee2c07fd 100644 --- a/doc/html/Manual.html +++ b/doc/html/Manual.html @@ -141,7 +141,9 @@

Version info:

The LAMMPS “version” is the date when it was released, such as 1 May 2010. LAMMPS is updated continuously. Whenever we fix a bug or add a -feature, we release it immediately, and post a notice on this page of the WWW site. Each dated copy of LAMMPS contains all the +feature, we release it immediately, and post a notice on this page of the WWW site. Every 2-4 months one of the incremental releases +is subjected to more thorough testing and labeled as a stable version.

+

Each dated copy of LAMMPS contains all the features and bug-fixes up to and including that version date. The version date is printed to the screen and logfile every time you run LAMMPS. It is also in the file src/version.h and in the LAMMPS @@ -174,7 +176,7 @@ under the terms of the GNU Public License (GPL).

  • Axel Kohlmeyer, akohlmey at gmail.com

    • Past core developers include Paul Crozier, Ray Shan and Mark Stevens, all at Sandia. -The LAMMPS WWW Site at “http://lammps.sandia.gov:_http://lammps.sandia.gov +The LAMMPS home page at http://lammps.sandia.gov has more information about the code and its uses.

    The LAMMPS documentation is organized into the following sections. If diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index 6b6760c3dc..e53fddef7d 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -28,7 +28,10 @@ Version info: :h4 The LAMMPS "version" is the date when it was released, such as 1 May 2010. LAMMPS is updated continuously. Whenever we fix a bug or add a feature, we release it immediately, and post a notice on "this page of -the WWW site"_bug. Each dated copy of LAMMPS contains all the +the WWW site"_bug. Every 2-4 months one of the incremental releases +is subjected to more thorough testing and labeled as a {stable} version. + +Each dated copy of LAMMPS contains all the features and bug-fixes up to and including that version date. The version date is printed to the screen and logfile every time you run LAMMPS. It is also in the file src/version.h and in the LAMMPS @@ -68,7 +71,7 @@ Stan Moore, stamoore at sandia.gov :l :ulb Past core developers include Paul Crozier, Ray Shan and Mark Stevens, all at Sandia. -The "LAMMPS WWW Site"_lws at "http://lammps.sandia.gov:_http://lammps.sandia.gov +The [LAMMPS home page] at "http://lammps.sandia.gov"_http://lammps.sandia.gov has more information about the code and its uses. :link(bug,http://lammps.sandia.gov/bug.html) From fc2d878305382c1760c71422f093cc7f49fdb6d6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 6 Sep 2016 21:20:47 -0400 Subject: [PATCH 05/18] update manual introduction to represent current status. correct some markup to better pass through sphinx --- doc/html/Manual.html | 12 ++++--- doc/html/Section_accelerate.html | 54 +++++++++++--------------------- doc/html/Section_howto.html | 2 +- doc/src/Manual.txt | 12 ++++--- doc/src/Section_accelerate.txt | 31 +++++++++--------- doc/src/Section_howto.txt | 8 +++-- 6 files changed, 55 insertions(+), 64 deletions(-) diff --git a/doc/html/Manual.html b/doc/html/Manual.html index 84440161a1..2281f57fbd 100644 --- a/doc/html/Manual.html +++ b/doc/html/Manual.html @@ -168,16 +168,20 @@ run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL).

    -

    The core group of LAMMPS developers is at Sandia National Labs and Temple University:

    +

    The current core group of LAMMPS developers is at Sandia National +Labs and Temple University:

    • Steve Plimpton, sjplimp at sandia.gov
    • Aidan Thompson, athomps at sandia.gov
    • Stan Moore, stamoore at sandia.gov
    • Axel Kohlmeyer, akohlmey at gmail.com
    -

    Past core developers include Paul Crozier, Ray Shan and Mark Stevens, all at Sandia. -The LAMMPS home page at http://lammps.sandia.gov -has more information about the code and its uses.

    +

    Past core developers include Paul Crozier, Ray Shan and Mark Stevens, +all at Sandia. The LAMMPS home page at +http://lammps.sandia.gov has more information +about the code and its uses. Interaction with external LAMMPS developers, +bug reports and feature requests are mainly coordinated through the +LAMMPS project on GitHub.

    The LAMMPS documentation is organized into the following sections. If you find errors or omissions in this manual or have suggestions for diff --git a/doc/html/Section_accelerate.html b/doc/html/Section_accelerate.html index 9fcd094369..331ea71448 100644 --- a/doc/html/Section_accelerate.html +++ b/doc/html/Section_accelerate.html @@ -346,8 +346,8 @@ package and are explained in the individual accelerator doc pages, listed above:

    --++ @@ -356,40 +356,24 @@ listed above:

    - -
    build the accelerator library
    install the accelerator package make yes-opt, make yes-user-intel, etc
    -
    -
    install the accelerator package | make yes-opt, make yes-user-intel, etc |
    -
    -
    -
    only for USER-INTEL, KOKKOS, USER-OMP, OPT packages |
    - ---- - - + + + + - -
    re-build LAMMPS
    add compile/link flags to Makefile.machine in src/MAKEonly for USER-INTEL, KOKKOS, USER-OMP, OPT packages
    re-build LAMMPS make machine
    -
    -
    re-build LAMMPS | make machine |
    -
    -
    -
    mpirun -np 32 lmp_machine -in in.script |
    -
    -
    only for KOKKOS package |
    -
    -
    package command, <br> -only if defaults need to be changed |
    -
    -
    suffix command |
    - -- - + + + + + + + + + + + +
    prepare and test a regular LAMMPS simulationlmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script
    enable specific accelerator support via ‘-k on’ command-line switch,only needed for KOKKOS package
    set any needed options for the package via “-pk” command-line switch or package command,only if defaults need to be changed
    use accelerated styles in your input via “-sf” command-line switch or suffix commandlmp_machine -in in.script -sf gpu

    Note that the first 4 steps can be done as a single command, using the @@ -528,7 +512,7 @@ full 16 lanes to each of the PCIe 2.0 16x slots.

  • The GPU package accelerates only pair force, neighbor list, and PPPM calculations.
  • The GPU package requires neighbor lists to be built on the CPU when using -exclusion lists or a triclinic simulation box.
    • +exclusion lists, hybrid pair styles, or a triclinic simulation box. diff --git a/doc/html/Section_howto.html b/doc/html/Section_howto.html index d29a4556f4..9ea709012e 100644 --- a/doc/html/Section_howto.html +++ b/doc/html/Section_howto.html @@ -933,7 +933,7 @@ vectors of a general parallelepiped, where there is no restriction on A x B . C > 0. The equivalent LAMMPS a,b,c are a linear rotation of A, B, and C and can be computed as follows:

    _images/transform.jpg -

    where A = |A| indicates the scalar length of A. The ^ hat symbol +

    where A = |A| indicates the scalar length of A. The hat symbol indicates the corresponding unit vector. beta and gamma are angles between the vectors described below. Note that by construction, a, b, and c have strictly positive x, y, and z components, respectively. diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index afbb824fd7..ab82bb0716 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -62,7 +62,8 @@ National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL). -The core group of LAMMPS developers is at Sandia National Labs and Temple University: +The current core group of LAMMPS developers is at Sandia National +Labs and Temple University: "Steve Plimpton"_sjp, sjplimp at sandia.gov :ulb,l Aidan Thompson, athomps at sandia.gov :l @@ -70,9 +71,12 @@ Stan Moore, stamoore at sandia.gov :l "Axel Kohlmeyer"_ako, akohlmey at gmail.com :l :ulb -Past core developers include Paul Crozier, Ray Shan and Mark Stevens, all at Sandia. -The [LAMMPS home page] at "http://lammps.sandia.gov"_http://lammps.sandia.gov -has more information about the code and its uses. +Past core developers include Paul Crozier, Ray Shan and Mark Stevens, +all at Sandia. The [LAMMPS home page] at +"http://lammps.sandia.gov"_http://lammps.sandia.gov has more information +about the code and its uses. Interaction with external LAMMPS developers, +bug reports and feature requests are mainly coordinated through the +"LAMMPS project on GitHub."_https://github.com/lammps/lammps :link(bug,http://lammps.sandia.gov/bug.html) :link(sjp,http://www.sandia.gov/~sjplimp) diff --git a/doc/src/Section_accelerate.txt b/doc/src/Section_accelerate.txt index e002cbb5f9..9489dee160 100644 --- a/doc/src/Section_accelerate.txt +++ b/doc/src/Section_accelerate.txt @@ -206,24 +206,18 @@ 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,
    +add compile/link flags to Makefile.machine in src/MAKE | only for USER-INTEL, KOKKOS, USER-OMP, OPT packages | re-build LAMMPS | make machine | -run a LAMMPS simulation | - lmp_machine < in.script
    - mpirun -np 32 lmp_machine -in in.script | -enable the accelerator package | - via "-c on" and "-k on" "command-line switches"_Section_start.html#start_7,
    - only for KOKKOS package | -set any needed options for the package | - via "-pk" "command-line switch"_Section_start.html#start_7 or - "package"_package.html command,
    +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_7, | + only needed for KOKKOS package | +set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_7 or "package"_package.html command, | only if defaults need to be changed | -use accelerated styles in your input script | - via "-sf" "command-line switch"_Section_start.html#start_7 or - "suffix"_suffix.html command :tb(c=2,s=|) +use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_7 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, using the src/Make.py tool. This tool is discussed in "Section @@ -303,7 +297,8 @@ 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 +CPU. :l +:ule The individual accelerator package doc pages explain: @@ -369,7 +364,8 @@ 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 +full 16 lanes to each of the PCIe 2.0 16x slots. :l +:ule [Differences between the two packages:] @@ -377,4 +373,5 @@ 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 or a triclinic simulation box. :l,ule +exclusion lists, hybrid pair styles, or a triclinic simulation box. :l +:ule diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt index 13798f8f88..f3283c8360 100644 --- a/doc/src/Section_howto.txt +++ b/doc/src/Section_howto.txt @@ -695,7 +695,8 @@ MD with quantum forces calculated by a density functional code :l lammps_spparks: coupling of LAMMPS and "SPPARKS"_spparks, to couple a kinetic Monte Carlo model for grain growth using MD to calculate -strain induced across grain boundaries :l,ule +strain induced across grain boundaries :l +:ule :link(quest,http://dft.sandia.gov/Quest) :link(spparks,http://www.sandia.gov/~sjplimp/spparks.html) @@ -829,7 +830,7 @@ rotation of [A], [B], and [C] and can be computed as follows: :c,image(Eqs/transform.jpg) -where A = |[A]| indicates the scalar length of [A]. The ^ hat symbol +where A = |[A]| indicates the scalar length of [A]. The hat symbol indicates the corresponding unit vector. {beta} and {gamma} are angles between the vectors described below. Note that by construction, [a], [b], and [c] have strictly positive x, y, and z components, respectively. @@ -1286,7 +1287,8 @@ print"_fix_print.html for single-line output of "variables"_variable.html. Fix print can also output to the screen. :l -"Restart files"_restart.html. :l,ule +"Restart files"_restart.html. :l +:ule A simulation prints one set of thermodynamic output and (optionally) restart files. It can generate any number of dump files and fix From a31c5073706c868ecb67ed9df686f81319468d95 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 6 Sep 2016 22:15:49 -0400 Subject: [PATCH 06/18] correct error message text, sync with source --- doc/html/Section_errors.html | 3 +-- doc/src/Section_errors.txt | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/doc/html/Section_errors.html b/doc/html/Section_errors.html index 658dfb8c2d..a8fd33e6b7 100644 --- a/doc/html/Section_errors.html +++ b/doc/html/Section_errors.html @@ -486,8 +486,7 @@ be computed.

    Bad TIP4P bond type for PPPMDisp/TIP4P
    Specified bond type is not valid.
    Bad fix ID in fix append/atoms command
    -
    The value of the fix_id for keyword spatial must start with the suffix -f_.
    +
    The value of the fix_id for keyword spatial must start with ‘f_‘.
    Bad grid of processors
    The 3d grid of processors defined by the processors command does not match the number of processors LAMMPS is being run on.
    diff --git a/doc/src/Section_errors.txt b/doc/src/Section_errors.txt index 52405f684b..7f5f7857a5 100644 --- a/doc/src/Section_errors.txt +++ b/doc/src/Section_errors.txt @@ -535,8 +535,7 @@ Specified bond type is not valid. :dd {Bad fix ID in fix append/atoms command} :dt -The value of the fix_id for keyword spatial must start with the suffix -f_. :dd +The value of the fix_id for keyword spatial must start with 'f_'. :dd {Bad grid of processors} :dt From 0d491d483c232312a4dfc6449e06cc441751fdfc Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Sep 2016 02:10:49 -0400 Subject: [PATCH 07/18] avoid Inline substitution_reference start-string without end-string --- doc/src/Section_howto.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt index f3283c8360..62550dc0dc 100644 --- a/doc/src/Section_howto.txt +++ b/doc/src/Section_howto.txt @@ -830,7 +830,7 @@ rotation of [A], [B], and [C] and can be computed as follows: :c,image(Eqs/transform.jpg) -where A = |[A]| indicates the scalar length of [A]. The hat symbol +where A = | [A] | indicates the scalar length of [A]. The hat symbol (^) indicates the corresponding unit vector. {beta} and {gamma} are angles between the vectors described below. Note that by construction, [a], [b], and [c] have strictly positive x, y, and z components, respectively. From 55022d126306b49c22e0ea0ec2d06e9762ce43c5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Sep 2016 02:11:59 -0400 Subject: [PATCH 08/18] replace :l,ule and :l,ole with :l :ule or :l :ole --- doc/src/Section_howto.txt | 9 +++++--- doc/src/Section_intro.txt | 3 ++- doc/src/Section_modify.txt | 3 ++- doc/src/Section_python.txt | 3 ++- doc/src/Section_start.txt | 6 ++++-- doc/src/accelerate_gpu.txt | 6 ++++-- doc/src/accelerate_intel.txt | 18 ++++++++++------ doc/src/accelerate_kokkos.txt | 3 ++- doc/src/accelerate_omp.txt | 6 ++++-- doc/src/compute.txt | 3 ++- doc/src/fix.txt | 3 ++- doc/src/fix_adapt_fep.txt | 3 ++- doc/src/fix_addtorque.txt | 3 ++- doc/src/fix_atc.txt | 3 ++- doc/src/fix_ave_correlate.txt | 6 ++++-- doc/src/fix_langevin_drude.txt | 3 ++- doc/src/fix_rigid.txt | 3 ++- doc/src/fix_temp_berendsen.txt | 3 ++- doc/src/fix_temp_csvr.txt | 3 ++- doc/src/fix_temp_rescale.txt | 3 ++- doc/src/neigh_modify.txt | 3 ++- doc/src/pair_bop.txt | 39 ++++++++++++++++++++++------------ doc/src/pair_buck_long.txt | 3 ++- doc/src/pair_gran.txt | 3 ++- doc/src/pair_modify.txt | 3 ++- doc/src/pair_table.txt | 3 ++- doc/src/pair_table_rx.txt | 3 ++- doc/src/read_data.txt | 3 ++- doc/src/region.txt | 3 ++- doc/src/rerun.txt | 3 ++- doc/src/tutorial_drude.txt | 4 ++-- doc/src/write_dump.txt | 3 ++- 32 files changed, 110 insertions(+), 56 deletions(-) diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt index 62550dc0dc..576c80f11f 100644 --- a/doc/src/Section_howto.txt +++ b/doc/src/Section_howto.txt @@ -2276,7 +2276,8 @@ molecule diffusion rates. :l As input to special functions of "equal-style variables"_variable.html, like sum() and max(). E.g. to find the -largest cluster or fastest diffusing molecule. :l,ule +largest cluster or fastest diffusing molecule. :l +:ule Example calculations with chunks :h5 @@ -2432,7 +2433,8 @@ package, :ulb,l the adiabatic core-shell method, implemented in the "CORESHELL"_#howto_26 package, :l the thermalized Drude dipole method, implemented in the -"USER-DRUDE"_#howto_27 package. :l,ule +"USER-DRUDE"_#howto_27 package. :l +:ule The fluctuating charge method calculates instantaneous charges on interacting atoms based on the electronegativity equalization @@ -2739,7 +2741,8 @@ too much. To avoid this, damping at short range can be done by Thole functions (for which there are physical grounds). This Thole damping is applied to the point charges composing the induced dipole (the charge of the Drude particle and the opposite charge on the core, not -to the total charge of the core atom). :l,ule +to the total charge of the core atom). :l +:ule A detailed tutorial covering the usage of Drude induced dipoles in LAMMPS is "available here"_tutorial_drude.html. diff --git a/doc/src/Section_intro.txt b/doc/src/Section_intro.txt index 089921d45d..1a015a4edf 100644 --- a/doc/src/Section_intro.txt +++ b/doc/src/Section_intro.txt @@ -241,7 +241,8 @@ Our group has also written and released a separate toolkit called "Pizza.py"_pizza which provides tools for doing setup, analysis, plotting, and visualization for LAMMPS simulations. Pizza.py is written in "Python"_python and is available for download from "the -Pizza.py WWW site"_pizza. :l,ule +Pizza.py WWW site"_pizza. :l +:ule :link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) :link(python,http://www.python.org) diff --git a/doc/src/Section_modify.txt b/doc/src/Section_modify.txt index e3447e5df8..a3ac505946 100644 --- a/doc/src/Section_modify.txt +++ b/doc/src/Section_modify.txt @@ -130,7 +130,8 @@ If you add something you think is truly useful and doesn't impact LAMMPS performance when it isn't used, send an email to the "developers"_http://lammps.sandia.gov/authors.html. We might be interested in adding it to the LAMMPS distribution. See further -details on this at the bottom of this page. :l,ule +details on this at the bottom of this page. :l +:ule :line :line diff --git a/doc/src/Section_python.txt b/doc/src/Section_python.txt index 231a9054fb..ce38053023 100644 --- a/doc/src/Section_python.txt +++ b/doc/src/Section_python.txt @@ -761,7 +761,8 @@ Add a wrapper method to python/lammps.py for this interface function. :l You should now be able to invoke the new interface function from a -Python script. Isn't ctypes amazing? :l,ule +Python script. Isn't ctypes amazing? :l +:ule :line :line diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt index 0231fb3357..2705e6fd83 100644 --- a/doc/src/Section_start.txt +++ b/doc/src/Section_start.txt @@ -1208,7 +1208,8 @@ Move to the directory where you have saved lmp_win_no-mpi.exe (e.g. by typing: cd "Documents"). :l At the command prompt, type "lmp_win_no-mpi -in in.lj", replacing in.lj -with the name of your LAMMPS input script. :l,ule +with the name of your LAMMPS input script. :l +:ule For the MPI version, which allows you to run LAMMPS under Windows on multiple processors, follow these steps: @@ -1237,7 +1238,8 @@ In this mode, output may not immediately show up on the screen, so if your input script takes a long time to execute, you may need to be patient before the output shows up. :l Alternatively, you can still use this executable to run on a single processor by typing something -like: "lmp_win_mpi -in in.lj". :l,ule +like: "lmp_win_mpi -in in.lj". :l +:ule :line diff --git a/doc/src/accelerate_gpu.txt b/doc/src/accelerate_gpu.txt index 8e76b85aa2..6b4cddf8be 100644 --- a/doc/src/accelerate_gpu.txt +++ b/doc/src/accelerate_gpu.txt @@ -42,7 +42,8 @@ LAMMPS-specific code is in the GPU package. It makes calls to a generic GPU library in the lib/gpu directory. This library provides NVIDIA support as well as more general OpenCL support, so that the same functionality can eventually be supported on a variety of GPU -hardware. :l,ule +hardware. :l +:ule Here is a quick overview of how to enable and use the GPU package: @@ -245,7 +246,8 @@ regardless of asynchronous CPU calculations. :l The output section "GPU Time Info (average)" reports "Max Mem / Proc". This is the maximum memory used at one time on the GPU for data -storage by a single MPI process. :l,ule +storage by a single MPI process. :l +:ule [Restrictions:] diff --git a/doc/src/accelerate_intel.txt b/doc/src/accelerate_intel.txt index c97b19b67d..e1b715e587 100644 --- a/doc/src/accelerate_intel.txt +++ b/doc/src/accelerate_intel.txt @@ -31,7 +31,8 @@ Fixes: nve, npt, nvt, nvt/sllod :l Improper Styles: cvff, harmonic :l Pair Styles: buck/coul/cut, buck/coul/long, buck, gayberne, charmm/coul/long, lj/cut, lj/cut/coul/long, sw, tersoff :l -K-Space Styles: pppm :l,ule +K-Space Styles: pppm :l +:ule [Speed-ups to expect:] @@ -70,7 +71,8 @@ For Intel Xeon CPUs: Edit src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi as necessary. :ulb,l If using {kspace_style pppm} in the input script, add "neigh_modify binsize 3" and "kspace_modify diff ad" to the input script for better performance. :l -"-pk intel 0 omp 2 -sf intel" added to LAMMPS command-line :l,ule +"-pk intel 0 omp 2 -sf intel" added to LAMMPS command-line :l +:ule For Intel Xeon Phi CPUs for simulations without {kspace_style pppm} in the input script : @@ -79,7 +81,8 @@ Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l Runs should be performed using MCDRAM. :l "-pk intel 0 omp 2 -sf intel" {or} "-pk intel 0 omp 4 -sf intel" should be added to the LAMMPS command-line. Choice for best -performance will depend on the simulation. :l,ule +performance will depend on the simulation. :l +:ule For Intel Xeon Phi CPUs for simulations with {kspace_style pppm} in the input script: @@ -93,13 +96,15 @@ performance. :l export KMP_AFFINITY=none :l "-pk intel 0 omp 3 lrt yes -sf intel" or "-pk intel 0 omp 1 lrt yes -sf intel" added to LAMMPS command-line. Choice for best performance -will depend on the simulation. :l,ule +will depend on the simulation. :l +:ule For Intel Xeon Phi coprocessors (Offload): Edit src/MAKE/OPTIONS/Makefile.intel_coprocessor as necessary :ulb,l "-pk intel N omp 1" added to command-line where N is the number of -coprocessors per node. :l,ule +coprocessors per node. :l +:ule :line @@ -463,7 +468,8 @@ Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Krake Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. 2016 International Conference for High Performance Computing. In press. :l -Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101. :l,ule +Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101. :l +:ule diff --git a/doc/src/accelerate_kokkos.txt b/doc/src/accelerate_kokkos.txt index a3d1c9efbd..c33e591712 100644 --- a/doc/src/accelerate_kokkos.txt +++ b/doc/src/accelerate_kokkos.txt @@ -381,7 +381,8 @@ When running large number of atoms per GPU, KOKKOS is typically faster than the GPU package. :l When running on Intel Xeon Phi, KOKKOS is not as fast as -the USER-INTEL package, which is optimized for that hardware. :l,ule +the USER-INTEL package, which is optimized for that hardware. :l +:ule See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS web site for performance of the KOKKOS package on different diff --git a/doc/src/accelerate_omp.txt b/doc/src/accelerate_omp.txt index 0f969d6de1..f31bbc42a3 100644 --- a/doc/src/accelerate_omp.txt +++ b/doc/src/accelerate_omp.txt @@ -163,7 +163,8 @@ sometimes be achived by increasing the length of the Coulombic cutoff and thus reducing the work done by the long-range solver. Using the "run_style verlet/split"_run_style.html command, which is compatible with the USER-OMP package, is an alternative way to reduce the number -of MPI tasks assigned to the KSpace calculation. :l,ule +of MPI tasks assigned to the KSpace calculation. :l +:ule Additional performance tips are as follows: @@ -178,7 +179,8 @@ NOTE: By default, several current MPI implementations use a processor affinity setting that restricts each MPI task to a single CPU core. Using multi-threading in this mode will force all threads to share the one core and thus is likely to be counterproductive. Instead, binding -MPI tasks to a (multi-core) socket, should solve this issue. :l,ule +MPI tasks to a (multi-core) socket, should solve this issue. :l +:ule [Restrictions:] diff --git a/doc/src/compute.txt b/doc/src/compute.txt index e680abaa33..8ecfd81af1 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -108,7 +108,8 @@ variable"_variable.html. :l Local values can be reduced by the "compute reduce"_compute_reduce.html command, or histogrammed by the "fix ave/histo"_fix_ave_histo.html command, or output by the "dump -local"_dump.html command. :l,ule +local"_dump.html command. :l +:ule The results of computes that calculate global quantities can be either "intensive" or "extensive" values. Intensive means the value is diff --git a/doc/src/fix.txt b/doc/src/fix.txt index 3fbeb013eb..d84ec2aad9 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -130,7 +130,8 @@ variable"_variable.html. :l Local values can be reduced by the "compute reduce"_compute_reduce.html command, or histogrammed by the "fix -ave/histo"_fix_ave_histo.html command. :l,ule +ave/histo"_fix_ave_histo.html command. :l +:ule See this "howto section"_Section_howto.html#howto_15 for a summary of various LAMMPS output options, many of which involve fixes. diff --git a/doc/src/fix_adapt_fep.txt b/doc/src/fix_adapt_fep.txt index 3037bc9317..5dd58bc39a 100644 --- a/doc/src/fix_adapt_fep.txt +++ b/doc/src/fix_adapt_fep.txt @@ -61,7 +61,8 @@ It is possible to modify the charges of chosen atom types only, instead of scaling all the charges in the system. :ulb,l There is a new option {after} for better compatibility with "fix -ave/time". :l,ule +ave/time". :l +:ule This version is suited for free energy calculations using "compute ti"_compute_ti.html or "compute fep"_compute_fep.html. diff --git a/doc/src/fix_addtorque.txt b/doc/src/fix_addtorque.txt index 25c7855c7d..793ec0e015 100644 --- a/doc/src/fix_addtorque.txt +++ b/doc/src/fix_addtorque.txt @@ -32,7 +32,8 @@ the components of the total torque applied on the group (around its center of mass) are Tx,Ty,Tz :ulb,l the group would move as a rigid body in the absence of other -forces. :l,ule +forces. :l +:ule This command can be used to drive a group of atoms into rotation. diff --git a/doc/src/fix_atc.txt b/doc/src/fix_atc.txt index eddfa52921..0df4e29c0b 100644 --- a/doc/src/fix_atc.txt +++ b/doc/src/fix_atc.txt @@ -19,7 +19,8 @@ type = {thermal} or {two_temperature} or {hardy} or {field} :l {two_temperature} = electron-phonon coupling with field: temperature and electron_temperature {hardy} = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields) {field} = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) :pre -parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file :l,ule +parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file :l +:ule [Examples:] diff --git a/doc/src/fix_ave_correlate.txt b/doc/src/fix_ave_correlate.txt index c4df7671aa..6f97d78219 100644 --- a/doc/src/fix_ave_correlate.txt +++ b/doc/src/fix_ave_correlate.txt @@ -232,7 +232,8 @@ so Npair = N*(N+1)/2. :l If {type} is set to {full} then each input value is correlated with itself and every other value. I.e. Cij = Vi*Vj, for i,j = 1,N so -Npair = N^2. :l,ule +Npair = N^2. :l +:ule The {ave} keyword determines what happens to the accumulation of correlation samples every {Nfreq} timesteps. If the {ave} setting is @@ -342,7 +343,8 @@ CNN. :l For {type} = {full}, the Npair = N^2 columns are ordered: C11, C12, ..., C1N, C21, C22, ..., C2N, C31, ..., C3N, ..., CN1, ..., CNN-1, -CNN. :l,ule +CNN. :l +:ule The array values calculated by this fix are treated as intensive. If you need to divide them by the number of atoms, you must do this in a diff --git a/doc/src/fix_langevin_drude.txt b/doc/src/fix_langevin_drude.txt index 47864e3e2c..4fee37fd31 100644 --- a/doc/src/fix_langevin_drude.txt +++ b/doc/src/fix_langevin_drude.txt @@ -229,7 +229,8 @@ computes the global pressure even if its group is {ATOMS}. This is what we want. If we thermostated {ATOMS} using {npt}, the pressure should be the global one, but the temperature should be only that of the cores. That's why the command {fix_modify} should be called in -that case. :l,ule +that case. :l +:ule :line diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt index f42c18d387..fb6f0e29cb 100644 --- a/doc/src/fix_rigid.txt +++ b/doc/src/fix_rigid.txt @@ -621,7 +621,8 @@ rigid styles for the rigid bodies. :l Use "fix press/berendsen"_fix_press_berendsen.html to compute the pressure and change the box dimensions. Use one of the 4 NVE or 2 NVT rigid styles for the rigid bodies. Use "fix nvt"_fix_nh.thml (or any -other thermostat) for the non-rigid particles. :l,ule +other thermostat) for the non-rigid particles. :l +:ule In all case, the rigid bodies and non-rigid particles both contribute to the global pressure and the box is scaled the same by any of the diff --git a/doc/src/fix_temp_berendsen.txt b/doc/src/fix_temp_berendsen.txt index 202be8921f..dd516d7f08 100644 --- a/doc/src/fix_temp_berendsen.txt +++ b/doc/src/fix_temp_berendsen.txt @@ -16,7 +16,8 @@ ID, group-ID are documented in "fix"_fix.html command :ulb,l temp/berendsen = style name of this fix command :l Tstart,Tstop = desired temperature at start/end of run :l Tstart can be a variable (see below) :pre -Tdamp = temperature damping parameter (time units) :l,ule +Tdamp = temperature damping parameter (time units) :l +:ule [Examples:] diff --git a/doc/src/fix_temp_csvr.txt b/doc/src/fix_temp_csvr.txt index 137654d1ec..7e53926516 100644 --- a/doc/src/fix_temp_csvr.txt +++ b/doc/src/fix_temp_csvr.txt @@ -19,7 +19,8 @@ temp/csvr or temp/csld = style name of this fix command :l Tstart,Tstop = desired temperature at start/end of run :l Tstart can be a variable (see below) :pre Tdamp = temperature damping parameter (time units) :l -seed = random number seed to use for white noise (positive integer) :l,ule +seed = random number seed to use for white noise (positive integer) :l +:ule [Examples:] diff --git a/doc/src/fix_temp_rescale.txt b/doc/src/fix_temp_rescale.txt index 4f8f216ce4..b5c1ec1b6c 100644 --- a/doc/src/fix_temp_rescale.txt +++ b/doc/src/fix_temp_rescale.txt @@ -18,7 +18,8 @@ N = perform rescaling every N steps :l Tstart,Tstop = desired temperature at start/end of run (temperature units) :l Tstart can be a variable (see below) :pre window = only rescale if temperature is outside this window (temperature units) :l -fraction = rescale to target temperature by this fraction :l,ule +fraction = rescale to target temperature by this fraction :l +:ule [Examples:] diff --git a/doc/src/neigh_modify.txt b/doc/src/neigh_modify.txt index b05fcf4d3e..c16b667f7d 100644 --- a/doc/src/neigh_modify.txt +++ b/doc/src/neigh_modify.txt @@ -123,7 +123,8 @@ to freeze a wall or portion of a bio-molecule. :l When one or more rigid bodies are specified, interactions within each body can be turned off to save needless computation. See the "fix -rigid"_fix_rigid.html command for more details. :l,ule +rigid"_fix_rigid.html command for more details. :l +:ule The {exclude type} option turns off the pairwise interaction if one atom is of type M and the other of type N. M can equal N. The diff --git a/doc/src/pair_bop.txt b/doc/src/pair_bop.txt index f08bc5413b..b569750c9c 100644 --- a/doc/src/pair_bop.txt +++ b/doc/src/pair_bop.txt @@ -162,7 +162,8 @@ Line 1: nr, nBOt (nr is the number of divisions the radius is broken into for function tables and MUST be a factor of 5; nBOt is the number of divisions for the tabulated values of THETA_(S,ij) :ulb,l Line 2: delta_1-delta_7 (if all are not used in the particular :l -formulation, set unused values to 0.0) :l,ule +formulation, set unused values to 0.0) :l +:ule Following this N lines for e_1-e_N containing p_pi. @@ -176,7 +177,8 @@ Line 1: r_cut (for e_1-e_1 interactions) :ulb,l Line 2: c_sigma, a_sigma, c_pi, a_pi :l Line 3: delta_sigma, delta_pi :l Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of -the previous section but is interaction type dependent) :l,ule +the previous section but is interaction type dependent) :l +:ule The next section contains a line for each three body interaction type e_j-e_i-e_k with i=0->N, j=0->N, k=j->N @@ -185,7 +187,8 @@ Line 1: g_(sigma0), g_(sigma1), g_(sigma2) (These are coefficients for g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. "Ward"_#Ward contains the full expressions for the constants as functions of b_(sigma,ijk), p_(sigma,ijk), u_(sigma,ijk)) :ulb,l -Line 2: g_(sigma0), g_(sigma1), g_(sigma2) (for e_1-e_1-e_2) :l,ule +Line 2: g_(sigma0), g_(sigma1), g_(sigma2) (for e_1-e_1-e_2) :l +:ule The next section contains a block for each interaction type for the phi_ij(r_ij). Each block has nr entries with 5 entries per line. @@ -196,7 +199,8 @@ Line 2: phi(r6), phi(r7), phi(r8), phi(r9), phi(r10) (this continues until nr) :l ... :l Line nr/5_1: phi(r1), phi(r2), phi(r3), phi(r4), phi(r5), (for the -e_1-e_1 interaction type) :l,ule +e_1-e_1 interaction type) :l +:ule The next section contains a block for each interaction type for the beta_(sigma,ij)(r_ij). Each block has nr entries with 5 entries per @@ -208,7 +212,8 @@ Line 2: beta_sigma(r6), beta_sigma(r7), beta_sigma(r8), beta_sigma(r9), beta_sigma(r10) (this continues until nr) :l ... :l Line nr/5+1: beta_sigma(r1), beta_sigma(r2), beta_sigma(r3), -beta_sigma(r4), beta_sigma(r5) (for the e_1-e_2 interaction type) :l,ule +beta_sigma(r4), beta_sigma(r5) (for the e_1-e_2 interaction type) :l +:ule The next section contains a block for each interaction type for beta_(pi,ij)(r_ij). Each block has nr entries with 5 entries per line. @@ -219,7 +224,8 @@ Line 2: beta_pi(r6), beta_pi(r7), beta_pi(r8), beta_pi(r9), beta_pi(r10) (this continues until nr) :l ... :l Line nr/5+1: beta_pi(r1), beta_pi(r2), beta_pi(r3), beta_pi(r4), -beta_pi(r5) (for the e_1-e_2 interaction type) :l,ule +beta_pi(r5) (for the e_1-e_2 interaction type) :l +:ule The next section contains a block for each interaction type for the THETA_(S,ij)((THETA_(sigma,ij))^(1/2), f_(sigma,ij)). Each block has @@ -231,7 +237,8 @@ Line 2: THETA_(S,ij)(r6), THETA_(S,ij)(r7), THETA_(S,ij)(r8), THETA_(S,ij)(r9), THETA_(S,ij)(r10) (this continues until nBOt) :l ... :l Line nBOt/5+1: THETA_(S,ij)(r1), THETA_(S,ij)(r2), THETA_(S,ij)(r3), -THETA_(S,ij)(r4), THETA_(S,ij)(r5) (for the e_1-e_2 interaction type) :l,ule +THETA_(S,ij)(r4), THETA_(S,ij)(r5) (for the e_1-e_2 interaction type) :l +:ule The next section contains a block of N lines for e_1-e_N @@ -266,7 +273,8 @@ into for function tables and MUST be a factor of 5; ntheta is the power of the power of the spline used to fit the angular function; nBOt is the number of divisions for the tabulated values of THETA_(S,ij) :ulb,l Line 2: delta_1-delta_7 (if all are not used in the particular :l -formulation, set unused values to 0.0) :l,ule +formulation, set unused values to 0.0) :l +:ule Following this N lines for e_1-e_N containing p_pi. @@ -280,7 +288,8 @@ Line 1: r_cut (for e_1-e_1 interactions) :ulb,l Line 2: c_sigma, a_sigma, c_pi, a_pi :l Line 3: delta_sigma, delta_pi :l Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of -the previous section but is interaction type dependent) :l,ule +the previous section but is interaction type dependent) :l +:ule The next section contains a line for each three body interaction type e_j-e_i-e_k with i=0->N, j=0->N, k=j->N @@ -292,7 +301,8 @@ can contain up to five constants. If the spline has more than five terms the second line will contain the remaining constants The following lines will then contain the constants for the remainaing g0, g1, g2... (for e_1-e_1-e_2) and the other three body -interactions :l,ule +interactions :l +:ule The rest of the table has the same structure as the previous section (see above). @@ -319,7 +329,8 @@ into for function tables and MUST be a factor of 5; ntheta is the number of divisions for the tabulated values of the g angular function; nBOt is the number of divisions for the tabulated values of THETA_(S,ij) :ulb,l Line 2: delta_1-delta_7 (if all are not used in the particular :l -formulation, set unused values to 0.0) :l,ule +formulation, set unused values to 0.0) :l +:ule Following this N lines for e_1-e_N containing p_pi. @@ -333,7 +344,8 @@ Line 1: r_cut (for e_1-e_1 interactions) :ulb,l Line 2: c_sigma, a_sigma, c_pi, a_pi :l Line 3: delta_sigma, delta_pi :l Line 4: f_sigma, k_sigma, delta_3 (This delta_3 is similar to that of -the previous section but is interaction type dependent) :l,ule +the previous section but is interaction type dependent) :l +:ule The next section contains a line for each three body interaction type e_j-e_i-e_k with i=0->N, j=0->N, k=j->N @@ -344,7 +356,8 @@ Line 2: g(theta6), g(theta7), g(theta8), g(theta9), g(theta10) (this continues until ntheta) :l ... :l Line ntheta/5+1: g(theta1), g(theta2), g(theta3), g(theta4), g(theta5), (for the -e_1-e_1-e_2 interaction type) :l,ule +e_1-e_1-e_2 interaction type) :l +:ule The rest of the table has the same structure as the previous section (see above). diff --git a/doc/src/pair_buck_long.txt b/doc/src/pair_buck_long.txt index aad5bdb0fe..50aee51dd3 100644 --- a/doc/src/pair_buck_long.txt +++ b/doc/src/pair_buck_long.txt @@ -20,7 +20,8 @@ flag_coul = {long} or {off} :l {long} = use Kspace long-range summation for the Coulombic term 1/r {off} = omit the Coulombic term :pre cutoff = global cutoff for Buckingham (and Coulombic if only 1 cutoff) (distance units) :l -cutoff2 = global cutoff for Coulombic (optional) (distance units) :l,ule +cutoff2 = global cutoff for Coulombic (optional) (distance units) :l +:ule [Examples:] diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt index 497d1d553f..baa1154fa5 100644 --- a/doc/src/pair_gran.txt +++ b/doc/src/pair_gran.txt @@ -23,7 +23,8 @@ Kt = elastic constant for tangential contact (force/distance units or pressure u gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) :l gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) :l xmu = static yield criterion (unitless value between 0.0 and 1.0e4) :l -dampflag = 0 or 1 if tangential damping force is excluded or included :l,ule +dampflag = 0 or 1 if tangential damping force is excluded or included :l +:ule NOTE: Versions of LAMMPS before 9Jan09 had different style names for granular force fields. This is to emphasize the fact that the diff --git a/doc/src/pair_modify.txt b/doc/src/pair_modify.txt index eb60c6b006..8a4f291583 100644 --- a/doc/src/pair_modify.txt +++ b/doc/src/pair_modify.txt @@ -187,7 +187,8 @@ enabled will not be thermodynamically consistent with the truncated force-field that was used. In other words, atoms do not feel any LJ pair interactions beyond the cutoff, but the energy and pressure reported by the simulation include an estimated contribution from -those interactions. :l,ule +those interactions. :l +:ule The {compute} keyword allows pairwise computations to be turned off, even though a "pair_style"_pair_style.html is defined. This is not diff --git a/doc/src/pair_table.txt b/doc/src/pair_table.txt index 8a667e40f4..560ff43590 100644 --- a/doc/src/pair_table.txt +++ b/doc/src/pair_table.txt @@ -118,7 +118,8 @@ consistent (dE/dr = -F) over the entire range of r values. LAMMPS will warn if this is not the case. :l Use as large an inner cutoff as possible. This avoids fitting splines -to very steep parts of the potential. :l,ule +to very steep parts of the potential. :l +:ule :line diff --git a/doc/src/pair_table_rx.txt b/doc/src/pair_table_rx.txt index 6c765d2093..6db0a3fa5c 100644 --- a/doc/src/pair_table_rx.txt +++ b/doc/src/pair_table_rx.txt @@ -111,7 +111,8 @@ Make sure that your tabulated forces and tabulated energies are consistent (dE/dr = -F) along the entire range of r values. :l Use as large an inner cutoff as possible. This avoids fitting splines -to very steep parts of the potential. :l,ule +to very steep parts of the potential. :l +:ule :line diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt index d040872e73..bcdc7ac434 100644 --- a/doc/src/read_data.txt +++ b/doc/src/read_data.txt @@ -698,7 +698,8 @@ atoms in such a bond. :l If you plan to "dump"_dump.html image flags and perform post-analysis that will unwrap atom coordinates, it may be important that a continued run (restarted from a data file) begins with image flags -that are consistent with the previous run. :l,ule +that are consistent with the previous run. :l +:ule NOTE: If your system is an infinite periodic crystal with bonds then it is impossible to have fully consistent image flags. This is because diff --git a/doc/src/region.txt b/doc/src/region.txt index 0dc415a8a8..0bc578c07e 100644 --- a/doc/src/region.txt +++ b/doc/src/region.txt @@ -243,7 +243,8 @@ to yz. :l For style {sphere}, the lattice spacing in dimensions x,y,z are applied to the sphere center x,y,z. The spacing in dimension x is -applied to the sphere radius. :l,ule +applied to the sphere radius. :l +:ule :line diff --git a/doc/src/rerun.txt b/doc/src/rerun.txt index c623d4bebc..da8c8d6895 100644 --- a/doc/src/rerun.txt +++ b/doc/src/rerun.txt @@ -60,7 +60,8 @@ Calculate the portion of per-atom forces resulting from a subset of the potential. E.g. compute only Coulombic forces. This can be done by only defining only a Coulombic pair style in the rerun script. Doing this in the original script would result in different (bad) -dynamics. :l,ule +dynamics. :l +:ule Conceptually, using the rerun command is like running an input script that has a loop in it (see the "next"_next.html and "jump"_jump.html diff --git a/doc/src/tutorial_drude.txt b/doc/src/tutorial_drude.txt index a6080fef27..10de99a80c 100644 --- a/doc/src/tutorial_drude.txt +++ b/doc/src/tutorial_drude.txt @@ -332,8 +332,8 @@ For the {thole} pair style the coefficients are the atom polarizability in units of cubic length :olb,l the screening factor of the Thole function (optional, default value specified by the pair_style command) :l -the cutoff (optional, default value defined by the pair_style command) -:l,ole +the cutoff (optional, default value defined by the pair_style command) :l +:ole The special neighbors have charge-charge and charge-dipole interactions screened by the {coul} factors of the {special_bonds} diff --git a/doc/src/write_dump.txt b/doc/src/write_dump.txt index 8f6e860a48..a4ed7b1664 100644 --- a/doc/src/write_dump.txt +++ b/doc/src/write_dump.txt @@ -17,7 +17,8 @@ style = any of the supported "dump styles"_dump.html :l file = name of file to write dump info to :l dump-args = any additional args needed for a particular "dump style"_dump.html :l modify = all args after this keyword are passed to "dump_modify"_dump_modify.html (optional) :l -dump-modify-args = args for "dump_modify"_dump_modify.html (optional) :l,ule +dump-modify-args = args for "dump_modify"_dump_modify.html (optional) :l +:ule [Examples:] From 3f312244a01d07495bfb18c727da5507684a4339 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 6 Sep 2016 23:31:58 -0400 Subject: [PATCH 09/18] Escape RST special character '*' in final output (cherry picked from commit 7cb39811d47b1f364286597acea21c3afd010733) --- doc/utils/converters/lammpsdoc/txt2rst.py | 5 +++++ doc/utils/converters/tests/test_txt2rst.py | 4 ++++ 2 files changed, 9 insertions(+) diff --git a/doc/utils/converters/lammpsdoc/txt2rst.py b/doc/utils/converters/lammpsdoc/txt2rst.py index f9ceb9b7ae..aec1b0d02d 100755 --- a/doc/utils/converters/lammpsdoc/txt2rst.py +++ b/doc/utils/converters/lammpsdoc/txt2rst.py @@ -57,10 +57,15 @@ class RSTMarkup(Markup): return text def convert(self, text): + text = self.escape_rst_chars(text) text = super().convert(text) text = self.inline_math(text) return text + def escape_rst_chars(self, text): + text = text.replace('*', '\\*') + return text + def inline_math(self, text): start_pos = text.find("\\(") end_pos = text.find("\\)") diff --git a/doc/utils/converters/tests/test_txt2rst.py b/doc/utils/converters/tests/test_txt2rst.py index e2c20434be..9403d419a8 100644 --- a/doc/utils/converters/tests/test_txt2rst.py +++ b/doc/utils/converters/tests/test_txt2rst.py @@ -77,6 +77,10 @@ class TestMarkup(unittest.TestCase): self.assertEqual("**bold** = [bold]\n" "*italic* = {italic}\n", s) + def test_escape_rst_characters(self): + s = self.markup.convert("[*bold] and {italic*}") + self.assertEqual("**\*bold** and *italic\**", s) + def test_paragraph_with_italic(self): self.assertEqual("A sentence with a *italic* word", self.markup.convert("A sentence with a {italic} word")) From 925f1bfb6fc997c61f42656109208a5336be2c11 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 6 Sep 2016 23:46:14 -0400 Subject: [PATCH 10/18] Escape RST special character '^' and take care of special math cases (cherry picked from commit 453521c8e682c6563226dfcc57c689052dacd21f) --- doc/utils/converters/lammpsdoc/txt2rst.py | 6 ++++++ doc/utils/converters/tests/test_txt2rst.py | 17 +++++++++++++++++ 2 files changed, 23 insertions(+) diff --git a/doc/utils/converters/lammpsdoc/txt2rst.py b/doc/utils/converters/lammpsdoc/txt2rst.py index aec1b0d02d..73c5ff91dc 100755 --- a/doc/utils/converters/lammpsdoc/txt2rst.py +++ b/doc/utils/converters/lammpsdoc/txt2rst.py @@ -64,6 +64,7 @@ class RSTMarkup(Markup): def escape_rst_chars(self, text): text = text.replace('*', '\\*') + text = text.replace('^', '\\^') return text def inline_math(self, text): @@ -73,6 +74,8 @@ class RSTMarkup(Markup): while start_pos >= 0 and end_pos >= 0: original = text[start_pos:end_pos+2] formula = original[2:-2] + formula = formula.replace('\\*', '*') + formula = formula.replace('\\^', '^') replacement = ":math:`" + formula.replace('\n', ' ').strip() + "`" text = text.replace(original, replacement) @@ -300,6 +303,9 @@ class RSTFormatting(Formatting): start = "" body = parts[0] + body = body.replace('\\*', '*') + body = body.replace('\\^', '^') + if len(start) > 0: text += start + "\n" text += "\n.. math::\n\n" diff --git a/doc/utils/converters/tests/test_txt2rst.py b/doc/utils/converters/tests/test_txt2rst.py index 9403d419a8..a4b059fbf3 100644 --- a/doc/utils/converters/tests/test_txt2rst.py +++ b/doc/utils/converters/tests/test_txt2rst.py @@ -81,6 +81,10 @@ class TestMarkup(unittest.TestCase): s = self.markup.convert("[*bold] and {italic*}") self.assertEqual("**\*bold** and *italic\**", s) + def test_escape_hat_character(self): + s = self.markup.convert("x^2") + self.assertEqual("x\^2", s) + def test_paragraph_with_italic(self): self.assertEqual("A sentence with a *italic* word", self.markup.convert("A sentence with a {italic} word")) @@ -411,6 +415,16 @@ class TestMathMarkup(unittest.TestCase): " \\frac{s_{ij} r_{ij} }{2} \\right)\n" " \\exp \\left( - s_{ij} r_{ij} \\right) \\end{equation}\n\n", s) + def test_detect_latex_equation_with_mult(self): + s = self.txt2rst.convert("\\begin\\{equation\\} a = b * c \\end\\{equation\\}\n") + self.assertEqual("\n.. math::\n\n" + " \\begin{equation} a = b * c \\end{equation}\n\n", s) + + def test_detect_latex_equation_with_pow(self): + s = self.txt2rst.convert("\\begin\\{equation\\} a = b^c \\end\\{equation\\}\n") + self.assertEqual("\n.. math::\n\n" + " \\begin{equation} a = b^c \\end{equation}\n\n", s) + def test_detect_inline_latex_equation(self): s = self.txt2rst.convert("Masses: \\begin\\{equation\\} M' = M + m \\end\\{equation\\}\n" "\\begin\\{equation\\} m' = \\frac \\{M\\, m \\} \\{M'\\} \\end\\{equation\\}\n") @@ -426,6 +440,9 @@ class TestMathMarkup(unittest.TestCase): def test_detect_inline_math(self): self.assertEqual(":math:`x^2`", self.markup.convert("\\( x^2 \\)")) + def test_detect_inline_math_mult(self): + self.assertEqual(":math:`x * 2`", self.markup.convert("\\( x * 2 \\)")) + def test_detect_multiline_inline_math(self): line = "\\(\\sqrt \\{ \\frac \\{2\, k_B \\mathtt\\{Tcom\\}\, m'\\}\n" \ "\\{\\mathrm dt\\, \\mathtt\\{damp\\_com\\} \\}\n" \ From 9e8256aeb0b7e4f8ffadb97e6a04256018b17138 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 7 Sep 2016 00:52:43 -0400 Subject: [PATCH 11/18] Refactored code and escape RST special character '_' (cherry picked from commit 4629a464f701f919633fd220860b6610d097c291) --- doc/utils/converters/lammpsdoc/txt2rst.py | 21 ++++++++++++++------- doc/utils/converters/tests/test_txt2rst.py | 4 ++++ 2 files changed, 18 insertions(+), 7 deletions(-) diff --git a/doc/utils/converters/lammpsdoc/txt2rst.py b/doc/utils/converters/lammpsdoc/txt2rst.py index 73c5ff91dc..a4196e501b 100755 --- a/doc/utils/converters/lammpsdoc/txt2rst.py +++ b/doc/utils/converters/lammpsdoc/txt2rst.py @@ -65,6 +65,13 @@ class RSTMarkup(Markup): def escape_rst_chars(self, text): text = text.replace('*', '\\*') text = text.replace('^', '\\^') + text = re.sub(r'([^"])_', r'\1\\_', text) + return text + + def unescape_rst_chars(self, text): + text = text.replace('\\*', '*') + text = text.replace('\\^', '^') + text = text.replace('\\_', '_') return text def inline_math(self, text): @@ -74,8 +81,7 @@ class RSTMarkup(Markup): while start_pos >= 0 and end_pos >= 0: original = text[start_pos:end_pos+2] formula = original[2:-2] - formula = formula.replace('\\*', '*') - formula = formula.replace('\\^', '^') + formula = self.unescape_rst_chars(formula) replacement = ":math:`" + formula.replace('\n', ' ').strip() + "`" text = text.replace(original, replacement) @@ -88,6 +94,8 @@ class RSTMarkup(Markup): content = content.strip() content = content.replace('\n', ' ') + href = self.unescape_rst_chars(href) + anchor_pos = href.find('#') if anchor_pos >= 0: @@ -130,11 +138,11 @@ class RSTFormatting(Formatting): link.lower().endswith('.jpeg') or link.lower().endswith('.png') or link.lower().endswith('.gif')): - converted = ".. thumbnail:: " + link + "\n" + converted = ".. thumbnail:: " + self.markup.unescape_rst_chars(link) + "\n" else: - converted = ".. image:: " + file + "\n" + converted = ".. image:: " + self.markup.unescape_rst_chars(file) + "\n" if link: - converted += " :target: " + link + "\n" + converted += " :target: " + self.markup.unescape_rst_chars(link) + "\n" if "c" in self.current_command_list: converted += " :align: center\n" @@ -303,8 +311,7 @@ class RSTFormatting(Formatting): start = "" body = parts[0] - body = body.replace('\\*', '*') - body = body.replace('\\^', '^') + body = self.markup.unescape_rst_chars(body) if len(start) > 0: text += start + "\n" diff --git a/doc/utils/converters/tests/test_txt2rst.py b/doc/utils/converters/tests/test_txt2rst.py index a4b059fbf3..1602fb61f9 100644 --- a/doc/utils/converters/tests/test_txt2rst.py +++ b/doc/utils/converters/tests/test_txt2rst.py @@ -85,6 +85,10 @@ class TestMarkup(unittest.TestCase): s = self.markup.convert("x^2") self.assertEqual("x\^2", s) + def test_escape_underscore(self): + s = self.markup.convert("x_") + self.assertEqual("x\_", s) + def test_paragraph_with_italic(self): self.assertEqual("A sentence with a *italic* word", self.markup.convert("A sentence with a {italic} word")) From 4c783ea3b7262ad49f70f010ece79cbc4f43e610 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 7 Sep 2016 01:31:56 -0400 Subject: [PATCH 12/18] Enforce l,ule or l,ole command order for RST (cherry picked from commit 79e867c213ee022685e5bb8a5089a112099e4f06) --- doc/utils/converters/lammpsdoc/txt2html.py | 5 ++++- doc/utils/converters/lammpsdoc/txt2rst.py | 8 ++++++++ doc/utils/converters/tests/test_txt2rst.py | 8 ++++++++ 3 files changed, 20 insertions(+), 1 deletion(-) diff --git a/doc/utils/converters/lammpsdoc/txt2html.py b/doc/utils/converters/lammpsdoc/txt2html.py index ab132a380d..6e559723b4 100755 --- a/doc/utils/converters/lammpsdoc/txt2html.py +++ b/doc/utils/converters/lammpsdoc/txt2html.py @@ -518,6 +518,9 @@ class TxtParser(object): def last_word(self, text): return text.split()[-1] + def order_commands(self, commands): + return list(reversed(commands)) + def do_formatting(self, paragraph): last_word = self.last_word(paragraph) format_str = paragraph[paragraph.rfind(last_word):] @@ -529,7 +532,7 @@ class TxtParser(object): commands = [x[0] for x in command_pattern.findall(commands)] - for command in reversed(commands): + for command in self.order_commands(commands): paragraph = self.format.convert(command, paragraph, commands) return paragraph + '\n' diff --git a/doc/utils/converters/lammpsdoc/txt2rst.py b/doc/utils/converters/lammpsdoc/txt2rst.py index a4196e501b..1bc279c0f3 100755 --- a/doc/utils/converters/lammpsdoc/txt2rst.py +++ b/doc/utils/converters/lammpsdoc/txt2rst.py @@ -347,6 +347,14 @@ class Txt2Rst(TxtParser): def is_raw_textblock_end(self, line): return line.startswith('END_RST -->') + def order_commands(self, commands): + if 'ule' in commands and 'l' in commands and commands.index('ule') > commands.index('l'): + return commands + elif 'ole' in commands and 'l' in commands and commands.index('ole') > commands.index('l'): + return commands + return super().order_commands(commands) + + class Txt2RstConverter(TxtConverter): def get_argument_parser(self): parser = argparse.ArgumentParser(description='converts a text file with simple formatting & markup into ' diff --git a/doc/utils/converters/tests/test_txt2rst.py b/doc/utils/converters/tests/test_txt2rst.py index 1602fb61f9..2fa2bd699e 100644 --- a/doc/utils/converters/tests/test_txt2rst.py +++ b/doc/utils/converters/tests/test_txt2rst.py @@ -236,6 +236,14 @@ class TestListFormatting(unittest.TestCase): "* two\n" "* three\n\n", s) + def test_elementwise_unordered_list_reverse(self): + s = self.txt2rst.convert("one :ulb,l\n" + "two :l\n" + "three :l,ule\n") + self.assertEqual("* one\n" + "* two\n" + "* three\n\n", s) + def test_multi_line_unordered_list_elements(self): s = self.txt2rst.convert("one :ulb,l\n" "two\n" From 348b677148cea0d57eaab992d233f7ab4eca9d19 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Sep 2016 07:41:17 -0400 Subject: [PATCH 13/18] Make formatting and links more consistent and unique --- doc/src/Section_packages.txt | 6 +++--- doc/src/Section_tools.txt | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt index 5282eaa4bb..38afb98de1 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -1160,9 +1160,9 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library "USER-QTB"_#USER-QTB, quantum nuclear effects, Yuan Shen (Stanford), "fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -, - "USER-QUIP"_#USER-QUIP, QUIP/libatoms interface, Albert Bartok-Partay (U Cambridge), "pair_style quip"_pair_quip.html, USER/quip, -, lib/quip "USER-REAXC"_#USER-REAXC, C version of ReaxFF, Metin Aktulga (LBNL), "pair_style reaxc"_pair_reax_c.html, reax, -, - -"USER-SMD"_#USER-SMD, smoothed Mach dynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, -, - +"USER-SMD"_#USER-SMD, smoothed Mach dynamics, Georg Ganzenmuller (EMI), "SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, -, - "USER-SMTBQ"_#USER-SMTBQ, Second Moment Tight Binding - QEq potential, Salles & Maras & Politano & Tetot (4), "pair_style smtbq"_pair_smtbq.html, USER/smtbq, -, - -"USER-SPH"_#USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, - +"USER-SPH"_#USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, - "USER-TALLY"_#USER-TALLY, Pairwise tallied computes, Axel Kohlmeyer (Temple U), "compute XXX/tally"_compute_tally.html, USER/tally, -, - "USER-VTK"_#USER-VTK, VTK-style dumps, Berger and Queteschiner (6), "compute custom/vtk"_dump_custom_vtk.html, -, -, lib/vtk :tb(ea=c) @@ -1336,7 +1336,7 @@ splitting algorithm. See src/USER-DPD/README for more details. Supporting info: /src/USER-DPD/README, "compute dpd"_compute_dpd.html "compute dpd/atom"_compute_dpd_atom.html "fix eos/cv"_fix_eos_table.html "fix eos/table"_fix_eos_table.html - "fix eos/table/rx"_fix_eos_table_rx.html "fix shardlow"_fix_shardlow.html +"fix eos/table/rx"_fix_eos_table_rx.html "fix shardlow"_fix_shardlow.html "fix rx"_fix_rx.html "pair table/rx"_pair_table_rx.html "pair dpd/fdt"_pair_dpd_fdt.html "pair dpd/fdt/energy"_pair_dpd_fdt.html "pair exp6/rx"_pair_exp6_rx.html "pair multi/lucy"_pair_multi_lucy.html diff --git a/doc/src/Section_tools.txt b/doc/src/Section_tools.txt index 6da0690f34..189bc1e35c 100644 --- a/doc/src/Section_tools.txt +++ b/doc/src/Section_tools.txt @@ -65,7 +65,7 @@ own sub-directories with their own Makefiles. "polymer bonding"_#polybond "pymol_asphere"_#pymol "python"_#pythontools -"reax"_#reax +"reax"_#reax_tool "restart2data"_#restart "vim"_#vim "xmgrace"_#xmgrace @@ -455,7 +455,7 @@ README for more info on Pizza.py and how to use these scripts. :line -reax tool :h4,link(reax) +reax tool :h4,link(reax_tool) The reax sub-directory contains stand-alond codes that can post-process the output of the "fix reax/bonds"_fix_reax_bonds.html From 70d6718aa31290689f0e7f52af48438e0de43366 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Sep 2016 07:42:06 -0400 Subject: [PATCH 14/18] Update discussion on parallel python packages. There seem to be only two left. --- doc/src/Section_python.txt | 65 +++++++++++++------------------------- 1 file changed, 22 insertions(+), 43 deletions(-) diff --git a/doc/src/Section_python.txt b/doc/src/Section_python.txt index ce38053023..b9049d87f7 100644 --- a/doc/src/Section_python.txt +++ b/doc/src/Section_python.txt @@ -277,35 +277,14 @@ your Python with an interface to MPI. This also allows you to make MPI calls directly from Python in your script, if you desire. There are several Python packages available that purport to wrap MPI -as a library and allow MPI functions to be called from Python. +as a library and allow MPI functions to be called from Python. However, +development on most of them seems to be halted except on: -These include +"mpi4py"_https://bitbucket.org/mpi4py/mpi4py +"PyPar"_https://github.com/daleroberts/pypar :ul -"pyMPI"_http://pympi.sourceforge.net/ -"maroonmpi"_http://code.google.com/p/maroonmpi/ -"mpi4py"_http://code.google.com/p/mpi4py/ -"myMPI"_http://nbcr.sdsc.edu/forum/viewtopic.php?t=89&sid=c997fefc3933bd66204875b436940f16 -"Pypar"_http://code.google.com/p/pypar :ul - -All of these except pyMPI work by wrapping the MPI library and -exposing (some portion of) its interface to your Python script. This -means Python cannot be used interactively in parallel, since they do -not address the issue of interactive input to multiple instances of -Python running on different processors. The one exception is pyMPI, -which alters the Python interpreter to address this issue, and (I -believe) creates a new alternate executable (in place of "python" -itself) as a result. - -In principle any of these Python/MPI packages should work to invoke -LAMMPS in parallel and to make MPI calls themselves from a Python -script which is itself running in parallel. However, when I -downloaded and looked at a few of them, their documentation was -incomplete and I had trouble with their installation. It's not clear -if some of the packages are still being actively developed and -supported. - -The packages Pypar and mpi4py have both been successfully tested with -LAMMPS. Pypar is simpler and easy to set up and use, but supports +Both packages, PyPar and mpi4py have been successfully tested with +LAMMPS. PyPar is simpler and easy to set up and use, but supports only a subset of MPI. Mpi4py is more MPI-feature complete, but also a bit more complex to use. As of version 2.0.0, mpi4py is the only python MPI wrapper that allows passing a custom MPI communicator to @@ -314,7 +293,7 @@ LAMMPS instances on subsets of the total MPI ranks. :line -Pypar requires the ubiquitous "Numpy package"_http://numpy.scipy.org +PyPar requires the ubiquitous "Numpy package"_http://numpy.scipy.org be installed in your Python. After launching Python, type import numpy :pre @@ -329,16 +308,16 @@ sudo python setup.py install :pre The "sudo" is only needed if required to copy Numpy files into your Python distribution's site-packages directory. -To install Pypar (version pypar-2.1.4_94 as of Aug 2012), unpack it +To install PyPar (version pypar-2.1.4_94 as of Aug 2012), unpack it and from its "source" directory, type python setup.py build sudo python setup.py install :pre -Again, the "sudo" is only needed if required to copy Pypar files into +Again, the "sudo" is only needed if required to copy PyPar files into your Python distribution's site-packages directory. -If you have successully installed Pypar, you should be able to run +If you have successully installed PyPar, you should be able to run Python and type import pypar :pre @@ -355,17 +334,17 @@ print "Proc %d out of %d procs" % (pypar.rank(),pypar.size()) :pre and see one line of output for each processor you run on. -NOTE: To use Pypar and LAMMPS in parallel from Python, you must insure +NOTE: To use PyPar and LAMMPS in parallel from Python, you must insure both are using the same version of MPI. If you only have one MPI installed on your system, this is not an issue, but it can be if you have multiple MPIs. Your LAMMPS build is explicit about which MPI it is using, since you specify the details in your lo-level -src/MAKE/Makefile.foo file. Pypar uses the "mpicc" command to find +src/MAKE/Makefile.foo file. PyPar uses the "mpicc" command to find information about the MPI it uses to build against. And it tries to load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find the MPI library that LAMMPS is using. If you have problems running -both Pypar and LAMMPS together, this is an issue you may need to -address, e.g. by moving other MPI installations so that Pypar finds +both PyPar and LAMMPS together, this is an issue you may need to +address, e.g. by moving other MPI installations so that PyPar finds the right one. :line @@ -467,8 +446,8 @@ lmp_g++ -in in.lj :pre [Test LAMMPS and Python in parallel:] :h5 To run LAMMPS in parallel, assuming you have installed the -"Pypar"_Pypar package as discussed above, create a test.py file -containing these lines: +"PyPar"_https://github.com/daleroberts/pypar package as discussed +above, create a test.py file containing these lines: import pypar from lammps import lammps @@ -478,8 +457,8 @@ print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp pypar.finalize() :pre To run LAMMPS in parallel, assuming you have installed the -"mpi4py"_mpi4py package as discussed above, create a test.py file -containing these lines: +"mpi4py"_https://bitbucket.org/mpi4py/mpi4py package as discussed +above, create a test.py file containing these lines: from mpi4py import MPI from lammps import lammps @@ -498,17 +477,17 @@ and you should see the same output as if you had typed % mpirun -np 4 lmp_g++ -in in.lj :pre -Note that if you leave out the 3 lines from test.py that specify Pypar +Note that if you leave out the 3 lines from test.py that specify PyPar commands you will instantiate and run LAMMPS independently on each of the P processors specified in the mpirun command. In this case you should get 4 sets of output, each showing that a LAMMPS run was made on a single processor, instead of one set of output showing that LAMMPS ran on 4 processors. If the 1-processor outputs occur, it -means that Pypar is not working correctly. +means that PyPar is not working correctly. -Also note that once you import the PyPar module, Pypar initializes MPI +Also note that once you import the PyPar module, PyPar initializes MPI for you, and you can use MPI calls directly in your Python script, as -described in the Pypar documentation. The last line of your Python +described in the PyPar documentation. The last line of your Python script should be pypar.finalize(), to insure MPI is shut down correctly. From 44ce6fac4b911c93bf14eea2b3ac1cd0111f8ab5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Sep 2016 08:29:16 -0400 Subject: [PATCH 15/18] replace backquote with regular quote and `` + '' with double quote. --- doc/src/Section_errors.txt | 8 ++++---- doc/src/Section_start.txt | 4 ++-- doc/src/tutorial_github.txt | 10 +++++----- src/KIM/pair_kim.h | 8 ++++---- 4 files changed, 15 insertions(+), 15 deletions(-) diff --git a/doc/src/Section_errors.txt b/doc/src/Section_errors.txt index 7f5f7857a5..6a18b1bbdb 100644 --- a/doc/src/Section_errors.txt +++ b/doc/src/Section_errors.txt @@ -11351,19 +11351,19 @@ have fully consistent image flags, since some bonds will cross periodic boundaries and connect two atoms with the same image flag. :dd -{KIM Model does not provide `energy'; Potential energy will be zero} :dt +{KIM Model does not provide 'energy'; Potential energy will be zero} :dt Self-explanatory. :dd -{KIM Model does not provide `forces'; Forces will be zero} :dt +{KIM Model does not provide 'forces'; Forces will be zero} :dt Self-explanatory. :dd -{KIM Model does not provide `particleEnergy'; energy per atom will be zero} :dt +{KIM Model does not provide 'particleEnergy'; energy per atom will be zero} :dt Self-explanatory. :dd -{KIM Model does not provide `particleVirial'; virial per atom will be zero} :dt +{KIM Model does not provide 'particleVirial'; virial per atom will be zero} :dt Self-explanatory. :dd diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt index 2705e6fd83..32bd5dae3c 100644 --- a/doc/src/Section_start.txt +++ b/doc/src/Section_start.txt @@ -1080,12 +1080,12 @@ Here is an example of such errors when the system FFTW or provided lib/colvars library have not been built as shared libraries: /usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation -R_X86_64_32 against `.rodata' can not be used when making a shared +R_X86_64_32 against '.rodata' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libfftw3.a: could not read symbols: Bad value :pre /usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o): -relocation R_X86_64_32 against `__pthread_key_create' can not be used +relocation R_X86_64_32 against '__pthread_key_create' can not be used when making a shared object; recompile with -fPIC ../../lib/colvars/libcolvars.a: error adding symbols: Bad value :pre diff --git a/doc/src/tutorial_github.txt b/doc/src/tutorial_github.txt index 06f15df874..f31de522cc 100644 --- a/doc/src/tutorial_github.txt +++ b/doc/src/tutorial_github.txt @@ -22,7 +22,7 @@ book"_http://git-scm.com/book/ to reacquaint yourself. First of all, you need a GitHub account. This is fairly simple, just go to "GitHub"_https://github.com and create an account by clicking -the ``Sign up for GitHub'' button. Once your account is created, you +the "Sign up for GitHub" button. Once your account is created, you can sign in by clicking the button in the top left and filling in your username or e-mail address and password. @@ -33,7 +33,7 @@ username or e-mail address and password. To get changes into LAMMPS, you need to first fork the repository. At the time of writing, LAMMPS-ICMS is the preferred fork. Go to "LAMMPS on GitHub"_https://github.com/lammps/lammps and make sure branch is -set to ``lammps-icms'', see the figure below. +set to "lammps-icms", see the figure below. :c,image(JPG/tutorial_branch.png) @@ -58,7 +58,7 @@ will contain these changes, a so-called feature branch. Since LAMMPS is such a big project and most user contributions come in small portions, the most ideal workflow for LAMMPS is the so-called -``Feature branch'' workflow. It is explained in great detail here: +"Feature branch" workflow. It is explained in great detail here: "feature branch workflow"_https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow. @@ -78,7 +78,7 @@ You can find the proper url to the right of the "HTTPS" block, see figure. :c,image(JPG/tutorial_https_block.png) -The above command copies (``clones'') the git repository to your local +The above command copies ("clones") the git repository to your local machine. You can use this local clone to make changes and test them without interfering with the repository on github. First, however, it is recommended to make a new branch for a particular feature you would @@ -101,7 +101,7 @@ you should switch branches! After everything is done, add the files to the branch and commit them: $ git add src/USER-MANIFOLD examples/USER/manifold/ - $ git add doc/fix_nv{t,e}_manifold_rattle.txt + $ git add doc/fix_nv\{t,e\}_manifold_rattle.txt $ git add doc/fix_manifoldforce.txt doc/user_manifolds.txt :pre After the files are added, the change should be comitted: diff --git a/src/KIM/pair_kim.h b/src/KIM/pair_kim.h index 6e2fd2e342..843fb6db2a 100644 --- a/src/KIM/pair_kim.h +++ b/src/KIM/pair_kim.h @@ -197,19 +197,19 @@ E: Unknown unit_style Self-explanatory. Check the input script or data file. -W: KIM Model does not provide `energy'; Potential energy will be zero +W: KIM Model does not provide 'energy'; Potential energy will be zero Self-explanatory. -W: KIM Model does not provide `forces'; Forces will be zero +W: KIM Model does not provide 'forces'; Forces will be zero Self-explanatory. -W: KIM Model does not provide `particleEnergy'; energy per atom will be zero +W: KIM Model does not provide 'particleEnergy'; energy per atom will be zero Self-explanatory. -W: KIM Model does not provide `particleVirial'; virial per atom will be zero +W: KIM Model does not provide 'particleVirial'; virial per atom will be zero Self-explanatory. From 5feedbd8291d2175fd7ee96332a32465a43c0dd0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Sep 2016 10:09:53 -0400 Subject: [PATCH 16/18] regenerate html pages with new txt2rst tool --- doc/html/Section_accelerate.html | 4 +- doc/html/Section_commands.html | 12 +- doc/html/Section_errors.html | 10 +- doc/html/Section_example.html | 20 +- doc/html/Section_howto.html | 316 +++++++------- doc/html/Section_modify.html | 102 ++--- doc/html/Section_packages.html | 257 ++++++------ doc/html/Section_python.html | 250 ++++++----- doc/html/Section_start.html | 130 +++--- doc/html/Section_tools.html | 12 +- doc/html/accelerate_gpu.html | 26 +- doc/html/accelerate_intel.html | 46 +- doc/html/accelerate_kokkos.html | 144 +++---- doc/html/accelerate_omp.html | 16 +- doc/html/angle_charmm.html | 14 +- doc/html/angle_class2.html | 18 +- doc/html/angle_cosine.html | 14 +- doc/html/angle_cosine_delta.html | 14 +- doc/html/angle_cosine_periodic.html | 14 +- doc/html/angle_cosine_shift.html | 14 +- doc/html/angle_cosine_shift_exp.html | 14 +- doc/html/angle_cosine_squared.html | 14 +- doc/html/angle_dipole.html | 14 +- doc/html/angle_fourier.html | 6 +- doc/html/angle_fourier_simple.html | 6 +- doc/html/angle_harmonic.html | 14 +- doc/html/angle_quartic.html | 14 +- doc/html/angle_sdk.html | 20 +- doc/html/atom_modify.html | 16 +- doc/html/atom_style.html | 24 +- doc/html/body.html | 20 +- doc/html/bond_class2.html | 14 +- doc/html/bond_fene.html | 14 +- doc/html/bond_fene_expand.html | 14 +- doc/html/bond_harmonic.html | 14 +- doc/html/bond_harmonic_shift.html | 14 +- doc/html/bond_harmonic_shift_cut.html | 14 +- doc/html/bond_morse.html | 14 +- doc/html/bond_nonlinear.html | 14 +- doc/html/bond_quartic.html | 22 +- doc/html/change_box.html | 56 +-- doc/html/compute.html | 14 +- doc/html/compute_bond_local.html | 10 +- doc/html/compute_centro_atom.html | 2 +- doc/html/compute_dipole_chunk.html | 10 +- doc/html/compute_fep.html | 10 +- doc/html/compute_gyration_chunk.html | 10 +- doc/html/compute_heat_flux.html | 26 +- doc/html/compute_inertia_chunk.html | 10 +- doc/html/compute_ke_atom_eff.html | 10 +- doc/html/compute_ke_eff.html | 10 +- doc/html/compute_modify.html | 14 +- doc/html/compute_pe_atom.html | 10 +- doc/html/compute_pressure.html | 14 +- doc/html/compute_property_atom.html | 38 +- doc/html/compute_property_chunk.html | 12 +- doc/html/compute_reduce.html | 62 +-- doc/html/compute_rigid_local.html | 8 +- doc/html/compute_saed.html | 18 +- doc/html/compute_sna_atom.html | 42 +- doc/html/compute_stress_atom.html | 12 +- doc/html/compute_temp_cs.html | 8 +- doc/html/compute_temp_eff.html | 10 +- doc/html/compute_ti.html | 10 +- doc/html/compute_voronoi_atom.html | 34 +- doc/html/compute_xrd.html | 10 +- doc/html/create_atoms.html | 38 +- doc/html/delete_bonds.html | 20 +- doc/html/dihedral_charmm.html | 18 +- doc/html/dihedral_class2.html | 24 +- doc/html/dihedral_cosine_shift_exp.html | 14 +- doc/html/dihedral_fourier.html | 14 +- doc/html/dihedral_harmonic.html | 14 +- doc/html/dihedral_helix.html | 14 +- doc/html/dihedral_multi_harmonic.html | 14 +- doc/html/dihedral_nharmonic.html | 14 +- doc/html/dihedral_opls.html | 18 +- doc/html/dihedral_quadratic.html | 14 +- doc/html/dihedral_spherical.html | 18 +- doc/html/dihedral_style.html | 16 +- doc/html/dihedral_table.html | 46 +- doc/html/dump.html | 62 +-- doc/html/dump_custom_vtk.html | 12 +- doc/html/dump_image.html | 48 +-- doc/html/dump_modify.html | 70 ++-- doc/html/fix.html | 4 +- doc/html/fix_adapt_fep.html | 34 +- doc/html/fix_addtorque.html | 12 +- doc/html/fix_atc.html | 120 +++--- doc/html/fix_atom_swap.html | 14 +- doc/html/fix_ave_atom.html | 52 ++- doc/html/fix_ave_chunk.html | 54 ++- doc/html/fix_ave_correlate.html | 82 ++-- doc/html/fix_ave_correlate_long.html | 30 +- doc/html/fix_ave_histo.html | 54 ++- doc/html/fix_ave_time.html | 52 ++- doc/html/fix_balance.html | 4 +- doc/html/fix_bond_break.html | 4 +- doc/html/fix_bond_create.html | 6 +- doc/html/fix_bond_swap.html | 6 +- doc/html/fix_box_relax.html | 24 +- doc/html/fix_colvars.html | 4 +- doc/html/fix_controller.html | 36 +- doc/html/fix_deform.html | 68 ++- doc/html/fix_deposit.html | 4 +- doc/html/fix_drag.html | 4 +- doc/html/fix_drude_transform.html | 36 +- doc/html/fix_efield.html | 12 +- doc/html/fix_ehex.html | 4 +- doc/html/fix_external.html | 22 +- doc/html/fix_gcmc.html | 32 +- doc/html/fix_gld.html | 6 +- doc/html/fix_gle.html | 6 +- doc/html/fix_gravity.html | 18 +- doc/html/fix_heat.html | 14 +- doc/html/fix_imd.html | 4 +- doc/html/fix_ipi.html | 4 +- doc/html/fix_langevin.html | 4 +- doc/html/fix_langevin_drude.html | 32 +- doc/html/fix_langevin_eff.html | 4 +- doc/html/fix_lb_fluid.html | 4 +- doc/html/fix_lb_momentum.html | 4 +- doc/html/fix_lb_pc.html | 6 +- doc/html/fix_lb_rigid_pc_sphere.html | 4 +- doc/html/fix_lb_viscous.html | 4 +- doc/html/fix_lineforce.html | 4 +- doc/html/fix_move.html | 38 +- doc/html/fix_msst.html | 30 +- doc/html/fix_neb.html | 4 +- doc/html/fix_nh.html | 26 +- doc/html/fix_nh_eff.html | 10 +- doc/html/fix_nph_asphere.html | 12 +- doc/html/fix_nph_sphere.html | 12 +- doc/html/fix_nphug.html | 22 +- doc/html/fix_npt_asphere.html | 12 +- doc/html/fix_npt_body.html | 12 +- doc/html/fix_npt_sphere.html | 12 +- doc/html/fix_nve_asphere.html | 4 +- doc/html/fix_nve_asphere_noforce.html | 4 +- doc/html/fix_nve_body.html | 4 +- doc/html/fix_nve_line.html | 4 +- doc/html/fix_nve_manifold_rattle.html | 14 +- doc/html/fix_nve_sphere.html | 4 +- doc/html/fix_nve_tri.html | 4 +- doc/html/fix_nvt_asphere.html | 10 +- doc/html/fix_nvt_body.html | 10 +- doc/html/fix_nvt_sllod.html | 10 +- doc/html/fix_nvt_sllod_eff.html | 4 +- doc/html/fix_nvt_sphere.html | 10 +- doc/html/fix_orient.html | 4 +- doc/html/fix_phonon.html | 10 +- doc/html/fix_pimd.html | 12 +- doc/html/fix_pour.html | 4 +- doc/html/fix_qbmsst.html | 32 +- doc/html/fix_qeq.html | 18 +- doc/html/fix_qeq_comb.html | 4 +- doc/html/fix_qeq_reax.html | 4 +- doc/html/fix_qmmm.html | 4 +- doc/html/fix_qtb.html | 14 +- doc/html/fix_reax_bonds.html | 4 +- doc/html/fix_reaxc_species.html | 4 +- doc/html/fix_restrain.html | 22 +- doc/html/fix_rigid.html | 34 +- doc/html/fix_rx.html | 16 +- doc/html/fix_saed_vtk.html | 60 ++- doc/html/fix_shake.html | 4 +- doc/html/fix_smd.html | 4 +- doc/html/fix_smd_adjust_dt.html | 16 +- doc/html/fix_smd_integrate_tlsph.html | 18 +- doc/html/fix_smd_integrate_ulsph.html | 24 +- .../fix_smd_move_triangulated_surface.html | 50 ++- doc/html/fix_smd_setvel.html | 10 +- doc/html/fix_smd_wall_surface.html | 16 +- doc/html/fix_spring.html | 4 +- doc/html/fix_spring_chunk.html | 4 +- doc/html/fix_spring_rg.html | 4 +- doc/html/fix_spring_self.html | 4 +- doc/html/fix_store_state.html | 78 ++-- doc/html/fix_temp_berendsen.html | 10 +- doc/html/fix_temp_csvr.html | 10 +- doc/html/fix_temp_rescale.html | 10 +- doc/html/fix_temp_rescale_eff.html | 4 +- doc/html/fix_tfmc.html | 4 +- doc/html/fix_thermal_conductivity.html | 16 +- doc/html/fix_ti_rs.html | 10 +- doc/html/fix_ti_spring.html | 10 +- doc/html/fix_ttm.html | 116 +++--- doc/html/fix_viscosity.html | 4 +- doc/html/fix_viscous.html | 4 +- doc/html/fix_wall.html | 60 ++- doc/html/fix_wall_gran.html | 16 +- doc/html/fix_wall_piston.html | 4 +- doc/html/fix_wall_reflect.html | 58 ++- doc/html/fix_wall_region.html | 4 +- doc/html/genindex.html | 394 +++++++++--------- doc/html/group.html | 36 +- doc/html/if.html | 16 +- doc/html/improper_class2.html | 16 +- doc/html/improper_cossq.html | 14 +- doc/html/improper_cvff.html | 14 +- doc/html/improper_distance.html | 8 +- doc/html/improper_fourier.html | 14 +- doc/html/improper_harmonic.html | 14 +- doc/html/improper_ring.html | 18 +- doc/html/improper_umbrella.html | 14 +- doc/html/jump.html | 24 +- doc/html/kspace_modify.html | 14 +- doc/html/kspace_style.html | 24 +- doc/html/lattice.html | 54 +-- doc/html/min_modify.html | 12 +- doc/html/min_style.html | 20 +- doc/html/neigh_modify.html | 20 +- doc/html/next.html | 12 +- doc/html/package.html | 10 +- doc/html/pair_adp.html | 22 +- doc/html/pair_airebo.html | 52 +-- doc/html/pair_beck.html | 16 +- doc/html/pair_body.html | 16 +- doc/html/pair_bop.html | 26 +- doc/html/pair_born.html | 56 +-- doc/html/pair_brownian.html | 16 +- doc/html/pair_buck.html | 58 +-- doc/html/pair_buck_long.html | 20 +- doc/html/pair_charmm.html | 54 +-- doc/html/pair_class2.html | 42 +- doc/html/pair_colloid.html | 20 +- doc/html/pair_comb.html | 32 +- doc/html/pair_coul.html | 124 +++--- doc/html/pair_coul_diel.html | 14 +- doc/html/pair_cs.html | 26 +- doc/html/pair_dipole.html | 52 +-- doc/html/pair_dpd.html | 28 +- doc/html/pair_dpd_fdt.html | 22 +- doc/html/pair_dsmc.html | 28 +- doc/html/pair_eam.html | 64 +-- doc/html/pair_edip.html | 12 +- doc/html/pair_eff.html | 26 +- doc/html/pair_eim.html | 24 +- doc/html/pair_exp6_rx.html | 18 +- doc/html/pair_gauss.html | 36 +- doc/html/pair_gayberne.html | 14 +- doc/html/pair_gran.html | 20 +- doc/html/pair_gromacs.html | 26 +- doc/html/pair_hbond_dreiding.html | 36 +- doc/html/pair_hybrid.html | 146 +++---- doc/html/pair_line_lj.html | 18 +- doc/html/pair_list.html | 24 +- doc/html/pair_lj.html | 106 ++--- doc/html/pair_lj96.html | 16 +- doc/html/pair_lj_cubic.html | 14 +- doc/html/pair_lj_expand.html | 16 +- doc/html/pair_lj_long.html | 32 +- doc/html/pair_lj_sf.html | 16 +- doc/html/pair_lj_smooth.html | 16 +- doc/html/pair_lj_smooth_linear.html | 16 +- doc/html/pair_lj_soft.html | 88 ++-- doc/html/pair_lubricate.html | 28 +- doc/html/pair_lubricateU.html | 16 +- doc/html/pair_mdf.html | 42 +- doc/html/pair_meam.html | 38 +- doc/html/pair_meam_spline.html | 22 +- doc/html/pair_meam_sw_spline.html | 16 +- doc/html/pair_mgpt.html | 22 +- doc/html/pair_mie.html | 18 +- doc/html/pair_modify.html | 46 +- doc/html/pair_morse.html | 16 +- doc/html/pair_multi_lucy.html | 32 +- doc/html/pair_multi_lucy_rx.html | 34 +- doc/html/pair_nb3b_harmonic.html | 20 +- doc/html/pair_nm.html | 36 +- doc/html/pair_peri.html | 38 +- doc/html/pair_polymorphic.html | 50 +-- doc/html/pair_quip.html | 16 +- doc/html/pair_reax.html | 40 +- doc/html/pair_reax_c.html | 48 +-- doc/html/pair_resquared.html | 14 +- doc/html/pair_sdk.html | 24 +- doc/html/pair_smd_hertz.html | 8 +- doc/html/pair_smd_triangulated_surface.html | 8 +- doc/html/pair_smtbq.html | 22 +- doc/html/pair_snap.html | 26 +- doc/html/pair_soft.html | 36 +- doc/html/pair_sph_idealgas.html | 14 +- doc/html/pair_sph_taitwater.html | 14 +- doc/html/pair_sph_taitwater_morris.html | 14 +- doc/html/pair_srp.html | 36 +- doc/html/pair_style.html | 26 +- doc/html/pair_sw.html | 22 +- doc/html/pair_table.html | 38 +- doc/html/pair_table_rx.html | 38 +- doc/html/pair_tersoff.html | 30 +- doc/html/pair_tersoff_mod.html | 20 +- doc/html/pair_tersoff_zbl.html | 20 +- doc/html/pair_thole.html | 28 +- doc/html/pair_tri_lj.html | 16 +- doc/html/pair_vashishta.html | 20 +- doc/html/pair_yukawa.html | 16 +- doc/html/pair_yukawa_colloid.html | 22 +- doc/html/pair_zbl.html | 16 +- doc/html/prd.html | 32 +- doc/html/processors.html | 20 +- doc/html/python.html | 106 ++--- doc/html/read_data.html | 32 +- doc/html/read_dump.html | 30 +- doc/html/region.html | 34 +- doc/html/restart.html | 24 +- doc/html/run_style.html | 60 +-- doc/html/set.html | 24 +- doc/html/special_bonds.html | 38 +- doc/html/tad.html | 52 +-- doc/html/thermo.html | 8 +- doc/html/thermo_style.html | 58 +-- doc/html/tutorial_drude.html | 192 +++++---- doc/html/tutorial_github.html | 16 +- doc/html/units.html | 2 +- doc/html/variable.html | 120 +++--- doc/html/velocity.html | 22 +- doc/html/write_coeff.html | 12 +- doc/html/write_dump.html | 28 +- 319 files changed, 4360 insertions(+), 4585 deletions(-) diff --git a/doc/html/Section_accelerate.html b/doc/html/Section_accelerate.html index 331ea71448..db8d8af4bd 100644 --- a/doc/html/Section_accelerate.html +++ b/doc/html/Section_accelerate.html @@ -346,8 +346,8 @@ package and are explained in the individual accelerator doc pages, listed above:

    --++ diff --git a/doc/html/Section_commands.html b/doc/html/Section_commands.html index 88bc54ce5a..69c6609b6c 100644 --- a/doc/html/Section_commands.html +++ b/doc/html/Section_commands.html @@ -247,15 +247,15 @@ inside the parenthesis is treated as an “immediate” variable and evaluated as an equal-style variable. This is a way to use numeric formulas in an input script without having to assign them to variable names. For example, these 3 input script lines:

    -
    variable X equal (xlo+xhi)/2+sqrt(v_area)
+
    +variable X equal (xlo+xhi)/2+sqrt(v_area)
 region 1 block $X 2 INF INF EDGE EDGE
 variable X delete
-
    -
    +

    can be replaced by

    -
    region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
-
    -
    +
    +region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
+

    so that you do not have to define (or discard) a temporary variable X.

    Note that neither the curly-bracket or immediate form of variables can contain nested $ characters for other variables to substitute for. diff --git a/doc/html/Section_errors.html b/doc/html/Section_errors.html index a8fd33e6b7..680f6140be 100644 --- a/doc/html/Section_errors.html +++ b/doc/html/Section_errors.html @@ -486,7 +486,7 @@ be computed.

    Bad TIP4P bond type for PPPMDisp/TIP4P
    Specified bond type is not valid.
    Bad fix ID in fix append/atoms command
    -
    The value of the fix_id for keyword spatial must start with ‘f_‘.
    +
    The value of the fix_id for keyword spatial must start with ‘f_’.
    Bad grid of processors
    The 3d grid of processors defined by the processors command does not match the number of processors LAMMPS is being run on.
    @@ -6358,13 +6358,13 @@ have an infinite periodic crystal with bonds then it is impossible to have fully consistent image flags, since some bonds will cross periodic boundaries and connect two atoms with the same image flag. -
    KIM Model does not provide `energy’; Potential energy will be zero
    +
    KIM Model does not provide ‘energy’; Potential energy will be zero
    Self-explanatory.
    -
    KIM Model does not provide `forces’; Forces will be zero
    +
    KIM Model does not provide ‘forces’; Forces will be zero
    Self-explanatory.
    -
    KIM Model does not provide `particleEnergy’; energy per atom will be zero
    +
    KIM Model does not provide ‘particleEnergy’; energy per atom will be zero
    Self-explanatory.
    -
    KIM Model does not provide `particleVirial’; virial per atom will be zero
    +
    KIM Model does not provide ‘particleVirial’; virial per atom will be zero
    Self-explanatory.
    Kspace_modify slab param < 2.0 may cause unphysical behavior
    The kspace_modify slab parameter should be larger to insure periodic diff --git a/doc/html/Section_example.html b/doc/html/Section_example.html index 95a590b02f..9c2e1a0c72 100644 --- a/doc/html/Section_example.html +++ b/doc/html/Section_example.html @@ -303,11 +303,11 @@ longer times, e.g. to measure a particular quantity.

    build the accelerator library

    Here is how you can run and visualize one of the sample problems:

    -
    cd indent
-cp ../../src/lmp_linux .           # copy LAMMPS executable to this dir
-lmp_linux -in in.indent            # run the problem
-
    -
    +
    +cd indent
+cp ../../src/lmp_linux .           # copy LAMMPS executable to this dir
+lmp_linux -in in.indent            # run the problem
+

    Running the simulation produces the files dump.indent and log.lammps. You can visualize the dump file of snapshots with a variety of 3rd-party tools highlighted on the @@ -321,17 +321,17 @@ ImageMagick or QuickTime or various Windows-based tools. See the dump image doc page for more details. E.g. this Imagemagick command would create a GIF file suitable for viewing in a browser.

    -
    % convert -loop 1 *.jpg foo.gif
-
    -
    +
    +% convert -loop 1 *.jpg foo.gif
+

    7.2. Uppercase directories

    --++ diff --git a/doc/html/Section_howto.html b/doc/html/Section_howto.html index 9ea709012e..feb6e5e5c9 100644 --- a/doc/html/Section_howto.html +++ b/doc/html/Section_howto.html @@ -252,13 +252,13 @@ scripts are based on. If that script had the line

    and tmp.restart.100) as it ran.

    This script could be used to read the 1st restart file and re-run the last 50 timesteps:

    -
    read_restart tmp.restart.50
-
    -
    -
    neighbor     0.4 bin
-neigh_modify every 1 delay 1
-
    -
    +
    +read_restart        tmp.restart.50
+
    +
    +neighbor     0.4 bin
+neigh_modify        every 1 delay 1
+
    fix          1 all nve
 fix          2 all langevin 1.0 1.0 10.0 904297
    @@ -281,25 +281,25 @@ notice that the thermodynamic data match at step 50 (if you also put a uses random numbers in a way that does not allow for perfect restarts.

    As an alternate approach, the restart file could be converted to a data file as follows:

    -
    lmp_g++ -r tmp.restart.50 tmp.restart.data
-
    -
    +
    +lmp_g++ -r tmp.restart.50 tmp.restart.data
+

    Then, this script could be used to re-run the last 50 steps:

    -
    units                lj
-atom_style   bond
-pair_style   lj/cut 1.12
-pair_modify  shift yes
-bond_style   fene
-special_bonds   0.0 1.0 1.0
-
    -
    -
    read_data    tmp.restart.data
-
    -
    -
    neighbor     0.4 bin
-neigh_modify every 1 delay 1
-
    -
    +
    +units                lj
+atom_style  bond
+pair_style  lj/cut 1.12
+pair_modify shift yes
+bond_style  fene
+special_bonds   0.0 1.0 1.0
+
    +
    +read_data   tmp.restart.data
+
    +
    +neighbor     0.4 bin
+neigh_modify        every 1 delay 1
+
    fix          1 all nve
 fix          2 all langevin 1.0 1.0 10.0 904297
    @@ -307,10 +307,10 @@ file as follows:

    timestep     0.012
    -
    reset_timestep       50
-run          50
-
    -
    +
    +reset_timestep      50
+run          50
+

    Note that nearly all the settings specified in the original in.chain script must be repeated, except the pair_coeff and bond_coeff commands since the new data file lists the force field coefficients. @@ -420,39 +420,40 @@ individual commands for more details on how these examples work.

    If “multiple simulations” means continue a previous simulation for more timesteps, then you simply use the run command multiple times. For example, this script

    -
    units lj
-atom_style atomic
-read_data data.lj
-run 10000
-run 10000
-run 10000
-run 10000
-run 10000
-
    -
    +
    +units lj
+atom_style atomic
+read_data data.lj
+run 10000
+run 10000
+run 10000
+run 10000
+run 10000
+

    would run 5 successive simulations of the same system for a total of 50,000 timesteps.

    If you wish to run totally different simulations, one after the other, the clear command can be used in between them to re-initialize LAMMPS. For example, this script

    -
    units lj
-atom_style atomic
-read_data data.lj
-run 10000
-clear
-units lj
-atom_style atomic
-read_data data.lj.new
-run 10000
-
    -
    +
    +units lj
+atom_style atomic
+read_data data.lj
+run 10000
+clear
+units lj
+atom_style atomic
+read_data data.lj.new
+run 10000
+

    would run 2 independent simulations, one after the other.

    For large numbers of independent simulations, you can use variables and the next and jump commands to loop over the same input script multiple times with different settings. For example, this script, named in.polymer

    -
    variable d index run1 run2 run3 run4 run5 run6 run7 run8
+
    +variable d index run1 run2 run3 run4 run5 run6 run7 run8
 shell cd $d
 read_data data.polymer
 run 10000
@@ -460,8 +461,7 @@ shell cd ..
 clear
 next d
 jump in.polymer
-
    -
    +

    would run 8 simulations in different directories, using a data.polymer file in each directory. The same concept could be used to run the same system at 8 different temperatures, using a temperature variable @@ -528,10 +528,10 @@ replica. The processors assigned to each replica are determined at run-time by using the -partition command-line switch to launch LAMMPS on multiple partitions, which in this context are the same as replicas. E.g. these commands:

    -
    mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
-mpirun -np 8 lmp_linux -partition 8x1 -in in.neb
-
    -
    +
    +mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
+mpirun -np 8 lmp_linux -partition 8x1 -in in.neb
+

    would each run 8 replicas, on either 16 or 8 processors. Note the use of the -in command-line switch to specify the input script which is required when running in multi-replica mode.

    @@ -933,7 +933,7 @@ vectors of a general parallelepiped, where there is no restriction on A x B . C > 0. The equivalent LAMMPS a,b,c are a linear rotation of A, B, and C and can be computed as follows:

    _images/transform.jpg -

    where A = |A| indicates the scalar length of A. The hat symbol +

    where A = | A | indicates the scalar length of A. The hat symbol (^) indicates the corresponding unit vector. beta and gamma are angles between the vectors described below. Note that by construction, a, b, and c have strictly positive x, y, and z components, respectively. @@ -1037,23 +1037,23 @@ BOUNDS for a snapshot is written to a dump file for a triclinic box, an orthogonal bounding box which encloses the triclinic simulation box is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic box, formatted as follows:

    -
    ITEM: BOX BOUNDS xy xz yz
-xlo_bound xhi_bound xy
-ylo_bound yhi_bound xz
-zlo_bound zhi_bound yz
-
    -
    +
    +ITEM: BOX BOUNDS xy xz yz
+xlo_bound xhi_bound xy
+ylo_bound yhi_bound xz
+zlo_bound zhi_bound yz
+

    This bounding box is convenient for many visualization programs and is calculated from the 9 triclinic box parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:

    -
    xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz)
-xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz)
-ylo_bound = ylo + MIN(0.0,yz)
-yhi_bound = yhi + MAX(0.0,yz)
-zlo_bound = zlo
-zhi_bound = zhi
-
    -
    +
    +xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz)
+xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz)
+ylo_bound = ylo + MIN(0.0,yz)
+yhi_bound = yhi + MAX(0.0,yz)
+zlo_bound = zlo
+zhi_bound = zhi
+

    These formulas can be inverted if you need to convert the bounding box back into the triclinic box parameters, e.g. xlo = xlo_bound - MIN(0.0,xy,xz,xy+xz).

    @@ -1136,9 +1136,9 @@ of individual particles, after then are created.

    The dipole style does not actually define finite-size particles, but is often used in conjunction with spherical particles, via a command like

    -
    atom_style hybrid sphere dipole
-
    -
    +
    +atom_style hybrid sphere dipole
+

    This is because when dipoles interact with each other, they induce torques, and a particle must be finite-size (i.e. have a moment of inertia) in order to respond and rotate. See the atom_style dipole command for details. The “set” command can be @@ -1372,11 +1372,11 @@ per-atom vector.

    When a quantity is accessed, as in many of the output commands discussed below, it can be referenced via the following bracket notation, where ID in this case is the ID of a compute. The leading -“c_” would be replaced by “f_” for a fix, or “v_” for a variable:

    +“c_” would be replaced by “f_” for a fix, or “v_” for a variable:

    ASPHERE
    --++ @@ -1911,13 +1911,13 @@ internal LAMMPS operations. Note that LAMMPS classes are defined within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++ application.

    Library.cpp contains these 5 basic functions:

    -
    void lammps_open(int, char **, MPI_Comm, void **)
-void lammps_close(void *)
-int lammps_version(void *)
-void lammps_file(void *, char *)
-char *lammps_command(void *, char *)
-
    -
    +
    +void lammps_open(int, char **, MPI_Comm, void **)
+void lammps_close(void *)
+int lammps_version(void *)
+void lammps_file(void *, char *)
+char *lammps_command(void *, char *)
+

    The lammps_open() function is used to initialize LAMMPS, passing in a list of strings as if they were command-line arguments when LAMMPS is run in stand-alone mode from the command line, and a MPI communicator for @@ -1951,17 +1951,17 @@ interleaving the lammps_command() calls with other calls to extract information from LAMMPS, perform its own operations, or call another code’s library.

    Other useful functions are also included in library.cpp. For example:

    -
    void *lammps_extract_global(void *, char *)
-void *lammps_extract_atom(void *, char *)
-void *lammps_extract_compute(void *, char *, int, int)
-void *lammps_extract_fix(void *, char *, int, int, int, int)
-void *lammps_extract_variable(void *, char *, char *)
-int lammps_set_variable(void *, char *, char *)
-int lammps_get_natoms(void *)
-void lammps_get_coords(void *, double *)
-void lammps_put_coords(void *, double *)
-
    -
    +
    +void *lammps_extract_global(void *, char *)
+void *lammps_extract_atom(void *, char *)
+void *lammps_extract_compute(void *, char *, int, int)
+void *lammps_extract_fix(void *, char *, int, int, int, int)
+void *lammps_extract_variable(void *, char *, char *)
+int lammps_set_variable(void *, char *, char *)
+int lammps_get_natoms(void *)
+void lammps_get_coords(void *, double *)
+void lammps_put_coords(void *, double *)
+

    These can extract various global or per-atom quantities from LAMMPS as well as values calculated by a compute, fix, or variable. The “set_variable” function can set an existing string-style variable to a @@ -2087,29 +2087,30 @@ liquid Ar via the GK formalism:

    # Sample LAMMPS input script for viscosity of liquid Ar
    -
    units       real
+
    +units       real
 variable    T equal 86.4956
 variable    V equal vol
 variable    dt equal 4.0
 variable    p equal 400     # correlation length
 variable    s equal 5       # sample interval
 variable    d equal $p*$s   # dump interval
-
    -
    +
    # convert from LAMMPS real units to SI
    -
    variable    kB equal 1.3806504e-23    # [J/K/** Boltzmann
+
    +variable    kB equal 1.3806504e-23    # [J/K/** Boltzmann
 variable    atm2Pa equal 101325.0
 variable    A2m equal 1.0e-10
 variable    fs2s equal 1.0e-15
 variable    convert equal ${atm2Pa}*${atm2Pa}*${fs2s}*${A2m}*${A2m}*${A2m}
-
    -
    +
    # setup problem
    -
    dimension    3
+
    +dimension    3
 boundary     p p p
 lattice      fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
 region       box block 0 4 0 4 0 4
@@ -2120,8 +2121,7 @@ pair_style   lj/cut 13.0
 pair_coeff   * * 0.2381 3.405
 timestep     ${dt}
 thermo            $d
-
    -
    +
    # equilibration and thermalization
    @@ -2137,7 +2137,8 @@ run 8000 #fix NVE all nve -
    reset_timestep 0
+
    +reset_timestep 0
 variable     pxy equal pxy
 variable     pxz equal pxz
 variable     pyz equal pyz
@@ -2151,9 +2152,8 @@ thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33
 run          100000
 variable     v equal (v_v11+v_v22+v_v33)/3.0
 variable     ndens equal count(all)/vol
-print        "average viscosity: $v [Pa.s/** @ $T K, ${ndens} /A^3"
-
    -
    +print "average viscosity: $v [Pa.s/** @ $T K, ${ndens} /A^3" +

    The fifth method is related to the above Green-Kubo method, but uses the Einstein formulation, analogous to the Einstein mean-square-displacement formulation for self-diffusivity. The @@ -2274,7 +2274,7 @@ fix produces a global array as output with one row of values per chunk.

    -

    6.23.3. Compute */chunk commands:

    +

    6.23.3. Compute */chunk commands:

    Currently the following computes operate on chunks of atoms to produce per-chunk values.

      @@ -2331,31 +2331,31 @@ velocity:

      1. Center of mass of each molecule:
      -
      compute cc1 all chunk/atom molecule
-compute myChunk all com/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
-
      -
      +
      +compute cc1 all chunk/atom molecule
+compute myChunk all com/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
+
      1. Total force on each molecule and ave/max across all molecules:
      -
      compute cc1 all chunk/atom molecule
-fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
-variable xave equal ave(f_1[2])
-variable xmax equal max(f_1[2])
-thermo 1000
-thermo_style custom step temp v_xave v_xmax
-
      -
      +
      +compute cc1 all chunk/atom molecule
+fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
+variable xave equal ave(f_1[2])
+variable xmax equal max(f_1[2])
+thermo 1000
+thermo_style custom step temp v_xave v_xmax
+
      1. Histogram of cluster sizes:
      -
      compute cluster all cluster/atom 1.0
-compute cc1 all chunk/atom c_cluster compress yes
-compute size all property/chunk cc1 count
-fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo
-
      -
      +
      +compute cluster all cluster/atom 1.0
+compute cc1 all chunk/atom c_cluster compress yes
+compute size all property/chunk cc1 count
+fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo
+
    @@ -2607,18 +2607,18 @@ by the Ewald solvers can be used.

    For the NaCL example problem, these pair style and bond style settings are used:

    -
    pair_style      born/coul/long/cs 20.0 20.0
-pair_coeff      * *      0.0 1.000   0.00  0.00   0.00
-pair_coeff      3 3    487.0 0.23768 0.00  1.05   0.50 #Na-Na
-pair_coeff      3 4 145134.0 0.23768 0.00  6.99   8.70 #Na-Cl
-pair_coeff      4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
-
    -
    -
    bond_style      harmonic
-bond_coeff      1 63.014 0.0
-bond_coeff      2 25.724 0.0
-
    -
    +
    +pair_style      born/coul/long/cs 20.0 20.0
+pair_coeff      * *      0.0 1.000   0.00  0.00   0.00
+pair_coeff      3 3    487.0 0.23768 0.00  1.05   0.50 #Na-Na
+pair_coeff      3 4 145134.0 0.23768 0.00  6.99   8.70 #Na-Cl
+pair_coeff      4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
+
    +
    +bond_style      harmonic
+bond_coeff      1 63.014 0.0
+bond_coeff      2 25.724 0.0
+

    When running dynamics with the adiabatic core/shell model, the following issues should be considered. Since the relative motion of the core and shell particles corresponds to the polarization, typical @@ -2645,15 +2645,15 @@ used to assign the compute to the thermostat fix. Likewise the thermo_modify temp command can be used to make this temperature be output for the overall system.

    For the NaCl example, this can be done as follows:

    -
    group cores type 1 2
-group shells type 3 4
-compute CSequ all temp/cs cores shells
-fix thermoberendsen all temp/berendsen 1427 1427 0.4    # thermostat for the true physical system
-fix thermostatequ all nve                               # integrator as needed for the berendsen thermostat
-fix_modify thermoberendsen temp CSequ
-thermo_modify temp CSequ                                # output of center-of-mass derived temperature
-
    -
    +
    +group cores type 1 2
+group shells type 3 4
+compute CSequ all temp/cs cores shells
+fix thermoberendsen all temp/berendsen 1427 1427 0.4    # thermostat for the true physical system
+fix thermostatequ all nve                               # integrator as needed for the berendsen thermostat
+fix_modify thermoberendsen temp CSequ
+thermo_modify temp CSequ                                # output of center-of-mass derived temperature
+

    If compute temp/cs is used, the decoupled relative motion of the core and the shell should in theory be stable. However numerical fluctuation can introduce a small @@ -2702,14 +2702,14 @@ accessed by the command, to use as input to the compute chunk/atom command to define the core/shell pairs as chunks.

    For example,

    -
    fix csinfo all property/atom i_CSID                       # property/atom command
-read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info  # atom property added in the data-file
-compute prop all property/atom i_CSID
-compute cs_chunk all chunk/atom c_prop
-compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0     # note the chosen degrees of freedom for the core/shell pairs
-fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector
-
    -
    +
    +fix csinfo all property/atom i_CSID                       # property/atom command
+read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info  # atom property added in the data-file
+compute prop all property/atom i_CSID
+compute cs_chunk all chunk/atom c_prop
+compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0     # note the chosen degrees of freedom for the core/shell pairs
+fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector
+

    The additional section in the date file would be formatted like this:

    CS-Info         # header of additional section
    diff --git a/doc/html/Section_modify.html b/doc/html/Section_modify.html index 1ddbd8f04a..41c466042e 100644 --- a/doc/html/Section_modify.html +++ b/doc/html/Section_modify.html @@ -193,8 +193,8 @@ C-style data structures (vectors and arrays).

    Most of the new features described in this section require you to write a new C++ derived class (except for exceptions described below, where you can make small edits to existing files). Creating a new -class requires 2 files, a source code file (.cpp) and a header file -(.h). The derived class must provide certain methods to work as a +class requires 2 files, a source code file (*.cpp) and a header file +(*.h). The derived class must provide certain methods to work as a new option. Depending on how different your new feature is compared to existing features, you can either derive from the base class itself, or from a derived class that already exists. Enabling LAMMPS @@ -209,19 +209,19 @@ and pair_foo.h that define a new class PairFoo that computes pairwise potentials described in the classic 1997 paper by Foo, et al. If you wish to invoke those potentials in a LAMMPS input script with a command like

    -
    pair_style foo 0.1 3.5
-
    -
    +
    +pair_style foo 0.1 3.5
+

    then your pair_foo.h file should be structured as follows:

    -
    #ifdef PAIR_CLASS
-PairStyle(foo,PairFoo)
-#else
-...
-(class definition for PairFoo)
-...
-#endif
-
    -
    +
    +#ifdef PAIR_CLASS
+PairStyle(foo,PairFoo)
+#else
+...
+(class definition for PairFoo)
+...
+#endif
+

    where “foo” is the style keyword in the pair_style command, and PairFoo is the class name defined in your pair_foo.cpp and pair_foo.h files.

    @@ -275,8 +275,8 @@ atoms.

    class. See atom_vec.h for details.

    c_ID
    --++ @@ -393,18 +393,18 @@ output the custom values.

    The code for these classes can use the per-atom properties defined by fix property/atom. The Atom class has a find_custom() method that is useful in this context:

    -
    int index = atom->find_custom(char *name, int &flag);
-
    -
    +
    +int index = atom->find_custom(char *name, int &flag);
+

    The “name” of a custom attribute, as specified in the fix property/atom command, is checked to verify that it exists and its index is returned. The method also sets flag = 0/1 depending on whether it is an integer or floating-point attribute. The vector of values associated with the attribute can then be accessed using the returned index as

    -
    int *ivector = atom->ivector[index];
-double *dvector = atom->dvector[index];
-
    -
    +
    +int *ivector = atom->ivector[index];
+double *dvector = atom->dvector[index];
+

    Ivector or dvector are vectors of length Nlocal = # of owned atoms, which store the attributes of individual atoms.

    @@ -474,8 +474,8 @@ per-atom kinetic energy.

    class. See compute.h for details.

    init
    --++ @@ -551,8 +551,8 @@ DumpCustom class contained in the dump_custom.cpp file.

    class. See dump.h for details.

    init
    --++ @@ -597,8 +597,8 @@ implement.

    derived class. See fix.h for details.

    write_header
    --++ @@ -823,8 +823,8 @@ styles can be created to add new K-space options to LAMMPS.

    class. See kspace.h for details.

    setmask
    --++ @@ -853,8 +853,8 @@ LAMMPS.

    class. See min.h for details.

    init
    --++ @@ -882,8 +882,8 @@ includes some optional methods to enable its use with rRESPA.

    Here is a brief description of the class methods in pair.h:

    init
    --++ @@ -929,8 +929,8 @@ styles can be created to add new region shapes to LAMMPS.

    class. See region.h for details.

    compute
    --++ @@ -965,8 +965,8 @@ a rigid body containing N sub-particles.

    class. See body.h for details.

    inside
    --++ @@ -1030,14 +1030,14 @@ via the print< thermo_style custom commands. Variables of style “equal” can compute complex equations that involve the following types of arguments:

    -
    thermo keywords = ke, vol, atoms, ...
-other variables = v_a, v_myvar, ...
-math functions = div(x,y), mult(x,y), add(x,y), ...
-group functions = mass(group), xcm(group,x), ...
-atom values = x[123], y[3], vx[34], ...
-compute values = c_mytemp[0], c_thermo_press[3], ...
-
    -
    +
    +thermo keywords = ke, vol, atoms, ...
+other variables = v_a, v_myvar, ...
+math functions = div(x,y), mult(x,y), add(x,y), ...
+group functions = mass(group), xcm(group,x), ...
+atom values = x[123], y[3], vx[34], ...
+compute values = c_mytemp[0], c_thermo_press[3], ...
+

    Adding keywords for the thermo_style custom command (which can then be accessed by variables) was discussed here on this page.

    @@ -1157,7 +1157,7 @@ structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
  • If you want your contribution to be added as a user-contributed -feature, and it’s a single file (actually a *.cpp and *.h file) it can +feature, and it’s a single file (actually a *.cpp and *.h file) it can rapidly be added to the USER-MISC directory. Send us the one-line entry to add to the USER-MISC/README file in that dir, along with the 2 source files. You can do this multiple times if you wish to @@ -1192,12 +1192,12 @@ to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing “make html pdf” in the doc folder. Thus the documentation source files must be in the same format and -style as other .txt files in the lammps/doc/src directory for similar +style as other *.txt files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. A description of the markup can also be found in lammps/doc/utils/txt2html/README.html As appropriate, the text files can include links to equations -(see doc/Eqs/.tex for examples, we auto-create the associated JPG +(see doc/Eqs/*.tex for examples, we auto-create the associated JPG files), or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the @@ -1220,7 +1220,7 @@ These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind
  • If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or -its implementation in LAMMPS), you can add the citation to the *.cpp +its implementation in LAMMPS), you can add the citation to the *.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the diff --git a/doc/html/Section_packages.html b/doc/html/Section_packages.html index fedd3cc1ae..2565c51206 100644 --- a/doc/html/Section_packages.html +++ b/doc/html/Section_packages.html @@ -630,9 +630,9 @@ for aspherical particle models: ellipsoids, 2d lines, 3d triangles.

    make machine -
    Make.py -p ^asphere -a machine
-
    -
    +
    +Make.py -p ^asphere -a machine
+

    Supporting info: Section howto 6.14, pair_style gayberne, pair_style resquared, doc/PDF/pair_gayberne_extra.pdf, @@ -658,9 +658,9 @@ themselves. See the make machine -

    Make.py -p ^body -a machine
-
    -
    +
    +Make.py -p ^body -a machine
+

    Supporting info: atom_style body, body, pair_style body, examples/body

    @@ -682,9 +682,9 @@ COMPASS CLASS2 molecular force field.

    make machine -
    Make.py -p ^class2 -a machine
-
    -
    +
    +Make.py -p ^class2 -a machine
+

    Supporting info: bond_style class2, angle_style class2, dihedral_style class2, improper_style class2, pair_style lj/class2

    @@ -708,9 +708,9 @@ approximation to Stokesian dynamics.

    make machine -
    Make.py -p ^colloid -a machine
-
    -
    +
    +Make.py -p ^colloid -a machine
+

    Supporting info: fix wall/colloid, pair_style colloid, pair_style yukawa/colloid, pair_style brownian, pair_style lubricate, pair_style lubricateU, examples/colloid, examples/srd

    @@ -737,9 +737,9 @@ zlib info it specifies.

    make machine -
    Make.py -p ^compress -a machine
-
    -
    +
    +Make.py -p ^compress -a machine
+

    Supporting info: src/COMPRESS/README, lib/compress/README, dump atom/gz, dump cfg/gz, dump custom/gz, dump xyz/gz

    @@ -764,9 +764,9 @@ package.

    make machine -
    Make.py -p ^coreshell -a machine
-
    -
    +
    +Make.py -p ^coreshell -a machine
+

    Supporting info: Section howto 6.26, compute temp/cs, pair_style born/coul/long/cs, pair_style buck/coul/long/cs, pair_style lj/cut/coul/long/cs”_pair_lj.html, examples/coreshell

    @@ -789,9 +789,9 @@ dipole models with short-range or long-range interactions.

    make machine -
    Make.py -p ^dipole -a machine
-
    -
    +
    +Make.py -p ^dipole -a machine
+

    Supporting info: atom_style dipole, pair_style lj/cut/dipole/cut, pair_style lj/cut/dipole/long, pair_style lj/long/dipole/long, examples/dipole

    @@ -841,9 +841,9 @@ one step, with Type “python src/Make.py -h -gpu” to see the details. make machine -
    Make.py -p ^gpu -a machine
-
    -
    +
    +Make.py -p ^gpu -a machine
+

    Supporting info: src/GPU/README, lib/gpu/README, Section acclerate, Section accelerate gpu, Pair Styles section of Section commands 3.5 for any pair style listed with a (g), kspace_style, package gpu, examples/accelerate, bench/FERMI, bench/KEPLER

    @@ -867,9 +867,9 @@ frictional and dissipative potentials.

    make machine -
    Make.py -p ^granular -a machine
-
    -
    +
    +Make.py -p ^granular -a machine
+

    Supporting info: Section howto 6.6, fix pour, fix wall/gran, pair_style gran/hooke, pair_style gran/hertz/history, examples/pour, bench/in.chute

    @@ -896,9 +896,9 @@ process. You should not need to edit this file.

    make machine -
    Make.py -p ^kim -a machine
-
    -
    +
    +Make.py -p ^kim -a machine
+

    Supporting info: src/KIM/README, lib/kim/README, pair_style kim, examples/kim

    @@ -928,12 +928,12 @@ choose which hardware to build for. Type “python src/Make.py -h system, you will need to read the Section accelerate kokkos doc page for details of what Makefile.machine settings are needed.

    To install via make or Make.py for each of 3 hardware options:

    -
    make yes-kokkos
-make kokkos_omp    # for CPUs with OpenMP
-make kokkos_cuda   # for GPUs, check the KOKKOS_ARCH setting in Makefile.kokkos_cuda
-make kokkos_phi    # for Xeon Phis
-
    -
    +
    +make yes-kokkos
+make kokkos_omp    # for CPUs with OpenMP
+make kokkos_cuda   # for GPUs, check the KOKKOS_ARCH setting in Makefile.kokkos_cuda
+make kokkos_phi    # for Xeon Phis
+

    Make.py -p kokkos -kokkos omp -a machine # for CPUs with OpenMP Make.py -p kokkos -kokkos cuda arch=35 -a machine # for GPUs of style arch Make.py -p kokkos -kokkos phi -a machine # for Xeon Phis

    @@ -942,9 +942,9 @@ Make.py -p kokkos -kokkos phi -a machine # for Xeon Phis

    make machine -
    Make.py -p ^kokkos -a machine
-
    -
    +
    +Make.py -p ^kokkos -a machine
+

    Supporting info: src/KOKKOS/README, lib/kokkos/README, Section acclerate, Section accelerate kokkos, Pair Styles section of Section commands 3.5 for any pair style listed with a (k), package kokkos, examples/accelerate, bench/FERMI, bench/KEPLER

    @@ -977,9 +977,9 @@ see the details.

    make machine -
    Make.py -p ^kspace -a machine
-
    -
    +
    +Make.py -p ^kspace -a machine
+

    Supporting info: kspace_style, doc/PDF/kspace.pdf, Section howto 6.7, Section howto 6.8, Section howto 6.9, pair_style coul, other pair style command doc pages which have “long” or “msm” in their @@ -1005,9 +1005,9 @@ the full list.

    make machine -
    Make.py -p ^manybody -a machine
-
    -
    +
    +Make.py -p ^manybody -a machine
+

    Supporting info:

    Examples: Pair Styles section of Section commands 3.5, examples/comb, examples/eim, examples/nb3d, examples/vashishta

    @@ -1032,9 +1032,9 @@ in conjuction with dynamics.

    make machine -
    Make.py -p ^mc -a machine
-
    -
    +
    +Make.py -p ^mc -a machine
+

    Supporting info: fix atom/swap, fix bond/break, fix bond/create, fix bond/swap, fix gcmc, pair_style dsmc

    @@ -1079,9 +1079,9 @@ Intel Fortran compiler, rather than the GNU Fortran compiler.

    make machine -
    Make.py -p ^meam -a machine
-
    -
    +
    +Make.py -p ^meam -a machine
+

    Supporting info: lib/meam/README, pair_style meam, examples/meam

    @@ -1104,9 +1104,9 @@ listing, “ls src/MISC”, to see the list of commands.

    make machine -
    Make.py -p ^misc -a machine
-
    -
    +
    +Make.py -p ^misc -a machine
+

    Supporting info: compute ti, fix evaporate, fix tmm, fix viscosity, examples/misc

    @@ -1129,9 +1129,9 @@ covalent bonds. The pair styles include terms for the Dreiding make machine -
    Make.py -p ^molecule -a machine
-
    -
    +
    +Make.py -p ^molecule -a machine
+

    Supporting info:atom_style, bond_style, angle_style, dihedral_style, @@ -1159,9 +1159,9 @@ are also written and read in parallel.

    make machine -
    Make.py -p ^mpiio -a machine
-
    -
    +
    +Make.py -p ^mpiio -a machine
+

    Supporting info: dump, restart, write_restart, read_restart

    @@ -1192,9 +1192,9 @@ creates and uses.

    make machine -
    Make.py -p ^opt -a machine
-
    -
    +
    +Make.py -p ^opt -a machine
+

    Supporting info: Section acclerate, Section accelerate opt, Pair Styles section of Section commands 3.5 for any pair style listed with an (o), examples/accelerate, bench/KEPLER

    @@ -1218,9 +1218,9 @@ styles which implement different materials models.

    make machine -
    Make.py -p ^peri -a machine
-
    -
    +
    +Make.py -p ^peri -a machine
+

    Supporting info: doc/PDF/PDLammps_overview.pdf, doc/PDF/PDLammps_EPS.pdf, @@ -1261,9 +1261,9 @@ one step. Type “python src/Make.py -h -poems” to see the details.make machine -

    Make.py -p ^meam -a machine
-
    -
    +
    +Make.py -p ^meam -a machine
+

    Supporting info: src/POEMS/README, lib/poems/README, fix poems, examples/rigid

    @@ -1296,9 +1296,9 @@ in one step. Type “python src/Make.py -h -python” to see the detail make machine -
    Make.py -p ^python -a machine
-
    -
    +
    +Make.py -p ^python -a machine
+

    Supporting info: examples/python

    @@ -1320,9 +1320,9 @@ that use QEq as part of their formulation.

    make machine -
    Make.py -p ^qeq -a machine
-
    -
    +
    +Make.py -p ^qeq -a machine
+

    Supporting info: fix qeq/*, examples/qeq

    @@ -1362,9 +1362,9 @@ one step. Type “python src/Make.py -h -reax” to see the details.

    make machine -
    Make.py -p ^reax -a machine
-
    -
    +
    +Make.py -p ^reax -a machine
+

    Supporting info: lib/reax/README, pair_style reax, fix reax/bonds, examples/reax

    @@ -1394,9 +1394,9 @@ field calcalation on another set.

    make machine -
    Make.py -p ^replica -a machine
-
    -
    +
    +Make.py -p ^replica -a machine
+

    Supporting info: Section howto 6.5, neb, prd, tad, temper, run_style verlet/split, examples/neb, examples/prd, @@ -1422,9 +1422,9 @@ few large bodies or many small bodies.

    make machine -
    Make.py -p ^rigid -a machine
-
    -
    +
    +Make.py -p ^rigid -a machine
+

    Supporting info: compute erotate/rigid, fix shake, fix rattle, fix rigid/*, examples/ASPHERE, examples/rigid

    @@ -1446,9 +1446,9 @@ simulations where a shock-wave passes through a material.

    make machine -
    Make.py -p ^shock -a machine
-
    -
    +
    +Make.py -p ^shock -a machine
+

    Supporting info: fix append/atoms, fix msst, fix nphug, fix wall/piston, examples/hugoniostat, examples/msst

    @@ -1471,9 +1471,9 @@ properties of the potential are also included.

    make machine -
    Make.py -p ^snap -a machine
-
    -
    +
    +Make.py -p ^snap -a machine
+

    Supporting info: pair snap, compute sna/atom, compute snad/atom, compute snav/atom, examples/snap

    @@ -1496,9 +1496,9 @@ colloidal-scale particles.

    make machine -
    Make.py -p ^srd -a machine
-
    -
    +
    +Make.py -p ^srd -a machine
+

    Supporting info: fix srd, fix wall/srd, examples/srd, examples/ASPHERE

    @@ -1541,9 +1541,9 @@ src/Make.py -h -voronoi” to see the details.

    make machine -
    Make.py -p ^voronoi -a machine
-
    -
    +
    +Make.py -p ^voronoi -a machine
+

    Supporting info: src/VORONOI/README, lib/voronoi/README, compute voronoi/atom, examples/voronoi

    @@ -1860,7 +1860,7 @@ src/Make.py -h -voronoi” to see the details.

    • - + - +
    data_body
    USER-SMD smoothed Mach dynamics Georg Ganzenmuller (EMI)userguide.pdfSMD User Guide USER/smd
    • @@ -1888,7 +1888,7 @@ src/Make.py -h -voronoi” to see the details.

    USER-SPH smoothed particle hydrodynamics Georg Ganzenmuller (EMI)userguide.pdfSPH User Guide USER/sph sph
      @@ -1986,9 +1986,9 @@ more details.

      make machine -
      Make.py -p ^atc -a machine
-
      -
      +
      +Make.py -p ^atc -a machine
+

      Supporting info:src/USER-ATC/README, fix atc, examples/USER/atc

      Authors: Reese Jones (rjones at sandia.gov), Jeremy Templeton (jatempl @@ -2064,10 +2064,9 @@ equations of motion are integrated efficiently through the Shardlow splitting algorithm. See src/USER-DPD/README for more details.

      Supporting info: /src/USER-DPD/README, compute dpd compute dpd/atom -fix eos/cv fix eos/table

      -
      -
      -

      fix rx pair table/rx +fix eos/cv fix eos/table +fix eos/table/rx fix shardlow +fix rx pair table/rx pair dpd/fdt pair dpd/fdt/energy pair exp6/rx pair multi/lucy pair multi/lucy/rx, examples/USER/dpd

      @@ -2213,7 +2212,7 @@ Contact them directly if you have any questions.

      Supporting info:

      The files in this package are a potpourri of (mostly) unrelated features contributed to LAMMPS by users. Each feature is a single -pair of files (*.cpp and *.h).

      +pair of files (*.cpp and *.h).

      More information about each feature can be found by reading its doc page in the LAMMPS doc directory. The doc page which lists all LAMMPS input script commands is as follows:

      @@ -2382,18 +2381,18 @@ questions.

      Supporting info:

      This package implements smoothed Mach dynamics (SMD) in LAMMPS. Currently, the package has the following features:

      -
        -
      • Does liquids via traditional Smooth Particle Hydrodynamics (SPH)
        • -
      • Also solves solids mechanics problems via a state of the art -stabilized meshless method with hourglass control.
        • -
      • Can specify hydrostatic interactions independently from material -strength models, i.e. pressure and deviatoric stresses are separated.
        • -
      • Many material models available (Johnson-Cook, plasticity with -hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new -material models.
        • -
      • Rigid boundary conditions (walls) can be loaded as surface geometries -from *.STL files.
        • -
      +

      * Does liquids via traditional Smooth Particle Hydrodynamics (SPH)

      +
      +
      * Also solves solids mechanics problems via a state of the art
      +
      stabilized meshless method with hourglass control.
      +
      * Can specify hydrostatic interactions independently from material
      +
      strength models, i.e. pressure and deviatoric stresses are separated.
      +
      * Many material models available (Johnson-Cook, plasticity with
      +
      hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new +material models.
      +
      * Rigid boundary conditions (walls) can be loaded as surface geometries
      +
      from *.STL files.
      +

      See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started.

      There are example scripts for using this package in examples/USER/smd.

      The person who created this package is Georg Ganzenmuller at the @@ -2424,16 +2423,18 @@ them directly if you have any questions.

      Supporting info:

      This package implements smoothed particle hydrodynamics (SPH) in LAMMPS. Currently, the package has the following features:

      -
        -
      • Tait, ideal gas, Lennard-Jones equation of states, full support for -complete (i.e. internal-energy dependent) equations of state
        • -
      • Plain or Monaghans XSPH integration of the equations of motion
        • -
      • Density continuity or density summation to propagate the density field
        • -
      • Commands to set internal energy and density of particles from the -input script
        • -
      • Output commands to access internal energy and density for dumping and -thermo output
        • -
      +
      +
      * Tait, ideal gas, Lennard-Jones equation of states, full support for
      +
      complete (i.e. internal-energy dependent) equations of state
      +
      +

      * Plain or Monaghans XSPH integration of the equations of motion

      +

      * Density continuity or density summation to propagate the density field

      +
      +
      * Commands to set internal energy and density of particles from the
      +
      input script
      +
      * Output commands to access internal energy and density for dumping and
      +
      thermo output
      +

      See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started.

      There are example scripts for using this package in examples/USER/sph.

      The person who created this package is Georg Ganzenmuller at the diff --git a/doc/html/Section_python.html b/doc/html/Section_python.html index 8b4dc1cffb..971aeb58dc 100644 --- a/doc/html/Section_python.html +++ b/doc/html/Section_python.html @@ -343,10 +343,10 @@ described above.

      If you set the paths to these files as environment variables, you only have to do it once. For the csh or tcsh shells, add something like this to your ~/.cshrc file, one line for each of the two files:

      -
      setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
+
      +setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
 setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
-
      -
      +

      If you use the python/install.py script, you need to invoke it every time you rebuild LAMMPS (as a shared library) or make changes to the python/lammps.py file.

      @@ -393,39 +393,21 @@ environment variable as described above.

      your Python with an interface to MPI. This also allows you to make MPI calls directly from Python in your script, if you desire.

      There are several Python packages available that purport to wrap MPI -as a library and allow MPI functions to be called from Python.

      -

      These include

      +as a library and allow MPI functions to be called from Python. However, +development on most of them seems to be halted except on:

      -

      All of these except pyMPI work by wrapping the MPI library and -exposing (some portion of) its interface to your Python script. This -means Python cannot be used interactively in parallel, since they do -not address the issue of interactive input to multiple instances of -Python running on different processors. The one exception is pyMPI, -which alters the Python interpreter to address this issue, and (I -believe) creates a new alternate executable (in place of “python” -itself) as a result.

      -

      In principle any of these Python/MPI packages should work to invoke -LAMMPS in parallel and to make MPI calls themselves from a Python -script which is itself running in parallel. However, when I -downloaded and looked at a few of them, their documentation was -incomplete and I had trouble with their installation. It’s not clear -if some of the packages are still being actively developed and -supported.

      -

      The packages Pypar and mpi4py have both been successfully tested with -LAMMPS. Pypar is simpler and easy to set up and use, but supports +

      Both packages, PyPar and mpi4py have been successfully tested with +LAMMPS. PyPar is simpler and easy to set up and use, but supports only a subset of MPI. Mpi4py is more MPI-feature complete, but also a bit more complex to use. As of version 2.0.0, mpi4py is the only python MPI wrapper that allows passing a custom MPI communicator to the LAMMPS constructor, which means one can easily run one or more LAMMPS instances on subsets of the total MPI ranks.

      -

      Pypar requires the ubiquitous Numpy package +

      PyPar requires the ubiquitous Numpy package be installed in your Python. After launching Python, type

      import numpy
      @@ -439,15 +421,15 @@ top-level directory, type

      The “sudo” is only needed if required to copy Numpy files into your Python distribution’s site-packages directory.

      -

      To install Pypar (version pypar-2.1.4_94 as of Aug 2012), unpack it +

      To install PyPar (version pypar-2.1.4_94 as of Aug 2012), unpack it and from its “source” directory, type

      python setup.py build
 sudo python setup.py install
      -

      Again, the “sudo” is only needed if required to copy Pypar files into +

      Again, the “sudo” is only needed if required to copy PyPar files into your Python distribution’s site-packages directory.

      -

      If you have successully installed Pypar, you should be able to run +

      If you have successully installed PyPar, you should be able to run Python and type

      import pypar
      @@ -465,17 +447,17 @@ on a simple test script

      and see one line of output for each processor you run on.

      Note

      -

      To use Pypar and LAMMPS in parallel from Python, you must insure +

      To use PyPar and LAMMPS in parallel from Python, you must insure both are using the same version of MPI. If you only have one MPI installed on your system, this is not an issue, but it can be if you have multiple MPIs. Your LAMMPS build is explicit about which MPI it is using, since you specify the details in your lo-level -src/MAKE/Makefile.foo file. Pypar uses the “mpicc” command to find +src/MAKE/Makefile.foo file. PyPar uses the “mpicc” command to find information about the MPI it uses to build against. And it tries to load “libmpi.so” from the LD_LIBRARY_PATH. This may or may not find the MPI library that LAMMPS is using. If you have problems running -both Pypar and LAMMPS together, this is an issue you may need to -address, e.g. by moving other MPI installations so that Pypar finds +both PyPar and LAMMPS together, this is an issue you may need to +address, e.g. by moving other MPI installations so that PyPar finds the right one.

      @@ -502,11 +484,11 @@ on a simple test script

      where test.py contains the lines

      -
      from mpi4py import MPI
-comm = MPI.COMM_WORLD
-print "Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size())
-
      -
      +
      +from mpi4py import MPI
+comm = MPI.COMM_WORLD
+print "Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size())
+

      and see one line of output for each processor you run on.

      Note

      @@ -568,15 +550,15 @@ interactively from the bench directory:

      Either way, you should see the results of running the in.lj benchmark on a single processor appear on the screen, the same as if you had typed something like:

      -
      lmp_g++ -in in.lj
-
      -
      +
      +lmp_g++ -in in.lj
+

      11.6.2. Test LAMMPS and Python in parallel:

      To run LAMMPS in parallel, assuming you have installed the -Pypar package as discussed above, create a test.py file -containing these lines:

      +PyPar package as discussed +above, create a test.py file containing these lines:

      import pypar
 from lammps import lammps
 lmp = lammps()
@@ -586,36 +568,36 @@ containing these lines:

      To run LAMMPS in parallel, assuming you have installed the -mpi4py package as discussed above, create a test.py file -containing these lines:

      -
      from mpi4py import MPI
-from lammps import lammps
-lmp = lammps()
-lmp.file("in.lj")
-me = MPI.COMM_WORLD.Get_rank()
-nprocs = MPI.COMM_WORLD.Get_size()
-print "Proc %d out of %d procs has" % (me,nprocs),lmp
-MPI.Finalize()
-
      -
      +mpi4py package as discussed +above, create a test.py file containing these lines:

      +
      +from mpi4py import MPI
+from lammps import lammps
+lmp = lammps()
+lmp.file("in.lj")
+me = MPI.COMM_WORLD.Get_rank()
+nprocs = MPI.COMM_WORLD.Get_size()
+print "Proc %d out of %d procs has" % (me,nprocs),lmp
+MPI.Finalize()
+

      You can either script in parallel as:

      % mpirun -np 4 python test.py

      and you should see the same output as if you had typed

      -
      % mpirun -np 4 lmp_g++ -in in.lj
-
      -
      -

      Note that if you leave out the 3 lines from test.py that specify Pypar +

      +% mpirun -np 4 lmp_g++ -in in.lj
+
      +

      Note that if you leave out the 3 lines from test.py that specify PyPar commands you will instantiate and run LAMMPS independently on each of the P processors specified in the mpirun command. In this case you should get 4 sets of output, each showing that a LAMMPS run was made on a single processor, instead of one set of output showing that LAMMPS ran on 4 processors. If the 1-processor outputs occur, it -means that Pypar is not working correctly.

      -

      Also note that once you import the PyPar module, Pypar initializes MPI +means that PyPar is not working correctly.

      +

      Also note that once you import the PyPar module, PyPar initializes MPI for you, and you can use MPI calls directly in your Python script, as -described in the Pypar documentation. The last line of your Python +described in the PyPar documentation. The last line of your Python script should be pypar.finalize(), to insure MPI is shut down correctly.

      @@ -661,14 +643,14 @@ Python script, as follows:

      the files src/library.cpp and src/library.h you will see that they correspond one-to-one with calls you can make to the LAMMPS library from a C++ or C or Fortran program.

      -
      lmp = lammps()           # create a LAMMPS object using the default liblammps.so library
-                         4 optional args are allowed: name, cmdargs, ptr, comm
-lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
-lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
-lmp = lammps(name="g++")   # create a LAMMPS object using the liblammps_g++.so library
-lmp = lammps(name="g++",cmdargs=list)    # add LAMMPS command-line args, e.g. list = ["-echo","screen"]
-
      -
      +
      +lmp = lammps()           # create a LAMMPS object using the default liblammps.so library
+                         4 optional args are allowed: name, cmdargs, ptr, comm
+lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
+lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
+lmp = lammps(name="g++")   # create a LAMMPS object using the liblammps_g++.so library
+lmp = lammps(name="g++",cmdargs=list)    # add LAMMPS command-line args, e.g. list = ["-echo","screen"]
+
      lmp.close()              # destroy a LAMMPS object
      @@ -677,49 +659,49 @@ from a C++ or C or Fortran program.

      lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100" -
      xlo = lmp.extract_global(name,type)  # extract a global quantity
-                                     # name = "boxxlo", "nlocal", etc
-                                  # type = 0 = int
-                                  #        1 = double
-
      -
      -
      coords = lmp.extract_atom(name,type)      # extract a per-atom quantity
-                                          # name = "x", "type", etc
-                                       # type = 0 = vector of ints
-                                       #        1 = array of ints
-                                       #        2 = vector of doubles
-                                       #        3 = array of doubles
-
      -
      -
      eng = lmp.extract_compute(id,style,type)  # extract value(s) from a compute
-v3 = lmp.extract_fix(id,style,type,i,j)   # extract value(s) from a fix
-                                          # id = ID of compute or fix
-                                       # style = 0 = global data
-                                       #         1 = per-atom data
-                                       #         2 = local data
-                                       # type = 0 = scalar
-                                       #        1 = vector
-                                       #        2 = array
-                                       # i,j = indices of value in global vector or array
-
      -
      -
      var = lmp.extract_variable(name,group,flag)  # extract value(s) from a variable
-                                          # name = name of variable
-                                          # group = group ID (ignored for equal-style variables)
-                                          # flag = 0 = equal-style variable
-                                          #        1 = atom-style variable
-
      -
      -
      flag = lmp.set_variable(name,value)       # set existing named string-style variable to value, flag = 0 if successful
-natoms = lmp.get_natoms()                 # total # of atoms as int
-data = lmp.gather_atoms(name,type,count)  # return atom attribute of all atoms gathered into data, ordered by atom ID
-                                          # name = "x", "charge", "type", etc
-                                          # count = # of per-atom values, 1 or 3, etc
-lmp.scatter_atoms(name,type,count,data)   # scatter atom attribute of all atoms from data, ordered by atom ID
-                                          # name = "x", "charge", "type", etc
-                                          # count = # of per-atom values, 1 or 3, etc
-
      -
      +
      +xlo = lmp.extract_global(name,type)  # extract a global quantity
+                                     # name = "boxxlo", "nlocal", etc
+                                  # type = 0 = int
+                                  #        1 = double
+
      +
      +coords = lmp.extract_atom(name,type)      # extract a per-atom quantity
+                                          # name = "x", "type", etc
+                                       # type = 0 = vector of ints
+                                       #        1 = array of ints
+                                       #        2 = vector of doubles
+                                       #        3 = array of doubles
+
      +
      +eng = lmp.extract_compute(id,style,type)  # extract value(s) from a compute
+v3 = lmp.extract_fix(id,style,type,i,j)   # extract value(s) from a fix
+                                          # id = ID of compute or fix
+                                       # style = 0 = global data
+                                       #         1 = per-atom data
+                                       #         2 = local data
+                                       # type = 0 = scalar
+                                       #        1 = vector
+                                       #        2 = array
+                                       # i,j = indices of value in global vector or array
+
      +
      +var = lmp.extract_variable(name,group,flag)  # extract value(s) from a variable
+                                          # name = name of variable
+                                          # group = group ID (ignored for equal-style variables)
+                                          # flag = 0 = equal-style variable
+                                          #        1 = atom-style variable
+
      +
      +flag = lmp.set_variable(name,value)       # set existing named string-style variable to value, flag = 0 if successful
+natoms = lmp.get_natoms()                 # total # of atoms as int
+data = lmp.gather_atoms(name,type,count)  # return atom attribute of all atoms gathered into data, ordered by atom ID
+                                          # name = "x", "charge", "type", etc
+                                          # count = # of per-atom values, 1 or 3, etc
+lmp.scatter_atoms(name,type,count,data)   # scatter atom attribute of all atoms from data, ordered by atom ID
+                                          # name = "x", "charge", "type", etc
+                                          # count = # of per-atom values, 1 or 3, etc
+

      The lines

      from lammps import lammps
@@ -767,8 +749,8 @@ argument.
      
 returned, which you can use via normal Python subscripting.  See the
 extract() method in the src/atom.cpp file for a list of valid names.
 Again, new names could easily be added.  A pointer to a vector of
-doubles or integers, or a pointer to an array of doubles (double **)
-or integers (int **) is returned.  You need to specify the appropriate
+doubles or integers, or a pointer to an array of doubles (double **)
+or integers (int **) is returned.  You need to specify the appropriate
 data type via the type argument.
      
 
      For extract_compute() and extract_fix(), the global, per-atom, or
 local data calulated by the compute or fix can be accessed.  What is
@@ -824,19 +806,19 @@ consecutively ordered, no coordinates are reset.
      
 
      The array of coordinates passed to scatter_atoms() must be a ctypes
 vector of ints or doubles, allocated and initialized something like
 this:
      
-
      from ctypes import *
-natoms = lmp.get_natoms()
-n3 = 3*natoms
-x = (n3*c_double)()
-x[0] = x coord of atom with ID 1
-x[1] = y coord of atom with ID 1
-x[2] = z coord of atom with ID 1
-x[3] = x coord of atom with ID 2
-...
-x[n3-1] = z coord of atom with ID natoms
-lmp.scatter_coords("x",1,3,x)
-
      
-
      
+
      +from ctypes import *
+natoms = lmp.get_natoms()
+n3 = 3*natoms
+x = (n3*c_double)()
+x[0] = x coord of atom with ID 1
+x[1] = y coord of atom with ID 1
+x[2] = z coord of atom with ID 1
+x[3] = x coord of atom with ID 2
+...
+x[n3-1] = z coord of atom with ID natoms
+lmp.scatter_coords("x",1,3,x)
+
      
 
      Alternatively, you can just change values in the vector returned by
 gather_atoms(“x”,1,3), since it is a ctypes vector of doubles.
      
 
      
@@ -915,10 +897,10 @@ capability needed by these Python scripts.
      
 open-source version of PyMol in your Python, so that you can import it
 from a Python script.  See the PyMol WWW pages here or
 here for more details:
      
-
      http://www.pymol.org
-http://sourceforge.net/scm/?type=svn&group_id=4546
-
      
-
      
+
      +http://www.pymol.org
+http://sourceforge.net/scm/?type=svn&group_id=4546
+
      
 
      The latter link is to the open-source version.
      
 
      Note that for VMD, you need a fairly current version (1.8.7 works for
 me) and there are some lines in the pizza/vmd.py script for 4 PIZZA
diff --git a/doc/html/Section_start.html b/doc/html/Section_start.html
index 4d422cdc2a..b3ebfd3dca 100644
--- a/doc/html/Section_start.html
+++ b/doc/html/Section_start.html
@@ -173,10 +173,10 @@ experienced users.
      
 
      When you download a LAMMPS tarball you will need to unzip and untar
 the downloaded file with the following commands, after placing the
 tarball in an appropriate directory.
      
-
      gunzip lammps*.tar.gz
-tar xvf lammps*.tar
-
      
-
      
+
      +gunzip lammps*.tar.gz
+tar xvf lammps*.tar
+
      
 
      This will create a LAMMPS directory containing two files and several
 sub-directories:
      
 
@@ -315,13 +315,13 @@ it will be never be touched by any LAMMPS updates.
      
 a list of available choices from src/MAKE and all of its
 sub-directories.  If one of those has the options you want or is the
 machine you want, you can type a command like:
      
-
      make mpi
-or
-make serial_icc
-or
-gmake mac
-
      
-
      
+
      +make mpi
+or
+make serial_icc
+or
+gmake mac
+
      Note that the corresponding Makefile.machine can exist in src/MAKE or
 any of its sub-directories.  If a file with the same name appears in
 multiple places (not a good idea), the order they are used is as
@@ -362,13 +362,13 @@ then you should list them as part of the LIB variable.  You should
 not need to do this if you use mpicxx.
      The DEPFLAGS setting is what triggers the C++ compiler to create a
 dependency list for a source file.  This speeds re-compilation when
-source (.cpp) or header (.h) files are edited.  Some compilers do
+source (*.cpp) or header (*.h) files are edited.  Some compilers do
 not support dependency file creation, or may use a different switch
 than -D.  GNU g++ and Intel icc works with -D.  If your compiler can’t
 create dependency files, then you’ll need to create a Makefile.foo
 patterned after Makefile.storm, which uses different rules that do not
 involve dependency files.  Note that when you build LAMMPS for the
-first time on a new platform, a long list of *.d files will be printed
+first time on a new platform, a long list of *.d files will be printed
 out rapidly.  This is not an error; it is the Makefile doing its
 normal creation of dependencies.
      Step 4
      
@@ -598,7 +598,7 @@ faster, depending on how many cores your compilation machine has.  N
 is the number of cores the build runs on.
      You should get the executable lmp_foo when the build is complete.
      
-
      **Errors that can occur when making LAMMPS:**
      
+
      **Errors that can occur when making LAMMPS:**
      
 
      Note
      
 
      If an error occurs when building LAMMPS, the compiler or linker
@@ -632,17 +632,17 @@ is undefined’, then your machine does not support “long long”
 integers.  Try using the -DLAMMPS_LONGLONG_TO_LONG setting described
 above in Step 4.
      
 
      
-
      **Additional build tips:**
      
+
      **Additional build tips:**
      
 
        
 
      1. Building LAMMPS for multiple platforms.
        2. 
 
      
 
      You can make LAMMPS for multiple platforms from the same src
 directory.  Each target creates its own object sub-directory called
-Obj_target where it stores the system-specific *.o files.
      
+Obj_target where it stores the system-specific *.o files.
      
 
        
 
      1. Cleaning up.
        2. 
 
      
-
      Typing “make clean-all” or “make clean-machine” will delete *.o object
+
      Typing “make clean-all” or “make clean-machine” will delete *.o object
 files created when LAMMPS is built, for either all builds or for a
 particular machine.
      
 
      (3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
@@ -686,11 +686,11 @@ basis is limited by 4-byte integer storage to 2^31 atoms per processor
 a problem would have a huge per-processor memory footprint due to
 neighbor lists and would run very slowly in terms of CPU secs/timestep.
      
 
      
-
      **Building for a Mac:**
      
+
      **Building for a Mac:**
      
 
      OS X is BSD Unix, so it should just work.  See the
 src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.
      
 
      
-
      **Building for Windows:**
      
+
      **Building for Windows:**
      
 
      The LAMMPS download page has an option to download both a serial and
 parallel pre-built Windows executable.  See the Running LAMMPS section for instructions on running these executables
 on a Windows box.
      
@@ -725,7 +725,7 @@ tool which can be used to install/un-install packages and build the
 auxiliary libraries which some of them use.  It can also auto-edit a
 Makefile.machine to add settings needed by some packages.
      
 
      
-
      **Package basics:**
      
+
      **Package basics:**
      
 
      The source code for LAMMPS is structured as a set of core files which
 are always included, plus optional packages.  Packages are groups of
 files that enable a specific set of features.  For example, force
@@ -742,9 +742,9 @@ package, you must have built LAMMPS with that package, else you will
 get an error that the style is invalid or the command is unknown.
 Every command’s doc page specfies if it is part of a package.  You can
 also type
      
-
      lmp_machine -h
-
      
-
      
+
      +lmp_machine -h
+
      
 
      to run your executable with the optional -h command-line switch for “help”, which will simply list the styles and
 commands known to your executable, and immediately exit.
      
 
      There are two kinds of packages in LAMMPS, standard and user packages.
@@ -768,7 +768,7 @@ Information on how to submit additions you make to LAMMPS as single
 files or either a standard or user-contributed package are given in
 this section of the documentation.
      
 
      
-
      **Including/excluding packages:**
      
+
      **Including/excluding packages:**
      
 
      To use (or not use) a package you must include it (or exclude it)
 before building LAMMPS.  From the src directory, this is typically as
 simple as:
      
@@ -837,7 +837,7 @@ sub-directory.  Typing “make package-diff” lists all differences
 between these files.  Again, type “make package” to see all of the
 package-related make options.
      
 
      
-
      **Packages that require extra libraries:**
      
+
      **Packages that require extra libraries:**
      
 
      A few of the standard and user packages require additional auxiliary
 libraries.  Many of them are provided with LAMMPS, in which case they
 must be compiled first, before LAMMPS is built, if you wish to include
@@ -908,7 +908,7 @@ needed soft links.  Type “python install.py” for further instruction
 or settings in the lib/package/Makefile.lammps files are not correct,
 the LAMMPS build will typically fail.
      
 
      
-
      **Packages that require Makefile.machine settings**
      
+
      **Packages that require Makefile.machine settings**
      
 
      A few packages require specific settings in Makefile.machine, to
 either build or use the package effectively.  These are the
 USER-INTEL, KOKKOS, USER-OMP, and OPT packages, used for accelerating
@@ -1081,7 +1081,7 @@ LAMMPS to other codes.  See 
 
      2.5.1. Static library:
      
-
      To build LAMMPS as a static library (*.a file on Linux), type
      
+
      To build LAMMPS as a static library (*.a file on Linux), type
      
 
      make foo mode=lib
 
      
 
      
@@ -1095,7 +1095,7 @@ point to the most recently built static library.
      
 
      
 
      2.5.2. Shared library:
      
-
      To build LAMMPS as a shared library (*.so file on Linux), which can be
+
      To build LAMMPS as a shared library (*.so file on Linux), which can be
 dynamically loaded, e.g. from Python, type
      
 
      make foo mode=shlib
 
      
@@ -1122,18 +1122,18 @@ of the auxiliary library.  The build instructions for the library
 should tell you how to do this.
      
 
      Here is an example of such errors when the system FFTW or provided
 lib/colvars library have not been built as shared libraries:
      
-
      /usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation
-R_X86_64_32 against `.rodata' can not be used when making a shared
+
      +/usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation
+R_X86_64_32 against '.rodata' can not be used when making a shared
 object; recompile with -fPIC
 /usr/local/lib/libfftw3.a: could not read symbols: Bad value
-
      
-
      
-
      /usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o):
-relocation R_X86_64_32 against `__pthread_key_create' can not be used
+
      
+
      +/usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o):
+relocation R_X86_64_32 against '__pthread_key_create' can not be used
 when making a shared object; recompile with -fPIC
 ../../lib/colvars/libcolvars.a: error adding symbols: Bad value
-
      
-
      
+
 
      As an example, here is how to build and install the MPICH library, a popular open-source version of MPI, distributed by
 Argonne National Labs, as a shared library in the default
 /usr/local/lib location:
      
@@ -1157,9 +1157,9 @@ current version of the shared library is always available to programs
 that use it.
      
 
      For the csh or tcsh shells, you would add something like this to your
 ~/.cshrc file:
      
-
      setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
-
      
-
      
+
      +setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
+
      
 
      
 
      
 
      2.5.4. Calling the LAMMPS library:
      
@@ -1188,20 +1188,20 @@ interface and how to extend it for your needs.
      
 
      2.6. Running LAMMPS
      
 
      By default, LAMMPS runs by reading commands from standard input.  Thus
 if you run the LAMMPS executable by itself, e.g.
      
-
      lmp_linux
-
      
-
      
+
      +lmp_linux
+
      
 
      it will simply wait, expecting commands from the keyboard.  Typically
 you should put commands in an input script and use I/O redirection,
 e.g.
      
-
      lmp_linux < in.file
-
      
-
      
+
      +lmp_linux < in.file
+
      
 
      For parallel environments this should also work.  If it does not, use
 the ‘-in’ command-line switch, e.g.
      
-
      lmp_linux -in in.file
-
      
-
      
+
      +lmp_linux -in in.file
+
      
 
      This section describes how input scripts are
 structured and what commands they contain.
      
 
      You can test LAMMPS on any of the sample inputs provided in the
@@ -1210,13 +1210,13 @@ outputs are named log.*.name.P where name is a machine and P is the
 number of processors it was run on.
      
 
      Here is how you might run a standard Lennard-Jones benchmark on a
 Linux box, using mpirun to launch a parallel job:
      
-
      cd src
-make linux
-cp lmp_linux ../bench
-cd ../bench
-mpirun -np 4 lmp_linux -in in.lj
-
      
-
      
+
      +cd src
+make linux
+cp lmp_linux ../bench
+cd ../bench
+mpirun -np 4 lmp_linux -in in.lj
+
      
 
      See this page for timings for this and the other benchmarks on
 various platforms.  Note that some of the example scripts require
 LAMMPS to be built with one or more of its optional packages.
      
@@ -1256,7 +1256,7 @@ in.lj”, replacing in.lj with the name of your LAMMPS input script.
 matter what you type).
 
    • In this mode, output may not immediately show up on the screen, so if
 your input script takes a long time to execute, you may need to be
-patient before the output shows up. :l Alternatively, you can still
+patient before the output shows up.  Alternatively, you can still
 use this executable to run on a single processor by typing something
 like: “lmp_win_mpi -in in.lj”.
      • 
 
@@ -1309,10 +1309,10 @@ letter abbreviation can be used:
      
 
    • -v or -var
      • 
 
 
      For example, lmp_ibm might be launched as follows:
      
-
      mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none -in in.alloy
-mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none -in in.alloy
-
      
-
      
+
      +mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none -in in.alloy
+mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none -in in.alloy
+
      
 
      Here are the details on the options:
      
 
      -echo style
 
      
@@ -1395,11 +1395,11 @@ are intended for computational work like running LAMMPS.  By default
 Ng = 1 and Ns is not set.
      
 
      Depending on which flavor of MPI you are running, LAMMPS will look for
 one of these 3 environment variables
      
-
      SLURM_LOCALID (various MPI variants compiled with SLURM support)
-MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
-OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI)
-
      
-
      
+
      +SLURM_LOCALID (various MPI variants compiled with SLURM support)
+MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
+OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI)
+
      
 
      which are initialized by the “srun”, “mpirun” or “mpiexec” commands.
 The environment variable setting for each MPI rank is used to assign a
 unique GPU ID to the MPI task.
      
diff --git a/doc/html/Section_tools.html b/doc/html/Section_tools.html
index 285debd48d..0e3948b6a0 100644
--- a/doc/html/Section_tools.html
+++ b/doc/html/Section_tools.html
@@ -218,7 +218,7 @@ own sub-directories with their own Makefiles.
      
 
    • polymer bonding
      • 
 
    • pymol_asphere
      • 
 
    • python
      • 
-
    • reax
      • 
+
    • reax
      • 
 
    • restart2data
      • 
 
    • vim
      • 
 
    • xmgrace
      • 
@@ -289,9 +289,9 @@ at: 
      Syntax: ./abf_integrate < filename > [-n < nsteps >] [-t < temp >] [-m [0|1] (metadynamics)] [-h < hill_height >] [-f < variable_hill_factor >]
-
      
-
      
+
      +Syntax: ./abf_integrate < filename > [-n < nsteps >] [-t < temp >] [-m [0|1] (metadynamics)] [-h < hill_height >] [-f < variable_hill_factor >]
+
      
 
      The LAMMPS interface to the colvars collective variable library, as
 well as these tools, were created by Axel Kohlmeyer (akohlmey at
 gmail.com) at ICTP, Italy.
      
@@ -419,7 +419,7 @@ Greathouse at Sandia (jagreat at sandia.gov).
      
 
      
 
      9.17. lmp2cfg tool
      
 
      The lmp2cfg sub-directory contains a tool for converting LAMMPS output
-files into a series of *.cfg files which can be read into the
+files into a series of *.cfg files which can be read into the
 AtomEye visualizer.  See
 the README file for more information.
      
 
      This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
      
@@ -538,7 +538,7 @@ README for more info on Pizza.py and how to use these scripts.
      
 
      
 
      
 
      
-
      9.27. reax tool
      
+
      9.27. reax tool
      
 
      The reax sub-directory contains stand-alond codes that can
 post-process the output of the fix reax/bonds
 command from a LAMMPS simulation using ReaxFF.  See
diff --git a/doc/html/accelerate_gpu.html b/doc/html/accelerate_gpu.html
index b4fc73c25e..33e9cc6d76 100644
--- a/doc/html/accelerate_gpu.html
+++ b/doc/html/accelerate_gpu.html
@@ -202,11 +202,11 @@ attention to 3 settings in this makefile.
      
 
      See lib/gpu/Makefile.linux.double for examples of the ARCH settings
 for different GPU choices, e.g. Fermi vs Kepler.  It also lists the
 possible precision settings:
      
-
      CUDA_PREC = -D_SINGLE_SINGLE  # single precision for all calculations
-CUDA_PREC = -D_DOUBLE_DOUBLE  # double precision for all calculations
-CUDA_PREC = -D_SINGLE_DOUBLE  # accumulation of forces, etc, in double
-
      
-
      
+
      +CUDA_PREC = -D_SINGLE_SINGLE  # single precision for all calculations
+CUDA_PREC = -D_DOUBLE_DOUBLE  # double precision for all calculations
+CUDA_PREC = -D_SINGLE_DOUBLE  # accumulation of forces, etc, in double
+
      
 
      The last setting is the mixed mode referred to above.  Note that your
 GPU must support double precision to use either the 2nd or 3rd of
 these settings.
      
@@ -253,11 +253,11 @@ shared by 4 MPI tasks.
      
 which will automatically append “gpu” to styles that support it.  Use
 the “-pk gpu Ng” command-line switch to
 set Ng = # of GPUs/node to use.
      
-
      lmp_machine -sf gpu -pk gpu 1 -in in.script                         # 1 MPI task uses 1 GPU
-mpirun -np 12 lmp_machine -sf gpu -pk gpu 2 -in in.script           # 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node
-mpirun -np 48 -ppn 12 lmp_machine -sf gpu -pk gpu 2 -in in.script   # ditto on 4 16-core nodes
-
      
-
      
+
      +lmp_machine -sf gpu -pk gpu 1 -in in.script                         # 1 MPI task uses 1 GPU
+mpirun -np 12 lmp_machine -sf gpu -pk gpu 2 -in in.script           # 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node
+mpirun -np 48 -ppn 12 lmp_machine -sf gpu -pk gpu 2 -in in.script   # ditto on 4 16-core nodes
+
      
 
      Note that if the “-sf gpu” switch is used, it also issues a default
 package gpu 1 command, which sets the number of
 GPUs/node to 1.
      
@@ -276,9 +276,9 @@ GPU package pair styles.
      
 and use of multiple MPI tasks/GPU is the same.
      
 
      Use the suffix gpu command, or you can explicitly add an
 “gpu” suffix to individual styles in your input script, e.g.
      
-
      pair_style lj/cut/gpu 2.5
-
      
-
      
+
      +pair_style lj/cut/gpu 2.5
+
      
 
      You must also use the package gpu command to enable the
 GPU package, unless the “-sf gpu” or “-pk gpu” command-line switches were used.  It specifies the
 number of GPUs/node to use, as well as other options.
      
diff --git a/doc/html/accelerate_intel.html b/doc/html/accelerate_intel.html
index ad8f8560d4..cc1a7a68b6 100644
--- a/doc/html/accelerate_intel.html
+++ b/doc/html/accelerate_intel.html
@@ -268,30 +268,30 @@ this information can normally be obtained with:
      
 
      
 
      Several example Makefiles for building with the Intel compiler are
 included with LAMMPS in the src/MAKE/OPTIONS/ directory:
      
-
      Makefile.intel_cpu_intelmpi # Intel Compiler, Intel MPI, No Offload
-Makefile.knl                # Intel Compiler, Intel MPI, No Offload
-Makefile.intel_cpu_mpich    # Intel Compiler, MPICH, No Offload
-Makefile.intel_cpu_openpmi  # Intel Compiler, OpenMPI, No Offload
-Makefile.intel_coprocessor  # Intel Compiler, Intel MPI, Offload
-
      
-
      
+
      +Makefile.intel_cpu_intelmpi # Intel Compiler, Intel MPI, No Offload
+Makefile.knl                # Intel Compiler, Intel MPI, No Offload
+Makefile.intel_cpu_mpich    # Intel Compiler, MPICH, No Offload
+Makefile.intel_cpu_openpmi  # Intel Compiler, OpenMPI, No Offload
+Makefile.intel_coprocessor  # Intel Compiler, Intel MPI, Offload
+
      
 
      Makefile.knl is identical to Makefile.intel_cpu_intelmpi except that
 it explicitly specifies that vectorization should be for Intel
 Xeon Phi x200 processors making it easier to cross-compile. For
 users with recent installations of Intel Parallel Studio, the
 process can be as simple as:
      
-
      make yes-user-intel
-source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
-# or psxevars.csh for C-shell
-make intel_cpu_intelmpi
-
      
-
      
+
      +make yes-user-intel
+source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
+# or psxevars.csh for C-shell
+make intel_cpu_intelmpi
+
      
 
      Alternatively, the build can be accomplished with the src/Make.py
 script, described in Section 2.4 of the
 manual. Type “Make.py -h” for help. For an example:
      
-
      Make.py -v -p intel omp -intel cpu -a file intel_cpu_intelmpi
-
      
-
      
+
      +Make.py -v -p intel omp -intel cpu -a file intel_cpu_intelmpi
+
      
 
      Note that if you build with support for a Phi coprocessor, the same
 binary can be used on nodes with or without coprocessors installed.
 However, if you do not have coprocessors on your system, building
@@ -385,10 +385,10 @@ set the number of OpenMP threads via the OMP_NUM_THREADS environment
 variable if desired.
      
 
      Examples (see documentation for your MPI/Machine for differences in
 launching MPI applications):
      
-
      mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script                                 # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads
-mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double   # Don't use any coprocessors that might be available, use 2 OpenMP threads for each task, use double precision
-
      
-
      
+
      +mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script                                 # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads
+mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double   # Don't use any coprocessors that might be available, use 2 OpenMP threads for each task, use double precision
+
      
 
      Or run with the USER-INTEL package by editing an input script:
      
 
      As an alternative to adding command-line arguments, the input script
 can be edited to enable the USER-INTEL package. This requires adding
@@ -399,9 +399,9 @@ script. For the second example above, this would be:
      
 
      
 
      To enable the USER-INTEL package only for individual styles, you can
 add an “intel” suffix to the individual style, e.g.:
      
-
      pair_style lj/cut/intel 2.5
-
      
-
      
+
      +pair_style lj/cut/intel 2.5
+
      
 
      Alternatively, the suffix intel command can be added to
 the input script to enable USER-INTEL styles for the commands that
 follow in the input script.
      
diff --git a/doc/html/accelerate_kokkos.html b/doc/html/accelerate_kokkos.html
index e517e0e2c5..c592745bea 100644
--- a/doc/html/accelerate_kokkos.html
+++ b/doc/html/accelerate_kokkos.html
@@ -166,19 +166,19 @@ produce an executable compatible with specific hardware.
      
 
      Here is a quick overview of how to use the KOKKOS package
 for CPU acceleration, assuming one or more 16-core nodes.
 More details follow.
      
-
      use a C++11 compatible compiler
-make yes-kokkos
-make mpi KOKKOS_DEVICES=OpenMP                 # build with the KOKKOS package
-make kokkos_omp                                # or Makefile.kokkos_omp already has variable set
-Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi   # or one-line build via Make.py
-
      
-
      
-
      mpirun -np 16 lmp_mpi -k on -sf kk -in in.lj              # 1 node, 16 MPI tasks/node, no threads
-mpirun -np 2 -ppn 1 lmp_mpi -k on t 16 -sf kk -in in.lj   # 2 nodes, 1 MPI task/node, 16 threads/task
-mpirun -np 2 lmp_mpi -k on t 8 -sf kk -in in.lj           # 1 node, 2 MPI tasks/node, 8 threads/task
-mpirun -np 32 -ppn 4 lmp_mpi -k on t 4 -sf kk -in in.lj   # 8 nodes, 4 MPI tasks/node, 4 threads/task
-
      
-
      
+
      +use a C++11 compatible compiler
+make yes-kokkos
+make mpi KOKKOS_DEVICES=OpenMP                 # build with the KOKKOS package
+make kokkos_omp                                # or Makefile.kokkos_omp already has variable set
+Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi   # or one-line build via Make.py
+
      
+
      +mpirun -np 16 lmp_mpi -k on -sf kk -in in.lj              # 1 node, 16 MPI tasks/node, no threads
+mpirun -np 2 -ppn 1 lmp_mpi -k on t 16 -sf kk -in in.lj   # 2 nodes, 1 MPI task/node, 16 threads/task
+mpirun -np 2 lmp_mpi -k on t 8 -sf kk -in in.lj           # 1 node, 2 MPI tasks/node, 8 threads/task
+mpirun -np 32 -ppn 4 lmp_mpi -k on t 4 -sf kk -in in.lj   # 8 nodes, 4 MPI tasks/node, 4 threads/task
+
      
 
        
 
      • specify variables and settings in your Makefile.machine that enable OpenMP, GPU, or Phi support
        • 
 
      • include the KOKKOS package and build LAMMPS
        • 
@@ -188,39 +188,39 @@ More details follow.
        
 assuming one or more nodes, each with 16 cores and a GPU.  More
 details follow.
        
 
        discuss use of NVCC, which Makefiles to examine
        
-
        use a C++11 compatible compiler
-KOKKOS_DEVICES = Cuda, OpenMP
-KOKKOS_ARCH = Kepler35
-make yes-kokkos
-make machine
-Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda
-
        
-
        
-
        mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj          # one MPI task, 6 threads on CPU
-mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj   # ditto on 4 nodes
-
        
-
        
-
        mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj           # two MPI tasks, 8 threads per CPU
-mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj   # ditto on 16 nodes
-
        
-
        
+
        +use a C++11 compatible compiler
+KOKKOS_DEVICES = Cuda, OpenMP
+KOKKOS_ARCH = Kepler35
+make yes-kokkos
+make machine
+Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda
+
        
+
        +mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj          # one MPI task, 6 threads on CPU
+mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj   # ditto on 4 nodes
+
        
+
        +mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj           # two MPI tasks, 8 threads per CPU
+mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj   # ditto on 16 nodes
+
        
 
        Here is a quick overview of how to use the KOKKOS package
 for the Intel Phi:
        
-
        use a C++11 compatible compiler
-KOKKOS_DEVICES = OpenMP
-KOKKOS_ARCH = KNC
-make yes-kokkos
-make machine
-Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi
-
        
-
        
-
        host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
-mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj           # 1 MPI task on 1 Phi, 1*240 = 240
-mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj            # 30 MPI tasks on 1 Phi, 30*8 = 240
-mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj           # 12 MPI tasks on 1 Phi, 12*20 = 240
-mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj   # ditto on 8 Phis
-
        
-
        
+
        +use a C++11 compatible compiler
+KOKKOS_DEVICES = OpenMP
+KOKKOS_ARCH = KNC
+make yes-kokkos
+make machine
+Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi
+
        
+
        +host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
+mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj           # 1 MPI task on 1 Phi, 1*240 = 240
+mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj            # 30 MPI tasks on 1 Phi, 30*8 = 240
+mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj           # 12 MPI tasks on 1 Phi, 12*20 = 240
+mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj   # ditto on 8 Phis
+
        
 
        Required hardware/software:
        
 
        Kokkos support within LAMMPS must be built with a C++11 compatible
 compiler.  If using gcc, version 4.8.1 or later is required.
        
@@ -257,40 +257,40 @@ respectively.  Or the effect of the “-pk” or “-sf” switc
 duplicated by adding the package kokkos or suffix kk commands respectively to your input script.
        
 
        Or you can follow these steps:
        
 
        CPU-only (run all-MPI or with OpenMP threading):
        
-
        cd lammps/src
-make yes-kokkos
-make g++ KOKKOS_DEVICES=OpenMP
-
        
-
        
+
        +cd lammps/src
+make yes-kokkos
+make g++ KOKKOS_DEVICES=OpenMP
+
        
 
        Intel Xeon Phi:
        
-
        cd lammps/src
-make yes-kokkos
-make g++ KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=KNC
-
        
-
        
+
        +cd lammps/src
+make yes-kokkos
+make g++ KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=KNC
+
        
 
        CPUs and GPUs:
        
-
        cd lammps/src
-make yes-kokkos
-make cuda KOKKOS_DEVICES=Cuda
-
        
-
        
+
        +cd lammps/src
+make yes-kokkos
+make cuda KOKKOS_DEVICES=Cuda
+
        
 
        These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
 make command line which requires a GNU-compatible make command.  Try
 “gmake” if your system’s standard make complains.
        
 
        
 
        Note
        
 
        If you build using make line variables and re-build LAMMPS twice
-with different KOKKOS options and the same target, e.g. g++ in the
-first two examples above, then you must perform a “make clean-all”
+with different KOKKOS options and the *same* target, e.g. g++ in the
+first two examples above, then you *must* perform a “make clean-all”
 or “make clean-machine” before each build.  This is to force all the
 KOKKOS-dependent files to be re-compiled with the new options.
        
 
        
 
        You can also hardwire these make variables in the specified machine
 makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above,
 with a line like:
        
-
        KOKKOS_ARCH = KNC
-
        
-
        
+
        +KOKKOS_ARCH = KNC
+
        
 
        Note that if you build LAMMPS multiple times in this manner, using
 different KOKKOS options (defined in different machine makefiles), you
 do not have to worry about doing a “clean” in between.  This is
@@ -342,7 +342,7 @@ with compute capability 3.x.  For the LINK setting, “nvcc” should no
 be used; instead use g++ or another compiler suitable for linking C++
 applications.  Often you will want to use your MPI compiler wrapper
 for this setting (i.e. mpicxx).  Finally, the lo-level Makefile must
-also have a “Compilation rule” for creating *.o files from *.cu files.
+also have a “Compilation rule” for creating *.o files from *.cu files.
 See src/Makefile.cuda for an example of a lo-level Makefile with all
 of these settings.
        
 
        KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not
@@ -430,9 +430,9 @@ specify its additional arguments for hardware options appopriate to
 your system, as documented above.
        
 
        Use the suffix kk command, or you can explicitly add a
 “kk” suffix to individual styles in your input script, e.g.
        
-
        pair_style lj/cut/kk 2.5
-
        
-
        
+
        +pair_style lj/cut/kk 2.5
+
        
 
        You only need to use the package kokkos command if you
 wish to change any of its option defaults, as set by the “-k on”
 command-line switch.
        
@@ -483,10 +483,10 @@ performance to bind both MPI tasks to physical cores, and threads to
 physical cores, so they do not migrate during a simulation.
        
 
        If you are not certain MPI tasks are being bound (check the defaults
 for your MPI installation), binding can be forced with these flags:
        
-
        OpenMPI 1.8: mpirun -np 2 -bind-to socket -map-by socket ./lmp_openmpi ...
-Mvapich2 2.0: mpiexec -np 2 -bind-to socket -map-by socket ./lmp_mvapich ...
-
        
-
        
+
        +OpenMPI 1.8: mpirun -np 2 -bind-to socket -map-by socket ./lmp_openmpi ...
+Mvapich2 2.0: mpiexec -np 2 -bind-to socket -map-by socket ./lmp_mvapich ...
+
        
 
        For binding threads with the KOKKOS OMP option, use thread affinity
 environment variables to force binding.  With OpenMP 3.1 (gcc 4.7 or
 later, intel 12 or later) setting the environment variable
diff --git a/doc/html/accelerate_omp.html b/doc/html/accelerate_omp.html
index b77f59e8cd..8409d38821 100644
--- a/doc/html/accelerate_omp.html
+++ b/doc/html/accelerate_omp.html
@@ -141,11 +141,11 @@ one or more 16-core nodes.  More details follow.
        
 Make.py -v -p omp -o mpi -a file mpi       # or one-line build via Make.py
 
      
-
      lmp_mpi -sf omp -pk omp 16 < in.script                         # 1 MPI task, 16 threads
-mpirun -np 4 lmp_mpi -sf omp -pk omp 4 -in in.script           # 4 MPI tasks, 4 threads/task
-mpirun -np 32 -ppn 4 lmp_mpi -sf omp -pk omp 4 -in in.script   # 8 nodes, 4 MPI tasks/node, 4 threads/task
-
      
-
      
+
      +lmp_mpi -sf omp -pk omp 16 < in.script                         # 1 MPI task, 16 threads
+mpirun -np 4 lmp_mpi -sf omp -pk omp 4 -in in.script           # 4 MPI tasks, 4 threads/task
+mpirun -np 32 -ppn 4 lmp_mpi -sf omp -pk omp 4 -in in.script   # 8 nodes, 4 MPI tasks/node, 4 threads/task
+
      Required hardware/software:
      Your compiler must support the OpenMP interface.  You should have one
 or more multi-core CPUs so that multiple threads can be launched by
@@ -184,9 +184,9 @@ threads via the OMP_NUM_THREADS environment variable.
      
 and threads/MPI task is the same.
      Use the suffix omp command, or you can explicitly add an
 “omp” suffix to individual styles in your input script, e.g.
      
-
      pair_style lj/cut/omp 2.5
-
      
-
      
+
      +pair_style lj/cut/omp 2.5
+
      You must also use the package omp command to enable the
 USER-OMP package.  When you do this you also specify how many threads
 per MPI task to use.  The command doc page explains other options and
diff --git a/doc/html/angle_charmm.html b/doc/html/angle_charmm.html
index df9e20c662..3d6bb4e8cd 100644
--- a/doc/html/angle_charmm.html
+++ b/doc/html/angle_charmm.html
@@ -137,16 +137,16 @@
 
      angle_style charmm/omp command
      
 
      Syntax
      
-
      angle_style charmm
-
      
-
      
+
      +angle_style charmm
+
      
 
      
 
      Examples
      
-
      angle_style charmm
-angle_coeff 1 300.0 107.0 50.0 3.0
-
      
-
      
+
      +angle_style charmm
+angle_coeff 1 300.0 107.0 50.0 3.0
+
      
 
      
 
      Description
      
diff --git a/doc/html/angle_class2.html b/doc/html/angle_class2.html
index 1977415a6d..1b800d6c0d 100644
--- a/doc/html/angle_class2.html
+++ b/doc/html/angle_class2.html
@@ -131,18 +131,18 @@
 
      angle_style class2/omp command
      
 
      
 
      Syntax
      
-
      angle_style class2
-
      
-
      
+
      +angle_style class2
+
      
 
      
 
      
 
      Examples
      
-
      angle_style class2
-angle_coeff * 75.0
-angle_coeff 1 bb 10.5872 1.0119 1.5228
-angle_coeff * ba 3.6551 24.895 1.0119 1.5228
-
      
-
      
+
      +angle_style class2
+angle_coeff * 75.0
+angle_coeff 1 bb 10.5872 1.0119 1.5228
+angle_coeff * ba 3.6551 24.895 1.0119 1.5228
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/angle_cosine.html b/doc/html/angle_cosine.html
index ef3eba806d..6876620bb5 100644
--- a/doc/html/angle_cosine.html
+++ b/doc/html/angle_cosine.html
@@ -131,16 +131,16 @@
 
      angle_style cosine/omp command
      
 
      
 
      Syntax
      
-
      angle_style cosine
-
      
-
      
+
      +angle_style cosine
+
      
 
      
 
      
 
      Examples
      
-
      angle_style cosine
-angle_coeff * 75.0
-
      
-
      
+
      +angle_style cosine
+angle_coeff * 75.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/angle_cosine_delta.html b/doc/html/angle_cosine_delta.html
index e3dedd0a2b..fda0b0a0a5 100644
--- a/doc/html/angle_cosine_delta.html
+++ b/doc/html/angle_cosine_delta.html
@@ -131,16 +131,16 @@
 
      angle_style cosine/delta/omp command
      
 
      
 
      Syntax
      
-
      angle_style cosine/delta
-
      
-
      
+
      +angle_style cosine/delta
+
      
 
      
 
      
 
      Examples
      
-
      angle_style cosine/delta
-angle_coeff 2*4 75.0 100.0
-
      
-
      
+
      +angle_style cosine/delta
+angle_coeff 2*4 75.0 100.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/angle_cosine_periodic.html b/doc/html/angle_cosine_periodic.html
index 8a358d76d2..9851cea9d4 100644
--- a/doc/html/angle_cosine_periodic.html
+++ b/doc/html/angle_cosine_periodic.html
@@ -131,16 +131,16 @@
 
      angle_style cosine/periodic/omp command
      
 
      
 
      Syntax
      
-
      angle_style cosine/periodic
-
      
-
      
+
      +angle_style cosine/periodic
+
      
 
      
 
      
 
      Examples
      
-
      angle_style cosine/periodic
-angle_coeff * 75.0 1 6
-
      
-
      
+
      +angle_style cosine/periodic
+angle_coeff * 75.0 1 6
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/angle_cosine_shift.html b/doc/html/angle_cosine_shift.html
index d9c19717bc..76d4b6dcb4 100644
--- a/doc/html/angle_cosine_shift.html
+++ b/doc/html/angle_cosine_shift.html
@@ -131,16 +131,16 @@
 
      angle_style cosine/shift/omp command
      
 
      
 
      Syntax
      
-
      angle_style cosine/shift
-
      
-
      
+
      +angle_style cosine/shift
+
      
 
      
 
      
 
      Examples
      
-
      angle_style cosine/shift
-angle_coeff * 10.0 45.0
-
      
-
      
+
      +angle_style cosine/shift
+angle_coeff * 10.0 45.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/angle_cosine_shift_exp.html b/doc/html/angle_cosine_shift_exp.html
index 60dcbf1a2d..2bb957b561 100644
--- a/doc/html/angle_cosine_shift_exp.html
+++ b/doc/html/angle_cosine_shift_exp.html
@@ -131,16 +131,16 @@
 
      angle_style cosine/shift/exp/omp command
      
 
      
 
      Syntax
      
-
      angle_style cosine/shift/exp
-
      
-
      
+
      +angle_style cosine/shift/exp
+
      
 
      
 
      
 
      Examples
      
-
      angle_style cosine/shift/exp
-angle_coeff * 10.0 45.0 2.0
-
      
-
      
+
      +angle_style cosine/shift/exp
+angle_coeff * 10.0 45.0 2.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/angle_cosine_squared.html b/doc/html/angle_cosine_squared.html
index 2797e23fda..e7f0d49193 100644
--- a/doc/html/angle_cosine_squared.html
+++ b/doc/html/angle_cosine_squared.html
@@ -131,16 +131,16 @@
 
      angle_style cosine/squared/omp command
      
 
      
 
      Syntax
      
-
      angle_style cosine/squared
-
      
-
      
+
      +angle_style cosine/squared
+
      
 
      
 
      
 
      Examples
      
-
      angle_style cosine/squared
-angle_coeff 2*4 75.0 100.0
-
      
-
      
+
      +angle_style cosine/squared
+angle_coeff 2*4 75.0 100.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/angle_dipole.html b/doc/html/angle_dipole.html
index 92fec1da89..13f560db0e 100644
--- a/doc/html/angle_dipole.html
+++ b/doc/html/angle_dipole.html
@@ -131,16 +131,16 @@
 
      angle_style dipole/omp command
      
 
      
 
      Syntax
      
-
      angle_style dipole
-
      
-
      
+
      +angle_style dipole
+
      
 
      
 
      
 
      Examples
      
-
      angle_style dipole
-angle_coeff 6 2.1 180.0
-
      
-
      
+
      +angle_style dipole
+angle_coeff 6 2.1 180.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/angle_fourier.html b/doc/html/angle_fourier.html
index ea480d563e..c49686daf1 100644
--- a/doc/html/angle_fourier.html
+++ b/doc/html/angle_fourier.html
@@ -131,9 +131,9 @@
 
      angle_style fourier/omp command
      
 
      
 
      Syntax
      
-
      angle_style fourier
-
      
-
      
+
      +angle_style fourier
+
      
 
      
 
      
 
      Examples
      
diff --git a/doc/html/angle_fourier_simple.html b/doc/html/angle_fourier_simple.html
index fb8db727a9..91c3ac4eeb 100644
--- a/doc/html/angle_fourier_simple.html
+++ b/doc/html/angle_fourier_simple.html
@@ -131,9 +131,9 @@
 
      angle_style fourier/simple/omp command
      
 
      
 
      Syntax
      
-
      angle_style fourier/simple
-
      
-
      
+
      +angle_style fourier/simple
+
      
 
      
 
      
 
      Examples
      
diff --git a/doc/html/angle_harmonic.html b/doc/html/angle_harmonic.html
index 8a15d8a8d6..403ca622ca 100644
--- a/doc/html/angle_harmonic.html
+++ b/doc/html/angle_harmonic.html
@@ -137,16 +137,16 @@
 
      angle_style harmonic/omp command
      
 
      
 
      Syntax
      
-
      angle_style harmonic
-
      
-
      
+
      +angle_style harmonic
+
      
 
      
 
      
 
      Examples
      
-
      angle_style harmonic
-angle_coeff 1 300.0 107.0
-
      
-
      
+
      +angle_style harmonic
+angle_coeff 1 300.0 107.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/angle_quartic.html b/doc/html/angle_quartic.html
index 3cd4e9b3ca..4134601496 100644
--- a/doc/html/angle_quartic.html
+++ b/doc/html/angle_quartic.html
@@ -131,16 +131,16 @@
 
      angle_style quartic/omp command
      
 
      
 
      Syntax
      
-
      angle_style quartic
-
      
-
      
+
      +angle_style quartic
+
      
 
      
 
      
 
      Examples
      
-
      angle_style quartic
-angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221
-
      
-
      
+
      +angle_style quartic
+angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/angle_sdk.html b/doc/html/angle_sdk.html
index ef4126c1f5..d94d31ccf8 100644
--- a/doc/html/angle_sdk.html
+++ b/doc/html/angle_sdk.html
@@ -128,19 +128,19 @@
 
      angle_style sdk command
      
 
      
 
      Syntax
      
-
      angle_style sdk
-
      
-
      
-
      angle_style sdk/omp
-
      
-
      
+
      +angle_style sdk
+
      
+
      +angle_style sdk/omp
+
      
 
      
 
      
 
      Examples
      
-
      angle_style sdk
-angle_coeff 1 300.0 107.0
-
      
-
      
+
      +angle_style sdk
+angle_coeff 1 300.0 107.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/atom_modify.html b/doc/html/atom_modify.html
index b2e3f8585d..0922591416 100644
--- a/doc/html/atom_modify.html
+++ b/doc/html/atom_modify.html
@@ -128,9 +128,9 @@
 
      atom_modify command
      
 
      
 
      Syntax
      
-
      atom_modify keyword values ...
-
      
-
      
+
      +atom_modify keyword values ...
+
      
 
        
 
      • one or more keyword/value pairs may be appended
        • 
 
      • keyword = id or map or first or sort
        • 
@@ -146,11 +146,11 @@
 
      
 
      
 
      Examples
      
-
      atom_modify map hash
-atom_modify map array sort 10000 2.0
-atom_modify first colloid
-
      
-
      
+
      +atom_modify map hash
+atom_modify map array sort 10000 2.0
+atom_modify first colloid
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/atom_style.html b/doc/html/atom_style.html
index 2ed9ccbab0..a2cbd22a72 100644
--- a/doc/html/atom_style.html
+++ b/doc/html/atom_style.html
@@ -128,9 +128,9 @@
 
      atom_style command
      
 
      
 
      Syntax
      
-
      atom_style style args
-
      
-
      
+
      +atom_style style args
+
      
 
        
 
      • style = angle or atomic or body or bond or charge or dipole or         dpd or electron or ellipsoid or full or line or meso or        molecular or peri or smd or sphere or tri or         template or hybrid
        • 
 
      
@@ -150,15 +150,15 @@ args = none for any style except the following
 
      
 
      
 
      Examples
      
-
      atom_style atomic
-atom_style bond
-atom_style full
-atom_style body nparticle 2 10
-atom_style hybrid charge bond
-atom_style hybrid charge body nparticle 2 5
-atom_style template myMols
-
      
-
      
+
      +atom_style atomic
+atom_style bond
+atom_style full
+atom_style body nparticle 2 10
+atom_style hybrid charge bond
+atom_style hybrid charge body nparticle 2 5
+atom_style template myMols
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/body.html b/doc/html/body.html
index 6a2be8aff8..5aaa8ec563 100644
--- a/doc/html/body.html
+++ b/doc/html/body.html
@@ -247,11 +247,11 @@ mentioned above, the 
 
      The atom_style body command for this body style takes two additional
 arguments:
      
-
      atom_style body nparticle Nmin Nmax
-Nmin = minimum # of sub-particles in any body in the system
-Nmax = maximum # of sub-particles in any body in the system
-
      
-
      
+
      +atom_style body nparticle Nmin Nmax
+Nmin = minimum # of sub-particles in any body in the system
+Nmax = maximum # of sub-particles in any body in the system
+
      
 
      The Nmin and Nmax arguments are used to bound the size of data
 structures used internally by each particle.
      
 
      When the read_data command reads a data file for this
@@ -313,11 +313,11 @@ used for 2d models.  One example use of this body style is for 2d
 discrete element models, as described in Fraige.  Similar to
 body style nparticle, the atom_style body command for this body
 style takes two additional arguments:
      
-
      atom_style body rounded/polygon Nmin Nmax
-Nmin = minimum # of vertices in any body in the system
-Nmax = maximum # of vertices in any body in the system
-
      
-
      
+
      +atom_style body rounded/polygon Nmin Nmax
+Nmin = minimum # of vertices in any body in the system
+Nmax = maximum # of vertices in any body in the system
+
      
 
      The Nmin and Nmax arguments are used to bound the size of data
 structures used internally by each particle.
      
 
      When the read_data command reads a data file for this
diff --git a/doc/html/bond_class2.html b/doc/html/bond_class2.html
index 7e3e5100ec..dad9e1dba9 100644
--- a/doc/html/bond_class2.html
+++ b/doc/html/bond_class2.html
@@ -131,16 +131,16 @@
 
      bond_style class2/omp command
      
 
      
 
      Syntax
      
-
      bond_style class2
-
      
-
      
+
      +bond_style class2
+
      
 
      
 
      
 
      Examples
      
-
      bond_style class2
-bond_coeff 1 1.0 100.0 80.0 80.0
-
      
-
      
+
      +bond_style class2
+bond_coeff 1 1.0 100.0 80.0 80.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/bond_fene.html b/doc/html/bond_fene.html
index 7a74e3c9ef..d836487156 100644
--- a/doc/html/bond_fene.html
+++ b/doc/html/bond_fene.html
@@ -137,16 +137,16 @@
 
      bond_style fene/omp command
      
 
      
 
      Syntax
      
-
      bond_style fene
-
      
-
      
+
      +bond_style fene
+
      
 
      
 
      
 
      Examples
      
-
      bond_style fene
-bond_coeff 1 30.0 1.5 1.0 1.0
-
      
-
      
+
      +bond_style fene
+bond_coeff 1 30.0 1.5 1.0 1.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/bond_fene_expand.html b/doc/html/bond_fene_expand.html
index e2b5ed6ad5..577a4cde04 100644
--- a/doc/html/bond_fene_expand.html
+++ b/doc/html/bond_fene_expand.html
@@ -131,16 +131,16 @@
 
      bond_style fene/expand/omp command
      
 
      
 
      Syntax
      
-
      bond_style fene/expand
-
      
-
      
+
      +bond_style fene/expand
+
      
 
      
 
      
 
      Examples
      
-
      bond_style fene/expand
-bond_coeff 1 30.0 1.5 1.0 1.0 0.5
-
      
-
      
+
      +bond_style fene/expand
+bond_coeff 1 30.0 1.5 1.0 1.0 0.5
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/bond_harmonic.html b/doc/html/bond_harmonic.html
index f1594a77d6..fc22160d18 100644
--- a/doc/html/bond_harmonic.html
+++ b/doc/html/bond_harmonic.html
@@ -137,16 +137,16 @@
 
      bond_style harmonic/omp command
      
 
      
 
      Syntax
      
-
      bond_style harmonic
-
      
-
      
+
      +bond_style harmonic
+
      
 
      
 
      
 
      Examples
      
-
      bond_style harmonic
-bond_coeff 5 80.0 1.2
-
      
-
      
+
      +bond_style harmonic
+bond_coeff 5 80.0 1.2
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/bond_harmonic_shift.html b/doc/html/bond_harmonic_shift.html
index 91a6674537..4ab86dc316 100644
--- a/doc/html/bond_harmonic_shift.html
+++ b/doc/html/bond_harmonic_shift.html
@@ -131,16 +131,16 @@
 
      bond_style harmonic/shift/omp command
      
 
      
 
      Syntax
      
-
      bond_style harmonic/shift
-
      
-
      
+
      +bond_style harmonic/shift
+
      
 
      
 
      
 
      Examples
      
-
      bond_style harmonic/shift
-bond_coeff 5 10.0 0.5 1.0
-
      
-
      
+
      +bond_style harmonic/shift
+bond_coeff 5 10.0 0.5 1.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/bond_harmonic_shift_cut.html b/doc/html/bond_harmonic_shift_cut.html
index c53ad2cc14..121eda2221 100644
--- a/doc/html/bond_harmonic_shift_cut.html
+++ b/doc/html/bond_harmonic_shift_cut.html
@@ -131,16 +131,16 @@
 
      bond_style harmonic/shift/cut/omp command
      
 
      
 
      Syntax
      
-
      bond_style harmonic/shift/cut
-
      
-
      
+
      +bond_style harmonic/shift/cut
+
      
 
      
 
      
 
      Examples
      
-
      bond_style harmonic/shift/cut
-bond_coeff 5 10.0 0.5 1.0
-
      
-
      
+
      +bond_style harmonic/shift/cut
+bond_coeff 5 10.0 0.5 1.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/bond_morse.html b/doc/html/bond_morse.html
index facb9a0c9c..42794978e3 100644
--- a/doc/html/bond_morse.html
+++ b/doc/html/bond_morse.html
@@ -131,16 +131,16 @@
 
      bond_style morse/omp command
      
 
      
 
      Syntax
      
-
      bond_style morse
-
      
-
      
+
      +bond_style morse
+
      
 
      
 
      
 
      Examples
      
-
      bond_style morse
-bond_coeff 5 1.0 2.0 1.2
-
      
-
      
+
      +bond_style morse
+bond_coeff 5 1.0 2.0 1.2
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/bond_nonlinear.html b/doc/html/bond_nonlinear.html
index 02540da242..ad8a574f82 100644
--- a/doc/html/bond_nonlinear.html
+++ b/doc/html/bond_nonlinear.html
@@ -131,16 +131,16 @@
 
      bond_style nonlinear/omp command
      
 
      
 
      Syntax
      
-
      bond_style nonlinear
-
      
-
      
+
      +bond_style nonlinear
+
      
 
      
 
      
 
      Examples
      
-
      bond_style nonlinear
-bond_coeff 2 100.0 1.1 1.4
-
      
-
      
+
      +bond_style nonlinear
+bond_coeff 2 100.0 1.1 1.4
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/bond_quartic.html b/doc/html/bond_quartic.html
index d2b57516a1..290a9f8055 100644
--- a/doc/html/bond_quartic.html
+++ b/doc/html/bond_quartic.html
@@ -131,16 +131,16 @@
 
      bond_style quartic/omp command
      
 
      
 
      Syntax
      
-
      bond_style quartic
-
      
-
      
+
      +bond_style quartic
+
      
 
      
 
      
 
      Examples
      
-
      bond_style quartic
-bond_coeff 2 1200 -0.55 0.25 1.3 34.6878
-
      
-
      
+
      +bond_style quartic
+bond_coeff 2 1200 -0.55 0.25 1.3 34.6878
+
      
 
      
 
      
 
      Description
      
@@ -184,10 +184,10 @@ to 1,1,1, as indicated as a restriction below.
      
 
      Note that when bonds are dumped to a file via the dump local command, bonds with type 0 are not included.  The
 delete_bonds command can also be used to query the
 status of broken bonds or permanently delete them, e.g.:
      
-
      delete_bonds all stats
-delete_bonds all bond 0 remove
-
      
-
      
+
      +delete_bonds all stats
+delete_bonds all bond 0 remove
+
      
 
      
 
      Styles with a gpu, intel, kk, omp, or opt suffix are
 functionally the same as the corresponding style without the suffix.
diff --git a/doc/html/change_box.html b/doc/html/change_box.html
index fc034cbe2f..5fd817925f 100644
--- a/doc/html/change_box.html
+++ b/doc/html/change_box.html
@@ -128,9 +128,9 @@
 
      change_box command
      
 
      
 
      Syntax
      
-
      change_box group-ID parameter args ... keyword args ...
-
      
-
      
+
      +change_box group-ID parameter args ... keyword args ...
+
      
 
        
 
      • group-ID = ID of group of atoms to (optionally) displace
        • 
 
      • one or more parameter/arg pairs may be appended
        • 
@@ -175,10 +175,10 @@ parameter = x or y or z or xy or xz
 
      
 
      
 
      Examples
      
-
      change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
-change_box all x scale 1.1 y volume z volume remap
-
      
-
      
+
      +change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
+change_box all x scale 1.1 y volume z volume remap
+
      
 
      
 
      
 
      Description
      
@@ -223,15 +223,15 @@ will be re-shrink-wrapped before the change_box command completes.
 Instead you could do something like this, assuming the simulation box
 is non-periodic and atoms extend from 0 to 20 in all dimensions:
      
 
      
-
      change_box all x final -10 20
-create_atoms 1 single -5 5 5   # this will fail to insert an atom
-
      
-
      
-
      change_box all x final -10 20 boundary f s s
-create_atoms 1 single -5 5 5
-change_box boundary s s s      # this will work
-
      
-
      
+
      +change_box all x final -10 20
+create_atoms 1 single -5 5 5   # this will fail to insert an atom
+
      
+
      +change_box all x final -10 20 boundary f s s
+create_atoms 1 single -5 5 5
+change_box boundary s s s      # this will work
+
      
 
      
 
      Note
      
 
      Unlike the earlier “displace_box” version of this command, atom
@@ -295,30 +295,30 @@ used following a keyword that changed the volume, which is any of the
 x, y, z keywords.  If the preceding keyword “key” had a volume
 style, then both it and the current keyword apply to the keyword
 preceding “key”.  I.e. this sequence of keywords is allowed:
      
-
      change_box all x scale 1.1 y volume z volume
-
      
-
      
+
      +change_box all x scale 1.1 y volume z volume
+
      
 
      The volume style changes the associated dimension so that the
 overall box volume is unchanged relative to its value before the
 preceding keyword was invoked.
      
 
      If the following command is used, then the z box length will shrink by
 the same 1.1 factor the x box length was increased by:
      
-
      change_box all x scale 1.1 z volume
-
      
-
      
+
      +change_box all x scale 1.1 z volume
+
      
 
      If the following command is used, then the y,z box lengths will each
 shrink by sqrt(1.1) to keep the volume constant.  In this case, the
 y,z box lengths shrink so as to keep their relative aspect ratio
 constant:
      
-
      change_box all"x scale 1.1 y volume z volume
-
      
-
      
+
      +change_box all"x scale 1.1 y volume z volume
+
      
 
      If the following command is used, then the final box will be a factor
 of 10% larger in x and y, and a factor of 21% smaller in z, so as to
 keep the volume constant:
      
-
      change_box all x scale 1.1 z volume y scale 1.1 z volume
-
      
-
      
+
      +change_box all x scale 1.1 z volume y scale 1.1 z volume
+
      
 
      
 
      Note
      
 
      For solids or liquids, when one dimension of the box is
diff --git a/doc/html/compute.html b/doc/html/compute.html
index b4f0375d18..ec28819bbb 100644
--- a/doc/html/compute.html
+++ b/doc/html/compute.html
@@ -186,8 +186,8 @@ discussed below, it can be referenced via the following bracket
 notation, where ID is the ID of the compute:
      
 
      
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
      --++
@@ -245,11 +245,11 @@ computes for further info.
      
 Three computes are always created, named “thermo_temp”,
 “thermo_press”, and “thermo_pe”, as if these commands had been invoked
 in the input script:
      
-
      compute thermo_temp all temp
-compute thermo_press all pressure thermo_temp
-compute thermo_pe all pe
-
      
-
      
+
      +compute thermo_temp all temp
+compute thermo_press all pressure thermo_temp
+compute thermo_pe all pe
+
      Additional computes for other quantities are created if the thermo
 style requires it.  See the documentation for the
 thermo_style command.
      
diff --git a/doc/html/compute_bond_local.html b/doc/html/compute_bond_local.html
index 5bde75437f..79f34ad60f 100644
--- a/doc/html/compute_bond_local.html
+++ b/doc/html/compute_bond_local.html
@@ -177,11 +177,11 @@ For example, bond output from the dump local
 command in a consistent way.
      Here is an example of how to do this:
      
-
      compute 1 all property/local btype batom1 batom2
-compute 2 all bond/local dist eng
-dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
-
      
-
      
+
      +compute 1 all property/local btype batom1 batom2
+compute 2 all bond/local dist eng
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
+
      Output info:
      This compute calculates a local vector or local array depending on the
 number of keywords.  The length of the vector or number of rows in the
diff --git a/doc/html/compute_centro_atom.html b/doc/html/compute_centro_atom.html
index 743a69e651..5b1779546e 100644
--- a/doc/html/compute_centro_atom.html
+++ b/doc/html/compute_centro_atom.html
@@ -234,7 +234,7 @@ simulation into gold (FCC).  These were provided by Jon Zimmerman
 Free surface ~ 23.0
 
 
-
      These values are not normalized by the square of the lattice
+
      These values are *not* normalized by the square of the lattice
 parameter.  If they were, normalized values would be:
      Bulk lattice = 0
 Dislocation core ~ 0.06 (0.03 to 0.075)
diff --git a/doc/html/compute_dipole_chunk.html b/doc/html/compute_dipole_chunk.html
index 55452e3a0f..efedfa0512 100644
--- a/doc/html/compute_dipole_chunk.html
+++ b/doc/html/compute_dipole_chunk.html
@@ -181,11 +181,11 @@ and how they are set for each atom.  You can reset the image flags
 
      The simplest way to output the results of the compute com/chunk
 calculation to a file is to use the fix ave/time
 command, for example:
      
-
      compute cc1 all chunk/atom molecule
-compute myChunk all dipole/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
-
      
-
      
+
      +compute cc1 all chunk/atom molecule
+compute myChunk all dipole/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
+
      
 
      Output info:
      
 
      This compute calculates a global array where the number of rows = the
 number of chunks Nchunk as calculated by the specified compute chunk/atom command.  The number of columns =
diff --git a/doc/html/compute_fep.html b/doc/html/compute_fep.html
index 5a7910465c..0824a98ae4 100644
--- a/doc/html/compute_fep.html
+++ b/doc/html/compute_fep.html
@@ -164,10 +164,10 @@
 
      
 
      
 
      Examples
      
-
      compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes
-compute 1 all fep 300 atom charge 2 v_delta
-
      
-
      
+
      +compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes
+compute 1 all fep 300 atom charge 2 v_delta
+
      
 
      
 
      
 
      Description
      
@@ -307,7 +307,7 @@ each, as in the 1st example above.  I <= J is required.  LAMMPS sets
 the coefficients for the symmetric J,I interaction to the same
 values. A wild-card asterisk can be used in place of or in conjunction
 with the I,J arguments to set the coefficients for multiple pairs of
-atom types.  This takes the form “*” or “n” or “n” or “m*n”.  If N =
+atom types.  This takes the form “*” or “*n” or “n*” or “m*n”.  If N =
 the number of atom types, then an asterisk with no numeric values
 means all types from 1 to N.  A leading asterisk means all types from
 1 to n (inclusive).  A trailing asterisk means all types from n to N
diff --git a/doc/html/compute_gyration_chunk.html b/doc/html/compute_gyration_chunk.html
index 388ee64c04..3ec0dca379 100644
--- a/doc/html/compute_gyration_chunk.html
+++ b/doc/html/compute_gyration_chunk.html
@@ -193,11 +193,11 @@ using the set im
 
      The simplest way to output the results of the compute gyration/chunk
 calculation to a file is to use the fix ave/time
 command, for example:
      
-
      compute cc1 all chunk/atom molecule
-compute myChunk all gyration/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
-
      
-
      
+
      +compute cc1 all chunk/atom molecule
+compute myChunk all gyration/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
+
      
 
      Output info:
      
 
      This compute calculates a global vector if the tensor keyword is not
 specified and a global array if it is.  The length of the vector or
diff --git a/doc/html/compute_heat_flux.html b/doc/html/compute_heat_flux.html
index 1ef755717d..1595174920 100644
--- a/doc/html/compute_heat_flux.html
+++ b/doc/html/compute_heat_flux.html
@@ -237,29 +237,30 @@ energy/area/time 
      # Sample LAMMPS input script for thermal conductivity of solid Ar
 
      
 
      
-
      units       real
+
      +units       real
 variable    T equal 70
 variable    V equal vol
 variable    dt equal 4.0
 variable    p equal 200     # correlation length
 variable    s equal 10      # sample interval
 variable    d equal $p*$s   # dump interval
-
      
-
      
+
 
      # convert from LAMMPS real units to SI
 
      
 
      
-
      variable    kB equal 1.3806504e-23    # [J/K] Boltzmann
+
      +variable    kB equal 1.3806504e-23    # [J/K] Boltzmann
 variable    kCal2J equal 4186.0/6.02214e23
 variable    A2m equal 1.0e-10
 variable    fs2s equal 1.0e-15
 variable    convert equal ${kCal2J}*${kCal2J}/${fs2s}/${A2m}
-
      
-
      
+
 
      # setup problem
 
      
 
      
-
      dimension    3
+
      +dimension    3
 boundary     p p p
 lattice      fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
 region       box block 0 4 0 4 0 4
@@ -270,8 +271,7 @@ pair_style   lj/cut 13.0
 pair_coeff   * * 0.2381 3.405
 timestep     ${dt}
 thermo            $d
-
      
-
      
+
 
      # equilibration and thermalization
 
      
 
      
@@ -287,7 +287,8 @@ run          8000
 #fix         NVE all nve
 
      
-
      reset_timestep 0
+
      +reset_timestep 0
 compute      myKE all ke/atom
 compute      myPE all pe/atom
 compute      myStress all stress/atom NULL virial
@@ -305,9 +306,8 @@ thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
 run          100000
 variable     k equal (v_k11+v_k22+v_k33)/3.0
 variable     ndens equal count(all)/vol
-print        "average conductivity: $k[W/mK] @ $T K, ${ndens} /A^3"
-
      
-
      
+print        "average conductivity: $k[W/mK] @ $T K, ${ndens} /A^3"
+
 
 
 
diff --git a/doc/html/compute_inertia_chunk.html b/doc/html/compute_inertia_chunk.html
index b93575cfc5..d718f90f47 100644
--- a/doc/html/compute_inertia_chunk.html
+++ b/doc/html/compute_inertia_chunk.html
@@ -177,11 +177,11 @@ how they are set for each atom.  You can reset the image flags
 
      The simplest way to output the results of the compute inertia/chunk
 calculation to a file is to use the fix ave/time
 command, for example:
      
-
      compute cc1 all chunk/atom molecule
-compute myChunk all inertia/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
-
      
-
      
+
      +compute cc1 all chunk/atom molecule
+compute myChunk all inertia/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
+
      Output info:
      This compute calculates a global array where the number of rows = the
 number of chunks Nchunk as calculated by the specified compute chunk/atom command.  The number of columns =
diff --git a/doc/html/compute_ke_atom_eff.html b/doc/html/compute_ke_atom_eff.html
index 00b22b9256..6a017dc79b 100644
--- a/doc/html/compute_ke_atom_eff.html
+++ b/doc/html/compute_ke_atom_eff.html
@@ -168,11 +168,11 @@ eFF.
      
 thermodynamic output by using the thermo_modify
 command, as shown in the following example:
      
-
      compute         effTemp all temp/eff
-thermo_style    custom step etotal pe ke temp press
-thermo_modify   temp effTemp
-
      
-
      
+
      +compute         effTemp all temp/eff
+thermo_style    custom step etotal pe ke temp press
+thermo_modify   temp effTemp
+
      The value of the kinetic energy will be 0.0 for atoms (nuclei or
 electrons) not in the specified compute group.
      Output info:
      
diff --git a/doc/html/compute_ke_eff.html b/doc/html/compute_ke_eff.html
index b614a9d25b..ff0e0b4e68 100644
--- a/doc/html/compute_ke_eff.html
+++ b/doc/html/compute_ke_eff.html
@@ -169,11 +169,11 @@ the thermo_modify command, as shown in the following
 example:
      
-
      compute         effTemp all temp/eff
-thermo_style    custom step etotal pe ke temp press
-thermo_modify   temp effTemp
-
      
-
      
+
      +compute         effTemp all temp/eff
+thermo_style    custom step etotal pe ke temp press
+thermo_modify   temp effTemp
+
      See compute temp/eff.
      Output info:
      This compute calculates a global scalar (the KE).  This value can be
diff --git a/doc/html/compute_modify.html b/doc/html/compute_modify.html
index 8c31af05b2..6556686bb9 100644
--- a/doc/html/compute_modify.html
+++ b/doc/html/compute_modify.html
@@ -128,9 +128,9 @@
 
      compute_modify command
      
 
      Syntax
      
-
      compute_modify compute-ID keyword value ...
-
      
-
      
+
      +compute_modify compute-ID keyword value ...
+
      
 
        
 
      • compute-ID = ID of the compute to modify
        • 
 
      • one or more keyword/value pairs may be listed
        • 
@@ -145,10 +145,10 @@
 
      
 
      Examples
      
-
      compute_modify myTemp extra 0
-compute_modify newtemp dynamic yes extra 600
-
      
-
      
+
      +compute_modify myTemp extra 0
+compute_modify newtemp dynamic yes extra 600
+
      
 
      
 
      Description
      
diff --git a/doc/html/compute_pe_atom.html b/doc/html/compute_pe_atom.html
index fafebf006b..b5de90dfdb 100644
--- a/doc/html/compute_pe_atom.html
+++ b/doc/html/compute_pe_atom.html
@@ -185,11 +185,11 @@ command.
      
 
      As an example of per-atom potential energy compared to total potential
 energy, these lines in an input script should yield the same result
 in the last 2 columns of thermo output:
      
-
      compute              peratom all pe/atom
-compute              pe all reduce sum c_peratom
-thermo_style custom step temp etotal press pe c_pe
-
      
-
      
+
      +compute              peratom all pe/atom
+compute              pe all reduce sum c_peratom
+thermo_style        custom step temp etotal press pe c_pe
+
      
 
      
 
      Note
      
 
      The per-atom energy does not any Lennard-Jones tail corrections
diff --git a/doc/html/compute_pressure.html b/doc/html/compute_pressure.html
index eb4ac742f3..1d117a4f5e 100644
--- a/doc/html/compute_pressure.html
+++ b/doc/html/compute_pressure.html
@@ -141,10 +141,10 @@
 
      
 
      
 
      Examples
      
-
      compute 1 all pressure thermo_temp
-compute 1 all pressure NULL pair bond
-
      
-
      
+
      +compute 1 all pressure thermo_temp
+compute 1 all pressure NULL pair bond
+
      
 
      
 
      
 
      Description
      
@@ -196,9 +196,9 @@ degrees-of-freedom divided by d = dimensionality, where the DOF value
 is calcluated by the temperature compute.  See the various compute temperature styles for details.
      
 
      A compute of this style with the ID of “thermo_press” is created when
 LAMMPS starts up, as if this command were in the input script:
      
-
      compute thermo_press all pressure thermo_temp
-
      
-
      
+
      +compute thermo_press all pressure thermo_temp
+
      
 
      where “thermo_temp” is the ID of a similarly defined compute of style
 “temp”.  See the “thermo_style” command for more details.
      
 
      
diff --git a/doc/html/compute_property_atom.html b/doc/html/compute_property_atom.html
index 9fdc98e352..f91b814e33 100644
--- a/doc/html/compute_property_atom.html
+++ b/doc/html/compute_property_atom.html
@@ -136,25 +136,25 @@
 
    • property/atom = style name of this compute command
      • 
 
    • input = one or more atom attributes
      • 
 
-
      possible attributes = id, mol, proc, type, mass,
-                   x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
-                   vx, vy, vz, fx, fy, fz,
-                      q, mux, muy, muz, mu,
-                      radius, diameter, omegax, omegay, omegaz,
-                   angmomx, angmomy, angmomz,
-                   shapex,shapey, shapez,
-                   quatw, quati, quatj, quatk, tqx, tqy, tqz,
-                   end1x, end1y, end1z, end2x, end2y, end2z,
-                   corner1x, corner1y, corner1z,
-                   corner2x, corner2y, corner2z,
-                   corner3x, corner3y, corner3z,
-                   nbonds,
-                      vfrac, s0,
-                   spin, eradius, ervel, erforce,
-                      rho, drho, e, de, cv,
-                      i_name, d_name
-
      
-
      
+
      +possible attributes = id, mol, proc, type, mass,
+                   x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
+                   vx, vy, vz, fx, fy, fz,
+                      q, mux, muy, muz, mu,
+                      radius, diameter, omegax, omegay, omegaz,
+                   angmomx, angmomy, angmomz,
+                   shapex,shapey, shapez,
+                   quatw, quati, quatj, quatk, tqx, tqy, tqz,
+                   end1x, end1y, end1z, end2x, end2y, end2z,
+                   corner1x, corner1y, corner1z,
+                   corner2x, corner2y, corner2z,
+                   corner3x, corner3y, corner3z,
+                   nbonds,
+                      vfrac, s0,
+                   spin, eradius, ervel, erforce,
+                      rho, drho, e, de, cv,
+                      i_name, d_name
+
      
 
      id = atom ID
 mol = molecule ID
 proc = ID of processor that owns atom
diff --git a/doc/html/compute_property_chunk.html b/doc/html/compute_property_chunk.html
index 2012335a47..7cf73b649d 100644
--- a/doc/html/compute_property_chunk.html
+++ b/doc/html/compute_property_chunk.html
@@ -192,12 +192,12 @@ will be in unitless reduced units (0-1).
      
 
      The simplest way to output the results of the compute property/chunk
 calculation to a file is to use the fix ave/time
 command, for example:
      
-
      compute cc1 all chunk/atom molecule
-compute myChunk1 all property/chunk cc1 count
-compute myChunk2 all com/chunk cc1
-fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2[*] file tmp.out mode vector
-
      
-
      
+
      +compute cc1 all chunk/atom molecule
+compute myChunk1 all property/chunk cc1 count
+compute myChunk2 all com/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2[*] file tmp.out mode vector
+
      
 
      Output info:
      
 
      This compute calculates a global vector or global array depending on
 the number of input values.  The length of the vector or number of
diff --git a/doc/html/compute_reduce.html b/doc/html/compute_reduce.html
index 519bc9ff3c..56a155c53a 100644
--- a/doc/html/compute_reduce.html
+++ b/doc/html/compute_reduce.html
@@ -148,14 +148,14 @@
 
    • one or more inputs can be listed
      • 
 
    • input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name
      • 
 
-
      x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
-c_ID = per-atom or local vector calculated by a compute with ID
-c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID, I can include wildcard (see below)
-f_ID = per-atom or local vector calculated by a fix with ID
-f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID, I can include wildcard (see below)
-v_name = per-atom vector calculated by an atom-style variable with name
-
      
-
      
+
      +x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
+c_ID = per-atom or local vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID, I can include wildcard (see below)
+f_ID = per-atom or local vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID, I can include wildcard (see below)
+v_name = per-atom vector calculated by an atom-style variable with name
+
      
 
        
 
      • zero or more keyword/args pairs may be appended
        • 
 
      • keyword = replace
        • 
@@ -168,13 +168,13 @@
 
      
 
      
 
      Examples
      
-
      compute 1 all reduce sum c_force
-compute 1 all reduce/region subbox sum c_force
-compute 2 all reduce min c_press[2] f_ave v_myKE
-compute 2 all reduce min c_press[*] f_ave v_myKE
-compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
-
      
-
      
+
      +compute 1 all reduce sum c_force
+compute 1 all reduce/region subbox sum c_force
+compute 2 all reduce min c_press[2] f_ave v_myKE
+compute 2 all reduce min c_press[*] f_ave v_myKE
+compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
+
      
 
      
 
      
 
      Description
      
@@ -211,7 +211,7 @@ component) or can be the result of a variable.
      
 
      Note that for values from a compute or fix, the bracketed index I can
 be specified using a wildcard asterisk with the index to effectively
-specify multiple values.  This takes the form “*” or “n” or “n” or
+specify multiple values.  This takes the form “*” or “*n” or “n*” or
 “m*n”.  If N = the size of the vector (for mode = scalar) or the
 number of columns in the array (for mode = vector), then an asterisk
 with no numeric values means all indices from 1 to N.  A leading
@@ -222,18 +222,18 @@ means all indices from m to n (inclusive).
      
 had been listed one by one.  E.g. these 2 compute reduce commands are
 equivalent, since the compute stress/atom
 command creates a per-atom array with 6 columns:
      
-
      compute myPress all stress/atom NULL
-compute 2 all reduce min myPress[*]
-compute 2 all reduce min myPress[1] myPress[2] myPress[3] &
-                         myPress[4] myPress[5] myPress[6]
-
      
-
      
+
      +compute myPress all stress/atom NULL
+compute 2 all reduce min myPress[*]
+compute 2 all reduce min myPress[1] myPress[2] myPress[3] &
+                         myPress[4] myPress[5] myPress[6]
+
      
 
      
 
      The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
 self-explanatory.  Note that other atom attributes can be used as
 inputs to this fix by using the compute property/atom command and then specifying
 an input value from that compute.
      
-
      If a value begins with “c_”, a compute ID must follow which has been
+
      If a value begins with “c_”, a compute ID must follow which has been
 previously defined in the input script.  Computes can generate
 per-atom or local quantities.  See the individual
 compute doc page for details.  If no bracketed integer
@@ -243,7 +243,7 @@ by the compute is used.  Users can also write code for their own
 compute styles and add them to LAMMPS.  See the
 discussion above for how I can be specified with a wildcard asterisk
 to effectively specify multiple values.
      
-
      If a value begins with “f_”, a fix ID must follow which has been
+
      If a value begins with “f_”, a fix ID must follow which has been
 previously defined in the input script.  Fixes can generate per-atom
 or local quantities.  See the individual fix doc page for
 details.  Note that some fixes only produce their values on certain
@@ -254,7 +254,7 @@ integer is appended, the Ith column of the array calculated by the fix
 is used.  Users can also write code for their own fix style and add them to LAMMPS.  See the discussion above for how
 I can be specified with a wildcard asterisk to effectively specify
 multiple values.
      
-
      If a value begins with “v_”, a variable name must follow which has
+
      If a value begins with “v_”, a variable name must follow which has
 been previously defined in the input script.  It must be an
 atom-style variable.  Atom-style variables can
 reference thermodynamic keywords and various per-atom attributes, or
@@ -271,12 +271,12 @@ Then, instead of performing a min/max on the vec1 input vector, the
 stored index is used to select the Nth element of the vec1 vector.
      
 
      Thus, for example, if you wish to use this compute to find the bond
 with maximum stretch, you can do it as follows:
      
-
      compute 1 all property/local batom1 batom2
-compute      2 all bond/local dist
-compute      3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3
-thermo_style custom step temp c_3[1] c_3[2] c_3[3]
-
      
-
      
+
      +compute 1 all property/local batom1 batom2
+compute      2 all bond/local dist
+compute      3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3
+thermo_style custom step temp c_3[1] c_3[2] c_3[3]
+
      
 
      The first two input values in the compute reduce command are vectors
 with the IDs of the 2 atoms in each bond, using the compute property/local command.  The last input
 value is bond distance, using the compute bond/local command.  Instead of taking the
diff --git a/doc/html/compute_rigid_local.html b/doc/html/compute_rigid_local.html
index 154d01a909..7f7d5630fa 100644
--- a/doc/html/compute_rigid_local.html
+++ b/doc/html/compute_rigid_local.html
@@ -202,10 +202,10 @@ there will be no consistent ordering of the entries within the local
 vector or array from one timestep to the next.
      
 
      Here is an example of how to use this compute to dump rigid body info
 to a file:
      
-
      compute 1 all rigid/local myRigid mol x y z fx fy fz
-dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_1[6] c_1[7]
-
      
-
      
+
      +compute 1 all rigid/local myRigid mol x y z fx fy fz
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_1[6] c_1[7]
+
      
 
      
 
      This section explains the rigid body attributes that can be specified.
      
 
      The id attribute is the atomID of the atom which owns the rigid body, which is
diff --git a/doc/html/compute_saed.html b/doc/html/compute_saed.html
index 5a40350a0d..bc78dd1378 100644
--- a/doc/html/compute_saed.html
+++ b/doc/html/compute_saed.html
@@ -157,14 +157,14 @@
 
      
 
      
 
      Examples
      
-
      compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
-compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
-
      
-
      
-
      fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
-fix saed/vtk 1 1 1 c_2 file Ni_000.saed
-
      
-
      
+
      +compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
+compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
+
      
+
      +fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
+fix saed/vtk 1 1 1 c_2 file Ni_000.saed
+
      
 
      
 
      
 
      Description
      
@@ -193,7 +193,7 @@ shown in the 2D diagram below.
      
                      height="auto"
                      alt=""/>
                 
      For a mesh defined by the simulation domain, a rectilinear grid is
-constructed with spacing c*inv(A) along each reciprocal lattice
+constructed with spacing c*inv(A) along each reciprocal lattice
 axis. Where A are the vectors corresponding to the edges of the
 simulation cell. If one or two directions has non-periodic boundary
 conditions, then the spacing in these directions is defined from the
diff --git a/doc/html/compute_sna_atom.html b/doc/html/compute_sna_atom.html
index e61705f25a..930f66a12e 100644
--- a/doc/html/compute_sna_atom.html
+++ b/doc/html/compute_sna_atom.html
@@ -134,11 +134,11 @@
 
      compute snav/atom command
      
 
      
 
      Syntax
      
-
      compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
-compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
-compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
-
      
-
      
+
      +compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
+compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
+compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
+
      
 
        
 
      • ID, group-ID are documented in compute command
        • 
 
      • sna/atom = style name of this compute command
        • 
@@ -276,22 +276,22 @@ corresponding to a particular bispectrum component.  The total number
 of columns and the identities of the bispectrum component contained in
 each column depend on the values of twojmax and diagonal, as
 described by the following piece of python code:
        
-
        for j1 in range(0,twojmax+1):
-    if(diagonal==2):
-        print j1/2.,j1/2.,j1/2.
-    elif(diagonal==1):
-        for j in range(0,min(twojmax,2*j1)+1,2):
-            print j1/2.,j1/2.,j/2.
-    elif(diagonal==0):
-        for j2 in range(0,j1+1):
-            for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
-                print j1/2.,j2/2.,j/2.
-    elif(diagonal==3):
-        for j2 in range(0,j1+1):
-            for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
-                if (j>=j1): print j1/2.,j2/2.,j/2.
-
        
-
        
+
        +for j1 in range(0,twojmax+1):
+    if(diagonal==2):
+        print j1/2.,j1/2.,j1/2.
+    elif(diagonal==1):
+        for j in range(0,min(twojmax,2*j1)+1,2):
+            print j1/2.,j1/2.,j/2.
+    elif(diagonal==0):
+        for j2 in range(0,j1+1):
+            for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
+                print j1/2.,j2/2.,j/2.
+    elif(diagonal==3):
+        for j2 in range(0,j1+1):
+            for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
+                if (j>=j1): print j1/2.,j2/2.,j/2.
+
        
 
        Compute snad/atom evaluates a per-atom array. The columns are
 arranged into ntypes blocks, listed in order of atom type I.  Each
 block contains three sub-blocks corresponding to the x, y, and z
diff --git a/doc/html/compute_stress_atom.html b/doc/html/compute_stress_atom.html
index e99ece1705..c4704bbbbd 100644
--- a/doc/html/compute_stress_atom.html
+++ b/doc/html/compute_stress_atom.html
@@ -234,12 +234,12 @@ d = dimension and V is the volume of the system, the result should be
 -P, where P is the total pressure of the system.
        
 
        These lines in an input script for a 3d system should yield that
 result.  I.e. the last 2 columns of thermo output will be the same:
        
-
        compute              peratom all stress/atom NULL
-compute              p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
-variable     press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
-thermo_style custom step temp etotal press v_press
-
        
-
        
+
        +compute              peratom all stress/atom NULL
+compute              p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
+variable     press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
+thermo_style        custom step temp etotal press v_press
+
        
 
        Output info:
        
 
        This compute calculates a per-atom array with 6 columns, which can be
 accessed by indices 1-6 by any command that uses per-atom values from
diff --git a/doc/html/compute_temp_cs.html b/doc/html/compute_temp_cs.html
index 4751726a56..81927952be 100644
--- a/doc/html/compute_temp_cs.html
+++ b/doc/html/compute_temp_cs.html
@@ -140,10 +140,10 @@
 
      
 
      
 
      Examples
      
-
      compute oxygen_c-s all temp/cs O_core O_shell
-compute core_shells all temp/cs cores shells
-
      
-
      
+
      +compute oxygen_c-s all temp/cs O_core O_shell
+compute core_shells all temp/cs cores shells
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/compute_temp_eff.html b/doc/html/compute_temp_eff.html
index 4dadf7de39..d11ad256a8 100644
--- a/doc/html/compute_temp_eff.html
+++ b/doc/html/compute_temp_eff.html
@@ -170,11 +170,11 @@ reported by LAMMPS in the thermodynamic quantities reported via the
 thermo_modify command, as shown in the following
 example:
      
 
      
-
      compute         effTemp all temp/eff
-thermo_style    custom step etotal pe ke temp press
-thermo_modify   temp effTemp
-
      
-
      
+
      +compute         effTemp all temp/eff
+thermo_style    custom step etotal pe ke temp press
+thermo_modify   temp effTemp
+
      
 
      A 6-component kinetic energy tensor is also calculated by this compute
 for use in the computation of a pressure tensor.  The formula for the
 components of the tensor is the same as the above formula, except that
diff --git a/doc/html/compute_ti.html b/doc/html/compute_ti.html
index 5701aeee75..8d6198637d 100644
--- a/doc/html/compute_ti.html
+++ b/doc/html/compute_ti.html
@@ -154,10 +154,10 @@ pair style args = atype v_name1 v_name2
 
      
 
      
 
      Examples
      
-
      compute 1 all ti lj/cut 1 v_lj v_dlj coul/long 2 v_c v_dc kspace 1 v_ks v_dks
-compute 1 all ti lj/cut 1*3 v_lj v_dlj coul/long * v_c v_dc kspace * v_ks v_dks
-
      
-
      
+
      +compute 1 all ti lj/cut 1 v_lj v_dlj coul/long 2 v_c v_dc kspace 1 v_ks v_dks
+compute 1 all ti lj/cut 1*3 v_lj v_dlj coul/long * v_c v_dc kspace * v_ks v_dks
+
      
 
      
 
      
 
      Description
      
@@ -192,7 +192,7 @@ with respect to lambda.
      
 numeric values can be used, as in the 1st example above.  Or a
 wildcard asterisk can be used in place of or in conjunction with the
 atype argument to select multiple atom types.  This takes the form
-“*” or “n” or “n” or “m*n”.  If N = the number of atom types, then
+“*” or “*n” or “n*” or “m*n”.  If N = the number of atom types, then
 an asterisk with no numeric values means all types from 1 to N.  A
 leading asterisk means all types from 1 to n (inclusive).  A trailing
 asterisk means all types from n to N (inclusive).  A middle asterisk
diff --git a/doc/html/compute_voronoi_atom.html b/doc/html/compute_voronoi_atom.html
index 630ee3bac6..ed4cd612a1 100644
--- a/doc/html/compute_voronoi_atom.html
+++ b/doc/html/compute_voronoi_atom.html
@@ -158,14 +158,14 @@ or face_threshold or neighbors or peratom
 
      
 
      
 
      Examples
      
-
      compute 1 all voronoi/atom
-compute 2 precipitate voronoi/atom surface matrix
-compute 3b precipitate voronoi/atom radius v_r
-compute 4 solute voronoi/atom only_group
-compute 5 defects voronoi/atom occupation
-compute 6 all voronoi/atom neighbors yes
-
      
-
      
+
      +compute 1 all voronoi/atom
+compute 2 precipitate voronoi/atom surface matrix
+compute 3b precipitate voronoi/atom radius v_r
+compute 4 solute voronoi/atom only_group
+compute 5 defects voronoi/atom occupation
+compute 6 all voronoi/atom neighbors yes
+
      
 
      
 
      
 
      Description
      
@@ -199,11 +199,11 @@ can be obtained by running a “reduce sum” compute on c_2[3]
      
 
      If the radius keyword is specified with an atom style variable as
 the argument, a poly-disperse Voronoi tessellation is
 performed. Examples for radius variables are
      
-
      variable r1 atom (type==1)*0.1+(type==2)*0.4
-compute radius all property/atom radius
-variable r2 atom c_radius
-
      
-
      
+
      +variable r1 atom (type==1)*0.1+(type==2)*0.4
+compute radius all property/atom radius
+variable r2 atom c_radius
+
      
 
      Here v_r1 specifies a per-type radius of 0.1 units for type 1 atoms
 and 0.4 units for type 2 atoms, and v_r2 accesses the radius property
 present in atom_style sphere for granular models.
      
@@ -247,10 +247,10 @@ uses local values from a compute as input.  See dump local command to write a file containing
 all the Voronoi neighbors in a system:
      
-
      compute 6 all voronoi/atom neighbors yes
-dump d2 all local 1 dump.neighbors index c_6[1] c_6[2] c_6[3]
-
      
-
      
+
      +compute 6 all voronoi/atom neighbors yes
+dump d2 all local 1 dump.neighbors index c_6[1] c_6[2] c_6[3]
+
      
 
      If the face_threshold keyword is used, then only faces
 with areas greater than the threshold are stored.
      
 
      
diff --git a/doc/html/compute_xrd.html b/doc/html/compute_xrd.html
index b16569ab91..caeec6cf77 100644
--- a/doc/html/compute_xrd.html
+++ b/doc/html/compute_xrd.html
@@ -159,10 +159,10 @@
 compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual
 
      
 
      
-
      fix 1 all ave/histo/weight 1 1 1 0.087 0.87 250 c_1[1] c_1[2] mode vector file Rad2Theta.xrd
-fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2[1] c_2[2] mode vector file Deg2Theta.xrd
-
      
-
      
+
      +fix 1 all ave/histo/weight 1 1 1 0.087 0.87 250 c_1[1] c_1[2] mode vector file Rad2Theta.xrd
+fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2[1] c_2[2] mode vector file Deg2Theta.xrd
+
      
 
      
 
      
 
      Description
      
@@ -196,7 +196,7 @@ shown in the 2D diagram below.
      
                      height="auto"
                      alt=""/>
                 
      For a mesh defined by the simulation domain, a rectilinear grid is
-constructed with spacing c*inv(A) along each reciprocal lattice
+constructed with spacing c*inv(A) along each reciprocal lattice
 axis. Where A are the vectors corresponding to the edges of the
 simulation cell. If one or two directions has non-periodic boundary
 conditions, then the spacing in these directions is defined from the
diff --git a/doc/html/create_atoms.html b/doc/html/create_atoms.html
index 03785a73f4..3786038236 100644
--- a/doc/html/create_atoms.html
+++ b/doc/html/create_atoms.html
@@ -128,9 +128,9 @@
 
      create_atoms command
      
 
      
 
      Syntax
      
-
      create_atoms type style args keyword values ...
-
      
-
      
+
      +create_atoms type style args keyword values ...
+
      
 
        
 
      • type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)
        • 
 
      • style = box or region or single or random
        • 
@@ -172,12 +172,12 @@
 
      
 
      
 
      Examples
      
-
      create_atoms 1 box
-create_atoms 3 region regsphere basis 2 3
-create_atoms 3 single 0 0 5
-create_atoms 1 box var v set x xpos set y ypos
-
      
-
      
+
      +create_atoms 1 box
+create_atoms 3 region regsphere basis 2 3
+create_atoms 3 single 0 0 5
+create_atoms 1 box var v set x xpos set y ypos
+
      
 
      
 
      
 
      Description
      
@@ -328,19 +328,19 @@ the sinusoid would appear to be “smoother”.  Also note the use of th
 “xlat” and “ylat” thermo_style keywords which
 converts lattice spacings to distance.  Click on the image for a
 larger version.
      
-
      variable        x equal 100
+
      +variable        x equal 100
 variable        y equal 25
 lattice              hex 0.8442
 region               box block 0 $x 0 $y -0.5 0.5
-create_box   1 box
-
      
-
      
-
      variable        xx equal 0.0
-variable        yy equal 0.0
-variable        v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
-create_atoms 1 box var v set x xx set y yy
-
      
-
      
+create_box  1 box
+
+
      +variable        xx equal 0.0
+variable        yy equal 0.0
+variable        v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
+create_atoms        1 box var v set x xx set y yy
+
      
 
      delete_bonds command
      
 
      
 
      Syntax
      
-
      delete_bonds group-ID style arg keyword ...
-
      
-
      
+
      +delete_bonds group-ID style arg keyword ...
+
      
 
        
 
      • group-ID = group ID
        
 
        • 
@@ -157,12 +157,12 @@
 
      
 
      
 
      Examples
      
-
      delete_bonds frozen multi remove
-delete_bonds all atom 4 special
-delete_bonds all bond 0*3 special
-delete_bonds all stats
-
      
-
      
+
      +delete_bonds frozen multi remove
+delete_bonds all atom 4 special
+delete_bonds all bond 0*3 special
+delete_bonds all stats
+
      
 
      
 
      
 
      Description
      
@@ -183,7 +183,7 @@ be an integer from 0 to N, where N is the number of relevant types
 (atom types, bond types, etc).  A value of 0 is only relevant for
 style bond; see details below.  In all cases, a wildcard asterisk
 can be used in place of or in conjunction with the type argument to
-specify a range of types.  This takes the form “*” or “n” or “n” or
+specify a range of types.  This takes the form “*” or “*n” or “n*” or
 “m*n”.  If N = the number of types, then an asterisk with no numeric
 values means all types from 0 to N.  A leading asterisk means all
 types from 0 to n (inclusive).  A trailing asterisk means all types
diff --git a/doc/html/dihedral_charmm.html b/doc/html/dihedral_charmm.html
index 80c9b47043..9794ca050e 100644
--- a/doc/html/dihedral_charmm.html
+++ b/doc/html/dihedral_charmm.html
@@ -137,18 +137,18 @@
 
      dihedral_style charmm/omp command
      
 
      
 
      Syntax
      
-
      dihedral_style charmm
-
      
-
      
+
      +dihedral_style charmm
+
      
 
      
 
      
 
      Examples
      
-
      dihedral_style charmm
-dihedral_coeff  1 0.2 1 180 1.0
-dihedral_coeff  2 1.8 1   0 1.0
-dihedral_coeff  1 3.1 2 180 0.5
-
      
-
      
+
      +dihedral_style charmm
+dihedral_coeff  1 0.2 1 180 1.0
+dihedral_coeff  2 1.8 1   0 1.0
+dihedral_coeff  1 3.1 2 180 0.5
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/dihedral_class2.html b/doc/html/dihedral_class2.html
index 40f10f1e74..e9556733e2 100644
--- a/doc/html/dihedral_class2.html
+++ b/doc/html/dihedral_class2.html
@@ -131,21 +131,21 @@
 
      dihedral_style class2/omp command
      
 
      
 
      Syntax
      
-
      dihedral_style class2
-
      
-
      
+
      +dihedral_style class2
+
      
 
      
 
      
 
      Examples
      
-
      dihedral_style class2
-dihedral_coeff 1 100 75 100 70 80 60
-dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228
-dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010
-dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270
-dihedral_coeff * aat -13.5271 110.2453 105.1270
-dihedral_coeff * bb13 0.0 1.0119 1.1010
-
      
-
      
+
      +dihedral_style class2
+dihedral_coeff 1 100 75 100 70 80 60
+dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228
+dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010
+dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270
+dihedral_coeff * aat -13.5271 110.2453 105.1270
+dihedral_coeff * bb13 0.0 1.0119 1.1010
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/dihedral_cosine_shift_exp.html b/doc/html/dihedral_cosine_shift_exp.html
index b6e718bce8..1cc73331be 100644
--- a/doc/html/dihedral_cosine_shift_exp.html
+++ b/doc/html/dihedral_cosine_shift_exp.html
@@ -131,16 +131,16 @@
 
      dihedral_style cosine/shift/exp/omp command
      
 
      
 
      Syntax
      
-
      dihedral_style cosine/shift/exp
-
      
-
      
+
      +dihedral_style cosine/shift/exp
+
      
 
      
 
      
 
      Examples
      
-
      dihedral_style cosine/shift/exp
-dihedral_coeff 1 10.0 45.0 2.0
-
      
-
      
+
      +dihedral_style cosine/shift/exp
+dihedral_coeff 1 10.0 45.0 2.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/dihedral_fourier.html b/doc/html/dihedral_fourier.html
index 0feb09036b..1470ba7346 100644
--- a/doc/html/dihedral_fourier.html
+++ b/doc/html/dihedral_fourier.html
@@ -131,16 +131,16 @@
 
      dihedral_style fourier/omp command
      
 
      
 
      Syntax
      
-
      dihedral_style fourier
-
      
-
      
+
      +dihedral_style fourier
+
      
 
      
 
      
 
      Examples
      
-
      dihedral_style fourier
-dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0
-
      
-
      
+
      +dihedral_style fourier
+dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/dihedral_harmonic.html b/doc/html/dihedral_harmonic.html
index 0c37cf26cc..2a8ed8a6f7 100644
--- a/doc/html/dihedral_harmonic.html
+++ b/doc/html/dihedral_harmonic.html
@@ -134,16 +134,16 @@
 
      dihedral_style harmonic/omp command
      
 
      
 
      Syntax
      
-
      dihedral_style harmonic
-
      
-
      
+
      +dihedral_style harmonic
+
      
 
      
 
      
 
      Examples
      
-
      dihedral_style harmonic
-dihedral_coeff 1 80.0 1 2
-
      
-
      
+
      +dihedral_style harmonic
+dihedral_coeff 1 80.0 1 2
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/dihedral_helix.html b/doc/html/dihedral_helix.html
index 14a06fac03..b8d5653099 100644
--- a/doc/html/dihedral_helix.html
+++ b/doc/html/dihedral_helix.html
@@ -131,16 +131,16 @@
 
      dihedral_style helix/omp command
      
 
      
 
      Syntax
      
-
      dihedral_style helix
-
      
-
      
+
      +dihedral_style helix
+
      
 
      
 
      
 
      Examples
      
-
      dihedral_style helix
-dihedral_coeff 1 80.0 100.0 40.0
-
      
-
      
+
      +dihedral_style helix
+dihedral_coeff 1 80.0 100.0 40.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/dihedral_multi_harmonic.html b/doc/html/dihedral_multi_harmonic.html
index c8f3b7b886..ec192b670e 100644
--- a/doc/html/dihedral_multi_harmonic.html
+++ b/doc/html/dihedral_multi_harmonic.html
@@ -131,16 +131,16 @@
 
      dihedral_style multi/harmonic/omp command
      
 
      
 
      Syntax
      
-
      dihedral_style multi/harmonic
-
      
-
      
+
      +dihedral_style multi/harmonic
+
      
 
      
 
      
 
      Examples
      
-
      dihedral_style multi/harmonic
-dihedral_coeff 1 20 20 20 20 20
-
      
-
      
+
      +dihedral_style multi/harmonic
+dihedral_coeff 1 20 20 20 20 20
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/dihedral_nharmonic.html b/doc/html/dihedral_nharmonic.html
index eb35a50a58..eb59b45627 100644
--- a/doc/html/dihedral_nharmonic.html
+++ b/doc/html/dihedral_nharmonic.html
@@ -131,16 +131,16 @@
 
      dihedral_style nharmonic/omp command
      
 
      
 
      Syntax
      
-
      dihedral_style nharmonic
-
      
-
      
+
      +dihedral_style nharmonic
+
      
 
      
 
      
 
      Examples
      
-
      dihedral_style nharmonic
-dihedral_coeff 3 10.0 20.0 30.0
-
      
-
      
+
      +dihedral_style nharmonic
+dihedral_coeff 3 10.0 20.0 30.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/dihedral_opls.html b/doc/html/dihedral_opls.html
index 2f73119b58..fd7c9f1e4f 100644
--- a/doc/html/dihedral_opls.html
+++ b/doc/html/dihedral_opls.html
@@ -137,18 +137,18 @@
 
      dihedral_style opls/omp command
      
 
      
 
      Syntax
      
-
      dihedral_style opls
-
      
-
      
+
      +dihedral_style opls
+
      
 
      
 
      
 
      Examples
      
-
      dihedral_style opls
-dihedral_coeff 1 1.740 -0.157 0.279 0.00   # CT-CT-CT-CT
-dihedral_coeff 2 0.000 0.000 0.366 0.000   # CT-CT-CT-HC
-dihedral_coeff 3 0.000 0.000 0.318 0.000   # HC-CT-CT-HC
-
      
-
      
+
      +dihedral_style opls
+dihedral_coeff 1 1.740 -0.157 0.279 0.00   # CT-CT-CT-CT
+dihedral_coeff 2 0.000 0.000 0.366 0.000   # CT-CT-CT-HC
+dihedral_coeff 3 0.000 0.000 0.318 0.000   # HC-CT-CT-HC
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/dihedral_quadratic.html b/doc/html/dihedral_quadratic.html
index 3cc35b63dd..3b490ae5d6 100644
--- a/doc/html/dihedral_quadratic.html
+++ b/doc/html/dihedral_quadratic.html
@@ -131,16 +131,16 @@
 
      dihedral_style quadratic/omp command
      
 
      
 
      Syntax
      
-
      dihedral_style quadratic
-
      
-
      
+
      +dihedral_style quadratic
+
      
 
      
 
      
 
      Examples
      
-
      dihedral_style quadratic
-dihedral_coeff 100.0 80.0
-
      
-
      
+
      +dihedral_style quadratic
+dihedral_coeff 100.0 80.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/dihedral_spherical.html b/doc/html/dihedral_spherical.html
index 1d9a9f7402..3e38d2d8ca 100644
--- a/doc/html/dihedral_spherical.html
+++ b/doc/html/dihedral_spherical.html
@@ -128,18 +128,18 @@
 
      dihedral_style spherical command
      
 
      
 
      Syntax
      
-
      dihedral_style spherical
-
      
-
      
+
      +dihedral_style spherical
+
      
 
      
 
      
 
      Examples
      
-
      dihedral_coeff 1 1  286.1  1 124 1   1 90.0 0   1 90.0 0
-dihedral_coeff 1 3  286.1  1 114 1   1 90  0    1 90.0  0  &
-                    17.3   0 0.0 0   1 158 1    0 0.0   0  &
-                    15.1   0 0.0 0   0 0.0 0    1 167.3 1
-
      
-
      
+
      +dihedral_coeff 1 1  286.1  1 124 1   1 90.0 0   1 90.0 0
+dihedral_coeff 1 3  286.1  1 114 1   1 90  0    1 90.0  0  &
+                    17.3   0 0.0 0   1 158 1    0 0.0   0  &
+                    15.1   0 0.0 0   0 0.0 0    1 167.3 1
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/dihedral_style.html b/doc/html/dihedral_style.html
index 9b21cd4640..c19d4a1a2e 100644
--- a/doc/html/dihedral_style.html
+++ b/doc/html/dihedral_style.html
@@ -128,20 +128,20 @@
 
      dihedral_style command
      
 
      
 
      Syntax
      
-
      dihedral_style style
-
      
-
      
+
      +dihedral_style style
+
      
 
        
 
      • style = none or hybrid or charmm or class2 or harmonic or helix or         multi/harmonic or opls
        • 
 
      
 
      
 
      
 
      Examples
      
-
      dihedral_style harmonic
-dihedral_style multi/harmonic
-dihedral_style hybrid harmonic charmm
-
      
-
      
+
      +dihedral_style harmonic
+dihedral_style multi/harmonic
+dihedral_style hybrid harmonic charmm
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/dihedral_table.html b/doc/html/dihedral_table.html
index d967731158..fe30f6ab11 100644
--- a/doc/html/dihedral_table.html
+++ b/doc/html/dihedral_table.html
@@ -131,9 +131,9 @@
 
      dihedral_style table/omp command
      
 
      
 
      Syntax
      
-
      dihedral_style table style Ntable
-
      
-
      
+
      +dihedral_style table style Ntable
+
      
 
        
 
      • style = linear or spline = method of interpolation
        • 
 
      • Ntable = size of the internal lookup table
        • 
@@ -141,12 +141,12 @@
 
      
 
      
 
      Examples
      
-
      dihedral_style table spline 400
-dihedral_style table linear 1000
-dihedral_coeff 1 file.table DIH_TABLE1
-dihedral_coeff 2 file.table DIH_TABLE2
-
      
-
      
+
      +dihedral_style table spline 400
+dihedral_style table linear 1000
+dihedral_coeff 1 file.table DIH_TABLE1
+dihedral_coeff 2 file.table DIH_TABLE2
+
      
 
      
 
      
 
      Description
      
@@ -185,23 +185,23 @@ or blank lines.
      
 
      # Table of the potential and its negative derivative
 
      
 
      
-
      DIH_TABLE1                   (keyword is the first text on line)
-N 30 DEGREES                 (N, NOF, DEGREES, RADIANS, CHECKU/F)
-                             (blank line)
-1 -168.0 -1.40351172223 0.0423346818422
-2 -156.0 -1.70447981034 0.00811786522531
-3 -144.0 -1.62956100432 -0.0184129719987
-...
-30 180.0 -0.707106781187 0.0719306095245
-
      
-
      
+
      +DIH_TABLE1                   (keyword is the first text on line)
+N 30 DEGREES                 (N, NOF, DEGREES, RADIANS, CHECKU/F)
+                             (blank line)
+1 -168.0 -1.40351172223 0.0423346818422
+2 -156.0 -1.70447981034 0.00811786522531
+3 -144.0 -1.62956100432 -0.0184129719987
+...
+30 180.0 -0.707106781187 0.0719306095245
+
      
 
      # Example 2: table of the potential. Forces omitted
 
      
 
      
-
      DIH_TABLE2
-N 30 NOF CHECKU testU.dat CHECKF testF.dat
-
      
-
      
+
      +DIH_TABLE2
+N 30 NOF CHECKU testU.dat CHECKF testF.dat
+
      
 
      1 -168.0 -1.40351172223
 2 -156.0 -1.70447981034
 3 -144.0 -1.62956100432
diff --git a/doc/html/dump.html b/doc/html/dump.html
index b47465bc33..d76697dbba 100644
--- a/doc/html/dump.html
+++ b/doc/html/dump.html
@@ -239,19 +239,19 @@ i_name = per-atom integer vector with name, managed by fix property/atom
 
      
 
      
 
      Examples
      
-
      dump myDump all atom 100 dump.atom
-dump myDump all atom/mpiio 100 dump.atom.mpiio
-dump myDump all atom/gz 100 dump.atom.gz
-dump 2 subgroup atom 50 dump.run.bin
-dump 2 subgroup atom 50 dump.run.mpiio.bin
-dump 4a all custom 100 dump.myforce.* id type x y vx fx
-dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
-dump 4b flow custom 100 dump.%.myforce id type c_myF[*] v_ke
-dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
-dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
-dump 1 all xtc 1000 file.xtc
-
      
-
      
+
      +dump myDump all atom 100 dump.atom
+dump myDump all atom/mpiio 100 dump.atom.mpiio
+dump myDump all atom/gz 100 dump.atom.gz
+dump 2 subgroup atom 50 dump.run.bin
+dump 2 subgroup atom 50 dump.run.mpiio.bin
+dump 4a all custom 100 dump.myforce.* id type x y vx fx
+dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
+dump 4b flow custom 100 dump.%.myforce id type c_myF[*] v_ke
+dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
+dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
+dump 1 all xtc 1000 file.xtc
+
      
 
      
 
      
 
      Description
      
@@ -347,12 +347,12 @@ or m = shrink wrapped with a minimum value.  See the
 bounding box which encloses the triclinic simulation box is output,
 along with the 3 tilt factors (xy, xz, yz) of the triclinic box,
 formatted as follows:
      
-
      ITEM: BOX BOUNDS xy xz yz xx yy zz
-xlo_bound xhi_bound xy
-ylo_bound yhi_bound xz
-zlo_bound zhi_bound yz
-
      
-
      
+
      +ITEM: BOX BOUNDS xy xz yz xx yy zz
+xlo_bound xhi_bound xy
+ylo_bound yhi_bound xz
+zlo_bound zhi_bound yz
+
      
 
      The presence of the text “xy xz yz” in the ITEM line indicates that
 the 3 tilt factors will be included on each of the 3 following lines.
 This bounding box is convenient for many visualization programs.  The
@@ -541,7 +541,7 @@ styles.
      
 reference values from a compute or fix, like the custom, cfg, or
 local styles, the bracketed index I can be specified using a
 wildcard asterisk with the index to effectively specify multiple
-values.  This takes the form “*” or “n” or “n” or “m*n”.  If N = the
+values.  This takes the form “*” or “*n” or “n*” or “m*n”.  If N = the
 size of the vector (for mode = scalar) or the number of columns in
 the array (for mode = vector), then an asterisk with no numeric
 values means all indices from 1 to N.  A leading asterisk means all
@@ -552,12 +552,12 @@ from m to n (inclusive).
      
 had been listed one by one.  E.g. these 2 dump commands are
 equivalent, since the compute stress/atom
 command creates a per-atom array with 6 columns:
      
-
      compute myPress all stress/atom NULL
-dump 2 all custom 100 tmp.dump id myPress[*]
-dump 2 all custom 100 tmp.dump id myPress[1] myPress[2] myPress[3] &
-                                  myPress[4] myPress[5] myPress[6]
-
      
-
      
+
      +compute myPress all stress/atom NULL
+dump 2 all custom 100 tmp.dump id myPress[*]
+dump 2 all custom 100 tmp.dump id myPress[1] myPress[2] myPress[3] &
+                                  myPress[4] myPress[5] myPress[6]
+
      
 
      
 
      This section explains the local attributes that can be specified as
 part of the local style.
      
@@ -598,11 +598,11 @@ be specified with a wildcard asterisk to effectively specify multiple
 values.
      
 
      Here is an example of how to dump bond info for a system, including
 the distance and energy of each bond:
      
-
      compute 1 all property/local batom1 batom2 btype
-compute 2 all bond/local dist eng
-dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
-
      
-
      
+
      +compute 1 all property/local batom1 batom2 btype
+compute 2 all bond/local dist eng
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
+
      
 
      
 
      This section explains the atom attributes that can be specified as
 part of the custom and cfg styles.
      
diff --git a/doc/html/dump_custom_vtk.html b/doc/html/dump_custom_vtk.html
index 8bd838f671..b77890476a 100644
--- a/doc/html/dump_custom_vtk.html
+++ b/doc/html/dump_custom_vtk.html
@@ -182,15 +182,15 @@ v_name = per-atom vector calculated by an atom-style variable with name
 
      
 
      
 
      Examples
      
-
      dump dmpvtk all custom/vtk 100 dump*.myforce.vtk id type vx fx
-dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD[1] c_myD[2] c_myD[3] v_ke
-dump e_data all custom/vtk 100 dump*.vtu id type spin eradius fx fy fz eforce
-
      
-
      
+
      +dump dmpvtk all custom/vtk 100 dump*.myforce.vtk id type vx fx
+dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD[1] c_myD[2] c_myD[3] v_ke
+dump e_data all custom/vtk 100 dump*.vtu id type spin eradius fx fy fz eforce
+
      
 
      The style custom/vtk is similar to the custom style but
 uses the VTK library to write data to VTK simple legacy or XML format
 depending on the filename extension specified. This can be either
-**.vtk* for the legacy format or **.vtp* and **.vtu*, respectively,
+*.vtk for the legacy format or *.vtp and *.vtu, respectively,
 for the XML format; see the VTK homepage for a detailed
 description of these formats.  Since this naming convention conflicts
 with the way binary output is usually specified (see below),
diff --git a/doc/html/dump_image.html b/doc/html/dump_image.html
index 2df937c169..356893b5d4 100644
--- a/doc/html/dump_image.html
+++ b/doc/html/dump_image.html
@@ -206,14 +206,14 @@
 
      
 
      
 
      Examples
      
-
      dump d0 all image 100 dump.*.jpg type type
-dump d1 mobile image 500 snap.*.png element element ssao yes 4539 0.6
-dump d2 all image 200 img-*.ppm type type zoom 2.5 adiam 1.5 size 1280 720
-dump m0 all movie 1000 movie.mpg type type size 640 480
-dump m1 all movie 1000 movie.avi type type size 640 480
-dump m2 all movie 100 movie.m4v type type zoom 1.8 adiam v_value size 1280 720
-
      
-
      
+
      +dump d0 all image 100 dump.*.jpg type type
+dump d1 mobile image 500 snap.*.png element element ssao yes 4539 0.6
+dump d2 all image 200 img-*.ppm type type zoom 2.5 adiam 1.5 size 1280 720
+dump m0 all movie 1000 movie.mpg type type size 640 480
+dump m1 all movie 1000 movie.avi type type size 640 480
+dump m2 all movie 100 movie.m4v type type zoom 1.8 adiam v_value size 1280 720
+
      
 
      
 
      
 
      Description
      
@@ -310,7 +310,7 @@ atoms rendered in the image.  They can be any atom attribute defined
 for the dump custom command, including type and
 element.  This includes per-atom quantities calculated by a
 compute, fix, or variable,
-which are prefixed by “c_”, “f_”, or “v_” respectively.  Note that the
+which are prefixed by “c_”, “f_”, or “v_” respectively.  Note that the
 diameter setting can be overridden with a numeric value applied to
 all atoms by the optional adiam keyword.
      
 
      If type is specified for the color setting, then the color of each
@@ -545,9 +545,9 @@ plane perpendicular to the view vector implied by the theta and
 pni values, and which is also in the plane defined by the view
 vector and user-specified up vector.  Thus this internal vector is
 computed from the user-specified up vector as
      
-
      up_internal = view cross (up cross view)
-
      
-
      
+
      +up_internal = view cross (up cross view)
+
      
 
      This means the only restriction on the specified up vector is that
 it cannot be parallel to the view vector, implied by the theta and
 phi values.
      
@@ -619,10 +619,10 @@ MPEG or other movie file you can use:
      
 
 
 
-
      % convert *.jpg foo.gif
-% convert -loop 1 *.ppm foo.mpg
-
      
-
      
+
      +% convert *.jpg foo.gif
+% convert -loop 1 *.ppm foo.mpg
+
      
 
      Animated GIF files from ImageMagick are unoptimized. You can use a
 program like gifsicle to optimize and massively shrink them.
 MPEG files created by ImageMagick are in MPEG-1 format with rather
@@ -635,7 +635,7 @@ inefficient compression and low quality.
      
 
 
      Select “Open Image Sequence” under the File menu Load the images into
 QuickTime to animate them Select “Export” under the File menu Save the
-movie as a QuickTime movie (*.mov) or in another format.  QuickTime
+movie as a QuickTime movie (*.mov) or in another format.  QuickTime
 can generate very high quality and efficiently compressed movie
 files. Some of the supported formats require to buy a license and some
 are not readable on all platforms until specific runtime libraries are
@@ -648,10 +648,10 @@ installed.
      
 
 
      FFmpeg is a command line tool that is available on many platforms and
 allows extremely flexible encoding and decoding of movies.
      
-
      cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v
-cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi
-
      
-
      
+
      +cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v
+cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi
+
      
 
      Frontends for FFmpeg exist for multiple platforms. For more
 information see the FFmpeg homepage
      
 
      
@@ -678,9 +678,9 @@ variety of file formats and decoders.
 animate tool,
 which works directly on a series of image files.
 
-
      a = animate("foo*.jpg")
-
      
-
      
+
      +a = animate("foo*.jpg")
+
      
 
        
 
      • d) QuickTime and other Windows- or MacOS-based media players can
 obviously play movie files directly. Similarly for corresponding tools
diff --git a/doc/html/dump_modify.html b/doc/html/dump_modify.html
index 492ef0a5f5..08afa5c7c6 100644
--- a/doc/html/dump_modify.html
+++ b/doc/html/dump_modify.html
@@ -128,9 +128,9 @@
 
        dump_modify command
        
 
        
 
        Syntax
        
-
        dump_modify dump-ID keyword values ...
-
        
-
        
+
        +dump_modify dump-ID keyword values ...
+
        
 
          
 
        • dump-ID = ID of dump to modify
          • 
 
        • one or more keyword/value pairs may be appended
          • 
@@ -228,16 +228,16 @@
 
        
 
        
 
        Examples
        
-
        dump_modify 1 format line "%d %d %20.15g %g %g" scale yes
-dump_modify 1 format float %20.15g scale yes
-dump_modify myDump image yes scale no flush yes
-dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
-dump_modify xtcdump precision 10000 sfactor 0.1
-dump_modify 1 every 1000 nfile 20
-dump_modify 1 every v_myVar
-dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
-
        
-
        
+
        +dump_modify 1 format line "%d %d %20.15g %g %g" scale yes
+dump_modify 1 format float %20.15g scale yes
+dump_modify myDump image yes scale no flush yes
+dump_modify 1 region mySphere thresh x < 0.0 thresh epair >= 3.2
+dump_modify xtcdump precision 10000 sfactor 0.1
+dump_modify 1 every 1000 nfile 20
+dump_modify 1 every v_myVar
+dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
+
        
 
        
 
        
 
        Description
        
@@ -318,19 +318,19 @@ to the dump file.  The every keyword cannot be used with the dump
 dcd style.
        
 
        For example, the following commands will
 write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:
        
-
        variable     s equal logfreq(10,3,10)
-dump         1 all atom 100 tmp.dump
-dump_modify  1 every v_s first yes
-
        
-
        
+
        +variable     s equal logfreq(10,3,10)
+dump         1 all atom 100 tmp.dump
+dump_modify 1 every v_s first yes
+
        
 
        The following commands would write snapshots at the timesteps listed
 in file tmp.times:
        
-
        variable        f file tmp.times
-variable     s equal next(f)
-dump         1 all atom 100 tmp.dump
-dump_modify  1 every v_s
-
        
-
        
+
        +variable        f file tmp.times
+variable     s equal next(f)
+dump         1 all atom 100 tmp.dump
+dump_modify 1 every v_s
+
        
 
        
 
        Note
        
 
        When using a file-style variable with the every keyword, the
@@ -406,11 +406,11 @@ an integer and you wish it to appear in the text dump file as a
 (large) integer, then you need to use an appropriate format.  For
 example, these commands:
        
 
        
-
        compute     1 all property/local batom1 batom2
-dump        1 all local 100 tmp.bonds index c_1[1] c_1[2]
-dump_modify 1 format "%d %0.0f %0.0f"
-
        
-
        
+
        +compute     1 all property/local batom1 batom2
+dump        1 all local 100 tmp.bonds index c_1[1] c_1[2]
+dump_modify 1 format "%d %0.0f %0.0f"
+
        
 
        will output the two atom IDs for atoms in each bond as integers.  If
 the dump_modify command were omitted, they would appear as
 floating-point values, assuming they were large integers (more than 6
@@ -566,7 +566,7 @@ atoms of each type will be drawn in the image.
        
 
        The specified type should be an integer from 1 to Ntypes = the
 number of atom types.  A wildcard asterisk can be used in place of or
 in conjunction with the type argument to specify a range of atom
-types.  This takes the form “*” or “n” or “n” or “m*n”.  If N = the
+types.  This takes the form “*” or “*n” or “n*” or “m*n”.  If N = the
 number of atom types, then an asterisk with no numeric values means
 all types from 1 to N.  A leading asterisk means all types from 1 to n
 (inclusive).  A trailing asterisk means all types from n to N
@@ -689,15 +689,15 @@ color map without having to specify where all the bin boundaries are.
        
 atoms in individual molecules with a different color.  See the
 examples/pour/in.pour.2d.molecule input script for an example of how
 this is used.
        
-
        variable        colors string &
+
        +variable        colors string &
                 "red green blue yellow white &
                 purple pink orange lime gray"
 variable     mol atom mol%10
 dump         1 all image 250 image.*.jpg v_mol type &
              zoom 1.6 adiam 1.5
-dump_modify  1 pad 5 amap 0 10 sa 1 10 ${colors}
-
        
-
        
+dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors}
+
 
        In this case, 10 colors are defined, and molecule IDs are
 mapped to one of the colors, even if there are 1000s of molecules.
        
 
        
@@ -711,7 +711,7 @@ set the color that bonds of each type will be drawn in the image.
        
 
        The specified type should be an integer from 1 to Nbondtypes = the
 number of bond types.  A wildcard asterisk can be used in place of or
 in conjunction with the type argument to specify a range of bond
-types.  This takes the form “*” or “n” or “n” or “m*n”.  If N = the
+types.  This takes the form “*” or “*n” or “n*” or “m*n”.  If N = the
 number of bond types, then an asterisk with no numeric values means
 all types from 1 to N.  A leading asterisk means all types from 1 to n
 (inclusive).  A trailing asterisk means all types from n to N
diff --git a/doc/html/fix.html b/doc/html/fix.html
index 885ad1653b..cc8435af47 100644
--- a/doc/html/fix.html
+++ b/doc/html/fix.html
@@ -210,8 +210,8 @@ discussed below, it can be referenced via the following bracket
 notation, where ID is the ID of the fix:
        
 
      
 




 
 
 
      c_ID
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
      --++
diff --git a/doc/html/fix_adapt_fep.html b/doc/html/fix_adapt_fep.html
index 51d29b8b76..908ef5b395 100644
--- a/doc/html/fix_adapt_fep.html
+++ b/doc/html/fix_adapt_fep.html
@@ -170,12 +170,12 @@
 
      
 
      Examples
      
-
      fix 1 all adapt/fep 1 pair soft a 1 1 v_prefactor
-fix 1 all adapt/fep 1 pair soft a 2* 3 v_prefactor
-fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
-fix 1 all adapt/fep 10 atom diameter 1 v_size
-
      
-
      
+
      +fix 1 all adapt/fep 1 pair soft a 1 1 v_prefactor
+fix 1 all adapt/fep 1 pair soft a 2* 3 v_prefactor
+fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
+fix 1 all adapt/fep 10 atom diameter 1 v_size
+
      
 
      
 
      Description
      
@@ -307,7 +307,7 @@ each, as in the 1st example above.  I <= J is required.  LAMMPS sets
 the coefficients for the symmetric J,I interaction to the same values.
      
 
      A wild-card asterisk can be used in place of or in conjunction with
 the I,J arguments to set the coefficients for multiple pairs of atom
-types.  This takes the form “*” or “n” or “n” or “m*n”.  If N = the
+types.  This takes the form “*” or “*n” or “n*” or “m*n”.  If N = the
 number of atom types, then an asterisk with no numeric values means
 all types from 1 to N.  A leading asterisk means all types from 1 to n
 (inclusive).  A trailing asterisk means all types from n to N
@@ -333,10 +333,10 @@ details.
      
 
      For example, these commands would change the prefactor coefficient of
 the pair_style soft potential from 10.0 to 30.0 in a
 linear fashion over the course of a simulation:
      
-
      variable prefactor equal ramp(10,30)
-fix 1 all adapt 1 pair soft a * * v_prefactor
-
      
-
      
+
      +variable prefactor equal ramp(10,30)
+fix 1 all adapt 1 pair soft a * * v_prefactor
+
      
 
      
 
      The kspace keyword used the specified variable as a scale factor on
 the energy, forces, virial calculated by whatever K-Space solver is
@@ -369,16 +369,14 @@ constant).
      
 
      For example, these commands would shrink the diameter of all granular
 particles in the “center” group from 1.0 to 0.1 in a linear fashion
 over the course of a 1000-step simulation:
      
-
      variable size equal ramp(1.0,0.1)
-fix 1 center adapt 10 atom diameter * v_size
-
      
-
      
+
      +variable size equal ramp(1.0,0.1)
+fix 1 center adapt 10 atom diameter * v_size
+
      
 
      For rRESPA time integration, this fix changes
 parameters on the outermost rRESPA level.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various output commands.  No parameter of this fix can
diff --git a/doc/html/fix_addtorque.html b/doc/html/fix_addtorque.html
index 8926210c55..2cc2a8b678 100644
--- a/doc/html/fix_addtorque.html
+++ b/doc/html/fix_addtorque.html
@@ -140,10 +140,10 @@
 
      
 
      Examples
      
-
      fix kick bead addtorque 2.0 3.0 5.0
-fix kick bead addtorque 0.0 0.0 v_oscillate
-
      
-
      
+
      +fix kick bead addtorque 2.0 3.0 5.0
+fix kick bead addtorque 0.0 0.0 v_oscillate
+
      
 
      
 
      Description
      
@@ -166,10 +166,8 @@ torque component.
      
 functions, and include thermo_style command
 keywords for the simulation box parameters and timestep and elapsed
 time.  Thus it is easy to specify a time-dependent torque.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.
      
 
      The fix_modify energy option is supported by this
 fix to add the potential “energy” inferred by the added forces to the
diff --git a/doc/html/fix_atc.html b/doc/html/fix_atc.html
index 2714ede1fe..d295f3cc18 100644
--- a/doc/html/fix_atc.html
+++ b/doc/html/fix_atc.html
@@ -128,9 +128,9 @@
 
      fix atc command
      
 
      
 
      Syntax
      
-
      fix <fixID> <group> atc <type> <parameter_file>
-
      
-
      
+
      +fix <fixID> <group> atc <type> <parameter_file>
+
      
 
        
 
      • fixID = name of fix
        • 
 
      • group = name of group fix is to be applied
        • 
@@ -148,12 +148,12 @@
 
      
 
      
 
      Examples
      
-
      fix AtC internal atc thermal Ar_thermal.dat
-fix AtC internal atc two_temperature Ar_ttm.mat
-fix AtC internal atc hardy
-fix AtC internal atc field
-
      
-
      
+
      +fix AtC internal atc thermal Ar_thermal.dat
+fix AtC internal atc two_temperature Ar_ttm.mat
+fix AtC internal atc hardy
+fix AtC internal atc field
+
      
 
      
 
      
 
      Description
      
@@ -163,31 +163,31 @@
  # ... commands to create and initialize the MD system
 
      
 
      
-
      # initial fix to designate coupling type and group to apply it to
-# tag group physics material_file
-fix AtC internal atc thermal Ar_thermal.mat
-
      
-
      
-
      # create a uniform 12 x 2 x 2 mesh that covers region contain the group
-# nx ny nz region periodicity
-fix_modify AtC mesh create 12 2 2 mdRegion f p p
-
      
-
      
-
      # specify the control method for the type of coupling
-# physics control_type
-fix_modify AtC thermal control flux
-
      
-
      
-
      # specify the initial values for the empirical field "temperature"
-# field node_group value
-fix_modify AtC initial temperature all 30
-
      
-
      
-
      # create an output stream for nodal fields
-# filename output_frequency
-fix_modify AtC output atc_fe_output 100
-
      
-
      
+
      +# initial fix to designate coupling type and group to apply it to
+# tag group physics material_file
+fix AtC internal atc thermal Ar_thermal.mat
+
      
+
      +# create a uniform 12 x 2 x 2 mesh that covers region contain the group
+# nx ny nz region periodicity
+fix_modify AtC mesh create 12 2 2 mdRegion f p p
+
      
+
      +# specify the control method for the type of coupling
+# physics control_type
+fix_modify AtC thermal control flux
+
      
+
      +# specify the initial values for the empirical field "temperature"
+# field node_group value
+fix_modify AtC initial temperature all 30
+
      
+
      +# create an output stream for nodal fields
+# filename output_frequency
+fix_modify AtC output atc_fe_output 100
+
      run 1000
 
      
 
      
@@ -200,30 +200,30 @@
 fixAtCinternalatchardy
-
      # for hardy fix, specific kernel function (function type and range) to # be used as a localization function
-fix AtC kernel quartic_sphere 10.0
-
      
-
      
-
      # create a uniform 1 x 1 x 1 mesh that covers region contain the group
-# with periodicity this effectively creats a system average
-fix_modify AtC mesh create 1 1 1 box p p p
-
      
-
      
-
      # change from default lagrangian map to eulerian
-# refreshed every 100 steps
-fix_modify AtC atom_element_map eulerian 100
-
      
-
      
-
      # start with no field defined
-# add mass density, potential energy density, stress and temperature
-fix_modify AtC fields add density energy stress temperature
-
      
-
      
-
      # create an output stream for nodal fields
-# filename output_frequency
-fix_modify AtC output nvtFE 100 text
-
      
-
      
+
      +# for hardy fix, specific kernel function (function type and range) to # be used as a localization function
+fix AtC kernel quartic_sphere 10.0
+
      
+
      +# create a uniform 1 x 1 x 1 mesh that covers region contain the group
+# with periodicity this effectively creats a system average
+fix_modify AtC mesh create 1 1 1 box p p p
+
      
+
      +# change from default lagrangian map to eulerian
+# refreshed every 100 steps
+fix_modify AtC atom_element_map eulerian 100
+
      
+
      +# start with no field defined
+# add mass density, potential energy density, stress and temperature
+fix_modify AtC fields add density energy stress temperature
+
      
+
      +# create an output stream for nodal fields
+# filename output_frequency
+fix_modify AtC output nvtFE 100 text
+
      run 1000
 
      
 
      
@@ -235,10 +235,8 @@
 
      fix_modify AtC mesh create 1 1 1 box p p p
      ...
      Note coupling and post-processing can be combined in the same simulations using separate fixes.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  The fix_modify options relevant to this fix are listed below.  No global scalar or vector or per-atom quantities are stored by this fix for access by various output commands.  No parameter of this fix can be used with the start/stop keywords of the run command.  This fix is not invoked during energy minimization.
      
 
      
diff --git a/doc/html/fix_atom_swap.html b/doc/html/fix_atom_swap.html
index 862d6932af..a56f3b4f8b 100644
--- a/doc/html/fix_atom_swap.html
+++ b/doc/html/fix_atom_swap.html
@@ -156,11 +156,11 @@
 
      
 
      Examples
      
-
      fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
-fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
-fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 0.0 4.3 -5.0
-
      
-
      
+
      +fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
+fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
+fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 0.0 4.3 -5.0
+
      
 
      
 
      Description
      
@@ -250,9 +250,7 @@ system (the quantity used when performing GCMC moves),
 you MUST enable the fix_modify energy option for
 that fix.  The doc pages for individual fix commands
 specify if this should be done.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      This fix writes the state of the fix to binary restart files.  This includes information about the random
 number generator seed, the next timestep for MC exchanges, etc.  See
 the read_restart command for info on how to
diff --git a/doc/html/fix_ave_atom.html b/doc/html/fix_ave_atom.html
index b8459a1d96..72641a5006 100644
--- a/doc/html/fix_ave_atom.html
+++ b/doc/html/fix_ave_atom.html
@@ -140,22 +140,22 @@
 one or more input values can be listed
 
    • value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[i], f_ID, f_ID[i], v_name
      • 
 
-
      x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
-c_ID = per-atom vector calculated by a compute with ID
-c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
-f_ID = per-atom vector calculated by a fix with ID
-f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
-v_name = per-atom vector calculated by an atom-style variable with name
-
      
-
      
+
      +x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
+c_ID = per-atom vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
+f_ID = per-atom vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
+v_name = per-atom vector calculated by an atom-style variable with name
+
      
 
      
 
      Examples
      
-
      fix 1 all ave/atom 1 100 100 vx vy vz
-fix 1 all ave/atom 10 20 1000 c_my_stress[1]
-fix 1 all ave/atom 10 20 1000 c_my_stress[*]
-
      
-
      
+
      +fix 1 all ave/atom 1 100 100 vx vy vz
+fix 1 all ave/atom 10 20 1000 c_my_stress[1]
+fix 1 all ave/atom 10 20 1000 c_my_stress[*]
+
      
 
      
 
      Description
      
@@ -181,7 +181,7 @@ are the only ones that can be used with this fix since they produce
 per-atom vectors.
      
 
      Note that for values from a compute or fix, the bracketed index I can
 be specified using a wildcard asterisk with the index to effectively
-specify multiple values.  This takes the form “*” or “n” or “n” or
+specify multiple values.  This takes the form “*” or “*n” or “n*” or
 “m*n”.  If N = the size of the vector (for mode = scalar) or the
 number of columns in the array (for mode = vector), then an asterisk
 with no numeric values means all indices from 1 to N.  A leading
@@ -192,13 +192,13 @@ means all indices from m to n (inclusive).
      
 had been listed one by one.  E.g. these 2 fix ave/atom commands are
 equivalent, since the compute stress/atom
 command creates a per-atom array with 6 columns:
      
-
      compute my_stress all stress/atom NULL
-fix 1 all ave/atom 10 20 1000 c_my_stress[*]
-fix 1 all ave/atom 10 20 1000 c_my_stress[1] c_my_stress[1] &
-                              c_my_stress[3] c_my_stress[4] &
-                              c_my_stress[5] c_my_stress[6]
-
      
-
      
+
      +compute my_stress all stress/atom NULL
+fix 1 all ave/atom 10 20 1000 c_my_stress[*]
+fix 1 all ave/atom 10 20 1000 c_my_stress[1] c_my_stress[1] &
+                              c_my_stress[3] c_my_stress[4] &
+                              c_my_stress[5] c_my_stress[6]
+
      
 
      
 
      The Nevery, Nrepeat, and Nfreq arguments specify on what
 timesteps the input values will be used in order to contribute to the
@@ -228,7 +228,7 @@ this is not what you want, consider averaging unwrapped coordinates,
 which can be provided by the compute property/atom command via its xu,yu,zu
 attributes.
      
 
      
-
      If a value begins with “c_”, a compute ID must follow which has been
+
      If a value begins with “c_”, a compute ID must follow which has been
 previously defined in the input script.  If no bracketed term is
 appended, the per-atom vector calculated by the compute is used.  If a
 bracketed term containing an index I is appended, the Ith column of
@@ -236,7 +236,7 @@ the per-atom array calculated by the compute is used.  Users can also
 write code for their own compute styles and add them to LAMMPS.  See the discussion above for how I can
 be specified with a wildcard asterisk to effectively specify multiple
 values.
      
-
      If a value begins with “f_”, a fix ID must follow which has been
+
      If a value begins with “f_”, a fix ID must follow which has been
 previously defined in the input script.  If no bracketed term is
 appended, the per-atom vector calculated by the fix is used.  If a
 bracketed term containing an index I is appended, the Ith column of
@@ -246,15 +246,13 @@ compatible with Nevery, else an error will result.  Users can also
 write code for their own fix styles and add them to LAMMPS.  See the discussion above for how I can
 be specified with a wildcard asterisk to effectively specify multiple
 values.
      
-
      If a value begins with “v_”, a variable name must follow which has
+
      If a value begins with “v_”, a variable name must follow which has
 been previously defined in the input script as an atom-style variable Variables of style atom can reference
 thermodynamic keywords, or invoke other computes, fixes, or variables
 when they are evaluated, so this is a very general means of generating
 per-atom quantities to time average.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global scalar or vector quantities are
 stored by this fix for access by various output commands.
      
diff --git a/doc/html/fix_ave_chunk.html b/doc/html/fix_ave_chunk.html
index 564b91e3ef..a6293fb62e 100644
--- a/doc/html/fix_ave_chunk.html
+++ b/doc/html/fix_ave_chunk.html
@@ -141,16 +141,16 @@
 
    • one or more input values can be listed
      • 
 
    • value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name
      • 
 
-
      vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
-density/number, density/mass = number or mass density
-temp = temperature
-c_ID = per-atom vector calculated by a compute with ID
-c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
-f_ID = per-atom vector calculated by a fix with ID
-f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
-v_name = per-atom vector calculated by an atom-style variable with name
-
      
-
      
+
      +vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
+density/number, density/mass = number or mass density
+temp = temperature
+c_ID = per-atom vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
+f_ID = per-atom vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
+v_name = per-atom vector calculated by an atom-style variable with name
+
      
 
        
 
      • zero or more keyword/arg pairs may be appended
        • 
 
      • keyword = norm or ave or bias or adof or cdof or file or overwrite or title1 or title2 or title3
        • 
@@ -185,12 +185,12 @@
 
      
 
      Examples
      
-
      fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro title1 "My output values"
-fix 1 flow ave/chunk 100 10 1000 molchunk vx vz norm sample file vel.profile
-fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
-fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
-
      
-
      
+
      +fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro title1 "My output values"
+fix 1 flow ave/chunk 100 10 1000 molchunk vx vz norm sample file vel.profile
+fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
+fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
+
      
 
      NOTE:
      
 
      If you are trying to replace a deprectated fix ave/spatial command
 with the newer, more flexible fix ave/chunk and compute chunk/atom commands, you simply need to split
@@ -242,7 +242,7 @@ ones that can be used with this fix since all other styles of variable
 produce global quantities.
      
 
      Note that for values from a compute or fix, the bracketed index I can
 be specified using a wildcard asterisk with the index to effectively
-specify multiple values.  This takes the form “*” or “n” or “n” or
+specify multiple values.  This takes the form “*” or “*n” or “n*” or
 “m*n”.  If N = the size of the vector (for mode = scalar) or the
 number of columns in the array (for mode = vector), then an asterisk
 with no numeric values means all indices from 1 to N.  A leading
@@ -253,11 +253,11 @@ means all indices from m to n (inclusive).
      
 had been listed one by one.  E.g. these 2 fix ave/chunk commands are
 equivalent, since the compute property/atom command creates, in this
 case, a per-atom array with 3 columns:
      
-
      compute myAng all property/atom angmomx angmomy angmomz
-fix 1 all ave/chunk 100 1 100 cc1 c_myAng[*] file tmp.angmom
-fix 2 all ave/chunk 100 1 100 cc1 c_myAng[1] c_myAng[2] c_myAng[3] file tmp.angmom
-
      
-
      
+
      +compute myAng all property/atom angmomx angmomy angmomz
+fix 1 all ave/chunk 100 1 100 cc1 c_myAng[*] file tmp.angmom
+fix 2 all ave/chunk 100 1 100 cc1 c_myAng[1] c_myAng[2] c_myAng[3] file tmp.angmom
+
      
 
      
 
      Note
      
 
      This fix works by creating an array of size Nchunk by Nvalues
@@ -349,7 +349,7 @@ in the chunk on different timesteps were collected together as one set
 of atoms to calculate their temperature.  The compute allows the
 center-of-mass velocity of each chunk to be subtracted before
 calculating the temperature; this fix does not.
      
-
      If a value begins with “c_”, a compute ID must follow which has been
+
      If a value begins with “c_”, a compute ID must follow which has been
 previously defined in the input script.  If no bracketed integer is
 appended, the per-atom vector calculated by the compute is used.  If a
 bracketed integer is appended, the Ith column of the per-atom array
@@ -357,7 +357,7 @@ calculated by the compute is used.  Users can also write code for
 their own compute styles and add them to LAMMPS.
 See the discussion above for how I can be specified with a wildcard
 asterisk to effectively specify multiple values.
      
-
      If a value begins with “f_”, a fix ID must follow which has been
+
      If a value begins with “f_”, a fix ID must follow which has been
 previously defined in the input script.  If no bracketed integer is
 appended, the per-atom vector calculated by the fix is used.  If a
 bracketed integer is appended, the Ith column of the per-atom array
@@ -367,7 +367,7 @@ their values on certain timesteps, which must be compatible with
 own fix styles and add them to LAMMPS.  See the
 discussion above for how I can be specified with a wildcard asterisk
 to effectively specify multiple values.
      
-
      If a value begins with “v_”, a variable name must follow which has
+
      If a value begins with “v_”, a variable name must follow which has
 been previously defined in the input script.  Variables of style
 atom can reference thermodynamic keywords and various per-atom
 attributes, or invoke other computes, fixes, or variables when they
@@ -502,10 +502,8 @@ value of the units keyword is reduced, the coordinate values w
 be in unitless reduced units (0-1).  This is not true for the Coord1 value
 of style bin/sphere or bin/cylinder which both represent radial
 dimensions.  Those values are always in distance units.
      
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.
      
 
      This fix computes a global array of values which can be accessed by
diff --git a/doc/html/fix_ave_correlate.html b/doc/html/fix_ave_correlate.html
index 5386d0dd57..c191ecefa1 100644
--- a/doc/html/fix_ave_correlate.html
+++ b/doc/html/fix_ave_correlate.html
@@ -140,14 +140,14 @@
 
    • one or more input values can be listed
      • 
 
    • value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
      • 
 
-
      c_ID = global scalar calculated by a compute with ID
-c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below)
-f_ID = global scalar calculated by a fix with ID
-f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below)
-v_name = global value calculated by an equal-style variable with name
-v_name[I] = Ith component of a vector-style variable with name
-
      
-
      
+
      +c_ID = global scalar calculated by a compute with ID
+c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below)
+f_ID = global scalar calculated by a fix with ID
+f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below)
+v_name = global value calculated by an equal-style variable with name
+v_name[I] = Ith component of a vector-style variable with name
+
      
 
        
 
      • zero or more keyword/arg pairs may be appended
        • 
 
      • keyword = type or ave or start or prefactor or file or overwrite or title1 or title2 or title3
        • 
@@ -180,12 +180,12 @@
 
      
 
      
 
      Examples
      
-
      fix 1 all ave/correlate 5 100 1000 c_myTemp file temp.correlate
-fix 1 all ave/correlate 1 50 10000 &
-          c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
-       type upper ave running title1 "My correlation data"
-
      
-
      
+
      +fix 1 all ave/correlate 5 100 1000 c_myTemp file temp.correlate
+fix 1 all ave/correlate 1 50 10000 &
+          c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
+       type upper ave running title1 "My correlation data"
+
      
 
      fix 1 all ave/correlate 1 50 10000 c_thermo_press[*]
      
 
      
 
      
@@ -221,7 +221,7 @@ ones that can be used with this fix.  Variables of style atom cannot
 be used, since they produce per-atom values.
      
 
      Note that for values from a compute or fix, the bracketed index I can
 be specified using a wildcard asterisk with the index to effectively
-specify multiple values.  This takes the form “*” or “n” or “n” or
+specify multiple values.  This takes the form “*” or “*n” or “n*” or
 “m*n”.  If N = the size of the vector (for mode = scalar) or the
 number of columns in the array (for mode = vector), then an asterisk
 with no numeric values means all indices from 1 to N.  A leading
@@ -232,13 +232,13 @@ means all indices from m to n (inclusive).
      
 vector had been listed one by one.  E.g. these 2 fix ave/correlate
 commands are equivalent, since the compute pressure command creates a global vector with 6
 values.
      
-
      compute myPress all pressure NULL
-fix 1 all ave/correlate 1 50 10000 c_myPress[*]
-fix 1 all ave/correlate 1 50 10000 &
-          c_myPress[1] c_myPress[2] c_myPress[3] &
-          c_myPress[4] c_myPress[5] c_myPress[6]
-
      
-
      
+
      +compute myPress all pressure NULL
+fix 1 all ave/correlate 1 50 10000 c_myPress[*]
+fix 1 all ave/correlate 1 50 10000 &
+          c_myPress[1] c_myPress[2] c_myPress[3] &
+          c_myPress[4] c_myPress[5] c_myPress[6]
+
      
 
      
 
      The Nevery, Nrepeat, and Nfreq arguments specify on what
 timesteps the input values will be used to calculate correlation data.
@@ -249,9 +249,9 @@ initial time up to an output timestep.  The initial time could be the
 beginning of the simulation or the last output time; see the ave
 keyword for options.  For the set of samples, the correlation value
 Cij is calculated as:
      
-
      Cij(delta) = ave(Vi(t)*Vj(t+delta))
-
      
-
      
+
      +Cij(delta) = ave(Vi(t)*Vj(t+delta))
+
      
 
      which is the correlation value between input values Vi and Vj,
 separated by time delta.  Note that the second value Vj in the pair is
 always the one sampled at the later time.  The ave() represents an
@@ -259,9 +259,9 @@ average over every pair of samples in the set that are separated by
 time delta.  The maximum delta used is of size (Nrepeat-1)*Nevery.
 Thus the correlation between a pair of input values yields Nrepeat
 correlation datums:
      
-
      Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij((Nrepeat-1)*Nevery)
-
      
-
      
+
      +Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij((Nrepeat-1)*Nevery)
+
      
 
      For example, if Nevery=5, Nrepeat=6, and Nfreq=100, then values on
 timesteps 0,5,10,15,...,100 will be used to compute the final averages
 on timestep 100.  Six averages will be computed: Cij(0), Cij(5),
@@ -272,7 +272,7 @@ Vi(10)*V j20), Vi(15)*Vj(25), ..., Vi(85)*Vj(95), Vi(90)*Vj(100).
      
 non-zero.  Also, if the ave keyword is set to one which is the
 default, then Nfreq >= (Nrepeat-1)*Nevery is required.
      
 
      
-
      If a value begins with “c_”, a compute ID must follow which has been
+
      If a value begins with “c_”, a compute ID must follow which has been
 previously defined in the input script.  If no bracketed term is
 appended, the global scalar calculated by the compute is used.  If a
 bracketed term is appended, the Ith element of the global vector
@@ -286,7 +286,7 @@ defined not in your input script, but by fix temp/rescale.  See the doc pages for
 these commands which give the IDs of these computes.  Users can also
 write code for their own compute styles and add them to LAMMPS.
      
-
      If a value begins with “f_”, a fix ID must follow which has been
+
      If a value begins with “f_”, a fix ID must follow which has been
 previously defined in the input script.  If no bracketed term is
 appended, the global scalar calculated by the fix is used.  If a
 bracketed term is appended, the Ith element of the global vector
@@ -296,7 +296,7 @@ values.
      
 
      Note that some fixes only produce their values on certain timesteps,
 which must be compatible with Nevery, else an error will result.
 Users can also write code for their own fix styles and add them to LAMMPS.
      
-
      If a value begins with “v_”, a variable name must follow which has
+
      If a value begins with “v_”, a variable name must follow which has
 been previously defined in the input script.  Only equal-style or
 vector-style variables can be referenced; the latter requires a
 bracketed term to specify the Ith element of the vector calculated by
@@ -366,11 +366,11 @@ the strings that will be printed as the first 3 lines of the output
 file, assuming the file keyword was used.  LAMMPS uses default
 values for each of these, so they do not need to be specified.
      
 
      By default, these header lines are as follows:
      
-
      # Time-correlated data for fix ID
-# TimeStep Number-of-time-windows
-# Index TimeDelta Ncount valueI*valueJ valueI*valueJ ...
-
      
-
      
+
      +# Time-correlated data for fix ID
+# TimeStep Number-of-time-windows
+# Index TimeDelta Ncount valueI*valueJ valueI*valueJ ...
+
      
 
      In the first line, ID is replaced with the fix-ID.  The second line
 describes the two values that are printed at the first of each section
 of output.  In the third line the value pairs are replaced with the
@@ -378,9 +378,9 @@ appropriate fields from the fix ave/correlate command.
      
 
      
 
      Let Sij = a set of time correlation data for input values I and J,
 namely the Nrepeat values:
      
-
      Sij = Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij(*Nrepeat-1)*Nevery)
-
      
-
      
+
      +Sij = Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij(*Nrepeat-1)*Nevery)
+
      
 
      As explained below, these datums are output as one column of a global
 array, which is effectively the correlation matrix.
      
 
      The trap function defined for equal-style variables
@@ -389,10 +389,8 @@ using a trapezoidal rule.  This is useful for calculating various
 quantities which can be derived from time correlation data.  If a
 normalization factor is needed for the time integration, it can be
 included in the variable formula or via the prefactor keyword.
      
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.
      
 
      This fix computes a global array of values which can be accessed by
diff --git a/doc/html/fix_ave_correlate_long.html b/doc/html/fix_ave_correlate_long.html
index ccd754dbaf..a673143beb 100644
--- a/doc/html/fix_ave_correlate_long.html
+++ b/doc/html/fix_ave_correlate_long.html
@@ -139,13 +139,13 @@
 
    • one or more input values can be listed
      • 
 
    • value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
      • 
 
-
      c_ID = global scalar calculated by a compute with ID
-c_ID[I] = Ith component of global vector calculated by a compute with ID
-f_ID = global scalar calculated by a fix with ID
-f_ID[I] = Ith component of global vector calculated by a fix with ID
-v_name = global value calculated by an equal-style variable with name
-
      
-
      
+
      +c_ID = global scalar calculated by a compute with ID
+c_ID[I] = Ith component of global vector calculated by a compute with ID
+f_ID = global scalar calculated by a fix with ID
+f_ID[I] = Ith component of global vector calculated by a fix with ID
+v_name = global value calculated by an equal-style variable with name
+
      
 
        
 
      • zero or more keyword/arg pairs may be appended
        • 
 
      • keyword = type or start or file or overwrite or title1 or title2 or ncorr or p or m
        • 
@@ -177,12 +177,12 @@
 
      
 
      
 
      Examples
      
-
      fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate
-fix 1 all ave/correlate/long 1 10000 &
-          c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
-       type upper title1 "My correlation data" nlen 15 ncount 3
-
      
-
      
+
      +fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate
+fix 1 all ave/correlate/long 1 10000 &
+          c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
+       type upper title1 "My correlation data" nlen 15 ncount 3
+
      
 
      
 
      
 
      Description
      
@@ -221,9 +221,7 @@ steps can be calculated.
      
 4*ncorr*nlen*8 bytes. With the default values of the parameters, this
 corresponds to about 10 KB.
      
 
      For the meaning of the additional optional keywords, see the fix ave/correlate doc page.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      Since this fix in intended for the calculation of time correlation
 functions over very long MD simulations, the information about this
 fix is written automatically to binary restart files, so that the time
diff --git a/doc/html/fix_ave_histo.html b/doc/html/fix_ave_histo.html
index e8291ddeb4..bb07687b4a 100644
--- a/doc/html/fix_ave_histo.html
+++ b/doc/html/fix_ave_histo.html
@@ -145,15 +145,15 @@
 
    • one or more input values can be listed
      • 
 
    • value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name
      • 
 
-
      x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
-c_ID = scalar or vector calculated by a compute with ID
-c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID, I can include wildcard (see below)
-f_ID = scalar or vector calculated by a fix with ID
-f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID, I can include wildcard (see below)
-v_name = value(s) calculated by an equal-style or vector-style or atom-style variable with name
-v_name[I] = value calculated by a vector-style variable with name
-
      
-
      
+
      +x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
+c_ID = scalar or vector calculated by a compute with ID
+c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID, I can include wildcard (see below)
+f_ID = scalar or vector calculated by a fix with ID
+f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID, I can include wildcard (see below)
+v_name = value(s) calculated by an equal-style or vector-style or atom-style variable with name
+v_name[I] = value calculated by a vector-style variable with name
+
      
 
        
 
      • zero or more keyword/arg pairs may be appended
        • 
 
      • keyword = mode or file or ave or start or beyond or overwrite or title1 or title2 or title3
        • 
@@ -185,13 +185,13 @@
 
      
 
      
 
      Examples
      
-
      fix 1 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running
-fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[2] c_thermo_press[3] title1 "My output values"
-fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[*]
-fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra
-fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD[1] c_XRD[2]
-
      
-
      
+
      +fix 1 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running
+fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[2] c_thermo_press[3] title1 "My output values"
+fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[*]
+fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra
+fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD[1] c_XRD[2]
+
      
 
      
 
      
 
      Description
      
@@ -232,7 +232,7 @@ with a bracketed term appended, indicating the Ith column of the array
 is used.
      
 
      Note that for values from a compute or fix, the bracketed index I can
 be specified using a wildcard asterisk with the index to effectively
-specify multiple values.  This takes the form “*” or “n” or “n” or
+specify multiple values.  This takes the form “*” or “*n” or “n*” or
 “m*n”.  If N = the size of the vector (for mode = scalar) or the
 number of columns in the array (for mode = vector), then an asterisk
 with no numeric values means all indices from 1 to N.  A leading
@@ -243,11 +243,11 @@ means all indices from m to n (inclusive).
      
 vector or columns of the array had been listed one by one.  E.g. these
 2 fix ave/histo commands are equivalent, since the compute com/chunk command creates a global array with
 3 columns:
      
-
      compute myCOM all com/chunk
-fix 1 all ave/histo 100 1 100 c_myCOM[*] file tmp1.com mode vector
-fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
-
      
-
      
+
      +compute myCOM all com/chunk
+fix 1 all ave/histo 100 1 100 c_myCOM[*] file tmp1.com mode vector
+fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
+
      
 
      If the fix ave/histo/weight command is used, exactly two values must
 be specified.  If the values are vectors, they must be the same
 length.  The first value (a scalar or vector) is what is histogrammed
@@ -278,7 +278,7 @@ simply generated on timesteps 100,200,etc.
      
 self-explanatory.  Note that other atom attributes can be used as
 inputs to this fix by using the compute property/atom command and then specifying
 an input value from that compute.
      
-
      If a value begins with “c_”, a compute ID must follow which has been
+
      If a value begins with “c_”, a compute ID must follow which has been
 previously defined in the input script.  If mode = scalar, then if
 no bracketed term is appended, the global scalar calculated by the
 compute is used.  If a bracketed term is appended, the Ith element of
@@ -295,7 +295,7 @@ can thus be accessed by fix ave/histo.  Or it can be a compute defined
 not in your input script, but by thermodynamic output or other fixes such as fix nvt or fix temp/rescale.  See
 the doc pages for these commands which give the IDs of these computes.
 Users can also write code for their own compute styles and add them to LAMMPS.
      
-
      If a value begins with “f_”, a fix ID must follow which has been
+
      If a value begins with “f_”, a fix ID must follow which has been
 previously defined in the input script.  If mode = scalar, then if
 no bracketed term is appended, the global scalar calculated by the fix
 is used.  If a bracketed term is appended, the Ith element of the
@@ -309,7 +309,7 @@ values.
      
 
      Note that some fixes only produce their values on certain timesteps,
 which must be compatible with Nevery, else an error will result.
 Users can also write code for their own fix styles and add them to LAMMPS.
      
-
      If a value begins with “v_”, a variable name must follow which has
+
      If a value begins with “v_”, a variable name must follow which has
 been previously defined in the input script.  If mode = scalar, then
 only equal-style or vector-style variables can be used, which both
 produce global values.  In this mode, a vector-style variable requires
@@ -399,10 +399,8 @@ values for each of these, so they do not need to be specified.
      
 describes the six values that are printed at the first of each section
 of output.  The third describes the 4 values printed for each bin in
 the histogram.
      
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.
      
 
      This fix produces a global vector and global array which can be
diff --git a/doc/html/fix_ave_time.html b/doc/html/fix_ave_time.html
index 6c6744c5e6..2d41fdc0dc 100644
--- a/doc/html/fix_ave_time.html
+++ b/doc/html/fix_ave_time.html
@@ -140,14 +140,14 @@
 
    • one or more input values can be listed
      • 
 
    • value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
      • 
 
-
      c_ID = global scalar or vector calculated by a compute with ID
-c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
-f_ID = global scalar or vector calculated by a fix with ID
-f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID, I can include wildcard (see below)
-v_name = value(s) calculated by an equal-style or vector-style variable with name
-v_name[I] = value calculated by a vector-style variable with name
-
      
-
      
+
      +c_ID = global scalar or vector calculated by a compute with ID
+c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
+f_ID = global scalar or vector calculated by a fix with ID
+f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID, I can include wildcard (see below)
+v_name = value(s) calculated by an equal-style or vector-style variable with name
+v_name[I] = value calculated by a vector-style variable with name
+
      
 
        
 
      • zero or more keyword/arg pairs may be appended
        • 
 
      • keyword = mode or file or ave or start or off or overwrite or title1 or title2 or title3
        • 
@@ -179,13 +179,13 @@
 
      
 
      
 
      Examples
      
-
      fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile
-fix 1 all ave/time 100 5 1000 c_thermo_press[2] ave window 20 &
-                              title1 "My output values"
-fix 1 all ave/time 100 5 1000 c_thermo_press[*]
-fix 1 all ave/time 1 100 1000 f_indent f_indent[1] file temp.indent off 1
-
      
-
      
+
      +fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile
+fix 1 all ave/time 100 5 1000 c_thermo_press[2] ave window 20 &
+                              title1 "My output values"
+fix 1 all ave/time 100 5 1000 c_thermo_press[*]
+fix 1 all ave/time 1 100 1000 f_indent f_indent[1] file temp.indent off 1
+
      
 
      
 
      
 
      Description
      
@@ -228,7 +228,7 @@ is used.  All vectors must be the same length, which is the length of
 the vector or number of rows in the array.
      
 
      Note that for values from a compute or fix, the bracketed index I can
 be specified using a wildcard asterisk with the index to effectively
-specify multiple values.  This takes the form “*” or “n” or “n” or
+specify multiple values.  This takes the form “*” or “*n” or “n*” or
 “m*n”.  If N = the size of the vector (for mode = scalar) or the
 number of columns in the array (for mode = vector), then an asterisk
 with no numeric values means all indices from 1 to N.  A leading
@@ -239,11 +239,11 @@ means all indices from m to n (inclusive).
      
 vector or columns of the array had been listed one by one.  E.g. these
 2 fix ave/time commands are equivalent, since the compute rdf command creates, in this case, a global array
 with 3 columns, each of length 50:
      
-
      compute myRDF all rdf 50 1 2
-fix 1 all ave/time 100 1 100 c_myRDF[*] file tmp1.rdf mode vector
-fix 2 all ave/time 100 1 100 c_myRDF[1] c_myRDF[2] c_myRDF[3] file tmp2.rdf mode vector
-
      
-
      
+
      +compute myRDF all rdf 50 1 2
+fix 1 all ave/time 100 1 100 c_myRDF[*] file tmp1.rdf mode vector
+fix 2 all ave/time 100 1 100 c_myRDF[1] c_myRDF[2] c_myRDF[3] file tmp2.rdf mode vector
+
      
 
      
 
      The Nevery, Nrepeat, and Nfreq arguments specify on what
 timesteps the input values will be used in order to contribute to the
@@ -261,7 +261,7 @@ timestep 200, etc.  If Nrepeat=1 and Nfreq = 100, then no time
 averaging is done; values are simply generated on timesteps
 100,200,etc.
      
 
      
-
      If a value begins with “c_”, a compute ID must follow which has been
+
      If a value begins with “c_”, a compute ID must follow which has been
 previously defined in the input script.  If mode = scalar, then if
 no bracketed term is appended, the global scalar calculated by the
 compute is used.  If a bracketed term is appended, the Ith element of
@@ -277,7 +277,7 @@ can thus be accessed by fix ave/time.  Or it can be a compute defined
 not in your input script, but by thermodynamic output or other fixes such as fix nvt or fix temp/rescale.  See
 the doc pages for these commands which give the IDs of these computes.
 Users can also write code for their own compute styles and add them to LAMMPS.
      
-
      If a value begins with “f_”, a fix ID must follow which has been
+
      If a value begins with “f_”, a fix ID must follow which has been
 previously defined in the input script.  If mode = scalar, then if
 no bracketed term is appended, the global scalar calculated by the fix
 is used.  If a bracketed term is appended, the Ith element of the
@@ -290,7 +290,7 @@ specify multiple values.
      
 
      Note that some fixes only produce their values on certain timesteps,
 which must be compatible with Nevery, else an error will result.
 Users can also write code for their own fix styles and add them to LAMMPS.
      
-
      If a value begins with “v_”, a variable name must follow which has
+
      If a value begins with “v_”, a variable name must follow which has
 been previously defined in the input script.  If mode = scalar, then
 only equal-style or vector-style variables can be used, which both
 produce global values.  In this mode, a vector-style variable requires
@@ -383,10 +383,8 @@ so the title3 setting is ignored when mode = scalar.
      
 describes the two values that are printed at the first of each section
 of output.  In the third line the values are replaced with the
 appropriate fields from the fix ave/time command.
      
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.
      
 
      This fix produces a global scalar or global vector or global array
diff --git a/doc/html/fix_balance.html b/doc/html/fix_balance.html
index 0415a0054b..56beb5da2b 100644
--- a/doc/html/fix_balance.html
+++ b/doc/html/fix_balance.html
@@ -432,10 +432,8 @@ will be duplicate nodes in the list.
      
 rectangle for each processor (1 to 4).
      
 
      For a 3d problem, the syntax is similar with 8 vertices listed for
 each processor, instead of 4, and “SQUARES” replaced by “CUBES”.
      
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.
      
 
      This fix computes a global scalar which is the imbalance factor
diff --git a/doc/html/fix_bond_break.html b/doc/html/fix_bond_break.html
index 9be191ab77..ef0c90e2a9 100644
--- a/doc/html/fix_bond_break.html
+++ b/doc/html/fix_bond_break.html
@@ -224,10 +224,8 @@ dramatically released when the bond is broken.  More generally, you
 may need to thermostat your system to compensate for energy changes
 resulting from broken bonds (and angles, dihedrals, impropers).
      
 
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.
      
 
      This fix computes two statistics which it stores in a global vector of
diff --git a/doc/html/fix_bond_create.html b/doc/html/fix_bond_create.html
index 8ab79a00a5..8854f57578 100644
--- a/doc/html/fix_bond_create.html
+++ b/doc/html/fix_bond_create.html
@@ -265,7 +265,7 @@ percolation simulation.
      
 1st, 2nd, and 3rd neighbors of each atom (within the bond topology of
 the system) for use in weighting pairwise interactions for bonded
 atoms.  Note that adding a single bond always adds a new 1st neighbor
-but may also induce many new 2nd and 3rd neighbors, depending on the
+but may also induce *many* new 2nd and 3rd neighbors, depending on the
 molecular topology of your system.  The “extra special per atom”
 parameter must typically be set to allow for the new maximum total
 size (1st + 2nd + 3rd neighbors) of this per-atom list.  There are 3
@@ -320,10 +320,8 @@ dramatically when the bond is formed.  More generally, you may need to
 thermostat your system to compensate for energy changes resulting from
 created bonds (and angles, dihedrals, impropers).
      
 
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.
      
 
      This fix computes two statistics which it stores in a global vector of
diff --git a/doc/html/fix_bond_swap.html b/doc/html/fix_bond_swap.html
index 27a56cba19..a3ae59400a 100644
--- a/doc/html/fix_bond_swap.html
+++ b/doc/html/fix_bond_swap.html
@@ -229,9 +229,9 @@ quantities or the printing of unwrapped coordinates to a dump file.
      
 
      This fix computes a temperature each time it is invoked for use by the
 Boltzmann criterion.  To do this, the fix creates its own compute of
 style temp, as if this command had been issued:
      
-
      compute fix-ID_temp all temp
-
      
-
      
+
      +compute fix-ID_temp all temp
+
      
 
      See the compute temp command for details.  Note
 that the ID of the new compute is the fix-ID with underscore + “temp”
 appended and the group for the new compute is “all”, so that the
diff --git a/doc/html/fix_box_relax.html b/doc/html/fix_box_relax.html
index ea16211584..e81bc87098 100644
--- a/doc/html/fix_box_relax.html
+++ b/doc/html/fix_box_relax.html
@@ -371,10 +371,10 @@ temperature is used to compute the kinetic contribution to the
 pressure, even though this is subsequently ignored by default.  To do
 this, the fix creates its own computes of style “temp” and “pressure”,
 as if these commands had been issued:
      
-
      compute fix-ID_temp group-ID temp
-compute fix-ID_press group-ID pressure fix-ID_temp virial
-
      
-
      
+
      +compute fix-ID_temp group-ID temp
+compute fix-ID_press group-ID pressure fix-ID_temp virial
+
      
 
      See the compute temp and compute pressure commands for details.  Note that the
 IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
 + underscore + “press”, and the group for the new computes is the same
@@ -388,10 +388,8 @@ fix’s temperature or pressure via the
 or pressure during thermodynamic output via the thermo_style custom command using the appropriate compute-ID.
 It also means that changing attributes of thermo_temp or
 thermo_press will have no effect on this fix.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.
      
 
      The fix_modify temp and press options are
 supported by this fix.  You can use them to assign a
@@ -425,12 +423,12 @@ potential energy. This fix does not support the
 because that would result in double-counting of the fix energy in the
 minimization energy. Instead, the fix energy can be explicitly
 added to the potential energy using one of these two variants:
      
-
      variable emin equal pe+f_1
-
      
-
      
-
      variable emin equal pe+f_1/atoms
-
      
-
      
+
      +variable emin equal pe+f_1
+
      
+
      +variable emin equal pe+f_1/atoms
+
      
 
      No parameter of this fix can be used with the start/stop keywords of
 the run command.
      
 
      This fix is invoked during energy minimization, but
diff --git a/doc/html/fix_colvars.html b/doc/html/fix_colvars.html
index 8ac1624b80..367d9b091c 100644
--- a/doc/html/fix_colvars.html
+++ b/doc/html/fix_colvars.html
@@ -200,9 +200,7 @@ wrapped back into the simulation cell at each re-neighboring instead.
      
 fix that thermostats all atoms in the fix colvars group. This will be
 used to provide the colvars module with the current thermostat target
 temperature.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      This fix writes the current status of the colvars module into
 binary restart files. This is in addition to the text
 mode status file that is written by the colvars module itself and the
diff --git a/doc/html/fix_controller.html b/doc/html/fix_controller.html
index e6608bc009..e9e662670c 100644
--- a/doc/html/fix_controller.html
+++ b/doc/html/fix_controller.html
@@ -141,13 +141,13 @@
 
    • Kd = derivative gain in PID equation (unitless)
      • 
 
    • pvar = process variable of form c_ID, c_ID[I], f_ID, f_ID[I], or v_name
      • 
 
-
      c_ID = global scalar calculated by a compute with ID
-c_ID[I] = Ith component of global vector calculated by a compute with ID
-f_ID = global scalar calculated by a fix with ID
-f_ID[I] = Ith component of global vector calculated by a fix with ID
-v_name = value calculated by an equal-style variable with name
-
      
-
      
+
      +c_ID = global scalar calculated by a compute with ID
+c_ID[I] = Ith component of global vector calculated by a compute with ID
+f_ID = global scalar calculated by a fix with ID
+f_ID[I] = Ith component of global vector calculated by a fix with ID
+v_name = value calculated by an equal-style variable with name
+
      
 
        
 
      • setpoint = desired value of process variable (same units as process variable)
        • 
 
      • cvar = name of control variable
        • 
@@ -155,11 +155,11 @@
 
      
 
      Examples
      
-
      fix 1 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol
-fix 1 all controller 100 0.2 0.5 0 100.0 v_pxxwall 1.01325 xwall
-fix 1 all controller 10000 0.2 0.5 0 2000 v_avpe -3.785 tcontrol
-
      
-
      
+
      +fix 1 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol
+fix 1 all controller 100 0.2 0.5 0 100.0 v_pxxwall 1.01325 xwall
+fix 1 all controller 10000 0.2 0.5 0 2000 v_avpe -3.785 tcontrol
+
      
 
      
 
      Description
      
@@ -269,14 +269,14 @@ because the value of e_n-1 is not yet defined.
      
 compute or fix or the evaluation of a
 variable.  In each case, the compute, fix, or variable
 must produce a global quantity, not a per-atom or local quantity.
      
-
      If pvar begins with “c_”, a compute ID must follow which has been
+
      If pvar begins with “c_”, a compute ID must follow which has been
 previously defined in the input script and which generates a global
 scalar or vector.  See the individual compute doc page
 for details.  If no bracketed integer is appended, the scalar
 calculated by the compute is used.  If a bracketed integer is
 appended, the Ith value of the vector calculated by the compute is
 used.  Users can also write code for their own compute styles and add them to LAMMPS.
      
-
      If pvar begins with “f_”, a fix ID must follow which has been
+
      If pvar begins with “f_”, a fix ID must follow which has been
 previously defined in the input script and which generates a global
 scalar or vector.  See the individual fix doc page for
 details.  Note that some fixes only produce their values on certain
@@ -285,7 +285,7 @@ references the values, or else an error results.  If no bracketed integer
 is appended, the scalar calculated by the fix is used.  If a bracketed
 integer is appended, the Ith value of the vector calculated by the fix
 is used.  Users can also write code for their own fix style and add them to LAMMPS.
      
-
      If pvar begins with “v_”, a variable name must follow which has been
+
      If pvar begins with “v_”, a variable name must follow which has been
 previously defined in the input script.  Only equal-style variables
 can be referenced.  See the variable command for
 details.  Note that variables of style equal define a formula which
@@ -296,14 +296,12 @@ variable.
      
 
      The target value setpoint for the process variable must be a numeric
 value, in whatever units pvar is defined for.
      
 
      The control variable cvar must be the name of an internal-style variable previously defined in the input script.  Note
-that it is not specified with a “v_” prefix, just the name of the
+that it is not specified with a “v_” prefix, just the name of the
 variable.  It must be an internal-style variable, because this fix
 updates its value directly.  Note that other commands can use an
 equal-style versus internal-style variable interchangeably.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      Currenlty, no information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.
      
 
      This fix produces a global vector with 3 values which can be accessed
diff --git a/doc/html/fix_deform.html b/doc/html/fix_deform.html
index e8ad31ffb0..d23425a85b 100644
--- a/doc/html/fix_deform.html
+++ b/doc/html/fix_deform.html
@@ -272,9 +272,9 @@ e.g. picoseconds for “metal” units).  Tensile strain is unitless and
 is defined as delta/L0, where L0 is the original box length and delta
 is the change relative to the original length.  The box length L as a
 function of time will change as
      
-
      L(t) = L0 (1 + erate*dt)
-
      
-
      
+
      +L(t) = L0 (1 + erate*dt)
+
      
 
      where dt is the elapsed time (in time units).  Thus if erate R is
 specified as 0.1 and time units are picoseconds, this means the box
 length will increase by 10% of its original length every picosecond.
@@ -295,9 +295,9 @@ e.g. picoseconds for “metal” units).  Tensile strain is unitless and
 is defined as delta/L0, where L0 is the original box length and delta
 is the change relative to the original length.
      
 
      The box length L as a function of time will change as
      
-
      L(t) = L0 exp(trate*dt)
-
      
-
      
+
      +L(t) = L0 exp(trate*dt)
+
      
 
      where dt is the elapsed time (in time units).  Thus if trate R is
 specified as ln(1.1) and time units are picoseconds, this means the
 box length will increase by 10% of its current (not original) length
@@ -341,9 +341,9 @@ dimensions, so that they respond to the tensile strain dynamically.
      
 
      The wiggle style oscillates the specified box length dimension
 sinusoidally with the specified amplitude and period.  I.e. the box
 length L as a function of time is given by
      
-
      L(t) = L0 + A sin(2*pi t/Tp)
-
      
-
      
+
      +L(t) = L0 + A sin(2*pi t/Tp)
+
      
 
      where L0 is its initial length.  If the amplitude A is a positive
 number the box initially expands, then contracts, etc.  If A is
 negative then the box initially contracts, then expands, etc.  The
@@ -370,13 +370,13 @@ arbitrary variable.
      
 
      Here is an example of using the variable style to perform the same
 box deformation as the wiggle style formula listed above, where we
 assume that the current timestep = 0.
      
-
      variable A equal 5.0
-variable Tp equal 10.0
-variable displace equal "v_A * sin(2*PI * step*dt/v_Tp)"
-variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)"
-fix 2 all deform 1 x variable v_displace v_rate remap v
-
      
-
      
+
      +variable A equal 5.0
+variable Tp equal 10.0
+variable displace equal "v_A * sin(2*PI * step*dt/v_Tp)"
+variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)"
+fix 2 all deform 1 x variable v_displace v_rate remap v
+
      
 
      For the scale, vel, erate, trate, volume, wiggle, and
 variable styles, the box length is expanded or compressed around its
 mid point.
      
@@ -413,9 +413,9 @@ to the shear direction (e.g. y box length for xy deformation) and
 offset is the displacement distance in the shear direction (e.g. x
 direction for xy deformation) from the unstrained orientation.
      
 
      The tilt factor T as a function of time will change as
      
-
      T(t) = T0 + L0*erate*dt
-
      
-
      
+
      +T(t) = T0 + L0*erate*dt
+
      
 
      where T0 is the initial tilt factor, L0 is the original length of the
 box perpendicular to the shear direction (e.g. y box length for xy
 deformation), and dt is the elapsed time (in time units).  Thus if
@@ -441,9 +441,9 @@ where length is the box length perpendicular to the shear direction
 distance in the shear direction (e.g. x direction for xy deformation)
 from the unstrained orientation.
      
 
      The tilt factor T as a function of time will change as
      
-
      T(t) = T0 exp(trate*dt)
-
      
-
      
+
      +T(t) = T0 exp(trate*dt)
+
      
 
      where T0 is the initial tilt factor and dt is the elapsed time (in
 time units).  Thus if trate R is specified as ln(1.1) and time units
 are picoseconds, this means the shear strain or tilt factor will
@@ -464,9 +464,9 @@ parameter), then this effect on the shear strain is ignored.
      
 
      The wiggle style oscillates the specified tilt factor sinusoidally
 with the specified amplitude and period.  I.e. the tilt factor T as a
 function of time is given by
      
-
      T(t) = T0 + A sin(2*pi t/Tp)
-
      
-
      
+
      +T(t) = T0 + A sin(2*pi t/Tp)
+
      
 
      where T0 is its initial value.  If the amplitude A is a positive
 number the tilt factor initially becomes more positive, then more
 negative, etc.  If A is negative then the tilt factor initially
@@ -492,13 +492,13 @@ arbitrary variable.
      
 
      Here is an example of using the variable style to perform the same
 box deformation as the wiggle style formula listed above, where we
 assume that the current timestep = 0.
      
-
      variable A equal 5.0
-variable Tp equal 10.0
-variable displace equal "v_A * sin(2*PI * step*dt/v_Tp)"
-variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)"
-fix 2 all deform 1 xy variable v_displace v_rate remap v
-
      
-
      
+
      +variable A equal 5.0
+variable Tp equal 10.0
+variable displace equal "v_A * sin(2*PI * step*dt/v_Tp)"
+variable rate equal "2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)"
+fix 2 all deform 1 xy variable v_displace v_rate remap v
+
      
 
      
 
      All of the tilt styles change the xy, xz, yz tilt factors during a
 simulation.  In LAMMPS, tilt factors (xy,xz,yz) for triclinic boxes
@@ -633,9 +633,7 @@ by including their suffix, or you can use the suffix command in your input script.
      
 
      See Section_accelerate of the manual for
 more instructions on how to use the accelerated styles effectively.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various output commands.
      
diff --git a/doc/html/fix_deposit.html b/doc/html/fix_deposit.html
index 6e7e0be54f..566b353255 100644
--- a/doc/html/fix_deposit.html
+++ b/doc/html/fix_deposit.html
@@ -355,9 +355,7 @@ count is changing due to adding particles, you typically should use
 the compute_modify dynamic yes command for the
 temperature compute you are using.
      
 
      
-
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      This fix writes the state of the deposition to binary restart files.  This includes information about how many
 particles have been depositied, the random number generator seed, the
 next timestep for deposition, etc.  See the
diff --git a/doc/html/fix_drag.html b/doc/html/fix_drag.html
index c464c735a2..5864fe2ce5 100644
--- a/doc/html/fix_drag.html
+++ b/doc/html/fix_drag.html
@@ -156,9 +156,7 @@ include that dimension in the distance calculation or force
 application.
      
 
      This command can be used to steer one or more atoms to a new location
 in the simulation.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.
      
 
      The fix_modify respa option is supported by this
 fix. This allows to set at which level of the r-RESPA
diff --git a/doc/html/fix_drude_transform.html b/doc/html/fix_drude_transform.html
index 7134e2dbf5..6a078677dc 100644
--- a/doc/html/fix_drude_transform.html
+++ b/doc/html/fix_drude_transform.html
@@ -219,14 +219,14 @@ Nose-Hoover thermostating fixes.  The fix drude/transform/inverse
 command must appear after any Nose-Hoover thermostating fixes.
      
 
      Example:
      
-
      fix fDIRECT all drude/transform/direct
-fix fNVT gCORES nvt temp 300.0 300.0 100
-fix fNVT gDRUDES nvt temp 1.0 1.0 100
-fix fINVERSE all drude/transform/inverse
-compute TDRUDE all temp/drude
-thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE[1] c_TDRUDE[2]
-
      
-
      
+
      +fix fDIRECT all drude/transform/direct
+fix fNVT gCORES nvt temp 300.0 300.0 100
+fix fNVT gDRUDES nvt temp 1.0 1.0 100
+fix fINVERSE all drude/transform/inverse
+compute TDRUDE all temp/drude
+thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE[1] c_TDRUDE[2]
+
      In this example, gCORES is the group of the atom cores and gDRUDES
 is the group of the Drude particles (electrons). The centers of mass
 of the Drude oscillators will be thermostated at 300.0 and the
@@ -240,14 +240,14 @@ the other one should be nvt. You must add a compute temp/com a
 that of its group (the Drude cores) but the pressure be the overall
 pressure thermo_press.
      Example:
      
-
      compute cTEMP_CORE gCORES temp/com
-fix fDIRECT all drude/transform/direct
-fix fNPT gCORES npt temp 298.0 298.0 100 iso 1.0 1.0 500
-fix_modify fNPT temp cTEMP_CORE press thermo_press
-fix fNVT gDRUDES nvt temp 5.0 5.0 100
-fix fINVERSE all drude/transform/inverse
-
      
-
      
+
      +compute cTEMP_CORE gCORES temp/com
+fix fDIRECT all drude/transform/direct
+fix fNPT gCORES npt temp 298.0 298.0 100 iso 1.0 1.0 500
+fix_modify fNPT temp cTEMP_CORE press thermo_press
+fix fNVT gDRUDES nvt temp 5.0 5.0 100
+fix fINVERSE all drude/transform/inverse
+
      In this example, gCORES is the group of the atom cores and gDRUDES
 is the group of the Drude particles. The centers of mass of the Drude
 oscillators will be thermostated at 298.0 and the internal degrees of
@@ -259,10 +259,8 @@ to add a fix momentum command:
      fix fMOMENTUM all momentum 100 linear 1 1 1
 
      
 
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.
      
 
      
diff --git a/doc/html/fix_efield.html b/doc/html/fix_efield.html
index c724217123..6ddd5f9067 100644
--- a/doc/html/fix_efield.html
+++ b/doc/html/fix_efield.html
@@ -148,10 +148,10 @@
 
      
 
      Examples
      
-
      fix kick external-field efield 1.0 0.0 0.0
-fix kick external-field efield 0.0 0.0 v_oscillate
-
      
-
      
+
      +fix kick external-field efield 1.0 0.0 0.0
+fix kick external-field efield 0.0 0.0 v_oscillate
+
      
 
      
 
      Description
      
@@ -218,10 +218,8 @@ variable formulas, i.e. that -Grad(E) = F.  For example, if the force
 due to the electric field were a spring-like F = kx, then the energy
 formula should be E = -0.5kx^2.  If you don’t do this correctly, the
 minimization will not converge properly.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.
      
 
      The fix_modify energy option is supported by this
 fix to add the potential “energy” inferred by the added force due to
diff --git a/doc/html/fix_ehex.html b/doc/html/fix_ehex.html
index f1cc66f404..a753adb554 100644
--- a/doc/html/fix_ehex.html
+++ b/doc/html/fix_ehex.html
@@ -262,10 +262,8 @@ be on the order of \(10^{-7}\) for relatively large
 temperature gradients.  A higher precision can be achieved by
 decreasing the timestep.
      
 
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.
      
 
      No parameter of this fix can be used with the start/stop keywords of
diff --git a/doc/html/fix_external.html b/doc/html/fix_external.html
index d2a176da50..264a4cf9ba 100644
--- a/doc/html/fix_external.html
+++ b/doc/html/fix_external.html
@@ -167,9 +167,9 @@ in the group, once every Napply steps, similar to the way the Napply, the force values produced by one callback will persist, and
 be used multiple times to update atom forces.
      
 
      The callback function “foo” is invoked by the fix as:
      
-
      foo(void *ptr, bigint timestep, int nlocal, int *ids, double **x, double **fexternal);
-
      
-
      
+
      +foo(void *ptr, bigint timestep, int nlocal, int *ids, double **x, double **fexternal);
+
      
 
      The arguments are as follows:
      
 
        
 
      • ptr = pointer provided by and simply passed back to external driver
        • 
@@ -194,9 +194,9 @@ array.  The fix adds these forces to each atom in the group, once
 every Napply steps, similar to the way the         fix addforce command works.
        
 
        The name of the public force array provided by the FixExternal
 class is
        
-
        double **fexternal;
-
        
-
        
+
        +double **fexternal;
+
        
 
        It is allocated by the FixExternal class as an (N,3) array where N is
 the number of atoms owned by a processor.  The 3 corresponds to the
 fx, fy, fz components of force.
        
@@ -212,18 +212,16 @@ to the added forces must also be set so as to be consistent with the
 added forces.  Otherwise the minimization will not converge correctly.
        
 
        This can be done from the external driver by calling this public
 method of the FixExternal class:
        
-
        void set_energy(double eng);
-
        
-
        
+
        +void set_energy(double eng);
+
        
 
        where eng is the potential energy.  Eng is an extensive quantity,
 meaning it should be the sum over per-atom energies of all affected
 atoms.  It should also be provided in energy units
 consistent with the simulation.  See the details below for how to
 insure this energy setting is used appropriately in a minimization.
        
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.
      
 
      The fix_modify energy option is supported by this
 fix to add the potential “energy” set by the external driver to the
diff --git a/doc/html/fix_gcmc.html b/doc/html/fix_gcmc.html
index 02f1da98e6..2210a5c5c4 100644
--- a/doc/html/fix_gcmc.html
+++ b/doc/html/fix_gcmc.html
@@ -168,11 +168,11 @@ keyword = mol, region, maxangle, pressure, <
 
      
 
      Examples
      
-
      fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
-fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
-fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
-
      
-
      
+
      +fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
+fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
+fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
+
      
 
      
 
      Description
      
@@ -239,12 +239,12 @@ used in fix nvt. Otherwise, the imaginary reservoir
 will not be in thermal equilibrium with the simulation cell. Also,
 it is important that the temperature used by fix nvt be dynamic,
 which can be achieved as follows:
      
-
      compute mdtemp mdatoms temp
-compute_modify mdtemp dynamic yes
-fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
-fix_modify mdnvt temp mdtemp
-
      
-
      
+
      +compute mdtemp mdatoms temp
+compute_modify mdtemp dynamic yes
+fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
+fix_modify mdnvt temp mdtemp
+
      
 
      Note that neighbor lists are re-built every timestep that this fix is
 invoked, so you should not set N to be too small.  However, periodic
 rebuilds are necessary in order to avoid dangerous rebuilds and missed
@@ -363,9 +363,9 @@ therefore, you will want to use the
 compute_modify command to insure that the
 current number of atoms is used as a normalizing factor each time
 temperature is computed.  Here is the necessary command:
      
-
      compute_modify thermo_temp dynamic yes
-
      
-
      
+
      +compute_modify thermo_temp dynamic yes
+
      
 
      If LJ units are used, note that a value of 0.18292026 is used by this
 fix as the reduced value for Planck’s constant.  This value was
 derived from LJ parameters for argon, where h* = h/sqrt(sigma^2 *
@@ -375,9 +375,7 @@ mass = 39.948 amu.
      
 of the group-ID value. The grouptype keyword assigns all
 inserted atoms of the specified type to the group
 of the group-ID value.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      This fix writes the state of the fix to binary restart files.  This includes information about the random
 number generator seed, the next timestep for MC exchanges, etc.  See
 the read_restart command for info on how to
diff --git a/doc/html/fix_gld.html b/doc/html/fix_gld.html
index aba80b6a9d..96beaab03f 100644
--- a/doc/html/fix_gld.html
+++ b/doc/html/fix_gld.html
@@ -128,9 +128,9 @@
 
      fix gld command
      
 
      
 
      Syntax
      
-
      fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k keyword values ...
-
      
-
      
+
      +fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k keyword values ...
+
      
 
        
 
      • ID, group-ID are documented in fix command
        • 
 
      • gld = style name of this fix command
        • 
diff --git a/doc/html/fix_gle.html b/doc/html/fix_gle.html
index 9f9296aea3..e51ed41bf3 100644
--- a/doc/html/fix_gle.html
+++ b/doc/html/fix_gle.html
@@ -145,7 +145,7 @@
 
        noneq Cmatrix  = file to read the non-equilibrium covariance matrix from
 every stride   = apply the GLE once every time steps. Reduces the accuracy
        
 
        
-
        of the integration of the GLE, but has no effect on the accuracy of equilibrium
+
        of the integration of the GLE, but has *no effect* on the accuracy of equilibrium
 sampling. It might change sampling properties when used together with noneq.
        
 
        
 
@@ -207,9 +207,7 @@ Prony series form of the memory kernel used by GLD into an appropriate
 input matrix for fix gle. While the GLE scheme is more
 general, the form used by fix gld can be more directly
 related to the representation of an implicit solvent environment.
        
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      The instantaneous values of the extended variables are written to
 binary restart files.  Because the state of the random
 number generator is not saved in restart files, this means you cannot
diff --git a/doc/html/fix_gravity.html b/doc/html/fix_gravity.html
index e770f8e7fe..f10e0f3416 100644
--- a/doc/html/fix_gravity.html
+++ b/doc/html/fix_gravity.html
@@ -156,13 +156,13 @@
 
      
 
      
 
      Examples
      
-
      fix 1 all gravity 1.0 chute 24.0
-fix 1 all gravity v_increase chute 24.0
-fix 1 all gravity 1.0 spherical 0.0 -180.0
-fix 1 all gravity 10.0 spherical v_phi v_theta
-fix 1 all gravity 100.0 vector 1 1 0
-
      
-
      
+
      +fix 1 all gravity 1.0 chute 24.0
+fix 1 all gravity v_increase chute 24.0
+fix 1 all gravity 1.0 spherical 0.0 -180.0
+fix 1 all gravity 10.0 spherical v_phi v_theta
+fix 1 all gravity 100.0 vector 1 1 0
+
      
 
      
 
      
 
      Description
      
@@ -220,10 +220,8 @@ by including their suffix, or you can use the suffix command in your input script.
      
 
      See Section_accelerate of the manual for
 more instructions on how to use the accelerated styles effectively.
      
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.
      
 
      The fix_modify energy option is supported by this
 fix to add the gravitational potential energy of the system to the
diff --git a/doc/html/fix_heat.html b/doc/html/fix_heat.html
index fb5b0f55e7..2e88845d31 100644
--- a/doc/html/fix_heat.html
+++ b/doc/html/fix_heat.html
@@ -147,11 +147,11 @@
 
      
 
      
 
      Examples
      
-
      fix 3 qin heat 1 1.0
-fix 3 qin heat 10 v_flux
-fix 4 qout heat 1 -1.0 region top
-
      
-
      
+
      +fix 3 qin heat 1 1.0
+fix 3 qin heat 10 v_flux
+fix 4 qout heat 1 -1.0 region top
+
      
 
      
 
      
 
      Description
      
@@ -219,9 +219,7 @@ their velocities.  Thus you must still use an integration fix
 (e.g. fix nve) on the affected atoms.  This fix should
 not normally be used on atoms that have their temperature controlled
 by another fix - e.g. fix nvt or fix langevin fix.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.
      
 
      This fix computes a global scalar which can be accessed by various
diff --git a/doc/html/fix_imd.html b/doc/html/fix_imd.html
index 5c92083e88..3245c8523d 100644
--- a/doc/html/fix_imd.html
+++ b/doc/html/fix_imd.html
@@ -237,9 +237,7 @@ they were real objects. See the 
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global scalar or vector or per-atom
 quantities are stored by this fix for access by various output commands.  No parameter of this fix can
diff --git a/doc/html/fix_ipi.html b/doc/html/fix_ipi.html
index 615515d668..40917601b7 100644
--- a/doc/html/fix_ipi.html
+++ b/doc/html/fix_ipi.html
@@ -173,9 +173,7 @@ configurations make sense. It is assumed that the species in the i-PI
 input are listed in the same order as in the data file of LAMMPS. The
 initial configuration is ignored, as it will be substituted with the
 coordinates received from i-PI before forces are ever evaluated.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      There is no restart information associated with this fix, since all
 the dynamical parameters are dealt with by i-PI.
      
 
      
diff --git a/doc/html/fix_langevin.html b/doc/html/fix_langevin.html
index 40cfbcd9cc..bf67a0e983 100644
--- a/doc/html/fix_langevin.html
+++ b/doc/html/fix_langevin.html
@@ -375,10 +375,8 @@ by including their suffix, or you can use the suffix command in your input script.
      
 
      See Section_accelerate of the manual for
 more instructions on how to use the accelerated styles effectively.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  Because the state of the random number generator
 is not saved in restart files, this means you cannot do “exact”
 restarts with this fix, where the simulation continues on the same as
diff --git a/doc/html/fix_langevin_drude.html b/doc/html/fix_langevin_drude.html
index f01d0bd451..ea9f9510a0 100644
--- a/doc/html/fix_langevin_drude.html
+++ b/doc/html/fix_langevin_drude.html
@@ -128,9 +128,9 @@
 
      fix langevin/drude command
      
 
      
 
      Syntax
      
-
      fix ID group-ID langevin/drude Tcom damp_com seed_com Tdrude damp_drude seed_drude keyword values ...
-
      
-
      
+
      +fix ID group-ID langevin/drude Tcom damp_com seed_com Tdrude damp_drude seed_drude keyword values ...
+
      
 
        
 
      • ID, group-ID are documented in fix command
        • 
 
      • langevin/drude = style name of this fix command
        • 
@@ -236,9 +236,9 @@ partner (electron).
        
 correctly.  You must use the comm_modify command to
 enable this, e.g.
        
 
      
-
      comm_modify vel yes
-
      
-
      
+
      +comm_modify vel yes
+
      
 
      
 
      Tcom is the target temperature of the centers of mass, which would
 be used to thermostate the non-polarizable atoms.  Tdrude is the
@@ -299,14 +299,14 @@ calculated using the 
 
      Usage example for rigid bodies in the NPT ensemble:
      
-
      comm_modify vel yes
-fix TEMP all langevin/drude 300. 100. 1256 1. 20. 13977 zero yes
-fix NPH ATOMS rigid/nph/small molecule iso 1. 1. 500.
-fix NVE DRUDES nve
-compute TDRUDE all temp/drude
-thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE[1] c_TDRUDE[2]
-
      
-
      
+
      +comm_modify vel yes
+fix TEMP all langevin/drude 300. 100. 1256 1. 20. 13977 zero yes
+fix NPH ATOMS rigid/nph/small molecule iso 1. 1. 500.
+fix NVE DRUDES nve
+compute TDRUDE all temp/drude
+thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE[1] c_TDRUDE[2]
+
      
 
      Comments:
      
 
        
 
      • Drude particles should not be in the rigid group, otherwise the Drude
@@ -332,10 +332,8 @@ should be the global one, but the temperature should be only that of
 the cores. That’s why the command fix_modify should be called in
 that case.
        • 
 
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  Because the state of the random number generator
 is not saved in restart files, this means you cannot do “exact”
 restarts with this fix, where the simulation continues on the same as
diff --git a/doc/html/fix_langevin_eff.html b/doc/html/fix_langevin_eff.html
index 506e61e35c..dea014ff7b 100644
--- a/doc/html/fix_langevin_eff.html
+++ b/doc/html/fix_langevin_eff.html
@@ -178,9 +178,7 @@ interactions ( command, except that the thermostatting
 is also applied to the radial electron velocity for electron
 particles.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  Because the state of the random number generator
 is not saved in restart files, this means you cannot do “exact”
 restarts with this fix, where the simulation continues on the same as
diff --git a/doc/html/fix_lb_fluid.html b/doc/html/fix_lb_fluid.html
index 51eefacda2..fadee5ceb3 100644
--- a/doc/html/fix_lb_fluid.html
+++ b/doc/html/fix_lb_fluid.html
@@ -374,10 +374,8 @@ screen every N timesteps.
      
 test runs, see Mackay et al..  Please include a citation to
 this paper if the lb_fluid fix is used in work contributing to
 published research.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      Due to the large size of the fluid data, this fix writes it’s own
 binary restart files, if requested, independent of the main LAMMPS
 binary restart files; no information about lb_fluid
diff --git a/doc/html/fix_lb_momentum.html b/doc/html/fix_lb_momentum.html
index aefe19517d..5ca4e990b6 100644
--- a/doc/html/fix_lb_momentum.html
+++ b/doc/html/fix_lb_momentum.html
@@ -167,9 +167,7 @@ and the fluid velocities at each lattice site.
      
 be changed by specifying the keyword linear, along with a set of
 three flags set to 0/1 in order to exclude/ include the corresponding
 dimension.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various output commands.  No parameter of this fix can be
diff --git a/doc/html/fix_lb_pc.html b/doc/html/fix_lb_pc.html
index 4fe4f72ced..8d27f6cd24 100644
--- a/doc/html/fix_lb_pc.html
+++ b/doc/html/fix_lb_pc.html
@@ -146,12 +146,10 @@
 
      Description
      
 
      Update the positions and velocities of the individual particles
 described by group-ID, experiencing velocity-dependent hydrodynamic
-forces, using the integration algorithm described in Mackay et al..  This integration algorithm should only be used if a
+forces, using the integration algorithm described in Mackay et al..  This integration algorithm should only be used if a
 user-specified value for the force-coupling constant used in fix lb/fluid has been set; do not use this integration
 algorithm if the force coupling constant has been set by default.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various output commands.  No parameter of this fix can be
diff --git a/doc/html/fix_lb_rigid_pc_sphere.html b/doc/html/fix_lb_rigid_pc_sphere.html
index ca3adc0748..8bda0b4a82 100644
--- a/doc/html/fix_lb_rigid_pc_sphere.html
+++ b/doc/html/fix_lb_rigid_pc_sphere.html
@@ -202,9 +202,7 @@ central atoms interact with one another.
      
 the rigid fix (although it includes fewer optional arguments, and
 assumes the constituent atoms are point particles); see
 fix rigid for a complete documentation.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about the rigid and rigid/nve fixes are written to
 binary restart files.
      
 
      Similar to the fix rigid command: The rigid
diff --git a/doc/html/fix_lb_viscous.html b/doc/html/fix_lb_viscous.html
index efc00565c9..876c9eb1f0 100644
--- a/doc/html/fix_lb_viscous.html
+++ b/doc/html/fix_lb_viscous.html
@@ -164,10 +164,8 @@ hydrodynamic forces to the particles.
      
 test runs, see Mackay et al..  Please include a citation to
 this paper if this fix is used in work contributing to published
 research.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      As described in the fix viscous documentation:
      
 
      “No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global or per-atom quantities are stored
diff --git a/doc/html/fix_lineforce.html b/doc/html/fix_lineforce.html
index 5ca8460a42..2734d0ff4e 100644
--- a/doc/html/fix_lineforce.html
+++ b/doc/html/fix_lineforce.html
@@ -151,9 +151,7 @@ remains.  This is done by subtracting out components of force in the
 plane perpendicular to the line.
      
 
      If the initial velocity of the atom is 0.0 (or along the line), then
 it should continue to move along the line thereafter.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various output commands.  No parameter of this fix can
diff --git a/doc/html/fix_move.html b/doc/html/fix_move.html
index 66cf61d80e..ad7177b2bd 100644
--- a/doc/html/fix_move.html
+++ b/doc/html/fix_move.html
@@ -160,11 +160,11 @@
 
      
 
      Examples
      
-
      fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box
-fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
-fix 2 boundary move variable v_myx v_myy NULL v_VX v_VY NULL
-
      
-
      
+
      +fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box
+fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
+fix 2 boundary move variable v_myx v_myy NULL v_VX v_VY NULL
+
      
 
      
 
      Description
      
@@ -202,9 +202,9 @@ command.
      
 
      The linear style moves atoms at a constant velocity, so that their
 position X = (x,y,z) as a function of time is given in vector
 notation as
      
-
      X(t) = X0 + V * delta
-
      
-
      
+
      +X(t) = X0 + V * delta
+
      
 
      where X0 = (x0,y0,z0) is their position at the time the fix is
 specified, V is the specified velocity vector with components
 (Vx,Vy,Vz), and delta is the time elapsed since the fix was
@@ -216,17 +216,17 @@ the corresponding force component on the atom.
      
 
      Note that the linear style is identical to using the variable
 style with an equal-style variable that uses the
 vdisplace() function.  E.g.
      
-
      variable V equal 10.0
+
      +variable V equal 10.0
 variable x equal vdisplace(0.0,$V)
 fix 1 boundary move variable v_x NULL NULL v_V NULL NULL
-
      
-
      
+
 
      The wiggle style moves atoms in an oscillatory fashion, so that
 their position X = (x,y,z) as a function of time is given in vector
 notation as
      
-
      X(t) = X0 + A sin(omega*delta)
-
      
-
      
+
      +X(t) = X0 + A sin(omega*delta)
+
      
 
      where X0 = (x0,y0,z0) is their position at the time the fix is
 specified, A is the specified amplitude vector with components
 (Ax,Ay,Az), omega is 2 PI / period, and delta is the time
@@ -239,14 +239,14 @@ corresponding force component on the atom.
      
 
      Note that the wiggle style is identical to using the variable
 style with equal-style variables that use the
 swiggle() and cwiggle() functions.  E.g.
      
-
      variable A equal 10.0
+
      +variable A equal 10.0
 variable T equal 5.0
 variable omega equal 2.0*PI/$T
 variable x equal swiggle(0.0,$A,$T)
 variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
 fix 1 boundary move variable v_x NULL NULL v_v NULL NULL
-
      
-
      
+
 
      The rotate style rotates atoms around a rotation axis R =
 (Rx,Ry,Rz) that goes thru a point P = (Px,Py,Pz).  The period of
 the rotation is also specified.  The direction of rotation for the
@@ -302,10 +302,8 @@ are in lattice spacings.  The 
 been previously used to define the lattice spacing.  Each of these 3
 quantities may be dependent on the x,y,z dimension, since the lattice
 spacings can be different in x,y,z.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      This fix writes the original coordinates of moving atoms to binary restart files, as well as the initial timestep, so that
 the motion can be continuous in a restarted simulation.  See the
 read_restart command for info on how to re-specify
diff --git a/doc/html/fix_msst.html b/doc/html/fix_msst.html
index f5a8d09ba8..c54106e01e 100644
--- a/doc/html/fix_msst.html
+++ b/doc/html/fix_msst.html
@@ -197,16 +197,14 @@ LAMMPS, but are not implemented for MSST.
      
 
      This fix computes a temperature and pressure each timestep. To do
 this, the fix creates its own computes of style “temp” and “pressure”,
 as if these commands had been issued:
      
-
      compute fix-ID_temp group-ID temp
-compute fix-ID_press group-ID pressure fix-ID_temp
-
      
-
      
+
      +compute fix-ID_temp group-ID temp
+compute fix-ID_press group-ID pressure fix-ID_temp
+
      
 
      See the compute temp and compute pressure commands for details.  Note that the
 IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
 + underscore + “press”.  The group for the new computes is “all”.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      This fix writes the state of all internal variables to binary restart files.  See the read_restart command
 for info on how to re-specify a fix in an input script that reads a
 restart file, so that the operation of the fix continues in an
@@ -230,15 +228,15 @@ equations. See also 
 
      To print these quantities to the log file with descriptive column
 headers, the following LAMMPS commands are suggested:
      
-
      fix           msst all msst z
-fix_modify       msst energy yes
-variable dhug    equal f_msst[1]
-variable dray    equal f_msst[2]
-variable lgr_vel equal f_msst[3]
-variable lgr_pos equal f_msst[4]
-thermo_style     custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
-
      
-
      
+
      +fix           msst all msst z
+fix_modify       msst energy yes
+variable dhug    equal f_msst[1]
+variable dray    equal f_msst[2]
+variable lgr_vel equal f_msst[3]
+variable lgr_pos equal f_msst[4]
+thermo_style     custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
+
      
 
      These fixes compute a global scalar and a global vector of 4
 quantities, which can be accessed by various output commands.  The scalar values calculated
 by this fix are “extensive”; the vector values are “intensive”.
      
diff --git a/doc/html/fix_neb.html b/doc/html/fix_neb.html
index 4b5777e1e2..1e50f393e0 100644
--- a/doc/html/fix_neb.html
+++ b/doc/html/fix_neb.html
@@ -190,9 +190,7 @@ forces on atoms in this replica are described in the
 
      The inter-replica forces for the other replicas are unchanged from the
 first equation.
      
-
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various output commands.  No parameter of this fix can
diff --git a/doc/html/fix_nh.html b/doc/html/fix_nh.html
index ff55e4e302..8cbee0b46f 100644
--- a/doc/html/fix_nh.html
+++ b/doc/html/fix_nh.html
@@ -158,9 +158,9 @@
 
      fix nph/omp command
      
 
      
 
      Syntax
      
-
      fix ID group-ID style_name keyword value ...
-
      
-
      
+
      +fix ID group-ID style_name keyword value ...
+
      
 
        
 
      • ID, group-ID are documented in fix command
        • 
 
      • style_name = nvt or npt or nph
        • 
@@ -508,14 +508,14 @@ thermostatting and barostatting.
        
 
        These fixes compute a temperature and pressure each timestep.  To do
 this, the fix creates its own computes of style “temp” and “pressure”,
 as if one of these two sets of commands had been issued:
        
-
        compute fix-ID_temp group-ID temp
-compute fix-ID_press group-ID pressure fix-ID_temp
-
        
-
        
-
        compute fix-ID_temp all temp
-compute fix-ID_press all pressure fix-ID_temp
-
        
-
        
+
        +compute fix-ID_temp group-ID temp
+compute fix-ID_press group-ID pressure fix-ID_temp
+
        
+
        +compute fix-ID_temp all temp
+compute fix-ID_press all pressure fix-ID_temp
+
        
 
        See the compute temp and compute pressure commands for details.  Note that the
 IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
 + underscore + “press”.  For fix nvt, the group for the new computes
@@ -606,10 +606,8 @@ by including their suffix, or you can use the suffix command in your input script.
        
 
        See Section_accelerate of the manual for
 more instructions on how to use the accelerated styles effectively.
        
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      These fixes writes the state of all the thermostat and barostat
 variables to binary restart files.  See the
 read_restart command for info on how to re-specify
diff --git a/doc/html/fix_nh_eff.html b/doc/html/fix_nh_eff.html
index 5e8d66853c..d11bbb105e 100644
--- a/doc/html/fix_nh_eff.html
+++ b/doc/html/fix_nh_eff.html
@@ -134,9 +134,9 @@
 
      fix nph/eff command
      
 
      
 
      Syntax
      
-
      fix ID group-ID style_name keyword value ...
-
      
-
      
+
      +fix ID group-ID style_name keyword value ...
+
      
 
      
-
      
-
diff --git a/doc/html/fix_nph_asphere.html b/doc/html/fix_nph_asphere.html
index d7c91846db..2c2d1a4d0a 100644
--- a/doc/html/fix_nph_asphere.html
+++ b/doc/html/fix_nph_asphere.html
@@ -175,10 +175,10 @@ unchanged and controlling the pressure of a surrounding fluid.
      
 
      This fix computes a temperature and pressure each timestep.  To do
 this, the fix creates its own computes of style “temp/asphere” and
 “pressure”, as if these commands had been issued:
      
-
      compute fix-ID_temp all temp/asphere
-compute fix-ID_press all pressure fix-ID_temp
-
      
-
      
+
      +compute fix-ID_temp all temp/asphere
+compute fix-ID_press all pressure fix-ID_temp
+
      
 
      See the compute temp/asphere and compute pressure commands for details.  Note that the
 IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
 + underscore + “press”, and the group for the new computes is “all”
@@ -207,9 +207,7 @@ by including their suffix, or you can use the suffix command in your input script.
      
 
      See Section_accelerate of the manual for
 more instructions on how to use the accelerated styles effectively.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      This fix writes the state of the Nose/Hoover barostat to binary restart files.  See the read_restart
 command for info on how to re-specify a fix in an input script that
 reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_nph_sphere.html b/doc/html/fix_nph_sphere.html
index 0529dba9db..ec7a15a0cd 100644
--- a/doc/html/fix_nph_sphere.html
+++ b/doc/html/fix_nph_sphere.html
@@ -175,10 +175,10 @@ unchanged and controlling the pressure of a surrounding fluid.
      
 
      This fix computes a temperature and pressure each timestep.  To do
 this, the fix creates its own computes of style “temp/sphere” and
 “pressure”, as if these commands had been issued:
      
-
      compute fix-ID_temp all temp/sphere
-compute fix-ID_press all pressure fix-ID_temp
-
      
-
      
+
      +compute fix-ID_temp all temp/sphere
+compute fix-ID_press all pressure fix-ID_temp
+
      
 
      See the compute temp/sphere and compute pressure commands for details.  Note that the
 IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
 + underscore + “press”, and the group for the new computes is “all”
@@ -207,9 +207,7 @@ by including their suffix, or you can use the suffix command in your input script.
      
 
      See Section_accelerate of the manual for
 more instructions on how to use the accelerated styles effectively.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      This fix writes the state of the Nose/Hoover barostat to binary restart files.  See the read_restart
 command for info on how to re-specify a fix in an input script that
 reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_nphug.html b/doc/html/fix_nphug.html
index da32f6307b..85dd234fe3 100644
--- a/doc/html/fix_nphug.html
+++ b/doc/html/fix_nphug.html
@@ -229,14 +229,14 @@ controlled by another fix - e.g. by 
      compute fix-ID_temp group-ID temp
-compute fix-ID_press group-ID pressure fix-ID_temp
-
      
-
      
-
      compute fix-ID_temp all temp
-compute fix-ID_press all pressure fix-ID_temp
-
      
-
      
+
      +compute fix-ID_temp group-ID temp
+compute fix-ID_press group-ID pressure fix-ID_temp
+
      
+
      +compute fix-ID_temp all temp
+compute fix-ID_press all pressure fix-ID_temp
+
      
 
      See the compute temp and compute pressure commands for details.  Note that the
 IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
 + underscore + “press”.  The group for
@@ -266,10 +266,8 @@ by including their suffix, or you can use the suffix command in your input script.
      See Section_accelerate of the manual for
 more instructions on how to use the accelerated styles effectively.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      This fix writes the values of E0, V0, and P0, as well as the
 state of all the thermostat and barostat
 variables to binary restart files.  See the
@@ -293,7 +291,7 @@ compute temperature on a subset of atoms.
      
 
      The fix_modify energy option is supported by these
 fixes to add the energy change induced by Nose/Hoover thermostatting
 and barostatting to the system’s potential energy as part of
-thermodynamic output. Either way, this energy is not
+thermodynamic output. Either way, this energy is *not*
 included in the definition of internal energy E when calculating the value
 of Delta in the above equation.
      
 
      These fixes compute a global scalar and a global vector of quantities,
diff --git a/doc/html/fix_npt_asphere.html b/doc/html/fix_npt_asphere.html
index 203bb248e0..2216a34678 100644
--- a/doc/html/fix_npt_asphere.html
+++ b/doc/html/fix_npt_asphere.html
@@ -182,10 +182,10 @@ unchanged and controlling the pressure of a surrounding fluid.
      
 
      This fix computes a temperature and pressure each timestep.  To do
 this, the fix creates its own computes of style “temp/asphere” and
 “pressure”, as if these commands had been issued:
      
-
      compute fix-ID_temp all temp/asphere
-compute fix-ID_press all pressure fix-ID_temp
-
      
-
      
+
      +compute fix-ID_temp all temp/asphere
+compute fix-ID_press all pressure fix-ID_temp
+
      
 
      See the compute temp/asphere and compute pressure commands for details.  Note that the
 IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
 + underscore + “press”, and the group for the new computes is “all”
@@ -227,9 +227,7 @@ by including their suffix, or you can use the suffix command in your input script.
      
 
      See Section_accelerate of the manual for
 more instructions on how to use the accelerated styles effectively.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      This fix writes the state of the Nose/Hoover thermostat and barostat
 to binary restart files.  See the
 read_restart command for info on how to re-specify
diff --git a/doc/html/fix_npt_body.html b/doc/html/fix_npt_body.html
index 7a21169513..b037898463 100644
--- a/doc/html/fix_npt_body.html
+++ b/doc/html/fix_npt_body.html
@@ -179,10 +179,10 @@ unchanged and controlling the pressure of a surrounding fluid.
      
 
      This fix computes a temperature and pressure each timestep.  To do
 this, the fix creates its own computes of style “temp/body” and
 “pressure”, as if these commands had been issued:
      
-
      compute fix-ID_temp all temp/body
-compute fix-ID_press all pressure fix-ID_temp
-
      
-
      
+
      +compute fix-ID_temp all temp/body
+compute fix-ID_press all pressure fix-ID_temp
+
      
 
      See the compute temp/body and compute pressure commands for details.  Note that the
 IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
 + underscore + “press”, and the group for the new computes is “all”
@@ -224,9 +224,7 @@ by including their suffix, or you can use the suffix command in your input script.
      
 
      See Section_accelerate of the manual for
 more instructions on how to use the accelerated styles effectively.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      This fix writes the state of the Nose/Hoover thermostat and barostat
 to binary restart files.  See the
 read_restart command for info on how to re-specify
diff --git a/doc/html/fix_npt_sphere.html b/doc/html/fix_npt_sphere.html
index 1d5d6ed867..f05e786221 100644
--- a/doc/html/fix_npt_sphere.html
+++ b/doc/html/fix_npt_sphere.html
@@ -181,10 +181,10 @@ unchanged and controlling the pressure of a surrounding fluid.
      
 
      This fix computes a temperature and pressure each timestep.  To do
 this, the fix creates its own computes of style “temp/sphere” and
 “pressure”, as if these commands had been issued:
      
-
      compute fix-ID_temp all temp/sphere
-compute fix-ID_press all pressure fix-ID_temp
-
      
-
      
+
      +compute fix-ID_temp all temp/sphere
+compute fix-ID_press all pressure fix-ID_temp
+
      
 
      See the compute temp/sphere and compute pressure commands for details.  Note that the
 IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
 + underscore + “press”, and the group for the new computes is “all”
@@ -226,9 +226,7 @@ by including their suffix, or you can use the suffix command in your input script.
      
 
      See Section_accelerate of the manual for
 more instructions on how to use the accelerated styles effectively.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      This fix writes the state of the Nose/Hoover thermostat and barostat
 to binary restart files.  See the
 read_restart command for info on how to re-specify
diff --git a/doc/html/fix_nve_asphere.html b/doc/html/fix_nve_asphere.html
index 435fea89b4..88dbabd521 100644
--- a/doc/html/fix_nve_asphere.html
+++ b/doc/html/fix_nve_asphere.html
@@ -153,9 +153,7 @@ group each timestep.  V is volume; E is energy.  This creates a system
 trajectory consistent with the microcanonical ensemble.
      
 
      This fix differs from the fix nve command, which
 assumes point particles and only updates their position and velocity.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various output commands.  No parameter of this fix can
diff --git a/doc/html/fix_nve_asphere_noforce.html b/doc/html/fix_nve_asphere_noforce.html
index 75760b0c6a..dd98e2ce40 100644
--- a/doc/html/fix_nve_asphere_noforce.html
+++ b/doc/html/fix_nve_asphere_noforce.html
@@ -150,10 +150,8 @@ angularm momenta are used to update their positions and orientation.
      
 
      This is useful as an implicit time integrator for Fast Lubrication
 Dynamics, since the velocity and angular momentum are updated by the
 pair_style lubricuteU command.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various output commands.  No parameter of this fix can
diff --git a/doc/html/fix_nve_body.html b/doc/html/fix_nve_body.html
index cd459a4379..45816df757 100644
--- a/doc/html/fix_nve_body.html
+++ b/doc/html/fix_nve_body.html
@@ -151,9 +151,7 @@ consistent with the microcanonical ensemble.  See 
 
      This fix differs from the fix nve command, which
 assumes point particles and only updates their position and velocity.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various output commands.  No parameter of this fix can
diff --git a/doc/html/fix_nve_line.html b/doc/html/fix_nve_line.html
index 5168b08db0..5b6a9bb8ab 100644
--- a/doc/html/fix_nve_line.html
+++ b/doc/html/fix_nve_line.html
@@ -152,9 +152,7 @@ trajectory consistent with the microcanonical ensemble.  See
 using line segment particles.
      
 
      This fix differs from the fix nve command, which
 assumes point particles and only updates their position and velocity.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various output commands.  No parameter of this fix can
diff --git a/doc/html/fix_nve_manifold_rattle.html b/doc/html/fix_nve_manifold_rattle.html
index 06d68cd6ae..149e6de046 100644
--- a/doc/html/fix_nve_manifold_rattle.html
+++ b/doc/html/fix_nve_manifold_rattle.html
@@ -159,7 +159,7 @@ keyword = every
 atoms constrained to a curved surface (manifold) in the group each
 timestep. The constraint is handled by RATTLE (Andersen)
 written out for the special case of single-particle constraints as
-explained in (Paquay).  V is volume; E is energy. This way,
+explained in (Paquay).  V is volume; E is energy. This way,
 the dynamics of particles constrained to curved surfaces can be
 studied. If combined with fix langevin, this
 generates Brownian motion of particles constrained to a curved
@@ -172,20 +172,18 @@ manifolds this can be achieved with region and create_atoms
 commands, but for more complex surfaces it might be more useful to
 write a script.
      
 
      The manifold args may be equal-style variables, like so:
      
-
      variable R equal "ramp(5.0,3.0)"
-fix shrink_sphere all nve/manifold/rattle 1e-4 10 sphere v_R
-
      
-
      
+
      +variable R equal "ramp(5.0,3.0)"
+fix shrink_sphere all nve/manifold/rattle 1e-4 10 sphere v_R
+
      
 
      In this case, the manifold parameter will change in time according to
 the variable.  This is not a problem for the time integrator as long
 as the change of the manifold is slow with respect to the dynamics of
 the particles.  Note that if the manifold has to exert work on the
 particles because of these changes, the total energy might not be
 conserved.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various output commands.  No parameter of this fix can
diff --git a/doc/html/fix_nve_sphere.html b/doc/html/fix_nve_sphere.html
index e0e8bf5189..2a70998598 100644
--- a/doc/html/fix_nve_sphere.html
+++ b/doc/html/fix_nve_sphere.html
@@ -189,10 +189,8 @@ by including their suffix, or you can use the suffix command in your input script.
      
 
      See Section_accelerate of the manual for
 more instructions on how to use the accelerated styles effectively.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various output commands.  No parameter of this fix can
diff --git a/doc/html/fix_nve_tri.html b/doc/html/fix_nve_tri.html
index e707401c30..1462555ef2 100644
--- a/doc/html/fix_nve_tri.html
+++ b/doc/html/fix_nve_tri.html
@@ -152,9 +152,7 @@ trajectory consistent with the microcanonical ensemble.  See
 using triangular particles.
      
 
      This fix differs from the fix nve command, which
 assumes point particles and only updates their position and velocity.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various output commands.  No parameter of this fix can
diff --git a/doc/html/fix_nvt_asphere.html b/doc/html/fix_nvt_asphere.html
index 08a1bea12b..473db13d7f 100644
--- a/doc/html/fix_nvt_asphere.html
+++ b/doc/html/fix_nvt_asphere.html
@@ -169,9 +169,9 @@ keywords.
      
 
      This fix computes a temperature each timestep.  To do this, the fix
 creates its own compute of style “temp/asphere”, as if this command
 had been issued:
      
-
      compute fix-ID_temp group-ID temp/asphere
-
      
-
      
+
      +compute fix-ID_temp group-ID temp/asphere
+
      
 
      See the compute temp/asphere command for
 details.  Note that the ID of the new compute is the fix-ID +
 underscore + “temp”, and the group for the new compute is the same as
@@ -213,9 +213,7 @@ by including their suffix, or you can use the suffix command in your input script.
      
 
      See Section_accelerate of the manual for
 more instructions on how to use the accelerated styles effectively.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      This fix writes the state of the Nose/Hoover thermostat to binary restart files.  See the read_restart
 command for info on how to re-specify a fix in an input script that
 reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_nvt_body.html b/doc/html/fix_nvt_body.html
index 9fecb55fc4..57ba66659d 100644
--- a/doc/html/fix_nvt_body.html
+++ b/doc/html/fix_nvt_body.html
@@ -166,9 +166,9 @@ keywords.
      
 
      This fix computes a temperature each timestep.  To do this, the fix
 creates its own compute of style “temp/body”, as if this command
 had been issued:
      
-
      compute fix-ID_temp group-ID temp/body
-
      
-
      
+
      +compute fix-ID_temp group-ID temp/body
+
      
 
      See the compute temp/body command for
 details.  Note that the ID of the new compute is the fix-ID +
 underscore + “temp”, and the group for the new compute is the same as
@@ -210,9 +210,7 @@ by including their suffix, or you can use the suffix command in your input script.
      
 
      See Section_accelerate of the manual for
 more instructions on how to use the accelerated styles effectively.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      This fix writes the state of the Nose/Hoover thermostat to binary restart files.  See the read_restart
 command for info on how to re-specify a fix in an input script that
 reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_nvt_sllod.html b/doc/html/fix_nvt_sllod.html
index a2592ab7e7..09875bceb8 100644
--- a/doc/html/fix_nvt_sllod.html
+++ b/doc/html/fix_nvt_sllod.html
@@ -194,9 +194,9 @@ keywords.
      
 
      This fix computes a temperature each timestep.  To do this, the fix
 creates its own compute of style “temp/deform”, as if this command had
 been issued:
      
-
      compute fix-ID_temp group-ID temp/deform
-
      
-
      
+
      +compute fix-ID_temp group-ID temp/deform
+
      
 
      See the compute temp/deform command for
 details.  Note that the ID of the new compute is the fix-ID +
 underscore + “temp”, and the group for the new compute is the same as
@@ -238,9 +238,7 @@ by including their suffix, or you can use the suffix command in your input script.
      
 
      See Section_accelerate of the manual for
 more instructions on how to use the accelerated styles effectively.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      This fix writes the state of the Nose/Hoover thermostat to binary restart files.  See the read_restart
 command for info on how to re-specify a fix in an input script that
 reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_nvt_sllod_eff.html b/doc/html/fix_nvt_sllod_eff.html
index 8492983e42..c175a68bdc 100644
--- a/doc/html/fix_nvt_sllod_eff.html
+++ b/doc/html/fix_nvt_sllod_eff.html
@@ -157,9 +157,7 @@ creates (as discussed in the compute temp/deform/eff commmand that includes
 the eFF contribution to the temperature from the electron radial
 velocity.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      This fix writes the state of the Nose/Hoover thermostat to binary restart files.  See the read_restart
 command for info on how to re-specify a fix in an input script that
 reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_nvt_sphere.html b/doc/html/fix_nvt_sphere.html
index fc5b3ddab1..6a27b967ed 100644
--- a/doc/html/fix_nvt_sphere.html
+++ b/doc/html/fix_nvt_sphere.html
@@ -169,9 +169,9 @@ keywords.
      
 
      This fix computes a temperature each timestep.  To do this, the fix
 creates its own compute of style “temp/sphere”, as if this command
 had been issued:
      
-
      compute fix-ID_temp group-ID temp/sphere
-
      
-
      
+
      +compute fix-ID_temp group-ID temp/sphere
+
      
 
      See the compute temp/sphere command for
 details.  Note that the ID of the new compute is the fix-ID +
 underscore + “temp”, and the group for the new compute is the same as
@@ -213,9 +213,7 @@ by including their suffix, or you can use the suffix command in your input script.
      
 
      See Section_accelerate of the manual for
 more instructions on how to use the accelerated styles effectively.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      This fix writes the state of the Nose/Hoover thermostat to binary restart files.  See the read_restart
 command for info on how to re-specify a fix in an input script that
 reads a restart file, so that the operation of the fix continues in an
diff --git a/doc/html/fix_orient.html b/doc/html/fix_orient.html
index 74dd4d3477..9b01605d28 100644
--- a/doc/html/fix_orient.html
+++ b/doc/html/fix_orient.html
@@ -232,9 +232,7 @@ symmetry, so the list must include one from each pair of
 equal-and-opposite neighbors.  A pair of orientation files for a
 Sigma=5 tilt boundary are shown below. A tutorial that can help for
 writing the orientation files is given in (Wicaksono2)
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.
      
 
      The fix_modify energy option is supported by this
 fix to add the potential energy of atom interactions with the grain
diff --git a/doc/html/fix_phonon.html b/doc/html/fix_phonon.html
index 40d369afee..3094e830ae 100644
--- a/doc/html/fix_phonon.html
+++ b/doc/html/fix_phonon.html
@@ -128,9 +128,9 @@
 
      fix phonon command
      
 
      
 
      Syntax
      
-
      fix ID group-ID phonon N Noutput Nwait map_file prefix keyword values ...
-
      
-
      
+
      +fix ID group-ID phonon N Noutput Nwait map_file prefix keyword values ...
+
      
 
        
 
      • ID, group-ID are documented in fix command
        • 
 
      • phonon = style name of this fix command
        • 
@@ -239,9 +239,7 @@ even degrade the performance of lammps in case the unit cell is too large.
        
 energy/distance^2/mass units.  The coordinates for q
 points in the log file is in the units of the basis vectors of the
 corresponding reciprocal lattice.
        
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.
      
 
      The fix_modify temp option is supported by this
 fix. You can use it to change the temperature compute from thermo_temp
diff --git a/doc/html/fix_pimd.html b/doc/html/fix_pimd.html
index 57ee90e294..545be26b57 100644
--- a/doc/html/fix_pimd.html
+++ b/doc/html/fix_pimd.html
@@ -232,9 +232,9 @@ ring.
      
 
      To run a PIMD simulation with M quasi-beads in each ring polymer using
 N MPI tasks for each partition’s domain-decomposition, you would use P
 = MxN processors (cores) and run the simulation as follows:
      
-
      mpirun -np P lmp_mpi -partition MxN -in script
-
      
-
      
+
      +mpirun -np P lmp_mpi -partition MxN -in script
+
      
 
      Note that in the LAMMPS input script for a multi-partition simulation,
 it is often very useful to define a uloop-style variable such as
      
 
      variable ibead uloop M pad
@@ -243,11 +243,11 @@ it is often very useful to define a 
      dump dcd all dcd 10 system_${ibead}.dcd
+
      +dump dcd all dcd 10 system_${ibead}.dcd
 restart 1000 system_${ibead}.restart1 system_${ibead}.restart2
 read_restart system_${ibead}.restart2
-
      
-
      
+
 
      
 
      
 
      Restrictions
      
diff --git a/doc/html/fix_pour.html b/doc/html/fix_pour.html
index ca471ec2c3..ee3f050be4 100644
--- a/doc/html/fix_pour.html
+++ b/doc/html/fix_pour.html
@@ -316,10 +316,8 @@ can prevent particles from being inserted.  The ignore keyword
 causes the overlap check to skip any line or triangle particles.
 Obviously you should only use it if there is in fact no overlap of the
 line or triangle particles with the insertion region.
      
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  This means you must be careful when restarting a
 pouring simulation, when the restart file was written in the middle of
 the pouring operation.  Specifically, you should use a new fix pour
diff --git a/doc/html/fix_qbmsst.html b/doc/html/fix_qbmsst.html
index 1fb67f4518..f3dca0ee47 100644
--- a/doc/html/fix_qbmsst.html
+++ b/doc/html/fix_qbmsst.html
@@ -157,10 +157,10 @@
 
      
 
      
 
      Examples
      
-
      fix 1 all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 seed 35082 f_max 0.3 N_f 100 eta 1 beta 400 T_init 110 (liquid methane modeled with the REAX force field, real units)
-fix 2 all qbmsst z 72 q 40 tscale 0.05 damp 1 seed 47508 f_max 120.0 N_f 100 eta 1.0 beta 500 T_init 300 (quartz modeled with the BKS force field, metal units)
-
      
-
      
+
      +fix 1 all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 seed 35082 f_max 0.3 N_f 100 eta 1 beta 400 T_init 110 (liquid methane modeled with the REAX force field, real units)
+fix 2 all qbmsst z 72 q 40 tscale 0.05 damp 1 seed 47508 f_max 120.0 N_f 100 eta 1.0 beta 500 T_init 300 (quartz modeled with the BKS force field, metal units)
+
      
 
      Two example input scripts are given, including shocked alpha quartz
 and shocked liquid methane. The input script first equilibrate an
 initial state with the quantum thermal bath at the target temperature
@@ -242,10 +242,8 @@ thermal bath and the system before shock loading.
      
 
      For all pressure styles, the simulation box stays orthorhombic in
 shape. Parrinello-Rahman boundary conditions (tilted box) are
 supported by LAMMPS, but are not implemented for QBMSST.
      
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      Because the state of the random number generator is not written to
 binary restart files, this fix cannot be restarted
 “exactly” in an uninterrupted fashion. However, in a statistical
@@ -271,16 +269,16 @@ headers, the following LAMMPS commands are suggested. Here the
 fix_modify energy command is also enabled to allow
 the thermo keyword etotal to print the quantity <i>etot</i>.  See
 also the thermo_style command.
      
-
      fix          fix_id all msst z
-fix_modify   fix_id energy yes
-variable     dhug    equal f_fix_id[1]
-variable     dray    equal f_fix_id[2]
-variable     lgr_vel equal f_fix_id[3]
-variable     lgr_pos equal f_fix_id[4]
-variable     T_qm    equal f_fix_id[5]
-thermo_style custom  step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id
-
      
-
      
+
      +fix          fix_id all msst z
+fix_modify  fix_id energy yes
+variable     dhug    equal f_fix_id[1]
+variable     dray    equal f_fix_id[2]
+variable     lgr_vel        equal f_fix_id[3]
+variable     lgr_pos        equal f_fix_id[4]
+variable     T_qm   equal f_fix_id[5]
+thermo_style        custom  step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id
+
      
 
      The global scalar under the entry f_fix_id is the quantity of thermo
 energy as an extra part of <i>etot</i>. This global scalar and the
 vector of 5 quantities can be accessed by various output commands. It is worth noting that the
diff --git a/doc/html/fix_qeq.html b/doc/html/fix_qeq.html
index addd4b9ecf..05e428f671 100644
--- a/doc/html/fix_qeq.html
+++ b/doc/html/fix_qeq.html
@@ -162,13 +162,13 @@
 
      
 
      
 
      Examples
      
-
      fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1
-fix 1 qeq qeq/shielded 1 8 1.0e-6 100 param.qeq2
-fix 1 all qeq/slater 5 10 1.0e-6 100 params alpha 0.2
-fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq
-fix 1 all qeq/fire 1 10 1.0e-3 100 my_qeq qdamp 0.2 qstep 0.1
-
      
-
      
+
      +fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1
+fix 1 qeq qeq/shielded 1 8 1.0e-6 100 param.qeq2
+fix 1 all qeq/slater 5 10 1.0e-6 100 params alpha 0.2
+fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq
+fix 1 all qeq/fire 1 10 1.0e-3 100 my_qeq qdamp 0.2 qstep 0.1
+
      
 
      
 
      
 
      Description
      
@@ -292,9 +292,7 @@ non-trivial.  Charges on atoms are not guaranteed to equilibrate with
 arbitrary choices of these parameters.  We do not develop these QEq
 paramters.  See the examples/qeq directory for some examples.
      
 
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about these fixes is written to binary restart files.  No global scalar or vector or per-atom
 quantities are stored by these fixes for access by various output commands.  No parameter of these fixes
 can be used with the start/stop keywords of the run
diff --git a/doc/html/fix_qeq_comb.html b/doc/html/fix_qeq_comb.html
index c7382d021d..3bf7a12a5c 100644
--- a/doc/html/fix_qeq_comb.html
+++ b/doc/html/fix_qeq_comb.html
@@ -195,10 +195,8 @@ by including their suffix, or you can use the suffix command in your input script.
      
 
      See Section_accelerate of the manual for
 more instructions on how to use the accelerated styles effectively.
      
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.
      
 
      The fix_modify respa option is supported by this
 fix. This allows to set at which level of the r-RESPA
diff --git a/doc/html/fix_qeq_reax.html b/doc/html/fix_qeq_reax.html
index cc02c2516a..665de2e845 100644
--- a/doc/html/fix_qeq_reax.html
+++ b/doc/html/fix_qeq_reax.html
@@ -180,9 +180,7 @@ exponent.  Note that these 3 quantities are also in the ReaxFF
 potential file, except that eta is defined here as twice the eta value
 in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
 of this fix are hard-coded to be A, eV, and electronic charge.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  No global scalar or vector or per-atom
 quantities are stored by this fix for access by various output commands.  No parameter of this fix can
 be used with the start/stop keywords of the run command.
      
diff --git a/doc/html/fix_qmmm.html b/doc/html/fix_qmmm.html
index 1adbcf6567..fa8cf47576 100644
--- a/doc/html/fix_qmmm.html
+++ b/doc/html/fix_qmmm.html
@@ -156,9 +156,7 @@ other QM codes.  This will allow the LAMMPS side of the implementation
 to be adapted if necessary before being finalized.
      
 
      Details about how to use this fix are currently documented in the
 description of the QM/MM interface code itself in lib/qmmm/README.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global scalar or vector or per-atom
 quantities are stored by this fix for access by various output commands.  No parameter of this fix can
diff --git a/doc/html/fix_qtb.html b/doc/html/fix_qtb.html
index 2f8934ddd0..cffd9b2764 100644
--- a/doc/html/fix_qtb.html
+++ b/doc/html/fix_qtb.html
@@ -147,12 +147,12 @@
 
      
 
      
 
      Examples
      
-
      fix 1 all nve
-fix 1 all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 100 (liquid methane modeled with the REAX force field, real units)
-fix 2 all nph iso 1.01325 1.01325 1
-fix 2 all qtb temp 300 damp 1 seed 47508 f_max 120.0 N_f 100 (quartz modeled with the BKS force field, metal units)
-
      
-
      
+
      +fix 1 all nve
+fix 1 all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 100 (liquid methane modeled with the REAX force field, real units)
+fix 2 all nph iso 1.01325 1.01325 1
+fix 2 all qtb temp 300 damp 1 seed 47508 f_max 120.0 N_f 100 (quartz modeled with the BKS force field, metal units)
+
      
 
      
 
      
 
      Description
      
@@ -219,7 +219,7 @@ runs on different numbers of processors.
      
 vibrational modes with frequencies higher than f_max will not be
 modulated. If we denote &Delta;<i>t</i> as the time interval for the
 MD integration, f_max is always reset by the code to make
-<i>&alpha;</i> = (int)(2f_max&Delta;<i>t</i>)<sup><i>-1</i></sup> a
+<i>&alpha;</i> = (int)(2*f_max*&Delta;<i>t</i>)<sup><i>-1</i></sup> a
 positive integer and print out relative information. An appropriate
 value for the cutoff frequency f_max would be around 2~3
 <i>f</i><sub>D</sub>, where <i>f</i><sub>D</sub> is the Debye
diff --git a/doc/html/fix_reax_bonds.html b/doc/html/fix_reax_bonds.html
index 0275b0ad0e..e8c6d12136 100644
--- a/doc/html/fix_reax_bonds.html
+++ b/doc/html/fix_reax_bonds.html
@@ -157,10 +157,8 @@ written to filename on timesteps that are multiples of Nevery,
 including timestep 0.  For time-averaged chemical species analysis,
 please see the fix reaxc/c/species command.
      
 
      The format of the output file should be self-explantory.
      
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various output commands.  No parameter of this fix can
diff --git a/doc/html/fix_reaxc_species.html b/doc/html/fix_reaxc_species.html
index d4f4f182bd..fb72dd69c4 100644
--- a/doc/html/fix_reaxc_species.html
+++ b/doc/html/fix_reaxc_species.html
@@ -215,10 +215,8 @@ i.e. Nrepeat*Nevery can not exceed Nfreq.
      
 
      For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order
 values on timesteps 90,92,94,96,98,100 will be used to compute the
 average bond-order for the species analysis output on timestep 100.
      
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.
      
 
      This fix computes both a global vector of length 2 and a per-atom
diff --git a/doc/html/fix_restrain.html b/doc/html/fix_restrain.html
index 34228509c9..ef8c9949c2 100644
--- a/doc/html/fix_restrain.html
+++ b/doc/html/fix_restrain.html
@@ -154,12 +154,12 @@
 
      
 
      
 
      Examples
      
-
      fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
-fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
-fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0
-fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0
-
      
-
      
+
      +fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
+fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
+fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0
+fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0
+
      
 
      
 
      
 
      Description
      
@@ -202,7 +202,8 @@ works best for a given application.
      
 molecule with particular restratins (e.g. for fitting forcefield
 parameters or constructing a potential energy surface), commands such
 as the following may be useful:
      
-
      # minimize molecule energy with restraints
+
      +# minimize molecule energy with restraints
 velocity all create 600.0 8675309 mom yes rot yes dist gaussian
 fix NVE all nve
 fix TFIX all langevin 600.0 0.0 100 24601
@@ -218,8 +219,7 @@ minimize 1e-6 1e-9 1000 100000
 # report unrestrained energies
 unfix REST
 run 0
-
      
-
      
+
 
      
 
      The bond keyword applies a bond restraint to the specified atoms
 using the same functional form used by the bond_style harmonic command.  The potential associated with
@@ -259,10 +259,8 @@ associated with the restraint is
      
 
      K and phi0 are specified with the fix.  Note that the value of n is
 hard-wired to 1.  Also note that the energy will be a minimum when the
 current dihedral angle phi is equal to phi0.
      
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.
      
 
      The fix_modify energy option is supported by this
 fix to add the potential energy associated with this fix to the
diff --git a/doc/html/fix_rigid.html b/doc/html/fix_rigid.html
index 8b0eef3e3a..3dc4ef9053 100644
--- a/doc/html/fix_rigid.html
+++ b/doc/html/fix_rigid.html
@@ -211,19 +211,19 @@
 
      
 
      
 
      Examples
      
-
      fix 1 clump rigid single
-fix 1 clump rigid/small molecule
-fix 1 clump rigid single force 1 off off on langevin 1.0 1.0 1.0 428984
-fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0
-fix 1 polychains rigid molecule force 1*5 off off off force 6*10 off off on
-fix 1 polychains rigid/small molecule langevin 1.0 1.0 1.0 428984
-fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off
-fix 1 rods rigid/npt molecule temp 300.0 300.0 100.0 iso 0.5 0.5 10.0
-fix 1 particles rigid/npt molecule temp 1.0 1.0 5.0 x 0.5 0.5 1.0 z 0.5 0.5 1.0 couple xz
-fix 1 water rigid/nph molecule iso 0.5 0.5 1.0
-fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0
-
      
-
      
+
      +fix 1 clump rigid single
+fix 1 clump rigid/small molecule
+fix 1 clump rigid single force 1 off off on langevin 1.0 1.0 1.0 428984
+fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0
+fix 1 polychains rigid molecule force 1*5 off off off force 6*10 off off on
+fix 1 polychains rigid/small molecule langevin 1.0 1.0 1.0 428984
+fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off
+fix 1 rods rigid/npt molecule temp 300.0 300.0 100.0 iso 0.5 0.5 10.0
+fix 1 particles rigid/npt molecule temp 1.0 1.0 5.0 x 0.5 0.5 1.0 z 0.5 0.5 1.0 couple xz
+fix 1 water rigid/nph molecule iso 0.5 0.5 1.0
+fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0
+
      
 
      
 
      
 
      Description
      
@@ -385,8 +385,8 @@ apply to is determined by the first argument of the force and
 torque keywords.  It can be an integer M from 1 to Nbody, where
 Nbody is the number of rigid bodies defined.  A wild-card asterisk can
 be used in place of, or in conjunction with, the M argument to set the
-flags for multiple rigid bodies.  This takes the form “*” or “n” or
-“n” or “m*n”.  If N = the number of rigid bodies, then an asterisk
+flags for multiple rigid bodies.  This takes the form “*” or “*n” or
+“n*” or “m*n”.  If N = the number of rigid bodies, then an asterisk
 with no numeric values means all bodies from 1 to N.  A leading
 asterisk means all bodies from 1 to n (inclusive).  A trailing
 asterisk means all bodies from n to N (inclusive).  A middle asterisk
@@ -745,10 +745,8 @@ by including their suffix, or you can use the suffix command in your input script.
      
 
      See Section_accelerate of the manual for
 more instructions on how to use the accelerated styles effectively.
      
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about the 4 NVE rigid styles is written to binary restart files.  The exception is if the infile or
 mol keyword is used, in which case an auxiliary file is written out
 with rigid body information each time a restart file is written, as
diff --git a/doc/html/fix_rx.html b/doc/html/fix_rx.html
index b39fe17f46..6d337133f8 100644
--- a/doc/html/fix_rx.html
+++ b/doc/html/fix_rx.html
@@ -147,13 +147,13 @@
 
      
 
      
 
      Examples
      
-
      fix 1 all rx kinetics.rx none dense lammps_rk4
-fix 1 all rx kinetics.rx none sparse lammps_rk4 1
-fix 1 all rx kinetics.rx lucy sparse lammps_rk4 10
-fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8
-fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8 -1
-
      
-
      
+
      +fix 1 all rx kinetics.rx none dense lammps_rk4
+fix 1 all rx kinetics.rx none sparse lammps_rk4 1
+fix 1 all rx kinetics.rx lucy sparse lammps_rk4 10
+fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8
+fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8 -1
+
      
 
      
 
      
 
      Description
      
@@ -271,7 +271,7 @@ temperature exponent n, and the activation energy Ea.
      
 are used by the fix eos/table/rx command to
 define the thermodynamic properties of each species.  Furthermore, the
 number of species molecules (i.e., concentration) can be specified
-either with the set command using the “d_” prefix or by
+either with the set command using the “d_” prefix or by
 reading directly the concentrations from a data file.  For the latter
 case, the read_data command with the fix keyword
 should be specified, where the fix-ID will be the “fix rx`ID with a <SPECIES”>`_ suffix, e.g.
      
diff --git a/doc/html/fix_saed_vtk.html b/doc/html/fix_saed_vtk.html
index 29f7570dc9..08de66a8eb 100644
--- a/doc/html/fix_saed_vtk.html
+++ b/doc/html/fix_saed_vtk.html
@@ -128,9 +128,9 @@
 
      fix saed/vtk command
      
 
      
 
      Syntax
      
-
      fix ID group-ID saed/vtk Nevery Nrepeat Nfreak c_ID attribute args ... keyword args ...
-
      
-
      
+
      +fix ID group-ID saed/vtk Nevery Nrepeat Nfreak c_ID attribute args ... keyword args ...
+
      
 
        
 
      • ID, group-ID are documented in fix command
        • 
 
      • saed/vtk = style name of this fix command
        • 
@@ -154,14 +154,14 @@ keyword = file or ave or start or file or 
 
        
 
        Examples
        
-
        compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
-compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
-
        
-
        
-
        fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
-fix saed/vtk 1 1 1 c_2 file Ni_000.saed
-
        
-
        
+
        +compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
+compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
+
        
+
        +fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
+fix saed/vtk 1 1 1 c_2 file Ni_000.saed
+
        
 
        
 
        
 
        Description
        
@@ -182,10 +182,10 @@ specified values may represent calculations performed by saed computes
 which store their own “group” definitions.
        
 
        Fix saed/vtk is designed to work only with compute saed
 values, e.g.
        
-
        compute 3 top saed 0.0251 Al O
-fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed
-
        
-
        
+
        +compute 3 top saed 0.0251 Al O
+fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed
+
        
 
        
 
        The Nevery, Nrepeat, and Nfreq arguments specify on what
 timesteps the input values will be used in order to contribute to the
@@ -209,19 +209,19 @@ vtk image data formatting.  The filename assigned by the file keyword i
 appended with _N.vtk where N is an index (0,1,2...) to account for multiple
 diffraction intensity outputs.
        
 
        By default the header contains the following information (with example data):
        
-
        # vtk DataFile Version 3.0 c_SAED
-Image data set
-ASCII
-DATASET STRUCTURED_POINTS
-DIMENSIONS 337 219 209
-ASPECT_RATIO 0.00507953 0.00785161 0.00821458
-ORIGIN -0.853361 -0.855826 -0.854316
-POINT_DATA 15424827
-SCALARS intensity float
-LOOKUP_TABLE default
-...data
-
        
-
        
+
        +# vtk DataFile Version 3.0 c_SAED
+Image data set
+ASCII
+DATASET STRUCTURED_POINTS
+DIMENSIONS 337 219 209
+ASPECT_RATIO 0.00507953 0.00785161 0.00821458
+ORIGIN -0.853361 -0.855826 -0.854316
+POINT_DATA 15424827
+SCALARS intensity float
+LOOKUP_TABLE default
+...data
+
        
 
        In this example, kspace is sampled across a 337 x 219 x 209 point mesh
 where the mesh spacing is approximately 0.005, 0.007, and 0.008
 inv(length) units in the k1, k2, and k3 directions, respectively.
@@ -264,9 +264,7 @@ intensity outputs.
        
 
        The overwrite keyword will continuously overwrite the output file
 with the latest output, so that it only contains one timestep worth of
 output.  This option can only be used with the ave running setting.
        
-
        
-
        
-
        Restart, fix_modify, output, run start/stop, minimize info
        
+
        Restart, fix_modify, output, run start/stop, minimize info:
        
 
        No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.
        
 
        No parameter of this fix can be used with the start/stop keywords of
diff --git a/doc/html/fix_shake.html b/doc/html/fix_shake.html
index 7cfb03e019..6c279062d0 100644
--- a/doc/html/fix_shake.html
+++ b/doc/html/fix_shake.html
@@ -289,10 +289,8 @@ the RATTLE constraints.  You can check whether the constraints work
 correctly by setting the value of RATTLE_DEBUG in src/fix_rattle.cpp
 to 1 and recompiling LAMMPS.
        
 
        
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about these fixes is written to binary restart files.  None of the fix_modify options
 are relevant to these fixes.  No global or per-atom quantities are
 stored by these fixes for access by various output commands.  No parameter of these fixes
diff --git a/doc/html/fix_smd.html b/doc/html/fix_smd.html
index 5be23f5d7b..0c2d9bc519 100644
--- a/doc/html/fix_smd.html
+++ b/doc/html/fix_smd.html
@@ -212,9 +212,7 @@ over the pulling force in direction of the spring is recorded and
 can then later be used to compute the potential of mean force (PMF)
 by averaging over multiple independent trajectories along the same
 pulling path.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      The fix stores the direction of the spring, current pulling target
 distance and the running PMF to binary restart files.
 See the read_restart command for info on how to
diff --git a/doc/html/fix_smd_adjust_dt.html b/doc/html/fix_smd_adjust_dt.html
index ebf49b94ca..734c433f36 100644
--- a/doc/html/fix_smd_adjust_dt.html
+++ b/doc/html/fix_smd_adjust_dt.html
@@ -128,9 +128,9 @@
 
      fix smd/adjust_dt command
      
 
      
 
      Syntax
      
-
      fix ID group-ID smd/adjust_dt arg
-
      
-
      
+
      +fix ID group-ID smd/adjust_dt arg
+
      
 
        
 
      • ID, group-ID are documented in fix command
        • 
 
      • smd/adjust_dt = style name of this fix command
        • 
@@ -142,9 +142,9 @@
 
      
 
      
 
      Examples
      
-
      fix 1 all smd/adjust_dt 0.1
-
      
-
      
+
      +fix 1 all smd/adjust_dt 0.1
+
      
 
      
 
      
 
      Description
      
@@ -157,9 +157,7 @@ stable maximum time step.
      
 
      This fix inquires the minimum stable time increment across all particles contained in the group for which this
 fix is defined. An additional safety factor s_fact is applied to the time increment.
      
 
      See this PDF guide to use Smooth Mach Dynamics in LAMMPS.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      Currently, no part of USER-SMD supports restarting nor minimization.
      
 
      
 
      
diff --git a/doc/html/fix_smd_integrate_tlsph.html b/doc/html/fix_smd_integrate_tlsph.html
index 194f99be37..04c9db062a 100644
--- a/doc/html/fix_smd_integrate_tlsph.html
+++ b/doc/html/fix_smd_integrate_tlsph.html
@@ -128,9 +128,9 @@
 
      fix smd/integrate_tlsph command
      
 
      
 
      Syntax
      
-
      fix ID group-ID smd/integrate_tlsph keyword values
-
      
-
      
+
      +fix ID group-ID smd/integrate_tlsph keyword values
+
      
 
        
 
      • ID, group-ID are documented in fix command
        • 
 
      • smd/integrate_tlsph = style name of this fix command
        • 
@@ -144,10 +144,10 @@
 
      
 
      
 
      Examples
      
-
      fix 1 all smd/integrate_tlsph
-fix 1 all smd/integrate_tlsph limit_velocity 1000
-
      
-
      
+
      +fix 1 all smd/integrate_tlsph
+fix 1 all smd/integrate_tlsph limit_velocity 1000
+
      
 
      
 
      
 
      Description
      
@@ -155,9 +155,7 @@
 
      See this PDF guide to using Smooth Mach Dynamics in LAMMPS.
      
 
      The limit_velocity keyword will control the velocity, scaling the norm of
 the velocity vector to max_vel in case it exceeds this velocity limit.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
      
 
      
 
      
diff --git a/doc/html/fix_smd_integrate_ulsph.html b/doc/html/fix_smd_integrate_ulsph.html
index e45d7d3f31..58bd9fda2c 100644
--- a/doc/html/fix_smd_integrate_ulsph.html
+++ b/doc/html/fix_smd_integrate_ulsph.html
@@ -128,9 +128,9 @@
 
      fix smd/integrate_ulsph command
      
 
      
 
      Syntax
      
-
      fix ID group-ID smd/integrate_ulsph keyword
-
      
-
      
+
      +fix ID group-ID smd/integrate_ulsph keyword
+
      
 
        
 
      • ID, group-ID are documented in fix command
        • 
 
      • smd/integrate_ulsph = style name of this fix command
        • 
@@ -148,12 +148,12 @@ max_nn = maximum number of neighbors
 
      
 
      
 
      Examples
      
-
      fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50
-
      
-
      
-
      fix 1 all smd/integrate_ulsph limit_velocity 1000
-
      
-
      
+
      +fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50
+
      
+
      +fix 1 all smd/integrate_ulsph limit_velocity 1000
+
      
 
      
 
      
 
      Description
      
@@ -161,12 +161,10 @@ max_nn = maximum number of neighbors
 See this PDF guide to using Smooth Mach Dynamics in LAMMPS.
      
 
      The adjust_radius keyword activates dynamic adjustment of the per-particle SPH smoothing kernel radius such that the number of neighbors per particles remains
 within the interval min_nn to max_nn. The parameter adjust_radius_factor determines the amount of adjustment per timestep. Typical values are
-adjust_radius_factor=1.02, min_nn=15, and max_nn=20.
      
+*adjust_radius_factor*=1.02, *min_nn*=15, and *max_nn*=20.
      
 
      The limit_velocity keyword will control the velocity, scaling the norm of
 the velocity vector to max_vel in case it exceeds this velocity limit.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
      
 
      
 
      
diff --git a/doc/html/fix_smd_move_triangulated_surface.html b/doc/html/fix_smd_move_triangulated_surface.html
index 689017806f..e3c04397e7 100644
--- a/doc/html/fix_smd_move_triangulated_surface.html
+++ b/doc/html/fix_smd_move_triangulated_surface.html
@@ -128,55 +128,53 @@
 
      fix smd/move_tri_surf command
      
 
      
 
      Syntax
      
-
      fix ID group-ID smd/move_tri_surf keyword
-
      
-
      
+
      +fix ID group-ID smd/move_tri_surf keyword
+
      
 
        
 
      • ID, group-ID are documented in fix command
        • 
 
      • smd/move_tri_surf keyword = style name of this fix command
        • 
-
      • keyword = **LINEAR* or **WIGGLE* or **ROTATE*
        • 
+
      • keyword = *LINEAR or *WIGGLE or *ROTATE
        • 
 
      
-
      **LINEAR* args = Vx Vy Vz
-   Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
-**WIGGLE* args = Vx Vy Vz max_travel
-   vx,vy,vz = components of velocity vector (velocity units), any component can be specified as NULL
-   max_travel = wiggle amplitude
-**ROTATE* args = Px Py Pz Rx Ry Rz period
-   Px,Py,Pz = origin point of axis of rotation (distance units)
-   Rx,Ry,Rz = axis of rotation vector
-   period = period of rotation (time units)
-
      
-
      
+
      +*LINEAR args = Vx Vy Vz
+   Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
+*WIGGLE args = Vx Vy Vz max_travel
+   vx,vy,vz = components of velocity vector (velocity units), any component can be specified as NULL
+   max_travel = wiggle amplitude
+*ROTATE args = Px Py Pz Rx Ry Rz period
+   Px,Py,Pz = origin point of axis of rotation (distance units)
+   Rx,Ry,Rz = axis of rotation vector
+   period = period of rotation (time units)
+
      
 
      
 
      
 
      Examples
      
-
      fix 1 tool smd/move_tri_surf *LINEAR 20 20 10
-fix 2 tool smd/move_tri_surf *WIGGLE 20 20 10
-fix 2 tool smd/move_tri_surf *ROTATE 0 0 0 5 2 1
-
      
-
      
+
      +fix 1 tool smd/move_tri_surf *LINEAR 20 20 10
+fix 2 tool smd/move_tri_surf *WIGGLE 20 20 10
+fix 2 tool smd/move_tri_surf *ROTATE 0 0 0 5 2 1
+
      
 
      
 
      
 
      Description
      
 
      This fix applies only to rigid surfaces read from .STL files via fix smd/wall_surface .
 It updates position and velocity for the particles in the group each timestep without regard to forces on the particles.
 The rigid surfaces can thus be moved along simple trajectories during the simulation.
      
-
      The **LINEAR* style moves particles with the specified constant velocity
+
      The *LINEAR style moves particles with the specified constant velocity
 vector V = (Vx,Vy,Vz). This style also sets the velocity of each particle
 to V = (Vx,Vy,Vz).
      
-
      The **WIGGLE* style moves particles in an oscillatory fashion.
+
      The *WIGGLE style moves particles in an oscillatory fashion.
 Particles are moved along (vx, vy, vz) with constant velocity until a
 displacement of max_travel is reached. Then, the velocity vector is
 reversed. This process is repeated.
      
-
      The **ROTATE* style rotates particles around a rotation axis R = (Rx,Ry,Rz) that
+
      The *ROTATE style rotates particles around a rotation axis R = (Rx,Ry,Rz) that
 goes through a point P = (Px,Py,Pz). The period of the rotation is also
 specified. This style also sets the velocity of each particle to (omega cross
 Rperp) where omega is its angular velocity around the rotation axis and
 Rperp is a perpendicular vector from the rotation axis to the particle.
      
 
      See this PDF guide to using Smooth Mach Dynamics in LAMMPS.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
      
 
      
 
      
diff --git a/doc/html/fix_smd_setvel.html b/doc/html/fix_smd_setvel.html
index cb8449f1c0..16fc5abc50 100644
--- a/doc/html/fix_smd_setvel.html
+++ b/doc/html/fix_smd_setvel.html
@@ -146,9 +146,9 @@
 
      
 
      
 
      Examples
      
-
      fix top_velocity top_group setvel 1.0 0.0 0.0
-
      
-
      
+
      +fix top_velocity top_group setvel 1.0 0.0 0.0
+
      
 
      
 
      
 
      Description
      
@@ -174,10 +174,8 @@ coordinates.  Thus it is easy to specify a spatially-dependent velocity
 field with optional time-dependence as well.
      
 
      If the region keyword is used, the particle must also be in the
 specified geometric region in order to have its velocity set by this command.
      
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      Currently, no part of USER-SMD supports restarting nor minimization
 None of the fix_modify options
 are relevant to this fix.
      
diff --git a/doc/html/fix_smd_wall_surface.html b/doc/html/fix_smd_wall_surface.html
index 92d197d542..f51d51f6a6 100644
--- a/doc/html/fix_smd_wall_surface.html
+++ b/doc/html/fix_smd_wall_surface.html
@@ -128,9 +128,9 @@
 
      fix smd/wall_surface command
      
 
      
 
      Syntax
      
-
      fix ID group-ID smd/wall_surface arg type mol-ID
-
      
-
      
+
      +fix ID group-ID smd/wall_surface arg type mol-ID
+
      
 
        
 
      • ID, group-ID are documented in fix command
        • 
 
      • smd/wall_surface = style name of this fix command
        • 
@@ -146,9 +146,9 @@
 
      
 
      
 
      Examples
      
-
      fix stl_surf all smd/wall_surface tool.stl 2 65535
-
      
-
      
+
      +fix stl_surf all smd/wall_surface tool.stl 2 65535
+
      
 
      
 
      
 
      Description
      
@@ -160,9 +160,7 @@ It is possible to move the triangulated surface via the this PDF guide to use Smooth Mach Dynamics in LAMMPS.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.
      
 
      
 
      
diff --git a/doc/html/fix_spring.html b/doc/html/fix_spring.html
index a1d40fbf68..413066a788 100644
--- a/doc/html/fix_spring.html
+++ b/doc/html/fix_spring.html
@@ -215,9 +215,7 @@ spring command, if the rigid body will cross a periodic boundary.
 This is because image flags for rigid bodies are used in a different
 way, as explained on the fix rigid doc page.
      
 
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.
      
 
      The fix_modify energy option is supported by this
 fix to add the energy stored in the spring to the system’s potential
diff --git a/doc/html/fix_spring_chunk.html b/doc/html/fix_spring_chunk.html
index 7373fd8e56..5ea20d8a43 100644
--- a/doc/html/fix_spring_chunk.html
+++ b/doc/html/fix_spring_chunk.html
@@ -166,9 +166,7 @@ the mass of the atom, and Mm is the total mass of all atoms in the
 chunk.  Note that K thus represents the spring constant for the
 total force on each chunk of atoms, not for a spring applied to each
 atom.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.
      
 
      The fix_modify energy option is supported by this
 fix to add the energy stored in all the springs to the system’s potential
diff --git a/doc/html/fix_spring_rg.html b/doc/html/fix_spring_rg.html
index aeaa3bece4..8cb641326c 100644
--- a/doc/html/fix_spring_rg.html
+++ b/doc/html/fix_spring_rg.html
@@ -166,9 +166,7 @@ the mass of the entire group.  Note that K is thus a force constant
 for the aggregate force on the group of atoms, not a per-atom force.
      
 
      If RG0 is specified as NULL, then the RG of the group is computed at
 the time the fix is specified, and that value is used as the target.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various output commands.  No parameter of this fix can
diff --git a/doc/html/fix_spring_self.html b/doc/html/fix_spring_self.html
index dbc542e600..28e33fc5ed 100644
--- a/doc/html/fix_spring_self.html
+++ b/doc/html/fix_spring_self.html
@@ -160,9 +160,7 @@ spring force is applied. By default, the restraint is applied in all
 directions, but it can be limited to the xy-, xz-, yz-plane and the
 x-, y-, or z-direction, thus restraining the atoms to a line or a
 plane, respectively.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      This fix writes the original coordinates of tethered atoms to binary restart files, so that the spring effect will be the
 same in a restarted simulation.  See the
 read_restart command for info on how to re-specify
diff --git a/doc/html/fix_store_state.html b/doc/html/fix_store_state.html
index 9d236aa13f..0a885ed683 100644
--- a/doc/html/fix_store_state.html
+++ b/doc/html/fix_store_state.html
@@ -137,43 +137,43 @@
 
    • N = store atom attributes every N steps, N = 0 for initial store only
      • 
 
    • input = one or more atom attributes
      • 
 
-
      possible attributes = id, mol, type, mass,
-                   x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz,
-                   vx, vy, vz, fx, fy, fz,
-                      q, mux, muy, muz, mu,
-                      radius, diameter, omegax, omegay, omegaz,
-                      angmomx, angmomy, angmomz, tqx, tqy, tqz,
-                      c_ID, c_ID[N], f_ID, f_ID[N], v_name,
-                      d_name, i_name
-
      
-
      
-
      id = atom ID
-mol = molecule ID
-type = atom type
-mass = atom mass
-x,y,z = unscaled atom coordinates
-xs,ys,zs = scaled atom coordinates
-xu,yu,zu = unwrapped atom coordinates
-xsu,ysu,zsu = scaled unwrapped atom coordinates
-ix,iy,iz = box image that the atom is in
-vx,vy,vz = atom velocities
-fx,fy,fz = forces on atoms
-q = atom charge
-mux,muy,muz = orientation of dipolar atom
-mu = magnitued of dipole moment of atom
-radius,diameter = radius.diameter of spherical particle
-omegax,omegay,omegaz = angular velocity of spherical particle
-angmomx,angmomy,angmomz = angular momentum of aspherical particle
-tqx,tqy,tqz = torque on finite-size particles
-c_ID = per-atom vector calculated by a compute with ID
-c_ID[I] = Ith column of per-atom array calculated by a compute with ID
-f_ID = per-atom vector calculated by a fix with ID
-f_ID[I] = Ith column of per-atom array calculated by a fix with ID
-v_name = per-atom vector calculated by an atom-style variable with name
-d_name = per-atom floating point vector name, managed by fix property/atom
-i_name = per-atom integer vector name, managed by fix property/atom
-
      
-
      
+
      +possible attributes = id, mol, type, mass,
+                   x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz,
+                   vx, vy, vz, fx, fy, fz,
+                      q, mux, muy, muz, mu,
+                      radius, diameter, omegax, omegay, omegaz,
+                      angmomx, angmomy, angmomz, tqx, tqy, tqz,
+                      c_ID, c_ID[N], f_ID, f_ID[N], v_name,
+                      d_name, i_name
+
      
+
      +id = atom ID
+mol = molecule ID
+type = atom type
+mass = atom mass
+x,y,z = unscaled atom coordinates
+xs,ys,zs = scaled atom coordinates
+xu,yu,zu = unwrapped atom coordinates
+xsu,ysu,zsu = scaled unwrapped atom coordinates
+ix,iy,iz = box image that the atom is in
+vx,vy,vz = atom velocities
+fx,fy,fz = forces on atoms
+q = atom charge
+mux,muy,muz = orientation of dipolar atom
+mu = magnitued of dipole moment of atom
+radius,diameter = radius.diameter of spherical particle
+omegax,omegay,omegaz = angular velocity of spherical particle
+angmomx,angmomy,angmomz = angular momentum of aspherical particle
+tqx,tqy,tqz = torque on finite-size particles
+c_ID = per-atom vector calculated by a compute with ID
+c_ID[I] = Ith column of per-atom array calculated by a compute with ID
+f_ID = per-atom vector calculated by a fix with ID
+f_ID[I] = Ith column of per-atom array calculated by a fix with ID
+v_name = per-atom vector calculated by an atom-style variable with name
+d_name = per-atom floating point vector name, managed by fix property/atom
+i_name = per-atom integer vector name, managed by fix property/atom
+
      
 
        
 
      • zero or more keyword/value pairs may be appended
        • 
 
      • keyword = com
        • 
@@ -217,9 +217,7 @@ of the group of atoms, instead of storing the absolute position.
        
 
        The requested values are stored in a per-atom vector or array as
 discussed below.  Zeroes are stored for atoms not in the specified
 group.
        
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      This fix writes the per-atom values it stores to binary restart files, so that the values can be restored when a
 simulation is restarted.  See the read_restart
 command for info on how to re-specify a fix in an input script that
diff --git a/doc/html/fix_temp_berendsen.html b/doc/html/fix_temp_berendsen.html
index d628854ba7..56ae7e3339 100644
--- a/doc/html/fix_temp_berendsen.html
+++ b/doc/html/fix_temp_berendsen.html
@@ -192,9 +192,9 @@ thermostatting.
      
 
      This fix computes a temperature each timestep.  To do this, the fix
 creates its own compute of style “temp”, as if this command had been
 issued:
      
-
      compute fix-ID_temp group-ID temp
-
      
-
      
+
      +compute fix-ID_temp group-ID temp
+
      
 
      See the compute temp command for details.  Note
 that the ID of the new compute is the fix-ID + underscore + “temp”,
 and the group for the new compute is the same as the fix group.
      
@@ -219,10 +219,8 @@ this case, the thermostat works in the following manner: the current
 temperature is calculated taking the bias into account, bias is
 removed from each atom, thermostatting is performed on the remaining
 thermal degrees of freedom, and the bias is added back in.
      
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.
      
 
      The fix_modify temp option is supported by this
 fix.  You can use it to assign a temperature compute
diff --git a/doc/html/fix_temp_csvr.html b/doc/html/fix_temp_csvr.html
index 0d3874ecdd..1a1b23cc0d 100644
--- a/doc/html/fix_temp_csvr.html
+++ b/doc/html/fix_temp_csvr.html
@@ -210,9 +210,9 @@ thermostatting.
      
 
      These fixes compute a temperature each timestep.  To do this, the fix
 creates its own compute of style “temp”, as if this command had been
 issued:
      
-
      compute fix-ID_temp group-ID temp
-
      
-
      
+
      +compute fix-ID_temp group-ID temp
+
      
 
      See the compute temp command for details.  Note
 that the ID of the new compute is the fix-ID + underscore + “temp”,
 and the group for the new compute is the same as the fix group.
      
@@ -237,10 +237,8 @@ this case, the thermostat works in the following manner: the current
 temperature is calculated taking the bias into account, bias is
 removed from each atom, thermostatting is performed on the remaining
 thermal degrees of freedom, and the bias is added back in.
      
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about these fixes are written to binary restart files.
      
 
      The fix_modify temp option is supported by these
 fixes.  You can use it to assign a temperature compute
diff --git a/doc/html/fix_temp_rescale.html b/doc/html/fix_temp_rescale.html
index bfa398c38e..2b96f60e2e 100644
--- a/doc/html/fix_temp_rescale.html
+++ b/doc/html/fix_temp_rescale.html
@@ -198,9 +198,9 @@ thermostatting.
      
 
      This fix computes a temperature each timestep.  To do this, the fix
 creates its own compute of style “temp”, as if one of this command had
 been issued:
      
-
      compute fix-ID_temp group-ID temp
-
      
-
      
+
      +compute fix-ID_temp group-ID temp
+
      
 
      See the compute temp for details.  Note that the
 ID of the new compute is the fix-ID + underscore + “temp”, and the
 group for the new compute is the same as the fix group.
      
@@ -225,10 +225,8 @@ this case, the thermostat works in the following manner: the current
 temperature is calculated taking the bias into account, bias is
 removed from each atom, thermostatting is performed on the remaining
 thermal degrees of freedom, and the bias is added back in.
      
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.
      
 
      The fix_modify temp option is supported by this
 fix.  You can use it to assign a temperature compute
diff --git a/doc/html/fix_temp_rescale_eff.html b/doc/html/fix_temp_rescale_eff.html
index 826fcfb6f4..4a5b09b42a 100644
--- a/doc/html/fix_temp_rescale_eff.html
+++ b/doc/html/fix_temp_rescale_eff.html
@@ -154,9 +154,7 @@ their velocities.
      
 
      The operation of this fix is exactly like that described by the fix temp/rescale command, except that the rescaling
 is also applied to the radial electron velocity for electron
 particles.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.
      
 
      The fix_modify temp option is supported by this
 fix.  You can use it to assign a temperature compute
diff --git a/doc/html/fix_tfmc.html b/doc/html/fix_tfmc.html
index 1fa84393e7..32b9de3cbb 100644
--- a/doc/html/fix_tfmc.html
+++ b/doc/html/fix_tfmc.html
@@ -228,10 +228,8 @@ translations or rotations of the fix group could be induced by these
 external forces, and removing them will lead to a violation of
 detailed balance.
      
 
      
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.
      
 
      None of the fix_modify options are relevant to this
 fix.
      
diff --git a/doc/html/fix_thermal_conductivity.html b/doc/html/fix_thermal_conductivity.html
index 97325bd91e..05f63ab2de 100644
--- a/doc/html/fix_thermal_conductivity.html
+++ b/doc/html/fix_thermal_conductivity.html
@@ -180,12 +180,12 @@ of the 2 atoms is performed, to conserve kinetic energy.  Over time,
 this induces a temperature gradient in the system which can be
 measured using commands such as the following, which writes the
 temperature profile (assuming z = edim) to the file tmp.profile:
      
-
      compute   ke all ke/atom
-variable  temp atom c_ke/1.5
-compute   layers all chunk/atom bin/1d z lower 0.05 units reduced
-fix       3 all ave/chunk 10 100 1000 layers v_temp file tmp.profile
-
      
-
      
+
      +compute   ke all ke/atom
+variable  temp atom c_ke/1.5
+compute   layers all chunk/atom bin/1d z lower 0.05 units reduced
+fix       3 all ave/chunk 10 100 1000 layers v_temp file tmp.profile
+
      
 
      Note that by default, Nswap = 1, though this can be changed by the
 optional swap keyword.  Setting this parameter appropriately, in
 conjunction with the swap rate N, allows the heat flux to be adjusted
@@ -221,9 +221,7 @@ not in a regime of linear response.  In this case you cannot
 accurately infer a thermal conductivity and should try increasing the
 Nevery parameter.
      
 
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.
      
 
      This fix computes a global scalar which can be accessed by various
diff --git a/doc/html/fix_ti_rs.html b/doc/html/fix_ti_rs.html
index 311cabb702..f298fc952d 100644
--- a/doc/html/fix_ti_rs.html
+++ b/doc/html/fix_ti_rs.html
@@ -128,9 +128,9 @@
 
      fix ti/rs command
      
 
      
 
      Syntax
      
-
      fix ID group-ID ti/rs lambda_initial lambda_final t_switch t_equil keyword value ...
-
      
-
      
+
      +fix ID group-ID ti/rs lambda_initial lambda_final t_switch t_equil keyword value ...
+
      
 
        
 
      • ID, group-ID are documented in fix command
        • 
 
      • ti/rs = style name of this fix command
        • 
@@ -198,9 +198,7 @@ scaling is faster at temperatures closer to the initial temperature of
 the procedure.
        
 
        An example script using this command is provided in the
 examples/USER/misc/ti directory.
        
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.
      
 
      This fix computes a global vector quantitie which can be accessed by
 various output commands. The vector has
diff --git a/doc/html/fix_ti_spring.html b/doc/html/fix_ti_spring.html
index a0a3a6db23..e7d63d947a 100644
--- a/doc/html/fix_ti_spring.html
+++ b/doc/html/fix_ti_spring.html
@@ -128,9 +128,9 @@
 
      fix ti/spring command
      
 
      
 
      Syntax
      
-
      fix ID group-ID ti/spring K t_switch t_equil keyword value ...
-
      
-
      
+
      +fix ID group-ID ti/spring K t_switch t_equil keyword value ...
+
      
 
        
 
      • ID, group-ID are documented in fix command
        • 
 
      • ti/spring = style name of this fix command
        • 
@@ -205,9 +205,7 @@ issues with the canonical sampling of harmonic degrees of freedom
 (notice that the chain option will NOT solve this problem). The
 Langevin thermostat (fix langevin) works fine.
        
 
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      This fix writes the original coordinates of tethered atoms to binary restart files, so that the spring effect will be the
 same in a restarted simulation. See the read restart command for info on how to re-specify a fix
 in an input script that reads a restart file, so that the operation of
diff --git a/doc/html/fix_ttm.html b/doc/html/fix_ttm.html
index af630d2964..1b12323895 100644
--- a/doc/html/fix_ttm.html
+++ b/doc/html/fix_ttm.html
@@ -131,50 +131,50 @@
 
      fix ttm/mod command
      
 
      
 
      Syntax
      
-
      fix ID group-ID ttm seed C_e rho_e kappa_e gamma_p gamma_s v_0 Nx Ny Nz T_infile N T_outfile
-fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile
-
      
-
      
+
      +fix ID group-ID ttm seed C_e rho_e kappa_e gamma_p gamma_s v_0 Nx Ny Nz T_infile N T_outfile
+fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile
+
      
 
        
 
      • ID, group-ID are documented in fix command
        • 
 
      • style = ttm or ttm_mod
        • 
 
      • seed = random number seed to use for white noise (positive integer)
        • 
 
      • remaining arguments for fix ttm:
        • 
 
      
-
      C_e  = electronic specific heat (energy/(electron*temperature) units)
-rho_e = electronic density (electrons/volume units)
-kappa_e = electronic thermal conductivity (energy/(time*distance*temperature) units)
-gamma_p = friction coefficient due to electron-ion interactions (mass/time units)
-gamma_s = friction coefficient due to electronic stopping (mass/time units)
-v_0 = electronic stopping critical velocity (velocity units)
-Nx = number of thermal solve grid points in the x-direction (positive integer)
-Ny = number of thermal solve grid points in the y-direction (positive integer)
-Nz = number of thermal solve grid points in the z-direction (positive integer)
-T_infile = filename to read initial electronic temperature from
-N = dump TTM temperatures every this many timesteps, 0 = no dump
-T_outfile = filename to write TTM temperatures to (only needed if N > 0)
-
      
-
      
+
      +C_e  = electronic specific heat (energy/(electron*temperature) units)
+rho_e = electronic density (electrons/volume units)
+kappa_e = electronic thermal conductivity (energy/(time*distance*temperature) units)
+gamma_p = friction coefficient due to electron-ion interactions (mass/time units)
+gamma_s = friction coefficient due to electronic stopping (mass/time units)
+v_0 = electronic stopping critical velocity (velocity units)
+Nx = number of thermal solve grid points in the x-direction (positive integer)
+Ny = number of thermal solve grid points in the y-direction (positive integer)
+Nz = number of thermal solve grid points in the z-direction (positive integer)
+T_infile = filename to read initial electronic temperature from
+N = dump TTM temperatures every this many timesteps, 0 = no dump
+T_outfile = filename to write TTM temperatures to (only needed if N > 0)
+
      
 
        
 
      • remaining arguments for fix ttm/mod:
        • 
 
      
-
      init_file = file with the parameters to TTM
-Nx = number of thermal solve grid points in the x-direction (positive integer)
-Ny = number of thermal solve grid points in the y-direction (positive integer)
-Nz = number of thermal solve grid points in the z-direction (positive integer)
-T_infile = filename to read initial electronic temperature from
-N = dump TTM temperatures every this many timesteps, 0 = no dump
-T_outfile = filename to write TTM temperatures to (only needed if N > 0)
-
      
-
      
+
      +init_file = file with the parameters to TTM
+Nx = number of thermal solve grid points in the x-direction (positive integer)
+Ny = number of thermal solve grid points in the y-direction (positive integer)
+Nz = number of thermal solve grid points in the z-direction (positive integer)
+T_infile = filename to read initial electronic temperature from
+N = dump TTM temperatures every this many timesteps, 0 = no dump
+T_outfile = filename to write TTM temperatures to (only needed if N > 0)
+
      
 
      
 
      
 
      Examples
      
-
      fix 2 all ttm 699489 1.0 1.0 10 0.1 0.0 2.0 1 12 1 initialTs 1000 T.out
-fix 2 all ttm 123456 1.0 1.0 1.0 1.0 1.0 5.0 5 5 5 Te.in 1 Te.out
-fix 2 all ttm/mod 34277 parameters.txt 5 5 5 T_init 10 T_out
-
      
-
      
+
      +fix 2 all ttm 699489 1.0 1.0 10 0.1 0.0 2.0 1 12 1 initialTs 1000 T.out
+fix 2 all ttm 123456 1.0 1.0 1.0 1.0 1.0 5.0 5 5 5 Te.in 1 Te.out
+fix 2 all ttm/mod 34277 parameters.txt 5 5 5 T_init 10 T_out
+
      
 
      
 
      
 
      Description
      
@@ -330,34 +330,32 @@ is calculated as
      
 
      The fix ttm/mod parameter file init_file has the following syntax/
 Every line with the odd number is considered as a comment and
 ignored. The lines with the even numbers are treated as follows:
      
-
      a_0, energy/(temperature*electron) units
-a_1, energy/(temperature^2*electron) units
-a_2, energy/(temperature^3*electron) units
-a_3, energy/(temperature^4*electron) units
-a_4, energy/(temperature^5*electron) units
-C_0, energy/(temperature*electron) units
-A, 1/temperature units
-rho_e, electrons/volume units
-D_e, length^2/time units
-gamma_p, mass/time units
-gamma_s, mass/time units
-v_0, length/time units
-I_0, energy/(time*length^2) units
-lsurface, electron grid units (positive integer)
-rsurface, electron grid units (positive integer)
-l_skin, length units
-tau, time units
-B, dimensionless
-lambda, length units
-n_ion, ions/volume units
-surface_movement: 0 to disable tracking of surface motion, 1 to enable
-T_e_min, temperature units
-
      
-
      
-
      
+
      +a_0, energy/(temperature*electron) units
+a_1, energy/(temperature^2*electron) units
+a_2, energy/(temperature^3*electron) units
+a_3, energy/(temperature^4*electron) units
+a_4, energy/(temperature^5*electron) units
+C_0, energy/(temperature*electron) units
+A, 1/temperature units
+rho_e, electrons/volume units
+D_e, length^2/time units
+gamma_p, mass/time units
+gamma_s, mass/time units
+v_0, length/time units
+I_0, energy/(time*length^2) units
+lsurface, electron grid units (positive integer)
+rsurface, electron grid units (positive integer)
+l_skin, length units
+tau, time units
+B, dimensionless
+lambda, length units
+n_ion, ions/volume units
+surface_movement: 0 to disable tracking of surface motion, 1 to enable
+T_e_min, temperature units
+
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      These fixes write the state of the electronic subsystem and the energy
 exchange between the subsystems to binary restart files.  See the read_restart command
 for info on how to re-specify a fix in an input script that reads a
diff --git a/doc/html/fix_viscosity.html b/doc/html/fix_viscosity.html
index 03773104e4..16fa977a8f 100644
--- a/doc/html/fix_viscosity.html
+++ b/doc/html/fix_viscosity.html
@@ -226,9 +226,7 @@ deform the simmulation box via the PPPM solver since PPPM does not currently support
 non-orthogonal boxes.  Using fix viscosity keeps the box orthogonal;
 thus it does not suffer from this limitation.
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.
      
 
      This fix computes a global scalar which can be accessed by various
diff --git a/doc/html/fix_viscous.html b/doc/html/fix_viscous.html
index 5bf3e54e0a..e63286eaeb 100644
--- a/doc/html/fix_viscous.html
+++ b/doc/html/fix_viscous.html
@@ -194,10 +194,8 @@ performing the same operation as fix viscous.  Also note that the
 gamma of fix viscous is related to the damping parameter of fix langevin, however the former is specified in units
 of force/velocity and the latter in units of time, so that it can more
 easily be used as a thermostat.
      
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various output commands.  No parameter of this fix can
diff --git a/doc/html/fix_wall.html b/doc/html/fix_wall.html
index 8f3ac46551..0a1d123b92 100644
--- a/doc/html/fix_wall.html
+++ b/doc/html/fix_wall.html
@@ -179,12 +179,12 @@ args = coord epsilon sigma cutoff
 
      
 
      
 
      Examples
      
-
      fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box
-fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5
-fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5
-fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858
-
      
-
      
+
      +fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box
+fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5
+fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5
+fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858
+
      
 
      
 
      
 
      Description
      
@@ -321,22 +321,22 @@ want.
      
 in a time-dependent fashion using equal-style
 variables.  The wall interaction parameters (epsilon,
 sigma) could be varied with additional variable definitions.
      
-
      variable ramp equal ramp(0,10)
-fix 1 all wall xlo v_ramp 1.0 1.0 2.5
-
      
-
      
-
      variable linear equal vdisplace(0,20)
-fix 1 all wall xlo v_linear 1.0 1.0 2.5
-
      
-
      
-
      variable wiggle equal swiggle(0.0,5.0,3.0)
-fix 1 all wall xlo v_wiggle 1.0 1.0 2.5
-
      
-
      
-
      variable wiggle equal cwiggle(0.0,5.0,3.0)
-fix 1 all wall xlo v_wiggle 1.0 1.0 2.5
-
      
-
      
+
      +variable ramp equal ramp(0,10)
+fix 1 all wall xlo v_ramp 1.0 1.0 2.5
+
      
+
      +variable linear equal vdisplace(0,20)
+fix 1 all wall xlo v_linear 1.0 1.0 2.5
+
      
+
      +variable wiggle equal swiggle(0.0,5.0,3.0)
+fix 1 all wall xlo v_wiggle 1.0 1.0 2.5
+
      
+
      +variable wiggle equal cwiggle(0.0,5.0,3.0)
+fix 1 all wall xlo v_wiggle 1.0 1.0 2.5
+
      
 
      The ramp(lo,hi) function adjusts the wall position linearly from lo to
 hi over the course of a run.  The vdisplace(c0,velocity) function does
 something similar using the equation position = c0 + velocity*delta,
@@ -344,20 +344,18 @@ where delta is the elapsed time.
      
 
      The swiggle(c0,A,period) function causes the wall position to
 oscillate sinusoidally according to this equation, where omega = 2 PI
 / period:
      
-
      position = c0 + A sin(omega*delta)
-
      
-
      
+
      +position = c0 + A sin(omega*delta)
+
      
 
      The cwiggle(c0,A,period) function causes the wall position to
 oscillate sinusoidally according to this equation, which will have an
 initial wall velocity of 0.0, and thus may impose a gentler
 perturbation on the particles:
      
-
      position = c0 + A (1 - cos(omega*delta))
-
      
-
      
-
      
+
      +position = c0 + A (1 - cos(omega*delta))
+
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.
      
 
      The fix_modify energy option is supported by this
 fix to add the energy of interaction between atoms and each wall to
diff --git a/doc/html/fix_wall_gran.html b/doc/html/fix_wall_gran.html
index 08178f888a..b6360f4ffb 100644
--- a/doc/html/fix_wall_gran.html
+++ b/doc/html/fix_wall_gran.html
@@ -128,9 +128,9 @@
 
      fix wall/gran command
      
 
      
 
      Syntax
      
-
      fix ID group-ID wall/gran Kn Kt fstyle gamma_n gamma_t xmu dampflag wallstyle args keyword values ...
-
      
-
      
+
      +fix ID group-ID wall/gran Kn Kt fstyle gamma_n gamma_t xmu dampflag wallstyle args keyword values ...
+
      
 
        
 
      • ID, group-ID are documented in fix command
        • 
 
      • wall/gran = style name of this fix command
        • 
@@ -241,9 +241,9 @@ is perpendicular to the wall, it is more of a shaking motion.  A
 zcylinder wall can only be wiggled in the z dimension.
        
 
        Each timestep, the position of a wiggled wall in the appropriate dim
 is set according to this equation:
        
-
        position = coord + A - A cos (omega * delta)
-
        
-
        
+
        +position = coord + A - A cos (omega * delta)
+
        
 
        where coord is the specified initial position of the wall, A is
 the amplitude, omega is 2 PI / period, and delta is the time
 elapsed since the fix was specified.  The velocity of the wall is set
@@ -257,9 +257,7 @@ cylinder is moving in the z-direction along it’s axis.  A dimension of
 the clockwise direction for vshear > 0 or counter-clockwise for
 vshear < 0.  In this case, vshear is the tangential velocity of
 the wall at whatever radius has been defined.
        
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      This fix writes the shear friction state of atoms interacting with the
 wall to binary restart files, so that a simulation can
 continue correctly if granular potentials with shear “history” effects
diff --git a/doc/html/fix_wall_piston.html b/doc/html/fix_wall_piston.html
index ade80b4497..baed71d961 100644
--- a/doc/html/fix_wall_piston.html
+++ b/doc/html/fix_wall_piston.html
@@ -199,10 +199,8 @@ to define a wall position, but only when a numeric constant is used.
      
 A lattice value means the distance units are in lattice spacings.
 The lattice command must have been previously used to
 define the lattice spacings.
      
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various output commands.  No parameter of this fix can
diff --git a/doc/html/fix_wall_reflect.html b/doc/html/fix_wall_reflect.html
index 4c6467cd42..9df5dfe8ef 100644
--- a/doc/html/fix_wall_reflect.html
+++ b/doc/html/fix_wall_reflect.html
@@ -162,11 +162,11 @@
 
      
 
      
 
      Examples
      
-
      fix xwalls all wall/reflect xlo EDGE xhi EDGE
-fix walls all wall/reflect xlo 0.0 ylo 10.0 units box
-fix top all wall/reflect zhi v_pressdown
-
      
-
      
+
      +fix xwalls all wall/reflect xlo EDGE xhi EDGE
+fix walls all wall/reflect xlo 0.0 ylo 10.0 units box
+fix top all wall/reflect zhi v_pressdown
+
      
 
      
 
      
 
      Description
      
@@ -215,22 +215,22 @@ define the lattice spacings.
      
 
      Here are examples of variable definitions that move the wall position
 in a time-dependent fashion using equal-style
 variables.
      
-
      variable ramp equal ramp(0,10)
-fix 1 all wall/reflect xlo v_ramp
-
      
-
      
-
      variable linear equal vdisplace(0,20)
-fix 1 all wall/reflect xlo v_linear
-
      
-
      
-
      variable wiggle equal swiggle(0.0,5.0,3.0)
-fix 1 all wall/reflect xlo v_wiggle
-
      
-
      
-
      variable wiggle equal cwiggle(0.0,5.0,3.0)
-fix 1 all wall/reflect xlo v_wiggle
-
      
-
      
+
      +variable ramp equal ramp(0,10)
+fix 1 all wall/reflect xlo v_ramp
+
      
+
      +variable linear equal vdisplace(0,20)
+fix 1 all wall/reflect xlo v_linear
+
      
+
      +variable wiggle equal swiggle(0.0,5.0,3.0)
+fix 1 all wall/reflect xlo v_wiggle
+
      
+
      +variable wiggle equal cwiggle(0.0,5.0,3.0)
+fix 1 all wall/reflect xlo v_wiggle
+
      
 
      The ramp(lo,hi) function adjusts the wall position linearly from lo to
 hi over the course of a run.  The vdisplace(c0,velocity) function does
 something similar using the equation position = c0 + velocity*delta,
@@ -238,16 +238,16 @@ where delta is the elapsed time.
      
 
      The swiggle(c0,A,period) function causes the wall position to
 oscillate sinusoidally according to this equation, where omega = 2 PI
 / period:
      
-
      position = c0 + A sin(omega*delta)
-
      
-
      
+
      +position = c0 + A sin(omega*delta)
+
      
 
      The cwiggle(c0,A,period) function causes the wall position to
 oscillate sinusoidally according to this equation, which will have an
 initial wall velocity of 0.0, and thus may impose a gentler
 perturbation on the particles:
      
-
      position = c0 + A (1 - cos(omega*delta))
-
      
-
      
+
      +position = c0 + A (1 - cos(omega*delta))
+
      
 
      
 
      Styles with a gpu, intel, kk, omp, or opt suffix are
 functionally the same as the corresponding style without the suffix.
@@ -264,10 +264,8 @@ by including their suffix, or you can use the suffix command in your input script.
      
 
      See Section_accelerate of the manual for
 more instructions on how to use the accelerated styles effectively.
      
-
      
 
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.  None of the fix_modify options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various output commands.  No parameter of this fix can
diff --git a/doc/html/fix_wall_region.html b/doc/html/fix_wall_region.html
index 4f24bee99a..ba645d66ef 100644
--- a/doc/html/fix_wall_region.html
+++ b/doc/html/fix_wall_region.html
@@ -280,9 +280,7 @@ and does not blow up as r -> 0, but you must use a large enough
 epsilon that particles always reamin on the correct side of the
 region surface (r > 0).
      
 
      
-
      
-
      
-
      Restart, fix_modify, output, run start/stop, minimize info
      
+
      Restart, fix_modify, output, run start/stop, minimize info:
      
 
      No information about this fix is written to binary restart files.
      
 
      The fix_modify energy option is supported by this
 fix to add the energy of interaction between atoms and the wall to the
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index b30e351edf..b40e27bf00 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -156,93 +156,93 @@
 
      
 




 
 
 
      f_ID
 
 
 
 
 
 
     
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
      
@@ -256,69 +256,69 @@
   
 
       
-  
      bond_coeff
+  
      bond\_coeff
   
      
 
       
-  
      bond_style
+  
      bond\_style
   
      
 
       
-  
      bond_style class2
+  
      bond\_style class2
   
      
 
       
-  
      bond_style fene
+  
      bond\_style fene
   
      
 
       
-  
      bond_style fene/expand
+  
      bond\_style fene/expand
   
      
 
       
-  
      bond_style harmonic
+  
      bond\_style harmonic
   
      
 
       
-  
      bond_style harmonic/shift
+  
      bond\_style harmonic/shift
   
      
 
       
-  
      bond_style harmonic/shift/cut
+  
      bond\_style harmonic/shift/cut
   
      
 
       
-  
      bond_style hybrid
+  
      bond\_style hybrid
   
      
 
   
   
      
   
      
       
-  
      angle_coeff
+  
      angle\_coeff
   
      
 
       
-  
      angle_style
+  
      angle\_style
   
      
 
       
-  
      angle_style charmm
+  
      angle\_style charmm
   
      
 
       
-  
      angle_style class2
+  
      angle\_style class2
   
      
 
       
-  
      angle_style cosine
+  
      angle\_style cosine
   
      
 
       
-  
      angle_style cosine/delta
+  
      angle\_style cosine/delta
   
      
 
       
-  
      angle_style cosine/periodic
+  
      angle\_style cosine/periodic
   
      
 
       
-  
      angle_style cosine/shift
+  
      angle\_style cosine/shift
   
      
 
       
-  
      angle_style cosine/shift/exp
+  
      angle\_style cosine/shift/exp
   
      
 
       
-  
      angle_style cosine/squared
+  
      angle\_style cosine/squared
   
      
 
       
-  
      angle_style dipole
+  
      angle\_style dipole
   
      
 
   
      		
   
      
       
-  
      angle_style fourier
+  
      angle\_style fourier
   
      
 
       
-  
      angle_style fourier/simple
+  
      angle\_style fourier/simple
   
      
 
       
-  
      angle_style harmonic
+  
      angle\_style harmonic
   
      
 
       
-  
      angle_style hybrid
+  
      angle\_style hybrid
   
      
 
       
-  
      angle_style none
+  
      angle\_style none
   
      
 
       
-  
      angle_style quartic
+  
      angle\_style quartic
   
      
 
       
-  
      angle_style sdk
+  
      angle\_style sdk
   
      
 
       
-  
      angle_style table
+  
      angle\_style table
   
      
 
       
-  
      angle_style zero
+  
      angle\_style zero
   
      
 
       
-  
      atom_modify
+  
      atom\_modify
   
      
 
       
-  
      atom_style
+  
      atom\_style
   
      
 
   
      
       
-  
      bond_style morse
+  
      bond\_style morse
   
      
 
       
-  
      bond_style none
+  
      bond\_style none
   
      
 
       
-  
      bond_style nonlinear
+  
      bond\_style nonlinear
   
      
 
       
-  
      bond_style quartic
+  
      bond\_style quartic
   
      
 
       
-  
      bond_style table
+  
      bond\_style table
   
      
 
       
-  
      bond_style zero
+  
      bond\_style zero
   
      
 
       
-  
      bond_write
+  
      bond\_write
   
      
 
       
@@ -336,7 +336,7 @@
 
@@ -820,11 +820,11 @@
 
      
   
      
       
-  
      change_box
+  
      change\_box
   
      
 
       
@@ -344,11 +344,11 @@
   
 
       
-  
      comm_modify
+  
      comm\_modify
   
      
 
       
-  
      comm_style
+  
      comm\_style
   
      
 
       
@@ -798,19 +798,19 @@
   
 
       
-  
      compute_modify
+  
      compute\_modify
   
      
 
       
-  
      create_atoms
+  
      create\_atoms
   
      
 
       
-  
      create_bonds
+  
      create\_bonds
   
      
 
       
-  
      create_box
+  
      create\_box
   
      
 
   
      
@@ -1408,19 +1408,19 @@
   
 
       
-  
      fix smd/adjust_dt
+  
      fix smd/adjust\_dt
   
      
 
       
-  
      fix smd/integrate_tlsph
+  
      fix smd/integrate\_tlsph
   
      
 
       
-  
      fix smd/integrate_ulsph
+  
      fix smd/integrate\_ulsph
   
      
 
       
-  
      fix smd/move_tri_surf
+  
      fix smd/move\_tri\_surf
   
      
 
       
@@ -1428,7 +1428,7 @@
   
 
       
-  
      fix smd/wall_surface
+  
      fix smd/wall\_surface
   
      
 
       
@@ -1540,7 +1540,7 @@
   
 
       
-  
      fix_modify
+  
      fix\_modify
   
      
@@ -1570,57 +1570,57 @@
   
 
       
-  
      improper_coeff
+  
      improper\_coeff
   
      
 
       
-  
      improper_style
+  
      improper\_style
   
      
 
       
-  
      improper_style class2
+  
      improper\_style class2
   
      
 
       
-  
      improper_style cossq
+  
      improper\_style cossq
   
      
 
       
-  
      improper_style cvff
+  
      improper\_style cvff
   
      
 
       
-  
      improper_style distance
+  
      improper\_style distance
   
      
 
       
-  
      improper_style fourier
+  
      improper\_style fourier
   
      
   
      
       
-  
      delete_atoms
+  
      delete\_atoms
   
      
 
       
-  
      delete_bonds
+  
      delete\_bonds
   
      
 
       
@@ -832,73 +832,73 @@
   
 
       
-  
      dihedral_coeff
+  
      dihedral\_coeff
   
      
 
       
-  
      dihedral_style
+  
      dihedral\_style
   
      
 
       
-  
      dihedral_style charmm
+  
      dihedral\_style charmm
   
      
 
       
-  
      dihedral_style class2
+  
      dihedral\_style class2
   
      
 
       
-  
      dihedral_style cosine/shift/exp
+  
      dihedral\_style cosine/shift/exp
   
      
 
       
-  
      dihedral_style fourier
+  
      dihedral\_style fourier
   
      
 
       
-  
      dihedral_style harmonic
+  
      dihedral\_style harmonic
   
      
 
       
-  
      dihedral_style helix
+  
      dihedral\_style helix
   
      
 
       
-  
      dihedral_style hybrid
+  
      dihedral\_style hybrid
   
      
 
       
-  
      dihedral_style multi/harmonic
+  
      dihedral\_style multi/harmonic
   
      
 
       
-  
      dihedral_style nharmonic
+  
      dihedral\_style nharmonic
   
      
 
   
      		
   
      
       
-  
      dihedral_style none
+  
      dihedral\_style none
   
      
 
       
-  
      dihedral_style opls
+  
      dihedral\_style opls
   
      
 
       
-  
      dihedral_style quadratic
+  
      dihedral\_style quadratic
   
      
 
       
-  
      dihedral_style spherical
+  
      dihedral\_style spherical
   
      
 
       
-  
      dihedral_style table
+  
      dihedral\_style table
   
      
 
       
-  
      dihedral_style zero
+  
      dihedral\_style zero
   
      
 
       
@@ -906,7 +906,7 @@
   
 
       
-  
      displace_atoms
+  
      displace\_atoms
   
      
 
       
@@ -930,7 +930,7 @@
   
 
       
-  
      dump_modify
+  
      dump\_modify
   
      
 
   
      		
 
   
 
   
   
      
       
-  
      improper_style harmonic
+  
      improper\_style harmonic
   
      
 
       
-  
      improper_style hybrid
+  
      improper\_style hybrid
   
      
 
       
-  
      improper_style none
+  
      improper\_style none
   
      
 
       
-  
      improper_style ring
+  
      improper\_style ring
   
      
 
       
-  
      improper_style umbrella
+  
      improper\_style umbrella
   
      
 
       
-  
      improper_style zero
+  
      improper\_style zero
   
      
 
       
@@ -1648,13 +1648,13 @@
 
@@ -1688,11 +1688,11 @@
   
 
       
-  
      min_modify
+  
      min\_modify
   
      
 
       
-  
      min_style
+  
      min\_style
   
      
@@ -1716,7 +1716,7 @@
   
 
       
-  
      neigh_modify
+  
      neigh\_modify
   
      
 
       
@@ -1744,385 +1744,385 @@
   
 
       
-  
      pair_coeff
+  
      pair\_coeff
   
      
 
       
-  
      pair_modify
+  
      pair\_modify
   
      
 
       
-  
      pair_style
+  
      pair\_style
   
      
 
       
-  
      pair_style adp
+  
      pair\_style adp
   
      
 
       
-  
      pair_style airebo
+  
      pair\_style airebo
   
      
 
       
-  
      pair_style awpmd/cut
+  
      pair\_style awpmd/cut
   
      
 
       
-  
      pair_style beck
+  
      pair\_style beck
   
      
 
       
-  
      pair_style body
+  
      pair\_style body
   
      
 
       
-  
      pair_style bop
+  
      pair\_style bop
   
      
 
       
-  
      pair_style born
+  
      pair\_style born
   
      
 
       
-  
      pair_style born/coul/long/cs
+  
      pair\_style born/coul/long/cs
   
      
 
       
-  
      pair_style brownian
+  
      pair\_style brownian
   
      
 
       
-  
      pair_style buck
+  
      pair\_style buck
   
      
 
       
-  
      pair_style buck/long/coul/long
+  
      pair\_style buck/long/coul/long
   
      
 
       
-  
      pair_style colloid
+  
      pair\_style colloid
   
      
 
       
-  
      pair_style comb
+  
      pair\_style comb
   
      
 
       
-  
      pair_style coul/cut
+  
      pair\_style coul/cut
   
      
 
       
-  
      pair_style coul/diel
+  
      pair\_style coul/diel
   
      
 
       
-  
      pair_style dpd
+  
      pair\_style dpd
   
      
 
       
-  
      pair_style dpd/fdt
+  
      pair\_style dpd/fdt
   
      
 
       
-  
      pair_style dsmc
+  
      pair\_style dsmc
   
      
 
       
-  
      pair_style eam
+  
      pair\_style eam
   
      
 
       
-  
      pair_style edip
+  
      pair\_style edip
   
      
 
       
-  
      pair_style eff/cut
+  
      pair\_style eff/cut
   
      
 
       
-  
      pair_style eim
+  
      pair\_style eim
   
      
 
       
-  
      pair_style exp6/rx
+  
      pair\_style exp6/rx
   
      
 
       
-  
      pair_style gauss
+  
      pair\_style gauss
   
      
 
       
-  
      pair_style gayberne
+  
      pair\_style gayberne
   
      
 
       
-  
      pair_style gran/hooke
+  
      pair\_style gran/hooke
   
      
 
       
-  
      pair_style hbond/dreiding/lj
+  
      pair\_style hbond/dreiding/lj
   
      
 
       
-  
      pair_style hybrid
+  
      pair\_style hybrid
   
      
 
       
-  
      pair_style kim
+  
      pair\_style kim
   
      
 
       
-  
      pair_style lcbop
+  
      pair\_style lcbop
   
      
 
       
-  
      pair_style line/lj
+  
      pair\_style line/lj
   
      
 
       
-  
      pair_style list
+  
      pair\_style list
   
      
 
       
-  
      pair_style lj/charmm/coul/charmm
+  
      pair\_style lj/charmm/coul/charmm
   
      
 
       
-  
      pair_style lj/class2
+  
      pair\_style lj/class2
   
      
 
       
-  
      pair_style lj/cubic
+  
      pair\_style lj/cubic
   
      
 
       
-  
      pair_style lj/cut
+  
      pair\_style lj/cut
   
      
 
       
-  
      pair_style lj/cut/dipole/cut
+  
      pair\_style lj/cut/dipole/cut
   
      
 
       
-  
      pair_style lj/cut/soft
+  
      pair\_style lj/cut/soft
   
      
 
       
-  
      pair_style lj/expand
+  
      pair\_style lj/expand
   
      
 
       
-  
      pair_style lj/gromacs
+  
      pair\_style lj/gromacs
   
      
 
       
-  
      pair_style lj/long/coul/long
+  
      pair\_style lj/long/coul/long
   
      
 
       
-  
      pair_style lj/mdf
+  
      pair\_style lj/mdf
   
      
 
       
-  
      pair_style lj/sdk
+  
      pair\_style lj/sdk
   
      
 
       
-  
      pair_style lj/sf
+  
      pair\_style lj/sf
   
      
 
       
-  
      pair_style lj/smooth
+  
      pair\_style lj/smooth
   
      
 
       
-  
      pair_style lj/smooth/linear
+  
      pair\_style lj/smooth/linear
   
      
 
       
-  
      pair_style lj96/cut
+  
      pair\_style lj96/cut
   
      
   
      
       
-  
      kspace_modify
+  
      kspace\_modify
   
      
 
   
      		
   
      
       
-  
      kspace_style
+  
      kspace\_style
   
      
 
   
      		
 
   
 
   
   
      
       
-  
      pair_style lubricate
+  
      pair\_style lubricate
   
      
 
       
-  
      pair_style lubricateU
+  
      pair\_style lubricateU
   
      
 
       
-  
      pair_style meam
+  
      pair\_style meam
   
      
 
       
-  
      pair_style mgpt
+  
      pair\_style mgpt
   
      
 
       
-  
      pair_style mie/cut
+  
      pair\_style mie/cut
   
      
 
       
-  
      pair_style morse
+  
      pair\_style morse
   
      
 
       
-  
      pair_style multi/lucy
+  
      pair\_style multi/lucy
   
      
 
       
-  
      pair_style multi/lucy/rx
+  
      pair\_style multi/lucy/rx
   
      
 
       
-  
      pair_style nb3b/harmonic
+  
      pair\_style nb3b/harmonic
   
      
 
       
-  
      pair_style nm/cut
+  
      pair\_style nm/cut
   
      
 
       
-  
      pair_style none
+  
      pair\_style none
   
      
 
       
-  
      pair_style peri/pmb
+  
      pair\_style peri/pmb
   
      
 
       
-  
      pair_style polymorphic
+  
      pair\_style polymorphic
   
      
 
       
-  
      pair_style quip
+  
      pair\_style quip
   
      
 
       
-  
      pair_style reax
+  
      pair\_style reax
   
      
 
       
-  
      pair_style reax/c
+  
      pair\_style reax/c
   
      
 
       
-  
      pair_style resquared
+  
      pair\_style resquared
   
      
 
       
-  
      pair_style smd/hertz
+  
      pair\_style smd/hertz
   
      
 
       
-  
      pair_style smd/tlsph
+  
      pair\_style smd/tlsph
   
      
 
       
-  
      pair_style smd/tri_surface
+  
      pair\_style smd/tri\_surface
   
      
 
       
-  
      pair_style smd/ulsph
+  
      pair\_style smd/ulsph
   
      
 
       
-  
      pair_style smtbq
+  
      pair\_style smtbq
   
      
 
       
-  
      pair_style snap
+  
      pair\_style snap
   
      
 
       
-  
      pair_style soft
+  
      pair\_style soft
   
      
 
       
-  
      pair_style sph/heatconduction
+  
      pair\_style sph/heatconduction
   
      
 
       
-  
      pair_style sph/idealgas
+  
      pair\_style sph/idealgas
   
      
 
       
-  
      pair_style sph/lj
+  
      pair\_style sph/lj
   
      
 
       
-  
      pair_style sph/rhosum
+  
      pair\_style sph/rhosum
   
      
 
       
-  
      pair_style sph/taitwater
+  
      pair\_style sph/taitwater
   
      
 
       
-  
      pair_style sph/taitwater/morris
+  
      pair\_style sph/taitwater/morris
   
      
 
       
-  
      pair_style srp
+  
      pair\_style srp
   
      
 
       
-  
      pair_style sw
+  
      pair\_style sw
   
      
 
       
-  
      pair_style table
+  
      pair\_style table
   
      
 
       
-  
      pair_style table/rx
+  
      pair\_style table/rx
   
      
 
       
-  
      pair_style tersoff
+  
      pair\_style tersoff
   
      
 
       
-  
      pair_style tersoff/mod
+  
      pair\_style tersoff/mod
   
      
 
       
-  
      pair_style tersoff/zbl
+  
      pair\_style tersoff/zbl
   
      
 
       
-  
      pair_style thole
+  
      pair\_style thole
   
      
 
       
-  
      pair_style tri/lj
+  
      pair\_style tri/lj
   
      
 
       
-  
      pair_style vashishta
+  
      pair\_style vashishta
   
      
 
       
-  
      pair_style yukawa
+  
      pair\_style yukawa
   
      
 
       
-  
      pair_style yukawa/colloid
+  
      pair\_style yukawa/colloid
   
      
 
       
-  
      pair_style zbl
+  
      pair\_style zbl
   
      
 
       
-  
      pair_style zero
+  
      pair\_style zero
   
      
 
       
-  
      pair_write
+  
      pair\_write
   
      
 
       
@@ -2162,15 +2162,15 @@
 
@@ -2220,7 +2220,7 @@
   
      
   
      
       
-  
      read_data
+  
      read\_data
   
      
 
       
-  
      read_dump
+  
      read\_dump
   
      
 
       
-  
      read_restart
+  
      read\_restart
   
      
 
       
@@ -2188,7 +2188,7 @@
   
 
       
-  
      reset_timestep
+  
      reset\_timestep
   
      
 
       
@@ -2200,7 +2200,7 @@
   
 
       
-  
      run_style
+  
      run\_style
   
      
 
   
      		
   
      
       
-  
      special_bonds
+  
      special\_bonds
   
      
 
       
@@ -2246,13 +2246,13 @@
   
 
       
-  
      thermo_modify
+  
      thermo\_modify
   
      
 
   
      		
   
      
       
-  
      thermo_style
+  
      thermo\_style
   
      
 
       
@@ -2310,21 +2310,21 @@
 
diff --git a/doc/html/group.html b/doc/html/group.html
index d21faf214a..009ce0deea 100644
--- a/doc/html/group.html
+++ b/doc/html/group.html
@@ -257,22 +257,22 @@ or exclude from a group.
      For example, these lines define a variable “eatom” that calculates the
 potential energy of each atom and includes it in the group if its
 potential energy is above the threshhold value -3.0.
      
-
      compute         1 all pe/atom
-compute         2 all reduce sum c_1
-thermo_style    custom step temp pe c_2
-run             0
-
      
-
      
-
      variable        eatom atom "c_1 > -3.0"
-group           hienergy variable eatom
-
      
-
      
+
      +compute         1 all pe/atom
+compute         2 all reduce sum c_1
+thermo_style    custom step temp pe c_2
+run             0
+
      
+
      +variable        eatom atom "c_1 > -3.0"
+group           hienergy variable eatom
+
      Note that these lines
      
-
      compute         2 all reduce sum c_1
-thermo_style    custom step temp pe c_2
-run             0
-
      
-
      
+
      +compute         2 all reduce sum c_1
+thermo_style    custom step temp pe c_2
+run             0
+
      are necessary to insure that the “eatom” variable is current when the
 group command invokes it.  Because the eatom variable computes the
 per-atom energy via the pe/atom compute, it will only be current if a
@@ -353,7 +353,8 @@ being integrated by using a spherical region with a variable radius
 used to model a quench of the system, freezing atoms outside the
 shrinking sphere, then converting the remaining atoms to a static
 group and running further.
      
-
      variable        nsteps equal 5000
+
      +variable        nsteps equal 5000
 variable        rad equal 18-(step/v_nsteps)*(18-5)
 region          ss sphere 20 20 0 v_rad
 group           mobile dynamic all region ss
@@ -361,8 +362,7 @@ fix             1 mobile nve
 run             ${nsteps}
 group           mobile static
 run          ${nsteps}
-
      
-
      
+
      
 
      Note
      
 
      All fixes and computes take a group ID as an argument, but they
diff --git a/doc/html/if.html b/doc/html/if.html
index f2ba9d34e7..fe0350f9d5 100644
--- a/doc/html/if.html
+++ b/doc/html/if.html
@@ -143,7 +143,8 @@
 
      
 
      Examples
      
-
      if "${steps} > 1000" then quit
+
      +if "${steps} > 1000" then quit
 if "${myString} == a10" then quit
 if "$x <= $y" then "print X is smaller = $x" else "print Y is smaller = $y"
 if "(${eng} > 0.0) || ($n < 1000)" then &
@@ -152,10 +153,9 @@ elif $n<10000 &
   "timestep 0.01" &
 else &
   "timestep 0.02" &
-  "print 'Max step reached'"
+  "print 'Max step reached'"
 if "${eng} > ${eng_previous}" then "jump file1" else "jump file2"
-
      
-
      
+
 
      
 
      Description
      
@@ -249,10 +249,10 @@ clarity, you must enclose the entire expression in quotes.
      
 
      An expression is built out of numbers (which start with a digit or
 period or minus sign) or strings (which start with a letter and can
 contain alphanumeric characters or underscores):
      
-
      0.2, 100, 1.0e20, -15.4, etc
-InP, myString, a123, ab_23_cd, etc
-
      
-
      
+
      +0.2, 100, 1.0e20, -15.4, etc
+InP, myString, a123, ab_23_cd, etc
+
      
 
      and Boolean operators:
      
 
      A == B, A != B, A < B, A <= B, A > B, A >= B, A && B, A || B, !A
 
      
diff --git a/doc/html/improper_class2.html b/doc/html/improper_class2.html
index c6758cff97..0d39e5935a 100644
--- a/doc/html/improper_class2.html
+++ b/doc/html/improper_class2.html
@@ -131,17 +131,17 @@
 
      improper_style class2/omp command
      
 
      
 
      Syntax
      
-
      improper_style class2
-
      
-
      
+
      +improper_style class2
+
      
 
      
 
      
 
      Examples
      
-
      improper_style class2
-improper_coeff 1 100.0 0
-improper_coeff * aa 0.0 0.0 0.0 115.06 130.01 115.06
-
      
-
      
+
      +improper_style class2
+improper_coeff 1 100.0 0
+improper_coeff * aa 0.0 0.0 0.0 115.06 130.01 115.06
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/improper_cossq.html b/doc/html/improper_cossq.html
index 9a7aa85c8d..28c2370f09 100644
--- a/doc/html/improper_cossq.html
+++ b/doc/html/improper_cossq.html
@@ -131,16 +131,16 @@
 
      improper_style cossq/omp command
      
 
      
 
      Syntax
      
-
      improper_style cossq
-
      
-
      
+
      +improper_style cossq
+
      
 
      
 
      
 
      Examples
      
-
      improper_style cossq
-improper_coeff 1 4.0 0.0
-
      
-
      
+
      +improper_style cossq
+improper_coeff 1 4.0 0.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/improper_cvff.html b/doc/html/improper_cvff.html
index 186c5aa3e1..461f02eeab 100644
--- a/doc/html/improper_cvff.html
+++ b/doc/html/improper_cvff.html
@@ -134,16 +134,16 @@
 
      improper_style cvff/omp command
      
 
      
 
      Syntax
      
-
      improper_style cvff
-
      
-
      
+
      +improper_style cvff
+
      
 
      
 
      
 
      Examples
      
-
      improper_style cvff
-improper_coeff 1 80.0 -1 4
-
      
-
      
+
      +improper_style cvff
+improper_coeff 1 80.0 -1 4
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/improper_distance.html b/doc/html/improper_distance.html
index 69718ece9a..3f42cef8d0 100644
--- a/doc/html/improper_distance.html
+++ b/doc/html/improper_distance.html
@@ -132,10 +132,10 @@
 
      
 
      
 
      Examples
      
-
      improper_style distance
-improper_coeff 1 80.0 100.0
-
      
-
      
+
      +improper_style distance
+improper_coeff 1 80.0 100.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/improper_fourier.html b/doc/html/improper_fourier.html
index 545282aa2a..be22144ccf 100644
--- a/doc/html/improper_fourier.html
+++ b/doc/html/improper_fourier.html
@@ -131,16 +131,16 @@
 
      improper_style fourier/omp command
      
 
      
 
      Syntax
      
-
      improper_style fourier
-
      
-
      
+
      +improper_style fourier
+
      
 
      
 
      
 
      Examples
      
-
      improper_style fourier
-improper_coeff 1 100.0 180.0
-
      
-
      
+
      +improper_style fourier
+improper_coeff 1 100.0 180.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/improper_harmonic.html b/doc/html/improper_harmonic.html
index d268c62014..11553c0187 100644
--- a/doc/html/improper_harmonic.html
+++ b/doc/html/improper_harmonic.html
@@ -137,16 +137,16 @@
 
      improper_style harmonic/omp command
      
 
      
 
      Syntax
      
-
      improper_style harmonic
-
      
-
      
+
      +improper_style harmonic
+
      
 
      
 
      
 
      Examples
      
-
      improper_style harmonic
-improper_coeff 1 100.0 0
-
      
-
      
+
      +improper_style harmonic
+improper_coeff 1 100.0 0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/improper_ring.html b/doc/html/improper_ring.html
index aa3b557a57..0e7e4330b0 100644
--- a/doc/html/improper_ring.html
+++ b/doc/html/improper_ring.html
@@ -131,16 +131,16 @@
 
      improper_style ring/omp command
      
 
      
 
      Syntax
      
-
      improper_style ring
-
      
-
      
+
      +improper_style ring
+
      
 
      
 
      
 
      Examples
      
-
      improper_style ring
-improper_coeff 1 8000 70.5
-
      
-
      
+
      +improper_style ring
+improper_coeff 1 8000 70.5
+
      
 
      
 
      
 
      Description
      
@@ -150,8 +150,8 @@
 specified by (i,j,k,l) indices and theta0 its equilibrium value.
      
 
      If the 4 atoms in an improper quadruplet (listed in the data file read
 by the read_data command) are ordered i,j,k,l then
-theta_ijl is the angle between atoms i,j and l, theta_ijk is the
-angle between atoms i,j and k, theta_kjl is the angle between atoms
+theta_ijl is the angle between atoms i,j and l, theta_ijk is the
+angle between atoms i,j and k, theta_kjl is the angle between atoms
 j,k, and l.
      
 
      The “ring” improper style implements the improper potential introduced
 by Destree et al., in Equation (9) of (Destree).  This
diff --git a/doc/html/improper_umbrella.html b/doc/html/improper_umbrella.html
index f1fb943d5e..de79db67ef 100644
--- a/doc/html/improper_umbrella.html
+++ b/doc/html/improper_umbrella.html
@@ -131,16 +131,16 @@
 
      improper_style umbrella/omp command
      
 
      
 
      Syntax
      
-
      improper_style umbrella
-
      
-
      
+
      +improper_style umbrella
+
      
 
      
 
      
 
      Examples
      
-
      improper_style umbrella
-improper_coeff 1 100.0 180.0
-
      
-
      
+
      +improper_style umbrella
+improper_coeff 1 100.0 180.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/jump.html b/doc/html/jump.html
index a87db9100d..8b2f4578a4 100644
--- a/doc/html/jump.html
+++ b/doc/html/jump.html
@@ -158,22 +158,22 @@ script is re-opened and read again.
      
 
      The SELF option is not guaranteed to work when the current input
 script is being read through stdin (standard input), e.g.
      
 
      
-
      lmp_g++ < in.script
-
      
-
      
+
      +lmp_g++ < in.script
+
      
 
      since the SELF option invokes the C-library rewind() call, which may
 not be supported for stdin on some systems or by some MPI
 implementations.  This can be worked around by using the -in command-line argument, e.g.
      
-
      lmp_g++ -in in.script
-
      
-
      
+
      +lmp_g++ -in in.script
+
      
 
      or by using the -var command-line argument to pass the script name as a
 variable to the input script.  In the latter case, a
 variable called “fname” could be used in place of
 SELF, e.g.
      
-
      lmp_g++ -var fname in.script < in.script
-
      
-
      
+
      +lmp_g++ -var fname in.script < in.script
+
      
 
      The 2nd argument to the jump command is optional.  If specified, it is
 treated as a label and the new file is scanned (without executing
 commands) until the label is found, and commands are executed from
@@ -198,9 +198,9 @@ scripts.  In this example, LAMMPS is run on 40 processors, with 4
 partitions of 10 procs each.  An in.file containing the example
 variable and jump command will cause each partition to run a different
 simulation.
      
-
      mpirun -np 40 lmp_ibm -partition 4x10 -in in.file
-
      
-
      
+
      +mpirun -np 40 lmp_ibm -partition 4x10 -in in.file
+
      
 
      variable f world script.1 script.2 script.3 script.4
 jump $f
 
      
diff --git a/doc/html/kspace_modify.html b/doc/html/kspace_modify.html
index 961ea342d6..2019d48cff 100644
--- a/doc/html/kspace_modify.html
+++ b/doc/html/kspace_modify.html
@@ -128,9 +128,9 @@
 
      kspace_modify command
      
 
      
 
      Syntax
      
-
      kspace_modify keyword value ...
-
      
-
      
+
      +kspace_modify keyword value ...
+
      
 
        
 
      • one or more keyword/value pairs may be listed
        • 
 
      
@@ -174,10 +174,10 @@ keyword = mesh or order or order/disp or mix/disp
 
      
 
      
 
      Examples
      
-
      kspace_modify mesh 24 24 30 order 6
-kspace_modify slab 3.0
-
      
-
      
+
      +kspace_modify mesh 24 24 30 order 6
+kspace_modify slab 3.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/kspace_style.html b/doc/html/kspace_style.html
index 53a0c22ce2..5cecc5b41d 100644
--- a/doc/html/kspace_style.html
+++ b/doc/html/kspace_style.html
@@ -128,9 +128,9 @@
 
      kspace_style command
      
 
      
 
      Syntax
      
-
      kspace_style style value
-
      
-
      
+
      +kspace_style style value
+
      
 
        
 
      • style = none or ewald or ewald/disp or ewald/omp or pppm or pppm/cg or pppm/disp or pppm/tip4p or pppm/stagger or pppm/disp/tip4p or pppm/gpu or pppm/kk or pppm/omp or pppm/cg/omp or pppm/tip4p/omp or msm or msm/cg or msm/omp or msm/cg/omp
        • 
 
      
@@ -179,12 +179,12 @@
 
      
 
      
 
      Examples
      
-
      kspace_style pppm 1.0e-4
-kspace_style pppm/cg 1.0e-5 1.0e-6
-kspace style msm 1.0e-4
-kspace_style none
-
      
-
      
+
      +kspace_style pppm 1.0e-4
+kspace_style pppm/cg 1.0e-5 1.0e-6
+kspace style msm 1.0e-4
+kspace_style none
+
      
 
      
 
      
 
      Description
      
@@ -422,9 +422,9 @@ must be periodic and the z dimension must be non-periodic.
      
 
      
 
      
 
      Default
      
-
      kspace_style none
-
      
-
      
+
      +kspace_style none
+
      
 
      
 
      (Darden) Darden, York, Pedersen, J Chem Phys, 98, 10089 (1993).
      
 
      (Deserno) Deserno and Holm, J Chem Phys, 109, 7694 (1998).
      
diff --git a/doc/html/lattice.html b/doc/html/lattice.html
index 636cba7437..07d659915c 100644
--- a/doc/html/lattice.html
+++ b/doc/html/lattice.html
@@ -135,10 +135,10 @@
 
    • style = none or sc or bcc or fcc or hcp or diamond or         sq or sq2 or hex or custom
      • 
 
    • scale = scale factor between lattice and simulation box
      • 
 
-
      scale = reduced density rho* (for LJ units)
-scale = lattice constant in distance units (for all other units)
-
      
-
      
+
      +scale = reduced density rho* (for LJ units)
+scale = lattice constant in distance units (for all other units)
+
      
 
        
 
      • zero or more keyword/value pairs may be appended
        • 
 
      • keyword = origin or orient or spacing or a1 or a2 or a3 or basis
        • 
@@ -349,20 +349,21 @@ in commands that use the spacings should be decipherable.
        
 
        
 
        Example commands for generating a Wurtzite crystal (courtesy
 of Aidan Thompson), with its 8 atom unit cell.
        
-
        variable a equal  4.340330
+
        +variable a equal  4.340330
 variable b equal  $a*sqrt(3.0)
 variable c equal  $a*sqrt(8.0/3.0)
-
        
-
        
-
        variable 1_3 equal 1.0/3.0
-variable 2_3 equal 2.0/3.0
-variable 1_6 equal 1.0/6.0
-variable 5_6 equal 5.0/6.0
-variable 1_12 equal 1.0/12.0
-variable 5_12 equal 5.0/12.0
-
        
-
        
-
        lattice custom    1.0     &
+
        
+
        +variable 1_3 equal 1.0/3.0
+variable 2_3 equal 2.0/3.0
+variable 1_6 equal 1.0/6.0
+variable 5_6 equal 5.0/6.0
+variable 1_12 equal 1.0/12.0
+variable 5_12 equal 5.0/12.0
+
        
+
        +lattice custom    1.0     &
         a1      $a      0.0     0.0     &
         a2      0.0     $b      0.0     &
         a3      0.0     0.0     $c      &
@@ -374,17 +375,16 @@ variable c equal  $a*sqrt(8.0/3.0)
         basis   0.5     0.5     0.625   &
         basis   ${1_3}  0.0     0.125   &
         basis   ${5_6}  0.5     0.125
-
        
-
        
-
        region myreg block 0 1 0 1 0 1
-create_box      2 myreg
-create_atoms    1 box      &
-        basis   5       2       &
-        basis   6       2       &
-        basis   7       2       &
-        basis   8       2
-
        
-
        
+
+
        +region myreg block 0 1 0 1 0 1
+create_box      2 myreg
+create_atoms    1 box      &
+        basis   5       2       &
+        basis   6       2       &
+        basis   7       2       &
+        basis   8       2
+
        
 
      
 
      
 
      
diff --git a/doc/html/min_modify.html b/doc/html/min_modify.html
index 5434586014..bd9a1f285f 100644
--- a/doc/html/min_modify.html
+++ b/doc/html/min_modify.html
@@ -128,9 +128,9 @@
 
      min_modify command
      
 
      
 
      Syntax
      
-
      min_modify keyword values ...
-
      
-
      
+
      +min_modify keyword values ...
+
      
 
        
 
      • one or more keyword/value pairs may be listed
        • 
 
      
@@ -144,9 +144,9 @@ keyword = dmax or line
 
      
 
      
 
      Examples
      
-
      min_modify dmax 0.2
-
      
-
      
+
      +min_modify dmax 0.2
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/min_style.html b/doc/html/min_style.html
index 158cf94d45..c2c66e37b9 100644
--- a/doc/html/min_style.html
+++ b/doc/html/min_style.html
@@ -128,19 +128,19 @@
 
      min_style command
      
 
      
 
      Syntax
      
-
      min_style style
-
      
-
      
+
      +min_style style
+
      
 
        
 
      • style = cg or hftn or sd or quickmin or fire
        • 
 
      
 
      
 
      
 
      Examples
      
-
      min_style cg
-min_style fire
-
      
-
      
+
      +min_style cg
+min_style fire
+
      
 
      
 
      
 
      Description
      
@@ -206,9 +206,9 @@ involving the electron radius in 
 
      Default
      
-
      min_style cg
-
      
-
      
+
      +min_style cg
+
      
 
      
 
      (Sheppard) Sheppard, Terrell, Henkelman, J Chem Phys, 128, 134106
 (2008).  See ref 1 in this paper for original reference to Qmin in
diff --git a/doc/html/neigh_modify.html b/doc/html/neigh_modify.html
index cdad858eee..991e8aaf9b 100644
--- a/doc/html/neigh_modify.html
+++ b/doc/html/neigh_modify.html
@@ -128,9 +128,9 @@
 
      neigh_modify command
      
 
      
 
      Syntax
      
-
      neigh_modify keyword values ...
-
      
-
      
+
      +neigh_modify keyword values ...
+
      
 
        
 
      • one or more keyword/value pairs may be listed
        • 
 
      
@@ -170,13 +170,13 @@ keyword = delay or every or check or once or
 
      
 
      
 
      Examples
      
-
      neigh_modify every 2 delay 10 check yes page 100000
-neigh_modify exclude type 2 3
-neigh_modify exclude group frozen frozen check no
-neigh_modify exclude group residue1 chain3
-neigh_modify exclude molecule rigid
-
      
-
      
+
      +neigh_modify every 2 delay 10 check yes page 100000
+neigh_modify exclude type 2 3
+neigh_modify exclude group frozen frozen check no
+neigh_modify exclude group residue1 chain3
+neigh_modify exclude molecule rigid
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/next.html b/doc/html/next.html
index 91a180f677..e8b2338450 100644
--- a/doc/html/next.html
+++ b/doc/html/next.html
@@ -196,7 +196,8 @@ see in your directory during and after such a LAMMPS run.
      
 command with an index-style variable.  If this input script is named
 in.polymer, 8 simulations would be run using data files from
 directories run1 thru run8.
      
-
      variable d index run1 run2 run3 run4 run5 run6 run7 run8
+
      +variable d index run1 run2 run3 run4 run5 run6 run7 run8
 shell cd $d
 read_data data.polymer
 run 10000
@@ -204,8 +205,7 @@ shell cd ..
 clear
 next d
 jump in.polymer
-
      
-
      
+
 
      If the variable “d” were of style universe, and the same in.polymer
 input script were run on 3 partitions of processors, then the first 3
 simulations would begin, one on each set of processors.  Whichever
@@ -214,7 +214,8 @@ and run another simulation, and so forth until all 8 simulations were
 finished.
      
 
      Jump and next commands can also be nested to enable multi-level loops.
 For example, this script will run 15 simulations in a double loop.
      
-
      variable i loop 3
+
      +variable i loop 3
   variable j loop 5
   clear
   ...
@@ -225,8 +226,7 @@ For example, this script will run 15 simulations in a double loop.
      
   jump in.script
 next i
 jump in.script
-
      
-
      
+
 
      Here is an example of a double loop which uses the if and
 jump commands to break out of the inner loop when a
 condition is met, then continues iterating thru the outer loop.
      
diff --git a/doc/html/package.html b/doc/html/package.html
index 90477fc5ec..7146faef4d 100644
--- a/doc/html/package.html
+++ b/doc/html/package.html
@@ -572,11 +572,11 @@ compilers is to use one thread for each available CPU core when
 performance.
      
 
      Here are examples of how to set the environment variable when
 launching LAMMPS:
      
-
      env OMP_NUM_THREADS=4 lmp_machine -sf omp -in in.script
-env OMP_NUM_THREADS=2 mpirun -np 2 lmp_machine -sf omp -in in.script
-mpirun -x OMP_NUM_THREADS=2 -np 2 lmp_machine -sf omp -in in.script
-
      
-
      
+
      +env OMP_NUM_THREADS=4 lmp_machine -sf omp -in in.script
+env OMP_NUM_THREADS=2 mpirun -np 2 lmp_machine -sf omp -in in.script
+mpirun -x OMP_NUM_THREADS=2 -np 2 lmp_machine -sf omp -in in.script
+
      
 
      or you can set it permanently in your shell’s start-up script.
 All three of these examples use a total of 4 CPU cores.
      
 
      Note that different MPI implementations have different ways of passing
diff --git a/doc/html/pair_adp.html b/doc/html/pair_adp.html
index c38bbab6b5..5bc88ab7d0 100644
--- a/doc/html/pair_adp.html
+++ b/doc/html/pair_adp.html
@@ -131,17 +131,17 @@
 
      pair_style adp/omp command
      
 
      
 
      Syntax
      
-
      pair_style adp
-
      
-
      
+
      +pair_style adp
+
      
 
      
 
      
 
      Examples
      
-
      pair_style adp
-pair_coeff * * Ta.adp Ta
-pair_coeff * * ../potentials/AlCu.adp Al Al Cu
-
      
-
      
+
      +pair_style adp
+pair_coeff * * Ta.adp Ta
+pair_coeff * * ../potentials/AlCu.adp Al Al Cu
+
      
 
      
 
      
 
      Description
      
@@ -188,9 +188,9 @@ file which has tabulated ADP values for w elements and their alloy
 interactions: Cu and Al.  If your LAMMPS simulation has 4 atoms types
 and you want the 1st 3 to be Al, and the 4th to be Cu, you would use
 the following pair_coeff command:
      
-
      pair_coeff * * AlCu.adp Al Al Al Cu
-
      
-
      
+
      +pair_coeff * * AlCu.adp Al Al Al Cu
+
      
 
      The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The first three Al arguments map LAMMPS atom types 1,2,3 to the Al
 element in the extended setfl file.  The final Cu argument maps
diff --git a/doc/html/pair_airebo.html b/doc/html/pair_airebo.html
index 503da5ef6a..6827568073 100644
--- a/doc/html/pair_airebo.html
+++ b/doc/html/pair_airebo.html
@@ -143,9 +143,9 @@
 
      pair_style rebo/omp command
      
 
      
 
      Syntax
      
-
      pair_style style cutoff LJ_flag TORSION_flag
-
      
-
      
+
      +pair_style style cutoff LJ_flag TORSION_flag
+
      
 
        
 
      • style = airebo or airebo/morse or rebo
        • 
 
      • cutoff = LJ or Morse cutoff (sigma scale factor) (AIREBO and AIREBO-M only)
        • 
@@ -155,19 +155,19 @@
 
      
 
      
 
      Examples
      
-
      pair_style airebo 3.0
-pair_style airebo 2.5 1 0
-pair_coeff * * ../potentials/CH.airebo H C
-
      
-
      
-
      pair_style airebo/morse 3.0
-pair_coeff * * ../potentials/CH.airebo-m H C
-
      
-
      
-
      pair_style rebo
-pair_coeff * * ../potentials/CH.airebo H C
-
      
-
      
+
      +pair_style airebo 3.0
+pair_style airebo 2.5 1 0
+pair_coeff * * ../potentials/CH.airebo H C
+
      
+
      +pair_style airebo/morse 3.0
+pair_coeff * * ../potentials/CH.airebo-m H C
+
      
+
      +pair_style rebo
+pair_coeff * * ../potentials/CH.airebo H C
+
      
 
      
 
      
 
      Description
      
@@ -242,9 +242,9 @@ to specify the path for the potential file.
      
 
      As an example, if your LAMMPS simulation has 4 atom types and you want
 the 1st 3 to be C, and the 4th to be H, you would use the following
 pair_coeff command:
      
-
      pair_coeff * * CH.airebo C C C H
-
      
-
      
+
      +pair_coeff * * CH.airebo C C C H
+
      
 
      The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The first three C arguments map LAMMPS atom types 1,2,3 to the C
 element in the AIREBO file.  The final H argument maps LAMMPS atom
@@ -273,13 +273,13 @@ The 3 values correspond to the following sub-categories:
      
 
 
      To print these quantities to the log file (with descriptive column
 headings) the following commands could be included in an input script:
      
-
      compute 0 all pair airebo
-variable REBO     equal c_0[1]
-variable LJ       equal c_0[2]
-variable TORSION  equal c_0[3]
-thermo_style custom step temp epair v_REBO v_LJ v_TORSION
-
      
-
      
+
      +compute 0 all pair airebo
+variable REBO     equal c_0[1]
+variable LJ       equal c_0[2]
+variable TORSION  equal c_0[3]
+thermo_style custom step temp epair v_REBO v_LJ v_TORSION
+
      
 
      
 
      Styles with a gpu, intel, kk, omp, or opt suffix are
 functionally the same as the corresponding style without the suffix.
diff --git a/doc/html/pair_beck.html b/doc/html/pair_beck.html
index 10325668e8..baf69eecfa 100644
--- a/doc/html/pair_beck.html
+++ b/doc/html/pair_beck.html
@@ -134,20 +134,20 @@
 
      pair_style beck/omp command
      
 
      
 
      Syntax
      
-
      pair_style beck Rc
-
      
-
      
+
      +pair_style beck Rc
+
      
 
        
 
      • Rc = cutoff for interactions (distance units)
        • 
 
      
 
      
 
      
 
      Examples
      
-
      pair_style beck 8.0
-pair_coeff * * 399.671876712 0.0000867636112694 0.675 4.390 0.0003746
-pair_coeff 1 1 399.671876712 0.0000867636112694 0.675 4.390 0.0003746 6.0
-
      
-
      
+
      +pair_style beck 8.0
+pair_coeff * * 399.671876712 0.0000867636112694 0.675 4.390 0.0003746
+pair_coeff 1 1 399.671876712 0.0000867636112694 0.675 4.390 0.0003746 6.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_body.html b/doc/html/pair_body.html
index 5f4df83aa4..5f623fb0b7 100644
--- a/doc/html/pair_body.html
+++ b/doc/html/pair_body.html
@@ -128,18 +128,18 @@
 
      pair_style body command
      
 
      
 
      Syntax
      
-
      pair_style body cutoff
-
      
-
      
+
      +pair_style body cutoff
+
      
 
      cutoff = global cutoff for interactions (distance units)
      
 
      
 
      
 
      Examples
      
-
      pair_style body 3.0
-pair_coeff * * 1.0 1.0
-pair_coeff 1 1 1.0 1.5 2.5
-
      
-
      
+
      +pair_style body 3.0
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 1.0 1.5 2.5
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_bop.html b/doc/html/pair_bop.html
index 1c1d5e2ce7..f3b0785cd0 100644
--- a/doc/html/pair_bop.html
+++ b/doc/html/pair_bop.html
@@ -128,9 +128,9 @@
 
      pair_style bop command
      
 
      
 
      Syntax
      
-
      pair_style bop keyword ...
-
      
-
      
+
      +pair_style bop keyword ...
+
      
 
        
 
      • zero or more keywords may be appended
        • 
 
      • keyword = save
        • 
@@ -141,13 +141,13 @@
 
      
 
      
 
      Examples
      
-
      pair_style bop
-pair_coeff * * ../potentials/CdTe_bop Cd Te
-pair_style bop save
-pair_coeff * * ../potentials/CdTe.bop.table Cd Te Te
-comm_modify cutoff 14.70
-
      
-
      
+
      +pair_style bop
+pair_coeff * * ../potentials/CdTe_bop Cd Te
+pair_style bop save
+pair_coeff * * ../potentials/CdTe.bop.table Cd Te Te
+comm_modify cutoff 14.70
+
      
 
      
 
      
 
      Description
      
@@ -238,9 +238,9 @@ where N is the number of LAMMPS atom types:
      
 and Te.  If your LAMMPS simulation has 4 atoms types and you want the
 1st 3 to be Cd, and the 4th to be Te, you would use the following
 pair_coeff command:
      
-
      pair_coeff * * CdTe Cd Cd Cd Te
-
      
-
      
+
      +pair_coeff * * CdTe Cd Cd Cd Te
+
      
 
      The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The first three Cd arguments map LAMMPS atom types 1,2,3 to the Cd
 element in the BOP file.  The final Te argument maps LAMMPS atom type
diff --git a/doc/html/pair_born.html b/doc/html/pair_born.html
index 3740bb4699..c73ca9761f 100644
--- a/doc/html/pair_born.html
+++ b/doc/html/pair_born.html
@@ -161,9 +161,9 @@
 
      pair_style born/coul/wolf/omp command
      
 
      
 
      Syntax
      
-
      pair_style style args
-
      
-
      
+
      +pair_style style args
+
      
 
        
 
      • style = born or born/coul/long or born/coul/long/cs or born/coul/msm or born/coul/wolf
        • 
 
      • args = list of arguments for a particular style
        • 
@@ -185,31 +185,31 @@
 
      
 
      
 
      Examples
      
-
      pair_style born 10.0
-pair_coeff * * 6.08 0.317 2.340 24.18 11.51
-pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
-
      
-
      
-
      pair_style born/coul/long 10.0
-pair_style born/coul/long/cs 10.0
-pair_style born/coul/long 10.0 8.0
-pair_style born/coul/long/cs 10.0 8.0
-pair_coeff * * 6.08 0.317 2.340 24.18 11.51
-pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
-
      
-
      
-
      pair_style born/coul/msm 10.0
-pair_style born/coul/msm 10.0 8.0
-pair_coeff * * 6.08 0.317 2.340 24.18 11.51
-pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
-
      
-
      
-
      pair_style born/coul/wolf 0.25 10.0
-pair_style born/coul/wolf 0.25 10.0 9.0
-pair_coeff * * 6.08 0.317 2.340 24.18 11.51
-pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
-
      
-
      
+
      +pair_style born 10.0
+pair_coeff * * 6.08 0.317 2.340 24.18 11.51
+pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
+
      
+
      +pair_style born/coul/long 10.0
+pair_style born/coul/long/cs 10.0
+pair_style born/coul/long 10.0 8.0
+pair_style born/coul/long/cs 10.0 8.0
+pair_coeff * * 6.08 0.317 2.340 24.18 11.51
+pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
+
      
+
      +pair_style born/coul/msm 10.0
+pair_style born/coul/msm 10.0 8.0
+pair_coeff * * 6.08 0.317 2.340 24.18 11.51
+pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
+
      
+
      +pair_style born/coul/wolf 0.25 10.0
+pair_style born/coul/wolf 0.25 10.0 9.0
+pair_coeff * * 6.08 0.317 2.340 24.18 11.51
+pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_brownian.html b/doc/html/pair_brownian.html
index eaf0a723c3..777cb46f10 100644
--- a/doc/html/pair_brownian.html
+++ b/doc/html/pair_brownian.html
@@ -137,9 +137,9 @@
 
      pair_style brownian/poly/omp command
      
 
      
 
      Syntax
      
-
      pair_style style mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF
-
      
-
      
+
      +pair_style style mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF
+
      
 
        
 
      • style = brownian or brownian/poly
        • 
 
      • mu = dynamic viscosity (dynamic viscosity units)
        • 
@@ -155,11 +155,11 @@
 
      
 
      
 
      Examples
      
-
      pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius = 1)
-pair_coeff 1 1 2.05 2.8
-pair_coeff * *
-
      
-
      
+
      +pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius = 1)
+pair_coeff 1 1 2.05 2.8
+pair_coeff * *
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_buck.html b/doc/html/pair_buck.html
index 58eccb8ce8..fa537931bf 100644
--- a/doc/html/pair_buck.html
+++ b/doc/html/pair_buck.html
@@ -179,9 +179,9 @@
 
      pair_style buck/coul/msm/omp command
      
 
      
 
      Syntax
      
-
      pair_style style args
-
      
-
      
+
      +pair_style style args
+
      
 
        
 
      • style = buck or buck/coul/cut or buck/coul/long or buck/coul/long/cs or buck/coul/msm
        • 
 
      • args = list of arguments for a particular style
        • 
@@ -202,32 +202,32 @@
 
      
 
      
 
      Examples
      
-
      pair_style buck 2.5
-pair_coeff * * 100.0 1.5 200.0
-pair_coeff * * 100.0 1.5 200.0 3.0
-
      
-
      
-
      pair_style buck/coul/cut 10.0
-pair_style buck/coul/cut 10.0 8.0
-pair_coeff * * 100.0 1.5 200.0
-pair_coeff 1 1 100.0 1.5 200.0 9.0
-pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0
-
      
-
      
-
      pair_style buck/coul/long 10.0
-pair_style buck/coul/long/cs 10.0
-pair_style buck/coul/long 10.0 8.0
-pair_style buck/coul/long/cs 10.0 8.0
-pair_coeff * * 100.0 1.5 200.0
-pair_coeff 1 1 100.0 1.5 200.0 9.0
-
      
-
      
-
      pair_style buck/coul/msm 10.0
-pair_style buck/coul/msm 10.0 8.0
-pair_coeff * * 100.0 1.5 200.0
-pair_coeff 1 1 100.0 1.5 200.0 9.0
-
      
-
      
+
      +pair_style buck 2.5
+pair_coeff * * 100.0 1.5 200.0
+pair_coeff * * 100.0 1.5 200.0 3.0
+
      
+
      +pair_style buck/coul/cut 10.0
+pair_style buck/coul/cut 10.0 8.0
+pair_coeff * * 100.0 1.5 200.0
+pair_coeff 1 1 100.0 1.5 200.0 9.0
+pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0
+
      
+
      +pair_style buck/coul/long 10.0
+pair_style buck/coul/long/cs 10.0
+pair_style buck/coul/long 10.0 8.0
+pair_style buck/coul/long/cs 10.0 8.0
+pair_coeff * * 100.0 1.5 200.0
+pair_coeff 1 1 100.0 1.5 200.0 9.0
+
      
+
      +pair_style buck/coul/msm 10.0
+pair_style buck/coul/msm 10.0 8.0
+pair_coeff * * 100.0 1.5 200.0
+pair_coeff 1 1 100.0 1.5 200.0 9.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_buck_long.html b/doc/html/pair_buck_long.html
index a9e6b7e670..82fc5d5641 100644
--- a/doc/html/pair_buck_long.html
+++ b/doc/html/pair_buck_long.html
@@ -131,9 +131,9 @@
 
      pair_style buck/long/coul/long/omp command
      
 
      
 
      Syntax
      
-
      pair_style buck/long/coul/long flag_buck flag_coul cutoff (cutoff2)
-
      
-
      
+
      +pair_style buck/long/coul/long flag_buck flag_coul cutoff (cutoff2)
+
      
 
        
 
      • flag_buck = long or cut
        • 
 
      
@@ -155,13 +155,13 @@
 
      
 
      
 
      Examples
      
-
      pair_style buck/long/coul/long cut off 2.5
-pair_style buck/long/coul/long cut long 2.5 4.0
-pair_style buck/long/coul/long long long 4.0
-pair_coeff * * 1 1
-pair_coeff 1 1 1 3 4
-
      
-
      
+
      +pair_style buck/long/coul/long cut off 2.5
+pair_style buck/long/coul/long cut long 2.5 4.0
+pair_style buck/long/coul/long long long 4.0
+pair_coeff * * 1 1
+pair_coeff 1 1 1 3 4
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_charmm.html b/doc/html/pair_charmm.html
index 75994eddd2..93e44709ce 100644
--- a/doc/html/pair_charmm.html
+++ b/doc/html/pair_charmm.html
@@ -158,9 +158,9 @@
 
      pair_style lj/charmm/coul/msm/omp command
      
 
      
 
      Syntax
      
-
      pair_style style args
-
      
-
      
+
      +pair_style style args
+
      
 
        
 
      • style = lj/charmm/coul/charmm or lj/charmm/coul/charmm/implicit or lj/charmm/coul/long or lj/charmm/coul/msm
        • 
 
      • args = list of arguments for a particular style
        • 
@@ -182,30 +182,30 @@
 
      
 
      
 
      Examples
      
-
      pair_style lj/charmm/coul/charmm 8.0 10.0
-pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
-pair_coeff * * 100.0 2.0
-pair_coeff 1 1 100.0 2.0 150.0 3.5
-
      
-
      
-
      pair_style lj/charmm/coul/charmm/implicit 8.0 10.0
-pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0
-pair_coeff * * 100.0 2.0
-pair_coeff 1 1 100.0 2.0 150.0 3.5
-
      
-
      
-
      pair_style lj/charmm/coul/long 8.0 10.0
-pair_style lj/charmm/coul/long 8.0 10.0 9.0
-pair_coeff * * 100.0 2.0
-pair_coeff 1 1 100.0 2.0 150.0 3.5
-
      
-
      
-
      pair_style lj/charmm/coul/msm 8.0 10.0
-pair_style lj/charmm/coul/msm 8.0 10.0 9.0
-pair_coeff * * 100.0 2.0
-pair_coeff 1 1 100.0 2.0 150.0 3.5
-
      
-
      
+
      +pair_style lj/charmm/coul/charmm 8.0 10.0
+pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
+pair_coeff * * 100.0 2.0
+pair_coeff 1 1 100.0 2.0 150.0 3.5
+
      
+
      +pair_style lj/charmm/coul/charmm/implicit 8.0 10.0
+pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0
+pair_coeff * * 100.0 2.0
+pair_coeff 1 1 100.0 2.0 150.0 3.5
+
      
+
      +pair_style lj/charmm/coul/long 8.0 10.0
+pair_style lj/charmm/coul/long 8.0 10.0 9.0
+pair_coeff * * 100.0 2.0
+pair_coeff 1 1 100.0 2.0 150.0 3.5
+
      
+
      +pair_style lj/charmm/coul/msm 8.0 10.0
+pair_style lj/charmm/coul/msm 8.0 10.0 9.0
+pair_coeff * * 100.0 2.0
+pair_coeff 1 1 100.0 2.0 150.0 3.5
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_class2.html b/doc/html/pair_class2.html
index 5e62dd99ef..a2dee8a442 100644
--- a/doc/html/pair_class2.html
+++ b/doc/html/pair_class2.html
@@ -158,9 +158,9 @@
 
      pair_style lj/class2/coul/long/omp command
      
 
      
 
      Syntax
      
-
      pair_style style args
-
      
-
      
+
      +pair_style style args
+
      
 
        
 
      • style = lj/class2 or lj/class2/coul/cut or lj/class2/coul/long
        • 
 
      • args = list of arguments for a particular style
        • 
@@ -178,24 +178,24 @@
 
      
 
      
 
      Examples
      
-
      pair_style lj/class2 10.0
-pair_coeff * * 100.0 2.5
-pair_coeff 1 2* 100.0 2.5 9.0
-
      
-
      
-
      pair_style lj/class2/coul/cut 10.0
-pair_style lj/class2/coul/cut 10.0 8.0
-pair_coeff * * 100.0 3.0
-pair_coeff 1 1 100.0 3.5 9.0
-pair_coeff 1 1 100.0 3.5 9.0 9.0
-
      
-
      
-
      pair_style lj/class2/coul/long 10.0
-pair_style lj/class2/coul/long 10.0 8.0
-pair_coeff * * 100.0 3.0
-pair_coeff 1 1 100.0 3.5 9.0
-
      
-
      
+
      +pair_style lj/class2 10.0
+pair_coeff * * 100.0 2.5
+pair_coeff 1 2* 100.0 2.5 9.0
+
      
+
      +pair_style lj/class2/coul/cut 10.0
+pair_style lj/class2/coul/cut 10.0 8.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+pair_coeff 1 1 100.0 3.5 9.0 9.0
+
      
+
      +pair_style lj/class2/coul/long 10.0
+pair_style lj/class2/coul/long 10.0 8.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_colloid.html b/doc/html/pair_colloid.html
index c4254f1606..a1520bc730 100644
--- a/doc/html/pair_colloid.html
+++ b/doc/html/pair_colloid.html
@@ -134,22 +134,22 @@
 
      pair_style colloid/omp command
      
 
      
 
      Syntax
      
-
      pair_style colloid cutoff
-
      
-
      
+
      +pair_style colloid cutoff
+
      
 
        
 
      • cutoff = global cutoff for colloidal interactions (distance units)
        • 
 
      
 
      
 
      
 
      Examples
      
-
      pair_style colloid 10.0
-pair_coeff * *  25 1.0 10.0 10.0
-pair_coeff 1 1 144 1.0 0.0 0.0 3.0
-pair_coeff 1 2  75.398 1.0 0.0 10.0 9.0
-pair_coeff 2 2  39.478 1.0 10.0 10.0 25.0
-
      
-
      
+
      +pair_style colloid 10.0
+pair_coeff * *  25 1.0 10.0 10.0
+pair_coeff 1 1 144 1.0 0.0 0.0 3.0
+pair_coeff 1 2  75.398 1.0 0.0 10.0 9.0
+pair_coeff 2 2  39.478 1.0 10.0 10.0 25.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_comb.html b/doc/html/pair_comb.html
index d7ca86f242..c0768ee36a 100644
--- a/doc/html/pair_comb.html
+++ b/doc/html/pair_comb.html
@@ -134,10 +134,10 @@
 
      pair_style comb3 command
      
 
      
 
      Syntax
      
-
      pair_style comb
-pair_style comb3 keyword
-
      
-
      
+
      +pair_style comb
+pair_style comb3 keyword
+
      
 
       keyword = polar
   polar value = polar_on or polar_off = whether or not to include atomic polarization
@@ -145,15 +145,15 @@ keyword = polar
 
      
 
      
 
      Examples
      
-
      pair_style comb
-pair_coeff * * ../potentials/ffield.comb Si
-pair_coeff * * ../potentials/ffield.comb Hf Si O
-
      
-
      
-
      pair_style comb3 polar_off
-pair_coeff * * ../potentials/ffield.comb3 O Cu N C O
-
      
-
      
+
      +pair_style comb
+pair_coeff * * ../potentials/ffield.comb Si
+pair_coeff * * ../potentials/ffield.comb Hf Si O
+
      
+
      +pair_style comb3 polar_off
+pair_coeff * * ../potentials/ffield.comb3 O Cu N C O
+
      
 
      
 
      
 
      Description
      
@@ -191,9 +191,9 @@ command, where N is the number of LAMMPS atom types.
      
 HfO<sub>2</sub> interface has 4 atom types, and you want the 1st and
 last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would
 use the following pair_coeff command:
      
-
      pair_coeff * * ../potentials/ffield.comb Si Hf O Si
-
      
-
      
+
      +pair_coeff * * ../potentials/ffield.comb Si Hf O Si
+
      
 
      The first two arguments must be * * so as to span all LAMMPS atom
 types.  The first and last Si arguments map LAMMPS atom types 1 and 4
 to the Si element in the ffield.comb file.  The second Hf argument
diff --git a/doc/html/pair_coul.html b/doc/html/pair_coul.html
index 1df9e6791a..98cba31724 100644
--- a/doc/html/pair_coul.html
+++ b/doc/html/pair_coul.html
@@ -206,18 +206,18 @@
 
      pair_style tip4p/long/omp command
      
 
      
 
      Syntax
      
-
      pair_style coul/cut cutoff
-pair_style coul/debye kappa cutoff
-pair_style coul/dsf alpha cutoff
-pair_style coul/long cutoff
-pair_style coul/long/cs cutoff
-pair_style coul/long/gpu cutoff
-pair_style coul/wolf alpha cutoff
-pair_style coul/streitz cutoff keyword alpha
-pair_style tip4p/cut otype htype btype atype qdist cutoff
-pair_style tip4p/long otype htype btype atype qdist cutoff
-
      
-
      
+
      +pair_style coul/cut cutoff
+pair_style coul/debye kappa cutoff
+pair_style coul/dsf alpha cutoff
+pair_style coul/long cutoff
+pair_style coul/long/cs cutoff
+pair_style coul/long/gpu cutoff
+pair_style coul/wolf alpha cutoff
+pair_style coul/streitz cutoff keyword alpha
+pair_style tip4p/cut otype htype btype atype qdist cutoff
+pair_style tip4p/long otype htype btype atype qdist cutoff
+
      
 
        
 
      • cutoff = global cutoff for Coulombic interactions
        • 
 
      • kappa = Debye length (inverse distance units)
        • 
@@ -226,46 +226,46 @@
 
      
 
      
 
      Examples
      
-
      pair_style coul/cut 2.5
-pair_coeff * *
-pair_coeff 2 2 3.5
-
      
-
      
-
      pair_style coul/debye 1.4 3.0
-pair_coeff * *
-pair_coeff 2 2 3.5
-
      
-
      
-
      pair_style coul/dsf 0.05 10.0
-pair_coeff * *
-
      
-
      
-
      pair_style coul/long 10.0
-pair_style coul/long/cs 10.0
-pair_coeff * *
-
      
-
      
-
      pair_style coul/msm 10.0
-pair_coeff * *
-
      
-
      
-
      pair_style coul/wolf 0.2 9.0
-pair_coeff * *
-
      
-
      
-
      pair_style coul/streitz 12.0 ewald
-pair_style coul/streitz 12.0 wolf 0.30
-pair_coeff * * AlO.streitz Al O
-
      
-
      
-
      pair_style tip4p/cut 1 2 7 8 0.15 12.0
-pair_coeff * *
-
      
-
      
-
      pair_style tip4p/long 1 2 7 8 0.15 10.0
-pair_coeff * *
-
      
-
      
+
      +pair_style coul/cut 2.5
+pair_coeff * *
+pair_coeff 2 2 3.5
+
      
+
      +pair_style coul/debye 1.4 3.0
+pair_coeff * *
+pair_coeff 2 2 3.5
+
      
+
      +pair_style coul/dsf 0.05 10.0
+pair_coeff * *
+
      
+
      +pair_style coul/long 10.0
+pair_style coul/long/cs 10.0
+pair_coeff * *
+
      
+
      +pair_style coul/msm 10.0
+pair_coeff * *
+
      
+
      +pair_style coul/wolf 0.2 9.0
+pair_coeff * *
+
      
+
      +pair_style coul/streitz 12.0 ewald
+pair_style coul/streitz 12.0 wolf 0.30
+pair_coeff * * AlO.streitz Al O
+
      
+
      +pair_style tip4p/cut 1 2 7 8 0.15 12.0
+pair_coeff * *
+
      
+
      +pair_style tip4p/long 1 2 7 8 0.15 10.0
+pair_coeff * *
+
      
 
      
 
      
 
      Description
      
@@ -317,21 +317,21 @@ used with p
 short-range potential that has been parameterized appropriately) via
 the pair_style hybrid/overlay command.  Likewise,
 charge equilibration must be performed via the fix qeq/slater command. For example:
      
-
      pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy
-pair_coeff * * coul/streitz AlO.streitz Al O
-pair_coeff * * eam/alloy AlO.eam.alloy Al O
-fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz
-
      
-
      
+
      +pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy
+pair_coeff * * coul/streitz AlO.streitz Al O
+pair_coeff * * eam/alloy AlO.eam.alloy Al O
+fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz
+
      
 
      The keyword wolf in the coul/streitz command denotes computing
 Coulombic interactions via Wolf summation.  An additional damping
 parameter is required for the Wolf summation, as described for the
 coul/wolf potential above.  Alternatively, Coulombic interactions can
 be computed via an Ewald summation.  For example:
      
-
      pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy
-kspace_style ewald 1e-6
-
      
-
      
+
      +pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy
+kspace_style ewald 1e-6
+
      
 
      Keyword ewald does not need a damping parameter, but a
 kspace_style must be defined, which can be style
 ewald or pppm.  The Ewald method was used in Streitz and
diff --git a/doc/html/pair_coul_diel.html b/doc/html/pair_coul_diel.html
index 1f7d3e04af..88e078dfd5 100644
--- a/doc/html/pair_coul_diel.html
+++ b/doc/html/pair_coul_diel.html
@@ -131,17 +131,17 @@
 
      pair_style coul/diel/omp command
      
 
      
 
      Syntax
      
-
      pair_style coul/diel cutoff
-
      
-
      
+
      +pair_style coul/diel cutoff
+
      
 
      cutoff = global cutoff (distance units)
      
 
      
 
      
 
      Examples
      
-
      pair_style coul/diel 3.5
-pair_coeff 1 4 78. 1.375 0.112
-
      
-
      
+
      +pair_style coul/diel 3.5
+pair_coeff 1 4 78. 1.375 0.112
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_cs.html b/doc/html/pair_cs.html
index 75b462f741..12d0c515ef 100644
--- a/doc/html/pair_cs.html
+++ b/doc/html/pair_cs.html
@@ -131,9 +131,9 @@
 
      pair_style buck/coul/long/cs command
      
 
      
 
      Syntax
      
-
      pair_style style args
-
      
-
      
+
      +pair_style style args
+
      
 
        
 
      • style = born/coul/long/cs or buck/coul/long/cs
        • 
 
      • args = list of arguments for a particular style
        • 
@@ -149,16 +149,16 @@
 
      
 
      
 
      Examples
      
-
      pair_style born/coul/long/cs 10.0 8.0
-pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
-
      
-
      
-
      pair_style buck/coul/long/cs 10.0
-pair_style buck/coul/long/cs 10.0 8.0
-pair_coeff * * 100.0 1.5 200.0
-pair_coeff 1 1 100.0 1.5 200.0 9.0
-
      
-
      
+
      +pair_style born/coul/long/cs 10.0 8.0
+pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
+
      
+
      +pair_style buck/coul/long/cs 10.0
+pair_style buck/coul/long/cs 10.0 8.0
+pair_coeff * * 100.0 1.5 200.0
+pair_coeff 1 1 100.0 1.5 200.0 9.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_dipole.html b/doc/html/pair_dipole.html
index a8b5437180..25e82fc6e3 100644
--- a/doc/html/pair_dipole.html
+++ b/doc/html/pair_dipole.html
@@ -149,12 +149,12 @@
 
      pair_style lj/long/dipole/long command
      
 
      
 
      Syntax
      
-
      pair_style lj/cut/dipole/cut cutoff (cutoff2)
-pair_style lj/sf/dipole/sf cutoff (cutoff2)
-pair_style lj/cut/dipole/long cutoff (cutoff2)
-pair_style lj/long/dipole/long flag_lj flag_coul cutoff (cutoff2)
-
      
-
      
+
      +pair_style lj/cut/dipole/cut cutoff (cutoff2)
+pair_style lj/sf/dipole/sf cutoff (cutoff2)
+pair_style lj/cut/dipole/long cutoff (cutoff2)
+pair_style lj/long/dipole/long flag_lj flag_coul cutoff (cutoff2)
+
      
 
        
 
      • cutoff = global cutoff LJ (and Coulombic if only 1 arg) (distance units)
        • 
 
      • cutoff2 = global cutoff for Coulombic and dipole (optional) (distance units)
        • 
@@ -175,26 +175,26 @@
 
      
 
      
 
      Examples
      
-
      pair_style lj/cut/dipole/cut 10.0
-pair_coeff * * 1.0 1.0
-pair_coeff 2 3 1.0 1.0 2.5 4.0
-
      
-
      
-
      pair_style lj/sf/dipole/sf 9.0
-pair_coeff * * 1.0 1.0
-pair_coeff 2 3 1.0 1.0 2.5 4.0
-
      
-
      
-
      pair_style lj/cut/dipole/long 10.0
-pair_coeff * * 1.0 1.0
-pair_coeff 2 3 1.0 1.0 2.5 4.0
-
      
-
      
-
      pair_style lj/long/dipole/long long long 3.5 10.0
-pair_coeff * * 1.0 1.0
-pair_coeff 2 3 1.0 1.0 2.5 4.0
-
      
-
      
+
      +pair_style lj/cut/dipole/cut 10.0
+pair_coeff * * 1.0 1.0
+pair_coeff 2 3 1.0 1.0 2.5 4.0
+
      
+
      +pair_style lj/sf/dipole/sf 9.0
+pair_coeff * * 1.0 1.0
+pair_coeff 2 3 1.0 1.0 2.5 4.0
+
      
+
      +pair_style lj/cut/dipole/long 10.0
+pair_coeff * * 1.0 1.0
+pair_coeff 2 3 1.0 1.0 2.5 4.0
+
      
+
      +pair_style lj/long/dipole/long long long 3.5 10.0
+pair_coeff * * 1.0 1.0
+pair_coeff 2 3 1.0 1.0 2.5 4.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_dpd.html b/doc/html/pair_dpd.html
index f605baaa87..1275469c41 100644
--- a/doc/html/pair_dpd.html
+++ b/doc/html/pair_dpd.html
@@ -143,10 +143,10 @@
 
      pair_style dpd/tstat/omp command
      
 
      
 
      Syntax
      
-
      pair_style dpd T cutoff seed
-pair_style dpd/tstat Tstart Tstop cutoff seed
-
      
-
      
+
      +pair_style dpd T cutoff seed
+pair_style dpd/tstat Tstart Tstop cutoff seed
+
      
 
        
 
      • T = temperature (temperature units)
        • 
 
      • Tstart,Tstop = desired temperature at start/end of run (temperature units)
        • 
@@ -156,16 +156,16 @@
 
      
 
      
 
      Examples
      
-
      pair_style dpd 1.0 2.5 34387
-pair_coeff * * 3.0 1.0
-pair_coeff 1 1 3.0 1.0 1.0
-
      
-
      
-
      pair_style dpd/tstat 1.0 1.0 2.5 34387
-pair_coeff * * 1.0
-pair_coeff 1 1 1.0 1.0
-
      
-
      
+
      +pair_style dpd 1.0 2.5 34387
+pair_coeff * * 3.0 1.0
+pair_coeff 1 1 3.0 1.0 1.0
+
      
+
      +pair_style dpd/tstat 1.0 1.0 2.5 34387
+pair_coeff * * 1.0
+pair_coeff 1 1 1.0 1.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_dpd_fdt.html b/doc/html/pair_dpd_fdt.html
index cd8033694c..e6132b19d2 100644
--- a/doc/html/pair_dpd_fdt.html
+++ b/doc/html/pair_dpd_fdt.html
@@ -131,9 +131,9 @@
 
      pair_style dpd/fdt/energy command
      
 
      
 
      Syntax
      
-
      pair_style style args
-
      
-
      
+
      +pair_style style args
+
      
 
        
 
      • style = dpd/fdt or dpd/fdt/energy
        • 
 
      • args = list of arguments for a particular style
        • 
@@ -150,14 +150,14 @@
 
      
 
      
 
      Examples
      
-
      pair_style dpd/fdt 300.0 2.5 34387
-pair_coeff * * 3.0 1.0 2.5
-
      
-
      
-
      pair_style dpd/fdt/energy 2.5 34387
-pair_coeff * * 3.0 1.0 0.1 2.5
-
      
-
      
+
      +pair_style dpd/fdt 300.0 2.5 34387
+pair_coeff * * 3.0 1.0 2.5
+
      
+
      +pair_style dpd/fdt/energy 2.5 34387
+pair_coeff * * 3.0 1.0 0.1 2.5
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_dsmc.html b/doc/html/pair_dsmc.html
index 5f8ddd5600..4c971f1dd1 100644
--- a/doc/html/pair_dsmc.html
+++ b/doc/html/pair_dsmc.html
@@ -128,9 +128,9 @@
 
      pair_style dsmc command
      
 
      
 
      Syntax
      
-
      pair_style dsmc max_cell_size seed weighting Tref Nrecompute Nsample
-
      
-
      
+
      +pair_style dsmc max_cell_size seed weighting Tref Nrecompute Nsample
+
      
 
        
 
      • max_cell_size = global maximum cell size for DSMC interactions (distance units)
        • 
 
      • seed = random # seed (positive integer)
        • 
@@ -142,11 +142,11 @@
 
      
 
      
 
      Examples
      
-
      pair_style dsmc 2.5 34387 10 1.0 100 20
-pair_coeff * * 1.0
-pair_coeff 1 1 1.0
-
      
-
      
+
      +pair_style dsmc 2.5 34387 10 1.0 100 20
+pair_coeff * * 1.0
+pair_coeff 1 1 1.0
+
      
 
      
 
      
 
      Description
      
@@ -191,12 +191,12 @@ neighboring processors every timestep as they move.  This makes it
 possible to perform all collisions between pairs of particles that are
 on the same processor.  To ensure this occurs, you should use
 these commands:
      
-
      neighbor 0.0 bin
-neigh_modify every 1 delay 0 check no
-atom_modify sort 0 0.0
-communicate single cutoff 0.0
-
      
-
      
+
      +neighbor 0.0 bin
+neigh_modify every 1 delay 0 check no
+atom_modify sort 0 0.0
+communicate single cutoff 0.0
+
      
 
      These commands ensure that LAMMPS communicates particles to
 neighboring processors every timestep and that no ghost atoms are
 created.  The output statistics for a simulation run should indicate
diff --git a/doc/html/pair_eam.html b/doc/html/pair_eam.html
index 81abf57a5a..62a0305a0c 100644
--- a/doc/html/pair_eam.html
+++ b/doc/html/pair_eam.html
@@ -176,32 +176,32 @@
 
      pair_style eam/fs/opt command
      
 
      
 
      Syntax
      
-
      pair_style style
-
      
-
      
+
      +pair_style style
+
      
 
        
 
      • style = eam or eam/alloy or eam/cd or eam/fs
        • 
 
      
 
      
 
      
 
      Examples
      
-
      pair_style eam
-pair_coeff * * cuu3
-pair_coeff 1*3 1*3 niu3.eam
-
      
-
      
-
      pair_style eam/alloy
-pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni
-
      
-
      
-
      pair_style eam/cd
-pair_coeff * * ../potentials/FeCr.cdeam Fe Cr
-
      
-
      
-
      pair_style eam/fs
-pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni
-
      
-
      
+
      +pair_style eam
+pair_coeff * * cuu3
+pair_coeff 1*3 1*3 niu3.eam
+
      
+
      +pair_style eam/alloy
+pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni
+
      
+
      +pair_style eam/cd
+pair_coeff * * ../potentials/FeCr.cdeam Fe Cr
+
      
+
      +pair_style eam/fs
+pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni
+
      
 
      
 
      
 
      Description
      
@@ -270,9 +270,9 @@ single argument:
      
 
    • filename
      • 
 
 
      Thus the following command
      
-
      pair_coeff *2 1*2 cuu3.eam
-
      
-
      
+
      +pair_coeff *2 1*2 cuu3.eam
+
      
 
      will read the cuu3 potential file and use the tabulated Cu values for
 F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs
 1,2 and 2,1 are ignored).  See the pair_coeff doc
@@ -315,9 +315,9 @@ density).  The units for the effective charge Z are “atomic charge”
 sqrt(Hartree * Bohr-radii).  For two interacting atoms i,j this is used
 by LAMMPS to compute the pair potential term in the EAM energy
 expression as r*phi, in units of eV-Angstroms, via the formula
      
-
      r*phi = 27.2 * 0.529 * Zi * Zj
-
      
-
      
+
      +r*phi = 27.2 * 0.529 * Zi * Zj
+
      
 
      where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms.
      
 
      
 
      Style eam/alloy computes pairwise interactions using the same
@@ -350,9 +350,9 @@ page for alternate ways to specify the path for the potential file.
 If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to
 be Ni, and the 4th to be Al, you would use the following pair_coeff
 command:
      
-
      pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al
-
      
-
      
+
      +pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al
+
      
 
      The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The first three Ni arguments map LAMMPS atom types 1,2,3 to the Ni
 element in the setfl file.  The final Al argument maps LAMMPS atom
@@ -446,9 +446,9 @@ require that; the user can tabulate any functional form desired in the
 FS potential files.
      
 
      For style eam/fs, the form of the pair_coeff command is exactly the
 same as for style eam/alloy, e.g.
      
-
      pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al
-
      
-
      
+
      +pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al
+
      
 
      where there are N additional arguments after the filename, where N is
 the number of LAMMPS atom types.  See the pair_coeff
 doc page for alternate ways to specify the path for the potential
diff --git a/doc/html/pair_edip.html b/doc/html/pair_edip.html
index 8c9d9ccdee..54a690dde1 100644
--- a/doc/html/pair_edip.html
+++ b/doc/html/pair_edip.html
@@ -128,12 +128,12 @@
 
      pair_style edip command
      
 
      
 
      Syntax
      
-
      pair_style edip
-
      
-
      
-
      pair_style edip/omp
-
      
-
      
+
      +pair_style edip
+
      
+
      +pair_style edip/omp
+
      
 
      
 
      
 
      Examples
      
diff --git a/doc/html/pair_eff.html b/doc/html/pair_eff.html
index 6bcd28cef2..939cdbbf5c 100644
--- a/doc/html/pair_eff.html
+++ b/doc/html/pair_eff.html
@@ -128,9 +128,9 @@
 
      pair_style eff/cut command
      
 
      
 
      Syntax
      
-
      pair_style eff/cut cutoff keyword args ...
-
      
-
      
+
      +pair_style eff/cut cutoff keyword args ...
+
      
 
        
 
      • cutoff = global cutoff for Coulombic interactions
        • 
 
      • zero or more keyword/value pairs may be appended
        • 
@@ -146,16 +146,16 @@ keyword = limit/eradius or pressure/evirials or ecp
 
      
 
      
 
      Examples
      
-
      pair_style eff/cut 39.7
-pair_style eff/cut 40.0 limit/eradius
-pair_style eff/cut 40.0 limit/eradius pressure/evirials
-pair_style eff/cut 40.0 ecp 1 Si 3 C
-pair_coeff * *
-pair_coeff 2 2 20.0
-pair_coeff 1 s 0.320852 2.283269 0.814857
-pair_coeff 3 p 22.721015 0.728733 1.103199 17.695345 6.693621
-
      
-
      
+
      +pair_style eff/cut 39.7
+pair_style eff/cut 40.0 limit/eradius
+pair_style eff/cut 40.0 limit/eradius pressure/evirials
+pair_style eff/cut 40.0 ecp 1 Si 3 C
+pair_coeff * *
+pair_coeff 2 2 20.0
+pair_coeff 1 s 0.320852 2.283269 0.814857
+pair_coeff 3 p 22.721015 0.728733 1.103199 17.695345 6.693621
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_eim.html b/doc/html/pair_eim.html
index 62c5a4a918..831c9f00dc 100644
--- a/doc/html/pair_eim.html
+++ b/doc/html/pair_eim.html
@@ -131,21 +131,21 @@
 
      pair_style eim/omp command
      
 
      
 
      Syntax
      
-
      pair_style style
-
      
-
      
+
      +pair_style style
+
      
 
        
 
      • style = eim
        • 
 
      
 
      
 
      
 
      Examples
      
-
      pair_style eim
-pair_coeff * * Na Cl ../potentials/ffield.eim Na Cl
-pair_coeff * * Na Cl ffield.eim  Na Na Na Cl
-pair_coeff * * Na Cl ../potentials/ffield.eim Cl NULL Na
-
      
-
      
+
      +pair_style eim
+pair_coeff * * Na Cl ../potentials/ffield.eim Na Cl
+pair_coeff * * Na Cl ffield.eim  Na Na Na Cl
+pair_coeff * * Na Cl ../potentials/ffield.eim Cl NULL Na
+
      
 
      
 
      
 
      Description
      
@@ -207,9 +207,9 @@ to specify the path for the potential file.
      
 system with Na and Cl atoms.  If your LAMMPS simulation has 4 atoms
 types and you want the 1st 3 to be Na, and the 4th to be Cl, you would
 use the following pair_coeff command:
      
-
      pair_coeff * * Na Cl ffield.eim Na Na Na Cl
-
      
-
      
+
      +pair_coeff * * Na Cl ffield.eim Na Na Na Cl
+
      
 
      The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The filename is the EIM potential file.  The Na and Cl arguments
 (before the file name) are the two elements for which info will be
diff --git a/doc/html/pair_exp6_rx.html b/doc/html/pair_exp6_rx.html
index 6bd4ae6865..79f0a9b4ae 100644
--- a/doc/html/pair_exp6_rx.html
+++ b/doc/html/pair_exp6_rx.html
@@ -128,21 +128,21 @@
 
      pair_style exp6/rx command
      
 
      
 
      Syntax
      
-
      pair_style exp6/rx cutoff
-
      
-
      
+
      +pair_style exp6/rx cutoff
+
      
 
        
 
      • cutoff = global cutoff for DPD interactions (distance units)
        • 
 
      
 
      
 
      
 
      Examples
      
-
      pair_style exp6/rx 10.0
-pair_coeff * * exp6.params h2o h2o 1.0 1.0 10.0
-pair_coeff * * exp6.params h2o 1fluid 1.0 1.0 10.0
-pair_coeff * * exp6.params 1fluid 1fluid 1.0 1.0 10.0
-
      
-
      
+
      +pair_style exp6/rx 10.0
+pair_coeff * * exp6.params h2o h2o 1.0 1.0 10.0
+pair_coeff * * exp6.params h2o 1fluid 1.0 1.0 10.0
+pair_coeff * * exp6.params 1fluid 1fluid 1.0 1.0 10.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_gauss.html b/doc/html/pair_gauss.html
index 2f167476f8..d90d449b83 100644
--- a/doc/html/pair_gauss.html
+++ b/doc/html/pair_gauss.html
@@ -140,25 +140,25 @@
 
      pair_style gauss/cut/omp command
      
 
      
 
      Syntax
      
-
      pair_style gauss cutoff
-pair_style gauss/cut cutoff
-
      
-
      
+
      +pair_style gauss cutoff
+pair_style gauss/cut cutoff
+
      
 
        
 
      • cutoff = global cutoff for Gauss interactions (distance units)
        • 
 
      
 
      
 
      
 
      Examples
      
-
      pair_style gauss 12.0
-pair_coeff * * 1.0 0.9
-pair_coeff 1 4 1.0 0.9 10.0
-
      
-
      
-
      pair_style gauss/cut 3.5
-pair_coeff 1 4 0.2805 1.45 0.112
-
      
-
      
+
      +pair_style gauss 12.0
+pair_coeff * * 1.0 0.9
+pair_coeff 1 4 1.0 0.9 10.0
+
      
+
      +pair_style gauss/cut 3.5
+pair_coeff 1 4 0.2805 1.45 0.112
+
      
 
      
 
      
 
      Description
      
@@ -239,11 +239,11 @@ sites have an atom within the distance at which the force is a maximum
 = sqrt(0.5/b).  This quantity can be accessed via the compute pair command as a vector of values of length 1.
      
 
      To print this quantity to the log file (with a descriptive column
 heading) the following commands could be included in an input script:
      
-
      compute gauss all pair gauss
-variable occ equal c_gauss[1]
-thermo_style custom step temp epair v_occ
-
      
-
      
+
      +compute gauss all pair gauss
+variable occ equal c_gauss[1]
+thermo_style custom step temp epair v_occ
+
      
 
      
 
      
 
      
diff --git a/doc/html/pair_gayberne.html b/doc/html/pair_gayberne.html
index 0b02a49a51..68e46bd2d8 100644
--- a/doc/html/pair_gayberne.html
+++ b/doc/html/pair_gayberne.html
@@ -137,9 +137,9 @@
 
      pair_style gayberne/omp command
      
 
      
 
      Syntax
      
-
      pair_style gayberne gamma upsilon mu cutoff
-
      
-
      
+
      +pair_style gayberne gamma upsilon mu cutoff
+
      
 
        
 
      • gamma = shift for potential minimum (typically 1)
        • 
 
      • upsilon = exponent for eta orientation-dependent energy function
        • 
@@ -149,10 +149,10 @@
 
      
 
      
 
      Examples
      
-
      pair_style gayberne 1.0 1.0 1.0 10.0
-pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0
-
      
-
      
+
      +pair_style gayberne 1.0 1.0 1.0 10.0
+pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_gran.html b/doc/html/pair_gran.html
index a1fb53f824..37946c96aa 100644
--- a/doc/html/pair_gran.html
+++ b/doc/html/pair_gran.html
@@ -143,9 +143,9 @@
 
      pair_style gran/hertz/history/omp command
      
 
      
 
      Syntax
      
-
      pair_style style Kn Kt gamma_n gamma_t xmu dampflag
-
      
-
      
+
      +pair_style style Kn Kt gamma_n gamma_t xmu dampflag
+
      
 
        
 
      • style = gran/hooke or gran/hooke/history or gran/hertz/history
        • 
 
      • Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
        • 
@@ -169,10 +169,10 @@ for details.
        
 
      
 
      
 
      Examples
      
-
      pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 1
-pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0
-
      
-
      
+
      +pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 1
+pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0
+
      
 
      
 
      
 
      Description
      
@@ -287,9 +287,9 @@ each pair of atom types via the pair_coeff for all
 pairs of granular atom types.  For example the command
      
-
      pair_coeff * *
-
      
-
      
+
      +pair_coeff * *
+
      
 
      should be used if all atoms in the simulation interact via a granular
 potential (i.e. one of the pair styles above is used).  If a granular
 potential is used as a sub-style of pair_style hybrid, then specific atom types can be used in the
diff --git a/doc/html/pair_gromacs.html b/doc/html/pair_gromacs.html
index 7cc3aee2ce..a58a10912a 100644
--- a/doc/html/pair_gromacs.html
+++ b/doc/html/pair_gromacs.html
@@ -140,9 +140,9 @@
 
      pair_style lj/gromacs/coul/gromacs/omp command
      
 
      
 
      Syntax
      
-
      pair_style style args
-
      
-
      
+
      +pair_style style args
+
      
 
        
 
      • style = lj/gromacs or lj/gromacs/coul/gromacs
        • 
 
      • args = list of arguments for a particular style
        • 
@@ -157,16 +157,16 @@
 
      
 
      
 
      Examples
      
-
      pair_style lj/gromacs 9.0 12.0
-pair_coeff * * 100.0 2.0
-pair_coeff 2 2 100.0 2.0 8.0 10.0
-
      
-
      
-
      pair_style lj/gromacs/coul/gromacs 9.0 12.0
-pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0
-pair_coeff * * 100.0 2.0
-
      
-
      
+
      +pair_style lj/gromacs 9.0 12.0
+pair_coeff * * 100.0 2.0
+pair_coeff 2 2 100.0 2.0 8.0 10.0
+
      
+
      +pair_style lj/gromacs/coul/gromacs 9.0 12.0
+pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0
+pair_coeff * * 100.0 2.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_hbond_dreiding.html b/doc/html/pair_hbond_dreiding.html
index 659f637dec..e639ba34e8 100644
--- a/doc/html/pair_hbond_dreiding.html
+++ b/doc/html/pair_hbond_dreiding.html
@@ -137,9 +137,9 @@
 
      pair_style hbond/dreiding/morse/omp command
      
 
      
 
      Syntax
      
-
      pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof
-
      
-
      
+
      +pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof
+
      
 
        
 
      • style = hbond/dreiding/lj or hbond/dreiding/morse
        • 
 
      • n = cosine angle periodicity
        • 
@@ -151,14 +151,14 @@
 
      
 
      
 
      Examples
      
-
      pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90
-pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 9.0 11.0 90.0
-
      
-
      
-
      pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/morse 2 9.0 11.0 90
-pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90
-
      
-
      
+
      +pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90
+pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 9.0 11.0 90.0
+
      
+
      +pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/morse 2 9.0 11.0 90
+pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90
+
      
 
      
 
      
 
      Description
      
@@ -265,7 +265,7 @@ follows:
      
 
      A single hydrogen atom type K can be specified, or a wild-card
 asterisk can be used in place of or in conjunction with the K
 arguments to select multiple types as hydrogens.  This takes the form
-“*” or “n” or “n” or “m*n”.  See the pair_coeff command
+“*” or “*n” or “n*” or “m*n”.  See the pair_coeff command
 doc page for details.
      
 
      If the donor flag is i, then the atom of type I in the pair_coeff
 command is treated as the donor, and J is the acceptor.  If the donor
@@ -321,12 +321,12 @@ quantities can be accessed via the 
      compute hb all pair hbond/dreiding/lj
-variable n_hbond equal c_hb[1] #number hbonds
-variable E_hbond equal c_hb[2] #hbond energy
-thermo_style custom step temp epair v_E_hbond
-
      
-
      
+
      +compute hb all pair hbond/dreiding/lj
+variable n_hbond equal c_hb[1] #number hbonds
+variable E_hbond equal c_hb[2] #hbond energy
+thermo_style custom step temp epair v_E_hbond
+
      
 
      
 
      
 
      
diff --git a/doc/html/pair_hybrid.html b/doc/html/pair_hybrid.html
index afe0cebcd6..60044d0faf 100644
--- a/doc/html/pair_hybrid.html
+++ b/doc/html/pair_hybrid.html
@@ -137,27 +137,27 @@
 
      pair_style hybrid/overlay/omp command
      
 
      
 
      Syntax
      
-
      pair_style hybrid style1 args style2 args ...
-pair_style hybrid/overlay style1 args style2 args ...
-
      
-
      
+
      +pair_style hybrid style1 args style2 args ...
+pair_style hybrid/overlay style1 args style2 args ...
+
      
 
        
 
      • style1,style2 = list of one or more pair styles and their arguments
        • 
 
      
 
      
 
      
 
      Examples
      
-
      pair_style hybrid lj/cut/coul/cut 10.0 eam lj/cut 5.0
-pair_coeff 1*2 1*2 eam niu3
-pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
-pair_coeff 1*2 3 lj/cut 0.5 1.2
-
      
-
      
-
      pair_style hybrid/overlay lj/cut 2.5 coul/long 2.0
-pair_coeff * * lj/cut 1.0 1.0
-pair_coeff * * coul/long
-
      
-
      
+
      +pair_style hybrid lj/cut/coul/cut 10.0 eam lj/cut 5.0
+pair_coeff 1*2 1*2 eam niu3
+pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
+pair_coeff 1*2 3 lj/cut 0.5 1.2
+
      
+
      +pair_style hybrid/overlay lj/cut 2.5 coul/long 2.0
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff * * coul/long
+
      
 
      
 
      
 
      Description
      
@@ -218,22 +218,22 @@ these coefficients apply to.
      
 
      For example, consider a simulation with 3 atom types: types 1 and 2
 are Ni atoms, type 3 are LJ atoms with charges.  The following
 commands would set up a hybrid simulation:
      
-
      pair_style hybrid eam/alloy lj/cut/coul/cut 10.0 lj/cut 8.0
-pair_coeff * * eam/alloy nialhjea Ni Ni NULL
-pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
-pair_coeff 1*2 3 lj/cut 0.8 1.3
-
      
-
      
+
      +pair_style hybrid eam/alloy lj/cut/coul/cut 10.0 lj/cut 8.0
+pair_coeff * * eam/alloy nialhjea Ni Ni NULL
+pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
+pair_coeff 1*2 3 lj/cut 0.8 1.3
+
      
 
      As an example of using the same pair style multiple times, consider a
 simulation with 2 atom types.  Type 1 is Si, type 2 is C.  The
 following commands would model the Si atoms with Tersoff, the C atoms
 with Tersoff, and the cross-interactions with Lennard-Jones:
      
-
      pair_style hybrid lj/cut 2.5 tersoff tersoff
-pair_coeff * * tersoff 1 Si.tersoff Si NULL
-pair_coeff * * tersoff 2 C.tersoff NULL C
-pair_coeff 1 2 lj/cut 1.0 1.5
-
      
-
      
+
      +pair_style hybrid lj/cut 2.5 tersoff tersoff
+pair_coeff * * tersoff 1 Si.tersoff Si NULL
+pair_coeff * * tersoff 2 C.tersoff NULL C
+pair_coeff 1 2 lj/cut 1.0 1.5
+
      
 
      If pair coefficients are specified in the data file read via the
 read_data command, then the same rule applies.
 E.g. “eam/alloy” or “lj/cut” must be added after the atom type, for
@@ -266,16 +266,16 @@ sub-style that has already been defined for that pair of atoms, then
 the new pair coefficients simply override the previous ones, as in the
 normal usage of the pair_coeff command.  E.g. these two sets of
 commands are the same:
      
-
      pair_style lj/cut 2.5
-pair_coeff * * 1.0 1.0
-pair_coeff 2 2 1.5 0.8
-
      
-
      
-
      pair_style hybrid/overlay lj/cut 2.5
-pair_coeff * * lj/cut 1.0 1.0
-pair_coeff 2 2 lj/cut 1.5 0.8
-
      
-
      
+
      +pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 2 2 1.5 0.8
+
      
+
      +pair_style hybrid/overlay lj/cut 2.5
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff 2 2 lj/cut 1.5 0.8
+
      
 
      Coefficients must be defined for each pair of atoms types via the
 pair_coeff command as described above, or in the
 data file or restart files read by the read_data or
@@ -293,9 +293,9 @@ command.  You can assign it to some sub-style and set the coefficients
 so that there is effectively no interaction (e.g. epsilon = 0.0 in a
 LJ potential).  Or, for hybrid and hybrid/overlay simulations, you
 can use this form of the pair_coeff command in your input script:
      
-
      pair_coeff   2 3 none
-
      
-
      
+
      +pair_coeff  2 3 none
+
      
 
      or this form in the “Pair Coeffs” section of the data file:
      
 
      3 none
 
      
@@ -321,29 +321,29 @@ described by the different force fields do not mix.
      
 
      Here is an example for mixing CHARMM and AMBER: The global amber
 setting sets the 1-4 interactions to non-zero scaling factors and
 then overrides them with 0.0 only for CHARMM:
      
-
      special_bonds amber
-pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
-pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
-
      
-
      
+
      +special_bonds amber
+pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
+pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
+
      
 
      The this input achieves the same effect:
      
-
      special_bonds 0.0 0.0 0.1
-pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
-pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
-pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333
-pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
-
      
-
      
+
      +special_bonds 0.0 0.0 0.1
+pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0
+pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5
+pair_modify pair lj/cut/coul/long special coul 0.0 0.0 0.83333333
+pair_modify pair lj/charmm/coul/long special lj/coul 0.0 0.0 0.0
+
      
 
      Here is an example for mixing Tersoff with OPLS/AA based on
 a data file that defines bonds for all atoms where for the
 Tersoff part of the system the force constants for the bonded
 interactions have been set to 0. Note the global settings are
 effectively lj/coul 0.0 0.0 0.5 as required for OPLS/AA:
      
-
      special_bonds lj/coul 1e-20 1e-20 0.5
-pair_hybrid tersoff lj/cut/coul/long 12.0
-pair_modify pair tersoff special lj/coul 1.0 1.0 1.0
-
      
-
      
+
      +special_bonds lj/coul 1e-20 1e-20 0.5
+pair_hybrid tersoff lj/cut/coul/long 12.0
+pair_modify pair tersoff special lj/coul 1.0 1.0 1.0
+
      
 
      See the pair_modify doc page for details on
 the specific syntax, requirements and restrictions.
      
 
      
@@ -358,7 +358,7 @@ ReaxFF, etc.  The way to think about using these potentials in a
 hybrid setting is as follows.
      
 
      
 
      A subset of atom types is assigned to the many-body potential with a
-single pair_coeff command, using “* *” to include
+single pair_coeff command, using “* *” to include
 all types and the NULL keywords described above to exclude specific
 types not assigned to that potential.  If types 1,3,4 were assigned in
 that way (but not type 2), this means that all many-body interactions
@@ -388,16 +388,16 @@ atoms in one surface, and type 2 for atoms in the other, and you wish
 to use a Tersoff potential to compute interactions within each
 surface, but not between surfaces.  Then either of these two command
 sequences would implement that model:
      
-
      pair_style hybrid tersoff
-pair_coeff * * tersoff SiC.tersoff C C
-pair_coeff 1 2 none
-
      
-
      
-
      pair_style tersoff
-pair_coeff * * SiC.tersoff C C
-neigh_modify exclude type 1 2
-
      
-
      
+
      +pair_style hybrid tersoff
+pair_coeff * * tersoff SiC.tersoff C C
+pair_coeff 1 2 none
+
      
+
      +pair_style tersoff
+pair_coeff * * SiC.tersoff C C
+neigh_modify exclude type 1 2
+
      
 
      Either way, only neighbor lists with 1-1 or 2-2 interactions would be
 passed to the Tersoff potential, which means it would compute no
 3-body interactions containing both type 1 and 2 atoms.
      
@@ -406,11 +406,11 @@ potentials together, in an overlapping manner.  Imagine you have CNT
 (C atoms) on a Si surface.  You want to use Tersoff for Si/Si and Si/C
 interactions, and AIREBO for C/C interactions.  Si atoms are type 1; C
 atoms are type 2.  Something like this will work:
      
-
      pair_style hybrid/overlay tersoff airebo 3.0
-pair_coeff * * tersoff SiC.tersoff.custom Si C
-pair_coeff * * airebo CH.airebo NULL C
-
      
-
      
+
      +pair_style hybrid/overlay tersoff airebo 3.0
+pair_coeff * * tersoff SiC.tersoff.custom Si C
+pair_coeff * * airebo CH.airebo NULL C
+
      
 
      Note that to prevent the Tersoff potential from computing C/C
 interactions, you would need to modify the SiC.tersoff file to turn
 off C/C interaction, i.e. by setting the appropriate coefficients to
diff --git a/doc/html/pair_line_lj.html b/doc/html/pair_line_lj.html
index f36f573822..c79f73301e 100644
--- a/doc/html/pair_line_lj.html
+++ b/doc/html/pair_line_lj.html
@@ -128,19 +128,19 @@
 
      pair_style line/lj command
      
 
      
 
      Syntax
      
-
      pair_style line/lj cutoff
-
      
-
      
+
      +pair_style line/lj cutoff
+
      
 
      cutoff = global cutoff for interactions (distance units)
      
 
      
 
      
 
      Examples
      
-
      pair_style line/lj 3.0
-pair_coeff * * 1.0 1.0 1.0 0.8 1.12
-pair_coeff 1 2 1.0 2.0 1.0 1.5 1.12 5.0
-pair_coeff 1 2 1.0 0.0 1.0 1.0 2.5
-
      
-
      
+
      +pair_style line/lj 3.0
+pair_coeff * * 1.0 1.0 1.0 0.8 1.12
+pair_coeff 1 2 1.0 2.0 1.0 1.5 1.12 5.0
+pair_coeff 1 2 1.0 0.0 1.0 1.0 2.5
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_list.html b/doc/html/pair_list.html
index f7d59aba21..2897df868b 100644
--- a/doc/html/pair_list.html
+++ b/doc/html/pair_list.html
@@ -128,9 +128,9 @@
 
      pair_style list command
      
 
      
 
      Syntax
      
-
      pair_style list listfile cutoff keyword
-
      
-
      
+
      +pair_style list listfile cutoff keyword
+
      
 
        
 
      • listfile = name of file with list of pairwise interactions
        • 
 
      • cutoff = global cutoff (distance units)
        • 
@@ -139,15 +139,15 @@
 
      
 
      
 
      Examples
      
-
      pair_style list restraints.txt 200.0
-pair_coeff * *
-
      
-
      
-
      pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0
-pair_coeff * * lj/cut 1.0 1.0
-pair_coeff 3* 3* list
-
      
-
      
+
      +pair_style list restraints.txt 200.0
+pair_coeff * *
+
      
+
      +pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0
+pair_coeff * * lj/cut 1.0 1.0
+pair_coeff 3* 3* list
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_lj.html b/doc/html/pair_lj.html
index fd46ab5d3b..73f9948c27 100644
--- a/doc/html/pair_lj.html
+++ b/doc/html/pair_lj.html
@@ -218,9 +218,9 @@
 
      pair_style lj/cut/tip4p/long/opt command
      
 
      
 
      Syntax
      
-
      pair_style style args
-
      
-
      
+
      +pair_style style args
+
      
 
        
 
      • style = lj/cut or lj/cut/coul/cut or lj/cut/coul/debye or lj/cut/coul/dsf or lj/cut/coul/long or lj/cut/coul/long/cs or lj/cut/coul/msm or lj/cut/tip4p/long
        • 
 
      • args = list of arguments for a particular style
        • 
@@ -261,56 +261,56 @@
 
      
 
      
 
      Examples
      
-
      pair_style lj/cut 2.5
-pair_coeff * * 1 1
-pair_coeff 1 1 1 1.1 2.8
-
      
-
      
-
      pair_style lj/cut/coul/cut 10.0
-pair_style lj/cut/coul/cut 10.0 8.0
-pair_coeff * * 100.0 3.0
-pair_coeff 1 1 100.0 3.5 9.0
-pair_coeff 1 1 100.0 3.5 9.0 9.0
-
      
-
      
-
      pair_style lj/cut/coul/debye 1.5 3.0
-pair_style lj/cut/coul/debye 1.5 2.5 5.0
-pair_coeff * * 1.0 1.0
-pair_coeff 1 1 1.0 1.5 2.5
-pair_coeff 1 1 1.0 1.5 2.5 5.0
-
      
-
      
-
      pair_style lj/cut/coul/dsf 0.05 2.5 10.0
-pair_coeff * * 1.0 1.0
-pair_coeff 1 1 1.0 1.0 2.5
-
      
-
      
-
      pair_style lj/cut/coul/long 10.0
-pair_style lj/cut/coul/long/cs 10.0
-pair_style lj/cut/coul/long 10.0 8.0
-pair_style lj/cut/coul/long/cs 10.0 8.0
-pair_coeff * * 100.0 3.0
-pair_coeff 1 1 100.0 3.5 9.0
-
      
-
      
-
      pair_style lj/cut/coul/msm 10.0
-pair_style lj/cut/coul/msm 10.0 8.0
-pair_coeff * * 100.0 3.0
-pair_coeff 1 1 100.0 3.5 9.0
-
      
-
      
-
      pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0
-pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0
-pair_coeff * * 100.0 3.0
-pair_coeff 1 1 100.0 3.5 9.0
-
      
-
      
-
      pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0
-pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0
-pair_coeff * * 100.0 3.0
-pair_coeff 1 1 100.0 3.5 9.0
-
      
-
      
+
      +pair_style lj/cut 2.5
+pair_coeff * * 1 1
+pair_coeff 1 1 1 1.1 2.8
+
      
+
      +pair_style lj/cut/coul/cut 10.0
+pair_style lj/cut/coul/cut 10.0 8.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+pair_coeff 1 1 100.0 3.5 9.0 9.0
+
      
+
      +pair_style lj/cut/coul/debye 1.5 3.0
+pair_style lj/cut/coul/debye 1.5 2.5 5.0
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 1.0 1.5 2.5
+pair_coeff 1 1 1.0 1.5 2.5 5.0
+
      
+
      +pair_style lj/cut/coul/dsf 0.05 2.5 10.0
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 1.0 1.0 2.5
+
      
+
      +pair_style lj/cut/coul/long 10.0
+pair_style lj/cut/coul/long/cs 10.0
+pair_style lj/cut/coul/long 10.0 8.0
+pair_style lj/cut/coul/long/cs 10.0 8.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+
      
+
      +pair_style lj/cut/coul/msm 10.0
+pair_style lj/cut/coul/msm 10.0 8.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+
      
+
      +pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0
+pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+
      
+
      +pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0
+pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_lj96.html b/doc/html/pair_lj96.html
index 25b68df4b4..3f7e8fdd9b 100644
--- a/doc/html/pair_lj96.html
+++ b/doc/html/pair_lj96.html
@@ -134,20 +134,20 @@
 
      pair_style lj96/cut/omp command
      
 
      
 
      Syntax
      
-
      pair_style lj96/cut cutoff
-
      
-
      
+
      +pair_style lj96/cut cutoff
+
      
 
        
 
      • cutoff = global cutoff for lj96/cut interactions (distance units)
        • 
 
      
 
      
 
      
 
      Examples
      
-
      pair_style lj96/cut 2.5
-pair_coeff * * 1.0 1.0 4.0
-pair_coeff 1 1 1.0 1.0
-
      
-
      
+
      +pair_style lj96/cut 2.5
+pair_coeff * * 1.0 1.0 4.0
+pair_coeff 1 1 1.0 1.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_lj_cubic.html b/doc/html/pair_lj_cubic.html
index 6032650397..6dad5de332 100644
--- a/doc/html/pair_lj_cubic.html
+++ b/doc/html/pair_lj_cubic.html
@@ -134,16 +134,16 @@
 
      pair_style lj/cubic/omp command
      
 
      
 
      Syntax
      
-
      pair_style lj/cubic
-
      
-
      
+
      +pair_style lj/cubic
+
      
 
      
 
      
 
      Examples
      
-
      pair_style lj/cubic
-pair_coeff * * 1.0 0.8908987
-
      
-
      
+
      +pair_style lj/cubic
+pair_coeff * * 1.0 0.8908987
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_lj_expand.html b/doc/html/pair_lj_expand.html
index fef3f21c46..69fc39c046 100644
--- a/doc/html/pair_lj_expand.html
+++ b/doc/html/pair_lj_expand.html
@@ -134,20 +134,20 @@
 
      pair_style lj/expand/omp command
      
 
      
 
      Syntax
      
-
      pair_style lj/expand cutoff
-
      
-
      
+
      +pair_style lj/expand cutoff
+
      
 
        
 
      • cutoff = global cutoff for lj/expand interactions (distance units)
        • 
 
      
 
      
 
      
 
      Examples
      
-
      pair_style lj/expand 2.5
-pair_coeff * * 1.0 1.0 0.5
-pair_coeff 1 1 1.0 1.0 -0.2 2.0
-
      
-
      
+
      +pair_style lj/expand 2.5
+pair_coeff * * 1.0 1.0 0.5
+pair_coeff 1 1 1.0 1.0 -0.2 2.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_lj_long.html b/doc/html/pair_lj_long.html
index fd2fa29241..2256d2d48e 100644
--- a/doc/html/pair_lj_long.html
+++ b/doc/html/pair_lj_long.html
@@ -137,9 +137,9 @@
 
      pair_style lj/long/tip4p/long command
      
 
      
 
      Syntax
      
-
      pair_style style args
-
      
-
      
+
      +pair_style style args
+
      
 
        
 
      • style = lj/long/coul/long or lj/long/tip4p/long
        • 
 
      • args = list of arguments for a particular style
        • 
@@ -171,19 +171,19 @@
 
      
 
      
 
      Examples
      
-
      pair_style lj/long/coul/long cut off 2.5
-pair_style lj/long/coul/long cut long 2.5 4.0
-pair_style lj/long/coul/long long long 2.5 4.0
-pair_coeff * * 1 1
-pair_coeff 1 1 1 3 4
-
      
-
      
-
      pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0
-pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 10.0
-pair_coeff * * 100.0 3.0
-pair_coeff 1 1 100.0 3.5 9.0
-
      
-
      
+
      +pair_style lj/long/coul/long cut off 2.5
+pair_style lj/long/coul/long cut long 2.5 4.0
+pair_style lj/long/coul/long long long 2.5 4.0
+pair_coeff * * 1 1
+pair_coeff 1 1 1 3 4
+
      
+
      +pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0
+pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 10.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_lj_sf.html b/doc/html/pair_lj_sf.html
index 8505d91cf5..b09ff7e036 100644
--- a/doc/html/pair_lj_sf.html
+++ b/doc/html/pair_lj_sf.html
@@ -131,20 +131,20 @@
 
      pair_style lj/sf/omp command
      
 
      
 
      Syntax
      
-
      pair_style lj/sf cutoff
-
      
-
      
+
      +pair_style lj/sf cutoff
+
      
 
        
 
      • cutoff = global cutoff for Lennard-Jones interactions (distance units)
        • 
 
      
 
      
 
      
 
      Examples
      
-
      pair_style lj/sf 2.5
-pair_coeff * * 1.0 1.0
-pair_coeff 1 1 1.0 1.0 3.0
-
      
-
      
+
      +pair_style lj/sf 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 1.0 1.0 3.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_lj_smooth.html b/doc/html/pair_lj_smooth.html
index 22565da2d7..0973d95ff9 100644
--- a/doc/html/pair_lj_smooth.html
+++ b/doc/html/pair_lj_smooth.html
@@ -131,9 +131,9 @@
 
      pair_style lj/smooth/omp command
      
 
      
 
      Syntax
      
-
      pair_style lj/smooth Rin Rc
-
      
-
      
+
      +pair_style lj/smooth Rin Rc
+
      
 
        
 
      • Rin = inner cutoff beyond which force smoothing will be applied (distance units)
        • 
 
      • Rc = outer cutoff for lj/smooth interactions (distance units)
        • 
@@ -141,11 +141,11 @@
 
      
 
      
 
      Examples
      
-
      pair_style lj/smooth 8.0 10.0
-pair_coeff * * 10.0 1.5
-pair_coeff 1 1 20.0 1.3 7.0 9.0
-
      
-
      
+
      +pair_style lj/smooth 8.0 10.0
+pair_coeff * * 10.0 1.5
+pair_coeff 1 1 20.0 1.3 7.0 9.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_lj_smooth_linear.html b/doc/html/pair_lj_smooth_linear.html
index f19e28551e..edd6d68386 100644
--- a/doc/html/pair_lj_smooth_linear.html
+++ b/doc/html/pair_lj_smooth_linear.html
@@ -131,20 +131,20 @@
 
      pair_style lj/smooth/linear/omp command
      
 
      
 
      Syntax
      
-
      pair_style lj/smooth/linear Rc
-
      
-
      
+
      +pair_style lj/smooth/linear Rc
+
      
 
        
 
      • Rc = cutoff for lj/smooth/linear interactions (distance units)
        • 
 
      
 
      
 
      
 
      Examples
      
-
      pair_style lj/smooth/linear 5.456108274435118
-pair_coeff * * 0.7242785984051078 2.598146797350056
-pair_coeff 1 1 20.0 1.3 9.0
-
      
-
      
+
      +pair_style lj/smooth/linear 5.456108274435118
+pair_coeff * * 0.7242785984051078 2.598146797350056
+pair_coeff 1 1 20.0 1.3 9.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_lj_soft.html b/doc/html/pair_lj_soft.html
index e253536083..f67e200935 100644
--- a/doc/html/pair_lj_soft.html
+++ b/doc/html/pair_lj_soft.html
@@ -173,9 +173,9 @@
 
      pair_style tip4p/long/soft/omp command
      
 
      
 
      Syntax
      
-
      pair_style style args
-
      
-
      
+
      +pair_style style args
+
      
 
        
 
      • style = lj/cut/soft or lj/cut/coul/cut/soft or lj/cut/coul/long/soft or lj/cut/tip4p/long/soft or lj/charmm/coul/long/soft or coul/cut/soft or coul/long/soft or tip4p/long/soft
        • 
 
      • args = list of arguments for a particular style
        • 
@@ -219,47 +219,47 @@
 
      
 
      
 
      Examples
      
-
      pair_style lj/cut/soft 2.0 0.5 9.5
-pair_coeff * * 0.28 3.1 1.0
-pair_coeff 1 1 0.28 3.1 1.0 9.5
-
      
-
      
-
      pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5
-pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 9.5
-pair_coeff * * 0.28 3.1 1.0
-pair_coeff 1 1 0.28 3.1 0.5 10.0
-pair_coeff 1 1 0.28 3.1 0.5 10.0 9.5
-
      
-
      
-
      pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5
-pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 9.5
-pair_coeff * * 0.28 3.1 1.0
-pair_coeff 1 1 0.28 3.1 0.0 10.0
-pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5
-
      
-
      
-
      pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
-pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 9.5
-pair_coeff * * 0.155 3.1536 1.0
-pair_coeff 1 1 0.155 3.1536 1.0 9.5
-
      
-
      
-
      pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0
-pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0
-pair_coeff * * 0.28 3.1 1.0
-pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1
-
      
-
      
-
      pair_style coul/long/soft 1.0 10.0 9.5
-pair_coeff * * 1.0
-pair_coeff 1 1 1.0 9.5
-
      
-
      
-
      pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
-pair_coeff * * 1.0
-pair_coeff 1 1 1.0 9.5
-
      
-
      
+
      +pair_style lj/cut/soft 2.0 0.5 9.5
+pair_coeff * * 0.28 3.1 1.0
+pair_coeff 1 1 0.28 3.1 1.0 9.5
+
      
+
      +pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5
+pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 9.5
+pair_coeff * * 0.28 3.1 1.0
+pair_coeff 1 1 0.28 3.1 0.5 10.0
+pair_coeff 1 1 0.28 3.1 0.5 10.0 9.5
+
      
+
      +pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5
+pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 9.5
+pair_coeff * * 0.28 3.1 1.0
+pair_coeff 1 1 0.28 3.1 0.0 10.0
+pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5
+
      
+
      +pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
+pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 9.5
+pair_coeff * * 0.155 3.1536 1.0
+pair_coeff 1 1 0.155 3.1536 1.0 9.5
+
      
+
      +pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0
+pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0
+pair_coeff * * 0.28 3.1 1.0
+pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1
+
      
+
      +pair_style coul/long/soft 1.0 10.0 9.5
+pair_coeff * * 1.0
+pair_coeff 1 1 1.0 9.5
+
      
+
      +pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
+pair_coeff * * 1.0
+pair_coeff 1 1 1.0 9.5
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_lubricate.html b/doc/html/pair_lubricate.html
index 2cae3906c3..b415ee6c3a 100644
--- a/doc/html/pair_lubricate.html
+++ b/doc/html/pair_lubricate.html
@@ -137,9 +137,9 @@
 
      pair_style lubricate/poly/omp command
      
 
      
 
      Syntax
      
-
      pair_style style mu flaglog flagfld cutinner cutoff flagHI flagVF
-
      
-
      
+
      +pair_style style mu flaglog flagfld cutinner cutoff flagHI flagVF
+
      
 
        
 
      • style = lubricate or lubricate/poly
        • 
 
      • mu = dynamic viscosity (dynamic viscosity units)
        • 
@@ -151,17 +151,17 @@
 
      • flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms
        • 
 
      
 
      Examples: (all assume radius = 1)
      
-
      pair_style lubricate 1.5 1 1 2.01 2.5
-pair_coeff 1 1 2.05 2.8
-pair_coeff * *
-
      
-
      
-
      pair_style lubricate 1.5 1 1 2.01 2.5
-pair_coeff * *
-variable mu equal ramp(1,2)
-fix 1 all adapt 1 pair lubricate mu * * v_mu
-
      
-
      
+
      +pair_style lubricate 1.5 1 1 2.01 2.5
+pair_coeff 1 1 2.05 2.8
+pair_coeff * *
+
      
+
      +pair_style lubricate 1.5 1 1 2.01 2.5
+pair_coeff * *
+variable mu equal ramp(1,2)
+fix 1 all adapt 1 pair lubricate mu * * v_mu
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_lubricateU.html b/doc/html/pair_lubricateU.html
index 4d518c72e8..deca70058e 100644
--- a/doc/html/pair_lubricateU.html
+++ b/doc/html/pair_lubricateU.html
@@ -131,9 +131,9 @@
 
      pair_style lubricateU/poly command
      
 
      
 
      Syntax
      
-
      pair_style style mu flaglog cutinner cutoff gdot flagHI flagVF
-
      
-
      
+
      +pair_style style mu flaglog cutinner cutoff gdot flagHI flagVF
+
      
 
        
 
      • style = lubricateU or lubricateU/poly
        • 
 
      • mu = dynamic viscosity (dynamic viscosity units)
        • 
@@ -145,11 +145,11 @@
 
      • flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms
        • 
 
      
 
      Examples: (all assume radius = 1)
      
-
      pair_style lubricateU 1.5 1 2.01 2.5 0.01 1 1
-pair_coeff 1 1 2.05 2.8
-pair_coeff * *
-
      
-
      
+
      +pair_style lubricateU 1.5 1 2.01 2.5 0.01 1 1
+pair_coeff 1 1 2.05 2.8
+pair_coeff * *
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_mdf.html b/doc/html/pair_mdf.html
index 9f78149009..477829e523 100644
--- a/doc/html/pair_mdf.html
+++ b/doc/html/pair_mdf.html
@@ -134,9 +134,9 @@
 
      pair_style lennard/mdf command
      
 
      
 
      Syntax
      
-
      pair_style style args
-
      
-
      
+
      +pair_style style args
+
      
 
        
 
      • style = lj/mdf or buck/mdf or lennard/mdf
        • 
 
      • args = list of arguments for a particular style
        • 
@@ -155,21 +155,21 @@
 
      
 
      
 
      Examples
      
-
      pair_style lj/mdf 2.5 3.0
-pair_coeff * * 1 1
-pair_coeff 1 1 1 1.1 2.8 3.0 3.2
-
      
-
      
-
      pair_style buck 2.5 3.0
-pair_coeff * * 100.0 1.5 200.0
-pair_coeff * * 100.0 1.5 200.0 3.0 3.5
-
      
-
      
-
      pair_style lennard/mdf 2.5 3.0
-pair_coeff * * 1 1
-pair_coeff 1 1 1 1.1 2.8 3.0 3.2
-
      
-
      
+
      +pair_style lj/mdf 2.5 3.0
+pair_coeff * * 1 1
+pair_coeff 1 1 1 1.1 2.8 3.0 3.2
+
      
+
      +pair_style buck 2.5 3.0
+pair_coeff * * 100.0 1.5 200.0
+pair_coeff * * 100.0 1.5 200.0 3.0 3.5
+
      
+
      +pair_style lennard/mdf 2.5 3.0
+pair_coeff * * 1 1
+pair_coeff 1 1 1 1.1 2.8 3.0 3.2
+
      
 
      
 
      
 
      Description
      
@@ -198,7 +198,7 @@ below:
      
 
    • epsilon (energy units)
      • 
 
    • sigma (distance units)
      • 
 
    • r_m (distance units)
      • 
-
    • r_cut (distance units)
      • 
+
    • r_cut (distance units)
      • 
 
 
      
 
      For the buck/mdf pair_style, the potential energy, E(r), is the
@@ -209,7 +209,7 @@ standard Buckingham potential:
      
 
    • rho (distance units)
      • 
 
    • C (energy-distance^6 units)
      • 
 
    • r_m (distance units)
      • 
-
    • r_cut$ (distance units)
      • 
+
    • r_cut$ (distance units)
      • 
 
 
      
 
      For the lennard/mdf pair_style, the potential energy, E(r), is the
@@ -223,7 +223,7 @@ commands, or by mixing as described below:
      
 
    • A (energy-distance^12 units)
      • 
 
    • B (energy-distance^6 units)
      • 
 
    • r_m (distance units)
      • 
-
    • r_cut (distance units)
      • 
+
    • r_cut (distance units)
      • 
 
 
      
 
      Mixing, shift, table, tail correction, restart, rRESPA info:
      
diff --git a/doc/html/pair_meam.html b/doc/html/pair_meam.html
index 4c704bc583..e9ec4ac13b 100644
--- a/doc/html/pair_meam.html
+++ b/doc/html/pair_meam.html
@@ -128,17 +128,17 @@
 
      pair_style meam command
      
 
      
 
      Syntax
      
-
      pair_style meam
-
      
-
      
+
      +pair_style meam
+
      
 
      
 
      
 
      Examples
      
-
      pair_style meam
-pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si
-pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni
-
      
-
      
+
      +pair_style meam
+pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si
+pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni
+
      
 
      
 
      
 
      Description
      
@@ -194,9 +194,9 @@ settings for a variety of elements.  The potentials/sic.meam file has
 specific parameter settings for a Si and C alloy system.  If your
 LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si,
 and the 4th to be C, you would use the following pair_coeff command:
      
-
      pair_coeff * * library.meam Si C sic.meam Si Si Si C
-
      
-
      
+
      +pair_coeff * * library.meam Si C sic.meam Si Si Si C
+
      
 
      The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The two filenames are for the library and parameter file respectively.
 The Si and C arguments (between the file names) are the two elements
@@ -390,14 +390,14 @@ parameter erose_form, can be used to modify the Rose energy function
 used to compute the pair potential.  This function gives the energy of
 the reference state as a function of interatomic spacing.  The form of
 this function is:
      
-
      astar = alpha * (r/re - 1.d0)
-if erose_form = 0: erose = -Ec*(1+astar+a3*(astar**3)/(r/re))*exp(-astar)
-if erose_form = 1: erose = -Ec*(1+astar+(-attrac+repuls/r)*(astar**3))*exp(-astar)
-if erose_form = 2: erose = -Ec*(1 +astar + a3*(astar**3))*exp(-astar)
-a3 = repuls, astar < 0
-a3 = attrac, astar >= 0
-
      
-
      
+
      +astar = alpha * (r/re - 1.d0)
+if erose_form = 0: erose = -Ec*(1+astar+a3*(astar**3)/(r/re))*exp(-astar)
+if erose_form = 1: erose = -Ec*(1+astar+(-attrac+repuls/r)*(astar**3))*exp(-astar)
+if erose_form = 2: erose = -Ec*(1 +astar + a3*(astar**3))*exp(-astar)
+a3 = repuls, astar < 0
+a3 = attrac, astar >= 0
+
      
 
      Most published MEAM parameter sets use the default values attrac=repulse=0.
 Setting repuls=attrac=delta corresponds to the form used in several
 recent published MEAM parameter sets, such as (Valone)
      
diff --git a/doc/html/pair_meam_spline.html b/doc/html/pair_meam_spline.html
index 04957d08ca..d0f57e43cb 100644
--- a/doc/html/pair_meam_spline.html
+++ b/doc/html/pair_meam_spline.html
@@ -131,17 +131,17 @@
 
      pair_style meam/spline/omp
      
 
      
 
      Syntax
      
-
      pair_style meam/spline
-
      
-
      
+
      +pair_style meam/spline
+
      
 
      
 
      
 
      Examples
      
-
      pair_style meam/spline
-pair_coeff * * Ti.meam.spline Ti
-pair_coeff * * Ti.meam.spline Ti Ti Ti
-
      
-
      
+
      +pair_style meam/spline
+pair_coeff * * Ti.meam.spline Ti
+pair_coeff * * Ti.meam.spline Ti Ti Ti
+
      
 
      
 
      
 
      Description
      
@@ -180,9 +180,9 @@ to specify the path for the potential file.
      
 your LAMMPS simulation has 3 atoms types and they are all to be
 treated with this potentials, you would use the following pair_coeff
 command:
      
-
      pair_coeff * * Ti.meam.spline Ti Ti Ti
-
      
-
      
+
      +pair_coeff * * Ti.meam.spline Ti Ti Ti
+
      
 
      The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The three Ti arguments map LAMMPS atom types 1,2,3 to the Ti element
 in the potential file.  If a mapping value is specified as NULL, the
diff --git a/doc/html/pair_meam_sw_spline.html b/doc/html/pair_meam_sw_spline.html
index 2608d4c901..f3b221fef6 100644
--- a/doc/html/pair_meam_sw_spline.html
+++ b/doc/html/pair_meam_sw_spline.html
@@ -131,17 +131,17 @@
 
      pair_style meam/sw/spline/omp
      
 
      
 
      Syntax
      
-
      pair_style meam/sw/spline
-
      
-
      
+
      +pair_style meam/sw/spline
+
      
 
      
 
      
 
      Examples
      
-
      pair_style meam/sw/spline
-pair_coeff * * Ti.meam.sw.spline Ti
-pair_coeff * * Ti.meam.sw.spline Ti Ti Ti
-
      
-
      
+
      +pair_style meam/sw/spline
+pair_coeff * * Ti.meam.sw.spline Ti
+pair_coeff * * Ti.meam.sw.spline Ti Ti Ti
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_mgpt.html b/doc/html/pair_mgpt.html
index b014cdeb42..9ac4b2224d 100644
--- a/doc/html/pair_mgpt.html
+++ b/doc/html/pair_mgpt.html
@@ -128,20 +128,20 @@
 
      pair_style mgpt command
      
 
      
 
      Syntax
      
-
      pair_style mgpt
-
      
-
      
+
      +pair_style mgpt
+
      
 
      
 
      
 
      Examples
      
-
      pair_style mgpt
-pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega
-cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin
-cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin
-pair_coeff * * parmin potin Omega volpress yes nbody 1234 precision double
-pair_coeff * * parmin potin Omega volpress yes nbody 12
-
      
-
      
+
      +pair_style mgpt
+pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega
+cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin
+cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin
+pair_coeff * * parmin potin Omega volpress yes nbody 1234 precision double
+pair_coeff * * parmin potin Omega volpress yes nbody 12
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_mie.html b/doc/html/pair_mie.html
index cdab3eaf53..517b4bbec6 100644
--- a/doc/html/pair_mie.html
+++ b/doc/html/pair_mie.html
@@ -131,21 +131,21 @@
 
      pair_style mie/cut/gpu command
      
 
      
 
      Syntax
      
-
      pair_style mie/cut cutoff
-
      
-
      
+
      +pair_style mie/cut cutoff
+
      
 
        
 
      • cutoff = global cutoff for mie/cut interactions (distance units)
        • 
 
      
 
      
 
      
 
      Examples
      
-
      pair_style mie/cut 10.0
-pair_coeff 1 1 0.72 3.40 23.00 6.66
-pair_coeff 2 2 0.30 3.55 12.65 6.00
-pair_coeff 1 2 0.46 3.32 16.90 6.31
-
      
-
      
+
      +pair_style mie/cut 10.0
+pair_coeff 1 1 0.72 3.40 23.00 6.66
+pair_coeff 2 2 0.30 3.55 12.65 6.00
+pair_coeff 1 2 0.46 3.32 16.90 6.31
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_modify.html b/doc/html/pair_modify.html
index 3dbe93a18c..2dfeb618aa 100644
--- a/doc/html/pair_modify.html
+++ b/doc/html/pair_modify.html
@@ -128,9 +128,9 @@
 
      pair_modify command
      
 
      
 
      Syntax
      
-
      pair_modify keyword values ...
-
      
-
      
+
      +pair_modify keyword values ...
+
      
 
        
 
      • one or more keyword/value pairs may be listed
        • 
 
      • keyword = pair or shift or mix or table or table/disp or tabinner or tabinner/disp or tail or compute
        • 
@@ -158,13 +158,13 @@
 
      
 
      
 
      Examples
      
-
      pair_modify shift yes mix geometric
-pair_modify tail yes
-pair_modify table 12
-pair_modify pair lj/cut compute no
-pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0
-
      
-
      
+
      +pair_modify shift yes mix geometric
+pair_modify tail yes
+pair_modify table 12
+pair_modify pair lj/cut compute no
+pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0
+
      
 
      
 
      
 
      Description
      
@@ -201,21 +201,21 @@ individual pair styles for those restrictions.  Note also that the
 coefficients for a specific I != J pairing, in which case no mixing is
 performed.
      
 
      mix geometric
      
-
      epsilon_ij = sqrt(epsilon_i * epsilon_j)
-sigma_ij = sqrt(sigma_i * sigma_j)
-
      
-
      
+
      +epsilon_ij = sqrt(epsilon_i * epsilon_j)
+sigma_ij = sqrt(sigma_i * sigma_j)
+
      
 
      mix arithmetic
      
-
      epsilon_ij = sqrt(epsilon_i * epsilon_j)
-sigma_ij = (sigma_i + sigma_j) / 2
-
      
-
      
+
      +epsilon_ij = sqrt(epsilon_i * epsilon_j)
+sigma_ij = (sigma_i + sigma_j) / 2
+
      
 
      mix sixthpower
      
-
      epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
-             (sigma_i^6 + sigma_j^6)
-sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6)
-
      
-
      
+
      +epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
+             (sigma_i^6 + sigma_j^6)
+sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6)
+
      
 
      The shift keyword determines whether a Lennard-Jones potential is
 shifted at its cutoff to 0.0.  If so, this adds an energy term to each
 pairwise interaction which will be included in the thermodynamic
diff --git a/doc/html/pair_morse.html b/doc/html/pair_morse.html
index bac9a4aa44..bcf7271af0 100644
--- a/doc/html/pair_morse.html
+++ b/doc/html/pair_morse.html
@@ -146,9 +146,9 @@
 
      pair_style morse/soft command
      
 
      
 
      Syntax
      
-
      pair_style style args
-
      
-
      
+
      +pair_style style args
+
      
 
        
 
      • style = morse or morse/smooth/linear or morse/soft
        • 
 
      • args = list of arguments for a particular style
        • 
@@ -170,11 +170,11 @@
 pair_style morse/smooth/linear 2.5
 pair_coeff * * 100.0 2.0 1.5
 pair_coeff 1 1 100.0 2.0 1.5 3.0
        
-
        pair_style morse/soft 4 0.9 10.0
-pair_coeff * * 100.0 2.0 1.5 1.0
-pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0
-
        
-
        
+
        +pair_style morse/soft 4 0.9 10.0
+pair_coeff * * 100.0 2.0 1.5 1.0
+pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0
+
        
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_multi_lucy.html b/doc/html/pair_multi_lucy.html
index 6835ef752e..4a16b32697 100644
--- a/doc/html/pair_multi_lucy.html
+++ b/doc/html/pair_multi_lucy.html
@@ -128,9 +128,9 @@
 
      pair_style multi/lucy command
      
 
      
 
      Syntax
      
-
      pair_style multi/lucy style N keyword ...
-
      
-
      
+
      +pair_style multi/lucy style N keyword ...
+
      
 
        
 
      • style = lookup or linear = method of interpolation
        • 
 
      • N = use N values in lookup, linear tables
        • 
@@ -138,10 +138,10 @@
 
      
 
      
 
      Examples
      
-
      pair_style multi/lucy linear 1000
-pair_coeff * * multibody.table ENTRY1 7.0
-
      
-
      
+
      +pair_style multi/lucy linear 1000
+pair_coeff * * multibody.table ENTRY1 7.0
+
      
 
      
 
      
 
      Description
      
@@ -196,15 +196,15 @@ defined as follows (without the parenthesized comments):
      
 
      # Density-dependent function (one or more comment or blank lines)
 
      
 
      
-
      DD-FUNCTION                (keyword is first text on line)
-N 500 R 1.0 10.0           (N, R, RSQ parameters)
-                           (blank)
-1 1.0 25.5 102.34          (index, density, energy/r^4, force)
-2 1.02 23.4 98.5
-...
-500 10.0 0.001 0.003
-
      
-
      
+
      +DD-FUNCTION                (keyword is first text on line)
+N 500 R 1.0 10.0           (N, R, RSQ parameters)
+                           (blank)
+1 1.0 25.5 102.34          (index, density, energy/r^4, force)
+2 1.02 23.4 98.5
+...
+500 10.0 0.001 0.003
+
      
 
      A section begins with a non-blank line whose 1st character is not a
 “#”; blank lines or lines starting with “#” can be used as comments
 between sections.  The first line begins with a keyword which
diff --git a/doc/html/pair_multi_lucy_rx.html b/doc/html/pair_multi_lucy_rx.html
index 380cdc22fa..ca4b859cdd 100644
--- a/doc/html/pair_multi_lucy_rx.html
+++ b/doc/html/pair_multi_lucy_rx.html
@@ -128,9 +128,9 @@
 
      pair_style multi/lucy/rx command
      
 
      
 
      Syntax
      
-
      pair_style multi/lucy/rx style N keyword ...
-
      
-
      
+
      +pair_style multi/lucy/rx style N keyword ...
+
      
 
        
 
      • style = lookup or linear = method of interpolation
        • 
 
      • N = use N values in lookup, linear tables
        • 
@@ -138,11 +138,11 @@
 
      
 
      
 
      Examples
      
-
      pair_style multi/lucy/rx linear 1000
-pair_coeff * * multibody.table ENTRY1 h2o h2o 7.0
-pair_coeff * * multibody.table ENTRY1 h2o 1fluid 7.0
-
      
-
      
+
      +pair_style multi/lucy/rx linear 1000
+pair_coeff * * multibody.table ENTRY1 h2o h2o 7.0
+pair_coeff * * multibody.table ENTRY1 h2o 1fluid 7.0
+
      
 
      
 
      
 
      Description
      
@@ -215,15 +215,15 @@ defined as follows (without the parenthesized comments):
      
 
      # Density-dependent function (one or more comment or blank lines)
 
      
 
      
-
      DD-FUNCTION                (keyword is first text on line)
-N 500 R 1.0 10.0           (N, R, RSQ parameters)
-                           (blank)
-1 1.0 25.5 102.34          (index, density, energy/r^4, force)
-2 1.02 23.4 98.5
-...
-500 10.0 0.001 0.003
-
      
-
      
+
      +DD-FUNCTION                (keyword is first text on line)
+N 500 R 1.0 10.0           (N, R, RSQ parameters)
+                           (blank)
+1 1.0 25.5 102.34          (index, density, energy/r^4, force)
+2 1.02 23.4 98.5
+...
+500 10.0 0.001 0.003
+
      
 
      A section begins with a non-blank line whose 1st character is not a
 “#”; blank lines or lines starting with “#” can be used as comments
 between sections.  The first line begins with a keyword which
diff --git a/doc/html/pair_nb3b_harmonic.html b/doc/html/pair_nb3b_harmonic.html
index 59fe5effb2..a24bb092e7 100644
--- a/doc/html/pair_nb3b_harmonic.html
+++ b/doc/html/pair_nb3b_harmonic.html
@@ -131,16 +131,16 @@
 
      pair_style nb3b/harmonic/omp command
      
 
      
 
      Syntax
      
-
      pair_style nb3b/harmonic
-
      
-
      
+
      +pair_style nb3b/harmonic
+
      
 
      
 
      
 
      Examples
      
-
      pair_style nb3b/harmonic
-pair_coeff * * MgOH.nb3bharmonic Mg O H
-
      
-
      
+
      +pair_style nb3b/harmonic
+pair_coeff * * MgOH.nb3bharmonic Mg O H
+
      
 
      
 
      
 
      Description
      
@@ -166,9 +166,9 @@ to specify the path for the potential file.
      
 for Si and C.  If your LAMMPS simulation has 4 atoms types and you
 want the 1st 3 to be Si, and the 4th to be C, you would use the
 following pair_coeff command:
      
-
      pair_coeff * * SiC.nb3b.harmonic Si Si Si C
-
      
-
      
+
      +pair_coeff * * SiC.nb3b.harmonic Si Si Si C
+
      
 
      The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
 element in the potential file.  The final C argument maps LAMMPS atom
diff --git a/doc/html/pair_nm.html b/doc/html/pair_nm.html
index 10052c9d20..c7759721cf 100644
--- a/doc/html/pair_nm.html
+++ b/doc/html/pair_nm.html
@@ -143,9 +143,9 @@
 
      pair_style nm/cut/coul/long/omp command
      
 
      
 
      Syntax
      
-
      pair_style style args
-
      
-
      
+
      +pair_style style args
+
      
 
        
 
      • style = nm/cut or nm/cut/coul/cut or nm/cut/coul/long
        • 
 
      • args = list of arguments for a particular style
        • 
@@ -163,21 +163,21 @@
 
      
 
      
 
      Examples
      
-
      pair_style nm/cut 12.0
-pair_coeff * * 0.01 5.4 8.0 7.0
-pair_coeff 1 1 0.01 4.4 7.0 6.0
-
      
-
      
-
      pair_style nm/cut/coul/cut 12.0 15.0
-pair_coeff * * 0.01 5.4 8.0 7.0
-pair_coeff 1 1 0.01 4.4 7.0 6.0
-
      
-
      
-
      pair_style nm/cut/coul/long 12.0 15.0
-pair_coeff * * 0.01 5.4 8.0 7.0
-pair_coeff 1 1 0.01 4.4 7.0 6.0
-
      
-
      
+
      +pair_style nm/cut 12.0
+pair_coeff * * 0.01 5.4 8.0 7.0
+pair_coeff 1 1 0.01 4.4 7.0 6.0
+
      
+
      +pair_style nm/cut/coul/cut 12.0 15.0
+pair_coeff * * 0.01 5.4 8.0 7.0
+pair_coeff 1 1 0.01 4.4 7.0 6.0
+
      
+
      +pair_style nm/cut/coul/long 12.0 15.0
+pair_coeff * * 0.01 5.4 8.0 7.0
+pair_coeff 1 1 0.01 4.4 7.0 6.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_peri.html b/doc/html/pair_peri.html
index a57e98bbb1..c2fa31cce8 100644
--- a/doc/html/pair_peri.html
+++ b/doc/html/pair_peri.html
@@ -143,31 +143,31 @@
 
      pair_style peri/eps command
      
 
      
 
      Syntax
      
-
      pair_style style
-
      
-
      
+
      +pair_style style
+
      
 
        
 
      • style = peri/pmb or peri/lps or peri/ves or peri/eps
        • 
 
      
 
      
 
      
 
      Examples
      
-
      pair_style peri/pmb
-pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
-
      
-
      
-
      pair_style peri/lps
-pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25
-
      
-
      
-
      pair_style peri/ves
-pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001
-
      
-
      
-
      pair_style peri/eps
-pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 118.43
-
      
-
      
+
      +pair_style peri/pmb
+pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
+
      
+
      +pair_style peri/lps
+pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25
+
      
+
      +pair_style peri/ves
+pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001
+
      
+
      +pair_style peri/eps
+pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 118.43
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_polymorphic.html b/doc/html/pair_polymorphic.html
index 550805f4da..017a5148d0 100644
--- a/doc/html/pair_polymorphic.html
+++ b/doc/html/pair_polymorphic.html
@@ -128,20 +128,20 @@
 
      pair_style polymorphic command
      
 
      
 
      Syntax
      
-
      pair_style polymorphic
-
      
-
      
+
      +pair_style polymorphic
+
      
 
      style = polymorphic
      
 
      
 
      
 
      Examples
      
-
      pair_style polymorphic
-pair_coeff * * TlBr_msw.polymorphic Tl Br
-pair_coeff * * AlCu_eam.polymorphic Al Cu
-pair_coeff * * GaN_tersoff.polymorphic Ga N
-pair_coeff * * GaN_sw.polymorphic GaN
-
      
-
      
+
      +pair_style polymorphic
+pair_coeff * * TlBr_msw.polymorphic Tl Br
+pair_coeff * * AlCu_eam.polymorphic Al Cu
+pair_coeff * * GaN_tersoff.polymorphic Ga N
+pair_coeff * * GaN_sw.polymorphic GaN
+
      
 
      
 
      
 
      Description
      
@@ -210,9 +210,9 @@ included in the potentials dir of the LAMMPS distro.  They have a
 functions for Si-C tersoff potential. If your LAMMPS simulation has 4
 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you
 would use the following pair_coeff command:
      
-
      pair_coeff * * SiC_tersoff.polymorphic Si Si Si C
-
      
-
      
+
      +pair_coeff * * SiC_tersoff.polymorphic Si Si Si C
+
      
 
      The 1st 2 arguments must be * * so as to span all LAMMPS atom
 types. The first three Si arguments map LAMMPS atom types 1,2,3 to the
 Si element in the polymorphic file. The final C argument maps LAMMPS
@@ -235,19 +235,19 @@ eta_ij defined in the potential functions above is set to 1 -
 delta_ij, otherwise eta_ij is set to delta_ij. The next ntypes lines
 each lists two numbers and a character string representing atomic
 number, atomic mass, and name of the species of the ntypes elements:
      
-
      atomic_number atomic-mass element (1)
-atomic_number atomic-mass element (2)
-...
-atomic_number atomic-mass element (ntypes)
-
      
-
      
+
      +atomic_number atomic-mass element (1)
+atomic_number atomic-mass element (2)
+...
+atomic_number atomic-mass element (ntypes)
+
      
 
      The next ntypes*(ntypes+1)/2 lines contain two numbers:
      
-
      cut xi (1)
-cut xi (2)
-...
-cut xi (ntypes*(ntypes+1)/2)
-
      
-
      
+
      +cut xi (1)
+cut xi (2)
+...
+cut xi (ntypes*(ntypes+1)/2)
+
      
 
      Here cut means the cutoff distance of the pair functions, xi is the
 same as defined in the potential functions above. The
 ntypes*(ntypes+1)/2 lines are related to the pairs according to the
diff --git a/doc/html/pair_quip.html b/doc/html/pair_quip.html
index e2bae6d90b..91f1131efb 100644
--- a/doc/html/pair_quip.html
+++ b/doc/html/pair_quip.html
@@ -128,17 +128,17 @@
 
      pair_style quip command
      
 
      
 
      Syntax
      
-
      pair_style quip
-
      
-
      
+
      +pair_style quip
+
      
 
      
 
      
 
      Examples
      
-
      pair_style      quip
-pair_coeff      * * gap_example.xml "Potential xml_label=GAP_2014_5_8_60_17_10_38_466" 14
-pair_coeff      * * sw_example.xml "IP SW" 14
-
      
-
      
+
      +pair_style      quip
+pair_coeff      * * gap_example.xml "Potential xml_label=GAP_2014_5_8_60_17_10_38_466" 14
+pair_coeff      * * sw_example.xml "IP SW" 14
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_reax.html b/doc/html/pair_reax.html
index 3093a0b62b..3929a8cd0d 100644
--- a/doc/html/pair_reax.html
+++ b/doc/html/pair_reax.html
@@ -128,9 +128,9 @@
 
      pair_style reax command
      
 
      
 
      Syntax
      
-
      pair_style reax hbcut hbnewflag tripflag precision
-
      
-
      
+
      +pair_style reax hbcut hbnewflag tripflag precision
+
      
 
        
 
      • hbcut = hydrogen-bond cutoff (optional) (distance units)
        • 
 
      • hbnewflag = use old or new hbond function style (0 or 1) (optional)
        • 
@@ -140,12 +140,12 @@
 
      
 
      
 
      Examples
      
-
      pair_style reax
-pair_style reax 10.0 0 1 1.0e-5
-pair_coeff * * ffield.reax 3 1 2 2
-pair_coeff * * ffield.reax 3 NULL NULL 3
-
      
-
      
+
      +pair_style reax
+pair_style reax 10.0 0 1 1.0e-5
+pair_coeff * * ffield.reax 3 1 2 2
+pair_coeff * * ffield.reax 3 NULL NULL 3
+
      
 
      
 
      
 
      Description
      
@@ -238,14 +238,14 @@ names in italics match those used in the ReaxFF FORTRAN library):
      
 
 
      To print these quantities to the log file (with descriptive column
 headings) the following commands could be included in an input script:
      
-
      compute reax all pair reax
-variable eb           equal c_reax[1]
-variable ea           equal c_reax[2]
-...
-variable eqeq         equal c_reax[14]
-thermo_style custom step temp epair v_eb v_ea ... v_eqeq
-
      
-
      
+
      +compute reax all pair reax
+variable eb           equal c_reax[1]
+variable ea           equal c_reax[2]
+...
+variable eqeq         equal c_reax[14]
+thermo_style custom step temp epair v_eb v_ea ... v_eqeq
+
      
 
      Only a single pair_coeff command is used with the reax style which
 specifies a ReaxFF potential file with parameters for all needed
 elements.  These are mapped to LAMMPS atom types by specifying N
@@ -286,9 +286,9 @@ enable this.
      
 elements are ordered as C, H, O, N in the ffield file.  If you want
 the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
 H, you would use the following pair_coeff command:
      
-
      pair_coeff * * ffield.reax 1 1 4 2
-
      
-
      
+
      +pair_coeff * * ffield.reax 1 1 4 2
+
      
 
      
 
      Mixing, shift, table, tail correction, restart, rRESPA info:
      
 
      This pair style does not support the pair_modify
diff --git a/doc/html/pair_reax_c.html b/doc/html/pair_reax_c.html
index bd96471c6b..38e27022b9 100644
--- a/doc/html/pair_reax_c.html
+++ b/doc/html/pair_reax_c.html
@@ -131,9 +131,9 @@
 
      pair_style reax/c/kk command
      
 
      
 
      Syntax
      
-
      pair_style reax/c cfile keyword value
-
      
-
      
+
      +pair_style reax/c cfile keyword value
+
      
 
        
 
      • cfile = NULL or name of a control file
        • 
 
      • zero or more keyword/value pairs may be appended
        • 
@@ -148,13 +148,13 @@ keyword = checkqeq or lgvdw or safezone or mincap
 
      
 
      
 
      Examples
      
-
      pair_style reax/c NULL
-pair_style reax/c controlfile checkqeq no
-pair_style reax/c NULL lgvdw yes
-pair_style reax/c NULL safezone 1.6 mincap 100
-pair_coeff * * ffield.reax C H O N
-
      
-
      
+
      +pair_style reax/c NULL
+pair_style reax/c controlfile checkqeq no
+pair_style reax/c NULL lgvdw yes
+pair_style reax/c NULL safezone 1.6 mincap 100
+pair_coeff * * ffield.reax C H O N
+
      
 
      
 
      
 
      Description
      
@@ -276,14 +276,14 @@ names in italics match those used in the original FORTRAN ReaxFF code):
      
 
 
      To print these quantities to the log file (with descriptive column
 headings) the following commands could be included in an input script:
      
-
      compute reax all pair reax/c
-variable eb           equal c_reax[1]
-variable ea           equal c_reax[2]
-...
-variable eqeq         equal c_reax[14]
-thermo_style custom step temp epair v_eb v_ea ... v_eqeq
-
      
-
      
+
      +compute reax all pair reax/c
+variable eb           equal c_reax[1]
+variable ea           equal c_reax[2]
+...
+variable eqeq         equal c_reax[14]
+thermo_style custom step temp epair v_eb v_ea ... v_eqeq
+
      
 
      Only a single pair_coeff command is used with the reax/c style which
 specifies a ReaxFF potential file with parameters for all needed
 elements.  These are mapped to LAMMPS atom types by specifying N
@@ -310,14 +310,14 @@ types that will be used with other potentials.
      
 elements are ordered as C, H, O, N in the ffield file.  If you want
 the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
 H, you would use the following pair_coeff command:
      
-
      pair_coeff * * ffield.reax C C N H
-
      
-
      
+
      +pair_coeff * * ffield.reax C C N H
+
      
 
      
 
      The format of a line in the control file is as follows:
      
-
      variable_name value
-
      
-
      
+
      +variable_name value
+
      
 
      and it may be followed by an ”!” character and a trailing comment.
      
 
      If the value of a control variable is not specified, then default
 values are used.  What follows is the list of variables along with a
diff --git a/doc/html/pair_resquared.html b/doc/html/pair_resquared.html
index edf33d6bdb..70c4fd0ba0 100644
--- a/doc/html/pair_resquared.html
+++ b/doc/html/pair_resquared.html
@@ -134,19 +134,19 @@
 
      pair_style resquared/omp command
      
 
      
 
      Syntax
      
-
      pair_style resquared cutoff
-
      
-
      
+
      +pair_style resquared cutoff
+
      
 
        
 
      • cutoff = global cutoff for interactions (distance units)
        • 
 
      
 
      
 
      
 
      Examples
      
-
      pair_style resquared 10.0
-pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0
-
      
-
      
+
      +pair_style resquared 10.0
+pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_sdk.html b/doc/html/pair_sdk.html
index a8cfc33d42..21a9ded1a5 100644
--- a/doc/html/pair_sdk.html
+++ b/doc/html/pair_sdk.html
@@ -146,9 +146,9 @@
 
      pair_style lj/sdk/coul/long/omp command
      
 
      
 
      Syntax
      
-
      pair_style style args
-
      
-
      
+
      +pair_style style args
+
      
 
        
 
      • style = lj/sdk or lj/sdk/coul/long
        • 
 
      • args = list of arguments for a particular style
        • 
@@ -163,15 +163,15 @@
 
      
 
      
 
      Examples
      
-
      pair_style lj/sdk 2.5
-pair_coeff 1 1 lj12_6 1 1.1 2.8
-
      
-
      
-
      pair_style lj/sdk/coul/long 10.0
-pair_style lj/sdk/coul/long 10.0 12.0
-pair_coeff 1 1 lj9_6 100.0 3.5 12.0
-
      
-
      
+
      +pair_style lj/sdk 2.5
+pair_coeff 1 1 lj12_6 1 1.1 2.8
+
      
+
      +pair_style lj/sdk/coul/long 10.0
+pair_style lj/sdk/coul/long 10.0 12.0
+pair_coeff 1 1 lj9_6 100.0 3.5 12.0
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/pair_smd_hertz.html b/doc/html/pair_smd_hertz.html
index 52dd7939f6..25cbc618da 100644
--- a/doc/html/pair_smd_hertz.html
+++ b/doc/html/pair_smd_hertz.html
@@ -128,9 +128,9 @@
 
      pair_style smd/hertz command
      
 
      
 
      Syntax
      
-
      pair_style smd/hertz scale_factor
-
      
-
      
+
      +pair_style smd/hertz scale_factor
+
      
 
      
 
      
 
      Examples
      
@@ -146,7 +146,7 @@ The effect is that a particles cannot penetrate into each other.
 The parameter <contact_stiffness> has units of pressure and should equal roughly one half
 of the Young’s modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particles.
      
 
      The parameter scale_factor can be used to scale the particles’ contact radii. This can be useful to control how close
-particles can approach each other. Usually, scale_factor=1.0.
      
+particles can approach each other. Usually, *scale_factor*=1.0.
      
 
      
 
      Mixing, shift, table, tail correction, restart, rRESPA info:
      
 
      No mixing is performed automatically.
diff --git a/doc/html/pair_smd_triangulated_surface.html b/doc/html/pair_smd_triangulated_surface.html
index 9f4ba0991d..428893dfc3 100644
--- a/doc/html/pair_smd_triangulated_surface.html
+++ b/doc/html/pair_smd_triangulated_surface.html
@@ -128,9 +128,9 @@
 
      pair_style smd/tri_surface command
      
 
      
 
      Syntax
      
-
      pair_style smd/tri_surface scale_factor
-
      
-
      
+
      +pair_style smd/tri_surface scale_factor
+
      
 
      
 
      
 
      Examples
      
@@ -147,7 +147,7 @@ The effect is that a particle cannot penetrate into the triangular surface.
 The parameter <contact_stiffness> has units of pressure and should equal roughly one half
 of the Young’s modulus (or bulk modulus in the case of fluids) of the material model associated with the SPH particle
      
 
      The parameter scale_factor can be used to scale the particles’ contact radii. This can be useful to control how close
-particles can approach the triangulated surface. Usually, scale_factor=1.0.
      
+particles can approach the triangulated surface. Usually, *scale_factor*=1.0.
      
 
      
 
      Mixing, shift, table, tail correction, restart, rRESPA info:
      
 
      No mixing is performed automatically.
diff --git a/doc/html/pair_smtbq.html b/doc/html/pair_smtbq.html
index 568539fd0c..f9b3de8f22 100644
--- a/doc/html/pair_smtbq.html
+++ b/doc/html/pair_smtbq.html
@@ -128,16 +128,16 @@
 
      pair_style smtbq command
      
 
      
 
      Syntax
      
-
      pair_style smtbq
-
      
-
      
+
      +pair_style smtbq
+
      
 
      
 
      
 
      Examples
      
-
      pair_style smtbq
-pair_coeff * * ffield.smtbq.Al2O3 O Al
-
      
-
      
+
      +pair_style smtbq
+pair_coeff * * ffield.smtbq.Al2O3 O Al
+
      
 
      
 
      
 
      Description
      
@@ -164,9 +164,9 @@ filename in the pair_coeff command. Note that atom type 1 must always
 correspond to oxygen atoms. As an example, to simulate a TiO2 system,
 atom type 1 has to be oxygen and atom type 2 Ti. The following
 pair_coeff command should then be used:
      
-
      pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti
-
      
-
      
+
      +pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti
+
      
 
      The electrostatic part of the energy consists of two components
      
 
      self-energy of atom i in the form of a second order charge dependent
 polynomial and a long-range Coulombic electrostatic interaction. The
@@ -271,7 +271,7 @@ quotation marks (‘’).
      
 
 
        
 
      • Keyword for element1, element2 and interaction potential (‘second_moment’ or ‘buck’ or ‘buckPlusAttr’) between element 1 and 2.  If the potential is ‘second_moment’, specify ‘oxide’ or ‘metal’ for metal-oxygen or metal-metal interactions respectively.
        • 
-
      • Potential parameter: <pre><br/>       If type of potential is ‘second_moment’ : A (eV), p, &#958<sup>0</sup> (eV) and q <br/>                                               r<sub>c1</sub> (&#197), r<sub>c2</sub> (&#197) and r<sub>0</sub> (&#197) <br/>  If type of potential is ‘buck’ : C (eV) and &#961 (&#197) <br/>     If type of potential is ‘buckPlusAttr’ : C (eV) and &#961 (&#197) <br/>                                              D (eV), B (&#197<sup>-1</sup>), r<sub>1</sub><sup>OO</sup> (&#197) and r<sub>2</sub><sup>OO</sup> (&#197) </pre>
        • 
+
      • Potential parameter: <pre><br/>       If type of potential is ‘second_moment’ : A (eV), p, &#958<sup>0</sup> (eV) and q <br/>                                              r<sub>c1</sub> (&#197), r<sub>c2</sub> (&#197) and r<sub>0</sub> (&#197) <br/>  If type of potential is ‘buck’ : C (eV) and &#961 (&#197) <br/>     If type of potential is ‘buckPlusAttr’ : C (eV) and &#961 (&#197) <br/>                                              D (eV), B (&#197<sup>-1</sup>), r<sub>1</sub><sup>OO</sup> (&#197) and r<sub>2</sub><sup>OO</sup> (&#197) </pre>
        • 
 
      • Divided line
        • 
 
      
 
        
diff --git a/doc/html/pair_snap.html b/doc/html/pair_snap.html
index bc82ce506e..0589cb40a5 100644
--- a/doc/html/pair_snap.html
+++ b/doc/html/pair_snap.html
@@ -128,16 +128,16 @@
 
        pair_style snap command
        
 
        
 
        Syntax
        
-
        pair_style snap
-
        
-
        
+
        +pair_style snap
+
        
 
        
 
        
 
        Examples
        
-
        pair_style snap
-pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P
-
        
-
        
+
        +pair_style snap
+pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P
+
        
 
        
 
        
 
        Description
        
@@ -180,9 +180,9 @@ command, where N is the number of LAMMPS atom types:
        
 
        As an example, if a LAMMPS indium phosphide simulation has 4 atoms
 types, with the first two being indium and the 3rd and 4th being
 phophorous, the pair_coeff command would look like this:
        
-
        pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P
-
        
-
        
+
        +pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P
+
        
 
        The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The two filenames are for the element and parameter files, respectively.
 The ‘In’ and ‘P’ arguments (between the file names) are the two elements
@@ -210,7 +210,8 @@ using the hybrid/overlay pair style. As an example, the SNAP
 tantalum potential provided in the LAMMPS potentials directory
 combines the snap and zbl pair styles. It is invoked
 by the following commands:
        
-
        variable zblcutinner equal 4
+
        +variable zblcutinner equal 4
 variable zblcutouter equal 4.8
 variable zblz equal 73
 pair_style hybrid/overlay &
@@ -219,8 +220,7 @@ pair_coeff * * zbl 0.0
 pair_coeff 1 1 zbl ${zblz}
 pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
 ../potentials/Ta06A.snapparam Ta
-
        
-
        
+
 
        It is convenient to keep these commands in a separate file that can
 be inserted in any LAMMPS input script using the include
 command.
        
diff --git a/doc/html/pair_soft.html b/doc/html/pair_soft.html
index 0929a1f6af..3443927106 100644
--- a/doc/html/pair_soft.html
+++ b/doc/html/pair_soft.html
@@ -134,26 +134,26 @@
 
        pair_style soft/omp command
        
 
        
 
        Syntax
        
-
        pair_style soft cutoff
-
        
-
        
+
        +pair_style soft cutoff
+
        
 
          
 
        • cutoff = global cutoff for soft interactions (distance units)
          • 
 
        
 
        
 
        
 
        Examples
        
-
        pair_style soft 1.0
-pair_coeff * * 10.0
-pair_coeff 1 1 10.0 3.0
-
        
-
        
-
        pair_style soft 1.0
-pair_coeff * * 0.0
-variable prefactor equal ramp(0,30)
-fix 1 all adapt 1 pair soft a * * v_prefactor
-
        
-
        
+
        +pair_style soft 1.0
+pair_coeff * * 10.0
+pair_coeff 1 1 10.0 3.0
+
        
+
        +pair_style soft 1.0
+pair_coeff * * 0.0
+variable prefactor equal ramp(0,30)
+fix 1 all adapt 1 pair soft a * * v_prefactor
+
        
 
        
 
        
 
        Description
        
@@ -193,10 +193,10 @@ pair_coeff settings for A must still be specified, but will be
 overridden.  For example these commands will vary the prefactor A for
 all pairwise interactions from 0.0 at the beginning to 30.0 at the end
 of a run:
        
-
        variable prefactor equal ramp(0,30)
-fix 1 all adapt 1 pair soft a * * v_prefactor
-
        
-
        
+
        +variable prefactor equal ramp(0,30)
+fix 1 all adapt 1 pair soft a * * v_prefactor
+
        
 
        Note that a formula defined by an equal-style variable
 can use the current timestep, elapsed time in the current run, elapsed
 time since the beginning of a series of runs, as well as access other
diff --git a/doc/html/pair_sph_idealgas.html b/doc/html/pair_sph_idealgas.html
index 130c193d90..602e66a277 100644
--- a/doc/html/pair_sph_idealgas.html
+++ b/doc/html/pair_sph_idealgas.html
@@ -128,16 +128,16 @@
 
        pair_style sph/idealgas command
        
 
        
 
        Syntax
        
-
        pair_style sph/idealgas
-
        
-
        
+
        +pair_style sph/idealgas
+
        
 
        
 
        
 
        Examples
        
-
        pair_style sph/idealgas
-pair_coeff * * 1.0 2.4
-
        
-
        
+
        +pair_style sph/idealgas
+pair_coeff * * 1.0 2.4
+
        
 
        
 
        
 
        Description
        
diff --git a/doc/html/pair_sph_taitwater.html b/doc/html/pair_sph_taitwater.html
index 0d56ce2bdd..0ce7b08918 100644
--- a/doc/html/pair_sph_taitwater.html
+++ b/doc/html/pair_sph_taitwater.html
@@ -128,16 +128,16 @@
 
        pair_style sph/taitwater command
        
 
        
 
        Syntax
        
-
        pair_style sph/taitwater
-
        
-
        
+
        +pair_style sph/taitwater
+
        
 
        
 
        
 
        Examples
        
-
        pair_style sph/taitwater
-pair_coeff * * 1000.0 1430.0 1.0 2.4
-
        
-
        
+
        +pair_style sph/taitwater
+pair_coeff * * 1000.0 1430.0 1.0 2.4
+
        
 
        
 
        
 
        Description
        
diff --git a/doc/html/pair_sph_taitwater_morris.html b/doc/html/pair_sph_taitwater_morris.html
index 8c6f8c913a..fda93bd07c 100644
--- a/doc/html/pair_sph_taitwater_morris.html
+++ b/doc/html/pair_sph_taitwater_morris.html
@@ -128,16 +128,16 @@
 
        pair_style sph/taitwater/morris command
        
 
        
 
        Syntax
        
-
        pair_style sph/taitwater/morris
-
        
-
        
+
        +pair_style sph/taitwater/morris
+
        
 
        
 
        
 
        Examples
        
-
        pair_style sph/taitwater/morris
-pair_coeff * * 1000.0 1430.0 1.0 2.4
-
        
-
        
+
        +pair_style sph/taitwater/morris
+pair_coeff * * 1000.0 1430.0 1.0 2.4
+
        
 
        
 
        
 
        Description
        
diff --git a/doc/html/pair_srp.html b/doc/html/pair_srp.html
index caddb4012a..a9e1607ab8 100644
--- a/doc/html/pair_srp.html
+++ b/doc/html/pair_srp.html
@@ -143,24 +143,24 @@
 
        
 
        
 
        Examples
        
-
        pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes
-pair_coeff 1 1 dpd 60.0 4.5 1.0
-pair_coeff 1 2 none
-pair_coeff 2 2 srp 100.0 0.8
-
        
-
        
-
        pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes
-pair_coeff 1 1 dpd 60.0 50 1.0
-pair_coeff 1 2 none
-pair_coeff 2 2 srp 40.0
-
        
-
        
-
        pair_style hybrid srp 0.8 2 mid
-pair_coeff 1 1 none
-pair_coeff 1 2 none
-pair_coeff 2 2 srp 100.0 0.8
-
        
-
        
+
        +pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes
+pair_coeff 1 1 dpd 60.0 4.5 1.0
+pair_coeff 1 2 none
+pair_coeff 2 2 srp 100.0 0.8
+
        
+
        +pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes
+pair_coeff 1 1 dpd 60.0 50 1.0
+pair_coeff 1 2 none
+pair_coeff 2 2 srp 40.0
+
        
+
        +pair_style hybrid srp 0.8 2 mid
+pair_coeff 1 1 none
+pair_coeff 1 2 none
+pair_coeff 2 2 srp 100.0 0.8
+
        
 
        
 
        
 
        Description
        
diff --git a/doc/html/pair_style.html b/doc/html/pair_style.html
index 4dc6adc479..86a80963cc 100644
--- a/doc/html/pair_style.html
+++ b/doc/html/pair_style.html
@@ -128,9 +128,9 @@
 
        pair_style command
        
 
        
 
        Syntax
        
-
        pair_style style args
-
        
-
        
+
        +pair_style style args
+
        
 
          
 
        • style = one of the styles from the list below
          • 
 
        • args = arguments used by a particular style
          • 
@@ -138,13 +138,13 @@
 
        
 
        
 
        Examples
        
-
        pair_style lj/cut 2.5
-pair_style eam/alloy
-pair_style hybrid lj/charmm/coul/long 10.0 eam
-pair_style table linear 1000
-pair_style none
-
        
-
        
+
        +pair_style lj/cut 2.5
+pair_style eam/alloy
+pair_style hybrid lj/charmm/coul/long 10.0 eam
+pair_style table linear 1000
+pair_style none
+
        
 
        
 
        
 
        Description
        
@@ -338,9 +338,9 @@ package.
        
 
        
 
        
 
        Default
        
-
        pair_style none
-
        
-
        
+
        +pair_style none
+
        
 
        
 
        
 
diff --git a/doc/html/pair_sw.html b/doc/html/pair_sw.html
index 099d2de727..687c162b34 100644
--- a/doc/html/pair_sw.html
+++ b/doc/html/pair_sw.html
@@ -140,17 +140,17 @@
 
        pair_style sw/omp command
        
 
        
 
        Syntax
        
-
        pair_style sw
-
        
-
        
+
        +pair_style sw
+
        
 
        
 
        
 
        Examples
        
-
        pair_style sw
-pair_coeff * * si.sw Si
-pair_coeff * * GaN.sw Ga N Ga
-
        
-
        
+
        +pair_style sw
+pair_coeff * * si.sw Si
+pair_coeff * * GaN.sw Ga N Ga
+
        
 
        
 
        
 
        Description
        
@@ -175,9 +175,9 @@ to specify the path for the potential file.
        
 Si and C.  If your LAMMPS simulation has 4 atoms types and you want
 the 1st 3 to be Si, and the 4th to be C, you would use the following
 pair_coeff command:
        
-
        pair_coeff * * SiC.sw Si Si Si C
-
        
-
        
+
        +pair_coeff * * SiC.sw Si Si Si C
+
        
 
        The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
 element in the SW file.  The final C argument maps LAMMPS atom type 4
diff --git a/doc/html/pair_table.html b/doc/html/pair_table.html
index 7dd8b8ecf1..703a6081cc 100644
--- a/doc/html/pair_table.html
+++ b/doc/html/pair_table.html
@@ -137,9 +137,9 @@
 
        pair_style table/omp command
        
 
        
 
        Syntax
        
-
        pair_style table style N keyword ...
-
        
-
        
+
        +pair_style table style N keyword ...
+
        
 
          
 
        • style = lookup or linear or spline or bitmap = method of interpolation
          • 
 
        • N = use N values in lookup, linear, spline tables
          • 
@@ -150,13 +150,13 @@
 
        
 
        
 
        Examples
        
-
        pair_style table linear 1000
-pair_style table linear 1000 pppm
-pair_style table bitmap 12
-pair_coeff * 3 morse.table ENTRY1
-pair_coeff * 3 morse.table ENTRY1 7.0
-
        
-
        
+
        +pair_style table linear 1000
+pair_style table linear 1000 pppm
+pair_style table bitmap 12
+pair_coeff * 3 morse.table ENTRY1
+pair_coeff * 3 morse.table ENTRY1 7.0
+
        
 
        
 
        
 
        Description
        
@@ -240,15 +240,15 @@ defined as follows (without the parenthesized comments):
        
 
        # Morse potential for Fe   (one or more comment or blank lines)
 
        
 
        
-
        MORSE_FE                   (keyword is first text on line)
-N 500 R 1.0 10.0           (N, R, RSQ, BITMAP, FPRIME parameters)
-                           (blank)
-1 1.0 25.5 102.34          (index, r, energy, force)
-2 1.02 23.4 98.5
-...
-500 10.0 0.001 0.003
-
        
-
        
+
        +MORSE_FE                   (keyword is first text on line)
+N 500 R 1.0 10.0           (N, R, RSQ, BITMAP, FPRIME parameters)
+                           (blank)
+1 1.0 25.5 102.34          (index, r, energy, force)
+2 1.02 23.4 98.5
+...
+500 10.0 0.001 0.003
+
        
 
        A section begins with a non-blank line whose 1st character is not a
 “#”; blank lines or lines starting with “#” can be used as comments
 between sections.  The first line begins with a keyword which
diff --git a/doc/html/pair_table_rx.html b/doc/html/pair_table_rx.html
index 18ecd7f404..eab8b7d00c 100644
--- a/doc/html/pair_table_rx.html
+++ b/doc/html/pair_table_rx.html
@@ -128,22 +128,22 @@
 
        pair_style table/rx command
        
 
        
 
        Syntax
        
-
        pair_style table style N
-
        
-
        
+
        +pair_style table style N
+
        
 
        style = lookup or linear or spline or bitmap = method of interpolation
 N = use N values in lookup, linear, spline tables
 N = use 2^N values in bitmap tables
        
 
        
 
        
 
        Examples
        
-
        pair_style table/rx linear 1000
-pair_style table/rx bitmap 12
-pair_coeff * * rxn.table ENTRY1 h2o h2o 10.0
-pair_coeff * * rxn.table ENTRY1 1fluid 1fluid 10.0
-pair_coeff * 3 rxn.table ENTRY1 h2o no2 10.0
-
        
-
        
+
        +pair_style table/rx linear 1000
+pair_style table/rx bitmap 12
+pair_coeff * * rxn.table ENTRY1 h2o h2o 10.0
+pair_coeff * * rxn.table ENTRY1 1fluid 1fluid 10.0
+pair_coeff * 3 rxn.table ENTRY1 h2o no2 10.0
+
        
 
        
 
        
 
        Description
        
@@ -226,15 +226,15 @@ defined as follows (without the parenthesized comments):
        
 
        # Morse potential for Fe   (one or more comment or blank lines)
 
        
 
        
-
        MORSE_FE                   (keyword is first text on line)
-N 500 R 1.0 10.0           (N, R, RSQ, BITMAP, FPRIME parameters)
-                           (blank)
-1 1.0 25.5 102.34          (index, r, energy, force)
-2 1.02 23.4 98.5
-...
-500 10.0 0.001 0.003
-
        
-
        
+
        +MORSE_FE                   (keyword is first text on line)
+N 500 R 1.0 10.0           (N, R, RSQ, BITMAP, FPRIME parameters)
+                           (blank)
+1 1.0 25.5 102.34          (index, r, energy, force)
+2 1.02 23.4 98.5
+...
+500 10.0 0.001 0.003
+
        
 
        A section begins with a non-blank line whose 1st character is not a
 “#”; blank lines or lines starting with “#” can be used as comments
 between sections.  The first line begins with a keyword which
diff --git a/doc/html/pair_tersoff.html b/doc/html/pair_tersoff.html
index 6ea2a43607..8345a1c90b 100644
--- a/doc/html/pair_tersoff.html
+++ b/doc/html/pair_tersoff.html
@@ -146,22 +146,22 @@
 
        pair_style tersoff/table/omp command
        
 
        
 
        Syntax
        
-
        pair_style style
-
        
-
        
+
        +pair_style style
+
        
 
        style = tersoff or tersoff/table or tersoff/gpu or tersoff/omp or tersoff/table/omp
        
 
        
 
        
 
        Examples
        
-
        pair_style tersoff
-pair_coeff * * Si.tersoff Si
-pair_coeff * * SiC.tersoff Si C Si
-
        
-
        
-
        pair_style tersoff/table
-pair_coeff * * SiCGe.tersoff Si(D)
-
        
-
        
+
        +pair_style tersoff
+pair_coeff * * Si.tersoff Si
+pair_coeff * * SiC.tersoff Si C Si
+
        
+
        +pair_style tersoff/table
+pair_coeff * * SiCGe.tersoff Si(D)
+
        
 
        
 
        
 
        Description
        
@@ -191,9 +191,9 @@ to specify the path for the potential file.
        
 and C.  If your LAMMPS simulation has 4 atoms types and you want the
 1st 3 to be Si, and the 4th to be C, you would use the following
 pair_coeff command:
        
-
        pair_coeff * * SiC.tersoff Si Si Si C
-
        
-
        
+
        +pair_coeff * * SiC.tersoff Si Si Si C
+
        
 
        The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
 element in the Tersoff file.  The final C argument maps LAMMPS atom
diff --git a/doc/html/pair_tersoff_mod.html b/doc/html/pair_tersoff_mod.html
index b88d02ee18..34a2120f67 100644
--- a/doc/html/pair_tersoff_mod.html
+++ b/doc/html/pair_tersoff_mod.html
@@ -137,16 +137,16 @@
 
        pair_style tersoff/mod/omp command
        
 
        
 
        Syntax
        
-
        pair_style tersoff/mod
-
        
-
        
+
        +pair_style tersoff/mod
+
        
 
        
 
        
 
        Examples
        
-
        pair_style tersoff/mod
-pair_coeff * * Si.tersoff.mod Si Si
-
        
-
        
+
        +pair_style tersoff/mod
+pair_coeff * * Si.tersoff.mod Si Si
+
        
 
        
 
        
 
        Description
        
@@ -180,9 +180,9 @@ where N is the number of LAMMPS atom types:
        
 
        As an example, imagine the Si.tersoff_mod file has Tersoff values for Si.
 If your LAMMPS simulation has 3 Si atoms types, you would use the following
 pair_coeff command:
        
-
        pair_coeff * * Si.tersoff_mod Si Si Si
-
        
-
        
+
        +pair_coeff * * Si.tersoff_mod Si Si Si
+
        
 
        The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The three Si arguments map LAMMPS atom types 1,2,3 to the Si element
 in the Tersoff/MOD file. If a mapping value is specified as NULL, the
diff --git a/doc/html/pair_tersoff_zbl.html b/doc/html/pair_tersoff_zbl.html
index 90e840acc3..694938f86e 100644
--- a/doc/html/pair_tersoff_zbl.html
+++ b/doc/html/pair_tersoff_zbl.html
@@ -137,16 +137,16 @@
 
        pair_style tersoff/zbl/omp command
        
 
        
 
        Syntax
        
-
        pair_style tersoff/zbl
-
        
-
        
+
        +pair_style tersoff/zbl
+
        
 
        
 
        
 
        Examples
        
-
        pair_style tersoff/zbl
-pair_coeff * * SiC.tersoff.zbl Si C Si
-
        
-
        
+
        +pair_style tersoff/zbl
+pair_coeff * * SiC.tersoff.zbl Si C Si
+
        
 
        
 
        
 
        Description
        
@@ -188,9 +188,9 @@ to specify the path for the potential file.
        
 for Si and C.  If your LAMMPS simulation has 4 atoms types and you
 want the 1st 3 to be Si, and the 4th to be C, you would use the
 following pair_coeff command:
        
-
        pair_coeff * * SiC.tersoff Si Si Si C
-
        
-
        
+
        +pair_coeff * * SiC.tersoff Si Si Si C
+
        
 
        The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
 element in the Tersoff/ZBL file.  The final C argument maps LAMMPS
diff --git a/doc/html/pair_thole.html b/doc/html/pair_thole.html
index e3a5f8b9cb..8e8f15daf2 100644
--- a/doc/html/pair_thole.html
+++ b/doc/html/pair_thole.html
@@ -134,9 +134,9 @@
 
        pair_style lj/cut/thole/long/omp command
        
 
        
 
        Syntax
        
-
        pair_style style args
-
        
-
        
+
        +pair_style style args
+
        
 
          
 
        • style = thole or lj/cut/thole/long or lj/cut/thole/long/omp
          • 
 
        • args = list of arguments for a particular style
          • 
@@ -153,15 +153,15 @@
 
        
 
        
 
        Examples
        
-
        pair_style hybrid/overlay ... thole 2.6 12.0
-pair_coeff 1 1 thole 1.0
-pair_coeff 1 2 thole 1.0 2.6 10.0
-pair_coeff * 2 thole 1.0 2.6
-
        
-
        
-
        pair_style lj/cut/thole/long 2.6 12.0
-
        
-
        
+
        +pair_style hybrid/overlay ... thole 2.6 12.0
+pair_coeff 1 1 thole 1.0
+pair_coeff 1 2 thole 1.0 2.6 10.0
+pair_coeff * 2 thole 1.0 2.6
+
        
+
        +pair_style lj/cut/thole/long 2.6 12.0
+
        
 
        
 
        
 
        Description
        
@@ -189,8 +189,8 @@ short distances by a function
        
 \frac{s_{ij} r_{ij} }{2} \right)
 \exp \left( - s_{ij} r_{ij} \right) \end{equation}\]
        
 
        This function results from an adaptation to point charges
-(Noskov) of the dipole screening scheme originally proposed
-by Thole. The scaling coefficient \(s_{ij}\) is determined
+(Noskov) of the dipole screening scheme originally proposed
+by Thole. The scaling coefficient \(s_{ij}\) is determined
 by the polarizability of the atoms, \(\alpha_i\), and by a Thole
 damping parameter \(a\).  This Thole damping parameter usually takes
 a value of 2.6, but in certain force fields the value can depend upon
diff --git a/doc/html/pair_tri_lj.html b/doc/html/pair_tri_lj.html
index e6c6b24ddd..bdda14e2e2 100644
--- a/doc/html/pair_tri_lj.html
+++ b/doc/html/pair_tri_lj.html
@@ -128,18 +128,18 @@
 
        pair_style tri/lj command
        
 
        
 
        Syntax
        
-
        pair_style tri/lj cutoff
-
        
-
        
+
        +pair_style tri/lj cutoff
+
        
 
        cutoff = global cutoff for interactions (distance units)
        
 
        
 
        
 
        Examples
        
-
        pair_style tri/lj 3.0
-pair_coeff * * 1.0 1.0
-pair_coeff 1 1 1.0 1.5 2.5
-
        
-
        
+
        +pair_style tri/lj 3.0
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 1.0 1.5 2.5
+
        
 
        
 
        
 
        Description
        
diff --git a/doc/html/pair_vashishta.html b/doc/html/pair_vashishta.html
index 0bfaceb06c..6dd3e02f8f 100644
--- a/doc/html/pair_vashishta.html
+++ b/doc/html/pair_vashishta.html
@@ -131,16 +131,16 @@
 
        pair_style vashishta/omp command
        
 
        
 
        Syntax
        
-
        pair_style vashishta
-
        
-
        
+
        +pair_style vashishta
+
        
 
        
 
        
 
        Examples
        
-
        pair_style vashishta
-pair_coeff * * SiC.vashishta Si C
-
        
-
        
+
        +pair_style vashishta
+pair_coeff * * SiC.vashishta Si C
+
        
 
        
 
        
 
        Description
        
@@ -178,9 +178,9 @@ to specify the path for the potential file.
        
 Si and C.  If your LAMMPS simulation has 4 atoms types and you want
 the 1st 3 to be Si, and the 4th to be C, you would use the following
 pair_coeff command:
        
-
        pair_coeff * * SiC.vashishta Si Si Si C
-
        
-
        
+
        +pair_coeff * * SiC.vashishta Si Si Si C
+
        
 
        The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
 element in the file.  The final C argument maps LAMMPS atom type 4
diff --git a/doc/html/pair_yukawa.html b/doc/html/pair_yukawa.html
index 826c7de7ff..3f0d3b3e2c 100644
--- a/doc/html/pair_yukawa.html
+++ b/doc/html/pair_yukawa.html
@@ -134,9 +134,9 @@
 
        pair_style yukawa/omp command
        
 
        
 
        Syntax
        
-
        pair_style yukawa kappa cutoff
-
        
-
        
+
        +pair_style yukawa kappa cutoff
+
        
 
          
 
        • kappa = screening length (inverse distance units)
          • 
 
        • cutoff = global cutoff for Yukawa interactions (distance units)
          • 
@@ -144,11 +144,11 @@
 
        
 
        
 
        Examples
        
-
        pair_style yukawa 2.0 2.5
-pair_coeff 1 1 100.0 2.3
-pair_coeff * * 100.0
-
        
-
        
+
        +pair_style yukawa 2.0 2.5
+pair_coeff 1 1 100.0 2.3
+pair_coeff * * 100.0
+
        
 
        
 
        
 
        Description
        
diff --git a/doc/html/pair_yukawa_colloid.html b/doc/html/pair_yukawa_colloid.html
index 560d253325..0c16f65c1d 100644
--- a/doc/html/pair_yukawa_colloid.html
+++ b/doc/html/pair_yukawa_colloid.html
@@ -134,9 +134,9 @@
 
        pair_style yukawa/colloid/omp command
        
 
        
 
        Syntax
        
-
        pair_style yukawa/colloid kappa cutoff
-
        
-
        
+
        +pair_style yukawa/colloid kappa cutoff
+
        
 
          
 
        • kappa = screening length (inverse distance units)
          • 
 
        • cutoff = global cutoff for colloidal Yukawa interactions (distance units)
          • 
@@ -144,11 +144,11 @@
 
        
 
        
 
        Examples
        
-
        pair_style yukawa/colloid 2.0 2.5
-pair_coeff 1 1 100.0 2.3
-pair_coeff * * 100.0
-
        
-
        
+
        +pair_style yukawa/colloid 2.0 2.5
+pair_coeff 1 1 100.0 2.3
+pair_coeff * * 100.0
+
        
 
        
 
        
 
        Description
        
@@ -182,9 +182,9 @@ charge and surface potential due to the presence of electrolyte.  Note
 that the A for this potential style has different units than the A
 used in pair_style yukawa.  For low surface
 potentials, i.e. less than about 25 mV, A can be written as:
        
-
        A = 2 * PI * R*eps*eps0 * kappa * psi^2
-
        
-
        
+
        +A = 2 * PI * R*eps*eps0 * kappa * psi^2
+
        
 
        where
        
 
          
 
        • R = colloid radius (distance units)
          • 
diff --git a/doc/html/pair_zbl.html b/doc/html/pair_zbl.html
index 71b3bea35c..54ad6b5344 100644
--- a/doc/html/pair_zbl.html
+++ b/doc/html/pair_zbl.html
@@ -134,9 +134,9 @@
 
          pair_style zbl/omp command
          
 
          
 
          Syntax
          
-
          pair_style zbl inner outer
-
          
-
          
+
          +pair_style zbl inner outer
+
          
 
            
 
          • inner = distance where switching function begins
            • 
 
          • outer = global cutoff for ZBL interaction
            • 
@@ -144,11 +144,11 @@
 
          
 
          
 
          Examples
          
-
          pair_style zbl 3.0 4.0
-pair_coeff * * 73.0 73.0
-pair_coeff 1 1 14.0 14.0
-
          
-
          
+
          +pair_style zbl 3.0 4.0
+pair_coeff * * 73.0 73.0
+pair_coeff 1 1 14.0 14.0
+
          
 
          
 
          
 
          Description
          
diff --git a/doc/html/prd.html b/doc/html/prd.html
index ee0c7948c0..a32fecfdce 100644
--- a/doc/html/prd.html
+++ b/doc/html/prd.html
@@ -128,9 +128,9 @@
 
          prd command
          
 
          
 
          Syntax
          
-
          prd N t_event n_dephase t_dephase t_correlate compute-ID seed keyword value ...
-
          
-
          
+
          +prd N t_event n_dephase t_dephase t_correlate compute-ID seed keyword value ...
+
          
 
            
 
          • N = # of timesteps to run (not including dephasing/quenching)
            • 
 
          • t_event = timestep interval between event checks
            • 
@@ -200,19 +200,19 @@ potentials, etc should be the same for every replica.
            
 
            A PRD run has several stages, which are repeated each time an “event”
 occurs in one of the replicas, as defined below.  The logic for a PRD
 run is as follows:
            
-
            while (time remains):
-  dephase for n_dephase*t_dephase steps
-  until (event occurs on some replica):
-    run dynamics for t_event steps
-    quench
-    check for uncorrelated event on any replica
-  until (no correlated event occurs):
-    run dynamics for t_correlate steps
-    quench
-    check for correlated event on this replica
-  event replica shares state with all replicas
-
            
-
            
+
            +while (time remains):
+  dephase for n_dephase*t_dephase steps
+  until (event occurs on some replica):
+    run dynamics for t_event steps
+    quench
+    check for uncorrelated event on any replica
+  until (no correlated event occurs):
+    run dynamics for t_correlate steps
+    quench
+    check for correlated event on this replica
+  event replica shares state with all replicas
+
            
 
            Before this loop begins, the state of the system on replica 0 is
 shared with all replicas, so that all replicas begin from the same
 initial state. The first potential energy basin is identified by
diff --git a/doc/html/processors.html b/doc/html/processors.html
index f0feeb91ba..15f24d6340 100644
--- a/doc/html/processors.html
+++ b/doc/html/processors.html
@@ -162,15 +162,15 @@
 
          
 
          
 
          Examples
          
-
          processors * * 5
-processors 2 4 4
-processors * * 8 map xyz
-processors * * * grid numa
-processors * * * grid twolevel 4 * * 1
-processors 4 8 16 grid custom myfile
-processors * * * part 1 2 multiple
-
          
-
          
+
          +processors * * 5
+processors 2 4 4
+processors * * 8 map xyz
+processors * * * grid numa
+processors * * * grid twolevel 4 * * 1
+processors 4 8 16 grid custom myfile
+processors * * * part 1 2 multiple
+
          
 
          
 
          
 
          Description
          
@@ -428,7 +428,7 @@ option.
          
 
          
 
          
 
          Default
          
-
          The option defaults are Px Py Pz = * * *, grid = onelevel, and map =
+
          The option defaults are Px Py Pz = * * *, grid = onelevel, and map =
 cart.
          
 
          
 
          
diff --git a/doc/html/python.html b/doc/html/python.html
index f78a9df834..6700435a9f 100644
--- a/doc/html/python.html
+++ b/doc/html/python.html
@@ -161,35 +161,35 @@ keyword = invoke or input or return or format
 
          
 
          Examples
          
-
          python pForce input 2 v_x 20.0 return v_f format fff file force.py
-python pForce invoke
-
          
-
          
-
          python factorial input 1 myN return v_fac format ii here """
-def factorial(n):
-  if n == 1: return n
-  return n * factorial(n-1)
- """
-
          
-
          
-
          python loop input 1 SELF return v_value format -f here """
-def loop(lmpptr,N,cut0):
-  from lammps import lammps
-  lmp = lammps(ptr=lmpptr)
-
          
-
          
+
          +python pForce input 2 v_x 20.0 return v_f format fff file force.py
+python pForce invoke
+
          
+
          +python factorial input 1 myN return v_fac format ii here """
+def factorial(n):
+  if n == 1: return n
+  return n * factorial(n-1)
+ """
+
          
+
          +python loop input 1 SELF return v_value format -f here """
+def loop(lmpptr,N,cut0):
+  from lammps import lammps
+  lmp = lammps(ptr=lmpptr)
+
          
 
          # loop N times, increasing cutoff each time
 
          
 
          
-
           for i in range(N):
-   cut = cut0 + i*0.1
-   lmp.set_variable("cut",cut)               # set a variable in LAMMPS
-   lmp.command("pair_style lj/cut ${cut}")   # LAMMPS commands
-   lmp.command("pair_coeff * * 1.0 1.0")
-   lmp.command("run 100")
-"""
-
          
-
          
+
          + for i in range(N):
+   cut = cut0 + i*0.1
+   lmp.set_variable("cut",cut)               # set a variable in LAMMPS
+   lmp.command("pair_style lj/cut ${cut}")   # LAMMPS commands
+   lmp.command("pair_coeff * * 1.0 1.0")
+   lmp.command("run 100")
+"""
+
          
 
          
 
          
 
          Description
          
@@ -263,10 +263,10 @@ numeric or string value, as specified by the format keyword.
          
 of a python-style variable associates a Python function name with the
 variable.  This must match the func setting for this command.  For
 exampe these two commands would be self-consistent:
          
-
          variable foo python myMultiply
-python myMultiply return v_foo format f file funcs.py
-
          
-
          
+
          +variable foo python myMultiply
+python myMultiply return v_foo format f file funcs.py
+
          
 
          The two commands can appear in either order in the input script so
 long as both are specified before the Python function is invoked for
 the first time.
          
@@ -417,29 +417,29 @@ Python wraps the various functions included in the LAMMPS library
 interface.
          
 
          A more interesting example is in the examples/python/in.python script
 which loads and runs the following function from examples/python/funcs.py:
          
-
          def loop(N,cut0,thresh,lmpptr):
-  print "LOOP ARGS",N,cut0,thresh,lmpptr
-  from lammps import lammps
-  lmp = lammps(ptr=lmpptr)
-  natoms = lmp.get_natoms()
-
          
-
          
-
          for i in range(N):
-  cut = cut0 + i*0.1
-
          
-
          
-
          lmp.set_variable("cut",cut)                 # set a variable in LAMMPS
-lmp.command("pair_style lj/cut ${cut}")     # LAMMPS command
-#lmp.command("pair_style lj/cut %d" % cut)  # LAMMPS command option
-
          
-
          
-
          lmp.command("pair_coeff * * 1.0 1.0")       # ditto
-lmp.command("run 10")                       # ditto
-pe = lmp.extract_compute("thermo_pe",0,0)   # extract total PE from LAMMPS
-print "PE",pe/natoms,thresh
-if pe/natoms < thresh: return
-
          
-
          
+
          +def loop(N,cut0,thresh,lmpptr):
+  print "LOOP ARGS",N,cut0,thresh,lmpptr
+  from lammps import lammps
+  lmp = lammps(ptr=lmpptr)
+  natoms = lmp.get_natoms()
+
          
+
          +for i in range(N):
+  cut = cut0 + i*0.1
+
          
+
          +lmp.set_variable("cut",cut)                 # set a variable in LAMMPS
+lmp.command("pair_style lj/cut ${cut}")     # LAMMPS command
+#lmp.command("pair_style lj/cut %d" % cut)  # LAMMPS command option
+
          
+
          +lmp.command("pair_coeff * * 1.0 1.0")       # ditto
+lmp.command("run 10")                       # ditto
+pe = lmp.extract_compute("thermo_pe",0,0)   # extract total PE from LAMMPS
+print "PE",pe/natoms,thresh
+if pe/natoms < thresh: return
+
          
 
          with these input script commands:
          
 
          python          loop input 4 10 1.0 -4.0 SELF format iffp file funcs.py
 python          loop invoke
diff --git a/doc/html/read_data.html b/doc/html/read_data.html
index 41ce8a8dc9..0087555e4b 100644
--- a/doc/html/read_data.html
+++ b/doc/html/read_data.html
@@ -128,9 +128,9 @@
 
          read_data command
          
 
          
 
          Syntax
          
-
          read_data file keyword args ...
-
          
-
          
+
          +read_data file keyword args ...
+
          
 
            
 
          • file = name of data file to read in
            • 
 
          • zero or more keyword/arg pairs may be appended
            • 
@@ -165,13 +165,13 @@
 
          
 
          
 
          Examples
          
-
          read_data data.lj
-read_data ../run7/data.polymer.gz
-read_data data.protein fix mycmap crossterm CMAP
-read_data data.water add append offset 3 1 1 1 1 shift 0.0 0.0 50.0
-read_data data.water add merge 1 group solvent
-
          
-
          
+
          +read_data data.lj
+read_data ../run7/data.polymer.gz
+read_data data.protein fix mycmap crossterm CMAP
+read_data data.water add append offset 3 1 1 1 1 shift 0.0 0.0 50.0
+read_data data.water add merge 1 group solvent
+
          
 
          
 
          
 
          Description
          
@@ -764,9 +764,9 @@ are those that are not the 5 standard ones (ID,type,x,y,z).  For
 example, for the “charge” sub-style, a “q” value would appear.  For
 the “full” sub-style, a “molecule-ID” and “q” would appear.  These are
 listed in the same order they appear as listed above.  Thus if
          
-
          atom_style hybrid charge sphere
-
          
-
          
+
          +atom_style hybrid charge sphere
+
          
 
          were used in the input script, each atom line would have these fields:
          
 
          atom-ID atom-type x y z q diameter density
 
          
@@ -1260,9 +1260,9 @@ are those that are not the 5 standard ones (ID,vx,vy,vz).  For
 example, for the “sphere” sub-style, “wx”, “wy”, “wz” values would
 appear.  These are listed in the same order they appear as listed
 above.  Thus if
          
-
          atom_style hybrid electron sphere
-
          
-
          
+
          +atom_style hybrid electron sphere
+
          
 
          were used in the input script, each velocity line would have these
 fields:
          
 
          atom-ID vx vy vz ervel wx wy wz
diff --git a/doc/html/read_dump.html b/doc/html/read_dump.html
index 603ab46785..5e2e9f96eb 100644
--- a/doc/html/read_dump.html
+++ b/doc/html/read_dump.html
@@ -128,9 +128,9 @@
 
          read_dump command
          
 
          
 
          Syntax
          
-
          read_dump file Nstep field1 field2 ... keyword values ...
-
          
-
          
+
          +read_dump file Nstep field1 field2 ... keyword values ...
+
          
 
            
 
          • file = name of dump file to read
            • 
 
          • Nstep = snapshot timestep to read from file
            • 
@@ -168,18 +168,18 @@ field = x or y or z or vx or vy or
 
          
 
          
 
          Examples
          
-
          read_dump dump.file 5000 x y z
-read_dump dump.xyz 5 x y z box no format xyz
-read_dump dump.xyz 10 x y z box no format molfile xyz "../plugins"
-read_dump dump.dcd 0 x y z box yes format molfile dcd
-read_dump dump.file 1000 x y z vx vy vz box yes format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
-read_dump dump.file 5000 x y vx vy trim yes
-read_dump ../run7/dump.file.gz 10000 x y z box yes
-read_dump dump.xyz 10 x y z box no format molfile xyz ../plugins
-read_dump dump.dcd 0 x y z format molfile dcd
-read_dump dump.file 1000 x y z vx vy vz format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
-
          
-
          
+
          +read_dump dump.file 5000 x y z
+read_dump dump.xyz 5 x y z box no format xyz
+read_dump dump.xyz 10 x y z box no format molfile xyz "../plugins"
+read_dump dump.dcd 0 x y z box yes format molfile dcd
+read_dump dump.file 1000 x y z vx vy vz box yes format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
+read_dump dump.file 5000 x y vx vy trim yes
+read_dump ../run7/dump.file.gz 10000 x y z box yes
+read_dump dump.xyz 10 x y z box no format molfile xyz ../plugins
+read_dump dump.dcd 0 x y z format molfile dcd
+read_dump dump.file 1000 x y z vx vy vz format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
+
          
 
          
 
          
 
          Description
          
diff --git a/doc/html/region.html b/doc/html/region.html
index de04067047..8e3f0aa71b 100644
--- a/doc/html/region.html
+++ b/doc/html/region.html
@@ -193,14 +193,14 @@
 
          
 
          
 
          Examples
          
-
          region 1 block -3.0 5.0 INF 10.0 INF INF
-region 2 sphere 0.0 0.0 0.0 5 side out
-region void cylinder y 2 3 5 -5.0 EDGE units box
-region 1 prism 0 10 0 10 0 10 2 0 0
-region outside union 4 side1 side2 side3 side4
-region 2 sphere 0.0 0.0 0.0 5 side out move v_left v_up NULL
-
          
-
          
+
          +region 1 block -3.0 5.0 INF 10.0 INF INF
+region 2 sphere 0.0 0.0 0.0 5 side out
+region void cylinder y 2 3 5 -5.0 EDGE units box
+region 1 prism 0 10 0 10 0 10 2 0 0
+region outside union 4 side1 side2 side3 side4
+region 2 sphere 0.0 0.0 0.0 5 side out move v_left v_up NULL
+
          
 
          
 
          
 
          Description
          
@@ -380,18 +380,18 @@ fashion.  For the latter, see the start and stop keywords of t
 
          For example, these commands would displace a region from its initial
 position, in the positive x direction, effectively at a constant
 velocity:
          
-
          variable dx equal ramp(0,10)
-region 2 sphere 10.0 10.0 0.0 5 move v_dx NULL NULL
-
          
-
          
+
          +variable dx equal ramp(0,10)
+region 2 sphere 10.0 10.0 0.0 5 move v_dx NULL NULL
+
          
 
          Note that the initial displacemet is 0.0, though that is not required.
          
 
          Either of these varaibles would “wiggle” the region back and forth in
 the y direction:
          
-
          variable dy equal swiggle(0,5,100)
-variable dysame equal 5*sin(2*PI*elaplong*dt/100)
-region 2 sphere 10.0 10.0 0.0 5 move NULL v_dy NULL
-
          
-
          
+
          +variable dy equal swiggle(0,5,100)
+variable dysame equal 5*sin(2*PI*elaplong*dt/100)
+region 2 sphere 10.0 10.0 0.0 5 move NULL v_dy NULL
+
          
 
          The rotate keyword rotates the region around a rotation axis R =
 (Rx,Ry,Rz) that goes thru a point P = (Px,Py,Pz).  The rotation
 angle is calculated, presumably as a function of time, by a variable
diff --git a/doc/html/restart.html b/doc/html/restart.html
index d6fc25f246..3f169da485 100644
--- a/doc/html/restart.html
+++ b/doc/html/restart.html
@@ -150,14 +150,14 @@
 
          
 
          
 
          Examples
          
-
          restart 0
-restart 1000 poly.restart
-restart 1000 poly.restart.mpiio
-restart 1000 restart.*.equil
-restart 10000 poly.%.1 poly.%.2 nfile 10
-restart v_mystep poly.restart
-
          
-
          
+
          +restart 0
+restart 1000 poly.restart
+restart 1000 poly.restart.mpiio
+restart 1000 restart.*.equil
+restart 10000 poly.%.1 poly.%.2 nfile 10
+restart v_mystep poly.restart
+
          
 
          
 
          
 
          Description
          
@@ -226,10 +226,10 @@ options for For example, the following commands will write restart files
 every step from 1100 to 1200, and could be useful for debugging
 a simulation where something goes wrong at step 1163:
          
-
          variable     s equal stride(1100,1200,1)
-restart              v_s tmp.restart
-
          
-
          
+
          +variable     s equal stride(1100,1200,1)
+restart              v_s tmp.restart
+
          
 
          
 
          See the read_restart command for information about
 what is stored in a restart file.
          
diff --git a/doc/html/run_style.html b/doc/html/run_style.html
index 9ef0e69f67..b00835c7e1 100644
--- a/doc/html/run_style.html
+++ b/doc/html/run_style.html
@@ -128,9 +128,9 @@
 
          run_style command
          
 
          
 
          Syntax
          
-
          run_style style args
-
          
-
          
+
          +run_style style args
+
          
 
            
 
          • style = verlet or verlet/split or respa or respa/omp
            • 
 
          
@@ -175,14 +175,14 @@
 
          
 
          
 
          Examples
          
-
          run_style verlet
-run_style respa 4 2 2 2 bond 1 dihedral 2 pair 3 kspace 4
-run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4
-
          
-
          
-
          run_style respa 3 4 2 bond 1 hybrid 2 2 1 kspace 3
-
          
-
          
+
          +run_style verlet
+run_style respa 4 2 2 2 bond 1 dihedral 2 pair 3 kspace 4
+run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4
+
          
+
          +run_style respa 3 4 2 bond 1 hybrid 2 2 1 kspace 3
+
          
 
          
 
          
 
          Description
          
@@ -219,9 +219,9 @@ its onn optimal layout, then require the 2nd partition’s layout to
 match the integer multiple constraint.  See the
 processors command with its part keyword for a way
 to control this, e.g.
          
-
          procssors * * * part 1 2 multiple
-
          
-
          
+
          +procssors * * * part 1 2 multiple
+
          
 
          You can also use the partition command to explicitly
 specity the processor layout on each partition.  E.g. for 2 partitions
 of 60 and 15 processors each:
          
@@ -314,10 +314,10 @@ angstrom “healing distance” (the distance between the outer and inne
 cutoffs) works reasonably well.  We thus recommend the following
 settings for use of the respa style without SHAKE in biomolecular
 simulations:
          
-
          timestep  4.0
-run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 8.0 10.0 outer 4
-
          
-
          
+
          +timestep  4.0
+run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 8.0 10.0 outer 4
+
          
 
          With these settings, users can expect good energy conservation and
 roughly a 2.5 fold speedup over the verlet style with a 0.5 fmsec
 timestep.
          
@@ -332,11 +332,11 @@ respa in order to freeze out these high frequency motions and increase
 the size of the time steps in the respa hierarchy.  The following
 settings can be used for biomolecular simulations with SHAKE and
 rRESPA:
          
-
          fix             2 all shake 0.000001 500 0 m 1.0 a 1
-timestep        4.0
-run_style    respa 2 2 inner 1 4.0 5.0 outer 2
-
          
-
          
+
          +fix             2 all shake 0.000001 500 0 m 1.0 a 1
+timestep        4.0
+run_style   respa 2 2 inner 1 4.0 5.0 outer 2
+
          
 
          With these settings, users can expect good energy conservation and
 roughly a 1.5 fold speedup over the verlet style with SHAKE and a
 2.0 fmsec timestep.
          
@@ -348,10 +348,10 @@ keywords.  A 2-fold or more speedup can be obtained while maintaining
 good energy conservation.  In real units, for a pure LJ fluid at
 liquid density, with a sigma of 3.0 angstroms, and epsilon of 0.1
 Kcal/mol, the following settings seem to work well:
          
-
          timestep  36.0
-run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3
-
          
-
          
+
          +timestep  36.0
+run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3
+
          
 
          
 
          The respa/omp styles is a variant of respa adapted for use with
 pair, bond, angle, dihedral, improper, or kspace styles with an omp
@@ -384,9 +384,9 @@ conserving energy to adequate precision.
          
 
          
 
          
 
          Default
          
-
          run_style verlet
-
          
-
          
+
          +run_style verlet
+
          
 
          
 
          (Tuckerman) Tuckerman, Berne and Martyna, J Chem Phys, 97, p 1990
 (1992).
          
diff --git a/doc/html/set.html b/doc/html/set.html
index 89ea2eb1ff..075dbb3510 100644
--- a/doc/html/set.html
+++ b/doc/html/set.html
@@ -214,17 +214,17 @@
 
          
 
          
 
          Examples
          
-
          set group solvent type 2
-set group solvent type/fraction 2 0.5 12393
-set group edge bond 4
-set region half charge 0.5
-set type 3 charge 0.5
-set type 1*3 charge 0.5
-set atom * charge v_atomfile
-set atom 100*200 x 0.5 y 1.0
-set atom 1492 type 3
-
          
-
          
+
          +set group solvent type 2
+set group solvent type/fraction 2 0.5 12393
+set group edge bond 4
+set region half charge 0.5
+set type 3 charge 0.5
+set type 1*3 charge 0.5
+set atom * charge v_atomfile
+set atom 100*200 x 0.5 y 1.0
+set atom 1492 type 3
+
          
 
          
 
          
 
          Description
          
@@ -252,7 +252,7 @@ style type selects all the atoms in a range of types.  The style
 mol selects all the atoms in a range of molecule IDs.
          
 
          In each of the range cases, the range can be specified as a single
 numeric value, or a wildcard asterisk can be used to specify a range
-of values.  This takes the form “*” or “n” or “n” or “m*n”.  For
+of values.  This takes the form “*” or “*n” or “n*” or “m*n”.  For
 example, for the style type, if N = the number of atom types, then
 an asterisk with no numeric values means all types from 1 to N.  A
 leading asterisk means all types from 1 to n (inclusive).  A trailing
diff --git a/doc/html/special_bonds.html b/doc/html/special_bonds.html
index 08a1e3f74c..d431cc49b3 100644
--- a/doc/html/special_bonds.html
+++ b/doc/html/special_bonds.html
@@ -128,9 +128,9 @@
 
          special_bonds command
          
 
          
 
          Syntax
          
-
          special_bonds keyword values ...
-
          
-
          
+
          +special_bonds keyword values ...
+
          
 
            
 
          • one or more keyword/value pairs may be appended
            • 
 
          • keyword = amber or charmm or dreiding or fene or lj/coul or lj or coul or angle or dihedral or extra
            • 
@@ -152,14 +152,14 @@
   N = number of extra 1-2,1-3,1-4 interactions to save space for
 
          
 
          Examples:
          
-
          special_bonds amber
-special_bonds charmm
-special_bonds fene dihedral no
-special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes
-special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
-special_bonds lj/coul 0 1 1 extra 2
-
          
-
          
+
          +special_bonds amber
+special_bonds charmm
+special_bonds fene dihedral no
+special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes
+special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
+special_bonds lj/coul 0 1 1 extra 2
+
          
 
          
 
          
 
          Description
          
@@ -301,7 +301,7 @@ current system has.
          
 the system).  If new bonds are created (or molecules added containing
 atoms with more special neighbors), the size of this list needs to
 grow.  Note that adding a single bond always adds a new 1st neighbor
-but may also induce many new 2nd and 3rd neighbors, depending on the
+but may also induce *many* new 2nd and 3rd neighbors, depending on the
 molecular topology of your system.  Using the extra keyword leaves
 empty space in the list for this N additional 1st, 2nd, or 3rd
 neighbors to be added.  If you do not do this, you may get an error
@@ -325,14 +325,14 @@ Coul: coul 0.0 0.0 1.0
          
 
          because the LJ settings are reset to their default values
 each time the command is issued.
          
 
          Likewise
          
-
          special_bonds amber
-special_bonds extra 2
-
          
-
          
+
          +special_bonds amber
+special_bonds extra 2
+
          
 
          is not the same as this single command:
          
-
          special_bonds amber extra 2
-
          
-
          
+
          +special_bonds amber extra 2
+
          
 
          since in the former case, the 2nd command will reset all the LJ and
 Coulombic weights to 0.0 (the default).
          
 
          One exception to this rule is the extra option itself.  It is not
diff --git a/doc/html/tad.html b/doc/html/tad.html
index d4f05d75ae..e4bab3f210 100644
--- a/doc/html/tad.html
+++ b/doc/html/tad.html
@@ -128,9 +128,9 @@
 
          tad command
          
 
          
 
          Syntax
          
-
          tad N t_event T_lo T_hi delta tmax compute-ID keyword value ...
-
          
-
          
+
          +tad N t_event T_lo T_hi delta tmax compute-ID keyword value ...
+
          
 
            
 
          • N = # of timesteps to run (not including dephasing/quenching)
            • 
 
          • t_event = timestep interval between event checks
            • 
@@ -162,15 +162,15 @@
 
          
 
          
 
          Examples
          
-
          tad 2000 50 1800 2300 0.01 0.01 event
-tad 2000 50 1800 2300 0.01 0.01 event &
-    min 1e-05 1e-05 100 100 &
-    neb 0.0 0.01 200 200 20 &
-    min_style cg &
-    neb_style fire &
-    neb_log log.neb
-
          
-
          
+
          +tad 2000 50 1800 2300 0.01 0.01 event
+tad 2000 50 1800 2300 0.01 0.01 event &
+    min 1e-05 1e-05 100 100 &
+    neb 0.0 0.01 200 200 20 &
+    min_style cg &
+    neb_style fire &
+    neb_log log.neb
+
          
 
          
 
+
          +while (time remains):
+  while (time < tstop):
+    until (event occurs):
+      run dynamics for t_event steps
+      quench
+    run neb calculation using all replicas
+    compute tlo from energy barrier
+    update earliest event
+    update tstop
+    reflect back into current basin
+  execute earliest event
+
          
 
          Before this outer loop begins, the initial potential energy basin is
 identified by quenching (an energy minimization, see below) the
 initial state and storing the resulting coordinates for reference.
          
@@ -298,7 +298,7 @@ at the low temperature.
          
 current basin to the stopping time. This last number can be used to
 judge whether the stopping time is too short or too long (see above).
          
 
          t_lo is the low-temperature event time when the current basin was
-entered, in units of timestep.  delt_lo is the time of each detected
+entered, in units of timestep.  del*t_lo* is the time of each detected
 event, measured relative to t_lo.  delt_lo is equal to the
 high-temperature time since entering the current basin, scaled by an
 exponential factor that depends on the hi/lo temperature ratio and the
diff --git a/doc/html/thermo.html b/doc/html/thermo.html
index 8567a3fd63..7a5cb15c32 100644
--- a/doc/html/thermo.html
+++ b/doc/html/thermo.html
@@ -162,10 +162,10 @@ this context.  Other similar math functions could easily be added as
 options for equal-style variables.
          
 
          For example, the following commands will output thermodynamic info at
 timesteps 0,10,20,30,100,200,300,1000,2000,etc:
          
-
          variable     s equal logfreq(10,3,10)
-thermo               v_s
-
          
-
          
+
          +variable     s equal logfreq(10,3,10)
+thermo               v_s
+
          
 
          
 
          
 
          Restrictions
          
diff --git a/doc/html/thermo_style.html b/doc/html/thermo_style.html
index 5a6e41bfc9..4f0f68acae 100644
--- a/doc/html/thermo_style.html
+++ b/doc/html/thermo_style.html
@@ -128,9 +128,9 @@
 
          thermo_style command
          
 
          
 
          Syntax
          
-
          thermo_style style args
-
          
-
          
+
          +thermo_style style args
+
          
 
            
 
          • style = one or multi or custom
            • 
 
          • args = list of arguments for a particular style
            • 
@@ -207,12 +207,12 @@
 
          
 
          
 
          Examples
          
-
          thermo_style multi
-thermo_style custom step temp pe etotal press vol
-thermo_style custom step temp etotal c_myTemp v_abc
-thermo_style custom step temp etotal c_myTemp[*] v_abc
-
          
-
          
+
          +thermo_style multi
+thermo_style custom step temp pe etotal press vol
+thermo_style custom step temp etotal c_myTemp v_abc
+thermo_style custom step temp etotal c_myTemp[*] v_abc
+
          
 
          
 
          
 
          Description
          
@@ -260,9 +260,9 @@ the thermo_modify command after it.
          
 computed: “temp”, “press”, “ke”, “etotal”, “enthalpy”, “pxx”, etc.  By
 default this is done by using a temperature compute which is created
 when LAMMPS starts up, as if this command had been issued:
          
-
          compute thermo_temp all temp
-
          
-
          
+
          +compute thermo_temp all temp
+
          
 
          See the compute temp command for details.  Note
 that the ID of this compute is thermo_temp and the group is all.
 You can change the attributes of this temperature (e.g. its
@@ -275,9 +275,9 @@ This is done via the pressure compute which is created when LAMMPS starts up, as
 if this command had been issued:
          
-
          compute thermo_press all pressure thermo_temp
-
          
-
          
+
          +compute thermo_press all pressure thermo_temp
+
          
 
          See the compute pressure command for details.
 Note that the ID of this compute is thermo_press and the group is
 all.  You can change the attributes of this pressure via the
@@ -290,9 +290,9 @@ that requires a pressure.  This is done via the
 be computed: “pe”, “etotal”, “ebond”, etc.  This is done by using a
 pe compute which is created when LAMMPS starts up, as if this
 command had been issued:
          
-
          compute thermo_pe all pe
-
          
-
          
+
          +compute thermo_pe all pe
+
          
 
          See the compute pe command for details.  Note that
 the ID of this compute is thermo_pe and the group is all.  You can
 change the attributes of this potential energy via the
@@ -394,7 +394,7 @@ of these quantities in terms of the internal LAMMPS cell dimensions
 
          For output values from a compute or fix, the bracketed index I used to
 index a vector, as in c_ID[I] or f_ID[I], can be specified
 using a wildcard asterisk with the index to effectively specify
-multiple values.  This takes the form “*” or “n” or “n” or “m*n”.
+multiple values.  This takes the form “*” or “*n” or “n*” or “m*n”.
 If N = the size of the vector (for mode = scalar) or the number of
 columns in the array (for mode = vector), then an asterisk with no
 numeric values means all indices from 1 to N.  A leading asterisk
@@ -405,13 +405,13 @@ indices from m to n (inclusive).
          
 vector had been listed one by one.  E.g. these 2 thermo_style commands
 are equivalent, since the compute temp command
 creates a global vector with 6 values.
          
-
          compute myTemp all temp
-thermo_style custom step temp etotal c_myTemp[*]
-thermo_style custom step temp etotal &
-             c_myTemp[1] c_myTemp[2] c_myTemp[3] &
-             c_myTemp[4] c_myTemp[5] c_myTemp[6]
-
          
-
          
+
          +compute myTemp all temp
+thermo_style custom step temp etotal c_myTemp[*]
+thermo_style custom step temp etotal &
+             c_myTemp[1] c_myTemp[2] c_myTemp[3] &
+             c_myTemp[4] c_myTemp[5] c_myTemp[6]
+
          
 
          
 
          The c_ID and c_ID[I] and c_ID[I][J] keywords allow global
 values calculated by a compute to be output.  As discussed on the
@@ -490,9 +490,9 @@ division by “natoms” in the variable formula if this is not the case
 
          
 
          
 
          Default
          
-
          thermo_style one
-
          
-
          
+
          +thermo_style one
+
          
 
          
 
          
 
diff --git a/doc/html/tutorial_drude.html b/doc/html/tutorial_drude.html
index e414d5d007..1f4763d477 100644
--- a/doc/html/tutorial_drude.html
+++ b/doc/html/tutorial_drude.html
@@ -204,14 +204,14 @@ The masses and charges of DCs and DPs are computed
 from phenol.dff, as well as the DC-DP bond constants.  The file
 phenol.dff contains the polarizabilities of the atom types
 and the mass of the Drude particles, for instance:
          
-
          # units: kJ/mol, A, deg
-# kforce is in the form k/2 r_D^2
-# type  m_D/u   q_D/e    k_D   alpha/A3  thole
-OH      0.4    -1.0    4184.0   0.63     0.67
-CA      0.4    -1.0    4184.0   1.36     2.51
-CAI     0.4    -1.0    4184.0   1.09     2.51
-
          
-
          
+
          +# units: kJ/mol, A, deg
+# kforce is in the form k/2 r_D^2
+# type  m_D/u   q_D/e    k_D   alpha/A3  thole
+OH      0.4    -1.0    4184.0   0.63     0.67
+CA      0.4    -1.0    4184.0   1.36     2.51
+CAI     0.4    -1.0    4184.0   1.09     2.51
+
          
 
          The hydrogen atoms are absent from this file, so they will be treated
 as non-polarizable atoms.  In the non-polarizable data file
 data.102494.lmp, atom names corresponding to the atom type numbers
@@ -252,9 +252,9 @@ be reserved by using the extra keyword of the special_bonds
 command.  With our phenol, there is 1 more special neighbor for which
 space is required.  Otherwise LAMMPS crashes and gives the required
 value.
          
-
          special_bonds lj/coul 0.0 0.0 0.5 extra 1
-
          
-
          
+
          +special_bonds lj/coul 0.0 0.0 0.5 extra 1
+
          
 
          Let us assume we want to run a simple NVT simulation at 300 K.  Note
 that Drude oscillators need to be thermalized at a low temperature in
 order to approximate a self-consistent field (SCF), therefore it is not
@@ -263,17 +263,17 @@ are approximated by a charged DC-DP pair, the pair_style must
 include Coulomb interactions, for instance lj/cut/coul/long with
 kspace_style pppm. For example, with a cutoff of 10. and a precision
 1.e-4:
          
-
          pair_style lj/cut/coul/long 10.0
-kspace_style pppm 1.0e-4
-
          
-
          
+
          +pair_style lj/cut/coul/long 10.0
+kspace_style pppm 1.0e-4
+
          
 
          As compared to the non-polarizable input file, pair_coeff lines need
 to be added for the DPs.  Since the DPs have no Lennard-Jones
 interactions, their epsilon is 0. so the only pair_coeff line
 that needs to be added is
          
-
          pair_coeff * 6* 0.0 0.0 # All-DPs
-
          
-
          
+
          +pair_coeff * 6* 0.0 0.0 # All-DPs
+
          
 
          Now for the thermalization, the simplest choice is to use the fix langevin/drude.
          
 
          fix LANG all langevin/drude 300. 100 12435 1. 20 13977
 
          
@@ -286,9 +286,9 @@ time 20 and random seed 13977.  Only the DCs and non-polarizable
 atoms need to be in this fix’s group.  LAMMPS will thermostate the DPs
 together with their DC.  For this, ghost atoms need to know their
 velocities. Thus you need to add the following command:
          
-
          comm_modify vel yes
-
          
-
          
+
          +comm_modify vel yes
+
          
 
          In order to avoid that the center of mass of the whole system
 drifts due to the random forces of the Langevin thermostat on DCs, you
 can add the zero yes option at the end of the fix line.
          
@@ -311,10 +311,10 @@ modification of forces but no position/velocity updates), the fix
 
          Finally, do not forget to update the atom type elements if you use
 them in a dump_modify ... element ... command, by adding the element
 type of the DPs. Here for instance
          
-
          dump DUMP all custom 10 dump.lammpstrj id mol type element x y z ix iy iz
-dump_modify DUMP element C C O H H D D D
-
          
-
          
+
          +dump DUMP all custom 10 dump.lammpstrj id mol type element x y z ix iy iz
+dump_modify DUMP element C C O H H D D D
+
          
 
          The input file should now be ready for use!
          
 
          You will notice that the global temperature thermo_temp computed by
 LAMMPS is not 300. K as wanted.  This is because LAMMPS treats DPs as
@@ -327,9 +327,9 @@ to their DCs, you should use the 
          thermo_style custom step temp c_TDRUDE[1] c_TDRUDE[2]
-
          
-
          
+
          +thermo_style custom step temp c_TDRUDE[1] c_TDRUDE[2]
+
          
 
          
 
          Thole screening
          
 
          Dipolar interactions represented by point charges on springs may not
@@ -346,9 +346,9 @@ correction to the Coulomb pair_styles, which dampens at short distance
 the interactions between the charges representing the induced dipoles.
 It is to be used as hybrid/overlay with any standard coul pair
 style.  In our example, we would use
          
-
          pair_style hybrid/overlay lj/cut/coul/long 10.0 thole 2.6 10.0
-
          
-
          
+
          +pair_style hybrid/overlay lj/cut/coul/long 10.0 thole 2.6 10.0
+
          
 
          This tells LAMMPS that we are using two pair_styles.  The first one is
 as above (lj/cut/coul/long 10.0).  The second one is a thole
 pair_style with default screening factor 2.6 (Noskov) and
@@ -358,50 +358,48 @@ coefficients of all the pairs of atom types with i < j should be
 explicitly defined.  The output of the polarizer script can be used
 to complete the pair_coeff section of the input file.  In our
 example, this will look like:
          
-
          pair_coeff    1    1 lj/cut/coul/long    0.0700   3.550
-pair_coeff    1    2 lj/cut/coul/long    0.0700   3.550
-pair_coeff    1    3 lj/cut/coul/long    0.1091   3.310
-pair_coeff    1    4 lj/cut/coul/long    0.0458   2.985
-pair_coeff    2    2 lj/cut/coul/long    0.0700   3.550
-pair_coeff    2    3 lj/cut/coul/long    0.1091   3.310
-pair_coeff    2    4 lj/cut/coul/long    0.0458   2.985
-pair_coeff    3    3 lj/cut/coul/long    0.1700   3.070
-pair_coeff    3    4 lj/cut/coul/long    0.0714   2.745
-pair_coeff    4    4 lj/cut/coul/long    0.0300   2.420
-pair_coeff    *    5 lj/cut/coul/long    0.0000   0.000
-pair_coeff    *   6* lj/cut/coul/long    0.0000   0.000
-pair_coeff    1    1 thole   1.090   2.510
-pair_coeff    1    2 thole   1.218   2.510
-pair_coeff    1    3 thole   0.829   1.590
-pair_coeff    1    6 thole   1.090   2.510
-pair_coeff    1    7 thole   1.218   2.510
-pair_coeff    1    8 thole   0.829   1.590
-pair_coeff    2    2 thole   1.360   2.510
-pair_coeff    2    3 thole   0.926   1.590
-pair_coeff    2    6 thole   1.218   2.510
-pair_coeff    2    7 thole   1.360   2.510
-pair_coeff    2    8 thole   0.926   1.590
-pair_coeff    3    3 thole   0.630   0.670
-pair_coeff    3    6 thole   0.829   1.590
-pair_coeff    3    7 thole   0.926   1.590
-pair_coeff    3    8 thole   0.630   0.670
-pair_coeff    6    6 thole   1.090   2.510
-pair_coeff    6    7 thole   1.218   2.510
-pair_coeff    6    8 thole   0.829   1.590
-pair_coeff    7    7 thole   1.360   2.510
-pair_coeff    7    8 thole   0.926   1.590
-pair_coeff    8    8 thole   0.630   0.670
-
          
-
          
+
          +pair_coeff    1    1 lj/cut/coul/long    0.0700   3.550
+pair_coeff    1    2 lj/cut/coul/long    0.0700   3.550
+pair_coeff    1    3 lj/cut/coul/long    0.1091   3.310
+pair_coeff    1    4 lj/cut/coul/long    0.0458   2.985
+pair_coeff    2    2 lj/cut/coul/long    0.0700   3.550
+pair_coeff    2    3 lj/cut/coul/long    0.1091   3.310
+pair_coeff    2    4 lj/cut/coul/long    0.0458   2.985
+pair_coeff    3    3 lj/cut/coul/long    0.1700   3.070
+pair_coeff    3    4 lj/cut/coul/long    0.0714   2.745
+pair_coeff    4    4 lj/cut/coul/long    0.0300   2.420
+pair_coeff    *    5 lj/cut/coul/long    0.0000   0.000
+pair_coeff    *   6* lj/cut/coul/long    0.0000   0.000
+pair_coeff    1    1 thole   1.090   2.510
+pair_coeff    1    2 thole   1.218   2.510
+pair_coeff    1    3 thole   0.829   1.590
+pair_coeff    1    6 thole   1.090   2.510
+pair_coeff    1    7 thole   1.218   2.510
+pair_coeff    1    8 thole   0.829   1.590
+pair_coeff    2    2 thole   1.360   2.510
+pair_coeff    2    3 thole   0.926   1.590
+pair_coeff    2    6 thole   1.218   2.510
+pair_coeff    2    7 thole   1.360   2.510
+pair_coeff    2    8 thole   0.926   1.590
+pair_coeff    3    3 thole   0.630   0.670
+pair_coeff    3    6 thole   0.829   1.590
+pair_coeff    3    7 thole   0.926   1.590
+pair_coeff    3    8 thole   0.630   0.670
+pair_coeff    6    6 thole   1.090   2.510
+pair_coeff    6    7 thole   1.218   2.510
+pair_coeff    6    8 thole   0.829   1.590
+pair_coeff    7    7 thole   1.360   2.510
+pair_coeff    7    8 thole   0.926   1.590
+pair_coeff    8    8 thole   0.630   0.670
+
          
 
          For the thole pair style the coefficients are
          
 
            
 
          1. the atom polarizability in units of cubic length
            2. 
 
          2. the screening factor of the Thole function (optional, default value
 specified by the pair_style command)
            3. 
-
          
-
            
 
          • the cutoff (optional, default value defined by the pair_style command)
            • 
-
          
+
      
 
      The special neighbors have charge-charge and charge-dipole
 interactions screened by the coul factors of the special_bonds
 command (0.0, 0.0, and 0.5 in the example above).  Without using the
@@ -458,14 +456,14 @@ We do want the pressure to correspond to the whole system, but we want
 the temperature to correspond to the fix group only.  We must then use
 the fix_modify command for this.  In the end, the block of
 instructions for thermostating and barostating will look like
      
-
      compute TATOMS ATOMS temp
-fix DIRECT all drude/transform/direct
-fix NPT ATOMS npt temp 300. 300. 100 iso 1. 1. 500
-fix_modify NPT temp TATOMS press thermo_press
-fix NVT DRUDES nvt temp 1. 1. 20
-fix INVERSE all drude/transform/inverse
-
      
-
      
+
      +compute TATOMS ATOMS temp
+fix DIRECT all drude/transform/direct
+fix NPT ATOMS npt temp 300. 300. 100 iso 1. 1. 500
+fix_modify NPT temp TATOMS press thermo_press
+fix NVT DRUDES nvt temp 1. 1. 20
+fix INVERSE all drude/transform/inverse
+
      
 
      
 
      Rigid bodies
      
 
      You may want to simulate molecules as rigid bodies (but polarizable).
@@ -474,12 +472,12 @@ kind of polarizable TIP4P water.  The rigid bodies and the DPs should
 be integrated separately, even with the Langevin thermostat.  Let us
 review the different thermostats and ensemble combinations.
      
 
      NVT ensemble using Langevin thermostat:
      
-
      comm_modify vel yes
-fix LANG all langevin/drude 300. 100 12435 1. 20 13977
-fix RIGID ATOMS rigid/nve/small molecule
-fix NVE DRUDES nve
-
      
-
      
+
      +comm_modify vel yes
+fix LANG all langevin/drude 300. 100 12435 1. 20 13977
+fix RIGID ATOMS rigid/nve/small molecule
+fix NVE DRUDES nve
+
      
 
      NVT ensemble using Nose-Hoover thermostat:
      
 
      fix DIRECT all drude/transform/direct
 fix RIGID ATOMS rigid/nvt/small molecule temp 300. 300. 100
@@ -488,21 +486,21 @@ review the different thermostats and ensemble combinations.
      
 
      
 
      
 
      NPT ensemble with Langevin thermostat:
      
-
      comm_modify vel yes
-fix LANG all langevin/drude 300. 100 12435 1. 20 13977
-fix RIGID ATOMS rigid/nph/small molecule iso 1. 1. 500
-fix NVE DRUDES nve
-
      
-
      
+
      +comm_modify vel yes
+fix LANG all langevin/drude 300. 100 12435 1. 20 13977
+fix RIGID ATOMS rigid/nph/small molecule iso 1. 1. 500
+fix NVE DRUDES nve
+
      
 
      NPT ensemble using Nose-Hoover thermostat:
      
-
      compute TATOM ATOMS temp
-fix DIRECT all drude/transform/direct
-fix RIGID ATOMS rigid/npt/small molecule temp 300. 300. 100 iso 1. 1. 500
-fix_modify RIGID temp TATOM press thermo_press
-fix NVT DRUDES nvt temp 1. 1. 20
-fix INVERSE all drude/transform/inverse
-
      
-
      
+
      +compute TATOM ATOMS temp
+fix DIRECT all drude/transform/direct
+fix RIGID ATOMS rigid/npt/small molecule temp 300. 300. 100 iso 1. 1. 500
+fix_modify RIGID temp TATOM press thermo_press
+fix NVT DRUDES nvt temp 1. 1. 20
+fix INVERSE all drude/transform/inverse
+
      
 
      
 
      (Lamoureux) Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003)
      
 
      (Schroeder)  Schroeder and Steinhauser, J Chem Phys, 133,
diff --git a/doc/html/tutorial_github.html b/doc/html/tutorial_github.html
index e6170b8961..ad4a731ba8 100644
--- a/doc/html/tutorial_github.html
+++ b/doc/html/tutorial_github.html
@@ -135,14 +135,14 @@ git. You may want to have a look at the GitHub and create an account by clicking
-the ``Sign up for GitHub’’ button. Once your account is created, you
+the “Sign up for GitHub” button. Once your account is created, you
 can sign in by clicking the button in the top left and filling in your
 username or e-mail address and password.
      
 
      
 
      Forking the repository
      
 
      To get changes into LAMMPS, you need to first fork the repository. At
 the time of writing, LAMMPS-ICMS is the preferred fork. Go to LAMMPS on GitHub and make sure branch is
-set to ``lammps-icms’‘, see the figure below.
      
+set to “lammps-icms”, see the figure below.
      
 _images/tutorial_branch.png
 
      Now, click on fork in the top right corner:
      
 _images/tutorial_fork.png
@@ -158,7 +158,7 @@ will contain these changes, a so-called feature branch.
      
 
      Feature branches
      
 
      Since LAMMPS is such a big project and most user contributions come in
 small portions, the most ideal workflow for LAMMPS is the so-called
-``Feature branch’’ workflow. It is explained in great detail here:
+“Feature branch” workflow. It is explained in great detail here:
 feature branch workflow.
      
 
      The idea is that every new feature for LAMMPS gets its own
 branch. This way, it is fairly painless to incorporate new features
@@ -172,7 +172,7 @@ to use a command line.
      
 
      
 
      You can find the proper url to the right of the “HTTPS” block, see figure.
      
 _images/tutorial_https_block.png
-
      The above command copies (``clones’‘) the git repository to your local
+
      The above command copies (“clones”) the git repository to your local
 machine. You can use this local clone to make changes and test them
 without interfering with the repository on github. First, however, it
 is recommended to make a new branch for a particular feature you would
@@ -192,7 +192,7 @@ you should switch branches!
      
 
      After everything is done, add the files to the branch and commit them:
      
 
       $ git add src/USER-MANIFOLD examples/USER/manifold/
-$ git add doc/fix_nvt,e_manifold_rattle.txt
+$ git add doc/fix_nv{t,e}_manifold_rattle.txt
 $ git add doc/fix_manifoldforce.txt doc/user_manifolds.txt
 
      
 
      After the files are added, the change should be comitted:
      
@@ -203,14 +203,14 @@ $ git add doc/fix_manifoldforce.txt doc/user_manifolds.txt
 indicate what type of change was commited.
      
 
      Wisdom by Axel
      
 
      “Do not use “git commit -a”.  the -a flag will automatically include
-*all modified or new files.  mercurial does that and it find it
+*all* modified or new files.  mercurial does that and it find it
 hugely annoying and often leading to accidental commits of files you
 don’t want.  use git add, git rm, git mv for adding, removing,
 renaming and then git commit to finalize the commit.  personally, i
 find it very convenient to use the bundled gui for commits, i.e. git
 gui.  typically, i will do git add and other operations, but then
 verify and review them with git gui.  git gui also allows to do
-line-by-line unstaging and other convenient operations.”*
      
+line-by-line unstaging and other convenient operations.”
      
 
      After the commit, the changes can be pushed to the same branch on GitHub:
      
 
      $ git push
 
      
@@ -234,7 +234,7 @@ branch. GitHub will now look like this:
      
 this case, is “add-user-manifold”. Now click “New pull request”. If
 done correctly, the only changes you will see are those that were made
 on this branch, so in my case, I will see nothing related to
-$mathrm*pair_dzugatov*.$
      
+$mathrm*pair\_dzugatov*.$
      
 
      This will open up a new window that lists changes made to the
 repository. If you are just adding new files, there is not much to do,
 but I suppose merge conflicts are to be resolved here if there are
diff --git a/doc/html/units.html b/doc/html/units.html
index 9dc8285c6d..e80e207a23 100644
--- a/doc/html/units.html
+++ b/doc/html/units.html
@@ -187,7 +187,7 @@ results from a unitless LJ simulation into physical quantities.
      
 
    • pressure = reduced LJ pressure, where P* = P sigma^3 / epsilon
      • 
 
    • dynamic viscosity = reduced LJ viscosity, where eta* = eta sigma^3 / epsilon / tau
      • 
 
    • charge = reduced LJ charge, where q* = q / (4 pi perm0 sigma epsilon)^1/2
      • 
-
    • dipole = reduced LJ dipole, moment where *mu = mu / (4 pi perm0 sigma^3 epsilon)^1/2
      • 
+
    • dipole = reduced LJ dipole, moment where *mu = mu / (4 pi perm0 sigma^3 epsilon)^1/2
      • 
 
    • electric field = force/charge, where E* = E (4 pi perm0 sigma epsilon)^1/2 sigma / epsilon
      • 
 
    • density = mass/volume, where rho* = rho sigma^dim
      • 
 
diff --git a/doc/html/variable.html b/doc/html/variable.html
index f5eb258506..f7fd72fac0 100644
--- a/doc/html/variable.html
+++ b/doc/html/variable.html
@@ -197,7 +197,8 @@
 
      
 
      
 
      Examples
      
-
      variable x index run1 run2 run3 run4 run5 run6 run7 run8
+
      +variable x index run1 run2 run3 run4 run5 run6 run7 run8
 variable LoopVar loop $n
 variable beta equal temp/3.0
 variable b1 equal x[234]+0.5*vol
@@ -214,8 +215,7 @@ variable x universe 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
 variable x uloop 15 pad
 variable str format x %.6g
 variable x delete
-
      
-
      
+
 
      
 
      
 
      Description
      
@@ -470,10 +470,10 @@ appear in the set, will remain 0.0.
      
 to match a function name specified in a python command
 which returns a value to this variable as defined by its return
 keyword.  For example these two commands would be self-consistent:
      
-
      variable foo python myMultiply
-python myMultiply return v_foo format f file funcs.py
-
      
-
      
+
      +variable foo python myMultiply
+python myMultiply return v_foo format f file funcs.py
+
      
 
      The two commands can appear in either order so long as both are
 specified before the Python function is invoked for the first time.
      
 
      Each time the variable is evaluated, the associated Python function is
@@ -527,9 +527,9 @@ variety of quantities.  The syntax for each kind of quantity is
 simple, but multiple quantities can be nested and combined in various
 ways to build up formulas of arbitrary complexity.  For example, this
 is a valid (though strange) variable formula:
      
-
      variable x equal "pe + c_MyTemp / vol^(1/3)"
-
      
-
      
+
      +variable x equal "pe + c_MyTemp / vol^(1/3)"
+
      
 
      Specifically, a formula can contain numbers, constants, thermo
 keywords, math operators, math functions, group functions, region
 functions, atom values, atom vectors, compute references, fix
@@ -618,9 +618,9 @@ of LAMMPS will be smaller. This can be used to have input scripts
 adapt automatically to LAMMPS versions, when non-backwards compatible
 syntax changes are introduced. Here is an illustrative example (which
 will not work, since the version has been introduced more recently):
      
-
      if $(version<20140513) then "communicate vel yes" else "comm_modify vel yes"
-
      
-
      
+
      +if $(version<20140513) then "communicate vel yes" else "comm_modify vel yes"
+
      
 
      The thermo keywords allowed in a formula are those defined by the
 thermo_style custom command.  Thermo keywords that
 require a compute to calculate their values such as
@@ -719,9 +719,9 @@ is the nearest integer to its argument.
      
 
      The ramp(x,y) function uses the current timestep to generate a value
 linearly intepolated between the specified x,y values over the course
 of a run, according to this formula:
      
-
      value = x + (y-x) * (timestep-startstep) / (stopstep-startstep)
-
      
-
      
+
      +value = x + (y-x) * (timestep-startstep) / (stopstep-startstep)
+
      
 
      The run begins on startstep and ends on stopstep.  Startstep and
 stopstep can span multiple runs, using the start and stop keywords
 of the run command.  See the run command for
@@ -790,9 +790,9 @@ sequence of output timesteps:
      
 velocity, and uses the elapsed time to change the value by a linear
 displacement due to the applied velocity over the course of a run,
 according to this formula:
      
-
      value = value0 + velocity*(timestep-startstep)*dt
-
      
-
      
+
      +value = value0 + velocity*(timestep-startstep)*dt
+
      
 
      where dt = the timestep size.
      
 
      The run begins on startstep.  Startstep can span multiple runs, using
 the start keyword of the run command.  See the
@@ -803,10 +803,10 @@ timestep-startstep.
      
 x = value0, y = amplitude, z = period.  They use the elapsed time to
 oscillate the value by a sin() or cos() function over the course of a
 run, according to one of these formulas, where omega = 2 PI / period:
      
-
      value = value0 + Amplitude * sin(omega*(timestep-startstep)*dt)
-value = value0 + Amplitude * (1 - cos(omega*(timestep-startstep)*dt))
-
      
-
      
+
      +value = value0 + Amplitude * sin(omega*(timestep-startstep)*dt)
+value = value0 + Amplitude * (1 - cos(omega*(timestep-startstep)*dt))
+
      
 
      where dt = the timestep size.
      
 
      The run begins on startstep.  Startstep can span multiple runs, using
 the start keyword of the run command.  See the
@@ -952,16 +952,16 @@ features or LAMMPS, respa allows to check whether the inner/middle/oute
 mode of r-RESPA is supported. In the various style categories,
 the checking is also done using suffix flags, if available and enabled.
      
 
      Example 1: disable use of suffix for pppm when using GPU package (i.e. run it on the CPU concurrently to running the pair style on the GPU), but do use the suffix otherwise (e.g. with USER-OMP).
      
-
      pair_style lj/cut/coul/long 14.0
+
      +pair_style lj/cut/coul/long 14.0
 if $(is_active(package,gpu)) then "suffix off"
 kspace_style pppm
-
      
-
      
+
 
      Example 2: use r-RESPA with inner/outer cutoff, if supported by pair style, otherwise fall back to using pair and reducing the outer time step
      
-
      timestep $(2.0*(1.0+*is_active(pair,respa))
+
      +timestep $(2.0*(1.0+*is_active(pair,respa))
 if $(is_active(pair,respa)) then "run_style respa 4 3 2 2  improper 1 inner 2 5.5 7.0 outer 3 kspace 4" else "run_style respa 3 3 2  improper 1 pair 2 kspace 3"
-
      
-
      
+
 
      The is_defined() function allows to query categories like compute,
 dump, fix, group, region, and variable whether an entry
 with the provided name or id is defined.
      
@@ -1022,8 +1022,8 @@ reference means, since computes only produce either global or per-atom
 quantities, never both.
      
 
      
   
      
       
-  
      write_coeff
+  
      write\_coeff
   
      
 
       
-  
      write_data
+  
      write\_data
   
      
 
   
      		
   
      
       
-  
      write_dump
+  
      write\_dump
   
      
 
       
-  
      write_restart
+  
      write\_restart
   
      
 
   
      		
 
 
 
 
 
 
      --++
@@ -1046,9 +1046,9 @@ variable refers to a compute that produces both a global scalar and a
 global vector.  Consider a compute with ID “foo” that does this,
 referenced as follows by variable “a”, where “myVec” is another
 vector-style variable:
      
-
      variable a vector c_foo*v_myVec
-
      
-
      
+
      +variable a vector c_foo*v_myVec
+
      
 
      The reference “c_foo” could refer to either the global scalar or
 global vector produced by compute “foo”.  In this case, “c_foo” will
 always refer to the global scalar, and “C_foo” can be used to
@@ -1077,14 +1077,14 @@ vector values.  A vector value can be a per-atom vector itself, or a
 column of an per-atom array.  See the doc pages for individual fixes
 to see what kind of values they produce.
      
 
      The different kinds of fix references are exactly the same as the
-compute references listed in the above table, where “c_” is replaced
-by “f_”.  Again, there is typically no ambiguity (see exception below)
+compute references listed in the above table, where “c_” is replaced
+by “f_”.  Again, there is typically no ambiguity (see exception below)
 as to what a reference means, since fixes only produce either global
 or per-atom quantities, never both.
      
 
      
 




 
 
 
      c_ID
      --++
@@ -1152,8 +1152,8 @@ There is no ambiguity as to what a reference means, since variables
 produce only a global scalar or global vector or per-atom vector.
      
 
      
 




 
 
 
      f_ID
      --++
@@ -1188,7 +1188,7 @@ same syntax as equal-style variables described on this page.  This
 effectively evaluates a formula immediately without using the variable
 command to define a named variable.
      
 
      More generally, there is a difference between referencing a variable
-with a leading $ sign (e.g. $x or ${abc}) versus with a leading “v_”
+with a leading $ sign (e.g. $x or ${abc}) versus with a leading “v_”
 (e.g. v_x or v_abc).  The former can be used in any input script
 command, including a variable command.  The input script parser
 evaluates the reference variable immediately and substitutes its value
@@ -1197,7 +1197,7 @@ un-named “immediate” variables for this purpose.  For example, a
 string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script
 command evaluates the string between the parenthesis as an equal-style
 variable formula.
      
-
      Referencing a variable with a leading “v_” is an optional or required
+
      Referencing a variable with a leading “v_” is an optional or required
 kind of argument for some commands (e.g. the fix ave/chunk or dump custom or
 thermo_style commands) if you wish it to evaluate
 a variable periodically during a run.  It can also be used in a
@@ -1224,9 +1224,9 @@ variable v0 equal $v
 
      The second command will force “v” to be evaluated (yielding the
 initial volume) and assign that value to the variable “v0”.  Thus the
 command
      
-
      thermo_style custom step v_v v_v0
-
      
-
      
+
      +thermo_style custom step v_v v_v0
+
      
 
      would print out both the current and initial volume periodically
 during the run.
      
 
      Note that it is a mistake to enclose a variable formula in double
@@ -1317,13 +1317,13 @@ a 0-timestep run before printing the variable has the desired effect.
      
 
      (3) The variable may be evaluated incorrectly and LAMMPS may have no
 way to detect this has occurred.  Consider the following sequence of
 commands:
      
-
      pair_coeff 1 1 1.0 1.0
-run 1000
-pair_coeff 1 1 1.5 1.0
-variable e equal pe
-print "Final potential energy = $e"
-
      
-
      
+
      +pair_coeff 1 1 1.0 1.0
+run 1000
+pair_coeff 1 1 1.5 1.0
+variable e equal pe
+print "Final potential energy = $e"
+
      
 
      The first run is performed using one setting for the pairwise
 potential defined by the pair_style and
 pair_coeff commands.  The potential energy is
@@ -1340,14 +1340,14 @@ perform a 0-timestep run before the variable is evaluated to insure
 the system is up-to-date.  For example, this sequence of commands
 would print a potential energy that reflected the changed pairwise
 coefficient:
      
-
      pair_coeff 1 1 1.0 1.0
-run 1000
-pair_coeff 1 1 1.5 1.0
-run 0
-variable e equal pe
-print "Final potential energy = $e"
-
      
-
      
+
      +pair_coeff 1 1 1.0 1.0
+run 1000
+pair_coeff 1 1 1.5 1.0
+run 0
+variable e equal pe
+print "Final potential energy = $e"
+
      
 
 
 
      
diff --git a/doc/html/velocity.html b/doc/html/velocity.html
index 06accf9593..af9be7196c 100644
--- a/doc/html/velocity.html
+++ b/doc/html/velocity.html
@@ -172,13 +172,13 @@
 
 
      
 
      Examples
      
-
      velocity all create 300.0 4928459 rot yes dist gaussian
-velocity border set NULL 4.0 v_vz sum yes units box
-velocity flow scale 300.0
-velocity flow ramp vx 0.0 5.0 y 5 25 temp mytemp
-velocity all zero linear
-
      
-
      
+
      +velocity all create 300.0 4928459 rot yes dist gaussian
+velocity border set NULL 4.0 v_vz sum yes units box
+velocity flow scale 300.0
+velocity flow ramp vx 0.0 5.0 y 5 25 temp mytemp
+velocity all zero linear
+
      
 
      
 
      
 
      Description
      
@@ -244,7 +244,7 @@ replace them if sum = no.
      
 
      The mom and rot keywords are used by create.  If mom = yes, the
 linear momentum of the newly created ensemble of velocities is zeroed;
 if rot = yes, the angular momentum is zeroed.
      
-
      *line
      
+
      *line
      
 
      If specified, the temp keyword is used by create and scale to
 specify a compute that calculates temperature in a
 desired way, e.g. by first subtracting out a velocity bias, as
@@ -252,9 +252,9 @@ discussed in create and scale
 calculate temperature using a compute that is defined internally as
 follows:
      
-
      compute velocity_temp group-ID temp
-
      
-
      
+
      +compute velocity_temp group-ID temp
+
      
 
      where group-ID is the same ID used in the velocity command. i.e. the
 group of atoms whose velocity is being altered.  This compute is
 deleted when the velocity command is finished.  See the compute temp command for details.  If the calculated
diff --git a/doc/html/write_coeff.html b/doc/html/write_coeff.html
index 1698ec2615..d4d15e1ddf 100644
--- a/doc/html/write_coeff.html
+++ b/doc/html/write_coeff.html
@@ -128,18 +128,18 @@
 
      write_coeff command
      
 
      
 
      Syntax
      
-
      write_coeff file
-
      
-
      
+
      +write_coeff file
+
      
 
      file = name of data file to write out
 
      
 
      
 
      
 
      
 
      Examples
      
-
      write_coeff polymer.coeff
-
      
-
      
+
      +write_coeff polymer.coeff
+
      
 
      
 
      
 
      Description
      
diff --git a/doc/html/write_dump.html b/doc/html/write_dump.html
index 413887f469..0fcd373eb7 100644
--- a/doc/html/write_dump.html
+++ b/doc/html/write_dump.html
@@ -128,9 +128,9 @@
 
      write_dump command
      
 
      
 
      Syntax
      
-
      write_dump group-ID style file dump-args modify dump_modify-args
-
      
-
      
+
      +write_dump group-ID style file dump-args modify dump_modify-args
+
      
 
        
 
      • group-ID = ID of the group of atoms to be dumped
        • 
 
      • style = any of the supported dump styles
        • 
@@ -142,17 +142,17 @@
 
      
 
      
 
      Examples
      
-
      write_dump all atom dump.atom
-write_dump subgroup atom dump.run.bin
-write_dump all custom dump.myforce.* id type x y vx fx
-write_dump flow custom dump.%.myforce id type c_myF[3] v_ke modify sort id
-write_dump all xyz system.xyz modify sort id elements O H
-write_dump all image snap*.jpg type type size 960 960 modify backcolor white
-write_dump all image snap*.jpg element element &
-   bond atom 0.3 shiny 0.1 ssao yes 6345 0.2 size 1600 1600  &
-   modify backcolor white element C C O H N C C C O H H S O H
-
      
-
      
+
      +write_dump all atom dump.atom
+write_dump subgroup atom dump.run.bin
+write_dump all custom dump.myforce.* id type x y vx fx
+write_dump flow custom dump.%.myforce id type c_myF[3] v_ke modify sort id
+write_dump all xyz system.xyz modify sort id elements O H
+write_dump all image snap*.jpg type type size 960 960 modify backcolor white
+write_dump all image snap*.jpg element element &
+   bond atom 0.3 shiny 0.1 ssao yes 6345 0.2 size 1600 1600  &
+   modify backcolor white element C C O H N C C C O H H S O H
+
      
 
      
 
      
 
      Description
      

From 346ff4249833619793efda918f5bc18b7fc5d0ba Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer 
Date: Wed, 7 Sep 2016 10:10:12 -0400
Subject: [PATCH 17/18] correct reference in modify section

---
 doc/src/Section_modify.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/src/Section_modify.txt b/doc/src/Section_modify.txt
index a3ac505946..d5657c7db6 100644
--- a/doc/src/Section_modify.txt
+++ b/doc/src/Section_modify.txt
@@ -21,7 +21,7 @@ and extending its source code.
 10.6 "Fix styles"_#mod_6 which include integrators, \
      temperature and pressure control, force constraints, \
      boundary conditions, diagnostic output, etc
-10.7 "Input script commands"_mod_7
+10.7 "Input script commands"_#mod_7
 10.8 "Kspace computations"_#mod_8
 10.9 "Minimization styles"_#mod_9
 10.10 "Pairwise potentials"_#mod_10

From 0fe7d1d3612cac3cee27ef0c9d2939f20fa65395 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer 
Date: Wed, 7 Sep 2016 10:13:34 -0400
Subject: [PATCH 18/18] correct internal links for Modify LAMMPS section

---
 doc/html/Section_modify.html | 4 ++--
 doc/src/Section_modify.txt   | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/doc/html/Section_modify.html b/doc/html/Section_modify.html
index 41c466042e..b760c3c002 100644
--- a/doc/html/Section_modify.html
+++ b/doc/html/Section_modify.html
@@ -1040,7 +1040,7 @@ compute values = c_mytemp[0], c_thermo_press[3], ...
 
 
      Adding keywords for the thermo_style custom command
 (which can then be accessed by variables) was discussed
-here on this page.
      
+here on this page.
      
 
      Adding a new math function of one or two arguments can be done by
 editing one section of the Variable::evaulate() method.  Search for
 the word “customize” to find the appropriate location.
      
@@ -1053,7 +1053,7 @@ of the Variable::evaulate() method.  Search for the word “customize”
 to find the appropriate location.
      
 
      Adding new compute styles (whose calculated values can
 then be accessed by variables) was discussed
-here on this page.
      
+here on this page.
      
 
      
 
      
 
      10.15. Submitting new features for inclusion in LAMMPS
      
diff --git a/doc/src/Section_modify.txt b/doc/src/Section_modify.txt
index d5657c7db6..67b38d6936 100644
--- a/doc/src/Section_modify.txt
+++ b/doc/src/Section_modify.txt
@@ -598,7 +598,7 @@ compute values = c_mytemp\[0\], c_thermo_press\[3\], ... :pre
 
 Adding keywords for the "thermo_style custom"_thermo_style.html command
 (which can then be accessed by variables) was discussed
-"here"_Section_modify.html#thermo on this page.
+"here"_Section_modify.html#mod_13 on this page.
 
 Adding a new math function of one or two arguments can be done by
 editing one section of the Variable::evaulate() method.  Search for
@@ -615,7 +615,7 @@ to find the appropriate location.
 
 Adding new "compute styles"_compute.html (whose calculated values can
 then be accessed by variables) was discussed
-"here"_Section_modify.html#compute on this page.
+"here"_Section_modify.html#mod_3 on this page.
 
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      v_name