patch 31Mar17 for stable release

Merge pull request #440 from ohenrich/user-cgdna
Updated lammps.book, USER-CGDNA install script
2017-03-30 10:07:27 -06:00 · 2017-03-30 09:34:35 -06:00 · 2017-03-29 11:18:04 +01:00 · 2017-03-29 08:28:03 +01:00 · 2017-03-28 13:26:12 -06:00 · 2017-03-28 13:12:23 -06:00
466 changed files with 300174 additions and 26077 deletions
--- a/doc/Makefile
+++ b/doc/Makefile
@ -6,6 +6,7 @@ BUILDDIR      = /tmp/lammps-docs-$(SHA1)
 RSTDIR        = $(BUILDDIR)/rst
 VENV          = $(BUILDDIR)/docenv
 TXT2RST       = $(VENV)/bin/txt2rst
+ANCHORCHECK   = $(VENV)/bin/doc_anchor_check

 PYTHON        = $(shell which python3)
 HAS_PYTHON3    = NO
@ -22,7 +23,7 @@ endif
 SOURCES=$(wildcard src/*.txt)
 OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)

-.PHONY: help clean-all clean epub html pdf old venv spelling
+.PHONY: help clean-all clean epub html pdf old venv spelling anchor_check

 # ------------------------------------------

@ -36,6 +37,7 @@ help:
 	@echo "  clean      remove all intermediate RST files"
 	@echo "  clean-all  reset the entire build environment"
 	@echo "  txt2html   build txt2html tool"
+	@echo "  anchor_check  scan for duplicate anchor labels"

 # ------------------------------------------

@ -49,11 +51,14 @@ clean:
 clean-spelling:
 	rm -rf spelling

-html: $(OBJECTS)
+html: $(OBJECTS) $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ;\
 		cp -r src/* $(RSTDIR)/ ;\
 		sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
+		echo "############################################" ;\
+		doc_anchor_check src/*.txt ;\
+		echo "############################################" ;\
 		deactivate ;\
 	)
 	-rm html/searchindex.js
@ -127,6 +132,13 @@ fetch:

 txt2html: utils/txt2html/txt2html.exe

+anchor_check : $(ANCHORCHECK)
+	@(\
+		. $(VENV)/bin/activate ;\
+		doc_anchor_check src/*.txt ;\
+		deactivate ;\
+	)
+
 # ------------------------------------------

 utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp
@ -151,7 +163,7 @@ $(VENV):
 		deactivate;\
 	)

-$(TXT2RST): $(VENV)
+$(TXT2RST) $(ANCHORCHECK): $(VENV)
 	@( \
 		. $(VENV)/bin/activate; \
 		(cd utils/converters;\
--- a/doc/src/Eqs/fix_gcmc1.jpg
+++ b/doc/src/Eqs/fix_gcmc1.jpg
--- a/doc/src/Eqs/fix_gcmc1.tex
+++ b/doc/src/Eqs/fix_gcmc1.tex
@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\mu &=&\mu^{id} + \mu^{ex}
+\end{eqnarray*}
+
+\end{document}
--- a/doc/src/Eqs/fix_gcmc2.jpg
+++ b/doc/src/Eqs/fix_gcmc2.jpg
--- a/doc/src/Eqs/fix_gcmc2.tex
+++ b/doc/src/Eqs/fix_gcmc2.tex
@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\mu^{id} &=& k T \ln{\rho \Lambda^3} \\
+&=& k T \ln{\frac{\phi P \Lambda^3}{k T}} 
+\end{eqnarray*}
+
+\end{document}
--- a/doc/src/Eqs/fix_gcmc3.jpg
+++ b/doc/src/Eqs/fix_gcmc3.jpg
--- a/doc/src/Eqs/fix_gcmc3.tex
+++ b/doc/src/Eqs/fix_gcmc3.tex
@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\Lambda &=& \sqrt{ \frac{h^2}{2 \pi m k T}}
+\end{eqnarray*}
+
+\end{document}
--- a/doc/src/Eqs/pair_momb.jpg
+++ b/doc/src/Eqs/pair_momb.jpg
--- a/doc/src/Eqs/pair_momb.tex
+++ b/doc/src/Eqs/pair_momb.tex
@ -0,0 +1,13 @@
+\documentclass[12pt,fleqn]{article}
+\usepackage{amsmath}
+\thispagestyle{empty}
+
+\begin{document}
+
+\setlength{\jot}{2ex}
+\begin{gather*}
+  E = D_0 [\exp^{-2 \alpha (r-r_0)} - 2\exp^{-\alpha (r-r_0)}] - s_6 \frac{C_6}{r^6} f_{damp}(r,R_r) \\
+  f_{damp}(r,R_r) = \frac{1}{1 + \exp^{-d(r/R_r - 1)}}
+\end{gather*}
+
+\end{document}
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="7 Mar 2017 version">
+<META NAME="docnumber" CONTENT="31 Mar 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
-7 Mar 2017 version :c,h4
+31 Mar 2017 version :c,h4

 Version info: :h4

@ -39,7 +39,7 @@ directory name created when you unpack a tarball, and at the top of
 the first page of the manual (this page).

 If you browse the HTML doc pages on the LAMMPS WWW site, they always
-describe the most current version of LAMMPS. :ulb,l
+describe the most current [development] version of LAMMPS. :ulb,l

 If you browse the HTML doc pages included in your tarball, they
 describe the version you have. :l
@ -67,7 +67,7 @@ Labs and Temple University:

 "Steve Plimpton"_sjp, sjplimp at sandia.gov :ulb,l
 Aidan Thompson, athomps at sandia.gov :l
-Stan Moore, stamoore at sandia.gov :l
+Stan Moore, stamoor at sandia.gov :l
 "Axel Kohlmeyer"_ako, akohlmey at gmail.com :l
 :ule

--- a/doc/src/PDF/USER-CGDNA-overview.pdf
+++ b/doc/src/PDF/USER-CGDNA-overview.pdf
--- a/doc/src/PDF/colvars-refman-lammps.pdf
+++ b/doc/src/PDF/colvars-refman-lammps.pdf
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@ -687,6 +687,7 @@ package"_Section_start.html#start_3.
 "eos/cv"_fix_eos_cv.html,
 "eos/table"_fix_eos_table.html,
 "eos/table/rx"_fix_eos_table_rx.html,
+"filter/corotate"_fix_filter_corotate.html,
 "flow/gauss"_fix_flow_gauss.html,
 "gle"_fix_gle.html,
 "grem"_fix_grem.html,
@ -939,6 +940,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
 "lj/charmm/coul/long (giko)"_pair_charmm.html,
 "lj/charmm/coul/msm"_pair_charmm.html,
+"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
+"lj/charmmfsw/coul/long"_pair_charmm.html,
 "lj/class2 (gko)"_pair_class2.html,
 "lj/class2/coul/cut (ko)"_pair_class2.html,
 "lj/class2/coul/long (gko)"_pair_class2.html,
@ -1034,6 +1037,7 @@ package"_Section_start.html#start_3.
 "meam/spline (o)"_pair_meam_spline.html,
 "meam/sw/spline"_pair_meam_sw_spline.html,
 "mgpt"_pair_mgpt.html,
+"momb"_pair_momb.html,
 "morse/smooth/linear"_pair_morse.html,
 "morse/soft"_pair_morse.html,
 "multi/lucy"_pair_multi_lucy.html,
@ -1043,6 +1047,10 @@ package"_Section_start.html#start_3.
 "oxdna/hbond"_pair_oxdna.html,
 "oxdna/stk"_pair_oxdna.html,
 "oxdna/xstk"_pair_oxdna.html,
+"oxdna2/coaxstk"_pair_oxdna2.html,
+"oxdna2/dh"_pair_oxdna2.html,
+"oxdna2/excv"_pair_oxdna2.html,
+"oxdna2/stk"_pair_oxdna2.html,
 "quip"_pair_quip.html,
 "reax/c (k)"_pair_reax_c.html,
 "smd/hertz"_pair_smd_hertz.html,
@ -1060,7 +1068,7 @@ package"_Section_start.html#start_3.
 "table/rx"_pair_table_rx.html,
 "tersoff/table (o)"_pair_tersoff.html,
 "thole"_pair_thole.html,
-"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
+"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c) 

 :line

@ -1092,7 +1100,8 @@ package"_Section_start.html#start_3.

 "harmonic/shift (o)"_bond_harmonic_shift.html,
 "harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
-"oxdna/fene"_bond_oxdna.html :tb(c=4,ea=c)
+"oxdna/fene"_bond_oxdna.html,
+"oxdna2/fene"_bond_oxdna.html :tb(c=4,ea=c)

 :line

@ -1146,6 +1155,7 @@ USER-OMP, t = OPT.
 "zero"_dihedral_zero.html,
 "hybrid"_dihedral_hybrid.html,
 "charmm (ko)"_dihedral_charmm.html,
+"charmmfsh"_dihedral_charmm.html,
 "class2 (ko)"_dihedral_class2.html,
 "harmonic (io)"_dihedral_harmonic.html,
 "helix (o)"_dihedral_helix.html,
--- a/doc/src/Section_example.txt
+++ b/doc/src/Section_example.txt
@ -25,9 +25,7 @@ files and image files.

 If you uncomment the "dump"_dump.html command in the input script, a
 text dump file will be produced, which can be animated by various
-"visualization programs"_http://lammps.sandia.gov/viz.html.  It can
-also be animated using the xmovie tool described in the "Additional
-Tools"_Section_tools.html section of the LAMMPS documentation.
+"visualization programs"_http://lammps.sandia.gov/viz.html.

 If you uncomment the "dump image"_dump.html command in the input
 script, and assuming you have built LAMMPS with a JPG library, JPG
@ -53,9 +51,11 @@ Lowercase directories :h4
 accelerate: run with various acceleration options (OpenMP, GPU, Phi)
 balance:  dynamic load balancing, 2d system
 body:     body particles, 2d system
+cmap:     CMAP 5-body contributions to CHARMM force field
 colloid:  big colloid particles in a small particle solvent, 2d system
 comb:     models using the COMB potential
 coreshell: core/shell model using CORESHELL package
+controller: use of fix controller as a thermostat
 crack:    crack propagation in a 2d solid
 deposit:  deposit atoms and molecules on a surface
 dipole:   point dipolar particles, 2d system
@ -64,6 +64,8 @@ eim:      NaCl using the EIM potential
 ellipse:  ellipsoidal particles in spherical solvent, 2d system
 flow:     Couette and Poiseuille flow in a 2d channel
 friction: frictional contact of spherical asperities between 2d surfaces
+gcmc:     Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
+granregion: use of fix wall/region/gran as boundary on granular particles
 hugoniostat: Hugoniostat shock dynamics
 indent:   spherical indenter into a 2d solid
 kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
@ -71,6 +73,7 @@ meam:     MEAM test for SiC and shear (same as shear examples)
 melt:     rapid melt of 3d LJ system
 micelle:  self-assembly of small lipid-like molecules into 2d bilayers
 min:      energy minimization of 2d LJ melt
+mscg:     parameterize a multi-scale coarse-graining (MSCG) model
 msst:     MSST shock dynamics
 nb3b:     use of nonbonded 3-body harmonic pair style
 neb:      nudged elastic band (NEB) calculation for barrier finding
@ -89,7 +92,8 @@ snap:     NVE dynamics for BCC tantalum crystal using SNAP potential
 srd:      stochastic rotation dynamics (SRD) particles as solvent
 streitz:  use of Streitz/Mintmire potential with charge equilibration
 tad:      temperature-accelerated dynamics of vacancy diffusion in bulk Si
-vashishta: use of the Vashishta potential :tb(s=:)
+vashishta: use of the Vashishta potential
+voronoi:  Voronoi tesselation via compute voronoi/atom command :tb(s=:)

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

--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@ -165,9 +165,16 @@ Many of the example input scripts included in the LAMMPS distribution
 are for 2d models.

 NOTE: Some models in LAMMPS treat particles as finite-size spheres, as
-opposed to point particles.  In 2d, the particles will still be
-spheres, not disks, meaning their moment of inertia will be the same
-as in 3d.
+opposed to point particles.  See the "atom_style
+sphere"_atom_style.html and "fix nve/sphere"_fix_nve_sphere.html
+commands for details.  By default, for 2d simulations, such particles
+will still be modeled as 3d spheres, not 2d discs (circles), meaning
+their moment of inertia will be that of a sphere.  If you wish to
+model them as 2d discs, see the "set density/disc"_set.html command
+and the {disc} option for the "fix nve/sphere"_fix_nve_sphere.html,
+"fix nvt/sphere"_fix_nvt_sphere.html, "fix
+nph/sphere"_fix_nph_sphere.html, "fix npt/sphere"_fix_npt_sphere.html
+commands.

 :line

@ -197,7 +204,10 @@ documentation for the formula it computes.

 "bond_style"_bond_harmonic.html harmonic
 "angle_style"_angle_charmm.html charmm
+"dihedral_style"_dihedral_charmm.html charmmfsh
 "dihedral_style"_dihedral_charmm.html charmm
+"pair_style"_pair_charmm.html lj/charmmfsw/coul/charmmfsh
+"pair_style"_pair_charmm.html lj/charmmfsw/coul/long
 "pair_style"_pair_charmm.html lj/charmm/coul/charmm
 "pair_style"_pair_charmm.html lj/charmm/coul/charmm/implicit
 "pair_style"_pair_charmm.html lj/charmm/coul/long :ul
@ -205,6 +215,12 @@ documentation for the formula it computes.
 "special_bonds"_special_bonds.html charmm
 "special_bonds"_special_bonds.html amber :ul

+NOTE: For CHARMM, the newer {charmmfsw} or {charmmfsh} styles were
+released in March 2017.  We recommend they be used instead of the
+older {charmm} styles.  See discussion of the differences on the "pair
+charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
+doc pages.
+
 DREIDING is a generic force field developed by the "Goddard
 group"_http://www.wag.caltech.edu at Caltech and is useful for
 predicting structures and dynamics of organic, biological and
@ -434,6 +450,12 @@ computations between frozen atoms by using this command:

 "neigh_modify"_neigh_modify.html exclude :ul

+NOTE: By default, for 2d systems, granular particles are still modeled
+as 3d spheres, not 2d discs (circles), meaning their moment of inertia
+will be the same as in 3d.  If you wish to model granular particles in
+2d as 2d discs, see the note on this topic in "Section
+6.2"_Section_howto.html#howto_2, where 2d simulations are disussed.
+
 :line

 6.7 TIP3P water model :link(howto_7),h4
@ -451,7 +473,7 @@ atoms and the water molecule to run a rigid TIP3P-CHARMM model with a
 cutoff.  The K values can be used if a flexible TIP3P model (without
 fix shake) is desired.  If the LJ epsilon and sigma for HH and OH are
 set to 0.0, it corresponds to the original 1983 TIP3P model
-"(Jorgensen)"_#Jorgensen.
+"(Jorgensen)"_#Jorgensen1.

 O mass = 15.9994
 H mass = 1.008
@ -469,7 +491,7 @@ K of HOH angle = 55
 theta of HOH angle = 104.52 :all(b),p

 These are the parameters to use for TIP3P with a long-range Coulombic
-solver (e.g. Ewald or PPPM in LAMMPS), see "(Price)"_#Price for
+solver (e.g. Ewald or PPPM in LAMMPS), see "(Price)"_#Price1 for
 details:

 O mass = 15.9994
@ -513,7 +535,7 @@ using the "fix shake"_fix_shake.html command.

 These are the additional parameters (in real units) to set for O and H
 atoms and the water molecule to run a rigid TIP4P model with a cutoff
-"(Jorgensen)"_#Jorgensen.  Note that the OM distance is specified in
+"(Jorgensen)"_#Jorgensen1.  Note that the OM distance is specified in
 the "pair_style"_pair_style.html command, not as part of the pair
 coefficients.

@ -737,23 +759,14 @@ LAMMPS itself does not do visualization, but snapshots from LAMMPS
 simulations can be visualized (and analyzed) in a variety of ways.

 LAMMPS snapshots are created by the "dump"_dump.html command which can
-create files in several formats.  The native LAMMPS dump format is a
+create files in several formats. The native LAMMPS dump format is a
 text file (see "dump atom" or "dump custom") which can be visualized
-by the "xmovie"_Section_tools.html#xmovie program, included with the
-LAMMPS package.  This produces simple, fast 2d projections of 3d
-systems, and can be useful for rapid debugging of simulation geometry
-and atom trajectories.
-
+by several popular visualization tools. The "dump image"_dump_image.html
+and "dump movie"_dump_image.html styles can output internally rendered
+images and convert a sequence of them to a movie during the MD run.
 Several programs included with LAMMPS as auxiliary tools can convert
-native LAMMPS dump files to other formats.  See the
-"Section 9"_Section_tools.html doc page for details.  The first is
-the "ch2lmp tool"_Section_tools.html#charmm, which contains a
-lammps2pdb Perl script which converts LAMMPS dump files into PDB
-files.  The second is the "lmp2arc tool"_Section_tools.html#arc which
-converts LAMMPS dump files into Accelrys' Insight MD program files.
-The third is the "lmp2cfg tool"_Section_tools.html#cfg which converts
-LAMMPS dump files into CFG files which can be read into the
-"AtomEye"_atomeye visualizer.
+between LAMMPS format files and other formats.
+See the "Section 9"_Section_tools.html doc page for details.

 A Python-based toolkit distributed by our group can read native LAMMPS
 dump files, including custom dump files with additional columns of
@ -766,22 +779,7 @@ RasMol visualization programs.  Pizza.py has tools that do interactive
 3d OpenGL visualization and one that creates SVG images of dump file
 snapshots.

-LAMMPS can create XYZ files directly (via "dump xyz") which is a
-simple text-based file format used by many visualization programs
-including "VMD"_vmd.
-
-LAMMPS can create DCD files directly (via "dump dcd") which can be
-read by "VMD"_vmd in conjunction with a CHARMM PSF file.  Using this
-form of output avoids the need to convert LAMMPS snapshots to PDB
-files.  See the "dump"_dump.html command for more information on DCD
-files.
-
-LAMMPS can create XTC files directly (via "dump xtc") which is GROMACS
-file format which can also be read by "VMD"_vmd for visualization.
-See the "dump"_dump.html command for more information on XTC files.
-
 :link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
-:link(vmd,http://www.ks.uiuc.edu/Research/vmd)
 :link(ensight,http://www.ensight.com)
 :link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)

@ -1032,6 +1030,10 @@ profile consistent with the applied shear strain rate.
 An alternative method for calculating viscosities is provided via the
 "fix viscosity"_fix_viscosity.html command.

+NEMD simulations can also be used to measure transport properties of a fluid
+through a pore or channel. Simulations of steady-state flow can be performed
+using the "fix flow/gauss"_fix_flow_gauss.html command.
+
 :line

 6.14 Finite-size spherical and aspherical particles :link(howto_14),h4
@ -1684,7 +1686,7 @@ nph) and Berendsen:
 The "fix npt"_fix_nh.html commands include a Nose-Hoover thermostat
 and barostat.  "Fix nph"_fix_nh.html is just a Nose/Hoover barostat;
 it does no thermostatting.  Both "fix nph"_fix_nh.html and "fix
-press/bernendsen"_fix_press_berendsen.html can be used in conjunction
+press/berendsen"_fix_press_berendsen.html can be used in conjunction
 with any of the thermostatting fixes.

 As with the thermostats, "fix npt"_fix_nh.html and "fix
@ -1834,7 +1836,7 @@ the deformation must be chosen judiciously, and care must be taken to
 fully equilibrate the deformed cell before sampling the stress
 tensor. Another approach is to sample the triclinic cell fluctuations
 that occur in an NPT simulation. This method can also be slow to
-converge and requires careful post-processing "(Shinoda)"_#Shinoda
+converge and requires careful post-processing "(Shinoda)"_#Shinoda1

 :line

@ -1957,9 +1959,12 @@ The extract functions return a pointer to various global or per-atom
 quantities stored in LAMMPS or to values calculated by a compute, fix,
 or variable.  The pointer returned by the extract_global() function
 can be used as a permanent reference to a value which may change.  For
-the other extract functions, the underlying storage may be reallocated
-as LAMMPS runs, so you need to re-call the function to assure a
-current pointer or returned value(s).
+the extract_atom() method, see the extract() method in the
+src/atom.cpp file for a list of valid per-atom properties.  New names
+could easily be added if the property you want is not listed.  For the
+other extract functions, the underlying storage may be reallocated as
+LAMMPS runs, so you need to re-call the function to assure a current
+pointer or returned value(s).

 The lammps_reset_box() function resets the size and shape of the
 simulation box, e.g. as part of restoring a previously extracted and
@ -1975,11 +1980,20 @@ keyword as a double precision value.
 The lammps_get_natoms() function returns the total number of atoms in
 the system and can be used by the caller to allocate space for the
 lammps_gather_atoms() and lammps_scatter_atoms() functions.  The
-gather function collects atom info of the requested type (atom coords,
-types, forces, etc) from all processors, orders them by atom ID, and
-returns a full list to each calling processor.  The scatter function
-does the inverse.  It distributes the same kinds of values, 
+gather function collects peratom info of the requested type (atom
+coords, types, forces, etc) from all processors, orders them by atom
+ID, and returns a full list to each calling processor.  The scatter
+function does the inverse.  It distributes the same peratom values,
 passed by the caller, to each atom owned by individual processors.
+Both methods are thus a means to extract or assign (overwrite) any
+peratom quantities within LAMMPS.  See the extract() method in the
+src/atom.cpp file for a list of valid per-atom properties.  New names
+could easily be added if the property you want is not listed.
+A special treatment is applied for accessing image flags via the
+"image" property. Image flags are stored in a packed format with all
+three image flags stored in a single integer. When signaling to access
+the image flags as 3 individual values per atom instead of 1, the data
+is transparently packed or unpacked by the library interface.

 The lammps_create_atoms() function takes a list of N atoms as input
 with atom types and coords (required), an optionally atom IDs and
@ -2899,14 +2913,14 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
 [(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
 (1990).

-:link(Jorgensen)
+:link(Jorgensen1)
 [(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
 Phys, 79, 926 (1983).

-:link(Price)
+:link(Price1)
 [(Price)] Price and Brooks, J Chem Phys, 121, 10096 (2004).

-:link(Shinoda)
+:link(Shinoda1)
 [(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).

 :link(MitchellFincham)
--- a/doc/src/Section_intro.txt
+++ b/doc/src/Section_intro.txt
@ -338,15 +338,13 @@ dynamics timestepping, particularly if the computations are not
 parallel, so it is often better to leave such analysis to
 post-processing codes.

-A very simple (yet fast) visualizer is provided with the LAMMPS
-package - see the "xmovie"_Section_tools.html#xmovie tool in "this
-section"_Section_tools.html.  It creates xyz projection views of
-atomic coordinates and animates them.  We find it very useful for
-debugging purposes.  For high-quality visualization we recommend the
+For high-quality visualization we recommend the
 following packages:

 "VMD"_http://www.ks.uiuc.edu/Research/vmd
 "AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A
+"OVITO"_http://www.ovito.org/
+"ParaView"_http://www.paraview.org/
 "PyMol"_http://www.pymol.org
 "Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html
 "RasMol"_http://www.openrasmol.org :ul
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@ -1140,7 +1140,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
 "USER-ATC"_#USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (1), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
 "USER-AWPMD"_#USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
 "USER-CG-CMM"_#USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
-"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, Oliver Henrich (U Edinburgh), src/USER-CGDNA/README, USER/cgdna, -, -
+"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, Oliver Henrich (U Strathclyde Glasgow), src/USER-CGDNA/README, USER/cgdna, -, -
 "USER-COLVARS"_#USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
 "USER-DIFFRACTION"_#USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -
 "USER-DPD"_#USER-DPD, reactive dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, -
@ -1288,25 +1288,29 @@ him directly if you have questions.
 USER-CGDNA package :link(USER-CGDNA),h5

 Contents: The CGDNA package implements coarse-grained force fields for
-single- and double-stranded DNA. This is at the moment mainly the
-oxDNA model, developed by Doye, Louis and Ouldridge at the University
+single- and double-stranded DNA. These are at the moment mainly the
+oxDNA and oxDNA2 models, developed by Doye, Louis and Ouldridge at the University
 of Oxford.  The package also contains Langevin-type rigid-body
 integrators with improved stability.

 See these doc pages to get started:

 "bond_style oxdna/fene"_bond_oxdna.html
+"bond_style oxdna2/fene"_bond_oxdna.html
 "pair_style oxdna/..."_pair_oxdna.html
+"pair_style oxdna2/..."_pair_oxdna2.html
 "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul

 Supporting info: /src/USER-CGDNA/README, "bond_style
-oxdna/fene"_bond_oxdna.html, "pair_style
-oxdna/..."_pair_oxdna.html, "fix
+oxdna/fene"_bond_oxdna.html, "bond_style
+oxdna2/fene"_bond_oxdna.html, "pair_style
+oxdna/..."_pair_oxdna.html, "pair_style
+oxdna2/..."_pair_oxdna2.html, "fix
 nve/dotc/langevin"_fix_nve_dotc_langevin.html

-Author: Oliver Henrich at the University of Edinburgh, UK (o.henrich
-at epcc.ed.ac.uk or ohenrich at ph.ed.ac.uk).  Contact him directly if
-you have any questions.
+Author: Oliver Henrich at the University of Strathclyde, Glasgow, UK and 
+University of Edinburgh (ohenrich@ph.ed.ac.uk).  
+Contact him directly if you have any questions.

 :line

--- a/doc/src/Section_python.txt
+++ b/doc/src/Section_python.txt
@ -594,10 +594,10 @@ flag = lmp.set_variable(name,value)       # set existing named string-style vari
 value = lmp.get_thermo(name)              # return current value of a thermo keyword

 natoms = lmp.get_natoms()                 # total # of atoms as int
-data = lmp.gather_atoms(name,type,count)  # return atom attribute of all atoms gathered into data, ordered by atom ID
+data = lmp.gather_atoms(name,type,count)  # return per-atom property of all atoms gathered into data, ordered by atom ID
                                          # name = "x", "charge", "type", etc
                                          # count = # of per-atom values, 1 or 3, etc
-lmp.scatter_atoms(name,type,count,data)   # scatter atom attribute of all atoms from data, ordered by atom ID
+lmp.scatter_atoms(name,type,count,data)   # scatter per-atom property to all atoms from data, ordered by atom ID
                                          # name = "x", "charge", "type", etc
                                          # count = # of per-atom values, 1 or 3, etc :pre

@ -656,10 +656,10 @@ argument.
 For extract_atom(), a pointer to internal LAMMPS atom-based data is
 returned, which you can use via normal Python subscripting.  See the
 extract() method in the src/atom.cpp file for a list of valid names.
-Again, new names could easily be added.  A pointer to a vector of
-doubles or integers, or a pointer to an array of doubles (double **)
-or integers (int **) is returned.  You need to specify the appropriate
-data type via the type argument.
+Again, new names could easily be added if the property you want is not
+listed.  A pointer to a vector of doubles or integers, or a pointer to
+an array of doubles (double **) or integers (int **) is returned.  You
+need to specify the appropriate data type via the type argument.

 For extract_compute() and extract_fix(), the global, per-atom, or
 local data calculated by the compute or fix can be accessed.  What is
@ -689,12 +689,21 @@ specified group.
 The get_natoms() method returns the total number of atoms in the
 simulation, as an int.

-The gather_atoms() method returns a ctypes vector of ints or doubles
-as specified by type, of length count*natoms, for the property of all
-the atoms in the simulation specified by name, ordered by count and
-then by atom ID.  The vector can be used via normal Python
-subscripting.  If atom IDs are not consecutively ordered within
-LAMMPS, a None is returned as indication of an error.
+The gather_atoms() method allows any per-atom property (coordinates,
+velocities, etc) to be extracted from LAMMPS.  It returns a ctypes
+vector of ints or doubles as specified by type, of length
+count*natoms, for the named property for all atoms in the simulation.
+The data is ordered by count and then by atom ID.  See the extract()
+method in the src/atom.cpp file for a list of valid names.  Again, new
+names could easily be added if the property you want is missing.  The
+vector can be used via normal Python subscripting.  If atom IDs are
+not consecutively ordered within LAMMPS, a None is returned as
+indication of an error. A special treatment is applied for image flags
+stored in the "image" property. All three image flags are stored in
+a packed format in a single integer, so count would be 1 to retrieve
+that integer, however also a count value of 3 can be used and then
+the image flags will be unpacked into 3 individual integers, ordered
+in a similar fashion as coordinates. 

 Note that the data structure gather_atoms("x") returns is different
 from the data structure returned by extract_atom("x") in four ways.
@ -711,14 +720,22 @@ assigning a new values to the extract_atom() array.  To do this with
 the gather_atoms() vector, you need to change values in the vector,
 then invoke the scatter_atoms() method.

-The scatter_atoms() method takes a vector of ints or doubles as
-specified by type, of length count*natoms, for the property of all the
-atoms in the simulation specified by name, ordered by bount and then
-by atom ID.  It uses the vector of data to overwrite the corresponding
-properties for each atom inside LAMMPS.  This requires LAMMPS to have
-its "map" option enabled; see the "atom_modify"_atom_modify.html
-command for details.  If it is not, or if atom IDs are not
-consecutively ordered, no coordinates are reset.
+The scatter_atoms() method allows any per-atom property (coordinates,
+velocities, etc) to be inserted into LAMMPS, overwriting the current
+property.  It takes a vector of ints or doubles as specified by type,
+of length count*natoms, for the named property for all atoms in the
+simulation.  The data should be ordered by count and then by atom ID.
+See the extract() method in the src/atom.cpp file for a list of valid
+names.  Again, new names could easily be added if the property you
+want is missing.  It uses the vector of data to overwrite the
+corresponding properties for each atom inside LAMMPS.  This requires
+LAMMPS to have its "map" option enabled; see the
+"atom_modify"_atom_modify.html command for details.  If it is not, or
+if atom IDs are not consecutively ordered, no coordinates are reset.
+Similar as for gather_atoms() a special treatment is applied for image
+flags, which can be provided in packed (count = 1) or unpacked (count = 3)
+format and in the latter case, they will be packed before applied to
+atoms.

 The array of coordinates passed to scatter_atoms() must be a ctypes
 vector of ints or doubles, allocated and initialized something like
@ -734,7 +751,7 @@ x\[2\] = z coord of atom with ID 1
 x\[3\] = x coord of atom with ID 2
 ...
 x\[n3-1\] = z coord of atom with ID natoms
-lmp.scatter_coords("x",1,3,x) :pre
+lmp.scatter_atoms("x",1,3,x) :pre

 Alternatively, you can just change values in the vector returned by
 gather_atoms("x",1,3), since it is a ctypes vector of doubles.
--- a/doc/src/Section_tools.txt
+++ b/doc/src/Section_tools.txt
@ -12,9 +12,12 @@ Section"_Section_modify.html :c

 LAMMPS is designed to be a computational kernel for performing
 molecular dynamics computations.  Additional pre- and post-processing
-steps are often necessary to setup and analyze a simulation.  A few
-additional tools are provided with the LAMMPS distribution and are
-described in this section.
+steps are often necessary to setup and analyze a simulation. A
+list of such tools can be found on the LAMMPS home page
+at "http://lammps.sandia.gov/prepost.html"_http://lammps.sandia.gov/prepost.html
+
+A few additional tools are provided with the LAMMPS distribution
+and are described in this section.

 Our group has also written and released a separate toolkit called
 "Pizza.py"_pizza which provides tools for doing setup, analysis,
@ -36,16 +39,16 @@ authors.
 The source code for each of these codes is in the tools sub-directory
 of the LAMMPS distribution.  There is a Makefile (which you may need
 to edit for your platform) which will build several of the tools which
-reside in that directory.  Some of them are larger packages in their
-own sub-directories with their own Makefiles.
+reside in that directory.  Most of them are larger packages in their
+own sub-directories with their own Makefiles and/or README files.

 "amber2lmp"_#amber
 "binary2txt"_#binary
 "ch2lmp"_#charmm
 "chain"_#chain
 "colvars"_#colvars
-"createatoms"_#create
-"data2xmovie"_#data
+"createatoms"_#createatoms
+"drude"_#drude
 "eam database"_#eamdb
 "eam generate"_#eamgn
 "eff"_#eff
@ -56,20 +59,18 @@ own sub-directories with their own Makefiles.
 "kate"_#kate
 "lmp2arc"_#arc
 "lmp2cfg"_#cfg
-"lmp2vmd"_#vmd
 "matlab"_#matlab
 "micelle2d"_#micelle
 "moltemplate"_#moltemplate
 "msi2lmp"_#msi
 "phonon"_#phonon
-"polymer bonding"_#polybond
+"polybond"_#polybond
 "pymol_asphere"_#pymol
 "python"_#pythontools
 "reax"_#reax_tool
-"restart2data"_#restart
+"smd"_#smd
 "vim"_#vim
 "xmgrace"_#xmgrace
-"xmovie"_#xmovie :ul

 :line

@ -158,7 +159,7 @@ gmail.com) at ICTP, Italy.

 :line

-createatoms tool :h4,link(create)
+createatoms tool :h4,link(createatoms)

 The tools/createatoms directory contains a Fortran program called
 createAtoms.f which can generate a variety of interesting crystal
@ -171,16 +172,16 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.

 :line

-data2xmovie tool :h4,link(data)
+drude tool :h4,link(drude)

-The file data2xmovie.c converts a LAMMPS data file into a snapshot
-suitable for visualizing with the "xmovie"_#xmovie tool, as if it had
-been output with a dump command from LAMMPS itself.  The syntax for
-running the tool is
+The tools/drude directory contains a Python script called
+polarizer.py which can add Drude oscillators to a LAMMPS
+data file in the required format.

-data2xmovie \[options\] < infile > outfile :pre
+See the header of the polarizer.py file for details.

-See the top of the data2xmovie.c file for a discussion of the options.
+The tool is authored by Agilio Padua and Alain Dequidt: agilio.padua
+at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr

 :line

@ -317,18 +318,6 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).

 :line

-lmp2vmd tool :h4,link(vmd)
-
-The lmp2vmd sub-directory contains a README.txt file that describes
-details of scripts and plugin support within the "VMD
-package"_http://www.ks.uiuc.edu/Research/vmd for visualizing LAMMPS
-dump files.
-
-The VMD plugins and other supporting scripts were written by Axel
-Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.
-
-:line
-
 matlab tool :h4,link(matlab)

 The matlab sub-directory contains several "MATLAB"_matlabhome scripts for
@ -381,16 +370,14 @@ supports it.  It has its own WWW page at
 msi2lmp tool :h4,link(msi)

 The msi2lmp sub-directory contains a tool for creating LAMMPS input
-data files from Accelrys' Insight MD code (formerly MSI/Biosym and
-its Discover MD code).  See the README file for more information.
+data files from BIOVIA's Materias Studio files (formerly Accelrys'
+Insight MD code, formerly MSI/Biosym and its Discover MD code).

 This tool was written by John Carpenter (Cray), Michael Peachey
-(Cray), and Steve Lustig (Dupont).  John is now at the Mayo Clinic
-(jec at mayo.edu), but still fields questions about the tool.
+(Cray), and Steve Lustig (Dupont). Several people contributed changes
+to remove bugs and adapt its output to changes in LAMMPS.

-This tool may be out-of-date with respect to the current LAMMPS and
-Insight versions.  Since we don't use it at Sandia, you'll need to
-experiment with it yourself.
+See the README file for more information.

 :line

@ -409,7 +396,7 @@ University.

 :line

-polymer bonding tool :h4,link(polybond)
+polybond tool :h4,link(polybond)

 The polybond sub-directory contains a Python-based tool useful for
 performing "programmable polymer bonding".  The Python file
@ -468,48 +455,19 @@ These tools were written by Aidan Thompson at Sandia.

 :line

-restart2data tool :h4,link(restart)
+smd tool :h4,link(smd)

-NOTE: This tool is now obsolete and is not included in the current
-LAMMPS distribution.  This is because there is now a
-"write_data"_write_data.html command, which can create a data file
-from within an input script.  Running LAMMPS with the "-r"
-"command-line switch"_Section_start.html#start_7 as follows:
+The smd sub-directory contains a C++ file dump2vtk_tris.cpp and
+Makefile which can be compiled and used to convert triangle output
+files created by the Smooth-Mach Dynamics (USER-SMD) package into a
+VTK-compatible unstructured grid file.  It could then be read in and
+visualized by VTK.

-lmp_g++ -r restartfile datafile
+See the header of dump2vtk.cpp for more details.

-is the same as running a 2-line input script:
-
-read_restart restartfile
-write_data datafile
-
-which will produce the same data file that the restart2data tool used
-to create.  The following information is included in case you have an
-older version of LAMMPS which still includes the restart2data tool.
-
-The file restart2data.cpp converts a binary LAMMPS restart file into
-an ASCII data file.  The syntax for running the tool is
-
-restart2data restart-file data-file (input-file) :pre
-
-Input-file is optional and if specified will contain LAMMPS input
-commands for the masses and force field parameters, instead of putting
-those in the data-file.  Only a few force field styles currently
-support this option.
-
-This tool must be compiled on a platform that can read the binary file
-created by a LAMMPS run, since binary files are not compatible across
-all platforms.
-
-Note that a text data file has less precision than a binary restart
-file.  Hence, continuing a run from a converted data file will
-typically not conform as closely to a previous run as will restarting
-from a binary restart file.
-
-If a "%" appears in the specified restart-file, the tool expects a set
-of multiple files to exist.  See the "restart"_restart.html and
-"write_restart"_write_restart.html commands for info on how such sets
-of files are written by LAMMPS, and how the files are named.
+This tool was written by the USER-SMD package author, Georg
+Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics,
+Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).

 :line

@ -537,32 +495,3 @@ See the README file for details.

 These files were provided by Vikas Varshney (vv0210 at gmail.com)

-:line
-
-xmovie tool :h4,link(xmovie)
-
-The xmovie tool is an X-based visualization package that can read
-LAMMPS dump files and animate them.  It is in its own sub-directory
-with the tools directory.  You may need to modify its Makefile so that
-it can find the appropriate X libraries to link against.
-
-The syntax for running xmovie is
-
-xmovie \[options\] dump.file1 dump.file2 ... :pre
-
-If you just type "xmovie" you will see a list of options.  Note that
-by default, LAMMPS dump files are in scaled coordinates, so you
-typically need to use the -scale option with xmovie.  When xmovie runs
-it opens a visualization window and a control window.  The control
-options are straightforward to use.
-
-Xmovie was mostly written by Mike Uttormark (U Wisconsin) while he
-spent a summer at Sandia.  It displays 2d projections of a 3d domain.
-While simple in design, it is an amazingly fast program that can
-render large numbers of atoms very quickly.  It's a useful tool for
-debugging LAMMPS input and output and making sure your simulation is
-doing what you think it should.  The animations on the Examples page
-of the "LAMMPS WWW site"_lws were created with xmovie.
-
-I've lost contact with Mike, so I hope he's comfortable with us
-distributing his great tool!
--- a/doc/src/accelerate_intel.txt
+++ b/doc/src/accelerate_intel.txt
@ -464,7 +464,7 @@ supported.

 [References:]

-Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., “Optimizing Classical Molecular Dynamics in LAMMPS,” in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l
+Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l

 Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. 2016 International Conference for High Performance Computing. In press. :l

--- a/doc/src/angle_dipole.txt
+++ b/doc/src/angle_dipole.txt
@ -41,7 +41,7 @@ angle.

 The torque on the dipole can be obtained by differentiating the
 potential using the 'chain rule' as in appendix C.3 of
-"(Allen)"_#Allen:
+"(Allen)"_#Allen1:

 :c,image(Eqs/angle_dipole_torque.jpg)

@ -121,6 +121,6 @@ This angle style should not be used with SHAKE.
 [(Orsi)] Orsi & Essex, The ELBA force field for coarse-grain modeling of
 lipid membranes, PloS ONE 6(12): e28637, 2011.

-:link(Allen)
+:link(Allen1)
 [(Allen)] Allen & Tildesley, Computer Simulation of Liquids,
 Clarendon Press, Oxford, 1987.
--- a/doc/src/atom_style.txt
+++ b/doc/src/atom_style.txt
@ -110,7 +110,12 @@ basis.
 For the {sphere} style, the particles are spheres and each stores a
 per-particle diameter and mass.  If the diameter > 0.0, the particle
 is a finite-size sphere.  If the diameter = 0.0, it is a point
-particle.
+particle.  Note that by use of the {disc} keyword with the "fix
+nve/sphere"_fix_nve_sphere.html, "fix nvt/sphere"_fix_nvt_sphere.html,
+"fix nph/sphere"_fix_nph_sphere.html, "fix
+npt/sphere"_fix_npt_sphere.html commands, spheres can be effectively
+treated as 2d discs for a 2d simulation if desired.  See also the "set
+density/disc"_set.html command.

 For the {ellipsoid} style, the particles are ellipsoids and each
 stores a flag which indicates whether it is a finite-size ellipsoid or
--- a/doc/src/balance.txt
+++ b/doc/src/balance.txt
@ -286,24 +286,32 @@ above.  It performs a recursive coordinate bisectioning (RCB) of the
 simulation domain. The basic idea is as follows.

 The simulation domain is cut into 2 boxes by an axis-aligned cut in
-the longest dimension, leaving one new box on either side of the cut.
-All the processors are also partitioned into 2 groups, half assigned
-to the box on the lower side of the cut, and half to the box on the
-upper side.  (If the processor count is odd, one side gets an extra
-processor.)  The cut is positioned so that the number of particles in
-the lower box is exactly the number that the processors assigned to
-that box should own for load balance to be perfect.  This also makes
-load balance for the upper box perfect.  The positioning is done
-iteratively, by a bisectioning method.  Note that counting particles
-on either side of the cut requires communication between all
-processors at each iteration.
+one of the dimensions, leaving one new sub-box on either side of the
+cut.  Which dimension is chosen for the cut depends on the particle
+(weight) distribution within the parent box.  Normally the longest
+dimension of the box is cut, but if all (or most) of the particles are
+at one end of the box, a cut may be performed in another dimension to
+induce sub-boxes that are more cube-ish (3d) or square-ish (2d) in
+shape.
+
+After the cut is made, all the processors are also partitioned into 2
+groups, half assigned to the box on the lower side of the cut, and
+half to the box on the upper side.  (If the processor count is odd,
+one side gets an extra processor.)  The cut is positioned so that the
+number of (weighted) particles in the lower box is exactly the number
+that the processors assigned to that box should own for load balance
+to be perfect.  This also makes load balance for the upper box
+perfect.  The positioning of the cut is done iteratively, by a
+bisectioning method (median search).  Note that counting particles on
+either side of the cut requires communication between all processors
+at each iteration.

 That is the procedure for the first cut.  Subsequent cuts are made
 recursively, in exactly the same manner.  The subset of processors
-assigned to each box make a new cut in the longest dimension of that
-box, splitting the box, the subset of processors, and the particles
-in the box in two.  The recursion continues until every processor is
-assigned a sub-box of the entire simulation domain, and owns the
+assigned to each box make a new cut in one dimension of that box,
+splitting the box, the subset of processors, and the particles in the
+box in two.  The recursion continues until every processor is assigned
+a sub-box of the entire simulation domain, and owns the (weighted)
 particles in that sub-box.

 :line
--- a/doc/src/bond_oxdna.txt
+++ b/doc/src/bond_oxdna.txt
@ -7,19 +7,24 @@
 :line

 bond_style oxdna/fene command :h3
+bond_style oxdna2/fene command :h3

 [Syntax:]

 bond_style oxdna/fene :pre
+bond_style oxdna2/fene :pre

 [Examples:]

 bond_style oxdna/fene
 bond_coeff * 2.0 0.25 0.7525 :pre

+bond_style oxdna2/fene
+bond_coeff * 2.0 0.25 0.7564 :pre
+
 [Description:]

-The {oxdna/fene} bond style uses the potential
+The {oxdna/fene} and {oxdna2/fene} bond styles use the potential

 :c,image(Eqs/bond_oxdna_fene.jpg)

@ -36,13 +41,16 @@ epsilon (energy)
 Delta (distance)
 r0 (distance) :ul

-NOTE: This bond style has to be used together with the corresponding oxDNA pair styles
+NOTE: The oxDNA bond style has to be used together with the corresponding oxDNA pair styles
 for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
 and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of 
-"pair_style oxdna/excv"_pair_oxdna.html). The coefficients 
+"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair 
+style {oxdna2/dh} have to be defined.
+
+The coefficients 
 in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.

-Example input and data files can be found in examples/USER/cgdna/examples/duplex1/ and /duplex2/.
+Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
 A simple python setup tool which creates single straight or helical DNA strands,
 DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
 A technical report with more information on the model, the structure of the input file,
@ -60,7 +68,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]

-"pair_style oxdna/excv"_pair_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html 
+"pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html 

 [Default:] none

@ -68,3 +76,6 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.

 :link(oxdna_fene)
 [(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
+
+:link(oxdna2)
+[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
--- a/doc/src/bonds.txt
+++ b/doc/src/bonds.txt
@ -16,6 +16,7 @@ Bond Styles :h1
   bond_none
   bond_nonlinear
   bond_oxdna
+   bond_oxdna2
   bond_quartic
   bond_table
   bond_zero
--- a/doc/src/change_box.txt
+++ b/doc/src/change_box.txt
@ -101,11 +101,11 @@ Instead you could do something like this, assuming the simulation box
 is non-periodic and atoms extend from 0 to 20 in all dimensions:

 change_box all x final -10 20
-create_atoms 1 single -5 5 5   # this will fail to insert an atom :pre
+create_atoms 1 single -5 5 5       # this will fail to insert an atom :pre

 change_box all x final -10 20 boundary f s s
 create_atoms 1 single -5 5 5
-change_box boundary s s s      # this will work :pre
+change_box all boundary s s s      # this will work :pre

 NOTE: Unlike the earlier "displace_box" version of this command, atom
 remapping is NOT performed by default.  This command allows remapping
--- a/doc/src/compute_chunk_atom.txt
+++ b/doc/src/compute_chunk_atom.txt
@ -148,7 +148,9 @@ described further below where the keywords are discussed.
 The {binning} styles perform a spatial binning of atoms, and assign an
 atom the chunk ID corresponding to the bin number it is in.  {Nchunk}
 is set to the number of bins, which can change if the simulation box
-size changes.
+size changes.  This also depends on the setting of the {units}
+keyword; e.g. for {reduced} units the number of chunks may not change
+even if the box size does.

 The {bin/1d}, {bin/2d}, and {bin/3d} styles define bins as 1d layers
 (slabs), 2d pencils, or 3d boxes.  The {dim}, {origin}, and {delta}
--- a/doc/src/compute_coord_atom.txt
+++ b/doc/src/compute_coord_atom.txt
@ -64,7 +64,7 @@ defined by the orientational order parameter calculated by the
 "compute orientorder/atom"_compute_orientorder_atom.html command.
 This {cstyle} thus allows one to apply the ten Wolde's criterion to
 identify crystal-like atoms in a system, as discussed in "ten
-Wolde"_#tenWolde.
+Wolde"_#tenWolde1.

 The ID of the previously specified "compute
 orientorder/atom"_compute_orientorder/atom command is specified as
@ -127,6 +127,6 @@ explained above.

 :line

-:link(tenWolde)
+:link(tenWolde1)
 [(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
 J. Chem. Phys. 104, 9932 (1996).
--- a/doc/src/compute_dpd.txt
+++ b/doc/src/compute_dpd.txt
@ -64,7 +64,7 @@ command.

 :line

-:link(Larentzos)
+:link(Larentzos1)
 [(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and
 W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
 Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
--- a/doc/src/compute_dpd_atom.txt
+++ b/doc/src/compute_dpd_atom.txt
@ -59,7 +59,7 @@ command.

 :line

-:link(Larentzos)
+:link(Larentzos2)
 [(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and
 W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
 Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
--- a/doc/src/compute_modify.txt
+++ b/doc/src/compute_modify.txt
@ -14,27 +14,29 @@ compute_modify compute-ID keyword value ... :pre

 compute-ID = ID of the compute to modify :ulb,l
 one or more keyword/value pairs may be listed :l
-keyword = {extra} or {dynamic} :l
-  {extra} value = N
+keyword = {extra/dof} or {extra} or {dynamic/dof} or {dynamic} :l
+  {extra/dof} value = N
    N = # of extra degrees of freedom to subtract
-  {dynamic} value = {yes} or {no}
-    yes/no = do or do not recompute the number of atoms contributing to the temperature :pre
+  {extra} syntax is identical to {extra/dof}, will be disabled at some point
+  {dynamic/dof} value = {yes} or {no}
+    yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature
+  {dynamic} syntax is identical to {dynamic/dof}, will be disabled at some point :pre
 :ule

 [Examples:]

-compute_modify myTemp extra 0
-compute_modify newtemp dynamic yes extra 600 :pre
+compute_modify myTemp extra/dof 0
+compute_modify newtemp dynamic/dof yes extra/dof 600 :pre

 [Description:]

 Modify one or more parameters of a previously defined compute.  Not
 all compute styles support all parameters.

-The {extra} keyword refers to how many degrees-of-freedom are
-subtracted (typically from 3N) as a normalizing factor in a
-temperature computation.  Only computes that compute a temperature use
-this option.  The default is 2 or 3 for "2d or 3d
+The {extra/dof} or {extra} keyword refers to how many
+degrees-of-freedom are subtracted (typically from 3N) as a normalizing
+factor in a temperature computation.  Only computes that compute a
+temperature use this option.  The default is 2 or 3 for "2d or 3d
 systems"_dimension.html which is a correction factor for an ensemble
 of velocities with zero total linear momentum. For compute
 temp/partial, if one or more velocity components are excluded, the
@ -43,14 +45,21 @@ number for the {extra} parameter if you need to add
 degrees-of-freedom.  See the "compute
 temp/asphere"_compute_temp_asphere.html command for an example.

-The {dynamic} keyword determines whether the number of atoms N in the
-compute group is re-computed each time a temperature is computed.
-Only compute styles that calculate a temperature use this option.  By
-default, N is assumed to be constant.  If you are adding atoms to the
-system (see the "fix pour"_fix_pour.html or "fix
-deposit"_fix_deposit.html commands) or expect atoms to be lost
-(e.g. due to evaporation), then this option should be used to insure
-the temperature is correctly normalized.
+The {dynamic/dof} or {dynamic} keyword determines whether the number
+of atoms N in the compute group and their associated degrees of
+freedom are re-computed each time a temperature is computed.  Only
+compute styles that calculate a temperature use this option.  By
+default, N and their DOF are assumed to be constant.  If you are
+adding atoms or molecules to the system (see the "fix
+pour"_fix_pour.html, "fix deposit"_fix_deposit.html, and "fix
+gcmc"_fix_gcmc.html commands) or expect atoms or molecules to be lost
+(e.g. due to exiting the simulation box or via "fix
+evaporate"_fix_evaporate.html), then this option should be used to
+insure the temperature is correctly normalized.
+
+NOTE: The {extra} and {dynamic} keywords should not be used as they
+are deprecated (March 2017) and will eventually be disabled.  Instead,
+use the equivalent {extra/dof} and {dynamic/dof} keywords.

 [Restrictions:] none

@ -60,5 +69,5 @@ the temperature is correctly normalized.

 [Default:]

-The option defaults are extra = 2 or 3 for 2d or 3d systems and
-dynamic = no.
+The option defaults are extra/dof = 2 or 3 for 2d or 3d systems and
+dynamic/dof = no.
--- a/doc/src/compute_orientorder_atom.txt
+++ b/doc/src/compute_orientorder_atom.txt
@ -78,7 +78,7 @@ normalized complex vector {Ybar_lm} of degree {ldegree}, which must be
 explicitly included in the keyword {degrees}. This option can be used
 in conjunction with "compute coord_atom"_compute_coord_atom.html to
 calculate the ten Wolde's criterion to identify crystal-like
-particles, as discussed in "ten Wolde"_#tenWolde.
+particles, as discussed in "ten Wolde"_#tenWolde2.

 The value of {Ql} is set to zero for atoms not in the
 specified compute group, as well as for atoms that have less than
@ -143,6 +143,6 @@ Phys. Rev. B 28, 784 (1983).
 [(Mickel)] W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke,
 J. Chem. Phys. 138, 044501 (2013).

-:link(tenWolde)
+:link(tenWolde2)
 [(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
 J. Chem. Phys. 104, 9932 (1996).
--- a/doc/src/compute_pe_atom.txt
+++ b/doc/src/compute_pe_atom.txt
@ -49,7 +49,7 @@ pairwise interactions between 1-4 atoms.  The energy contribution of
 these terms is included in the pair energy, not the dihedral energy.

 The KSpace contribution is calculated using the method in
-"(Heyes)"_#Heyes for the Ewald method and a related method for PPPM,
+"(Heyes)"_#Heyes1 for the Ewald method and a related method for PPPM,
 as specified by the "kspace_style pppm"_kspace_style.html command.
 For PPPM, the calculation requires 1 extra FFT each timestep that
 per-atom energy is calculated.  This "document"_PDF/kspace.pdf
@ -97,5 +97,5 @@ stress/atom"_compute_stress_atom.html

 :line

-:link(Heyes)
+:link(Heyes1)
 [(Heyes)] Heyes, Phys Rev B 49, 755 (1994),
--- a/doc/src/compute_pressure.txt
+++ b/doc/src/compute_pressure.txt
@ -70,7 +70,7 @@ means include all terms except the kinetic energy {ke}.
 Details of how LAMMPS computes the virial efficiently for the entire
 system, including for manybody potentials and accounting for the
 effects of periodic boundary conditions are discussed in
-"(Thompson)"_#Thompson.
+"(Thompson)"_#Thompson1.

 The temperature and kinetic energy tensor is not calculated by this
 compute, but rather by the temperature compute specified with the
@ -150,5 +150,5 @@ stress/atom"_compute_stress_atom.html,

 :line

-:link(Thompson)
+:link(Thompson1)
 [(Thompson)] Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009).
--- a/doc/src/compute_sna_atom.txt
+++ b/doc/src/compute_sna_atom.txt
@ -24,7 +24,7 @@ twojmax = band limit for bispectrum components (non-negative integer) :l
 R_1, R_2,... = list of cutoff radii, one for each type (distance units) :l
 w_1, w_2,... = list of neighbor weights, one for each type  :l
 zero or more keyword/value pairs may be appended :l
-keyword = {diagonal} or {rmin0} or {switchflag} :l
+keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} :l
  {diagonal} value = {0} or {1} or {2} or {3}
     {0} = all j1, j2, j <= twojmax, j2 <= j1
     {1} = subset satisfying j1 == j2
@ -33,7 +33,10 @@ keyword = {diagonal} or {rmin0} or {switchflag} :l
  {rmin0} value = parameter in distance to angle conversion (distance units)
  {switchflag} value = {0} or {1}
     {0} = do not use switching function
-     {1} = use switching function :pre
+     {1} = use switching function
+  {bzeroflag} value = {0} or {1}
+     {0} = do not subtract B0
+     {1} = subtract B0 :pre
 :ule

 [Examples:]
@ -50,12 +53,12 @@ for each atom in a group.
 Bispectrum components of an atom are order parameters characterizing
 the radial and angular distribution of neighbor atoms. The detailed
 mathematical definition is given in the paper by Thompson et
-al. "(Thompson)"_#Thompson2014
+al. "(Thompson)"_#Thompson20141

 The position of a neighbor atom {i'} relative to a central atom {i} is
 a point within the 3D ball of radius {R_ii' = rcutfac*(R_i + R_i')}

-Bartok et al. "(Bartok)"_#Bartok2010, proposed mapping this 3D ball
+Bartok et al. "(Bartok)"_#Bartok20101, proposed mapping this 3D ball
 onto the 3-sphere, the surface of the unit ball in a four-dimensional
 space.  The radial distance {r} within {R_ii'} is mapped on to a third
 polar angle {theta0} defined by,
@ -92,7 +95,7 @@ The expansion coefficients {u^j_m,m'} are complex-valued and they are
 not directly useful as descriptors, because they are not invariant
 under rotation of the polar coordinate frame. However, the following
 scalar triple products of expansion coefficients can be shown to be
-real-valued and invariant under rotation "(Bartok)"_#Bartok2010.
+real-valued and invariant under rotation "(Bartok)"_#Bartok20101.

 :c,image(Eqs/compute_sna_atom3.jpg)

@ -153,6 +156,12 @@ ordered in which they are listed
 The keyword {switchflag} can be used to turn off the switching
 function.

+The keyword {bzeroflag} determines whether or not {B0}, the bispectrum
+components of an atom with no neighbors, are subtracted from
+the calculated bispectrum components. This optional keyword is only
+available for compute {sna/atom}, as {snad/atom} and {snav/atom}
+are unaffected by the removal of constant terms.
+
 NOTE: If you have a bonded system, then the settings of
 "special_bonds"_special_bonds.html command can remove pairwise
 interactions between atoms in the same bond, angle, or dihedral.  This
@ -222,15 +231,15 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 [Default:]

 The optional keyword defaults are {diagonal} = 0, {rmin0} = 0,
-{switchflag} = 1.
+{switchflag} = 1, {bzeroflag} = 0.

 :line

-:link(Thompson2014)
+:link(Thompson20141)
 [(Thompson)] Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint
 available at "arXiv:1409.3880"_http://arxiv.org/abs/1409.3880

-:link(Bartok2010)
+:link(Bartok20101)
 [(Bartok)] Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).

 :link(Meremianin2006)
--- a/doc/src/compute_stress_atom.txt
+++ b/doc/src/compute_stress_atom.txt
@ -74,7 +74,7 @@ other atoms in the simulation, not just with other atoms in the group.

 Details of how LAMMPS computes the virial for individual atoms for
 either pairwise or manybody potentials, and including the effects of
-periodic boundary conditions is discussed in "(Thompson)"_#Thompson.
+periodic boundary conditions is discussed in "(Thompson)"_#Thompson2.
 The basic idea for manybody potentials is to treat each component of
 the force computation between a small cluster of atoms in the same
 manner as in the formula above for bond, angle, dihedral, etc
@ -89,8 +89,8 @@ pairwise interactions between 1-4 atoms.  The virial contribution of
 these terms is included in the pair virial, not the dihedral virial.

 The KSpace contribution is calculated using the method in
-"(Heyes)"_#Heyes for the Ewald method and by the methodology described
-in "(Sirk)"_#Sirk for PPPM.  The choice of KSpace solver is specified
+"(Heyes)"_#Heyes2 for the Ewald method and by the methodology described
+in "(Sirk)"_#Sirk1 for PPPM.  The choice of KSpace solver is specified
 by the "kspace_style pppm"_kspace_style.html command.  Note that for
 PPPM, the calculation requires 6 extra FFTs each timestep that
 per-atom stress is calculated.  Thus it can significantly increase the
@ -159,11 +159,11 @@ The per-atom array values will be in pressure*volume

 :line

-:link(Heyes)
+:link(Heyes2)
 [(Heyes)] Heyes, Phys Rev B 49, 755 (1994),

-:link(Sirk)
+:link(Sirk1)
 [(Sirk)] Sirk, Moore, Brown, J Chem Phys, 138, 064505 (2013).

-:link(Thompson)
+:link(Thompson2)
 [(Thompson)] Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009).
--- a/doc/src/compute_temp_cs.txt
+++ b/doc/src/compute_temp_cs.txt
@ -27,7 +27,7 @@ compute core_shells all temp/cs cores shells :pre
 Define a computation that calculates the temperature of a system based
 on the center-of-mass velocity of atom pairs that are bonded to each
 other.  This compute is designed to be used with the adiabatic
-core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham.  See
+core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham1.  See
 "Section 6.25"_Section_howto.html#howto_25 of the manual for an
 overview of the model as implemented in LAMMPS.  Specifically, this
 compute enables correct temperature calculation and thermostatting of
@ -114,6 +114,6 @@ temp/chunk"_compute_temp_chunk.html

 :line

-:link(MitchellFinchham)
+:link(MitchellFinchham1)
 [(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter,
 5, 1031-1038 (1993).
--- a/doc/src/compute_temp_profile.txt
+++ b/doc/src/compute_temp_profile.txt
@ -43,7 +43,7 @@ atoms, after subtracting out a spatially-averaged center-of-mass
 velocity field, before computing the kinetic energy.  This can be
 useful for thermostatting a collection of atoms undergoing a complex
 flow, e.g. via a profile-unbiased thermostat (PUT) as described in
-"(Evans)"_#Evans.  A compute of this style can be used by any command
+"(Evans)"_#Evans1.  A compute of this style can be used by any command
 that computes a temperature, e.g. "thermo_modify"_thermo_modify.html,
 "fix temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc.

@ -75,7 +75,7 @@ atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the
 simulation, N = number of atoms in the group, k = Boltzmann constant,
 and T = temperature.  The dim*Nx*Ny*Nz term are degrees of freedom
 subtracted to adjust for the removal of the center-of-mass velocity in
-each of Nx*Ny*Nz bins, as discussed in the "(Evans)"_#Evans paper.
+each of Nx*Ny*Nz bins, as discussed in the "(Evans)"_#Evans1 paper.

 If the {out} keyword is used with a {tensor} value, which is the
 default, a kinetic energy tensor, stored as a 6-element vector, is
@ -126,7 +126,7 @@ See "this howto section"_Section_howto.html#howto_16 of the manual for
 a discussion of different ways to compute temperature and perform
 thermostatting.  Using this compute in conjunction with a
 thermostatting fix, as explained there, will effectively implement a
-profile-unbiased thermostat (PUT), as described in "(Evans)"_#Evans.
+profile-unbiased thermostat (PUT), as described in "(Evans)"_#Evans1.

 [Output info:]

@ -178,5 +178,5 @@ The option default is out = tensor.

 :line

-:link(Evans)
+:link(Evans1)
 [(Evans)] Evans and Morriss, Phys Rev Lett, 56, 2172-2175 (1986).
--- a/doc/src/create_atoms.txt
+++ b/doc/src/create_atoms.txt
@ -134,6 +134,17 @@ not overlap existing atoms inappropriately, especially if molecules
 are being added.  The "delete_atoms"_delete_atoms.html command can be
 used to remove overlapping atoms or molecules.

+NOTE: You cannot use any of the styles explained above to create atoms
+that are outside the simulation box; they will just be ignored by
+LAMMPS.  This is true even if you are using shrink-wrapped box
+boundaries, as specified by the "boundary"_boundary.html command.
+However, you can first use the "change_box"_change_box.html command to
+temporarily expand the box, then add atoms via create_atoms, then
+finally use change_box command again if needed to re-shrink-wrap the
+new atoms.  See the "change_box"_change_box.html doc page for an
+example of how to do this, using the create_atoms {single} style to
+insert a new atom outside the current simulation box.
+
 :line

 Individual atoms are inserted by this command, unless the {mol}
--- a/doc/src/dihedral_charmm.txt
+++ b/doc/src/dihedral_charmm.txt
@ -10,21 +10,25 @@ dihedral_style charmm command :h3
 dihedral_style charmm/intel command :h3
 dihedral_style charmm/kk command :h3
 dihedral_style charmm/omp command :h3
+dihedral_style charmmfsh command :h3

 [Syntax:]

-dihedral_style charmm :pre
+dihedral_style style :pre
+
+style = {charmm} or {charmmfsh} :ul

 [Examples:]

 dihedral_style charmm
+dihedral_style charmmfsh
 dihedral_coeff  1 0.2 1 180 1.0
 dihedral_coeff  2 1.8 1   0 1.0
 dihedral_coeff  1 3.1 2 180 0.5 :pre

 [Description:]

-The {charmm} dihedral style uses the potential
+The {charmm} and {charmmfsh} dihedral styles use the potential

 :c,image(Eqs/dihedral_charmm.jpg)

@ -34,6 +38,14 @@ field (see comment on weighting factors below).  See
 "(Cornell)"_#dihedral-Cornell for a description of the AMBER force
 field.

+NOTE: The newer {charmmfsh} style was released in March 2017.  We
+recommend it be used instead of the older {charmm} style when running
+a simulation with the CHARMM force field and Coulomb cutoffs, via the
+"pair_style lj/charmmfsw/coul/charmmfsh"_pair_charmm.html command.
+Otherwise the older {charmm} style is fine to use.  See the discussion
+below and more details on the "pair_style charmm"_pair_charmm.html doc
+page.
+
 The following coefficients must be defined for each dihedral type via the
 "dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
 the data file or restart files read by the "read_data"_read_data.html
@ -73,13 +85,28 @@ special_bonds 1-4 scaling factor to 0.0 (which is the
 default). Otherwise 1-4 non-bonded interactions in dihedrals will be
 computed twice.

-Also note that for AMBER force fields, which use pair styles with
-"lj/cut", the special_bonds 1-4 scaling factor should be set to the
-AMBER defaults (1/2 and 5/6) and all the dihedral weighting factors
-(4th coeff above) must be set to 0.0. In this case, you can use any
-pair style you wish, since the dihedral does not need any
-Lennard-Jones parameter information and will not compute any 1-4
-non-bonded interactions.
+For simulations using the CHARMM force field with a Coulomb cutoff,
+the difference between the {charmm} and {charmmfsh} styles is in the
+computation of the 1-4 non-bond interactions, though only if the
+distance between the two atoms is within the switching region of the
+pairwise potential defined by the corresponding CHARMM pair style,
+i.e. within the outer cutoff specified for the pair style.  The
+{charmmfsh} style should only be used when using the "pair_style
+lj/charmmfsw/coul/charmmfsh"_pair_charmm.html to make the Coulombic
+pairwise calculations consistent.  Use the {charmm} style with
+long-range Coulombics or the older "pair_style
+lj/charmm/coul/charmm"_pair_charmm.html command.  See the discussion
+on the "CHARMM pair_style"_pair_charmm.html doc page for details.
+
+Note that for AMBER force fields, which use pair styles with "lj/cut",
+the special_bonds 1-4 scaling factor should be set to the AMBER
+defaults (1/2 and 5/6) and all the dihedral weighting factors (4th
+coeff above) must be set to 0.0. In this case, you can use any pair
+style you wish, since the dihedral does not need any Lennard-Jones
+parameter information and will not compute any 1-4 non-bonded
+interactions.  Likewise the {charmm} or {charmmfsh} styles are
+identical in this case since no 1-4 non-bonded interactions are
+computed.

 :line

--- a/doc/src/dump.txt
+++ b/doc/src/dump.txt
@ -331,10 +331,7 @@ bonds and colors.

 Note that {atom}, {custom}, {dcd}, {xtc}, and {xyz} style dump files
 can be read directly by "VMD"_http://www.ks.uiuc.edu/Research/vmd, a
-popular molecular viewing program.  See
-"Section 9"_Section_tools.html#vmd of the manual and the
-tools/lmp2vmd/README.txt file for more information about support in
-VMD for reading and visualizing LAMMPS dump files.
+popular molecular viewing program.

 :line

--- a/doc/src/dump_custom_vtk.txt
+++ b/doc/src/dump_custom_vtk.txt
@ -26,7 +26,6 @@ args = list of arguments for a particular style :l
                          q, mux, muy, muz, mu,
                          radius, diameter, omegax, omegay, omegaz,
                          angmomx, angmomy, angmomz, tqx, tqy, tqz,
-                          spin, eradius, ervel, erforce,
                          c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre

      id = atom ID
@ -51,17 +50,18 @@ args = list of arguments for a particular style :l
      angmomx,angmomy,angmomz = angular momentum of aspherical particle
      tqx,tqy,tqz = torque on finite-size particles
      c_ID = per-atom vector calculated by a compute with ID
-      c_ID\[N\] = Nth column of per-atom array calculated by a compute with ID
+      c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
      f_ID = per-atom vector calculated by a fix with ID
-      f_ID\[N\] = Nth column of per-atom array calculated by a fix with ID
-      v_name = per-atom vector calculated by an atom-style variable with name :pre
+      f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
+      v_name = per-atom vector calculated by an atom-style variable with name
+      d_name = per-atom floating point vector with name, managed by fix property/atom
+      i_name = per-atom integer vector with name, managed by fix property/atom :pre
 :ule

 [Examples:]

 dump dmpvtk all custom/vtk 100 dump*.myforce.vtk id type vx fx
-dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD\[1\] c_myD\[2\] c_myD\[3\] v_ke
-dump e_data all custom/vtk 100 dump*.vtu id type spin eradius fx fy fz eforce :pre
+dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD\[1\] c_myD\[2\] c_myD\[3\] v_ke :pre

 The style {custom/vtk} is similar to the "custom"_dump.html style but
 uses the VTK library to write data to VTK simple legacy or XML format
@ -199,32 +199,38 @@ part of the {custom/vtk} style.
 The {id}, {mol}, {proc}, {procp1}, {type}, {element}, {mass}, {vx},
 {vy}, {vz}, {fx}, {fy}, {fz}, {q} attributes are self-explanatory.

-{id} is the atom ID.  {mol} is the molecule ID, included in the data
-file for molecular systems.  {type} is the atom type.  {element} is
-typically the chemical name of an element, which you must assign to
-each type via the "dump_modify element"_dump_modify.html command.
-More generally, it can be any string you wish to associate with an
-atom type.  {mass} is the atom mass.  {vx}, {vy}, {vz}, {fx}, {fy},
-{fz}, and {q} are components of atom velocity and force and atomic
-charge.
+{Id} is the atom ID.  {Mol} is the molecule ID, included in the data
+file for molecular systems.  {Proc} is the ID of the processor (0 to
+Nprocs-1) that currently owns the atom.  {Procp1} is the proc ID+1,
+which can be convenient in place of a {type} attribute (1 to Ntypes)
+for coloring atoms in a visualization program.  {Type} is the atom
+type (1 to Ntypes).  {Element} is typically the chemical name of an
+element, which you must assign to each type via the "dump_modify
+element"_dump_modify.html command.  More generally, it can be any
+string you wish to associated with an atom type.  {Mass} is the atom
+mass.  {Vx}, {vy}, {vz}, {fx}, {fy}, {fz}, and {q} are components of
+atom velocity and force and atomic charge.

 There are several options for outputting atom coordinates.  The {x},
-{y}, {z} attributes are used to write atom coordinates "unscaled", in
-the appropriate distance "units"_units.html (Angstroms, sigma, etc).
-Additionally, you can use {xs}, {ys}, {zs} if you want to also save the
-coordinates "scaled" to the box size, so that each value is 0.0 to
-1.0.  If the simulation box is triclinic (tilted), then all atom
-coords will still be between 0.0 and 1.0.  Use {xu}, {yu}, {zu} if you
-want the coordinates "unwrapped" by the image flags for each atom.
-Unwrapped means that if the atom has passed through a periodic
-boundary one or more times, the value is printed for what the
-coordinate would be if it had not been wrapped back into the periodic
-box.  Note that using {xu}, {yu}, {zu} means that the coordinate
-values may be far outside the box bounds printed with the snapshot.
-Using {xsu}, {ysu}, {zsu} is similar to using {xu}, {yu}, {zu}, except
-that the unwrapped coordinates are scaled by the box size. Atoms that
-have passed through a periodic boundary will have the corresponding
-coordinate increased or decreased by 1.0.
+{y}, {z} attributes write atom coordinates "unscaled", in the
+appropriate distance "units"_units.html (Angstroms, sigma, etc).  Use
+{xs}, {ys}, {zs} if you want the coordinates "scaled" to the box size,
+so that each value is 0.0 to 1.0.  If the simulation box is triclinic
+(tilted), then all atom coords will still be between 0.0 and 1.0.
+I.e. actual unscaled (x,y,z) = xs*A + ys*B + zs*C, where (A,B,C) are
+the non-orthogonal vectors of the simulation box edges, as discussed
+in "Section 6.12"_Section_howto.html#howto_12.
+
+Use {xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the
+image flags for each atom.  Unwrapped means that if the atom has
+passed thru a periodic boundary one or more times, the value is
+printed for what the coordinate would be if it had not been wrapped
+back into the periodic box.  Note that using {xu}, {yu}, {zu} means
+that the coordinate values may be far outside the box bounds printed
+with the snapshot.  Using {xsu}, {ysu}, {zsu} is similar to using
+{xu}, {yu}, {zu}, except that the unwrapped coordinates are scaled by
+the box size. Atoms that have passed through a periodic boundary will
+have the corresponding coordinate increased or decreased by 1.0.

 The image flags can be printed directly using the {ix}, {iy}, {iz}
 attributes.  For periodic dimensions, they specify which image of the
@ -255,13 +261,7 @@ The {tqx}, {tqy}, {tqz} attributes are for finite-size particles that
 can sustain a rotational torque due to interactions with other
 particles.

-The {spin}, {eradius}, {ervel}, and {erforce} attributes are for
-particles that represent nuclei and electrons modeled with the
-electronic force field (EFF).  See "atom_style
-electron"_atom_style.html and "pair_style eff"_pair_eff.html for more
-details.
-
-The {c_ID} and {c_ID\[N\]} attributes allow per-atom vectors or arrays
+The {c_ID} and {c_ID\[I\]} attributes allow per-atom vectors or arrays
 calculated by a "compute"_compute.html to be output.  The ID in the
 attribute should be replaced by the actual ID of the compute that has
 been defined previously in the input script.  See the
@ -275,12 +275,14 @@ command.  Instead, global quantities can be output by the
 "thermo_style custom"_thermo_style.html command, and local quantities
 can be output by the dump local command.

-If {c_ID} is used as an attribute, then the per-atom vector calculated
-by the compute is printed.  If {c_ID\[N\]} is used, then N must be in
-the range from 1-M, which will print the Nth column of the M-length
-per-atom array calculated by the compute.
+If {c_ID} is used as a attribute, then the per-atom vector calculated
+by the compute is printed.  If {c_ID\[I\]} is used, then I must be in
+the range from 1-M, which will print the Ith column of the per-atom
+array with M columns calculated by the compute.  See the discussion
+above for how I can be specified with a wildcard asterisk to
+effectively specify multiple values.

-The {f_ID} and {f_ID\[N\]} attributes allow vector or array per-atom
+The {f_ID} and {f_ID\[I\]} attributes allow vector or array per-atom
 quantities calculated by a "fix"_fix.html to be output.  The ID in the
 attribute should be replaced by the actual ID of the fix that has been
 defined previously in the input script.  The "fix
@ -291,9 +293,11 @@ any "compute"_compute.html, "fix"_fix.html, or atom-style
 be written to a dump file.

 If {f_ID} is used as a attribute, then the per-atom vector calculated
-by the fix is printed.  If {f_ID\[N\]} is used, then N must be in the
-range from 1-M, which will print the Nth column of the M-length
-per-atom array calculated by the fix.
+by the fix is printed.  If {f_ID\[I\]} is used, then I must be in the
+range from 1-M, which will print the Ith column of the per-atom array
+with M columns calculated by the fix.  See the discussion above for
+how I can be specified with a wildcard asterisk to effectively specify
+multiple values.

 The {v_name} attribute allows per-atom vectors calculated by a
 "variable"_variable.html to be output.  The name in the attribute
@ -306,6 +310,10 @@ invoke other computes, fixes, or variables when they are evaluated, so
 this is a very general means of creating quantities to output to a
 dump file.

+The {d_name} and {i_name} attributes allow to output custom per atom
+floating point or integer properties that are managed by
+"fix property/atom"_fix_property_atom.html.
+
 See "Section 10"_Section_modify.html of the manual for information
 on how to add new compute and fix styles to LAMMPS to calculate
 per-atom quantities which could then be output into dump files.
--- a/doc/src/dump_molfile.txt
+++ b/doc/src/dump_molfile.txt
@ -34,10 +34,7 @@ to one or more files every N timesteps in one of several formats.
 Only information for atoms in the specified group is dumped.  This
 specific dump style uses molfile plugins that are bundled with the
 "VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and
-analysis program.  See "Section 9"_Section_tools.html#vmd of the
-manual and the tools/lmp2vmd/README.txt file for more information
-about support in VMD for reading and visualizing native LAMMPS dump
-files.
+analysis program.

 Unless the filename contains a * character, the output will be written
 to one single file with the specified format. Otherwise there will be
--- a/doc/src/fix_ave_chunk.txt
+++ b/doc/src/fix_ave_chunk.txt
@ -191,8 +191,15 @@ remain constant for the duration of the simulation.  This fix forces
 the chunk/atom compute specified by chunkID to hold {Nchunk} constant
 for the appropriate time windows, by not allowing it to re-calculate
 {Nchunk}, which can also affect how it assigns chunk IDs to atoms.
-More details are given on the "compute
-chunk/atom"_compute_chunk_atom.html doc page.
+This is particularly important to understand if the chunks defined by
+the "compute chunk/atom"_compute_chunk_atom.html command are spatial
+bins.  If its {units} keyword is set to {box} or {lattice}, then the
+number of bins {Nchunk} and size of each bin will be fixed over the
+{Nfreq} time window, which can affect which atoms are discarded if the
+simulation box size changes.  If its {units} keyword is set to
+{reduced}, then the number of bins {Nchunk} will still be fixed, but
+the size of each bin can vary at each timestep if the simulation box
+size changes, e.g. for an NPT simulation.

 :line

@ -290,24 +297,32 @@ It the {norm} setting is {all}, which is the default, a chunk value is
 summed over all atoms in all {Nrepeat} samples, as is the count of
 atoms in the chunk.  The averaged output value for the chunk on the
 {Nfreq} timesteps is Total-sum / Total-count.  In other words it is an
-average over atoms across the entire {Nfreq} timescale.
+average over atoms across the entire {Nfreq} timescale.  For the
+{density/number} and {density/mass} values, the volume (bin volume or
+system volume) used in the final normalization will be the volume at
+the final {Nfreq} timestep.

-If the {norm} setting is {sample}, the chunk value is summed over atoms
-for each sample, as is the count, and an "average sample value" is
-computed for each sample, i.e. Sample-sum / Sample-count.  The output
-value for the chunk on the {Nfreq} timesteps is the average of the
-{Nrepeat} "average sample values", i.e. the sum of {Nrepeat} "average
-sample values" divided by {Nrepeat}.  In other words it is an average
-of an average.
+If the {norm} setting is {sample}, the chunk value is summed over
+atoms for each sample, as is the count, and an "average sample value"
+is computed for each sample, i.e. Sample-sum / Sample-count.  The
+output value for the chunk on the {Nfreq} timesteps is the average of
+the {Nrepeat} "average sample values", i.e. the sum of {Nrepeat}
+"average sample values" divided by {Nrepeat}.  In other words it is an
+average of an average.  For the {density/number} and {density/mass}
+values, the volume (bin volume or system volume) used in the
+per-sample normalization will be the current volume at each sampling
+step.

 If the {norm} setting is {none}, a similar computation as for the
-{sample} setting is done, except the individual "average sample values"
-are "summed sample values".  A summed sample value is simply the chunk
-value summed over atoms in the sample, without dividing by the number
-of atoms in the sample.  The output value for the chunk on the
-{Nfreq} timesteps is the average of the {Nrepeat} "summed sample
+{sample} setting is done, except the individual "average sample
+values" are "summed sample values".  A summed sample value is simply
+the chunk value summed over atoms in the sample, without dividing by
+the number of atoms in the sample.  The output value for the chunk on
+the {Nfreq} timesteps is the average of the {Nrepeat} "summed sample
 values", i.e. the sum of {Nrepeat} "summed sample values" divided by
-{Nrepeat}.
+{Nrepeat}.  For the {density/number} and {density/mass} values, the
+volume (bin volume or system volume) used in the per-sample sum
+normalization will be the current volume at each sampling step.

 The {ave} keyword determines how the per-chunk values produced every
 {Nfreq} steps are averaged with values produced on previous steps that
--- a/doc/src/fix_cmap.txt
+++ b/doc/src/fix_cmap.txt
@ -27,7 +27,7 @@ fix_modify     myCMAP energy yes :pre
 This command enables CMAP crossterms to be added to simulations which
 use the CHARMM force field.  These are relevant for any CHARMM model
 of a peptide or protein sequences that is 3 or more amino-acid
-residues long; see "(Buck)"_#Buck and "(Brooks)"_#Brooks for details,
+residues long; see "(Buck)"_#Buck and "(Brooks)"_#Brooks2 for details,
 including the analytic energy expressions for CMAP interactions.  The
 CMAP crossterms add additional potential energy contributions to pairs
 of overlapping phi-psi dihedrals of amino-acids, which are important
@ -128,5 +128,5 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 [(Buck)] Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36
 (2006).

-:link(Brooks)
+:link(Brooks2)
 [(Brooks)] Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009).
--- a/doc/src/fix_deposit.txt
+++ b/doc/src/fix_deposit.txt
@ -150,6 +150,12 @@ treated as rigid bodies, use the {rigid} keyword, specifying as its
 value the ID of a separate "fix rigid/small"_fix_rigid.html
 command which also appears in your input script.

+NOTE: If you wish the new rigid molecules (and other rigid molecules)
+to be thermostatted correctly via "fix rigid/small/nvt"_fix_rigid.html
+or "fix rigid/small/npt"_fix_rigid.html, then you need to use the
+"fix_modify dynamic/dof yes" command for the rigid fix.  This is to
+inform that fix that the molecule count will vary dynamically.
+
 If you wish to insert molecules via the {mol} keyword, that will have
 their bonds or angles constrained via SHAKE, use the {shake} keyword,
 specifying as its value the ID of a separate "fix
--- a/doc/src/fix_dpd_energy.txt
+++ b/doc/src/fix_dpd_energy.txt
@ -70,13 +70,13 @@ mesoparticle equation of state for each particle.

 :line

-:link(Lisal)
+:link(Lisal1)
 [(Lisal)] M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative
 particle dynamics at isothermal, isobaric, isoenergetic, and
 isoenthalpic conditions using Shardlow-like splitting algorithms.",
 J. Chem. Phys., 135, 204105 (2011).

-:link(Larentzos)
+:link(Larentzos3)
 [(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and
 W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
 Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
--- a/doc/src/fix_drude_transform.txt
+++ b/doc/src/fix_drude_transform.txt
@ -32,7 +32,7 @@ fix 1 all drude/transform/inverse :pre

 Transform the coordinates of Drude oscillators from real to reduced
 and back for thermalizing the Drude oscillators as described in
-"(Lamoureux)"_#Lamoureux using a Nose-Hoover thermostat.  This fix is
+"(Lamoureux)"_#Lamoureux1 using a Nose-Hoover thermostat.  This fix is
 designed to be used with the "thermalized Drude oscillator
 model"_tutorial_drude.html.  Polarizable models in LAMMPS are
 described in "this Section"_Section_howto.html#howto_25.
@ -160,5 +160,5 @@ files"_restart.html.

 :line

-:link(Lamoureux)
+:link(Lamoureux1)
 [(Lamoureux)] Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003).
--- a/doc/src/fix_eos_cv.txt
+++ b/doc/src/fix_eos_cv.txt
@ -53,7 +53,7 @@ command.

 :line

-:link(Larentzos)
+:link(Larentzos4)
 [(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and
 W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
 Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
--- a/doc/src/fix_filter_corotate.txt
+++ b/doc/src/fix_filter_corotate.txt
@ -0,0 +1,87 @@
+"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 filter/corotate command :h3
+
+[Syntax:]
+
+fix ID group-ID filter/corotate keyword value ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+one or more constraint/value pairs are appended :l
+constraint = {b} or {a} or {t} or {m} :l
+  {b} values = one or more bond types
+  {a} values = one or more angle types
+  {t} values = one or more atom types
+  {m} value = one or more mass values :pre
+:ule
+
+[Examples:]
+
+timestep 8
+run_style respa 3 2 8 bond 1 pair 2 kspace 3
+fix cor all filter/corotate m 1.0 :pre
+
+fix cor all filter/corotate b 4 19 a 3 5 2 :pre
+
+[Description:]
+
+This fix implements a corotational filter for a mollified impulse
+method. In biomolecular simulations, it allows the usage of larger
+timesteps for long-range electrostatic interactions.  For details, see
+"(Fath)"_#Fath2017.
+
+When using "run_style respa"_run_style.html for a biomolecular
+simulation with high-frequency covalent bonds, the outer time-step is
+restricted to below ~ 4fs due to resonance problems. This fix filters
+the outer stage of the respa and thus a larger (outer) time-step can
+be used. Since in large biomolecular simulations the computation of
+the long-range electrostatic contributions poses a major bottleneck,
+this can significantly accelerate the simulation.
+
+The filter computes a cluster decomposition of the molecular structure
+following the criteria indicated by the options a, b, t and m. This
+process is similar to the approach in "fix shake"_fix_shake.html,
+however, the clusters are not kept contrained. Instead, the position
+is slightly modified only for the computation of long-range forces. A
+good cluster decomposition constitutes in building clusters which
+contain the fastest covalent bonds inside clusters.
+
+If the clusters are chosen suitably, the "run_style
+respa"_run_style.html is stable for outer time-steps of at least 8fs.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about these fixes is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to these fixes.  No global or per-atom quantities are
+stored by these fixes for access by various "output
+commands"_Section_howto.html#howto_15.  No parameter of these fixes
+can be used with the {start/stop} keywords of the "run"_run.html
+command.  These fixes are not invoked during "energy
+minimization"_minimize.html.
+
+[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.
+
+Currently, it does not support "molecule templates"_molecule.html.
+
+[Related commands:]
+
+
+[Default:] none
+
+:line
+
+:link(Fath2017)
+[(Fath)] Fath, Hochbruck, Singh, J Comp Phys, 333, 180-198 (2017).
--- a/doc/src/fix_flow_gauss.txt
+++ b/doc/src/fix_flow_gauss.txt
@ -153,7 +153,7 @@ The option default for the {energy} keyword is energy = no.
 :link(Strong)
 [(Strong)] Strong and Eaves, J. Phys. Chem. B 121, 189 (2017).

-:link(Evans)
+:link(Evans2)
 [(Evans)] Evans and Morriss, Phys. Rev. Lett. 56, 2172 (1986).

 :link(Zhu)
--- a/doc/src/fix_gcmc.txt
+++ b/doc/src/fix_gcmc.txt
@ -23,9 +23,11 @@ T = temperature of the ideal gas reservoir (temperature units) :l
 mu = chemical potential of the ideal gas reservoir (energy units) :l
 displace = maximum Monte Carlo translation distance (length units) :l
 zero or more keyword/value pairs may be appended to args :l
-keyword = {mol}, {region}, {maxangle}, {pressure}, {fugacity_coeff}, {full_energy}, {charge}, {group}, {grouptype}, {intra_energy}, or {tfac_insert}
+keyword = {mol}, {region}, {maxangle}, {pressure}, {fugacity_coeff}, {full_energy}, {charge}, {group}, {grouptype}, {intra_energy}, {tfac_insert}, or {overlap_cutoff}
  {mol} value = template-ID
    template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
+  {rigid} value = fix-ID
+    fix-ID = ID of "fix rigid/small"_fix_rigid.html command
  {shake} value = fix-ID
    fix-ID = ID of "fix shake"_fix_shake.html command
  {region} value = region-ID
@ -41,7 +43,8 @@ keyword = {mol}, {region}, {maxangle}, {pressure}, {fugacity_coeff}, {full_energ
    type = atom type (int)
    group-ID = group-ID for inserted atoms (string)
  {intra_energy} value = intramolecular energy (energy units)
-  {tfac_insert} value = scale up/down temperature of inserted atoms (unitless) :pre
+  {tfac_insert} value = scale up/down temperature of inserted atoms (unitless)
+  {overlap_cutoff} value = maximum pair distance for overlap rejection (distance units) :pre
 :ule

 [Examples:]
@ -53,26 +56,25 @@ fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk :pre
 [Description:]

 This fix performs grand canonical Monte Carlo (GCMC) exchanges of
-atoms or molecules of the given type with an imaginary ideal gas reservoir at
-the specified T and chemical potential (mu) as discussed in
-"(Frenkel)"_#Frenkel. If used with the "fix nvt"_fix_nh.html command,
-simulations in the grand canonical ensemble (muVT, constant chemical
-potential, constant volume, and constant temperature) can be
+atoms or molecules of the given type with an imaginary ideal gas
+reservoir at the specified T and chemical potential (mu) as discussed
+in "(Frenkel)"_#Frenkel. If used with the "fix nvt"_fix_nh.html
+command, simulations in the grand canonical ensemble (muVT, constant
+chemical potential, constant volume, and constant temperature) can be
 performed.  Specific uses include computing isotherms in microporous
 materials, or computing vapor-liquid coexistence curves.

-Every N timesteps the fix attempts a number of GCMC exchanges (insertions
-or deletions) of gas atoms or molecules of
-the given type between the simulation cell and the imaginary
-reservoir. It also attempts a number of Monte Carlo
-moves (translations and molecule rotations) of gas of the given type
-within the simulation cell or region.  The average number of
-attempted GCMC exchanges is X. The average number of attempted MC moves is M.
-M should typically be chosen to be
-approximately equal to the expected number of gas atoms or molecules
-of the given type within the simulation cell or region,
-which will result in roughly one
-MC translation per atom or molecule per MC cycle.
+Every N timesteps the fix attempts a number of GCMC exchanges
+(insertions or deletions) of gas atoms or molecules of the given type
+between the simulation cell and the imaginary reservoir. It also
+attempts a number of Monte Carlo moves (translations and molecule
+rotations) of gas of the given type within the simulation cell or
+region.  The average number of attempted GCMC exchanges is X. The
+average number of attempted MC moves is M.  M should typically be
+chosen to be approximately equal to the expected number of gas atoms
+or molecules of the given type within the simulation cell or region,
+which will result in roughly one MC translation per atom or molecule
+per MC cycle.

 For MC moves of molecular gasses, rotations and translations are each
 attempted with 50% probability. For MC moves of atomic gasses,
@ -80,50 +82,50 @@ translations are attempted 100% of the time. For MC exchanges of
 either molecular or atomic gasses, deletions and insertions are each
 attempted with 50% probability.

-All inserted particles are always assigned to two groups: the default group
-"all" and the group specified in the fix gcmc command (which can also
-be "all"). In addition, particles are also added to any groups specified
-by the {group} and {grouptype} keywords.
-If inserted particles are individual atoms, they are
-assigned the atom type given by the type argument.  If they are molecules,
-the type argument has no effect and must be set to zero. Instead,
-the type of each atom in the inserted molecule is specified
-in the file read by the "molecule"_molecule.html command.
+All inserted particles are always assigned to two groups: the default
+group "all" and the group specified in the fix gcmc command (which can
+also be "all"). In addition, particles are also added to any groups
+specified by the {group} and {grouptype} keywords.  If inserted
+particles are individual atoms, they are assigned the atom type given
+by the type argument.  If they are molecules, the type argument has no
+effect and must be set to zero. Instead, the type of each atom in the
+inserted molecule is specified in the file read by the
+"molecule"_molecule.html command.

 This fix cannot be used to perform MC insertions of gas atoms or
 molecules other than the exchanged type, but MC deletions,
 translations, and rotations can be performed on any atom/molecule in
 the fix group.  All atoms in the simulation cell can be moved using
-regular time integration translations, e.g. via
-"fix nvt"_fix_nh.html, resulting in a hybrid GCMC+MD simulation. A
-smaller-than-usual timestep size may be needed when running such a
-hybrid simulation, especially if the inserted molecules are not well
-equilibrated.
+regular time integration translations, e.g. via "fix nvt"_fix_nh.html,
+resulting in a hybrid GCMC+MD simulation. A smaller-than-usual
+timestep size may be needed when running such a hybrid simulation,
+especially if the inserted molecules are not well equilibrated.

 This command may optionally use the {region} keyword to define an
 exchange and move volume.  The specified region must have been
 previously defined with a "region"_region.html command.  It must be
 defined with side = {in}.  Insertion attempts occur only within the
-specified region. For non-rectangular regions, random trial
-points are generated within the rectangular bounding box until a point is found
-that lies inside the region. If no valid point is generated after 1000 trials,
-no insertion is performed, but it is counted as an attempted insertion.
-Move and deletion attempt candidates are selected
-from gas atoms or molecules within the region. If there are no candidates,
-no move or deletion is performed, but it is counted as an attempt move
-or deletion. If an attempted move places the atom or molecule center-of-mass outside
-the specified region, a new attempted move is generated. This process is repeated
-until the atom or molecule center-of-mass is inside the specified region.
+specified region. For non-rectangular regions, random trial points are
+generated within the rectangular bounding box until a point is found
+that lies inside the region. If no valid point is generated after 1000
+trials, no insertion is performed, but it is counted as an attempted
+insertion.  Move and deletion attempt candidates are selected from gas
+atoms or molecules within the region. If there are no candidates, no
+move or deletion is performed, but it is counted as an attempt move or
+deletion. If an attempted move places the atom or molecule
+center-of-mass outside the specified region, a new attempted move is
+generated. This process is repeated until the atom or molecule
+center-of-mass is inside the specified region.

 If used with "fix nvt"_fix_nh.html, the temperature of the imaginary
 reservoir, T, should be set to be equivalent to the target temperature
-used in fix nvt. Otherwise, the imaginary reservoir
-will not be in thermal equilibrium with the simulation cell. Also,
-it is important that the temperature used by fix nvt be dynamic,
-which can be achieved as follows:
+used in fix nvt. Otherwise, the imaginary reservoir will not be in
+thermal equilibrium with the simulation cell. Also, it is important
+that the temperature used by fix nvt be dynamic/dof, which can be
+achieved as follows:

 compute mdtemp mdatoms temp
-compute_modify mdtemp dynamic yes
+compute_modify mdtemp dynamic/dof yes
 fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
 fix_modify mdnvt temp mdtemp :pre

@ -134,16 +136,16 @@ interactions. Specifically, avoid performing so many MC translations
 per timestep that atoms can move beyond the neighbor list skin
 distance. See the "neighbor"_neighbor.html command for details.

-When an atom or molecule is to be inserted, its
-coordinates are chosen at a random position within the current
-simulation cell or region, and new atom velocities are randomly chosen from
-the specified temperature distribution given by T. The effective
-temperature for new atom velocities can be increased or decreased
-using the optional keyword {tfac_insert} (see below). Relative
-coordinates for atoms in a molecule are taken from the template
-molecule provided by the user. The center of mass of the molecule
-is placed at the insertion point. The orientation of the molecule
-is chosen at random by rotating about this point.
+When an atom or molecule is to be inserted, its coordinates are chosen
+at a random position within the current simulation cell or region, and
+new atom velocities are randomly chosen from the specified temperature
+distribution given by T. The effective temperature for new atom
+velocities can be increased or decreased using the optional keyword
+{tfac_insert} (see below). Relative coordinates for atoms in a
+molecule are taken from the template molecule provided by the
+user. The center of mass of the molecule is placed at the insertion
+point. The orientation of the molecule is chosen at random by rotating
+about this point.

 Individual atoms are inserted, unless the {mol} keyword is used.  It
 specifies a {template-ID} previously defined using the
@ -155,53 +157,97 @@ command for details.  The only settings required to be in this file
 are the coordinates and types of atoms in the molecule.

 When not using the {mol} keyword, you should ensure you do not delete
-atoms that are bonded to other atoms, or LAMMPS will
-soon generate an error when it tries to find bonded neighbors.  LAMMPS will
-warn you if any of the atoms eligible for deletion have a non-zero
-molecule ID, but does not check for this at the time of deletion.
+atoms that are bonded to other atoms, or LAMMPS will soon generate an
+error when it tries to find bonded neighbors.  LAMMPS will warn you if
+any of the atoms eligible for deletion have a non-zero molecule ID,
+but does not check for this at the time of deletion.
+
+If you wish to insert molecules via the {mol} keyword, that will be
+treated as rigid bodies, use the {rigid} keyword, specifying as its
+value the ID of a separate "fix rigid/small"_fix_rigid.html command
+which also appears in your input script.
+
+NOTE: If you wish the new rigid molecules (and other rigid molecules)
+to be thermostatted correctly via "fix rigid/small/nvt"_fix_rigid.html
+or "fix rigid/small/npt"_fix_rigid.html, then you need to use the
+"fix_modify dynamic/dof yes" command for the rigid fix.  This is to
+inform that fix that the molecule count will vary dynamically.

 If you wish to insert molecules via the {mol} keyword, that will have
 their bonds or angles constrained via SHAKE, use the {shake} keyword,
 specifying as its value the ID of a separate "fix
 shake"_fix_shake.html command which also appears in your input script.

-Optionally, users may specify the maximum rotation angle for
-molecular rotations using the {maxangle} keyword and specifying
-the angle in degrees. Rotations are performed by generating a random
-point on the unit sphere and a random rotation angle on the
-range \[0,maxangle). The molecule is then rotated by that angle about an
+Optionally, users may specify the maximum rotation angle for molecular
+rotations using the {maxangle} keyword and specifying the angle in
+degrees. Rotations are performed by generating a random point on the
+unit sphere and a random rotation angle on the range
+\[0,maxangle). The molecule is then rotated by that angle about an
 axis passing through the molecule center of mass. The axis is parallel
-to the unit vector defined by the point on the unit sphere.
-The same procedure is used for randomly rotating molecules when they
-are inserted, except that the maximum angle is 360 degrees.
+to the unit vector defined by the point on the unit sphere.  The same
+procedure is used for randomly rotating molecules when they are
+inserted, except that the maximum angle is 360 degrees.

-Note that fix GCMC does not use configurational bias
-MC or any other kind of sampling of intramolecular degrees of freedom.
-Inserted molecules can have different orientations, but they will all
-have the same intramolecular configuration,
-which was specified in the molecule command input.
+Note that fix GCMC does not use configurational bias MC or any other
+kind of sampling of intramolecular degrees of freedom.  Inserted
+molecules can have different orientations, but they will all have the
+same intramolecular configuration, which was specified in the molecule
+command input.

 For atomic gasses, inserted atoms have the specified atom type, but
-deleted atoms are any atoms that have been inserted or that belong
-to the user-specified fix group. For molecular gasses, exchanged
-molecules use the same atom types as in the template molecule
-supplied by the user.  In both cases, exchanged
-atoms/molecules are assigned to two groups: the default group "all"
-and the group specified in the fix gcmc command (which can also be
-"all").
+deleted atoms are any atoms that have been inserted or that belong to
+the user-specified fix group. For molecular gasses, exchanged
+molecules use the same atom types as in the template molecule supplied
+by the user.  In both cases, exchanged atoms/molecules are assigned to
+two groups: the default group "all" and the group specified in the fix
+gcmc command (which can also be "all").

-The gas reservoir pressure can be specified using the {pressure}
-keyword, in which case the user-specified chemical potential is
-ignored. For non-ideal gas reservoirs, the user may also specify the
-fugacity coefficient using the {fugacity_coeff} keyword.
+The chemical potential is a user-specified input parameter defined
+as:
+
+:c,image(Eqs/fix_gcmc1.jpg)
+
+The second term mu_ex is the excess chemical potential due to
+energetic interactions and is formally zero for the fictitious gas
+reservoir but is non-zero for interacting systems. So, while the
+chemical potential of the reservoir and the simulation cell are equal,
+mu_ex is not, and as a result, the densities of the two are generally
+quite different.  The first term mu_id is the ideal gas contribution
+to the chemical potential.  mu_id can be related to the density or
+pressure of the fictitious gas reservoir by:
+
+:c,image(Eqs/fix_gcmc2.jpg)
+
+where k is Boltzman's constant,
+T is the user-specified temperature, rho is the number density,
+P is the pressure, and phi is the fugacity coefficient.
+The constant Lambda is required for dimensional consistency.
+For all unit styles except {lj} it is defined as the thermal
+de Broglie wavelength
+
+:c,image(Eqs/fix_gcmc3.jpg)
+
+where h is Planck's constant, and m is the mass of the exchanged atom
+or molecule.  For unit style {lj}, Lambda is simply set to the
+unity. Note that prior to March 2017, lambda for unit style {lj} was
+calculated using the above formula with h set to the rather specific
+value of 0.18292026.  Chemical potential under the old definition can
+be converted to an equivalent value under the new definition by
+subtracting 3kTln(Lambda_old).
+
+As an alternative to specifying mu directly, the ideal gas reservoir
+can be defined by its pressure P using the {pressure} keyword, in
+which case the user-specified chemical potential is ignored. The user
+may also specify the fugacity coefficient phi using the
+{fugacity_coeff} keyword, which defaults to unity.

 The {full_energy} option means that fix GCMC will compute the total
 potential energy of the entire simulated system. The total system
 energy before and after the proposed GCMC move is then used in the
 Metropolis criterion to determine whether or not to accept the
-proposed GCMC move. By default, this option is off, in which case
-only partial energies are computed to determine the difference in
-energy that would be caused by the proposed GCMC move.
+proposed GCMC move. By default, this option is off, in which case only
+partial energies are computed to determine the difference in energy
+that would be caused by the proposed GCMC move.

 The {full_energy} option is needed for systems with complicated
 potential energy calculations, including the following:
@ -210,7 +256,7 @@ potential energy calculations, including the following:
  many-body pair styles
  hybrid pair styles
  eam pair styles
-  triclinic systems
+  tail corrections
  need to include potential energy contributions from other fixes :ul

 In these cases, LAMMPS will automatically apply the {full_energy}
@ -219,42 +265,43 @@ keyword and issue a warning message.
 When the {mol} keyword is used, the {full_energy} option also includes
 the intramolecular energy of inserted and deleted molecules. If this
 is not desired, the {intra_energy} keyword can be used to define an
-amount of energy that is subtracted from the final energy when a molecule
-is inserted, and added to the initial energy when a molecule is
-deleted. For molecules that have a non-zero intramolecular energy, this
-will ensure roughly the same behavior whether or not the {full_energy}
-option is used.
+amount of energy that is subtracted from the final energy when a
+molecule is inserted, and added to the initial energy when a molecule
+is deleted. For molecules that have a non-zero intramolecular energy,
+this will ensure roughly the same behavior whether or not the
+{full_energy} option is used.

-Inserted atoms and molecules are assigned random velocities based on the
-specified temperature T. Because the relative velocity of
-all atoms in the molecule is zero, this may result in inserted molecules
-that are systematically too cold. In addition, the intramolecular potential
-energy of the inserted molecule may cause the kinetic energy
-of the molecule to quickly increase or decrease after insertion.
-The {tfac_insert} keyword allows the user to counteract these effects
-by changing the temperature used to assign velocities to
-inserted atoms and molecules by a constant factor. For a
-particular application, some experimentation may be required
-to find a value of {tfac_insert} that results in inserted molecules that
-equilibrate quickly to the correct temperature.
+Inserted atoms and molecules are assigned random velocities based on
+the specified temperature T. Because the relative velocity of all
+atoms in the molecule is zero, this may result in inserted molecules
+that are systematically too cold. In addition, the intramolecular
+potential energy of the inserted molecule may cause the kinetic energy
+of the molecule to quickly increase or decrease after insertion.  The
+{tfac_insert} keyword allows the user to counteract these effects by
+changing the temperature used to assign velocities to inserted atoms
+and molecules by a constant factor. For a particular application, some
+experimentation may be required to find a value of {tfac_insert} that
+results in inserted molecules that equilibrate quickly to the correct
+temperature.

 Some fixes have an associated potential energy. Examples of such fixes
 include: "efield"_fix_efield.html, "gravity"_fix_gravity.html,
 "addforce"_fix_addforce.html, "langevin"_fix_langevin.html,
-"restrain"_fix_restrain.html, "temp/berendsen"_fix_temp_berendsen.html,
+"restrain"_fix_restrain.html,
+"temp/berendsen"_fix_temp_berendsen.html,
 "temp/rescale"_fix_temp_rescale.html, and "wall fixes"_fix_wall.html.
 For that energy to be included in the total potential energy of the
-system (the quantity used when performing GCMC moves),
-you MUST enable the "fix_modify"_fix_modify.html {energy} option for
-that fix.  The doc pages for individual "fix"_fix.html commands
-specify if this should be done.
+system (the quantity used when performing GCMC moves), you MUST enable
+the "fix_modify"_fix_modify.html {energy} option for that fix.  The
+doc pages for individual "fix"_fix.html commands specify if this
+should be done.

 Use the {charge} option to insert atoms with a user-specified point
-charge. Note that doing so will cause the system to become non-neutral.
-LAMMPS issues a warning when using long-range electrostatics (kspace)
-with non-neutral systems. See the
-"compute group/group"_compute_group_group.html documentation for more
-details about simulating non-neutral systems with kspace on.
+charge. Note that doing so will cause the system to become
+non-neutral.  LAMMPS issues a warning when using long-range
+electrostatics (kspace) with non-neutral systems. See the "compute
+group/group"_compute_group_group.html documentation for more details
+about simulating non-neutral systems with kspace on.

 Use of this fix typically will cause the number of atoms to fluctuate,
 therefore, you will want to use the
@ -262,6 +309,24 @@ therefore, you will want to use the
 current number of atoms is used as a normalizing factor each time
 temperature is computed.  Here is the necessary command:

+NOTE: If the density of the cell is initially very small or zero, and
+increases to a much larger density after a period of equilibration,
+then certain quantities that are only calculated once at the start
+(kspace parameters, tail corrections) may no longer be accurate.  The
+solution is to start a new simulation after the equilibrium density
+has been reached.
+
+With some pair_styles, such as "Buckingham"_pair_buck.html,
+"Born-Mayer-Huggins"_pair_born.html and "ReaxFF"_pair_reax_c.html, two
+atoms placed close to each other may have an arbitrary large, negative
+potential energy due to the functional form of the potential.  While
+these unphysical configurations are inaccessible to typical dynamical
+trajectories, they can be generated by Monte Carlo moves. The
+{overlap_cutoff} keyword suppresses these moves by effectively
+assigning an infinite positive energy to all new configurations that
+place any pair of atoms closer than the specified overlap cutoff
+distance.
+
 compute_modify thermo_temp dynamic yes :pre

 If LJ units are used, note that a value of 0.18292026 is used by this
@ -270,10 +335,10 @@ derived from LJ parameters for argon, where h* = h/sqrt(sigma^2 *
 epsilon * mass), sigma = 3.429 angstroms, epsilon/k = 121.85 K, and
 mass = 39.948 amu.

-The {group} keyword assigns all inserted atoms to the "group"_group.html
-of the group-ID value. The {grouptype} keyword assigns all
-inserted atoms of the specified type to the "group"_group.html
-of the group-ID value.
+The {group} keyword assigns all inserted atoms to the
+"group"_group.html of the group-ID value. The {grouptype} keyword
+assigns all inserted atoms of the specified type to the
+"group"_group.html of the group-ID value.

 [Restart, fix_modify, output, run start/stop, minimize info:]

@ -321,19 +386,15 @@ well in parallel. Only usable for 3D simulations.
 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
-simulations. Likewise, very large molecules have not been tested
-and may turn out to be problematic.
+simulations. Likewise, very large molecules have not been tested and
+may turn out to be problematic.

 Use of multiple fix gcmc commands in the same input script can be
 problematic if using a template molecule. The issue is that the
-user-referenced template molecule in the second fix gcmc command
-may no longer exist since it might have been deleted by the first
-fix gcmc command. An existing template molecule will need to be
-referenced by the user for each subsequent fix gcmc command.
-
-Because molecule insertion does not work in combination with
-fix rigid, simulataneous use of fix rigid or fix rigid/small
-with this fix is not allowed.
+user-referenced template molecule in the second fix gcmc command may
+no longer exist since it might have been deleted by the first fix gcmc
+command. An existing template molecule will need to be referenced by
+the user for each subsequent fix gcmc command.

 [Related commands:]

@ -344,7 +405,8 @@ with this fix is not allowed.

 [Default:]

-The option defaults are mol = no, maxangle = 10, full_energy = no,
+The option defaults are mol = no, maxangle = 10, overlap_cutoff = 0.0,
+fugacity_coeff = 1, and full_energy = no, 
 except for the situations where full_energy is required, as
 listed above.

--- a/doc/src/fix_halt.txt
+++ b/doc/src/fix_halt.txt
@ -15,15 +15,16 @@ fix ID group-ID halt N attribute operator avalue keyword value ... :pre
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 halt = style name of this fix command :l
 N = check halt condition every N steps :l
-attribute = hstyle or v_name :l
-  hstyle = {bondmax}
+attribute = {bondmax} or {tlimit} or v_name :l
+  bondmax = length of longest bond in the system
+  tlimit = elapsed CPU time
  v_name = name of "equal-style variable"_variable.html :pre
 operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" :l
 avalue = numeric value to compare attribute to :l
-string = text string to print with optional variable names :l
 zero or more keyword/value pairs may be appended :l
-keyword = {error} :l
-  {error} value = {hard} or {soft} or {continue} :pre
+keyword = {error} or {message} :l
+  {error} value = {hard} or {soft} or {continue}
+  {message} value = {yes} or {no} :pre
 :ule

 [Examples:]
@ -40,14 +41,33 @@ specified by the "run"_run.html or "minimize"_minimize.html command.

 The specified group-ID is ignored by this fix.

-The specified {attribute} can be one of the {hstyle} options listed
-above, or an "equal-style variable"_variable.html referenced as
-{v_name}, where "name" is the name of a variable that has been defined
-previously in the input script.
+The specified {attribute} can be one of the options listed above,
+namely {bondmax} or {tlimit}, or an "equal-style
+variable"_variable.html referenced as {v_name}, where "name" is the
+name of a variable that has been defined previously in the input
+script.

-The only {hstyle} option currently implemented is {bondmax}.  This
-will loop over all bonds in the system, compute their current
-lengths, and set {attribute} to the longest bond distance.
+The {bondmax} attribute will loop over all bonds in the system,
+compute their current lengths, and set {attribute} to the longest bond
+distance.
+
+The {tlimit} attribute queries the elapsed CPU time (in seconds) since
+the current run began, and sets {attribute} to that value.  This is an
+alternative way to limit the length of a simulation run, similar to
+the "timer"_timer.html timeout command.  There are two differences in
+using this method versus the timer command option.  The first is that
+the clock starts at the beginning of the current run (not when the
+timer or fix command is specified), so that any setup time for the run
+is not included in the elapsed time.  The second is that the timer
+invocation and syncing across all processors (via MPI_Allreduce) is
+not performed once every {N} steps by this command.  Instead it is
+performed (typically) only a small number of times and the elapsed
+times are used to predict when the end-of-the-run will be.  Both of
+these attributes can be useful when performing benchmark calculations
+for a desired length of time with minmimal overhead.  For example, if
+a run is performing 1000s of timesteps/sec, the overhead for syncing
+the timer frequently across a large number of processors may be
+non-negligble.

 Equal-style variables evaluate to a numeric value.  See the
 "variable"_variable.html command for a description.  They calculate
@ -100,6 +120,14 @@ Note that you may wish use the "unfix"_unfix.html command on the fix
 halt ID, so that the same condition is not immediately triggered in a
 subsequent run.

+The optional {message} keyword determines whether a message is printed
+to the screen and logfile when the halt condition is triggered.  If
+{message} is set to yes, a one line message with the values that
+triggered the halt is printed.  If {message} is set to no, no message
+is printed; the run simply exits.  The latter may be desirable for
+post-processing tools that extract thermodyanmic information from log
+files.
+
 [Restart, fix_modify, output, run start/stop, minimize info:]

 No information about this fix is written to "binary restart
@ -118,4 +146,4 @@ This fix is not invoked during "energy minimization"_minimize.html.

 [Default:]

-The option defaults are error = hard.
+The option defaults are error = hard and message = yes.
--- a/doc/src/fix_langevin.txt
+++ b/doc/src/fix_langevin.txt
@ -49,7 +49,7 @@ fix 1 all langevin 1.0 1.1 100.0 48279 angmom 3.333 :pre

 [Description:]

-Apply a Langevin thermostat as described in "(Schneider)"_#Schneider
+Apply a Langevin thermostat as described in "(Schneider)"_#Schneider1
 to a group of atoms which models an interaction with a background
 implicit solvent.  Used with "fix nve"_fix_nve.html, this command
 performs Brownian dynamics (BD), since the total force on each atom
@ -80,7 +80,7 @@ dt damp), where Kb is the Boltzmann constant, T is the desired
 temperature, m is the mass of the particle, dt is the timestep size,
 and damp is the damping factor.  Random numbers are used to randomize
 the direction and magnitude of this force as described in
-"(Dunweg)"_#Dunweg, where a uniform random number is used (instead of
+"(Dunweg)"_#Dunweg1, where a uniform random number is used (instead of
 a Gaussian random number) for speed.

 Note that unless you use the {omega} or {angmom} keywords, the
@ -332,10 +332,10 @@ types, tally = no, zero = no, gjf = no.

 :line

-:link(Dunweg)
+:link(Dunweg1)
 [(Dunweg)] Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).

-:link(Schneider)
+:link(Schneider1)
 [(Schneider)] Schneider and Stoll, Phys Rev B, 17, 1302 (1978).

 :link(Gronbech-Jensen)
--- a/doc/src/fix_langevin_drude.txt
+++ b/doc/src/fix_langevin_drude.txt
@ -41,7 +41,7 @@ fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes :pre

 [Description:]

-Apply two Langevin thermostats as described in "(Jiang)"_#Jiang for
+Apply two Langevin thermostats as described in "(Jiang)"_#Jiang1 for
 thermalizing the reduced degrees of freedom of Drude oscillators.
 This link describes how to use the "thermalized Drude oscillator
 model"_tutorial_drude.html in LAMMPS and polarizable models in LAMMPS
@ -268,6 +268,6 @@ The option defaults are zero = no.

 :line

-:link(Jiang)
+:link(Jiang1)
 [(Jiang)] Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J
 Phys Chem Lett, 2, 87-92 (2011).
--- a/doc/src/fix_langevin_eff.txt
+++ b/doc/src/fix_langevin_eff.txt
@ -37,7 +37,7 @@ fix 1 all langevin/eff 1.0 1.1 10.0 48279 scale 3 1.5 :pre

 [Description:]

-Apply a Langevin thermostat as described in "(Schneider)"_#Schneider
+Apply a Langevin thermostat as described in "(Schneider)"_#Schneider2
 to a group of nuclei and electrons in the "electron force
 field"_pair_eff.html model.  Used with "fix nve/eff"_fix_nve_eff.html,
 this command performs Brownian dynamics (BD), since the total force on
@ -106,8 +106,8 @@ The option defaults are scale = 1.0 for all types and tally = no.

 :line

-:link(Dunweg)
+:link(Dunweg2)
 [(Dunweg)] Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).

-:link(Schneider)
+:link(Schneider2)
 [(Schneider)] Schneider and Stoll, Phys Rev B, 17, 1302 (1978).
--- a/doc/src/fix_lb_pc.txt
+++ b/doc/src/fix_lb_pc.txt
@ -24,7 +24,7 @@ fix 1 all lb/pc :pre
 Update the positions and velocities of the individual particles
 described by {group-ID}, experiencing velocity-dependent hydrodynamic
 forces, using the integration algorithm described in "Mackay et
-al."_#Mackay.  This integration algorithm should only be used if a
+al."_#Mackay1.  This integration algorithm should only be used if a
 user-specified value for the force-coupling constant used in "fix
 lb/fluid"_fix_lb_fluid.html has been set; do not use this integration
 algorithm if the force coupling constant has been set by default.
@ -58,5 +58,5 @@ lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html

 :line

-:link(Mackay)
+:link(Mackay1)
 [(Mackay et al.)] Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.
--- a/doc/src/fix_lb_viscous.txt
+++ b/doc/src/fix_lb_viscous.txt
@ -44,7 +44,7 @@ hydrodynamic forces to the particles.
 :line

 For further details, as well as descriptions and results of several
-test runs, see "Mackay et al."_#Mackay.  Please include a citation to
+test runs, see "Mackay et al."_#Mackay3.  Please include a citation to
 this paper if this fix is used in work contributing to published
 research.

@ -90,5 +90,5 @@ lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html

 :line

-:link(Mackay)
+:link(Mackay3)
 [(Mackay et al.)] Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.
--- a/doc/src/fix_modify.txt
+++ b/doc/src/fix_modify.txt
@ -14,11 +14,13 @@ fix_modify fix-ID keyword value ... :pre

 fix-ID = ID of the fix to modify :ulb,l
 one or more keyword/value pairs may be appended :l
-keyword = {temp} or {press} or {energy} or {respa} :l
+keyword = {temp} or {press} or {energy} or {respa} or {dynamic/dof} :l
  {temp} value = compute ID that calculates a temperature
  {press} value = compute ID that calculates a pressure
  {energy} value = {yes} or {no}
-  {respa} value = {1} to {max respa level} or {0} (for outermost level) :pre
+  {respa} value = {1} to {max respa level} or {0} (for outermost level)
+  {dynamic/dof} value = {yes} or {no}
+    yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature :pre
 :ule

 [Examples:]
@ -78,6 +80,27 @@ enabled to support this feature; if not, {fix_modify} will report an
 error. Active fixes with a custom RESPA level setting are reported
 with their specified level at the beginning of a r-RESPA run.

+The {dynamic/dof} keyword determines whether the number of atoms N in
+the fix group and their associated degrees of freedom are re-computed
+each time a temperature is computed.  Only fix styles that calculate
+their own internal temperature use this option.  Currently this is
+only the "fix rigid/nvt/small"_fix_rigid.html and "fix
+rigid/npt/small"_fix_rigid.html commands for the purpose of
+thermostatting rigid body translation and rotation.  By default, N and
+their DOF are assumed to be constant.  If you are adding atoms or
+molecules to the system (see the "fix pour"_fix_pour.html, "fix
+deposit"_fix_deposit.html, and "fix gcmc"_fix_gcmc.html commands) or
+expect atoms or molecules to be lost (e.g. due to exiting the
+simulation box or via "fix evaporate"_fix_evaporate.html), then
+this option should be used to insure the temperature is correctly
+normalized.
+
+NOTE: Other thermostatting fixes, such as "fix nvt"_fix_nh.html, do
+not use the {dynamic/dof} keyword because they use a temperature
+compute to calculate temperature.  See the "compute_modify
+dynamic/dof"_compute_modify.html command for a similar way to insure
+correct temperature normalization for those thermostats.
+
 [Restrictions:] none

 [Related commands:]
--- a/doc/src/fix_nh.txt
+++ b/doc/src/fix_nh.txt
@ -466,16 +466,6 @@ to undergo a slow random walk. This can be mitigated by resetting
 the momentum at infrequent intervals using the
 "fix momentum"_fix_momentum.html command.

-NOTE: This implementation has been shown to conserve linear momentum
-up to machine precision under NVT dynamics. Under NPT dynamics,
-for a system with zero initial total linear momentum, the total
-momentum fluctuates close to zero. It may occasionally undergo brief
-excursions to non-negligible values, before returning close to zero.
-Over long simulations, this has the effect of causing the center-of-mass
-to undergo a slow random walk. This can be mitigated by resetting
-the momentum at infrequent intervals using the
-"fix momentum"_fix_momentum.html command.
-
 :line

 The fix npt and fix nph commands can be used with rigid bodies or
--- a/doc/src/fix_nh_eff.txt
+++ b/doc/src/fix_nh_eff.txt
@ -128,15 +128,15 @@ ploop = 1, nreset = 0, drag = 0.0, dilate = all, and couple = none.

 :line

-:link(Martyna)
+:link(Martyna1)
 [(Martyna)] Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).

 :link(Parrinello)
 [(Parrinello)] Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).

-:link(Tuckerman)
+:link(Tuckerman1)
 [(Tuckerman)] Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
 Martyna, J Phys A: Math Gen, 39, 5629 (2006).

-:link(Shinoda)
+:link(Shinoda2)
 [(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
--- a/doc/src/fix_nph_sphere.txt
+++ b/doc/src/fix_nph_sphere.txt
@ -13,14 +13,17 @@ fix nph/sphere/omp command :h3

 fix ID group-ID nph/sphere args keyword value ... :pre

-ID, group-ID are documented in "fix"_fix.html command
-nph/sphere = style name of this fix command
-additional barostat related keyword/value pairs from the "fix nph"_fix_nh.html command can be appended :ul
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+nph/sphere = style name of this fix command :l
+keyword = {disc} :l
+  {disc} value = none = treat particles as 2d discs, not spheres :pre
+additional barostat related keyword/value pairs from the "fix nph"_fix_nh.html command can be appended :l,ule

 [Examples:]

 fix 1 all nph/sphere iso 0.0 0.0 1000.0
 fix 2 all nph/sphere x 5.0 5.0 1000.0
+fix 2 all nph/sphere x 5.0 5.0 1000.0 disc
 fix 2 all nph/sphere x 5.0 5.0 1000.0 drag 0.2
 fix 2 water nph/sphere aniso 0.0 0.0 1000.0 dilate partial :pre

@ -35,6 +38,12 @@ isenthalpic ensemble.
 This fix differs from the "fix nph"_fix_nh.html command, which assumes
 point particles and only updates their position and velocity.

+If the {disc} keyword is used, then each particle is treated as a 2d
+disc (circle) instead of as a sphere.  This is only possible for 2d
+simulations, as defined by the "dimension"_dimension.html keyword.
+The only difference between discs and spheres in this context is their
+moment of inertia, as used in the time integration.
+
 Additional parameters affecting the barostat are specified by keywords
 and values documented with the "fix nph"_fix_nh.html command.  See,
 for example, discussion of the {aniso}, and {dilate} keywords.
@ -139,6 +148,9 @@ command.
 All particles in the group must be finite-size spheres.  They cannot
 be point particles.

+Use of the {disc} keyword is only allowed for 2d simulations, as
+defined by the "dimension"_dimension.html keyword.
+
 [Related commands:]

 "fix nph"_fix_nh.html, "fix nve_sphere"_fix_nve_sphere.html, "fix
--- a/doc/src/fix_nphug.txt
+++ b/doc/src/fix_nphug.txt
@ -49,7 +49,7 @@ fix myhug all nphug temp 1.0 1.0 10.0 iso 40.0 40.0 70.0 drag 200.0 tchain 1 pch
 This command is a variant of the Nose-Hoover
 "fix npt"_fix_nh.html fix style.
 It performs time integration of the Hugoniostat equations
-of motion developed by Ravelo et al. "(Ravelo)"_#Ravelo.
+of motion developed by Ravelo et al. "(Ravelo)"_#Ravelo1.
 These equations compress the system to a state with average
 axial stress or pressure equal to the specified target value
 and that satisfies the Rankine-Hugoniot (RH)
@ -225,5 +225,5 @@ The keyword defaults are the same as those for "fix npt"_fix_nh.html

 :line

-:link(Ravelo)
+:link(Ravelo1)
 [(Ravelo)] Ravelo, Holian, Germann and Lomdahl, Phys Rev B, 70, 014103 (2004).
--- a/doc/src/fix_npt_sphere.txt
+++ b/doc/src/fix_npt_sphere.txt
@ -15,12 +15,17 @@ fix ID group-ID npt/sphere keyword value ... :pre

 ID, group-ID are documented in "fix"_fix.html command
 npt/sphere = style name of this fix command
-additional thermostat and barostat related keyword/value pairs from the "fix npt"_fix_nh.html command can be appended :ul
+zero or more keyword/value pairs may be appended :l
+keyword = {disc} :l
+  {disc} value = none = treat particles as 2d discs, not spheres :pre
+additional thermostat and barostat related keyword/value pairs from the "fix npt"_fix_nh.html command can be appended :l,ule
+

 [Examples:]

 fix 1 all npt/sphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
 fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
+fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 disc
 fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2
 fix 2 water npt/sphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial :pre

@ -42,6 +47,12 @@ degrees of freedom (see below).  The translational degrees of freedom
 can also have a bias velocity removed from them before thermostatting
 takes place; see the description below.

+If the {disc} keyword is used, then each particle is treated as a 2d
+disc (circle) instead of as a sphere.  This is only possible for 2d
+simulations, as defined by the "dimension"_dimension.html keyword.
+The only difference between discs and spheres in this context is their
+moment of inertia, as used in the time integration.
+
 Additional parameters affecting the thermostat and barostat are
 specified by keywords and values documented with the "fix
 npt"_fix_nh.html command.  See, for example, discussion of the {temp},
@ -163,6 +174,9 @@ command.
 All particles in the group must be finite-size spheres.  They cannot
 be point particles.

+Use of the {disc} keyword is only allowed for 2d simulations, as
+defined by the "dimension"_dimension.html keyword.
+
 [Related commands:]

 "fix npt"_fix_nh.html, "fix nve_sphere"_fix_nve_sphere.html, "fix
--- a/doc/src/fix_nve_dot.txt
+++ b/doc/src/fix_nve_dot.txt
@ -22,11 +22,11 @@ fix 1 all nve/dot :pre

 [Description:]

-Apply a rigid-body integrator as described in "(Davidchack)"_#Davidchack
+Apply a rigid-body integrator as described in "(Davidchack)"_#Davidchack1
 to a group of atoms, but without Langevin dynamics. 
 This command performs Molecular dynamics (MD)
 via a velocity-Verlet algorithm and an evolution operator that rotates 
-the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller. 
+the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller1. 

 This command is the equivalent of the "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
 without damping and noise and can be used to determine the stability range 
@ -55,7 +55,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.

 :line

-:link(Davidchack)
+:link(Davidchack1)
 [(Davidchack)] R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
-:link(Miller)
+:link(Miller1)
 [(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
--- a/doc/src/fix_nve_dotc_langevin.txt
+++ b/doc/src/fix_nve_dotc_langevin.txt
@ -29,14 +29,14 @@ fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 :pre
 [Description:]

 Apply a rigid-body Langevin-type integrator of the kind "Langevin C" 
-as described in "(Davidchack)"_#Davidchack
+as described in "(Davidchack)"_#Davidchack2
 to a group of atoms, which models an interaction with an implicit background
 solvent.  This command performs Brownian dynamics (BD)
 via a technique that splits the integration into a deterministic Hamiltonian 
 part and the Ornstein-Uhlenbeck process for noise and damping. 
 The quaternion degrees of freedom are updated though an evolution
 operator which performs a rotation in quaternion space, preserves
-the quaternion norm and is akin to "(Miller)"_#Miller.
+the quaternion norm and is akin to "(Miller)"_#Miller2.

 In terms of syntax this command has been closely modelled on the 
 "fix langevin"_fix_langevin.html and its {angmom} option. But it combines 
@ -72,7 +72,7 @@ dt damp), where Kb is the Boltzmann constant, T is the desired
 temperature, m is the mass of the particle, dt is the timestep size,
 and damp is the damping factor.  Random numbers are used to randomize
 the direction and magnitude of this force as described in
-"(Dunweg)"_#Dunweg, where a uniform random number is used (instead of
+"(Dunweg)"_#Dunweg3, where a uniform random number is used (instead of
 a Gaussian random number) for speed.

 :line
@ -126,9 +126,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.

 :line

-:link(Davidchack)
+:link(Davidchack2)
 [(Davidchack)] R.L Davidchack, T.E. Ouldridge, M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
-:link(Miller)
+:link(Miller2)
 [(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
-:link(Dunweg)
+:link(Dunweg3)
 [(Dunweg)] B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991).
--- a/doc/src/fix_nve_manifold_rattle.txt
+++ b/doc/src/fix_nve_manifold_rattle.txt
@ -33,7 +33,7 @@ fix step all nve/manifold/rattle 1e-8 100 ellipsoid 2.5 2.5 5.0 every 25 :pre

 Perform constant NVE integration to update position and velocity for
 atoms constrained to a curved surface (manifold) in the group each
-timestep. The constraint is handled by RATTLE "(Andersen)"_#Andersen
+timestep. The constraint is handled by RATTLE "(Andersen)"_#Andersen1
 written out for the special case of single-particle constraints as
 explained in "(Paquay)"_#Paquay2.  V is volume; E is energy. This way,
 the dynamics of particles constrained to curved surfaces can be
@ -92,7 +92,7 @@ manifoldforce"_fix_manifoldforce.html

 :line

-:link(Andersen)
+:link(Andersen1)
 [(Andersen)] Andersen, J. Comp. Phys. 52, 24, (1983).

 :link(Paquay2)
--- a/doc/src/fix_nve_sphere.txt
+++ b/doc/src/fix_nve_sphere.txt
@ -16,16 +16,18 @@ fix ID group-ID nve/sphere :pre
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 nve/sphere = style name of this fix command :l
 zero or more keyword/value pairs may be appended :l
-keyword = {update}
+keyword = {update} or {disc} :l
  {update} value = {dipole} or {dipole/dlm}
    dipole = update orientation of dipole moment during integration
-    dipole/dlm = use DLM integrator to update dipole orientation :pre
+    dipole/dlm = use DLM integrator to update dipole orientation
+  {disc} value = none = treat particles as 2d discs, not spheres :pre
 :ule

 [Examples:]

 fix 1 all nve/sphere
 fix 1 all nve/sphere update dipole
+fix 1 all nve/sphere disc
 fix 1 all nve/sphere update dipole/dlm :pre

 [Description:]
@ -52,6 +54,12 @@ Dullweber-Leimkuhler-McLachlan integration scheme
 giving better energy conservation and allows slightly longer timesteps
 at only a small additional computational cost.

+If the {disc} keyword is used, then each particle is treated as a 2d
+disc (circle) instead of as a sphere.  This is only possible for 2d
+simulations, as defined by the "dimension"_dimension.html keyword.
+The only difference between discs and spheres in this context is their
+moment of inertia, as used in the time integration.
+
 :line

 Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
@ -98,6 +106,9 @@ command.
 All particles in the group must be finite-size spheres.  They cannot
 be point particles.

+Use of the {disc} keyword is only allowed for 2d simulations, as
+defined by the "dimension"_dimension.html keyword.
+
 [Related commands:]

 "fix nve"_fix_nve.html, "fix nve/asphere"_fix_nve_asphere.html
--- a/doc/src/fix_nvt_manifold_rattle.txt
+++ b/doc/src/fix_nvt_manifold_rattle.txt
@ -37,7 +37,7 @@ fix 1 all nvt/manifold/rattle 1e-4 10 cylinder 3.0 temp 1.0 1.0 10.0

 [Description:]

-This fix combines the RATTLE-based "(Andersen)"_#Andersen time integrator of "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html "(Paquay)"_#Paquay3 with a Nose-Hoover-chain thermostat to sample the
+This fix combines the RATTLE-based "(Andersen)"_#Andersen2 time integrator of "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html "(Paquay)"_#Paquay3 with a Nose-Hoover-chain thermostat to sample the
 canonical ensemble of particles constrained to a curved surface (manifold). This sampling does suffer from discretization bias of O(dt).
 For a list of currently supported manifolds and their parameters, see "manifolds"_manifolds.html

@ -72,7 +72,7 @@ section for more info.

 :line

-:link(Andersen)
+:link(Andersen2)
 [(Andersen)] Andersen, J. Comp. Phys. 52, 24, (1983).

 :link(Paquay3)
--- a/doc/src/fix_nvt_sllod.txt
+++ b/doc/src/fix_nvt_sllod.txt
@ -54,9 +54,9 @@ by fix nvt/sllod.  LAMMPS will give an error if this setting is not
 consistent.

 The SLLOD equations of motion, originally proposed by Hoover and Ladd
-(see "(Evans and Morriss)"_#Evans), were proven to be equivalent to
+(see "(Evans and Morriss)"_#Evans3), were proven to be equivalent to
 Newton's equations of motion for shear flow by "(Evans and
-Morriss)"_#Evans. They were later shown to generate the desired
+Morriss)"_#Evans3. They were later shown to generate the desired
 velocity gradient and the correct production of work by stresses for
 all forms of homogeneous flow by "(Daivis and Todd)"_#Daivis.  As
 implemented in LAMMPS, they are coupled to a Nose/Hoover chain
@ -173,7 +173,7 @@ Same as "fix nvt"_fix_nh.html, except tchain = 1.

 :line

-:link(Evans)
+:link(Evans3)
 [(Evans and Morriss)] Evans and Morriss, Phys Rev A, 30, 1528 (1984).

 :link(Daivis)
--- a/doc/src/fix_nvt_sllod_eff.txt
+++ b/doc/src/fix_nvt_sllod_eff.txt
@ -89,6 +89,6 @@ Same as "fix nvt/eff"_fix_nh_eff.html, except tchain = 1.

 :line

-:link(Tuckerman)
+:link(Tuckerman2)
 [(Tuckerman)] Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys,
 106, 5615 (1997).
--- a/doc/src/fix_nvt_sphere.txt
+++ b/doc/src/fix_nvt_sphere.txt
@ -13,13 +13,17 @@ fix nvt/sphere/omp command :h3

 fix ID group-ID nvt/sphere keyword value ... :pre

-ID, group-ID are documented in "fix"_fix.html command
-nvt/sphere = style name of this fix command
-additional thermostat related keyword/value pairs from the "fix nvt"_fix_nh.html command can be appended :ul
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+nvt/sphere = style name of this fix command :l
+zero or more keyword/value pairs may be appended :l
+keyword = {disc} :l
+  {disc} value = none = treat particles as 2d discs, not spheres :pre
+additional thermostat related keyword/value pairs from the "fix nvt"_fix_nh.html command can be appended :l,ule

 [Examples:]

 fix 1 all nvt/sphere temp 300.0 300.0 100.0
+fix 1 all nvt/sphere temp 300.0 300.0 100.0 disc
 fix 1 all nvt/sphere temp 300.0 300.0 100.0 drag 0.2 :pre

 [Description:]
@ -40,6 +44,12 @@ degrees of freedom (see below).  The translational degrees of freedom
 can also have a bias velocity removed from them before thermostatting
 takes place; see the description below.

+If the {disc} keyword is used, then each particle is treated as a 2d
+disc (circle) instead of as a sphere.  This is only possible for 2d
+simulations, as defined by the "dimension"_dimension.html keyword.
+The only difference between discs and spheres in this context is their
+moment of inertia, as used in the time integration.
+
 Additional parameters affecting the thermostat are specified by
 keywords and values documented with the "fix nvt"_fix_nh.html
 command.  See, for example, discussion of the {temp} and {drag}
@ -140,6 +150,9 @@ command.
 All particles in the group must be finite-size spheres.  They cannot
 be point particles.

+Use of the {disc} keyword is only allowed for 2d simulations, as
+defined by the "dimension"_dimension.html keyword.
+
 [Related commands:]

 "fix nvt"_fix_nh.html, "fix nve_sphere"_fix_nve_sphere.html, "fix
--- a/doc/src/fix_pour.txt
+++ b/doc/src/fix_pour.txt
@ -117,6 +117,12 @@ treated as rigid bodies, use the {rigid} keyword, specifying as its
 value the ID of a separate "fix rigid/small"_fix_rigid.html
 command which also appears in your input script.

+NOTE: If you wish the new rigid molecules (and other rigid molecules)
+to be thermostatted correctly via "fix rigid/small/nvt"_fix_rigid.html
+or "fix rigid/small/npt"_fix_rigid.html, then you need to use the
+"fix_modify dynamic/dof yes" command for the rigid fix.  This is to
+inform that fix that the molecule count will vary dynamically.
+
 If you wish to insert molecules via the {mol} keyword, that will have
 their bonds or angles constrained via SHAKE, use the {shake} keyword,
 specifying as its value the ID of a separate "fix
--- a/doc/src/fix_press_berendsen.txt
+++ b/doc/src/fix_press_berendsen.txt
@ -35,7 +35,7 @@ fix 2 all press/berendsen aniso 0.0 0.0 1000.0 dilate partial :pre
 [Description:]

 Reset the pressure of the system by using a Berendsen barostat
-"(Berendsen)"_#Berendsen, which rescales the system volume and
+"(Berendsen)"_#Berendsen1, which rescales the system volume and
 (optionally) the atoms coordinates within the simulation box every
 timestep.

@ -221,7 +221,7 @@ pressure for whatever "units"_units.html are defined.

 :line

-:link(Berendsen)
+:link(Berendsen1)

 [(Berendsen)] Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
 Phys, 81, 3684 (1984).
--- a/doc/src/fix_qeq.txt
+++ b/doc/src/fix_qeq.txt
@ -43,8 +43,8 @@ fix 1 all qeq/fire 1 10 1.0e-3 100 my_qeq qdamp 0.2 qstep 0.1 :pre
 [Description:]

 Perform the charge equilibration (QEq) method as described in "(Rappe
-and Goddard)"_#Rappe and formulated in "(Nakano)"_#Nakano (also known
-as the matrix inversion method) and in "(Rick and Stuart)"_#Rick (also
+and Goddard)"_#Rappe1 and formulated in "(Nakano)"_#Nakano1 (also known
+as the matrix inversion method) and in "(Rick and Stuart)"_#Rick1 (also
 known as the extended Lagrangian method) based on the
 electronegativity equilization principle.

@ -97,8 +97,8 @@ below, thus the others can be set to 0.0 if desired.
 {chi} = electronegativity in energy units
 {eta} = self-Coulomb potential in energy units
 {gamma} = shielded Coulomb constant defined by "ReaxFF force field"_#vanDuin in distance units
-{zeta} = Slater type orbital exponent defined by the "Streitz-Mintmire"_#Streitz potential in reverse distance units
-{qcore} = charge of the nucleus defined by the "Streitz-Mintmire potential"_#Streitz potential in charge units :ul
+{zeta} = Slater type orbital exponent defined by the "Streitz-Mintmire"_#Streitz1 potential in reverse distance units
+{qcore} = charge of the nucleus defined by the "Streitz-Mintmire potential"_#Streitz1 potential in charge units :ul

 The {qeq/point} style describes partial charges on atoms as point
 charges.  Interaction between a pair of charged particles is 1/r,
@ -126,7 +126,7 @@ charge densities centered around atoms via the Slater 1{s} orbital, so
 that the interaction between a pair of charged particles is the
 product of two Slater 1{s} orbitals.  The expression for the Slater
 1{s} orbital is given under equation (6) of the
-"Streitz-Mintmire"_#Streitz paper.  Only the {chi}, {eta}, {zeta}, and
+"Streitz-Mintmire"_#Streitz1 paper.  Only the {chi}, {eta}, {zeta}, and
 {qcore} parameters from the {qfile} file are used.  This style solves
 partial charges on atoms via the matrix inversion method.  A tolerance
 of 1.0e-6 is usually a good number.  Keyword {alpha} can be used to
@ -194,18 +194,18 @@ LAMMPS"_Section_start.html#start_3 section for more info.

 :line

-:link(Rappe)
+:link(Rappe1)
 [(Rappe and Goddard)] A. K. Rappe and W. A. Goddard III, J Physical
 Chemistry, 95, 3358-3363 (1991).

-:link(Nakano)
+:link(Nakano1)
 [(Nakano)] A. Nakano, Computer Physics Communications, 104, 59-69 (1997).

-:link(Rick)
+:link(Rick1)
 [(Rick and Stuart)] S. W. Rick, S. J. Stuart, B. J. Berne, J Chemical Physics
 101, 16141 (1994).

-:link(Streitz)
+:link(Streitz1)
 [(Streitz-Mintmire)] F. H. Streitz, J. W. Mintmire, Physical Review B, 50,
 16, 11996 (1994)

--- a/doc/src/fix_qeq_reax.txt
+++ b/doc/src/fix_qeq_reax.txt
@ -28,7 +28,7 @@ fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq :pre
 [Description:]

 Perform the charge equilibration (QEq) method as described in "(Rappe
-and Goddard)"_#Rappe and formulated in "(Nakano)"_#Nakano.  It is
+and Goddard)"_#Rappe2 and formulated in "(Nakano)"_#Nakano2.  It is
 typically used in conjunction with the ReaxFF force field model as
 implemented in the "pair_style reax/c"_pair_reax_c.html command, but
 it can be used with any potential in LAMMPS, so long as it defines and
@ -36,7 +36,7 @@ uses charges on each atom.  The "fix qeq/comb"_fix_qeq_comb.html
 command should be used to perform charge equilibration with the "COMB
 potential"_pair_comb.html.  For more technical details about the
 charge equilibration performed by fix qeq/reax, see the
-"(Aktulga)"_#Aktulga paper.
+"(Aktulga)"_#qeq-Aktulga paper.

 The QEq method minimizes the electrostatic energy of the system by
 adjusting the partial charge on individual atoms based on interactions
@ -112,13 +112,13 @@ be used for periodic cell dimensions less than 10 angstroms.

 :line

-:link(Rappe)
+:link(Rappe2)
 [(Rappe)] Rappe and Goddard III, Journal of Physical Chemistry, 95,
 3358-3363 (1991).

-:link(Nakano)
+:link(Nakano2)
 [(Nakano)] Nakano, Computer Physics Communications, 104, 59-69 (1997).

-:link(Aktulga)
-(Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
+:link(qeq-Aktulga)
+[(Aktulga)] Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
 245-259 (2012).
--- a/doc/src/fix_rigid.txt
+++ b/doc/src/fix_rigid.txt
@ -93,7 +93,7 @@ Examples of large rigid bodies are a colloidal particle, or portions
 of a biomolecule such as a protein.

 Example of small rigid bodies are patchy nanoparticles, such as those
-modeled in "this paper"_#Zhang by Sharon Glotzer's group, clumps of
+modeled in "this paper"_#Zhang1 by Sharon Glotzer's group, clumps of
 granular particles, lipid molecules consiting of one or more point
 dipoles connected to other spheroids or ellipsoids, irregular
 particles built from line segments (2d) or triangles (3d), and
@ -299,12 +299,12 @@ perform constant NVE time integration.  They are referred to below as
 the 4 NVE rigid styles.  The only difference is that the {rigid} and
 {rigid/small} styles use an integration technique based on Richardson
 iterations.  The {rigid/nve} and {rigid/small/nve} styles uses the
-methods described in the paper by "Miller"_#Miller, which are thought
+methods described in the paper by "Miller"_#Miller3, which are thought
 to provide better energy conservation than an iterative approach.

 The {rigid/nvt} and {rigid/nvt/small} styles performs constant NVT
 integration using a Nose/Hoover thermostat with chains as described
-originally in "(Hoover)"_#Hoover and "(Martyna)"_#Martyna, which
+originally in "(Hoover)"_#Hoover and "(Martyna)"_#Martyna2, which
 thermostats both the translational and rotational degrees of freedom
 of the rigid bodies.  They are referred to below as the 2 NVT rigid
 styles.  The rigid-body algorithm used by {rigid/nvt} is described in
@ -788,13 +788,13 @@ torque.  Also Tchain = Pchain = 10, Titer = 1, Torder = 3.
 :link(Kamberaj)
 [(Kamberaj)] Kamberaj, Low, Neal, J Chem Phys, 122, 224114 (2005).

-:link(Martyna)
+:link(Martyna2)
 [(Martyna)] Martyna, Klein, Tuckerman, J Chem Phys, 97, 2635 (1992);
 Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117.

-:link(Miller)
+:link(Miller3)
 [(Miller)] Miller, Eleftheriou, Pattnaik, Ndirango, and Newns,
 J Chem Phys, 116, 8649 (2002).

-:link(Zhang)
+:link(Zhang1)
 [(Zhang)] Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004).
--- a/doc/src/fix_shake.txt
+++ b/doc/src/fix_shake.txt
@ -53,7 +53,7 @@ velocities are approximated as finite differences to the trajectories
 integrated explicitly, as with velocity Verlet which is what LAMMPS
 uses as an integration method, a second set of constraining forces is
 required in order to eliminate velocity components along the bonds
-("Andersen (1983)"_#Andersen).
+("Andersen (1983)"_#Andersen3).

 In order to formulate individual constraints for SHAKE and RATTLE,
 focus on a single molecule whose bonds are constrained.  Let Ri and Vi
@ -171,7 +171,7 @@ more instructions on how to use the accelerated styles effectively.

 The velocity constraints lead to a linear system of equations which
 can be solved analytically.  The implementation of the algorithm in
-LAMMPS closely follows ("Andersen (1983)"_#Andersen).
+LAMMPS closely follows ("Andersen (1983)"_#Andersen3).

 NOTE: The fix rattle command modifies forces and velocities and thus
 should be defined after all other integration fixes in your input
@ -223,5 +223,5 @@ SHAKE or RATTLE should not be used to constrain an angle at 180 degrees
 [(Ryckaert)] J.-P. Ryckaert, G. Ciccotti and H. J. C. Berendsen,
 J of Comp Phys, 23, 327-341 (1977).

-:link(Andersen)
+:link(Andersen3)
 [(Andersen)] H. Andersen, J of Comp Phys, 52, 24-34 (1983).
--- a/doc/src/fix_shardlow.txt
+++ b/doc/src/fix_shardlow.txt
@ -30,7 +30,7 @@ nve"_fix_nve.html or "fix nph"_fix_nh.html).  The stochastic
 integration of the dissipative and random forces is performed prior to
 the deterministic integration of the conservative force. Further
 details regarding the method are provided in "(Lisal)"_#Lisal and
-"(Larentzos1)"_#Larentzos1.
+"(Larentzos1)"_#Larentzos1sh.

 The fix {shardlow} must be used with the "pair_style
 dpd/fdt"_pair_style.html or "pair_style
@ -83,13 +83,13 @@ particle dynamics as isothermal, isobaric, isoenergetic, and
 isoenthalpic conditions using Shardlow-like splitting algorithms.",
 J. Chem. Phys., 135, 204105 (2011).

-:link(Larentzos1)
+:link(Larentzos1sh)
 [(Larentzos1)] J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and
 W.D. Mattson, "Parallel Implementation of Isothermal and Isoenergetic
 Dissipative Particle Dynamics Using Shardlow-Like Splitting
 Algorithms", Comput. Phys. Commun., 185, 1987-1998 (2014).

-:link(Larentzos2)
+:link(Larentzos2sh)
 [(Larentzos2)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and
 W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
 Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
--- a/doc/src/fix_srd.txt
+++ b/doc/src/fix_srd.txt
@ -72,7 +72,7 @@ viscosity"_fix_viscosity.html, and "fix nvt/sllod"_fix_nvt_sllod.html,
 can be used in conjunction with the SRD model.

 For more details on how the SRD model is implemented in LAMMPS, "this
-paper"_#Petersen describes the implementation and usage of pure SRD
+paper"_#Petersen1 describes the implementation and usage of pure SRD
 fluids.  "This paper"_#Lechman, which is nearly complete, describes
 the implementation and usage of mixture systems (solute particles in
 an SRD fluid).  See the examples/srd directory for sample input
@ -390,7 +390,7 @@ rescale = yes.
 :link(Hecht)
 [(Hecht)] Hecht, Harting, Ihle, Herrmann, Phys Rev E, 72, 011408 (2005).

-:link(Petersen)
+:link(Petersen1)
 [(Petersen)] Petersen, Lechman, Plimpton, Grest, in' t Veld, Schunk, J
 Chem Phys, 132, 174106 (2010).

--- a/doc/src/fix_temp_berendsen.txt
+++ b/doc/src/fix_temp_berendsen.txt
@ -26,7 +26,7 @@ fix 1 all temp/berendsen 300.0 300.0 100.0 :pre
 [Description:]

 Reset the temperature of a group of atoms by using a Berendsen
-thermostat "(Berendsen)"_#Berendsen, which rescales their velocities
+thermostat "(Berendsen)"_#Berendsen2, which rescales their velocities
 every timestep.

 The thermostat is applied to only the translational degrees of freedom
@ -157,7 +157,7 @@ temp/rescale"_fix_temp_rescale.html, "fix langevin"_fix_langevin.html,

 :line

-:link(Berendsen)
+:link(Berendsen2)

 [(Berendsen)] Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
 Phys, 81, 3684 (1984).
--- a/doc/src/fix_thermal_conductivity.txt
+++ b/doc/src/fix_thermal_conductivity.txt
@ -31,7 +31,7 @@ fix 1 all thermal/conductivity 50 z 20 swap 2 :pre
 [Description:]

 Use the Muller-Plathe algorithm described in "this
-paper"_#Muller-Plathe to exchange kinetic energy between two particles
+paper"_#Muller-Plathe1 to exchange kinetic energy between two particles
 in different regions of the simulation box every N steps.  This
 induces a temperature gradient in the system.  As described below this
 enables the thermal conductivity of a material to be calculated.  This
@ -85,7 +85,7 @@ quantity by time and the cross-sectional area of the simulation box
 yields a heat flux.  The ratio of heat flux to the slope of the
 temperature profile is proportional to the thermal conductivity of the
 fluid, in appropriate units.  See the "Muller-Plathe
-paper"_#Muller-Plathe for details.
+paper"_#Muller-Plathe1 for details.

 NOTE: If your system is periodic in the direction of the heat flux,
 then the flux is going in 2 directions.  This means the effective heat
@ -136,7 +136,7 @@ kinetic energy of atoms that are in constrained molecules, e.g. via
 "fix shake"_fix_shake.html or "fix rigid"_fix_rigid.html.  This is
 because application of the constraints will alter the amount of
 transferred momentum.  You should, however, be able to use flexible
-molecules.  See the "Zhang paper"_#Zhang for a discussion and results
+molecules.  See the "Zhang paper"_#Zhang2 for a discussion and results
 of this idea.

 When running a simulation with large, massive particles or molecules
@ -155,9 +155,9 @@ The option defaults are swap = 1.

 :line

-:link(Muller-Plathe)
+:link(Muller-Plathe1)
 [(Muller-Plathe)] Muller-Plathe, J Chem Phys, 106, 6082 (1997).

-:link(Zhang)
+:link(Zhang2)
 [(Zhang)] Zhang, Lussetti, de Souza, Muller-Plathe, J Phys Chem B,
 109, 15060-15067 (2005).
--- a/doc/src/fix_viscosity.txt
+++ b/doc/src/fix_viscosity.txt
@ -33,7 +33,7 @@ fix 1 all viscosity 50 x z 20 swap 2 vtarget 1.5 :pre
 [Description:]

 Use the Muller-Plathe algorithm described in "this
-paper"_#Muller-Plathe to exchange momenta between two particles in
+paper"_#Muller-Plathe2 to exchange momenta between two particles in
 different regions of the simulation box every N steps.  This induces a
 shear velocity profile in the system.  As described below this enables
 a viscosity of the fluid to be calculated.  This algorithm is
@ -83,7 +83,7 @@ quantity by time and the cross-sectional area of the simulation box
 yields a momentum flux.  The ratio of momentum flux to the slope of
 the shear velocity profile is proportional to the viscosity of the
 fluid, in appropriate units.  See the "Muller-Plathe
-paper"_#Muller-Plathe for details.
+paper"_#Muller-Plathe2 for details.

 NOTE: If your system is periodic in the direction of the momentum
 flux, then the flux is going in 2 directions.  This means the
@ -161,7 +161,7 @@ The option defaults are swap = 1 and vtarget = INF.

 :line

-:link(Muller-Plathe)
+:link(Muller-Plathe2)
 [(Muller-Plathe)] Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999).

 :link(Maginn)
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@ -42,6 +42,7 @@ Fixes :h1
   fix_eos_table_rx
   fix_evaporate
   fix_external
+   fix_filter_corotate
   fix_flow_gauss
   fix_freeze
   fix_gcmc
--- a/doc/src/info.txt
+++ b/doc/src/info.txt
@ -12,7 +12,7 @@ info command :h3

 info args :pre

-args = one or more of the following keywords: {out}, {all}, {system}, {communication}, {computes}, {dumps}, {fixes}, {groups}, {regions}, {variables}, {styles}, {time}, or {configuration}
+args = one or more of the following keywords: {out}, {all}, {system}, {memory}, {communication}, {computes}, {dumps}, {fixes}, {groups}, {regions}, {variables}, {styles}, {time}, or {configuration}
     {out} values = {screen}, {log}, {append} filename, {overwrite} filename
     {styles} values = {all}, {angle}, {atom}, {bond}, {compute}, {command}, {dump}, {dihedral}, {fix}, {improper}, {integrate}, {kspace}, {minimize}, {pair}, {region} :ul

@ -40,6 +40,17 @@ to that file, which is either appended to or overwritten, respectively.

 The {all} flag activates printing all categories listed below.

+The {configuration} category prints some information about the
+LAMMPS version as well as architecture and OS it is run on.
+
+The {memory} category prints some information about the current
+memory allocation of MPI rank 0 (this the amount of dynamically
+allocated memory reported by LAMMPS classes). Where supported,
+also some OS specific information about the size of the reserved
+memory pool size (this is where malloc() and the new operator
+request memory from) and the maximum resident set size is reported
+(this is the maximum amount of physical memory occupied so far).
+
 The {system} category prints a general system overview listing.  This
 includes the unit style, atom style, number of atoms, bonds, angles,
 dihedrals, and impropers and the number of the respective types, box
@ -93,11 +104,6 @@ region :ul
 The {time} category prints the accumulated CPU and wall time for the
 process that writes output (usually MPI rank 0).

-The {configuration} command prints some information about the LAMMPS
-version and architecture and OS it is run on. Where supported, also
-information about the memory consumption provided by the OS is
-reported.
-
 [Restrictions:] none

 [Related commands:]
--- a/doc/src/kspace_modify.txt
+++ b/doc/src/kspace_modify.txt
@ -206,7 +206,7 @@ beginning of the run to give the desired estimated error. Other
 cutoffs such as LJ will not be affected. If the grid is not set using
 the {mesh} command, this command will also attempt to use the optimal
 grid that minimizes cost using an estimate given by
-"(Hardy)"_#Hardy. Note that this cost estimate is not exact, somewhat
+"(Hardy)"_#Hardy1. Note that this cost estimate is not exact, somewhat
 experimental, and still may not yield the optimal parameters.

 The {pressure/scalar} keyword applies only to MSM. If this option is
@ -235,7 +235,7 @@ collective operations and adequate hardware.
 The {diff} keyword specifies the differentiation scheme used by the
 PPPM method to compute forces on particles given electrostatic
 potentials on the PPPM mesh.  The {ik} approach is the default for
-PPPM and is the original formulation used in "(Hockney)"_#Hockney.  It
+PPPM and is the original formulation used in "(Hockney)"_#Hockney1.  It
 performs differentiation in Kspace, and uses 3 FFTs to transfer each
 component of the computed fields back to real space for total of 4
 FFTs per timestep.
@ -271,7 +271,7 @@ speed-up the simulations but introduces some error in the force
 computations, as shown in "(Wennberg)"_#Wennberg.  With {none}, it is
 assumed that no mixing rule is applicable. Splitting of the dispersion
 coefficients will be performed as described in
-"(Isele-Holder)"_#Isele-Holder.  This splitting can be influenced with
+"(Isele-Holder)"_#Isele-Holder1.  This splitting can be influenced with
 the {splittol} keywords. Only the eigenvalues that are larger than tol
 compared to the largest eigenvalues are included. Using this keywords
 the original matrix of dispersion coefficients is approximated. This
@ -280,7 +280,7 @@ computations of the dispersion part is decreased.

 The {force/disp/real} and {force/disp/kspace} keywords set the force
 accuracy for the real and space computations for the dispersion part
-of pppm/disp. As shown in "(Isele-Holder)"_#Isele-Holder, optimal
+of pppm/disp. As shown in "(Isele-Holder)"_#Isele-Holder1, optimal
 performance and accuracy in the results is obtained when these values
 are different.

@ -311,7 +311,7 @@ split = 0, tol = 1.0e-6, and disp/auto = no.

 :line

-:link(Hockney)
+:link(Hockney1)
 [(Hockney)] Hockney and Eastwood, Computer Simulation Using Particles,
 Adam Hilger, NY (1989).

@ -325,7 +325,7 @@ Adam Hilger, NY (1989).
 :link(Klapp)
 [(Klapp)] Klapp, Schoen, J Chem Phys, 117, 8050 (2002).

-:link(Hardy)
+:link(Hardy1)
 [(Hardy)] David Hardy thesis: Multilevel Summation for the Fast
 Evaluation of Forces for the Simulation of Biomolecules, University of
 Illinois at Urbana-Champaign, (2006).
@ -333,7 +333,7 @@ Illinois at Urbana-Champaign, (2006).
 :link(Hummer)
 [(Hummer)] Hummer, Gronbech-Jensen, Neumann, J Chem Phys, 109, 2791 (1998)

-:link(Isele-Holder)
+:link(Isele-Holder1)
 [(Isele-Holder)] Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J
 Chem Theory Comput, 9, 5412 (2013).

--- a/doc/src/kspace_style.txt
+++ b/doc/src/kspace_style.txt
@ -152,7 +152,7 @@ such as when using a barostat.
 :line

 The {pppm/disp} and {pppm/disp/tip4p} styles add a mesh-based long-range
-dispersion sum option for 1/r^6 potentials "(Isele-Holder)"_#Isele-Holder,
+dispersion sum option for 1/r^6 potentials "(Isele-Holder)"_#Isele-Holder2012,
 similar to the {ewald/disp} style. The 1/r^6 capability means
 that Lennard-Jones or Buckingham potentials can be used without a cutoff,
 i.e. they become full long-range potentials.
@ -163,8 +163,8 @@ This can be done by either choosing the Ewald and grid parameters, or
 by specifying separate accuracies for the real and kspace
 calculations. When not making any settings, the simulation will stop with
 an error message. Further information on the influence of the parameters
-and how to choose them is described in "(Isele-Holder)"_#Isele-Holder,
-"(Isele-Holder2)"_#Isele-Holder2 and the
+and how to choose them is described in "(Isele-Holder)"_#Isele-Holder2012,
+"(Isele-Holder2)"_#Isele-Holder2013 and the
 "How-To"_Section_howto.html#howto_24 discussion.

 :line
@ -182,13 +182,13 @@ currently support the -DFFT_SINGLE compiler switch.
 :line

 The {msm} style invokes a multi-level summation method MSM solver,
-"(Hardy)"_#Hardy or "(Hardy2)"_#Hardy2, which maps atom charge to a 3d
-mesh, and uses a multi-level hierarchy of coarser and coarser meshes
-on which direct coulomb solves are done.  This method does not use
-FFTs and scales as N. It may therefore be faster than the other
+"(Hardy)"_#Hardy2006 or "(Hardy2)"_#Hardy2009, which maps atom charge
+to a 3d mesh, and uses a multi-level hierarchy of coarser and coarser
+meshes on which direct coulomb solves are done.  This method does not
+use FFTs and scales as N. It may therefore be faster than the other
 K-space solvers for relatively large problems when running on large
-core counts. MSM can also be used for non-periodic boundary conditions and
-for mixed periodic and non-periodic boundaries.
+core counts. MSM can also be used for non-periodic boundary conditions
+and for mixed periodic and non-periodic boundaries.

 MSM is most competitive versus Ewald and PPPM when only relatively
 low accuracy forces, about 1e-4 relative error or less accurate,
@ -247,7 +247,7 @@ equation 9 of "(Petersen)"_#Petersen. RMS force errors in K-space for
 which is similar to equation 32 of "(Kolafa)"_#Kolafa. RMS force
 errors in K-space for {pppm} are estimated using equation 38 of
 "(Deserno)"_#Deserno. RMS force errors for {msm} are estimated
-using ideas from chapter 3 of "(Hardy)"_#Hardy, with equation 3.197
+using ideas from chapter 3 of "(Hardy)"_#Hardy2006, with equation 3.197
 of particular note. When using {msm} with non-periodic boundary
 conditions, it is expected that the error estimation will be too
 pessimistic. RMS force errors for dipoles when using {ewald/disp}
@ -366,19 +366,19 @@ and Computation 5, 2322 (2009)
 [(Toukmaji)] Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113,
 10913 (2000).

-:link(Isele-Holder)
+:link(Isele-Holder2012)
 [(Isele-Holder)] Isele-Holder, Mitchell, Ismail, J Chem Phys, 137,
 174107 (2012).

-:link(Isele-Holder2)
+:link(Isele-Holder2013)
 [(Isele-Holder2)] Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail,
 J Chem Theory Comput 9, 5412 (2013).

-:link(Hardy)
+:link(Hardy2006)
 [(Hardy)] David Hardy thesis: Multilevel Summation for the Fast
 Evaluation of Forces for the Simulation of Biomolecules, University of
 Illinois at Urbana-Champaign, (2006).

-:link(Hardy2)
-[(Hardy)] Hardy, Stone, Schulten, Parallel Computing 35 (2009)
+:link(Hardy2009)
+[(Hardy2)] Hardy, Stone, Schulten, Parallel Computing 35 (2009)
 164-177.
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@ -168,6 +168,7 @@ fix_eos_table.html
 fix_eos_table_rx.html
 fix_evaporate.html
 fix_external.html
+fix_filter_corotate.html
 fix_flow_gauss.html
 fix_freeze.html
 fix_gcmc.html
@ -455,6 +456,7 @@ pair_meam_spline.html
 pair_meam_sw_spline.html
 pair_mgpt.html
 pair_mie.html
+pair_momb.html
 pair_morse.html
 pair_multi_lucy.html
 pair_multi_lucy_rx.html
@ -462,6 +464,7 @@ pair_nb3b_harmonic.html
 pair_nm.html
 pair_none.html
 pair_oxdna.html
+pair_oxdna2.html
 pair_peri.html
 pair_polymorphic.html
 pair_quip.html
--- a/doc/src/neb.txt
+++ b/doc/src/neb.txt
@ -44,7 +44,7 @@ of the energy barrier associated with a transition state, e.g. for an
 atom to perform a diffusive hop from one energy basin to another in a
 coordinated fashion with its neighbors.  The implementation in LAMMPS
 follows the discussion in these 3 papers: "(HenkelmanA)"_#HenkelmanA,
-"(HenkelmanB)"_#HenkelmanB, and "(Nakano)"_#Nakano.
+"(HenkelmanB)"_#HenkelmanB, and "(Nakano)"_#Nakano3.

 Each replica runs on a partition of one or more processors.  Processor
 partitions are defined at run-time using the -partition command-line
@ -412,5 +412,5 @@ langevin"_fix_langevin.html, "fix viscous"_fix_viscous.html
 [(HenkelmanB)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
 9901-9904 (2000).

-:link(Nakano)
+:link(Nakano3)
 [(Nakano)] Nakano, Comp Phys Comm, 178, 280-289 (2008).
--- a/doc/src/package.txt
+++ b/doc/src/package.txt
@ -62,12 +62,13 @@ args = arguments specific to the style :l
      {no_affinity} values = none
  {kokkos} args = keyword value ...
    zero or more keyword/value pairs may be appended
-    keywords = {neigh} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward}
-      {neigh} value = {full} or {half} or {n2} or {full/cluster}
+    keywords = {neigh} or {neigh/qeq} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward}
+      {neigh} value = {full} or {half}
+        full = full neighbor list
+        half = half neighbor list built in thread-safe manner
+      {neigh/qeq} value = {full} or {half}
        full = full neighbor list
        half = half neighbor list built in thread-safe manner
-        n2 = non-binning neighbor list build, O(N^2) algorithm
-        full/cluster = full neighbor list with clustered groups of atoms
      {newton} = {off} or {on}
        off = set Newton pairwise and bonded flags off (default)
        on = set Newton pairwise and bonded flags on
@ -392,10 +393,7 @@ default value as listed below.

 The {neigh} keyword determines how neighbor lists are built.  A value
 of {half} uses a thread-safe variant of half-neighbor lists,
-the same as used by most pair styles in LAMMPS.  A value of
-{n2} uses an O(N^2) algorithm to build the neighbor list without
-binning, where N = # of atoms on a processor.  It is typically slower
-than the other methods, which use binning.
+the same as used by most pair styles in LAMMPS.

 A value of {full} uses a full neighbor lists and is the default.  This
 performs twice as much computation as the {half} option, however that
@ -403,15 +401,9 @@ is often a win because it is thread-safe and doesn't require atomic
 operations in the calculation of pair forces.  For that reason, {full}
 is the default setting.  However, when running in MPI-only mode with 1
 thread per MPI task, {half} neighbor lists will typically be faster,
-just as it is for non-accelerated pair styles.
-
-A value of {full/cluster} is an experimental neighbor style, where
-particles interact with all particles within a small cluster, if at
-least one of the clusters particles is within the neighbor cutoff
-range.  This potentially allows for better vectorization on
-architectures such as the Intel Phi.  If also reduces the size of the
-neighbor list by roughly a factor of the cluster size, thus reducing
-the total memory footprint considerably.
+just as it is for non-accelerated pair styles. Similarly, the {neigh/qeq}
+keyword determines how neighbor lists are built for "fix qeq/reax/kk"_fix_qeq_reax.html.
+If not explicitly set, the value of {neigh/qeq} will match {neigh}.

 The {newton} keyword sets the Newton flags for pairwise and bonded
 interactions to {off} or {on}, the same as the "newton"_newton.html
@ -582,9 +574,9 @@ is used.  If it is not used, you must invoke the package intel
 command in your input script or or via the "-pk intel" "command-line
 switch"_Section_start.html#start_7.

-For the KOKKOS package, the option defaults neigh = full, newton =
-off, binsize = 0.0, and comm = device.  These settings are made
-automatically by the required "-k on" "command-line
+For the KOKKOS package, the option defaults neigh = full, neigh/qeq
+ = full, newton = off, binsize = 0.0, and comm = device.  These settings
+ are made automatically by the required "-k on" "command-line
 switch"_Section_start.html#start_7.  You can change them bu using the
 package kokkos command in your input script or via the "-pk kokkos"
 "command-line switch"_Section_start.html#start_7.
--- a/doc/src/pair_bop.txt
+++ b/doc/src/pair_bop.txt
@ -137,7 +137,7 @@ and beta_pi,ij)(r_ij).

 The parameters/coefficients format for the different kinds of BOP
 files are given below with variables matching the formulation of Ward
-("Ward"_#Ward) and Zhou ("Zhou"_#Zhou). Each header line containing a
+("Ward"_#Ward) and Zhou ("Zhou"_#Zhou1). Each header line containing a
 ":" is preceded by a blank line.


@ -258,7 +258,7 @@ Line 2: (A_ij)^(mu*nu) (for e1-e2 and repeats as above) :ul
 The parameters/coefficients format for the BOP potentials input file
 containing pre-tabulated functions of g is given below with variables
 matching the formulation of Ward ("Ward"_#Ward).  This format also
-assumes the angular functions have the formulation of ("Zhou"_#Zhou).
+assumes the angular functions have the formulation of ("Zhou"_#Zhou1).

 Line 1: # elements N :ul

@ -314,7 +314,7 @@ The rest of the table has the same structure as the previous section
 The parameters/coefficients format for the BOP potentials input file
 containing pre-tabulated functions of g is given below with variables
 matching the formulation of Ward ("Ward"_#Ward).  This format also
-assumes the angular functions have the formulation of ("Zhou"_#Zhou).
+assumes the angular functions have the formulation of ("Zhou"_#Zhou1).

 Line 1: # elements N :ul

@ -425,5 +425,5 @@ Drautz, and D.G. Pettifor, Phys. Rev. B, 73, 45206 (2006).
 [(Ward)] D.K. Ward, X.W. Zhou, B.M. Wong, F.P. Doty, and J.A.
 Zimmerman, Phys. Rev. B, 85,115206 (2012).

-:link(Zhou)
+:link(Zhou1)
 [(Zhou)] X.W. Zhou, D.K. Ward, M. Foster (TBP).
--- a/doc/src/pair_charmm.txt
+++ b/doc/src/pair_charmm.txt
@ -17,12 +17,14 @@ pair_style lj/charmm/coul/long/opt command :h3
 pair_style lj/charmm/coul/long/omp command :h3
 pair_style lj/charmm/coul/msm command :h3
 pair_style lj/charmm/coul/msm/omp command :h3
+pair_style lj/charmmfsw/coul/charmmfsh command :h3
+pair_style lj/charmmfsw/coul/long command :h3

 [Syntax:]

 pair_style style args :pre

-style = {lj/charmm/coul/charmm} or {lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long} or {lj/charmm/coul/msm}
+style = {lj/charmm/coul/charmm} or {lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long} or {lj/charmm/coul/msm} or {lj/charmmfsw/coul/charmmfsh} or {lj/charmmfsw/coul/long}
 args = list of arguments for a particular style :ul
  {lj/charmm/coul/charmm} args = inner outer (inner2) (outer2)
    inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
@ -35,12 +37,20 @@ args = list of arguments for a particular style :ul
    cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
  {lj/charmm/coul/msm} args = inner outer (cutoff)
    inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
+    cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
+  {lj/charmmfsw/coul/charmmfsh} args = inner outer (cutoff)
+    inner, outer = global cutoffs for LJ (and Coulombic if only 2 args)
+    cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
+  {lj/charmmfsw/coul/long} args = inner outer (cutoff)
+    inner, outer = global cutoffs for LJ (and Coulombic if only 2 args)
    cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args) :pre

 [Examples:]

 pair_style lj/charmm/coul/charmm 8.0 10.0
 pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
+pair_style lj/charmmfsw/coul/charmmfsh 10.0 12.0
+pair_style lj/charmmfsw/coul/charmmfsh 10.0 12.0 9.0
 pair_coeff * * 100.0 2.0
 pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre

@ -51,6 +61,8 @@ pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre

 pair_style lj/charmm/coul/long 8.0 10.0
 pair_style lj/charmm/coul/long 8.0 10.0 9.0
+pair_style lj/charmmfsw/coul/long 8.0 10.0
+pair_style lj/charmmfsw/coul/long 8.0 10.0 9.0
 pair_coeff * * 100.0 2.0
 pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre

@ -61,21 +73,57 @@ pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre

 [Description:]

-The {lj/charmm} styles compute LJ and Coulombic interactions with an
-additional switching function S(r) that ramps the energy and force
-smoothly to zero between an inner and outer cutoff.  It is a widely
-used potential in the "CHARMM"_http://www.scripps.edu/brooks MD code.
-See "(MacKerell)"_#pair-MacKerell for a description of the CHARMM force
-field.
+These pair styles compute Lennard Jones (LJ) and Coulombic
+interactions with additional switching or shifting functions that ramp
+the energy and/or force smoothly to zero between an inner and outer
+cutoff.  They are implementations of the widely used CHARMM force
+field used in the "CHARMM"_http://www.scripps.edu/brooks MD code (and
+others).  See "(MacKerell)"_#pair-MacKerell for a description of the
+CHARMM force field.
+
+The styles with {charmm} (not {charmmfsw} or {charmmfsh}) in their
+name are the older, original LAMMPS implementations.  They compute the
+LJ and Coulombic interactions with an energy switching function (esw,
+shown in the formula below as S(r)), which ramps the energy smoothly
+to zero between the inner and outer cutoff.  This can cause
+irregularities in pair-wise forces (due to the discontinuous 2nd
+derivative of energy at the boundaries of the switching region), which
+in some cases can result in detectable artifacts in an MD simulation.
+
+The newer styles with {charmmfsw} or {charmmfsh} in their name replace
+the energy switching with force switching (fsw) and force shifting
+(fsh) functions, for LJ and Coulombic interactions respectively.
+These follow the formulas and description given in
+"(Steinbach)"_#Steinbach and "(Brooks)"_#Brooks1 to minimize these
+artifacts.
+
+NOTE: The newer {charmmfsw} or {charmmfsh} styles were released in
+March 2017.  We recommend they be used instead of the older {charmm}
+styles.  Eventually code from the new styles will propagate into the
+related pair styles (e.g. implicit, accelerator, free energy
+variants).
+
+The general CHARMM formulas are as follows

 :c,image(Eqs/pair_charmm.jpg)

-Both the LJ and Coulombic terms require an inner and outer cutoff.
-They can be the same for both formulas or different depending on
-whether 2 or 4 arguments are used in the pair_style command.  In each
-case, the inner cutoff distance must be less than the outer cutoff.
-It it typical to make the difference between the 2 cutoffs about 1.0
-Angstrom.
+where S(r) is the energy switching function mentioned above for the
+{charmm} styles.  See the "(Steinbach)"_#Steinbach paper for the
+functional forms of the force switching and force shifting functions
+used in the {charmmfsw} and {charmmfsh} styles.
+
+When using the {lj/charmm/coul/charmm styles}, both the LJ and
+Coulombic terms require an inner and outer cutoff. They can be the
+same for both formulas or different depending on whether 2 or 4
+arguments are used in the pair_style command.  For the
+{lj/charmmfsw/coul/charmmfsh} style, the LJ term requires both an
+inner and outer cutoff, while the Coulombic term requires only one
+cutoff.  If the Coulomb cutoff is not specified (2 instead of 3
+arguments), the LJ outer cutoff is used for the Coulombic cutoff.  In
+all cases where an inner and outer cutoff are specified, the inner
+cutoff distance must be less than the outer cutoff.  It is typical to
+make the difference between the inner and outer cutoffs about 2.0
+Angstroms.

 Style {lj/charmm/coul/charmm/implicit} computes the same formulas as
 style {lj/charmm/coul/charmm} except that an additional 1/r term is
@ -86,12 +134,18 @@ screening.  It is designed for use in a simulation of an unsolvated
 biomolecule (no explicit water molecules).

 Styles {lj/charmm/coul/long} and {lj/charmm/coul/msm} compute the same
-formulas as style {lj/charmm/coul/charmm} except that an additional
-damping factor is applied to the Coulombic term, as described for the
-"lj/cut"_pair_lj.html pair styles.  Only one Coulombic cutoff is
-specified for {lj/charmm/coul/long} and {lj/charmm/coul/msm}; if only
-2 arguments are used in the pair_style command, then the outer LJ
-cutoff is used as the single Coulombic cutoff.
+formulas as style {lj/charmm/coul/charmm} and style
+{lj/charmmfsw/coul/long} computes the same formulas as style
+{lj/charmmfsw/coul/charmmfsh}, except that an additional damping
+factor is applied to the Coulombic term, so it can be used in
+conjunction with the "kspace_style"_kspace_style.html command and its
+{ewald} or {pppm} or {msm} option.  Only one Coulombic cutoff is
+specified for these styles; if only 2 arguments are used in the
+pair_style command, then the outer LJ cutoff is used as the single
+Coulombic cutoff.  The Coulombic cutoff specified for these styles
+means that pairwise interactions within this distance are computed
+directly; interactions outside that distance are computed in
+reciprocal space.

 The following coefficients must be defined for each pair of atoms
 types via the "pair_coeff"_pair_coeff.html command as in the examples
@ -111,7 +165,7 @@ sigma.
 The latter 2 coefficients are optional.  If they are specified, they
 are used in the LJ formula between 2 atoms of these types which are
 also first and fourth atoms in any dihedral.  No cutoffs are specified
-because this CHARMM force field does not allow varying cutoffs for
+because the CHARMM force field does not allow varying cutoffs for
 individual atom pairs; all pairs use the global cutoff(s) specified in
 the pair_style command.

@ -148,38 +202,41 @@ mixed.  The default mix value is {arithmetic} to coincide with the
 usual settings for the CHARMM force field.  See the "pair_modify"
 command for details.

-None of the lj/charmm pair styles support the
+None of the {lj/charmm} or {lj/charmmfsw} pair styles support the
 "pair_modify"_pair_modify.html shift option, since the Lennard-Jones
 portion of the pair interaction is smoothed to 0.0 at the cutoff.

-The {lj/charmm/coul/long} style supports the
-"pair_modify"_pair_modify.html table option since it can tabulate the
-short-range portion of the long-range Coulombic interaction.
+The {lj/charmm/coul/long} and {lj/charmmfsw/coul/long} styles support
+the "pair_modify"_pair_modify.html table option since they can
+tabulate the short-range portion of the long-range Coulombic
+interaction.

-None of the lj/charmm pair styles support the
+None of the {lj/charmm} or {lj/charmmfsw} pair styles support the
 "pair_modify"_pair_modify.html tail option for adding long-range tail
 corrections to energy and pressure, since the Lennard-Jones portion of
 the pair interaction is smoothed to 0.0 at the cutoff.

-All of the lj/charmm pair styles write their information to "binary
-restart files"_restart.html, so pair_style and pair_coeff commands do
-not need to be specified in an input script that reads a restart file.
+All of the {lj/charmm} and {lj/charmmfsw} pair styles write their
+information to "binary restart files"_restart.html, so pair_style and
+pair_coeff commands do not need to be specified in an input script
+that reads a restart file.

-The lj/charmm/coul/long pair style supports the use of the {inner},
-{middle}, and {outer} keywords of the "run_style respa"_run_style.html
-command, meaning the pairwise forces can be partitioned by distance at
-different levels of the rRESPA hierarchy.  The other styles only
-support the {pair} keyword of run_style respa.  See the
-"run_style"_run_style.html command for details.
+The {lj/charmm/coul/long} and {lj/charmmfsw/coul/long} pair styles
+support the use of the {inner}, {middle}, and {outer} keywords of the
+"run_style respa"_run_style.html command, meaning the pairwise forces
+can be partitioned by distance at different levels of the rRESPA
+hierarchy.  The other styles only support the {pair} keyword of
+run_style respa.  See the "run_style"_run_style.html command for
+details.

 :line

 [Restrictions:]

-The {lj/charmm/coul/charmm} and {lj/charmm/coul/charmm/implicit}
-styles are part of the MOLECULE package.  The {lj/charmm/coul/long}
-style is part of the KSPACE package.  They are only enabled if LAMMPS
-was built with those packages.  See the "Making
+All the styles with {coul/charmm} or {coul/charmmfsh} styles are part
+of the MOLECULE package.  All the styles with {coul/long} style are
+part of the KSPACE package.  They are only enabled if LAMMPS was built
+with those packages.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.  Note that
 the MOLECULE and KSPACE packages are installed by default.

@ -191,6 +248,13 @@ the MOLECULE and KSPACE packages are installed by default.

 :line

+:link(Brooks1)
+[(Brooks)] Brooks, et al, J Comput Chem, 30, 1545 (2009).
+
 :link(pair-MacKerell)
 [(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
 Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
+
+:link(Steinbach)
+[(Steinbach)] Steinbach, Brooks, J Comput Chem, 15, 667 (1994).
+
--- a/doc/src/pair_colloid.txt
+++ b/doc/src/pair_colloid.txt
@ -39,7 +39,7 @@ where A_cc is the Hamaker constant, a1 and a2 are the radii of the two
 colloidal particles, and Rc is the cutoff.  This equation results from
 describing each colloidal particle as an integrated collection of
 Lennard-Jones particles of size sigma and is derived in
-"(Everaers)"_#Everaers.
+"(Everaers)"_#Everaers1.

 The colloid-solvent interaction energy is given by

@ -201,5 +201,5 @@ only per-type polydispersity is enabled via the pair_coeff parameters.

 :line

-:link(Everaers)
+:link(Everaers1)
 [(Everaers)] Everaers, Ejtehadi, Phys Rev E, 67, 041710 (2003).
--- a/doc/src/pair_comb.txt
+++ b/doc/src/pair_comb.txt
@ -50,7 +50,7 @@ atoms {i} and {j},

 The COMB potentials (styles {comb} and {comb3}) are variable charge
 potentials.  The equilibrium charge on each atom is calculated by the
-electronegativity equalization (QEq) method.  See "Rick"_#Rick for
+electronegativity equalization (QEq) method.  See "Rick"_#Rick2 for
 further details.  This is implemented by the "fix
 qeq/comb"_fix_qeq_comb.html command, which should normally be
 specified in the input script when running a model with the COMB
@ -187,6 +187,6 @@ S. R. Phillpot, Phys. Rev. B 81, 125328 (2010)
 Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74,
 255-279 (2013).

-:link(Rick)
+:link(Rick2)
 [(Rick)] S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
 (1994).
--- a/doc/src/pair_coul.txt
+++ b/doc/src/pair_coul.txt
@ -109,7 +109,7 @@ mimic the screening effect of a polar solvent.
 :line

 Style {coul/dsf} computes Coulombic interactions via the damped
-shifted force model described in "Fennell"_#Fennell, given by:
+shifted force model described in "Fennell"_#Fennell1, given by:

 :c,image(Eqs/pair_coul_dsf.jpg)

@ -122,7 +122,7 @@ decay to zero.
 :line

 Style {coul/wolf} computes Coulombic interactions via the Wolf
-summation method, described in "Wolf"_#Wolf, given by:
+summation method, described in "Wolf"_#Wolf1, given by:

 :c,image(Eqs/pair_coul_wolf.jpg)

@ -143,7 +143,7 @@ interactions with a short-range potential.

 Style {coul/streitz} is the Coulomb pair interaction defined as part
 of the Streitz-Mintmire potential, as described in "this
-paper"_#Streitz, in which charge distribution about an atom is modeled
+paper"_#Streitz2, in which charge distribution about an atom is modeled
 as a Slater 1{s} orbital.  More details can be found in the referenced
 paper.  To fully reproduce the published Streitz-Mintmire potential,
 which is a variable charge potential, style {coul/streitz} must be
@ -205,7 +205,7 @@ added for the "core/shell model"_Section_howto.html#howto_25 to allow
 charges on core and shell particles to be separated by r = 0.0.

 Styles {tip4p/cut} and {tip4p/long} implement the coulomb part of
-the TIP4P water model of "(Jorgensen)"_#Jorgensen, which introduces
+the TIP4P water model of "(Jorgensen)"_#Jorgensen3, which introduces
 a massless site located a short distance away from the oxygen atom
 along the bisector of the HOH angle.  The atomic types of the oxygen and
 hydrogen atoms, the bond and angle types for OH and HOH interactions,
@ -325,14 +325,18 @@ hybrid/overlay"_pair_hybrid.html, "kspace_style"_kspace_style.html

 :line

-:link(Wolf)
+:link(Wolf1)
 [(Wolf)] D. Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem
 Phys, 110, 8254 (1999).

-:link(Fennell)
+:link(Fennell1)
 [(Fennell)] C. J. Fennell, J. D. Gezelter, J Chem Phys, 124,
 234104 (2006).

-:link(Streitz)
+:link(Streitz2)
 [(Streitz)] F. H. Streitz, J. W. Mintmire, Phys Rev B, 50, 11996-12003
 (1994).
+
+:link(Jorgensen3)
+[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
+Phys, 79, 926 (1983).
--- a/doc/src/pair_coul_diel.txt
+++ b/doc/src/pair_coul_diel.txt
@ -46,10 +46,10 @@ for water at 298K.

 Examples of the use of this type of Coulomb interaction include implicit
 solvent simulations of salt ions
-"(Lenart)"_#Lenart and of ionic surfactants "(Jusufi)"_#Jusufi.
+"(Lenart)"_#Lenart1 and of ionic surfactants "(Jusufi)"_#Jusufi1.
 Note that this potential is only reasonable for implicit solvent simulations
 and in combination with coul/cut or coul/long. It is also usually combined
-with gauss/cut, see "(Lenart)"_#Lenart or "(Jusufi)"_#Jusufi.
+with gauss/cut, see "(Lenart)"_#Lenart1 or "(Jusufi)"_#Jusufi1.

 The following coefficients must be defined for each pair of atom
 types via the "pair_coeff"_pair_coeff.html command as in the example
@ -103,10 +103,10 @@ LAMMPS"_Section_start.html#start_2_3 section for more info.
 [(Stiles)] Stiles , Hubbard, and Kayser, J Chem Phys, 77,
 6189 (1982).

-:link(Lenart)
+:link(Lenart1)
 [(Lenart)] Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126,
 044509 (2007).

-:link(Jusufi)
+:link(Jusufi1)
 [(Jusufi)] Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112,
 13783 (2008).
--- a/doc/src/pair_cs.txt
+++ b/doc/src/pair_cs.txt
@ -44,7 +44,7 @@ pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre
 [Description:]

 These pair styles are designed to be used with the adiabatic
-core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham.  See
+core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham2.  See
 "Section 6.25"_Section_howto.html#howto_25 of the manual for an
 overview of the model as implemented in LAMMPS.

@ -95,6 +95,6 @@ LAMMPS"_Section_start.html#start_3 section for more info.

 :line

-:link(MitchellFinchham)
+:link(MitchellFinchham2)
 [(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter,
 5, 1031-1038 (1993).
--- a/doc/src/pair_dipole.txt
+++ b/doc/src/pair_dipole.txt
@ -69,7 +69,7 @@ distance, and the vector r = Ri - Rj is the separation vector between
 the two particles.  Note that Eqq and Fqq are simply Coulombic energy
 and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
 torques do not act symmetrically.  These formulas are discussed in
-"(Allen)"_#Allen and in "(Toukmaji)"_#Toukmaji.
+"(Allen)"_#Allen2 and in "(Toukmaji)"_#Toukmaji2.

 Style {lj/sf/dipole/sf} computes "shifted-force" interactions between
 pairs of particles that each have a charge and/or a point dipole
@ -77,7 +77,7 @@ moment. In general, a shifted-force potential is a (sligthly) modified
 potential containing extra terms that make both the energy and its
 derivative go to zero at the cutoff distance; this removes
 (cutoff-related) problems in energy conservation and any numerical
-instability in the equations of motion "(Allen)"_#Allen. Shifted-force
+instability in the equations of motion "(Allen)"_#Allen2. Shifted-force
 interactions for the Lennard-Jones (E_LJ), charge-charge (Eqq),
 charge-dipole (Eqp), dipole-charge (Epq) and dipole-dipole (Epp)
 potentials are computed by these formulas for the energy (E), force
@ -95,11 +95,11 @@ and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
 torques do not act symmetrically.  The shifted-force formula for the
 Lennard-Jones potential is reported in "(Stoddard)"_#Stoddard.  The
 original (unshifted) formulas for the electrostatic potentials, forces
-and torques can be found in "(Price)"_#Price.  The shifted-force
+and torques can be found in "(Price)"_#Price2.  The shifted-force
 electrostatic potentials have been obtained by applying equation 5.13
-of "(Allen)"_#Allen. The formulas for the corresponding forces and
+of "(Allen)"_#Allen2. The formulas for the corresponding forces and
 torques have been obtained by applying the 'chain rule' as in appendix
-C.3 of "(Allen)"_#Allen.
+C.3 of "(Allen)"_#Allen2.

 If one cutoff is specified in the pair_style command, it is used for
 both the LJ and Coulombic (q,p) terms.  If two cutoffs are specified,
@ -110,7 +110,7 @@ scaled according to this factor. This scale factor is also made available
 for use with fix adapt.

 Style {lj/cut/dipole/long} computes long-range point-dipole
-interactions as discussed in "(Toukmaji)"_#Toukmaji. Dipole-dipole,
+interactions as discussed in "(Toukmaji)"_#Toukmaji2. Dipole-dipole,
 dipole-charge, and charge-charge interactions are all supported, along
 with the standard 12/6 Lennard-Jones interactions, which are computed
 with a cutoff.  A "kspace_style"_kspace_style.html must be defined to
@ -119,7 +119,7 @@ ewald/disp"_kspace_style.html support long-range point-dipole
 interactions.

 Style {lj/long/dipole/long} also computes point-dipole interactions as
-discussed in "(Toukmaji)"_#Toukmaji. Long-range dipole-dipole,
+discussed in "(Toukmaji)"_#Toukmaji2. Long-range dipole-dipole,
 dipole-charge, and charge-charge interactions are all supported, along
 with the standard 12/6 Lennard-Jones interactions.  LJ interactions
 can be cutoff or long-ranged.
@ -252,16 +252,16 @@ currently supported.

 :line

-:link(Allen)
+:link(Allen2)
 [(Allen)] Allen and Tildesley, Computer Simulation of Liquids,
 Clarendon Press, Oxford, 1987.

-:link(Toukmaji)
+:link(Toukmaji2)
 [(Toukmaji)] Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113,
 10913 (2000).

 :link(Stoddard)
 [(Stoddard)] Stoddard and Ford, Phys Rev A, 8, 1504 (1973).

-:link(Price)
+:link(Price2)
 [(Price)] Price, Stone and Alderton, Mol Phys, 52, 987 (1984).
--- a/doc/src/pair_dpd_fdt.txt
+++ b/doc/src/pair_dpd_fdt.txt
@ -37,7 +37,7 @@ Styles {dpd/fdt} and {dpd/fdt/energy} compute the force for dissipative
 particle dynamics (DPD) simulations.  The {dpd/fdt} style is used to
 perform DPD simulations under isothermal and isobaric conditions,
 while the {dpd/fdt/energy} style is used to perform DPD simulations
-under isoenergetic and isoenthalpic conditions (see "(Lisal)"_#Lisal).
+under isoenergetic and isoenthalpic conditions (see "(Lisal)"_#Lisal3).
 For DPD simulations in general, the force on atom I due to atom J is
 given as a sum of 3 terms

@ -111,7 +111,7 @@ calculated using only the conservative term.

 The forces computed through the {dpd/fdt} and {dpd/fdt/energy} styles
 can be integrated with the velocity-Verlet integration scheme or the
-Shardlow splitting integration scheme described by "(Lisal)"_#Lisal.
+Shardlow splitting integration scheme described by "(Lisal)"_#Lisal3.
 In the cases when these pair styles are combined with the
 "fix shardlow"_fix_shardlow.html, these pair styles differ from the
 other dpd styles in that the dissipative and random forces are split
@ -147,7 +147,7 @@ energies and temperatures.

 :line

-:link(Lisal)
+:link(Lisal3)
 [(Lisal)] M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative
 particle dynamics at isothermal, isobaric, isoenergetic, and
 isoenthalpic conditions using Shardlow-like splitting algorithms.",
--- a/doc/src/pair_eim.txt
+++ b/doc/src/pair_eim.txt
@ -25,7 +25,7 @@ pair_coeff * * Na Cl ../potentials/ffield.eim Cl NULL Na :pre
 [Description:]

 Style {eim} computes pairwise interactions for ionic compounds
-using embedded-ion method (EIM) potentials "(Zhou)"_#Zhou.  The
+using embedded-ion method (EIM) potentials "(Zhou)"_#Zhou2.  The
 energy of the system E is given by

 :c,image(Eqs/pair_eim1.jpg)
@ -169,6 +169,6 @@ LAMMPS was built with that package.

 :line

-:link(Zhou)
+:link(Zhou2)
 [(Zhou)] Zhou, submitted for publication (2010).  Please contact
 Xiaowang Zhou (Sandia) for details via email at xzhou at sandia.gov.
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
Steve Plimpton	ae56b9ad89	patch 31Mar17 for stable release	2017-03-30 10:07:27 -06:00
sjplimp	4466d9fb4a	Merge pull request #440 from ohenrich/user-cgdna Updated lammps.book, USER-CGDNA install script	2017-03-30 09:34:35 -06:00
Oliver Henrich	ac1aa9edea	Updated README	2017-03-29 11:18:04 +01:00
Oliver Henrich	c733204a70	Updated lammps.book and install script	2017-03-29 08:28:03 +01:00
Steve Plimpton	4b9d0a9566	sync with SVN	2017-03-28 13:26:12 -06:00
Steve Plimpton	0637f23875	patch 28Mar17	2017-03-28 13:12:23 -06:00
sjplimp	9f6e126a2f	Merge pull request #437 from ohenrich/user-cgdna User cgdna	2017-03-28 12:52:26 -06:00
sjplimp	645f56cf70	Merge pull request #436 from Pakketeretet2/better_incorrect_input_handling_nh Changed the check on initial and final temperature to <= 0 for both.	2017-03-28 12:51:17 -06:00
sjplimp	80e5111dca	Merge pull request #434 from akohlmey/imgflags-in-library improved image flag handling in library interface	2017-03-28 12:50:13 -06:00
sjplimp	7e9f05b617	Merge pull request #433 from akohlmey/fixes-for-stable More small fixes for stable release	2017-03-28 12:49:09 -06:00
Axel Kohlmeyer	1d8f0c762d	Merge branch 'master' into fixes-for-stable	2017-03-28 14:37:30 -04:00
Axel Kohlmeyer	ef6070cbde	remove executable permissions for potential files	2017-03-28 14:35:58 -04:00
Steve Plimpton	61f3ff1d2b	Merge branch 'master' of github.com:lammps/lammps	2017-03-28 12:35:33 -06:00
Steve Plimpton	111d350a22	fix gcmc units change for chemical potential	2017-03-28 12:34:46 -06:00
sjplimp	1dfd61f532	Merge pull request #432 from Pakketeretet2/user_manifold_fix Fixed a bug with equal-style variables as manifold params.	2017-03-28 12:33:45 -06:00
Oliver Henrich	5c1f5462e7	Removed contribution line from header files	2017-03-28 19:08:24 +01:00
Oliver Henrich	66a6375405	Resolved merge conflict	2017-03-28 18:58:31 +01:00
Oliver Henrich	604afebf6f	Update to oxDNA2	2017-03-28 18:22:02 +01:00
Oliver Henrich	8afed61db1	Upgrade to oxDNA2	2017-03-28 18:16:36 +01:00
Stefan Paquay	ee55a98103	Changed the check on initial and final temperature to <= 0 for both.	2017-03-28 11:22:10 -04:00
Axel Kohlmeyer	f8da9a866a	synchronize dump custom/vtk documentation with that of dump custom	2017-03-28 11:00:22 -04:00
Axel Kohlmeyer	28bdebd3c0	avoid segfault when calling PPPM*::memory_usage() before grid communication is initialized	2017-03-28 07:50:48 -04:00
Axel Kohlmeyer	fc51c38abb	add some docs for the special treatment of image flags	2017-03-28 02:22:45 -04:00
Axel Kohlmeyer	443ea13eff	add image flag packing/unpacking to library/python interface	2017-03-28 02:05:05 -04:00
Axel Kohlmeyer	5feeb79c13	one more line of dead code removed	2017-03-27 15:16:28 -04:00
Axel Kohlmeyer	a241b2d0f7	fix problems with references	2017-03-27 15:01:32 -04:00
Axel Kohlmeyer	61e7595a94	remove references to xmovie, streamline dump and viz descriptions	2017-03-27 14:59:58 -04:00
Axel Kohlmeyer	da9096750e	update .gitignore for newly added files	2017-03-27 14:30:21 -04:00
Axel Kohlmeyer	87ea9ba661	bugfix for library interface	2017-03-27 14:29:13 -04:00
Axel Kohlmeyer	c041727e4f	remove dead code and reduce trivial compiler warnings (clang++)	2017-03-27 14:28:50 -04:00
Stefan Paquay	3feffbe1de	Removed diagnostics.	2017-03-27 13:49:53 -04:00
Stefan Paquay	04fd038d35	Fixed a bug with equal-style variables as manifold params.	2017-03-27 13:46:57 -04:00
Steve Plimpton	3dfe4505dd	24Mar17 patch sync with SVN	2017-03-24 15:17:51 -06:00
Steve Plimpton	394e9b42b0	new CHARMM pair styles with force swithing/shifting	2017-03-24 13:53:07 -06:00
sjplimp	e6fcaefe95	Merge pull request #431 from v0i0/fix-airebo-morse Fix airebo/morse	2017-03-24 10:03:29 -06:00
sjplimp	f5a85d68ad	Merge pull request #429 from akohlmey/updates-for-stable Collected updates for stable release	2017-03-24 10:01:23 -06:00
sjplimp	277b93cb89	Merge pull request #417 from tonnamb/add-pair-zhou add new pair potential for metal-organic interactions - pair style momb	2017-03-24 09:41:30 -06:00
Axel Kohlmeyer	8820315ff9	Merge branch 'master' into updates-for-stable	2017-03-23 17:57:02 -04:00
Steve Plimpton	44841f6891	fix ave/chunk fixes, 2d disc option, fix_modify dynamic/dof	2017-03-23 15:31:27 -06:00
Axel Kohlmeyer	2cdcd6d630	remove one more reference to xmovie	2017-03-23 16:03:25 -04:00
Axel Kohlmeyer	47cade2bcf	re-arranged functions to make it easier to compare with non-threaded. port bugfixes to airebo to USER-OMP	2017-03-23 15:19:02 -04:00
Axel Kohlmeyer	a72efbea36	whitespace cleanup	2017-03-23 15:18:23 -04:00
Axel Kohlmeyer	5c9892c083	apply airebo/m bugfix also to USER-OMP version	2017-03-23 14:14:49 -04:00
Axel Kohlmeyer	9ecc5c8cf7	Merge branch 'fix-airebo-morse' of https://github.com/v0i0/lammps into pull-431	2017-03-23 14:12:37 -04:00
Markus Hoehnerbach	47cebb0d23	And getting it right...	2017-03-23 17:43:27 +01:00
Markus Hoehnerbach	f127e428cc	Fix airebo/morse Introduced in `b3d2fb91`, PCCf_2_0 does not get initialized in ::settings in PairAIREBOMorse. Future proof by calling super-class.	2017-03-23 17:37:49 +01:00
Axel Kohlmeyer	568b67eee9	include citation for reference paper into pair style momb	2017-03-23 12:00:53 -04:00
Axel Kohlmeyer	865b41e201	make pair style momb example follow LAMMPS conventions more closely	2017-03-23 11:50:10 -04:00
Axel Kohlmeyer	b88a749680	rename a couple more references to pair style zhou into momb	2017-03-23 11:38:33 -04:00
Tonnam Balankura	02e65900e6	add example log file generated from 17Nov16 version of lammps, make minimize and run short in system.in	2017-03-23 11:03:00 -04:00
Tonnam Balankura	343c9eda82	change zhou to momb in src/USER-MISC/README	2017-03-23 10:24:13 -04:00
Tonnam Balankura	df8dbec676	rename pair_zhou to pair_momb in src and change class name from PairZhou to PairMomb	2017-03-23 10:22:49 -04:00
Tonnam Balankura	1075be7eca	rename zhou to momb in examples	2017-03-23 10:18:15 -04:00
Tonnam Balankura	6d395ec511	change name zhou to momb in docs, fix grammar	2017-03-23 10:08:47 -04:00
Tonnam Balankura	bf560e78f3	edit description and add related commands and default	2017-03-22 16:56:40 -04:00
Tonnam Balankura	daae76c465	Add names Tonnam and Ya to README	2017-03-22 15:59:00 -04:00
Tonnam Balankura	1ea9a14121	Add Tonnam and Ya names	2017-03-22 15:55:34 -04:00
Axel Kohlmeyer	1db5834b99	Revert "Cleanup of a few more references to obsoleted and removed tools like xmovie" This reverts commit `127597023d`.	2017-03-22 15:12:49 -04:00
Axel Kohlmeyer	3070b043be	Revert "correct inconsistent anchors" This reverts commit `a14d58259c`.	2017-03-22 15:12:47 -04:00
Axel Kohlmeyer	ef3f323fc4	Revert "remove reference to removed section on VMD scripts" This reverts commit `66eb9c2486`.	2017-03-22 15:12:43 -04:00
Axel Kohlmeyer	43a304f564	remove reference to removed section on VMD scripts	2017-03-22 15:12:09 -04:00
Axel Kohlmeyer	a79aef65e8	correct inconsistent anchors	2017-03-22 15:12:09 -04:00
Axel Kohlmeyer	dc1d93a491	some more whitespace cleanup	2017-03-22 15:08:09 -04:00
Axel Kohlmeyer	66eb9c2486	remove reference to removed section on VMD scripts	2017-03-22 15:01:11 -04:00
Axel Kohlmeyer	a14d58259c	correct inconsistent anchors	2017-03-22 15:00:57 -04:00
Axel Kohlmeyer	127597023d	Cleanup of a few more references to obsoleted and removed tools like xmovie	2017-03-22 14:57:37 -04:00
Axel Kohlmeyer	3ec16f3630	fully integrate support for doc_anchor_check into docs makefile	2017-03-22 14:40:30 -04:00
Axel Kohlmeyer	cb9059652d	a few more small changes to integrate pair style zhou properly	2017-03-22 14:39:46 -04:00
Axel Kohlmeyer	43f27250b5	Merge branch 'add-pair-zhou' of https://github.com/tonnamb/lammps into pull-417	2017-03-22 14:05:16 -04:00
Oliver Henrich	af0b5b0e84	Removed dead code	2017-03-22 16:23:29 +00:00
Tonnam Balankura	c5d561a312	pair_zhou docs: add equation, add link in section_commands and pairs	2017-03-22 12:00:32 -04:00
Oliver Henrich	7435084375	Verified oxDNA with modified nucleotide layout	2017-03-22 15:59:10 +00:00
Axel Kohlmeyer	734e639c5d	correct typo reported on lammps-users	2017-03-21 14:12:00 -04:00
Steve Plimpton	dcede304df	changes for next patch, 2d disc options for spheres, fix external upgrade, bug fixes for fix ave/chunk for density calcs, Aidan doc page citation deconvolution	2017-03-21 08:56:37 -06:00
sjplimp	145e682ad3	Merge pull request #427 from akohlmey/small-updates-and-corrections Various updates and corrections for upcoming stable release	2017-03-21 08:18:21 -06:00
Axel Kohlmeyer	6482df6c2f	remove references to deleted tools. update/clarify section on restart2data	2017-03-20 18:57:30 -04:00
Axel Kohlmeyer	0c9cd11b4e	have the relevant LAMMPS version embedded into top part of the html manual	2017-03-20 18:25:11 -04:00
Axel Kohlmeyer	82d952ae0e	mention NumPy dependency instead of Numeric for python tools	2017-03-20 17:26:19 -04:00
Axel Kohlmeyer	47d6451d03	fix compilation for pymol_asphere tool	2017-03-20 17:18:24 -04:00
Axel Kohlmeyer	e110d6961a	remove obsolete tools and files	2017-03-20 17:17:35 -04:00
Axel Kohlmeyer	a42b0b7dcb	update colvars abf integrate tool from git repo	2017-03-20 17:04:16 -04:00
Axel Kohlmeyer	03828b5836	adapt binary2txt.cpp source to current coding conventions	2017-03-20 16:57:32 -04:00
Axel Kohlmeyer	3b44c3ff1d	remove non-ASCII characters from doc source files	2017-03-20 16:55:14 -04:00
Axel Kohlmeyer	0d0c2b65f7	correct stan's email address	2017-03-20 16:32:16 -04:00
Axel Kohlmeyer	2218a9d704	emphasize that the online manual is following the latest development version	2017-03-20 16:32:04 -04:00
Axel Kohlmeyer	0a6b33cd78	remove duplicate paragraph in nose-hoover fix docs	2017-03-20 16:27:00 -04:00
Axel Kohlmeyer	ecf17621aa	more permission fixes	2017-03-20 16:25:06 -04:00
Axel Kohlmeyer	f0c6ed004d	remove xmovie	2017-03-20 16:24:38 -04:00
Axel Kohlmeyer	554531a302	update permissions	2017-03-20 13:51:36 -04:00
sjplimp	d496c0fdfa	Merge pull request #426 from dstelter92/master fix for temper_grem exchange probability	2017-03-20 08:57:29 -06:00
dstelter92	5c39dfd740	re-ran example with fixed exchanges	2017-03-20 09:22:09 -04:00
dstelter92	5b842f0010	Teff and exchange bugfix, as per Greg Dignon to match python examples	2017-03-20 09:15:48 -04:00
Tonnam Balankura	52987a3615	Started writing pair_zhou.txt	2017-03-18 22:32:39 -04:00
Tonnam Balankura	b6ecfb91c4	deleted pair_zhou in main/src (moved to USER-MISC)	2017-03-18 21:22:02 -04:00
Tonnam Balankura	d04ea8653d	add examples for pair_zhou	2017-03-18 21:21:25 -04:00
Tonnam Balankura	2ab77caa8b	adapt to LAMMPS coding style	2017-03-18 21:01:40 -04:00
Tonnam Balankura	da81531906	move pair_zhou to USER-MISC and update USER-MISC/README	2017-03-18 20:54:12 -04:00
Tonnam Balankura	5be32f5d8d	remove pair_zhou from Makefile.list	2017-03-18 20:48:49 -04:00
Steve Plimpton	4a90bca7a3	patch 17Mar17	2017-03-17 11:29:23 -06:00
sjplimp	9f35b764f8	Merge pull request #424 from timattox/dpd_restart_fix Remove unneeded restart_peratom flags in USER-DPD package	2017-03-17 11:19:04 -06:00
sjplimp	7ca5dce2f5	Merge pull request #423 from timattox/master_bugfix_irregular bugfix for irregular::create_atom and create_data	2017-03-17 11:18:52 -06:00
sjplimp	fcc3b3bd36	Merge pull request #421 from akohlmey/memory-output improve memory usage reporting in info and output class	2017-03-17 11:18:08 -06:00
sjplimp	53a3877c3d	Merge pull request #420 from rbberger/doc_anchor_check Add utility to detect duplicate anchors in docs	2017-03-17 11:17:28 -06:00
sjplimp	a936b7b2ab	Merge pull request #419 from rbberger/python_fixes Library interface fixes, Python example fixes and better Python 3 compatibility	2017-03-17 11:16:58 -06:00
sjplimp	a91b851f3d	Merge pull request #416 from lukin17/filter_corotate Added fix filter/corotate.	2017-03-17 11:14:59 -06:00
Stan Moore	d31c591b60	Remove unneeded restart_peratom flags	2017-03-17 09:40:39 -06:00
Axel Kohlmeyer	ae5ebf6001	add support for MPI_Request_free() to MPI STUBS library	2017-03-17 11:40:09 -04:00
Axel Kohlmeyer	7fb741d53d	Revert "In irregular.cpp use simpler and slightly faster MPI_Reduce_scatter_block()" This reverts commit `8e75616c14`.	2017-03-17 11:35:59 -04:00
Tim Mattox	8e75616c14	In irregular.cpp use simpler and slightly faster MPI_Reduce_scatter_block()	2017-03-17 03:02:42 -04:00
Tim Mattox	411c069ba6	BUGFIX: Prevent possible deadlock in Irregular::create_atom and create_data	2017-03-17 03:02:19 -04:00
Axel Kohlmeyer	ac82d041cc	ignore package pair style	2017-03-16 23:12:49 -04:00
Richard Berger	621d7d5ce0	Correct off-by-one error in line number reported	2017-03-16 23:05:03 -04:00
Richard Berger	1bb9c7da42	Remove some duplicate anchors in documentation	2017-03-16 22:36:13 -04:00
Richard Berger	f893104b18	Add anchor_check to doc Makefile	2017-03-16 22:21:55 -04:00
Richard Berger	efb2a942e0	Add utility to detect duplicate anchors in documentation files	2017-03-16 22:21:12 -04:00
Axel Kohlmeyer	070ce33a13	improve memory usage reporting in info and output class	2017-03-16 18:35:04 -04:00
Axel Kohlmeyer	f604f86cfc	add fix filter/corotate to some administrative files	2017-03-16 15:08:17 -04:00
Axel Kohlmeyer	bed288339e	simplify and shorten examples for fix filter/corotate and combine into a single folder	2017-03-16 15:02:50 -04:00
Axel Kohlmeyer	1995f434f3	fix some more code formatting issues, add newline at EOF	2017-03-16 14:24:28 -04:00
Axel Kohlmeyer	db0281b4df	Merge branch 'filter_corotate' of https://github.com/lukin17/lammps into pull-416	2017-03-16 12:14:09 -04:00
lukin17	2f5e711acd	Merge remote-tracking branch 'upstream/master' into filter_corotate	2017-03-16 10:00:12 +01:00
lukin17	bdb7669e27	Fixed coding style.	2017-03-16 09:44:07 +01:00
Richard Berger	cda8213892	Added Python matplotlib plot example	2017-03-16 01:41:28 -04:00
Richard Berger	ef940d226c	Improve Python 3 compatibility of pizza tools and simplify read_snapshot code	2017-03-16 01:38:05 -04:00
Richard Berger	36da9223ec	Fix dump cfg in vizplotgui_atomeye.py example	2017-03-15 22:55:51 -04:00
Richard Berger	eb29ef32b1	Fix space/tab error in pizza/gl.py	2017-03-15 22:43:00 -04:00
Richard Berger	29550d472d	Fix dump cfg in viz_atomeye.py example	2017-03-15 22:31:14 -04:00
Richard Berger	79cae51156	Document property 'uses_exceptions' of Python interface	2017-03-15 22:20:30 -04:00
Richard Berger	a210867025	Fixes lammps_create_atoms library function and its Python interface variant The interface of that function has changed and includes two additional parameters, which haven't been added to the Python interface either. This showed up by trying to run the simple.py example.	2017-03-15 22:13:06 -04:00
Richard Berger	0262a54ecf	Fix Python 3 compatibility by encoding strings passed as c_char_p	2017-03-15 22:00:43 -04:00
Axel Kohlmeyer	0d8f74f0c5	Merge branch 'filter_corotate' of https://github.com/lukin17/lammps into pull-416	2017-03-15 18:54:41 -04:00
sjplimp	3a2da51a82	Merge pull request #413 from ohenrich/user-cgdna User cgdna	2017-03-15 13:12:43 -06:00
sjplimp	b1c59126f7	Merge pull request #415 from stanmoore1/kk_qeq Add neigh/qeq option to Kokkos package	2017-03-15 13:12:08 -06:00
sjplimp	4c77838514	Merge pull request #414 from sstrong99/flow-gauss-doc-addition flow/gauss documentation update	2017-03-15 13:11:26 -06:00
sjplimp	f9468f46f5	Merge pull request #412 from timattox/master_typofix Correct a typo in the fix_halt.txt documentation.	2017-03-15 13:10:58 -06:00
Tonnam Balankura	ec1778b586	add pair_zhou	2017-03-15 11:10:04 -04:00
lukin17	c3ce3747e0	Added fix filter/corotate.	2017-03-15 11:34:01 +01:00
Stan Moore	fdc390ad05	Tweaking docs for Kokkos package	2017-03-14 14:08:14 -06:00
Stan Moore	580f6b567b	Add neigh/qeq option to Kokkos	2017-03-14 10:44:31 -06:00
Steven Strong	27b1c33a16	updated the NEMD discussion in the how-to documentation about flow/gauss	2017-03-14 10:39:06 -06:00
Oliver Henrich	7a75cd111c	Minor updates in documentation and setup tool, merge before upgrade to oxDNA2	2017-03-14 11:39:09 +00:00
Oliver Henrich	23b8287933	Updated documentation and simple setup tool	2017-03-14 11:36:44 +00:00
Tim Mattox	4cfe623bc1	Correct a typo in the fix_halt.txt documentation.	2017-03-10 21:30:03 -05:00
Steve Plimpton	f871ecdc67	change to RCB cuts in load-balancing commands, also a new option for fix halt	2017-03-10 15:55:07 -07:00
sjplimp	470353e320	Merge pull request #408 from giacomofiorin/colvars-update-2017-03-10 Colvars update 2017-03-10	2017-03-10 14:51:16 -07:00
sjplimp	ffe02d20ca	Merge pull request #406 from stanmoore1/kokkos_bugfix Fix Kokkos issues	2017-03-10 14:51:04 -07:00
Giacomo Fiorin	f70752c18f	Include PDF of Colvars doc missing in previous commit	2017-03-10 15:58:35 -05:00
sjplimp	07fcfd6d54	Merge pull request #405 from stanmoore1/ev_setup_kk Add alloc flag to ev_setup	2017-03-10 11:01:51 -07:00
sjplimp	c97feafca6	Merge pull request #407 from frobnitzem/master Add error check to lammps_gather_atoms/lammps_scatter_atoms in library.cpp	2017-03-10 11:00:30 -07:00
sjplimp	b20d95d495	Merge pull request #402 from timattox/USER-DPD_spelling Fix spelling "correction" from `3a054d1a`: iterations not interactions and imd_writen not imd_written	2017-03-10 10:59:43 -07:00
Giacomo Fiorin	0b4adaa9e6	Backport typo fixes that were not previously pushed to the Colvars repository	2017-03-10 09:24:46 -05:00
Giacomo Fiorin	5fe6206638	Update Colvars module to version 2017-03-10	2017-03-10 09:16:58 -05:00
David M. Rogers	65964f3b31	Add error check to lammps_gather_atoms/lammps_scatter_atoms in library.cpp	2017-03-09 16:49:07 -05:00
Stan Moore	b28b84d444	Fix half from full nlist issue with Kokkos	2017-03-09 14:00:27 -07:00
Stan Moore	a001a5ceb0	Fixing memory overflow issue in comm_kokkos	2017-03-09 12:20:49 -07:00
Axel Kohlmeyer	2ef713ea1b	restore incorrect change due to spell checking in fix imd	2017-03-08 16:40:16 -05:00
Stan Moore	1f6c1942b3	Disable allocation of per-atom arrays in ev_setup for Kokkos styles	2017-03-08 12:42:44 -07:00
Stan Moore	683023d820	Adding alloc flag to ev_setup	2017-03-08 12:36:23 -07:00
Tim Mattox	42d3a8f498	Fix spelling "correction" from `3a054d1a`: iterations not interactions. :-)	2017-03-07 15:41:06 -05:00
Oliver Henrich	3626496c7c	Corrected comment in 3' to 5' directionality check	2017-02-22 20:06:49 +00:00
Oliver Henrich	458b6749e7	Corrected comment in 3' to 5' directionality check.	2017-02-22 20:03:41 +00:00
Oliver Henrich	0efd209480	Merge branch 'master' into user-cgdna	2017-02-09 11:50:03 +00:00
Oliver Henrich	ed0a347fbf	Merge branch 'master' into user-cgdna	2017-01-30 10:31:50 +00:00
Oliver Henrich	149f37e764	Corrected reference to Fig.1	2017-01-26 19:08:59 +00:00