patch 24Jul17

LICENSE: update address of Free Software Foundation

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="24 Jul 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
+24 Jul 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
+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_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

@@ -369,7 +369,7 @@ 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,
 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
@@ -427,8 +427,8 @@ 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
@@ -529,7 +529,7 @@ 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.
 
@@ -597,9 +597,9 @@ 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
@@ -926,7 +926,7 @@ 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.
 
@@ -953,7 +953,7 @@ CCFLAGS: add -restrict :ul
 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
 
@@ -1863,7 +1863,7 @@ 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.
 
@@ -1919,8 +1919,8 @@ 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
@@ -2193,7 +2193,7 @@ 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.
@@ -2226,8 +2226,8 @@ 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

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
@@ -685,7 +714,7 @@ 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

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.
@@ -75,7 +75,7 @@ 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.
+described in "Section 4"_Section_packages.html 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:
@@ -151,9 +151,9 @@ 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 +188,7 @@ 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

@@ -226,7 +226,7 @@ source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
 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
+script, described in "Section 4"_Section_packages.html 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
@@ -301,7 +301,7 @@ 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 +314,7 @@ 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 +387,7 @@ 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 +486,7 @@ 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

@@ -136,7 +136,7 @@ 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.
+described in "Section 4"_Section_packages.html of the manual.
 Type "Make.py -h" for help.  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
@@ -144,7 +144,7 @@ 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 +280,10 @@ 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 +304,12 @@ 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 +323,7 @@ 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 +332,7 @@ 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 +343,7 @@ 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 +389,7 @@ 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 +429,7 @@ 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

@@ -41,7 +41,7 @@ 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
+4"_Section_packages.html of the manual.  Type "Make.py -h" for
 help.
 
 Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
@@ -62,14 +62,14 @@ 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

@@ -36,7 +36,7 @@ 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
+4"_Section_packages.html of the manual.  Type "Make.py -h" for
 help.
 
 Note that if you use an Intel compiler to build with the OPT package,
@@ -46,7 +46,7 @@ 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/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)"_#Goldman 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)"_#Goldman 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(Goldman)
+[(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

doc/src/fix_qeq_comb.txt

@@ -74,7 +74,7 @@ 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_qeq_reax.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_reax_bonds.txt

@@ -82,7 +82,7 @@ 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_accelerate"_Section_accelerate.html of the manual for

doc/src/fix_reaxc_species.txt

@@ -151,7 +151,7 @@ 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_accelerate"_Section_accelerate.html of the manual for

doc/src/fix_rigid.txt

@@ -212,8 +212,9 @@ pour"_fix_pour.html.
 For bodystyle {single} the entire fix group of atoms is treated as one
 rigid body.  This option is only allowed for the {rigid} styles.
 
-For bodystyle {molecule}, each set of atoms in the fix group with a
-different molecule ID is treated as a rigid body.  This option is
+For bodystyle {molecule}, atoms are grouped into rigid bodies by their
+respective molecule IDs: each set of atoms in the fix group with the
+same molecule ID is treated as a different rigid body.  This option is
 allowed for both the {rigid} and {rigid/small} styles.  Note that
 atoms with a molecule ID = 0 will be treated as a single rigid body.
 For a system with atomic solvent (typically this is atoms with
@@ -675,7 +676,7 @@ 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_setforce.txt

@@ -82,7 +82,7 @@ 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_shake.txt

@@ -159,7 +159,7 @@ 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_wall_ees.txt

@@ -0,0 +1,117 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix wall/ees command :h3
+fix wall/region/ees command :h3
+
+[Syntax:]
+
+fix ID group-ID style args :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+style = {wall/ees} or {wall/region/ees} :l
+  args for style {wall/ees}: one or more {face parameters} groups may be appended
+  face = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi}
+  parameters = coord epsilon sigma cutoff
+    coord = position of wall = EDGE or constant or variable
+      EDGE = current lo or hi edge of simulation box
+      constant = number like 0.0 or -30.0 (distance units)
+      variable = "equal-style variable"_variable.html like v_x or v_wiggle
+    epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
+      epsilon can be a variable (see below)
+    sigma = size factor for wall-particle interaction (distance units)
+      sigma can be a variable (see below)
+    cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre
+
+  args for style {wall/region/ees}: {region-ID} {epsilon} {sigma} {cutoff}
+    region-ID = region whose boundary will act as wall
+    epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
+    sigma = size factor for wall-particle interaction (distance units)
+    cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :pre
+  :ule
+
+[Examples:]
+
+fix wallhi all wall/ees xlo -1.0 1.0 1.0 2.5 units box
+fix wallhi all wall/ees xhi EDGE 1.0 1.0 2.5
+fix wallhi all wall/ees v_wiggle 23.2 1.0 1.0 2.5
+fix zwalls all wall/ees zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 :pre
+
+fix ees_cube all wall/region/ees myCube 1.0 1.0 2.5 :pre
+
+
+[Description:]
+
+Fix {wall/ees} bounds the simulation domain on one or more of its
+faces with a flat wall that interacts with the ellipsoidal atoms in the
+group by generating a force on the atom in a direction perpendicular to
+the wall and a torque parallel with the wall.  The energy of
+wall-particle interactions E is given by:
+
+:c,image(Eqs/fix_wall_ees.jpg)
+
+Introduced by Babadi and Ejtehadi in "(Babadi)"_#BabadiEjtehadi. Here,
+{r} is the distance from the particle to the wall at position {coord},
+and Rc is the {cutoff} distance at which the  particle and wall no
+longer interact. Also,  sigma_n is the distance between center of
+ellipsoid and the nearest point of its surface to the wall  The energy
+of the wall (see the image below).
+
+:c,image(JPG/fix_wall_ees_image.jpg)
+
+Details of using this command and specifications are the same as
+fix/wall command. You can also find an example in USER/ees/ under
+examples/ directory.
+
+The prefactor {epsilon} can be thought of as an
+effective Hamaker constant with energy units for the strength of the
+ellipsoid-wall interaction.  More specifically, the {epsilon} pre-factor
+= 8 * pi^2 * rho_wall * rho_ellipsoid * epsilon
+* sigma_a * sigma_b * sigma_c, where epsilon is the LJ parameters for
+the constituent LJ particles and sigma_a, sigma_b, and sigma_c are radii
+of ellipsoidal particles. Rho_wall and rho_ellipsoid are the number
+density of the constituent particles, in the wall and ellipsoid
+respectively, in units of 1/volume.
+
+NOTE: You must insure that r is always bigger than sigma_n for
+all particles in the group, or LAMMPS will generate an error.  This
+means you cannot start your simulation with particles touching the wall
+position {coord} (r = sigma_n) or with particles penetrating the wall (0 =< r < sigma_n) or with particles on the wrong side of the
+wall (r < 0). 
+
+
+Fix {wall/region/ees} treats the surface of the geometric region defined
+by the {region-ID} as a bounding wall which interacts with nearby
+ellipsoidal particles according to the EES potential introduced above.
+
+Other details of this command are the same as for the "fix
+wall/region"_fix_wall_region.html command.  One may also find an example
+of using this fix in the examples/USER/misc/ees/ directory.
+
+[Restrictions:] 
+
+This fix is part of the USER-MISC 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.
+
+This fix requires that atoms be ellipsoids as defined by the
+"atom_style ellipsoid"_atom_style.html command.
+
+[Related commands:]
+
+"fix wall"_fix_wall.html,
+"pair resquared"_pair_resquared.html
+
+[Default:]
+
+none
+
+:line
+
+:link(BabadiEjtehadi)
+[(Babadi)] Babadi and Ejtehadi, EPL, 77 (2007) 23002.

doc/src/fix_wall_reflect.txt

@@ -142,7 +142,7 @@ 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/fixes.txt

@@ -156,6 +156,7 @@ Fixes :h1
    fix_viscosity
    fix_viscous
    fix_wall
+   fix_wall_ees
    fix_wall_gran
    fix_wall_gran_region
    fix_wall_piston

doc/src/improper_class2.txt

@@ -99,7 +99,7 @@ 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/improper_cossq.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/improper_cvff.txt

@@ -66,7 +66,7 @@ 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/improper_fourier.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/improper_harmonic.txt

@@ -70,7 +70,7 @@ 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/improper_ring.txt

@@ -69,7 +69,7 @@ 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