patch 11Aug17

Fixes for stable

LICENSE

@@ -3,7 +3,7 @@ GNU GENERAL PUBLIC LICENSE
 Version 2, June 1991 
 
 Copyright (C) 1989, 1991 Free Software Foundation, Inc.  
-59 Temple Place - Suite 330, Boston, MA  02111-1307, USA
+51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 
 Everyone is permitted to copy and distribute verbatim copies of this
 license document, but changing it is not allowed.

bench/FERMI/README

@@ -1,55 +1,21 @@
 These are input scripts used to run versions of several of the
-benchmarks in the top-level bench directory using the GPU and
-USER-CUDA accelerator packages.  The results of running these scripts
-on two different machines (a desktop with 2 Tesla GPUs and the ORNL
-Titan supercomputer) are shown on the "GPU (Fermi)" section of the
-Benchmark page of the LAMMPS WWW site: lammps.sandia.gov/bench.
+benchmarks in the top-level bench directory using the GPU accelerator
+package.  The results of running these scripts on two different machines
+(a desktop with 2 Tesla GPUs and the ORNL Titan supercomputer) are shown
+on the "GPU (Fermi)" section of the Benchmark page of the LAMMPS WWW
+site: lammps.sandia.gov/bench.
 
 Examples are shown below of how to run these scripts.  This assumes
-you have built 3 executables with both the GPU and USER-CUDA packages
+you have built 3 executables with the GPU package
 installed, e.g.
 
 lmp_linux_single
 lmp_linux_mixed
 lmp_linux_double
 
-The precision (single, mixed, double) refers to the GPU and USER-CUDA
-package precision.  See the README files in the lib/gpu and lib/cuda
-directories for instructions on how to build the packages with
-different precisions.  The GPU and USER-CUDA sub-sections of the
-doc/Section_accelerate.html file also describes this process.
-
-Make.py -d ~/lammps -j 16 -p #all orig -m linux -o cpu -a exe
-Make.py -d ~/lammps -j 16 -p #all opt orig -m linux -o opt -a exe
-Make.py -d ~/lammps -j 16 -p #all omp orig -m linux -o omp -a exe
-Make.py -d ~/lammps -j 16 -p #all gpu orig -m linux \
-        -gpu mode=double arch=20 -o gpu_double -a libs exe
-Make.py -d ~/lammps -j 16 -p #all gpu orig -m linux \
-        -gpu mode=mixed arch=20 -o gpu_mixed -a libs exe
-Make.py -d ~/lammps -j 16 -p #all gpu orig -m linux \
-        -gpu mode=single arch=20 -o gpu_single -a libs exe
-Make.py -d ~/lammps -j 16 -p #all cuda orig -m linux \
-        -cuda mode=double arch=20 -o cuda_double -a libs exe
-Make.py -d ~/lammps -j 16 -p #all cuda orig -m linux \
-        -cuda mode=mixed arch=20 -o cuda_mixed -a libs exe
-Make.py -d ~/lammps -j 16 -p #all cuda orig -m linux \
-        -cuda mode=single arch=20 -o cuda_single -a libs exe
-Make.py -d ~/lammps -j 16 -p #all intel orig -m linux -o intel_cpu -a exe
-Make.py -d ~/lammps -j 16 -p #all kokkos orig -m linux -o kokkos_omp -a exe
-Make.py -d ~/lammps -j 16 -p #all kokkos orig -kokkos cuda arch=20 \
-        -m cuda -o kokkos_cuda -a exe
-
-Make.py -d ~/lammps -j 16 -p #all opt omp gpu cuda intel kokkos orig \
-        -gpu mode=double arch=20 -cuda mode=double arch=20 -m linux \
-        -o all -a libs exe
-
-Make.py -d ~/lammps -j 16 -p #all opt omp gpu cuda intel kokkos orig \
-        -kokkos cuda arch=20 -gpu mode=double arch=20 \
-        -cuda mode=double arch=20 -m cuda -o all_cuda -a libs exe
-
 ------------------------------------------------------------------------
 
-To run on just CPUs (without using the GPU or USER-CUDA styles),
+To run on just CPUs (without using the GPU styles),
 do something like the following:
 
 mpirun -np 1 lmp_linux_double -v x 8 -v y 8 -v z 8 -v t 100 < in.lj
@@ -81,23 +47,5 @@ node via a "-ppn" setting.
 
 ------------------------------------------------------------------------
 
-To run with the USER-CUDA package, do something like the following:
-
-mpirun -np 1 lmp_linux_single -c on -sf cuda -v x 16 -v y 16 -v z 16 -v t 100 < in.lj
-mpirun -np 2 lmp_linux_double -c on -sf cuda -pk cuda 2 -v x 32 -v y 64 -v z 64 -v t 100 < in.eam
-
-The "xyz" settings determine the problem size.  The "t" setting
-determines the number of timesteps.  The "np" setting determines how
-many MPI tasks (per node) the problem will run on.  The numeric
-argument to the "-pk" setting is the number of GPUs (per node); 1 GPU
-is the default.  Note that the number of MPI tasks must equal the
-number of GPUs (both per node) with the USER-CUDA package.
-
-These mpirun commands run on a single node.  To run on multiple nodes,
-scale up the "-np" setting, and control the number of MPI tasks per
-node via a "-ppn" setting.
-
-------------------------------------------------------------------------
-
 If the script has "titan" in its name, it was run on the Titan
 supercomputer at ORNL.

bench/README

@@ -71,49 +71,33 @@ integration
 
 ----------------------------------------------------------------------
 
-Here is a src/Make.py command which will perform a parallel build of a
-LAMMPS executable "lmp_mpi" with all the packages needed by all the
-examples.  This assumes you have an MPI installed on your machine so
-that "mpicxx" can be used as the wrapper compiler.  It also assumes
-you have an Intel compiler to use as the base compiler.  You can leave
-off the "-cc mpi wrap=icc" switch if that is not the case.  You can
-also leave off the "-fft fftw3" switch if you do not have the FFTW
-(v3) installed as an FFT package, in which case the default KISS FFT
-library will be used.
-
-cd src
-Make.py -j 16 -p none molecule manybody kspace granular rigid orig \
-  -cc mpi wrap=icc -fft fftw3 -a file mpi
-
-----------------------------------------------------------------------
-
 Here is how to run each problem, assuming the LAMMPS executable is
 named lmp_mpi, and you are using the mpirun command to launch parallel
 runs:
 
 Serial (one processor runs):
 
-lmp_mpi < in.lj
-lmp_mpi < in.chain
-lmp_mpi < in.eam
-lmp_mpi < in.chute
-lmp_mpi < in.rhodo
+lmp_mpi -in in.lj
+lmp_mpi -in in.chain
+lmp_mpi -in in.eam
+lmp_mpi -in in.chute
+lmp_mpi -in in.rhodo
 
 Parallel fixed-size runs (on 8 procs in this case):
 
-mpirun -np 8 lmp_mpi < in.lj
-mpirun -np 8 lmp_mpi < in.chain
-mpirun -np 8 lmp_mpi < in.eam
-mpirun -np 8 lmp_mpi < in.chute
-mpirun -np 8 lmp_mpi < in.rhodo
+mpirun -np 8 lmp_mpi -in in.lj
+mpirun -np 8 lmp_mpi -in in.chain
+mpirun -np 8 lmp_mpi -in in.eam
+mpirun -np 8 lmp_mpi -in in.chute
+mpirun -np 8 lmp_mpi -in in.rhodo
 
 Parallel scaled-size runs (on 16 procs in this case):
 
-mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 < in.lj
-mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 < in.chain.scaled
-mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 < in.eam
-mpirun -np 16 lmp_mpi -var x 4 -var y 4 < in.chute.scaled
-mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 < in.rhodo.scaled
+mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 -in in.lj
+mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 -in in.chain.scaled
+mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 -in in.eam
+mpirun -np 16 lmp_mpi -var x 4 -var y 4 -in in.chute.scaled
+mpirun -np 16 lmp_mpi -var x 2 -var y 2 -var z 4 -in in.rhodo.scaled
 
 For each of the scaled-size runs you must set 3 variables as -var
 command line switches.  The variables x,y,z are used in the input

doc/src/Eqs/fix_wall_ees.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$ 
+E = \epsilon \left[ \frac{2  \sigma_{LJ}^{12} \left(7 r^5+14 r^3 \sigma_{n}^2+3 r \sigma_{n}^4\right) }{945 \left(r^2-\sigma_{n}^2\right)^7} -\frac{ \sigma_{LJ}^6 \left(2 r \sigma_{n}^3+\sigma_{n}^2 \left(r^2-\sigma_{n}^2\right)\log{ \left[\frac{r-\sigma_{n}}{r+\sigma_{n}}\right]}\right) }{12 \sigma_{n}^5 \left(r^2-\sigma_{n}^2\right)} \right]\qquad \sigma_n < r < r_c
+$$
+
+
+\end{document}

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="6 Jul 2017 version">
+<META NAME="docnumber" CONTENT="11 Aug 2017 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@@ -21,7 +21,7 @@
 <H1></H1>
 
 LAMMPS Documentation :c,h3
-6 Jul 2017 version :c,h4
+11 Aug 2017 version :c,h4
 
 Version info: :h4
 
@@ -261,7 +261,6 @@ END_RST -->
 :link(start_6,Section_start.html#start_6)
 :link(start_7,Section_start.html#start_7)
 :link(start_8,Section_start.html#start_8)
-:link(start_9,Section_start.html#start_9)
 
 :link(cmd_1,Section_commands.html#cmd_1)
 :link(cmd_2,Section_commands.html#cmd_2)

doc/src/Section_accelerate.txt

@@ -56,7 +56,7 @@ timings; you can simply extrapolate from short runs.
 
 For the set of runs, look at the timing data printed to the screen and
 log file at the end of each LAMMPS run.  "This
-section"_Section_start.html#start_8 of the manual has an overview.
+section"_Section_start.html#start_7 of the manual has an overview.
 
 Running on one (or a few processors) should give a good estimate of
 the serial performance and what portions of the timestep are taking
@@ -226,16 +226,16 @@ re-build LAMMPS |
   make machine |
 prepare and test a regular LAMMPS simulation |
   lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script |
-enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_7, |
+enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_6, |
   only needed for KOKKOS package |
-set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_7 or "package"_package.html command, |
+set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_6 or "package"_package.html command, |
   only if defaults need to be changed |
-use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_7 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
+use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
 :tb(c=2,s=|)
 
-Note that the first 4 steps can be done as a single command, using the
-src/Make.py tool.  This tool is discussed in "Section
-2.4"_Section_start.html#start_4 of the manual, and its use is
+Note that the first 4 steps can be done as a single command with
+suitable make command invocations. This is discussed in "Section
+4"_Section_packages.html of the manual, and its use is
 illustrated in the individual accelerator sections.  Typically these
 steps only need to be done once, to create an executable that uses one
 or more accelerator packages.

doc/src/Section_commands.txt

@@ -734,7 +734,9 @@ package"_Section_start.html#start_3.
 "smd/wall/surface"_fix_smd_wall_surface.html,
 "temp/rescale/eff"_fix_temp_rescale_eff.html,
 "ti/spring"_fix_ti_spring.html,
-"ttm/mod"_fix_ttm.html :tb(c=6,ea=c)
+"ttm/mod"_fix_ttm.html,
+"wall/ees"_fix_wall_ees.html,
+"wall/region/ees"_fix_wall_ees.html :tb(c=6,ea=c)
 
 :line
 

doc/src/Section_errors.txt

@@ -71,7 +71,7 @@ style", with ... being fix, compute, pair, etc, it means that you
 mistyped the style name or that the command is part of an optional
 package which was not compiled into your executable.  The list of
 available styles in your executable can be listed by using "the -h
-command-line argument"_Section_start.html#start_7.  The installation
+command-line argument"_Section_start.html#start_6.  The installation
 and compilation of optional packages is explained in the "installation
 instructions"_Section_start.html#start_3.
 

doc/src/Section_example.txt

@@ -49,6 +49,7 @@ Lists of both kinds of directories are given below.
 Lowercase directories :h4
 
 accelerate: run with various acceleration options (OpenMP, GPU, Phi)
+airebo:   polyethylene with AIREBO potential
 balance:  dynamic load balancing, 2d system
 body:     body particles, 2d system
 cmap:     CMAP 5-body contributions to CHARMM force field

doc/src/Section_howto.txt

@@ -54,7 +54,7 @@ restart files can be saved to disk using the "restart"_restart.html
 command.  At a later time, these binary files can be read via a
 "read_restart"_read_restart.html command in a new script.  Or they can
 be converted to text data files using the "-r command-line
-switch"_Section_start.html#start_7 and read by a
+switch"_Section_start.html#start_6 and read by a
 "read_data"_read_data.html command in a new script.
 
 Here we give examples of 2 scripts that read either a binary restart
@@ -337,7 +337,7 @@ All of the above examples work whether you are running on 1 or
 multiple processors, but assumed you are running LAMMPS on a single
 partition of processors.  LAMMPS can be run on multiple partitions via
 the "-partition" command-line switch as described in "this
-section"_Section_start.html#start_7 of the manual.
+section"_Section_start.html#start_6 of the manual.
 
 In the last 2 examples, if LAMMPS were run on 3 partitions, the same
 scripts could be used if the "index" and "loop" variables were
@@ -387,7 +387,7 @@ for more info on packages.
 In all these cases, you must run with one or more processors per
 replica.  The processors assigned to each replica are determined at
 run-time by using the "-partition command-line
-switch"_Section_start.html#start_7 to launch LAMMPS on multiple
+switch"_Section_start.html#start_6 to launch LAMMPS on multiple
 partitions, which in this context are the same as replicas.  E.g.
 these commands:
 
@@ -395,7 +395,7 @@ mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
 mpirun -np 8 lmp_linux -partition 8x1 -in in.neb :pre
 
 would each run 8 replicas, on either 16 or 8 processors.  Note the use
-of the "-in command-line switch"_Section_start.html#start_7 to specify
+of the "-in command-line switch"_Section_start.html#start_6 to specify
 the input script which is required when running in multi-replica mode.
 
 Also note that with MPI installed on a machine (e.g. your desktop),
@@ -1872,7 +1872,7 @@ void lammps_free(void *) :pre
 
 The lammps_open() function is used to initialize LAMMPS, passing in a
 list of strings as if they were "command-line
-arguments"_Section_start.html#start_7 when LAMMPS is run in
+arguments"_Section_start.html#start_6 when LAMMPS is run in
 stand-alone mode from the command line, and a MPI communicator for
 LAMMPS to run under.  It returns a ptr to the LAMMPS object that is
 created, and which is used in subsequent library calls.  The

doc/src/Section_packages.txt

@@ -25,6 +25,17 @@ There are two kinds of packages in LAMMPS, standard and user packages:
 "Table of standard packages"_#table_standard
 "Table of user packages"_#table_user :ul
 
+Either of these kinds of packages may work as is, may require some
+additional code compiled located in the lib folder, or may require
+an external library to be downloaded, compiled, installed, and LAMMPS
+configured to know about its location and additional compiler flags.
+You can often do the build of the internal or external libraries
+in one step by typing "make lib-name args='...'" from the src dir,
+with appropriate arguments included in args='...'. If you just type
+"make lib-name" you should see a help message about supported flags
+and some examples. For more details about this, please study the
+tables below and the sections about the individual packages.
+
 Standard packages are supported by the LAMMPS developers and are
 written in a syntax and style consistent with the rest of LAMMPS.
 This means the developers will answer questions about them, debug and
@@ -34,7 +45,9 @@ LAMMPS.
 User packages have been contributed by users, and begin with the
 "user" prefix.  If they are a single command (single file), they are
 typically in the user-misc package.  User packages don't necessarily
-meet the requirements of the standard packages.  If you have problems
+meet the requirements of the standard packages. This means the
+developers will try to keep things working and usually can answer
+technical questions about compiling the package. If you have problems
 using a feature provided in a user package, you may need to contact
 the contributor directly to get help.  Information on how to submit
 additions you make to LAMMPS as single files or as a standard or user
@@ -78,10 +91,10 @@ Package, Description, Doc page, Example, Library
 "COMPRESS"_#COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys
 "CORESHELL"_#CORESHELL, adiabatic core/shell model, "Section 6.6.25"_Section_howto.html#howto_25, coreshell, -
 "DIPOLE"_#DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, -
-"GPU"_#GPU, GPU-enabled styles, "Section 5.3.1"_accelerate_gpu.html, WWW bench, int
+"GPU"_#GPU, GPU-enabled styles, "Section 5.3.1"_accelerate_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int
 "GRANULAR"_#GRANULAR, granular systems, "Section 6.6.6"_Section_howto.html#howto_6, pour, -
-"KIM"_#KIM, openKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
-"KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, WWW bench, -
+"KIM"_#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
+"KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
 "KSPACE"_#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
 "MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
 "MC"_#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
@@ -90,7 +103,7 @@ Package, Description, Doc page, Example, Library
 "MOLECULE"_#MOLECULE, molecular system force fields, "Section 6.6.3"_Section_howto.html#howto_3, peptide, -
 "MPIIO"_#MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, -
 "MSCG"_#MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext
-"OPT"_#OPT, optimized pair styles, "Section 5.3.5"_accelerate_opt.html, WWW bench, -
+"OPT"_#OPT, optimized pair styles, "Section 5.3.5"_accelerate_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
 "PERI"_#PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, -
 "POEMS"_#POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
 "PYTHON"_#PYTHON, embed Python code in an input script, "python"_python.html, python, sys
@@ -101,8 +114,7 @@ Package, Description, Doc page, Example, Library
 "SHOCK"_#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
 "SNAP"_#SNAP, quantum-fitted potential, "pair snap"_pair_snap.html, snap, -
 "SRD"_#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
-"VORONOI"_#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext
-:tb(ea=c,ca1=l)
+"VORONOI"_#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)
 
 [USER packages] :link(table_user),p
 
@@ -118,7 +130,7 @@ Package, Description, Doc page, Example, Library
 "USER-EFF"_#USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, -
 "USER-FEP"_#USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, -
 "USER-H5MD"_#USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext
-"USER-INTEL"_#USER-INTEL, optimized Intel CPU and KNL styles,"Section 5.3.2"_accelerate_intel.html, WWW bench, -
+"USER-INTEL"_#USER-INTEL, optimized Intel CPU and KNL styles,"Section 5.3.2"_accelerate_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
 "USER-LB"_#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, -
 "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
 "USER-MEAMC"_#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, -
@@ -126,7 +138,7 @@ Package, Description, Doc page, Example, Library
 "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
 "USER-MOLFILE"_#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
 "USER-NETCDF"_#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
-"USER-OMP"_#USER-OMP, OpenMP-enabled styles,"Section 5.3.4"_accelerate_omp.html, WWW bench, -
+"USER-OMP"_#USER-OMP, OpenMP-enabled styles,"Section 5.3.4"_accelerate_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
 "USER-PHONON"_#USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, -
 "USER-QMMM"_#USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
 "USER-QTB"_#USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -
@@ -136,8 +148,7 @@ Package, Description, Doc page, Example, Library
 "USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
 "USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
 "USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
-"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext
-:tb(ea=c,ca1=l)
+"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)
 
 :line
 :line
@@ -364,12 +375,15 @@ GPU package :link(GPU),h4
 [Contents:]
 
 Dozens of pair styles and a version of the PPPM long-range Coulombic
-solver optimized for NVIDIA GPUs.  All such styles have a "gpu" as a
-suffix in their style name.  "Section 5.3.1"_accelerate_gpu.html gives
-details of what hardware and Cuda software is required on your system,
+solver optimized for GPUs.  All such styles have a "gpu" as a
+suffix in their style name. The GPU code can be compiled with either
+CUDA or OpenCL, however the OpenCL variants are no longer actively
+maintained and only the CUDA versions are regularly tested.
+"Section 5.3.1"_accelerate_gpu.html gives details of what
+hardware and GPU software is required on your system,
 and details on how to build and use this package.  Its styles can be
 invoked at run time via the "-sf gpu" or "-suffix gpu" "command-line
-switches"_Section_start.html#start_7.  See also the "KOKKOS"_#KOKKOS
+switches"_Section_start.html#start_6.  See also the "KOKKOS"_#KOKKOS
 package, which has GPU-enabled styles.
 
 [Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
@@ -378,32 +392,41 @@ package, which has GPU-enabled styles.
 [Install or un-install:]
 
 Before building LAMMPS with this package, you must first build the GPU
-library in lib/gpu from a set of provided C and Cuda files.  You can
+library in lib/gpu from a set of provided C and CUDA files.  You can
 do this manually if you prefer; follow the instructions in
-lib/gpu/README.  You can also do it in one step from the lammps/src
+lib/gpu/README. Please note, that the GPU library uses MPI calls, so
+you have to make certain to use the same MPI library (or the STUBS
+library) settings as the main LAMMPS code. That same applies to the
+-DLAMMPS_BIGBIG, -DLAMMPS_SMALLBIG, or -DLAMMPS_SMALLSMALL define.
+
+You can also do it in one step from the lammps/src
 dir, using a command like these, which simply invoke the
 lib/gpu/Install.py script with the specified args:
 
-make lib-gpu                                # print help message
-make lib-gpu args="-m"                      # build GPU library with default Makefile.linux
-make lib-gpu args="-i xk7 -p single -o xk7.single"      # create new Makefile.xk7.single, altered for single-precision
-make lib-gpu args="-i xk7 -p single -o xk7.single -m"   # ditto, also build GPU library
+make lib-gpu               # print help message
+make lib-gpu args="-b"     # build GPU library with default Makefile.linux
+make lib-gpu args="-m xk7 -p single -o xk7.single"  # create new Makefile.xk7.single, altered for single-precision
+make lib-gpu args="-m mpi -p mixed -b" # build GPU library with mixed precision using settings in Makefile.mpi :pre
 
-Note that this procedure starts with one of the existing
-Makefile.machine files in lib/gpu.  It allows you to alter 4 important
-settings in that Makefile, via the -h, -a, -p, -e switches,
-and save the new Makefile, if desired:
+Note that this procedure through the '-m machine' flag starts with one of
+the existing Makefile.machine files in lib/gpu. For your convenience,
+machine makefiles for "mpi" and "serial" are provided, which have the
+same settings as the corresponding machine makefiles in the main LAMMPS
+source folder. In addition you can alter 4 important settings in that
+Makefile, via the -h, -a, -p, -e switches, and also save a copy of the
+new Makefile, if desired:
 
-CUDA_HOME = where NVIDIA Cuda software is installed on your system
+CUDA_HOME = where NVIDIA CUDA software is installed on your system
 CUDA_ARCH = what GPU hardware you have (see help message for details)
 CUDA_PRECISION = precision (double, mixed, single)
 EXTRAMAKE = which Makefile.lammps.* file to copy to Makefile.lammps :ul
 
-If the library build is successful, 2 files should be created:
-lib/gpu/libgpu.a and lib/gpu/Makefile.lammps.  The latter has settings
-that enable LAMMPS to link with Cuda libraries.  If the settings in
-Makefile.lammps for your machine are not correct, the LAMMPS build
-will fail.
+If the library build is successful, at least 3 files should be created:
+lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, and lib/gpu/Makefile.lammps.
+The latter has settings that enable LAMMPS to link with CUDA libraries.
+If the settings in Makefile.lammps for your machine are not correct,
+the LAMMPS build will fail, and lib/gpu/Makefile.lammps may need to
+be edited.
 
 You can then install/un-install the package and build LAMMPS in the
 usual manner:
@@ -427,8 +450,8 @@ src/GPU/README
 lib/gpu/README
 "Section 5.3"_Section_accelerate.html#acc_3
 "Section 5.3.1"_accelerate_gpu.html
-"Section 2.7 -sf gpu"_Section_start.html#start_7
-"Section 2.7 -pk gpu"_Section_start.html#start_7
+"Section 2.6 -sf gpu"_Section_start.html#start_6
+"Section 2.6 -pk gpu"_Section_start.html#start_6
 "package gpu"_package.html
 Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (g)
 "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@@ -492,14 +515,40 @@ Minnesota).
 
 [Install or un-install:]
 
-Using this package requires the KIM library and its models
-(interatomic potentials) to be downloaded and installed on your
-system.  The library can be downloaded and built in lib/kim or
-elsewhere on your system.  Details of the download, build, and install
-process for KIM are given in the lib/kim/README file.
+Before building LAMMPS with this package, you must first download and
+build the KIM library and include the KIM models that you want to
+use. You can do this manually if you prefer; follow the instructions
+in lib/kim/README.  You can also do it in one step from the lammps/src
+dir, using a command like these, which simply invoke the
+lib/kim/Install.py script with the specified args.
 
-Once that process is complete, you can then install/un-install the
-package and build LAMMPS in the usual manner:
+make lib-kim              # print help message
+make lib-kim args="-b "   # (re-)install KIM API lib with only example models
+make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"  # ditto plus one model
+make lib-kim args="-b -a everything"     # install KIM API lib with all models
+make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002"       # add one model or model driver
+make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location
+make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
+
+Note that in LAMMPS lingo, a KIM model driver is a pair style
+(e.g. EAM or Tersoff).  A KIM model is a pair style for a particular
+element or alloy and set of parameters, e.g. EAM for Cu with a
+specific EAM potential file.  Also note that installing the KIM API
+library with all its models, may take around 30 min to build.  Of
+course you only need to do that once.
+
+See the list of KIM model drivers here:
+https://openkim.org/kim-items/model-drivers/alphabetical
+
+See the list of all KIM models here:
+https://openkim.org/kim-items/models/by-model-drivers
+
+See the list of example KIM models included by default here:
+https://openkim.org/kim-api in the "What is in the KIM API source
+package?" section
+
+You can then install/un-install the package and build LAMMPS in the
+usual manner:
 
 make yes-kim
 make machine :pre
@@ -523,13 +572,13 @@ KOKKOS package :link(KOKKOS),h4
 
 Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute
 styles adapted to compile using the Kokkos library which can convert
-them to OpenMP or Cuda code so that they run efficiently on multicore
+them to OpenMP or CUDA code so that they run efficiently on multicore
 CPUs, KNLs, or GPUs.  All the styles have a "kk" as a suffix in their
 style name.  "Section 5.3.3"_accelerate_kokkos.html gives details of
 what hardware and software is required on your system, and how to
 build and use this package.  Its styles can be invoked at run time via
 the "-sf kk" or "-suffix kk" "command-line
-switches"_Section_start.html#start_7.  Also see the "GPU"_#GPU,
+switches"_Section_start.html#start_6.  Also see the "GPU"_#GPU,
 "OPT"_#OPT, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP
 packages, which have styles optimized for CPUs, KNLs, and GPUs.
 
@@ -553,28 +602,28 @@ files for examples.
 For multicore CPUs using OpenMP:
 
 KOKKOS_DEVICES = OpenMP
-KOKKOS_ARCH = HSW           # HSW = Haswell, SNB = SandyBridge, BDW = Broadwell, etc
+KOKKOS_ARCH = HSW           # HSW = Haswell, SNB = SandyBridge, BDW = Broadwell, etc :pre
 
 For Intel KNLs using OpenMP:
 
 KOKKOS_DEVICES = OpenMP
-KOKKOS_ARCH = KNL
+KOKKOS_ARCH = KNL :pre
 
-For NVIDIA GPUs using Cuda:
+For NVIDIA GPUs using CUDA:
 
 KOKKOS_DEVICES = Cuda
 KOKKOS_ARCH = Pascal60,Power8     # P100 hosted by an IBM Power8, etc
-KOKKOS_ARCH = Kepler37,Power8     # K80 hosted by an IBM Power8, etc
+KOKKOS_ARCH = Kepler37,Power8     # K80 hosted by an IBM Power8, etc :pre
 
 For GPUs, you also need these 2 lines in your Makefile.machine before
 the CC line is defined, in this case for use with OpenMPI mpicxx.  The
 2 lines define a nvcc wrapper compiler, which will use nvcc for
-compiling Cuda files or use a C++ compiler for non-Kokkos, non-Cuda
+compiling CUDA files or use a C++ compiler for non-Kokkos, non-CUDA
 files.
 
 KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
 export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
-CC =		mpicxx
+CC =		mpicxx :pre
 
 Once you have an appropriate Makefile.machine, you can
 install/un-install the package and build LAMMPS in the usual manner.
@@ -597,9 +646,9 @@ src/KOKKOS/README
 lib/kokkos/README
 "Section 5.3"_Section_accelerate.html#acc_3
 "Section 5.3.3"_accelerate_kokkos.html
-"Section 2.7 -k on ..."_Section_start.html#start_7
-"Section 2.7 -sf kk"_Section_start.html#start_7
-"Section 2.7 -pk kokkos"_Section_start.html#start_7
+"Section 2.6 -k on ..."_Section_start.html#start_6
+"Section 2.6 -sf kk"_Section_start.html#start_6
+"Section 2.6 -pk kokkos"_Section_start.html#start_6
 "package kokkos"_package.html
 Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (k)
 "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@@ -710,6 +759,12 @@ MEAM package :link(MEAM),h4
 
 A pair style for the modified embedded atom (MEAM) potential.
 
+Please note that the MEAM package has been superseded by the
+"USER-MEAMC"_#USER-MEAMC package, which is a direct translation
+of the MEAM package to C++. USER-MEAMC contains additional
+optimizations making it run faster than MEAM on most machines,
+while providing the identical features and USER interface.
+
 [Author:] Greg Wagner (Northwestern U) while at Sandia.
 
 [Install or un-install:]
@@ -720,9 +775,10 @@ follow the instructions in lib/meam/README.  You can also do it in one
 step from the lammps/src dir, using a command like these, which simply
 invoke the lib/meam/Install.py script with the specified args:
 
-make lib-meam                      # print help message
-make lib-meam args="-m gfortran"   # build with GNU Fortran compiler
-make lib-meam args="-m ifort"      # build with Intel ifort compiler :pre
+make lib-meam                  # print help message
+make lib-meam args="-m mpi"    # build with default Fortran compiler compatible with your MPI library
+make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran)
+make lib-meam args="-m ifort"  # build with Intel Fortran compiler using Makefile.ifort :pre
 
 The build should produce two files: lib/meam/libmeam.a and
 lib/meam/Makefile.lammps.  The latter is copied from an existing
@@ -765,6 +821,9 @@ A variety of compute, fix, pair, dump styles with specialized
 capabilities that don't align with other packages.  Do a directory
 listing, "ls src/MISC", to see the list of commands.
 
+NOTE: the MISC package contains styles that require using the
+-restrict flag, when compiling with Intel compilers.
+
 [Install or un-install:]
 
 make yes-misc
@@ -878,9 +937,9 @@ University of Chicago.
 
 Before building LAMMPS with this package, you must first download and
 build the MS-CG library.  Building the MS-CG library and using it from
-LAMMPS requires a C++11 compatible compiler, and that LAPACK and GSL
-(GNU Scientific Library) libraries be installed on your machine.  See
-the lib/mscg/README and MSCG/Install files for more details.
+LAMMPS requires a C++11 compatible compiler and that the GSL
+(GNU Scientific Library) headers and libraries are installed on your
+machine.  See the lib/mscg/README and MSCG/Install files for more details.
 
 Assuming these libraries are in place, you can do the download and
 build of MS-CG manually if you prefer; follow the instructions in
@@ -888,15 +947,16 @@ lib/mscg/README.  You can also do it in one step from the lammps/src
 dir, using a command like these, which simply invoke the
 lib/mscg/Install.py script with the specified args:
 
-make lib-mscg                                # print help message
-make lib-mscg args="-g -b -l"                # download and build in default lib/mscg/MSCG-release-master
-make lib-mscg args="-h . MSCG -g -b -l"      # download and build in lib/mscg/MSCG
-make lib-mscg args="-h ~ MSCG -g -b -l"      # download and build in ~/mscg :pre
+make lib-mscg             # print help message
+make lib-mscg args="-b -m serial"   # download and build in lib/mscg/MSCG-release-master
+                                    # with the settings compatible with "make serial"
+make lib-mscg args="-b -m mpi"      # download and build in lib/mscg/MSCG-release-master
+                                    # with the settings compatible with "make mpi"
+make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release :pre
 
-Note that the final -l switch is to create 2 symbolic (soft) links,
-"includelink" and "liblink", in lib/mscg to point to the MS-CG src
-dir.  When LAMMPS builds it will use these links.  You should not need
-to edit the lib/mscg/Makefile.lammps file.
+Note that 2 symbolic (soft) links, "includelink" and "liblink", will be created in lib/mscg
+to point to the MS-CG src/installation dir.  When LAMMPS is built in src it will use these links.
+You should not need to edit the lib/mscg/Makefile.lammps file.
 
 You can then install/un-install the package and build LAMMPS in the
 usual manner:
@@ -926,7 +986,7 @@ CHARMM, and Morse potentials.  The styles have an "opt" suffix in
 their style name.  "Section 5.3.5"_accelerate_opt.html gives details
 of how to build and use this package.  Its styles can be invoked at
 run time via the "-sf opt" or "-suffix opt" "command-line
-switches"_Section_start.html#start_7.  See also the "KOKKOS"_#KOKKOS,
+switches"_Section_start.html#start_6.  See also the "KOKKOS"_#KOKKOS,
 "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which
 have styles optimized for CPU performance.
 
@@ -942,18 +1002,18 @@ make no-opt
 make machine :pre
 
 NOTE: The compile flag "-restrict" must be used to build LAMMPS with
-the OPT package.  It should be added to the CCFLAGS line of your
-Makefile.machine.  See Makefile.opt in src/MAKE/OPTIONS for an
-example.
+the OPT package when using Intel compilers.  It should be added to
+the CCFLAGS line of your Makefile.machine.  See Makefile.opt in
+src/MAKE/OPTIONS for an example.
 
-CCFLAGS: add -restrict :ul
+CCFLAGS: add -restrict for Intel compilers :ul
 
 [Supporting info:]
 
 src/OPT: filenames -> commands
 "Section 5.3"_Section_accelerate.html#acc_3
 "Section 5.3.5"_accelerate_opt.html
-"Section 2.7 -sf opt"_Section_start.html#start_7
+"Section 2.6 -sf opt"_Section_start.html#start_6
 Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (t)
 "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
 
@@ -1015,9 +1075,10 @@ follow the instructions in lib/poems/README.  You can also do it in
 one step from the lammps/src dir, using a command like these, which
 simply invoke the lib/poems/Install.py script with the specified args:
 
-make lib-poems                      # print help message
-make lib-poems args="-m g++"        # build with GNU g++ compiler
-make lib-poems args="-m icc"        # build with Intel icc compiler :pre
+make lib-poems                   # print help message
+make lib-poems args="-m serial"  # build with GNU g++ compiler (settings as with "make serial")
+make lib-poems args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
+make lib-poems args="-m icc"     # build with Intel icc compiler :pre
 
 The build should produce two files: lib/poems/libpoems.a and
 lib/poems/Makefile.lammps.  The latter is copied from an existing
@@ -1127,9 +1188,10 @@ follow the instructions in lib/reax/README.  You can also do it in one
 step from the lammps/src dir, using a command like these, which simply
 invoke the lib/reax/Install.py script with the specified args:
 
-make lib-reax                      # print help message
-make lib-reax args="-m gfortran"   # build with GNU Fortran compiler
-make lib-reax args="-m ifort"      # build with Intel ifort compiler :pre
+make lib-reax                    # print help message
+make lib-reax args="-m serial"   # build with GNU Fortran compiler (settings as with "make serial")
+make lib-reax args="-m mpi"      # build with default MPI Fortran compiler (settings as with "make mpi")
+make lib-reax args="-m ifort"    # build with Intel ifort compiler :pre
 
 The build should produce two files: lib/reax/libreax.a and
 lib/reax/Makefile.lammps.  The latter is copied from an existing
@@ -1346,15 +1408,15 @@ one step from the lammps/src dir, using a command like these, which
 simply invoke the lib/voronoi/Install.py script with the specified
 args:
 
-make lib-voronoi                                # print help message
-make lib-voronoi args="-g -b -l"                # download and build in default lib/voronoi/voro++-0.4.6
-make lib-voronoi args="-h . voro++ -g -b -l"    # download and build in lib/voronoi/voro++
-make lib-voronoi args="-h ~ voro++ -g -b -l"    # download and build in ~/voro++ :pre
+make lib-voronoi                          # print help message
+make lib-voronoi args="-b"                # download and build the default version in lib/voronoi/voro++-<version>
+make lib-voronoi args="-p $HOME/voro++"   # use existing Voro++ installation in $HOME/voro++
+make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6 :pre
 
-Note that the final -l switch is to create 2 symbolic (soft) links,
-"includelink" and "liblink", in lib/voronoi to point to the Voro++ src
-dir.  When LAMMPS builds it will use these links.  You should not need
-to edit the lib/voronoi/Makefile.lammps file.
+Note that 2 symbolic (soft) links, "includelink" and "liblink", are
+created in lib/voronoi to point to the Voro++ src dir.  When LAMMPS
+builds in src it will use these links.  You should not need to edit
+the lib/voronoi/Makefile.lammps file.
 
 You can then install/un-install the package and build LAMMPS in the
 usual manner:
@@ -1396,7 +1458,8 @@ from the lammps/src dir, using a command like these, which simply
 invoke the lib/atc/Install.py script with the specified args:
 
 make lib-atc                      # print help message
-make lib-atc args="-m g++"        # build with GNU g++ compiler
+make lib-atc args="-m serial"     # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+make lib-atc args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
 make lib-atc args="-m icc"        # build with Intel icc compiler :pre
 
 The build should produce two files: lib/atc/libatc.a and
@@ -1413,8 +1476,10 @@ can either exist on your system, or you can use the files provided in
 lib/linalg.  In the latter case you also need to build the library
 in lib/linalg with a command like these:
 
-make lib-linalg                      # print help message
-make lib-atc args="-m gfortran"      # build with GNU Fortran compiler
+make lib-linalg                     # print help message
+make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
+make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
+make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler :pre
 
 You can then install/un-install the package and build LAMMPS in the
 usual manner:
@@ -1454,9 +1519,10 @@ follow the instructions in lib/awpmd/README.  You can also do it in
 one step from the lammps/src dir, using a command like these, which
 simply invoke the lib/awpmd/Install.py script with the specified args:
 
-make lib-awpmd                      # print help message
-make lib-awpmd args="-m g++"        # build with GNU g++ compiler
-make lib-awpmd args="-m icc"        # build with Intel icc compiler :pre
+make lib-awpmd                   # print help message
+make lib-awpmd args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+make lib-awpmd args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
+make lib-awpmd args="-m icc"     # build with Intel icc compiler :pre
 
 The build should produce two files: lib/awpmd/libawpmd.a and
 lib/awpmd/Makefile.lammps.  The latter is copied from an existing
@@ -1472,8 +1538,10 @@ these can either exist on your system, or you can use the files
 provided in lib/linalg.  In the latter case you also need to build the
 library in lib/linalg with a command like these:
 
-make lib-linalg                      # print help message
-make lib-atc args="-m gfortran"      # build with GNU Fortran compiler
+make lib-linalg                     # print help message
+make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
+make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
+make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler :pre
 
 You can then install/un-install the package and build LAMMPS in the
 usual manner:
@@ -1566,9 +1634,11 @@ Restraints.  A "fix colvars"_fix_colvars.html command is implemented
 which wraps a COLVARS library, which implements these methods.
 simulations.
 
-[Authors:] Axel Kohlmeyer (Temple U).  The COLVARS library was written
-by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and
-Jerome Henin (LISM, CNRS, Marseille, France).
+[Authors:] The COLVARS library is written and maintained by
+Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA)
+and Jerome Henin (LISM, CNRS, Marseille, France), originally for
+the NAMD MD code, but with portability in mind.  Axel Kohlmeyer
+(Temple U) provided the interface to LAMMPS.
 
 [Install or un-install:]
 
@@ -1580,7 +1650,9 @@ which simply invoke the lib/colvars/Install.py script with the
 specified args:
 
 make lib-colvars                      # print help message
-make lib-colvars args="-m g++"        # build with GNU g++ compiler :pre
+make lib-colvars args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
+make lib-colvars args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
+make lib-colvars args="-m g++-debug"  # build with GNU g++ compiler and colvars debugging enabled :pre
 
 The build should produce two files: lib/colvars/libcolvars.a and
 lib/colvars/Makefile.lammps.  The latter is copied from an existing
@@ -1863,12 +1935,17 @@ All of them have an "intel" in their style name.  "Section
 5.3.2"_accelerate_intel.html gives details of what hardware and
 compilers are required on your system, and how to build and use this
 package.  Its styles can be invoked at run time via the "-sf intel" or
-"-suffix intel" "command-line switches"_Section_start.html#start_7.
+"-suffix intel" "command-line switches"_Section_start.html#start_6.
 Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-OMP"_#USER-OMP
 packages, which have styles optimized for CPUs and KNLs.
 
 You need to have an Intel compiler, version 14 or higher to take full
-advantage of this package.
+advantage of this package. While compilation with GNU compilers is
+supported, performance will be suboptimal.
+
+NOTE: the USER-INTEL package contains styles that require using the
+-restrict flag, when compiling with Intel compilers.
+
 
 [Author:] Mike Brown (Intel).
 
@@ -1885,17 +1962,17 @@ For CPUs:
 
 OPTFLAGS =      -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
 CCFLAGS =	-g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
-                -fno-alias -ansi-alias -restrict $(OPTFLAGS)
+-fno-alias -ansi-alias -restrict $(OPTFLAGS)
 LINKFLAGS =	-g -qopenmp $(OPTFLAGS)
-LIB =           -ltbbmalloc -ltbbmalloc_proxy
+LIB =           -ltbbmalloc -ltbbmalloc_proxy :pre
 
 For KNLs:
 
 OPTFLAGS =      -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
 CCFLAGS =	-g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
-                -fno-alias -ansi-alias -restrict $(OPTFLAGS)
+-fno-alias -ansi-alias -restrict $(OPTFLAGS)
 LINKFLAGS =	-g -qopenmp $(OPTFLAGS)
-LIB =           -ltbbmalloc
+LIB =           -ltbbmalloc :pre
 
 Once you have an appropriate Makefile.machine, you can
 install/un-install the package and build LAMMPS in the usual manner.
@@ -1919,8 +1996,8 @@ src/USER-INTEL: filenames -> commands
 src/USER-INTEL/README
 "Section 5.3"_Section_accelerate.html#acc_3
 "Section 5.3.2"_accelerate_gpu.html
-"Section 2.7 -sf intel"_Section_start.html#start_7
-"Section 2.7 -pk intel"_Section_start.html#start_7
+"Section 2.6 -sf intel"_Section_start.html#start_6
+"Section 2.6 -pk intel"_Section_start.html#start_6
 "package intel"_package.html
 Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (i)
 src/USER-INTEL/TEST
@@ -2193,18 +2270,22 @@ via OpenMP directives.  All of them have an "omp" in their style name.
 "Section 5.3.4"_accelerate_omp.html gives details of what hardware and
 compilers are required on your system, and how to build and use this
 package.  Its styles can be invoked at run time via the "-sf omp" or
-"-suffix omp" "command-line switches"_Section_start.html#start_7.
+"-suffix omp" "command-line switches"_Section_start.html#start_6.
 Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and
 "USER-INTEL"_#USER-INTEL packages, which have styles optimized for
 CPUs.
 
 [Author:] Axel Kohlmeyer (Temple U).
 
-NOTE: The compile flags "-restrict" and "-fopenmp" must be used to
-build LAMMPS with the USER-OMP package, as well as the link flag
-"-fopenmp".  They should be added to the CCFLAGS and LINKFLAGS lines
-of your Makefile.machine.  See src/MAKE/OPTIONS/Makefile.omp for an
-example.
+NOTE: To enable multi-threading support the compile flag "-fopenmp"
+and the link flag "-fopenmp" (for GNU compilers, you have to look up
+the equivalent flags for other compilers) must be used to build LAMMPS.
+When using Intel compilers, also the "-restrict" flag is required.
+The USER-OMP package can be compiled without enabling OpenMP; then
+all code will be compiled as serial and the only improvement over the
+regular styles are some data access optimization. These flags should
+be added to the CCFLAGS and LINKFLAGS lines of your Makefile.machine.
+See src/MAKE/OPTIONS/Makefile.omp for an example.
 
 Once you have an appropriate Makefile.machine, you can
 install/un-install the package and build LAMMPS in the usual manner:
@@ -2217,7 +2298,7 @@ make machine :pre
 make no-user-omp
 make machine :pre
 
-CCFLAGS: add -fopenmp and -restrict
+CCFLAGS: add -fopenmp (and -restrict when using Intel compilers)
 LINKFLAGS: add -fopenmp :ul
 
 [Supporting info:]
@@ -2226,8 +2307,8 @@ src/USER-OMP: filenames -> commands
 src/USER-OMP/README
 "Section 5.3"_Section_accelerate.html#acc_3
 "Section 5.3.4"_accelerate_omp.html
-"Section 2.7 -sf omp"_Section_start.html#start_7
-"Section 2.7 -pk omp"_Section_start.html#start_7
+"Section 2.6 -sf omp"_Section_start.html#start_6
+"Section 2.6 -pk omp"_Section_start.html#start_6
 "package omp"_package.html
 Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (o)
 "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
@@ -2286,12 +2367,14 @@ without changes to LAMMPS itself.
 
 Before building LAMMPS with this package, you must first build the
 QMMM library in lib/qmmm.  You can do this manually if you prefer;
-follow the first two steps explained in lib/colvars/README.  You can
+follow the first two steps explained in lib/qmmm/README.  You can
 also do it in one step from the lammps/src dir, using a command like
-these, which simply invoke the lib/colvars/Install.py script with the
+these, which simply invoke the lib/qmmm/Install.py script with the
 specified args:
 
 make lib-qmmm                      # print help message
+make lib-qmmm args="-m serial"     # build with GNU Fortran compiler (settings as in "make serial")
+make lib-qmmm args="-m mpi"        # build with default MPI compiler (settings as in "make mpi")
 make lib-qmmm args="-m gfortran"   # build with GNU Fortran compiler :pre
 
 The build should produce two files: lib/qmmm/libqmmm.a and
@@ -2468,15 +2551,13 @@ follow the instructions in lib/smd/README.  You can also do it in one
 step from the lammps/src dir, using a command like these, which simply
 invoke the lib/smd/Install.py script with the specified args:
 
-make lib-smd                            # print help message
-make lib-smd args="-g -l"               # download in default lib/smd/eigen-eigen-*
-make lib-smd args="-h . eigen -g -l"    # download in lib/smd/eigen
-make lib-smd args="-h ~ eigen -g -l"    # download and build in ~/eigen :pre
+make lib-smd                         # print help message
+make lib-smd args="-b"               # download and build in default lib/smd/eigen-eigen-...
+make lib-smd args="-p /usr/include/eigen3"    # use existing Eigen installation in /usr/include/eigen3 :pre
 
-Note that the final -l switch is to create a symbolic (soft) link
-named "includelink" in lib/smd to point to the Eigen dir.  When LAMMPS
-builds it will use this link.  You should not need to edit the
-lib/smd/Makefile.lammps file.
+Note that a symbolic (soft) link named "includelink" is created in
+lib/smd to point to the Eigen dir.  When LAMMPS builds it will use
+this link.  You should not need to edit the lib/smd/Makefile.lammps file.
 
 You can then install/un-install the package and build LAMMPS in the
 usual manner:

doc/src/Section_python.txt

@@ -198,7 +198,7 @@ file and the shared library.
 11.3 Building LAMMPS as a shared library :link(py_3),h4
 
 Instructions on how to build LAMMPS as a shared library are given in
-"Section 2.5"_Section_start.html#start_5.  A shared library is one
+"Section 2.4"_Section_start.html#start_4.  A shared library is one
 that is dynamically loadable, which is what Python requires to wrap
 LAMMPS.  On Linux this is a library file that ends in ".so", not ".a".
 
@@ -217,7 +217,7 @@ NOTE: If you are building LAMMPS with an MPI or FFT library or other
 auxiliary libraries (used by various packages), then all of these
 extra libraries must also be shared libraries.  If the LAMMPS
 shared-library build fails with an error complaining about this, see
-"Section 2.5"_Section_start.html#start_5 for more details.
+"Section 2.4"_Section_start.html#start_4 for more details.
 
 :line
 
@@ -439,7 +439,7 @@ first importing from the lammps.py file:
 >>> CDLL("liblammps.so") :pre
 
 If an error occurs, carefully go thru the steps in "Section
-2.5"_Section_start.html#start_5 and above about building a shared
+2.4"_Section_start.html#start_4 and above about building a shared
 library and about insuring Python can find the necessary two files
 it needs.
 

doc/src/Section_start.txt

@@ -14,11 +14,11 @@ experienced users.
 2.1 "What's in the LAMMPS distribution"_#start_1
 2.2 "Making LAMMPS"_#start_2
 2.3 "Making LAMMPS with optional packages"_#start_3
-2.5 "Building LAMMPS as a library"_#start_4
-2.6 "Running LAMMPS"_#start_5
-2.7 "Command-line options"_#start_6
-2.8 "Screen output"_#start_7
-2.9 "Tips for users of previous versions"_#start_8 :all(b)
+2.4 "Building LAMMPS as a library"_#start_4
+2.5 "Running LAMMPS"_#start_5
+2.6 "Command-line options"_#start_6
+2.7 "Screen output"_#start_7
+2.8 "Tips for users of previous versions"_#start_8 :all(b)
 
 :line
 
@@ -434,20 +434,39 @@ files.  Note that on some large parallel machines which use "modules"
 for their compile/link environements, you may simply need to include
 the correct module in your build environment.  Or the parallel machine
 may have a vendor-provided FFT library which the compiler has no
-trouble finding.
+trouble finding.  See the src/MAKE/OPTIONS/Makefile.fftw file for an
+example of how to specify these variables to use the FFTW3 library.
 
-FFTW is a fast, portable library that should also work on any
-platform.  You can download it from
+FFTW is fast, portable library that should also work on any platform
+and typically be faster than KISS FFT.  You can download it from
 "www.fftw.org"_http://www.fftw.org.  Both the legacy version 2.1.X and
 the newer 3.X versions are supported as -DFFT_FFTW2 or -DFFT_FFTW3.
-Building FFTW for your box should be as simple as ./configure; make.
-Note that on some platforms FFTW2 has been pre-installed, and uses
-renamed files indicating the precision it was compiled with,
-e.g. sfftw.h, or dfftw.h instead of fftw.h.  In this case, you can
-specify an additional define variable for FFT_INC called -DFFTW_SIZE,
-which will select the correct include file.  In this case, for FFT_LIB
-you must also manually specify the correct library, namely -lsfftw or
--ldfftw.
+Building FFTW for your box should be as simple as ./configure; make;
+make install.  The install command typically requires root privileges
+(e.g. invoke it via sudo), unless you specify a local directory with
+the "--prefix" option of configure.  Type "./configure --help" to see
+various options.
+
+If you wish to have FFTW support for single-precision FFTs (see below
+about -DFFT_SINGLE) in addition to the default double-precision FFTs,
+you will need to build FFTW a second time for single-precision.  For
+FFTW3, do this via:
+
+make clean
+./configure --enable-single; make; make install :pre
+
+which should produce the additional library libfftw3f.a.
+
+For FFTW2, do this:
+
+make clean
+./configure --enable-float --enable-type-prefix; make; make install :pre
+
+which should produce the additional library libsfftw.a and additional
+include file sfttw.a.  Note that on some platforms FFTW2 has been
+pre-installed for both single- and double-precision, and may already
+have these files as well as libdfftw.a and dfftw.h for double
+precision.
 
 The FFT_INC variable also allows for a -DFFT_SINGLE setting that will
 use single-precision FFTs with PPPM, which can speed-up long-range
@@ -459,6 +478,16 @@ accuracy for reduced memory use and parallel communication costs for
 transposing 3d FFT data.  Note that single precision FFTs have only
 been tested with the FFTW3, FFTW2, MKL, and KISS FFT options.
 
+When using -DFFT_SINGLE with FFTW3 or FFTW2, you need to build FFTW
+with support for single-precision, as explained above.  For FFTW3 you
+also need to include -lfftw3f with the FFT_LIB setting, in addition to
+-lfftw3.  For FFTW2, you also need to specify -DFFT_SIZE with the
+FFT_INC setting and -lsfftw with the FFT_LIB setting (in place of
+-lfftw).  Similarly, if FFTW2 has been preinstalled with an explicit
+double-precision library (libdfftw.a and not the default libfftw.a),
+then you can specify -DFFT_SIZE (and not -DFFT_SINGLE), and specify
+-ldfftw to use double-precision FFTs.
+
 Step 7 :h6
 
 The 3 JPG variables allow you to specify a JPEG and/or PNG library
@@ -558,8 +587,7 @@ 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.
 
-Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
--DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
+Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
 
 As explained above, any of these 3 settings can be specified on the
 LMP_INC line in your low-level src/MAKE/Makefile.foo.
@@ -630,7 +658,16 @@ utilities.
 For Cygwin and the MinGW cross-compilers, suitable makefiles are
 provided in src/MAKE/MACHINES. When using other compilers, like
 Visual C++ or Intel compilers for Windows, you may have to implement
-your own build system. Since none of the current LAMMPS core developers
+your own build system. Due to differences between the Windows OS
+and Windows system libraries to Unix-like environments like Linux
+or MacOS, when compiling for Windows a few adjustments may be needed:
+
+Do not set the -DLAMMPS_MEMALIGN define (see LMP_INC makefile variable)
+Add -lwsock32 -lpsapi to the linker flags (see LIB makefile variable)
+Try adding -static-libgcc or -static or both to the linker flags when your
+LAMMPS executable complains about missing .dll files  :ul
+
+Since none of the current LAMMPS core developers
 has significant experience building executables on Windows, we are
 happy to distribute contributed instructions and modifications, but
 we cannot provide support for those.
@@ -685,7 +722,7 @@ type
 lmp_machine -h :pre
 
 to run your executable with the optional "-h command-line
-switch"_#start_7 for "help", which will list the styles and commands
+switch"_#start_6 for "help", which will list the styles and commands
 known to your executable, and immediately exit.
 
 :line
@@ -880,7 +917,7 @@ src/MAKE/OPTIONS, which include the settings.  Note that the
 USER-INTEL and KOKKOS packages can use settings that build LAMMPS for
 different hardware.  The USER-INTEL package can be compiled for Intel
 CPUs and KNLs; the KOKKOS package builds for CPUs (OpenMP), GPUs
-(Cuda), and Intel KNLs.
+(CUDA), and Intel KNLs.
 
 Makefile.intel_cpu
 Makefile.intel_phi

doc/src/accelerate_gpu.txt

@@ -54,7 +54,7 @@ specify the # of GPUs per node
 use GPU styles in your input script :ul
 
 The latter two steps can be done using the "-pk gpu" and "-sf gpu"
-"command-line switches"_Section_start.html#start_7 respectively.  Or
+"command-line switches"_Section_start.html#start_6 respectively.  Or
 the effect of the "-pk" or "-sf" switches can be duplicated by adding
 the "package gpu"_package.html or "suffix gpu"_suffix.html commands
 respectively to your input script.
@@ -62,7 +62,7 @@ respectively to your input script.
 [Required hardware/software:]
 
 To use this package, you currently need to have an NVIDIA GPU and
-install the NVIDIA Cuda software on your system:
+install the NVIDIA CUDA software on your system:
 
 Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/0/information
 Go to http://www.nvidia.com/object/cuda_get.html
@@ -74,13 +74,8 @@ Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) t
 This requires two steps (a,b): build the GPU library, then build
 LAMMPS with the GPU package.
 
-You can do both these steps in one line, using the src/Make.py script,
-described in "Section 2.4"_Section_start.html#start_4 of the manual.
-Type "Make.py -h" for help.  If run from the src directory, this
-command will create src/lmp_gpu using src/MAKE/Makefile.mpi as the
-starting Makefile.machine:
-
-Make.py -p gpu -gpu mode=single arch=31 -o gpu -a lib-gpu file mpi :pre
+You can do both these steps in one line as described in
+"Section 4"_Section_packages.html of the manual.
 
 Or you can follow these two (a,b) steps:
 
@@ -90,7 +85,7 @@ The GPU library is in lammps/lib/gpu.  Select a Makefile.machine (in
 lib/gpu) appropriate for your system.  You should pay special
 attention to 3 settings in this makefile.
 
-CUDA_HOME = needs to be where NVIDIA Cuda software is installed on your system
+CUDA_HOME = needs to be where NVIDIA CUDA software is installed on your system
 CUDA_ARCH = needs to be appropriate to your GPUs
 CUDA_PREC = precision (double, mixed, single) you desire :ul
 
@@ -151,9 +146,9 @@ automatically if you create more MPI tasks/node than there are
 GPUs/mode.  E.g. with 8 MPI tasks/node and 2 GPUs, each GPU will be
 shared by 4 MPI tasks.
 
-Use the "-sf gpu" "command-line switch"_Section_start.html#start_7,
+Use the "-sf gpu" "command-line switch"_Section_start.html#start_6,
 which will automatically append "gpu" to styles that support it.  Use
-the "-pk gpu Ng" "command-line switch"_Section_start.html#start_7 to
+the "-pk gpu Ng" "command-line switch"_Section_start.html#start_6 to
 set Ng = # of GPUs/node to use.
 
 lmp_machine -sf gpu -pk gpu 1 -in in.script                         # 1 MPI task uses 1 GPU
@@ -188,7 +183,7 @@ pair_style lj/cut/gpu 2.5 :pre
 
 You must also use the "package gpu"_package.html command to enable the
 GPU package, unless the "-sf gpu" or "-pk gpu" "command-line
-switches"_Section_start.html#start_7 were used.  It specifies the
+switches"_Section_start.html#start_6 were used.  It specifies the
 number of GPUs/node to use, as well as other options.
 
 [Speed-ups to expect:]

doc/src/accelerate_intel.txt

@@ -225,11 +225,9 @@ source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
 # or psxevars.csh for C-shell
 make intel_cpu_intelmpi :pre
 
-Alternatively, the build can be accomplished with the src/Make.py
-script, described in "Section 2.4"_Section_start.html#start_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 :pre
+Alternatively this can be done as a single command with
+suitable make command invocations. This is discussed in "Section
+4"_Section_packages.html of the manual.
 
 Note that if you build with support for a Phi coprocessor, the same
 binary can be used on nodes with or without coprocessors installed.
@@ -244,8 +242,7 @@ highly recommended for CCFLAGS and LINKFLAGS. LIB should include
 is required for CCFLAGS and "-qoffload" is required for LINKFLAGS.
 Other recommended CCFLAG options for best performance are
 "-O2 -fno-alias -ansi-alias -qoverride-limits fp-model fast=2
--no-prec-div". The Make.py command will add all of these
-automatically.
+-no-prec-div".
 
 NOTE: The vectorization and math capabilities can differ depending on
 the CPU. For Intel compilers, the "-x" flag specifies the type of
@@ -301,7 +298,7 @@ Hyper-Threading technology disabled.
 
 To enable USER-INTEL optimizations for all available styles used in
 the input script, the "-sf intel"
-"command-line switch"_Section_start.html#start_7 can be used without
+"command-line switch"_Section_start.html#start_6 can be used without
 any requirement for editing the input script. This switch will
 automatically append "intel" to styles that support it. It also
 invokes a default command: "package intel 1"_package.html. This
@@ -314,7 +311,7 @@ support, that 1 coprocessor per node will be used with automatic
 balancing of work between the CPU and the coprocessor.
 
 You can specify different options for the USER-INTEL package by using
-the "-pk intel Nphi" "command-line switch"_Section_start.html#start_7
+the "-pk intel Nphi" "command-line switch"_Section_start.html#start_6
 with keyword/value pairs as specified in the documentation. Here,
 Nphi = # of Xeon Phi coprocessors/node (ignored without offload
 support). Common options to the USER-INTEL package include {omp} to
@@ -387,7 +384,7 @@ can performed automatically by using "-sf hybrid intel opt" or
 and "omp" suffixes can be appended manually in the input script. For
 the latter, the "package omp"_package.html command must be in the
 input script or the "-pk omp Nt" "command-line
-switch"_Section_start.html#start_7 must be used where Nt is the
+switch"_Section_start.html#start_6 must be used where Nt is the
 number of OpenMP threads. The number of OpenMP threads should not be
 set differently for the different packages. Note that the "suffix
 hybrid intel omp"_suffix.html command can also be used within the
@@ -486,7 +483,7 @@ sorting"_atom_modify.html is changed to 1 so that the per-atom data is
 effectively sorted at every rebuild of the neighbor lists. All the
 available coprocessor threads on each Phi will be divided among MPI
 tasks, unless the {tptask} option of the "-pk intel" "command-line
-switch"_Section_start.html#start_7 is used to limit the coprocessor
+switch"_Section_start.html#start_6 is used to limit the coprocessor
 threads per MPI task.
 
 [Restrictions:]

doc/src/accelerate_kokkos.txt

@@ -60,8 +60,7 @@ 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 :pre
+make kokkos_omp                                # or Makefile.kokkos_omp already has variable set :pre
 
 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
@@ -82,8 +81,7 @@ 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 :pre
+make machine :pre
 
 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 :pre
@@ -98,8 +96,7 @@ 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 :pre
+make machine :pre
 
 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
@@ -116,7 +113,7 @@ To build with Kokkos support for CPUs, your compiler must support the
 OpenMP interface.  You should have one or more multi-core CPUs so that
 multiple threads can be launched by each MPI task running on a CPU.
 
-To build with Kokkos support for NVIDIA GPUs, NVIDIA Cuda software
+To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA software
 version 7.5 or later must be installed on your system.  See the
 discussion for the "GPU"_accelerate_gpu.html package for details of
 how to check and do this.
@@ -135,16 +132,16 @@ mode like the USER-INTEL package supports.
 You must choose at build time whether to build for CPUs (OpenMP),
 GPUs, or Phi.
 
-You can do any of these in one line, using the src/Make.py script,
-described in "Section 2.4"_Section_start.html#start_4 of the manual.
-Type "Make.py -h" for help.  If run from the src directory, these
+You can do any of these in one line, using the suitable make command
+line flags as described in "Section 4"_Section_packages.html of the
+manual. If run from the src directory, these
 commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda, and
 lmp_kokkos_phi.  Note that the OMP and PHI options use
 src/MAKE/Makefile.mpi as the starting Makefile.machine.  The CUDA
 option uses src/MAKE/OPTIONS/Makefile.kokkos_cuda.
 
 The latter two steps can be done using the "-k on", "-pk kokkos" and
-"-sf kk" "command-line switches"_Section_start.html#start_7
+"-sf kk" "command-line switches"_Section_start.html#start_6
 respectively.  Or the effect of the "-pk" or "-sf" switches can be
 duplicated by adding the "package kokkos"_package.html or "suffix
 kk"_suffix.html commands respectively to your input script.
@@ -280,10 +277,10 @@ specify how many Phi coprocessors there are per node; each
 coprocessors is simply treated as running some number of MPI tasks.
 
 You must use the "-k on" "command-line
-switch"_Section_start.html#start_7 to enable the KOKKOS package.  It
+switch"_Section_start.html#start_6 to enable the KOKKOS package.  It
 takes additional arguments for hardware settings appropriate to your
 system.  Those arguments are "documented
-here"_Section_start.html#start_7.  The two most commonly used
+here"_Section_start.html#start_6.  The two most commonly used
 options are:
 
 -k on t Nt g Ng :pre
@@ -304,12 +301,12 @@ The "-k on" switch also issues a "package kokkos" command (with no
 additional arguments) which sets various KOKKOS options to default
 values, as discussed on the "package"_package.html command doc page.
 
-Use the "-sf kk" "command-line switch"_Section_start.html#start_7,
+Use the "-sf kk" "command-line switch"_Section_start.html#start_6,
 which will automatically append "kk" to styles that support it.  Use
-the "-pk kokkos" "command-line switch"_Section_start.html#start_7 if
+the "-pk kokkos" "command-line switch"_Section_start.html#start_6 if
 you wish to change any of the default "package kokkos"_package.html
 optionns set by the "-k on" "command-line
-switch"_Section_start.html#start_7.
+switch"_Section_start.html#start_6.
 
 
 
@@ -323,7 +320,7 @@ However, when running in MPI-only mode with 1 thread per MPI task, it
 will typically be faster to use "half" neighbor lists and set the
 Newton flag to "on", just as is the case for non-accelerated pair
 styles.  You can do this with the "-pk" "command-line
-switch"_Section_start.html#start_7.
+switch"_Section_start.html#start_6.
 
 [Or run with the KOKKOS package by editing an input script:]
 
@@ -332,7 +329,7 @@ appropriate thread and GPU values for host=OMP or host=MIC or
 device=CUDA are the same.
 
 You must still use the "-k on" "command-line
-switch"_Section_start.html#start_7 to enable the KOKKOS package, and
+switch"_Section_start.html#start_6 to enable the KOKKOS package, and
 specify its additional arguments for hardware options appropriate to
 your system, as documented above.
 
@@ -343,7 +340,7 @@ pair_style lj/cut/kk 2.5 :pre
 
 You only need to use the "package kokkos"_package.html command if you
 wish to change any of its option defaults, as set by the "-k on"
-"command-line switch"_Section_start.html#start_7.
+"command-line switch"_Section_start.html#start_6.
 
 [Speed-ups to expect:]
 
@@ -389,7 +386,7 @@ If N is the number of physical cores/node, then the number of MPI
 tasks/node * number of threads/task should not exceed N, and should
 typically equal N.  Note that the default threads/task is 1, as set by
 the "t" keyword of the "-k" "command-line
-switch"_Section_start.html#start_7.  If you do not change this, no
+switch"_Section_start.html#start_6.  If you do not change this, no
 additional parallelism (beyond MPI) will be invoked on the host
 CPU(s).
 
@@ -429,7 +426,7 @@ details).
 The -np setting of the mpirun command should set the number of MPI
 tasks/node to be equal to the # of physical GPUs on the node.
 
-Use the "-k" "command-line switch"_Section_commands.html#start_7 to
+Use the "-k" "command-line switch"_Section_commands.html#start_6 to
 specify the number of GPUs per node, and the number of threads per MPI
 task.  As above for multi-core CPUs (and no GPU), if N is the number
 of physical cores/node, then the number of MPI tasks/node * number of

doc/src/accelerate_omp.txt

@@ -23,8 +23,7 @@ one or more 16-core nodes.  More details follow.
 use -fopenmp with CCFLAGS and LINKFLAGS in Makefile.machine
 make yes-user-omp
 make mpi                                   # build with USER-OMP package, if settings added to Makefile.mpi
-make omp                                   # or Makefile.omp already has settings
-Make.py -v -p omp -o mpi -a file mpi       # or one-line build via Make.py :pre
+make omp                                   # or Makefile.omp already has settings :pre
 
 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
@@ -40,14 +39,11 @@ each MPI task running on a CPU.
 
 The lines above illustrate how to include/build with the USER-OMP
 package in two steps, using the "make" command.  Or how to do it with
-one command via the src/Make.py script, described in "Section
-2.4"_Section_start.html#start_4 of the manual.  Type "Make.py -h" for
-help.
+one command as described in "Section 4"_Section_packages.html of the manual.
 
 Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
 include "-fopenmp".  Likewise, if you use an Intel compiler, the
-CCFLAGS setting must include "-restrict".  The Make.py command will
-add these automatically.
+CCFLAGS setting must include "-restrict".
 
 [Run with the USER-OMP package from the command line:]
 
@@ -62,14 +58,14 @@ threads/task should not exceed the physical number of cores (on a
 node), otherwise performance will suffer.
 
 As in the lines above, use the "-sf omp" "command-line
-switch"_Section_start.html#start_7, which will automatically append
+switch"_Section_start.html#start_6, which will automatically append
 "omp" to styles that support it.  The "-sf omp" switch also issues a
 default "package omp 0"_package.html command, which will set the
 number of threads per MPI task via the OMP_NUM_THREADS environment
 variable.
 
 You can also use the "-pk omp Nt" "command-line
-switch"_Section_start.html#start_7, to explicitly set Nt = # of OpenMP
+switch"_Section_start.html#start_6, to explicitly set Nt = # of OpenMP
 threads per MPI task to use, as well as additional options.  Its
 syntax is the same as the "package omp"_package.html command whose doc
 page gives details, including the default values used if it is not

doc/src/accelerate_opt.txt

@@ -21,8 +21,7 @@ Here is a quick overview of how to use the OPT package.  More details
 follow.
 
 make yes-opt
-make mpi                               # build with the OPT package
-Make.py -v -p opt -o mpi -a file mpi   # or one-line build via Make.py :pre
+make mpi                               # build with the OPT package :pre
 
 lmp_mpi -sf opt -in in.script                # run in serial
 mpirun -np 4 lmp_mpi -sf opt -in in.script   # run in parallel :pre
@@ -35,18 +34,15 @@ None.
 
 The lines above illustrate how to build LAMMPS with the OPT package in
 two steps, using the "make" command.  Or how to do it with one command
-via the src/Make.py script, described in "Section
-2.4"_Section_start.html#start_4 of the manual.  Type "Make.py -h" for
-help.
+as described in "Section 4"_Section_packages.html of the manual.
 
 Note that if you use an Intel compiler to build with the OPT package,
 the CCFLAGS setting in your Makefile.machine must include "-restrict".
-The Make.py command will add this automatically.
 
 [Run with the OPT package from the command line:]
 
 As in the lines above, use the "-sf opt" "command-line
-switch"_Section_start.html#start_7, which will automatically append
+switch"_Section_start.html#start_6, which will automatically append
 "opt" to styles that support it.
 
 [Or run with the OPT package by editing an input script:]

doc/src/angle_charmm.txt

@@ -63,7 +63,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_class2.txt

@@ -94,7 +94,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_cosine.txt

@@ -50,7 +50,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_cosine_delta.txt

@@ -55,7 +55,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_cosine_periodic.txt

@@ -63,7 +63,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_cosine_shift.txt

@@ -53,7 +53,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_cosine_shift_exp.txt

@@ -65,7 +65,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_cosine_squared.txt

@@ -55,7 +55,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_fourier.txt

@@ -51,7 +51,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_fourier_simple.txt

@@ -50,7 +50,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_harmonic.txt

@@ -57,7 +57,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_quartic.txt

@@ -57,7 +57,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/angle_table.txt

@@ -136,7 +136,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/balance.txt

@@ -394,7 +394,7 @@ weights.  It assigns the same weight to each particle owned by a
 processor based on the total computational time spent by that
 processor.  See details below on what time window is used.  It uses
 the same timing information as is used for the "MPI task timing
-breakdown"_Section_start.html#start_8, namely, for sections {Pair},
+breakdown"_Section_start.html#start_7, namely, for sections {Pair},
 {Bond}, {Kspace}, and {Neigh}.  The time spent in those portions of
 the timestep are measured for each MPI rank, summed, then divided by
 the number of particles owned by that processor.  I.e. the weight is

doc/src/bond_class2.txt

@@ -56,7 +56,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/bond_fene.txt

@@ -59,7 +59,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/bond_fene_expand.txt

@@ -62,7 +62,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/bond_harmonic.txt

@@ -54,7 +54,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/bond_harmonic_shift.txt

@@ -55,7 +55,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/bond_harmonic_shift_cut.txt

@@ -55,7 +55,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/bond_morse.txt

@@ -53,7 +53,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/bond_nonlinear.txt

@@ -53,7 +53,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/bond_quartic.txt

@@ -88,7 +88,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/bond_table.txt

@@ -133,7 +133,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/compute_pressure.txt

@@ -117,7 +117,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/compute_rdf.txt

@@ -180,9 +180,18 @@ will register an arbitrarily large spike at whatever distance they
 happen to be at, and zero everywhere else.  Coord(r) will show a step
 change from zero to one at the location of the spike in g(r).
 
+NOTE: compute rdf can handle dynamic groups and systems where atoms
+are added or removed, but this causes that certain normalization
+parameters need to be recomputed in every step and include collective
+communication operations. This will reduce performance and limit
+parallel efficiency and scaling. For systems, where only the type
+of atoms changes (e.g. when using "fix atom/swap"_fix_atom_swap.html),
+you need to explicitly request the dynamic normalization updates
+via "compute_modify dynamic yes"_compute_modify.html
+
 [Related commands:]
 
-"fix ave/time"_fix_ave_time.html
+"fix ave/time"_fix_ave_time.html, "compute_modify"_compute_modify.html
 
 [Default:]
 

doc/src/compute_temp.txt

@@ -79,7 +79,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/compute_temp_partial.txt

@@ -86,7 +86,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/compute_voronoi_atom.txt

@@ -217,7 +217,7 @@ This compute is part of the VORONOI package.  It is only enabled if
 LAMMPS was built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
-It also requiers you have a copy of the Voro++ library built and
+It also requires you have a copy of the Voro++ library built and
 installed on your system.  See instructions on obtaining and
 installing the Voro++ software in the src/VORONOI/README file.
 

doc/src/dihedral_charmm.txt

@@ -128,7 +128,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/dihedral_class2.txt

@@ -153,7 +153,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/dihedral_cosine_shift_exp.txt

@@ -64,7 +64,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/dihedral_fourier.txt

@@ -55,7 +55,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/dihedral_harmonic.txt

@@ -65,7 +65,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/dihedral_helix.txt

@@ -58,7 +58,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/dihedral_multi_harmonic.txt

@@ -52,7 +52,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/dihedral_nharmonic.txt

@@ -52,7 +52,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/dihedral_opls.txt

@@ -60,7 +60,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/dihedral_quadratic.txt

@@ -53,7 +53,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/echo.txt

@@ -26,7 +26,7 @@ command to the screen and/or log file as it is read and processed.  If
 an input script has errors, it can be useful to look at echoed output
 to see the last command processed.
 
-The "command-line switch"_Section_start.html#start_5 -echo can be used
+The "command-line switch"_Section_start.html#start_6 -echo can be used
 in place of this command.
 
 [Restrictions:] none

doc/src/fix_addforce.txt

@@ -117,7 +117,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_aveforce.txt

@@ -77,7 +77,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_deform.txt

@@ -557,7 +557,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_enforce2d.txt

@@ -41,7 +41,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_freeze.txt

@@ -45,7 +45,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_gcmc.txt

@@ -383,6 +383,9 @@ called.  Reneighboring is required.
 Can be run in parallel, but aspects of the GCMC part will not scale
 well in parallel. Only usable for 3D simulations.
 
+When using fix gcmc in combination with fix shake or fix rigid,
+only gcmc exchange moves are supported.
+
 Note that very lengthy simulations involving insertions/deletions of
 billions of gas molecules may run out of atom or molecule IDs and
 trigger an error, so it is better to run multiple shorter-duration

doc/src/fix_gravity.txt

@@ -102,7 +102,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_langevin.txt

@@ -276,7 +276,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_momentum.txt

@@ -73,7 +73,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_msst.txt

@@ -25,7 +25,7 @@ keyword = {q} or {mu} or {p0} or {v0} or {e0} or {tscale} or {beta} or {dftb} :l
   {e0} value = initial total energy (energy units)
   {tscale} value = reduction in initial temperature (unitless fraction between 0.0 and 1.0) 
   {dftb} value = {yes} or {no} for whether using MSST in conjunction with DFTB+
-  {beta} value = scale factor on energy contribution of DFTB+ :pre
+  {beta} value = scale factor for improved energy conservation :pre
 :ule
 
 [Examples:]
@@ -72,6 +72,14 @@ be calculated on the first step, after the energy specified by
 {tscale} is removed.  The value of {e0} is not used in the dynamical
 equations, but is used in calculating the deviation from the Hugoniot.
 
+The keyword {beta} is a scaling term that can be added to the MSST
+ionic equations of motion to account for drift in the conserved
+quantity during long timescale simulations, similar to a Berendson
+thermostat. See "(Reed)"_#Reed and "(Goldman)"_#Goldman2 for more
+details.  The value of {beta} must be between 0.0 and 1.0 inclusive.
+A value of 0.0 means no contribution, a value of 1.0 means a full
+contribution.
+
 Values of shockvel less than a critical value determined by the
 material response will not have compressive solutions. This will be
 reflected in lack of significant change of the volume in the MSST.
@@ -95,23 +103,15 @@ or "_MSST_pe".  The group for the new computes is "all".
 
 :line
 
-The {dftb} and {beta} keywords are to allow this fix to be used when
-LAMMPS is being driven by DFTB+, a density-functional tight-binding
-code.
-
-If the keyword {dftb} is used with a value of {yes}, then the MSST
-equations are altered to account for an energy contribution compute by
-DFTB+.  In this case, you must define a "fix
-external"_fix_external.html command in your input script, which is
-used to callback to DFTB+ during the LAMMPS timestepping.  DFTB+ will
-communicate its info to LAMMPS via that fix.
-
-The keyword {beta} is a scale factor on the DFTB+ energy contribution.
-The value of {beta} must be between 0.0 and 1.0 inclusive.  A value of
-0.0 means no contribution, a value of 1.0 means a full contribution.
-
-(July 2017) More information about these keywords and the use of
-LAMMPS with DFTB+ will be added to the LAMMMPS documention soon.
+The {dftb} keyword is to allow this fix to be used when LAMMPS is
+being driven by DFTB+, a density-functional tight-binding code. If the
+keyword {dftb} is used with a value of {yes}, then the MSST equations
+are altered to account for the electron entropy contribution to the
+Hugonio relations and total energy.  See "(Reed2)"_#Reed2 and
+"(Goldman)"_#Goldman2 for details on this contribution.  In this case,
+you must define a "fix external"_fix_external.html command in your
+input script, which is used to callback to DFTB+ during the LAMMPS
+timestepping.  DFTB+ will communicate its info to LAMMPS via that fix.
 
 :line
 
@@ -182,4 +182,12 @@ timestep.
 :line
 
 :link(Reed)
-[(Reed)] Reed, Fried, and Joannopoulos, Phys. Rev. Lett., 90, 235503 (2003).
+[(Reed)] Reed, Fried, and Joannopoulos, Phys. Rev. Lett., 90, 235503
+(2003).
+
+:link(Reed2)
+[(Reed2)] Reed, J. Phys. Chem. C, 116, 2205 (2012).
+
+:link(Goldman2)
+[(Goldman)] Goldman, Srinivasan, Hamel, Fried, Gaus, and Elstner,
+J. Phys. Chem. C, 117, 7885 (2013).

doc/src/fix_nh.txt

@@ -492,7 +492,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_nph_asphere.txt

@@ -93,7 +93,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_nph_body.txt

@@ -92,7 +92,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_nph_sphere.txt

@@ -102,7 +102,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_nphug.txt

@@ -152,7 +152,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_npt_asphere.txt

@@ -117,7 +117,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_npt_body.txt

@@ -116,7 +116,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_npt_sphere.txt

@@ -127,7 +127,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_nve.txt

@@ -46,7 +46,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_nve_asphere.txt

@@ -57,7 +57,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_nve_sphere.txt

@@ -77,7 +77,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_nvt_asphere.txt

@@ -98,7 +98,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_nvt_body.txt

@@ -97,7 +97,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_nvt_sllod.txt

@@ -121,7 +121,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for

doc/src/fix_nvt_sphere.txt

@@ -108,7 +108,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
 See "Section 5"_Section_accelerate.html of the manual for