17Dec16 patch

extra python_wrapper change needed for last patch
patch 16Dec16
2016-12-16 11:36:54 -07:00 · 2016-12-16 11:35:42 -07:00 · 2016-12-16 10:30:57 -07:00 · 2016-12-16 10:25:29 -07:00 · 2016-12-16 10:24:25 -07:00 · 2016-12-16 11:22:25 -05:00
1254 changed files with 68557 additions and 19229 deletions
--- a/doc/Makefile
+++ b/doc/Makefile
@ -43,7 +43,7 @@ clean-all:
 	rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe

 clean:
-	rm -rf $(RSTDIR)
+	rm -rf $(RSTDIR) html

 html: $(OBJECTS)
 	@(\
--- a/doc/src/Eqs/fix_grem.jpg
+++ b/doc/src/Eqs/fix_grem.jpg
--- a/doc/src/Eqs/fix_grem.tex
+++ b/doc/src/Eqs/fix_grem.tex
@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  T_{eff} = \lambda + \eta (H - H_0)
+$$
+
+\end{document}
--- a/doc/src/Eqs/pair_agni.jpg
+++ b/doc/src/Eqs/pair_agni.jpg
--- a/doc/src/Eqs/pair_tersoff_mod_c.jpg
+++ b/doc/src/Eqs/pair_tersoff_mod_c.jpg
--- a/doc/src/Eqs/pair_tersoff_mod_c.tex
+++ b/doc/src/Eqs/pair_tersoff_mod_c.tex
@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+
+\begin{document}
+
+\begin{eqnarray*}
+  V_{ij}  & =  & f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) + c_0 \right]
+\end{eqnarray*}
+
+\end{document}
--- a/doc/src/Eqs/pressure.jpg
+++ b/doc/src/Eqs/pressure.jpg
--- a/doc/src/Eqs/pressure.tex
+++ b/doc/src/Eqs/pressure.tex
@ -3,7 +3,7 @@
 \begin{document}

 $$
-   P = \frac{N k_B T}{V} + \frac{\sum_{i}^{N} r_i \bullet f_i}{dV}
+   P = \frac{N k_B T}{V} + \frac{\sum_{i}^{N'} r_i \bullet f_i}{dV}
 $$

 \end{document}
--- a/doc/src/Eqs/pressure_tensor.jpg
+++ b/doc/src/Eqs/pressure_tensor.jpg
--- a/doc/src/Eqs/pressure_tensor.tex
+++ b/doc/src/Eqs/pressure_tensor.tex
@ -4,7 +4,7 @@

 $$
   P_{IJ} = \frac{\sum_{k}^{N} m_k v_{k_I} v_{k_J}}{V} + 
-   \frac{\sum_{k}^{N} r_{k_I} f_{k_J}}{V}
+   \frac{\sum_{k}^{N'} r_{k_I} f_{k_J}}{V}
 $$

 \end{document}
--- a/doc/src/JPG/pylammps_dihedral.jpg
+++ b/doc/src/JPG/pylammps_dihedral.jpg
--- a/doc/src/JPG/pylammps_mc_disordered.jpg
+++ b/doc/src/JPG/pylammps_mc_disordered.jpg
--- a/doc/src/JPG/pylammps_mc_energies_plot.jpg
+++ b/doc/src/JPG/pylammps_mc_energies_plot.jpg
--- a/doc/src/JPG/pylammps_mc_minimum.jpg
+++ b/doc/src/JPG/pylammps_mc_minimum.jpg
--- 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="27 Oct 2016 version">
+<META NAME="docnumber" CONTENT="17 Dec 2016 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
-27 Oct 2016 version :c,h4
+17 Dec 2016 version :c,h4

 Version info: :h4

--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@ -531,7 +531,8 @@ package"_Section_start.html#start_3.
 "dump nc"_dump_nc.html,
 "dump nc/mpiio"_dump_nc.html,
 "group2ndx"_group2ndx.html,
-"ndx2group"_group2ndx.html :tb(c=3,ea=c)
+"ndx2group"_group2ndx.html,
+"temper/grem"_temper_grem.html :tb(c=3,ea=c)

 :line

@ -632,10 +633,10 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "rigid/nve (o)"_fix_rigid.html,
 "rigid/nvt (o)"_fix_rigid.html,
 "rigid/small (o)"_fix_rigid.html,
-"rigid/small/nph"_fix_rigid.html,
-"rigid/small/npt"_fix_rigid.html,
-"rigid/small/nve"_fix_rigid.html,
-"rigid/small/nvt"_fix_rigid.html,
+"rigid/small/nph (o)"_fix_rigid.html,
+"rigid/small/npt (o)"_fix_rigid.html,
+"rigid/small/nve (o)"_fix_rigid.html,
+"rigid/small/nvt (o)"_fix_rigid.html,
 "setforce (k)"_fix_setforce.html,
 "shake"_fix_shake.html,
 "spring"_fix_spring.html,
@ -687,6 +688,7 @@ package"_Section_start.html#start_3.
 "eos/table/rx"_fix_eos_table_rx.html,
 "flow/gauss"_fix_flow_gauss.html,
 "gle"_fix_gle.html,
+"grem"_fix_grem.html,
 "imd"_fix_imd.html,
 "ipi"_fix_ipi.html,
 "langevin/drude"_fix_langevin_drude.html,
@ -765,6 +767,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "erotate/sphere"_compute_erotate_sphere.html,
 "erotate/sphere/atom"_compute_erotate_sphere_atom.html,
 "event/displace"_compute_event_displace.html,
+"global/atom"_compute_global_atom.html,
 "group/group"_compute_group_group.html,
 "gyration"_compute_gyration.html,
 "gyration/chunk"_compute_gyration_chunk.html,
@ -886,6 +889,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "body"_pair_body.html,
 "bop"_pair_bop.html,
 "born (go)"_pair_born.html,
+"born/coul/dsf"_pair_born.html,
+"born/coul/dsf/cs"_pair_born.html,
 "born/coul/long (go)"_pair_born.html,
 "born/coul/long/cs"_pair_born.html,
 "born/coul/msm (o)"_pair_born.html,
@ -909,8 +914,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "coul/msm"_pair_coul.html,
 "coul/streitz"_pair_coul.html,
 "coul/wolf (ko)"_pair_coul.html,
-"dpd (o)"_pair_dpd.html,
-"dpd/tstat (o)"_pair_dpd.html,
+"dpd (go)"_pair_dpd.html,
+"dpd/tstat (go)"_pair_dpd.html,
 "dsmc"_pair_dsmc.html,
 "eam (gkot)"_pair_eam.html,
 "eam/alloy (gkot)"_pair_eam.html,
@ -979,11 +984,12 @@ KOKKOS, o = USER-OMP, t = OPT.
 "table (gko)"_pair_table.html,
 "tersoff (gkio)"_pair_tersoff.html,
 "tersoff/mod (gko)"_pair_tersoff_mod.html,
+"tersoff/mod/c (o)"_pair_tersoff_mod.html,
 "tersoff/zbl (gko)"_pair_tersoff_zbl.html,
 "tip4p/cut (o)"_pair_coul.html,
 "tip4p/long (o)"_pair_coul.html,
 "tri/lj"_pair_tri_lj.html,
-"vashishta (o)"_pair_vashishta.html,
+"vashishta (ko)"_pair_vashishta.html,
 "vashishta/table (o)"_pair_vashishta.html,
 "yukawa (go)"_pair_yukawa.html,
 "yukawa/colloid (go)"_pair_yukawa_colloid.html,
@ -993,6 +999,7 @@ These are additional pair styles in USER packages, which can be used
 if "LAMMPS is built with the appropriate
 package"_Section_start.html#start_3.

+"agni (o)"_pair_agni.html,
 "awpmd/cut"_pair_awpmd.html,
 "buck/mdf"_pair_mdf.html,
 "coul/cut/soft (o)"_pair_lj_soft.html,
--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@ -1936,18 +1936,22 @@ documentation in the src/library.cpp file for details, including
 which quantities can be queried by name:

 void *lammps_extract_global(void *, char *)
+void lammps_extract_box(void *, double *, double *, 
+                        double *, double *, double *, int *, int *)
 void *lammps_extract_atom(void *, char *)
 void *lammps_extract_compute(void *, char *, int, int)
 void *lammps_extract_fix(void *, char *, int, int, int, int)
 void *lammps_extract_variable(void *, char *, char *) :pre

-int lammps_set_variable(void *, char *, char *)
-double lammps_get_thermo(void *, char *) :pre
+void lammps_reset_box(void *, double *, double *, double, double, double)
+int lammps_set_variable(void *, char *, char *) :pre

+double lammps_get_thermo(void *, char *)
 int lammps_get_natoms(void *)
 void lammps_gather_atoms(void *, double *)
 void lammps_scatter_atoms(void *, double *) :pre
-void lammps_create_atoms(void *, int, tagint *, int *, double *, double *) :pre
+void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
+                         imageint *, int) :pre

 The extract functions return a pointer to various global or per-atom
 quantities stored in LAMMPS or to values calculated by a compute, fix,
@ -1957,10 +1961,16 @@ 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
+saved state of a simulation.
+
 The lammps_set_variable() function can set an existing string-style
 variable to a new string value, so that subsequent LAMMPS commands can
-access the variable.  The lammps_get_thermo() function returns the
-current value of a thermo keyword as a double.
+access the variable.
+
+The lammps_get_thermo() function returns the current value of a thermo
+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
@ -1973,10 +1983,13 @@ passed by the caller, to each atom owned by individual processors.

 The lammps_create_atoms() function takes a list of N atoms as input
 with atom types and coords (required), an optionally atom IDs and
-velocities.  It uses the coords of each atom to assign it as a new
-atom to the processor that owns it.  Additional properties for the new
-atoms can be assigned via the lammps_scatter_atoms() or
-lammps_extract_atom() functions.
+velocities and image flags.  It uses the coords of each atom to assign
+it as a new atom to the processor that owns it.  This function is
+useful to add atoms to a simulation or (in tandem with
+lammps_reset_box()) to restore a previously extracted and saved state
+of a simulation.  Additional properties for the new atoms can then be
+assigned via the lammps_scatter_atoms() or lammps_extract_atom()
+functions.

 The examples/COUPLE and python directories have example C++ and C and
 Python codes which show how a driver code can link to LAMMPS as a
@ -2729,7 +2742,7 @@ production runs and is only required during equilibration. This way one
 is consistent with literature (based on the code packages DL_POLY or
 GULP for instance).

-The mentioned energy transfer will typically lead to a a small drift
+The mentioned energy transfer will typically lead to a small drift
 in total energy over time.  This internal energy can be monitored
 using the "compute chunk/atom"_compute_chunk_atom.html and "compute
 temp/chunk"_compute_temp_chunk.html commands.  The internal kinetic
@ -2830,7 +2843,7 @@ temp/drude"_compute_temp_drude.html. This requires also to use the
 command {comm_modify vel yes}.

 Short-range damping of the induced dipole interactions can be achieved
-using Thole functions through the the "pair style
+using Thole functions through the "pair style
 thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html
 with a Coulomb pair style. It may be useful to use {coul/long/cs} or
 similar from the CORESHELL package if the core and Drude particle come
--- a/doc/src/Section_intro.txt
+++ b/doc/src/Section_intro.txt
@ -366,11 +366,11 @@ complementary modeling tasks.
 "DL_POLY"_dlpoly
 "Tinker"_tinker :ul

-:link(charmm,http://www.scripps.edu/brooks)
-:link(amber,http://amber.scripps.edu)
+:link(charmm,http://www.charmm.org)
+:link(amber,http://ambermd.org)
 :link(namd,http://www.ks.uiuc.edu/Research/namd/)
 :link(nwchem,http://www.emsl.pnl.gov/docs/nwchem/nwchem.html)
-:link(dlpoly,http://www.cse.clrc.ac.uk/msi/software/DL_POLY)
+:link(dlpoly,http://www.ccp5.ac.uk/DL_POLY_CLASSIC)
 :link(tinker,http://dasher.wustl.edu/tinker)

 CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for
--- a/doc/src/Section_python.txt
+++ b/doc/src/Section_python.txt
@ -8,19 +8,26 @@

 11. Python interface to LAMMPS :h3

-LAMMPS can work together with Python in two ways.  First, Python can
+LAMMPS can work together with Python in three ways.  First, Python can
 wrap LAMMPS through the "LAMMPS library
 interface"_Section_howto.html#howto_19, so that a Python script can
 create one or more instances of LAMMPS and launch one or more
 simulations.  In Python lingo, this is "extending" Python with LAMMPS.

-Second, LAMMPS can use the Python interpreter, so that a LAMMPS input
+Second, the low-level Python interface can be used indirectly through the
+PyLammps and IPyLammps wrapper classes in Python. These wrappers try to
+simplify the usage of LAMMPS in Python by providing an object-based interface
+to common LAMMPS functionality. It also reduces the amount of code necessary to
+parameterize LAMMPS scripts through Python and makes variables and computes
+directly accessible. See "PyLammps interface"_#py_9 for more details.
+
+Third, LAMMPS can use the Python interpreter, so that a LAMMPS input
 script can invoke Python code, and pass information back-and-forth
 between the input script and Python functions you write.  The Python
 code can also callback to LAMMPS to query or change its attributes.
 In Python lingo, this is "embedding" Python in LAMMPS.

-This section describes how to do both.
+This section describes how to use these three approaches.

 11.1 "Overview of running LAMMPS from Python"_#py_1
 11.2 "Overview of using Python from a LAMMPS script"_#py_2
@ -29,7 +36,8 @@ This section describes how to do both.
 11.5 "Extending Python with MPI to run in parallel"_#py_5
 11.6 "Testing the Python-LAMMPS interface"_#py_6
 11.7 "Using LAMMPS from Python"_#py_7
-11.8 "Example Python scripts that use LAMMPS"_#py_8 :ul
+11.8 "Example Python scripts that use LAMMPS"_#py_8
+11.9 "PyLammps interface"_#py_9 :ul

 If you are not familiar with it, "Python"_http://www.python.org is a
 powerful scripting and programming language which can essentially do
@ -824,3 +832,7 @@ different visualization package options.  Click to see larger images:
 :image(JPG/screenshot_atomeye_small.jpg,JPG/screenshot_atomeye.jpg)
 :image(JPG/screenshot_pymol_small.jpg,JPG/screenshot_pymol.jpg)
 :image(JPG/screenshot_vmd_small.jpg,JPG/screenshot_vmd.jpg)
+
+11.9 PyLammps interface :link(py_9),h4
+
+Please see the "PyLammps Tutorial"_tutorial_pylammps.html.
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@ -706,7 +706,7 @@ future changes to LAMMPS.
 User packages, such as user-atc or user-omp, have been contributed by
 users, and always begin with the user prefix.  If they are a single
 command (single file), they are typically in the user-misc package.
-Otherwise, they are a a set of files grouped together which add a
+Otherwise, they are a set of files grouped together which add a
 specific functionality to the code.

 User packages don't necessarily meet the requirements of the standard
--- a/doc/src/angle_charmm.txt
+++ b/doc/src/angle_charmm.txt
@ -74,7 +74,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/angle_cosine.txt
+++ b/doc/src/angle_cosine.txt
@ -61,7 +61,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/angle_cosine_delta.txt
+++ b/doc/src/angle_cosine_delta.txt
@ -66,7 +66,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/angle_cosine_periodic.txt
+++ b/doc/src/angle_cosine_periodic.txt
@ -74,7 +74,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/angle_cosine_squared.txt
+++ b/doc/src/angle_cosine_squared.txt
@ -66,7 +66,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/angle_harmonic.txt
+++ b/doc/src/angle_harmonic.txt
@ -65,11 +65,11 @@ more instructions on how to use the accelerated styles effectively.

 :line

-[Restrictions:] none
+[Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package.  See the "Making LAMMPS"_Section_start.html#start_3
+section for more info on packages.

 [Related commands:]

--- a/doc/src/angle_hybrid.txt
+++ b/doc/src/angle_hybrid.txt
@ -76,7 +76,7 @@ for specific angle types.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 Unlike other angle styles, the hybrid angle style does not store angle
--- a/doc/src/angle_table.txt
+++ b/doc/src/angle_table.txt
@ -147,7 +147,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/bond_fene.txt
+++ b/doc/src/bond_fene.txt
@ -70,7 +70,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 You typically should specify "special_bonds fene"_special_bonds.html
--- a/doc/src/bond_fene_expand.txt
+++ b/doc/src/bond_fene_expand.txt
@ -73,7 +73,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 You typically should specify "special_bonds fene"_special_bonds.html
--- a/doc/src/bond_harmonic.txt
+++ b/doc/src/bond_harmonic.txt
@ -65,7 +65,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/bond_hybrid.txt
+++ b/doc/src/bond_hybrid.txt
@ -59,7 +59,7 @@ bond types.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 Unlike other bond styles, the hybrid bond style does not store bond
--- a/doc/src/bond_morse.txt
+++ b/doc/src/bond_morse.txt
@ -64,7 +64,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/bond_nonlinear.txt
+++ b/doc/src/bond_nonlinear.txt
@ -64,7 +64,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/bond_quartic.txt
+++ b/doc/src/bond_quartic.txt
@ -99,7 +99,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 The {quartic} style requires that "special_bonds"_special_bonds.html
--- a/doc/src/bond_table.txt
+++ b/doc/src/bond_table.txt
@ -144,7 +144,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/compute_bond_local.txt
+++ b/doc/src/compute_bond_local.txt
@ -51,12 +51,12 @@ relative to the center of mass (COM) velocity of the 2 atoms in the
 bond.

 The value {engvib} is the vibrational kinetic energy of the two atoms
-in the bond, which is simply 1/2 m1 v1^2 + 1/2 m1 v2^2, where v1 and
+in the bond, which is simply 1/2 m1 v1^2 + 1/2 m2 v2^2, where v1 and
 v2 are the magnitude of the velocity of the 2 atoms along the bond
 direction, after the COM velocity has been subtracted from each.

 The value {engrot} is the rotationsl kinetic energy of the two atoms
-in the bond, which is simply 1/2 m1 v1^2 + 1/2 m1 v2^2, where v1 and
+in the bond, which is simply 1/2 m1 v1^2 + 1/2 m2 v2^2, where v1 and
 v2 are the magnitude of the velocity of the 2 atoms perpendicular to
 the bond direction, after the COM velocity has been subtracted from
 each.
@ -67,7 +67,7 @@ Vcm^2 where Vcm = magnitude of the velocity of the COM.

 Note that these 3 kinetic energy terms are simply a partitioning of
 the summed kinetic energy of the 2 atoms themselves.  I.e. total KE =
-1/2 m1 v1^2 + 1/2 m2 v3^2 = engvib + engrot + engtrans, where v1,v2
+1/2 m1 v1^2 + 1/2 m2 v2^2 = engvib + engrot + engtrans, where v1,v2
 are the magnitude of the velocities of the 2 atoms, without any
 adjustment for the COM velocity.

--- a/doc/src/compute_centro_atom.txt
+++ b/doc/src/compute_centro_atom.txt
@ -114,7 +114,7 @@ local defects surrounding the central atom, as described above.  For
 the {axes yes} case, the vector components are also unitless, since
 they represent spatial directions.

-Here are typical centro-symmetry values, from a a nanoindentation
+Here are typical centro-symmetry values, from a nanoindentation
 simulation into gold (FCC).  These were provided by Jon Zimmerman
 (Sandia):

--- a/doc/src/compute_chunk_atom.txt
+++ b/doc/src/compute_chunk_atom.txt
@ -536,7 +536,7 @@ For the {bin/cylinder} style the details are as follows.  If {discard}
 is set to {yes}, an out-of-domain atom will have its chunk ID set to
 0.  If {discard} is set to {no}, the atom will have its chunk ID set
 to the first or last bin in both the radial and axis dimensions.  If
-{discard} is set to {mixed}, which is the default, the the radial
+{discard} is set to {mixed}, which is the default, the radial
 dimension is treated the same as for {discard} = no.  But for the axis
 dimensinon, it will only have its chunk ID set to the first or last
 bin if bins extend to the simulation box boundary in the axis
@ -641,7 +641,8 @@ the restarted simulation begins.

 [Related commands:]

-"fix ave/chunk"_fix_ave_chunk.html
+"fix ave/chunk"_fix_ave_chunk.html,
+"compute global/atom"_compute_global_atom.html

 [Default:]

--- a/doc/src/compute_cluster_atom.txt
+++ b/doc/src/compute_cluster_atom.txt
@ -37,7 +37,7 @@ The neighbor list needed to compute this quantity is constructed each
 time the calculation is performed (i.e. each time a snapshot of atoms
 is dumped).  Thus it can be inefficient to compute/dump this quantity
 too frequently or to have multiple compute/dump commands, each of a
-{clsuter/atom} style.
+{cluster/atom} style.

 NOTE: If you have a bonded system, then the settings of
 "special_bonds"_special_bonds.html command can remove pairwise
--- a/doc/src/compute_global_atom.txt
+++ b/doc/src/compute_global_atom.txt
@ -0,0 +1,220 @@
+"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
+
+compute global/atom command :h3
+
+[Syntax:]
+
+compute ID group-ID style index input1 input2 ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
+global/atom = style name of this compute command :l
+index = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l
+  c_ID = per-atom vector calculated by a compute with ID
+  c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID
+  f_ID = per-atom vector calculated by a fix with ID
+  f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID
+  v_name = per-atom vector calculated by an atom-style variable with name :pre
+one or more inputs can be listed :l
+input = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l
+  c_ID = global vector calculated by a compute with ID
+  c_ID\[I\] = Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
+  f_ID = global vector calculated by a fix with ID
+  f_ID\[I\] = Ith column of global array calculated by a fix with ID, I can include wildcard (see below)
+  v_name = global vector calculated by a vector-style variable with name :pre
+:ule
+
+[Examples:]
+
+compute 1 all global/atom c_chunk c_com\[1\\] c_com\[2\\] c_com\[3\\]
+compute 1 all global/atom c_chunk c_com\[*\\] :pre
+
+[Description:]
+
+Define a calculation that assigns global values to each atom from
+vectors or arrays of global values.  The specified {index} parameter
+is used to determine which global value is assigned to each atom.
+
+The {index} parameter must reference a per-atom vector or array from a
+"compute"_compute.html or "fix"_fix.html or the evaluation of an
+atom-style "variable"_variable.html.  Each {input} value must
+reference a global vector or array from a "compute"_compute.html or
+"fix"_fix.html or the evaluation of an vector-style
+"variable"_variable.html.  Details are given below.
+
+The {index} value for an atom is used as a index I (from 1 to N) into
+the vector associated with each of the input values.  The Ith value
+from the input vector becomes one output value for that atom.  If the
+atom is not in the specified group, or the index I < 1 or I > M, where
+M is the actual length of the input vector, then an output value of
+0.0 is assigned to the atom.
+
+An example of how this command is useful, is in the context of
+"chunks" which are static or dyanmic subsets of atoms.  The "compute
+chunk/atom"_compute_chunk_atom.html command assigns unique chunk IDs
+to each atom.  It's output can be used as the {index} parameter for
+this command.  Various other computes with "chunk" in their style
+name, such as "compute com/chunk"_compute_com_chunk.html or "compute
+msd/chunk"_compute_msd_chunk.html, calculate properties for each
+chunk.  The output of these commands are global vectors or arrays,
+with one or more values per chunk, and can be used as input values for
+this command.  This command will then assign the global chunk value to
+each atom in the chunk, producing a per-atom vector or per-atom array
+as output.  The per-atom values can then be output to a dump file or
+used by any command that uses per-atom values from a compute as input,
+as discussed in "Section 6.15"_Section_howto.html#howto_15.
+
+As a concrete example, these commands will calculate the displacement
+of each atom from the center-of-mass of the molecule it is in, and
+dump those values to a dump file.  In this case, each molecule is a
+chunk.
+
+compute cc1 all chunk/atom molecule
+compute myChunk all com/chunk cc1
+compute prop all property/atom xu yu zu
+compute glob all global/atom c_cc1 c_myChunk\[*\]
+variable dx atom c_prop\[1\]-c_glob\[1\]
+variable dy atom c_prop\[2\]-c_glob\[2\]
+variable dz atom c_prop\[3\]-c_glob\[3\]
+variable dist atom sqrt(v_dx*v_dx+v_dy*v_dy+v_dz*v_dz)
+dump 1 all custom 100 tmp.dump id xu yu zu c_glob\[1\] c_glob\[2\] c_glob\[3\] &
+     v_dx v_dy v_dz v_dist
+dump_modify 1 sort id :pre
+
+You can add these commands to the bench/in.chain script to see how
+they work.
+
+:line
+
+Note that for input values from a compute or fix, the bracketed index
+I can be specified using a wildcard asterisk with the index to
+effectively specify multiple values.  This takes the form "*" or "*n"
+or "n*" or "m*n".  If N = the size of the vector (for {mode} = scalar)
+or the number of columns in the array (for {mode} = vector), then an
+asterisk with no numeric values means all indices from 1 to N.  A
+leading asterisk means all indices from 1 to n (inclusive).  A
+trailing asterisk means all indices from n to N (inclusive).  A middle
+asterisk means all indices from m to n (inclusive).
+
+Using a wildcard is the same as if the individual columns of the array
+had been listed one by one.  E.g. these 2 compute global/atom commands
+are equivalent, since the "compute com/chunk"_compute_com_chunk.html
+command creates a global array with 3 columns:
+
+compute cc1 all chunk/atom molecule
+compute com all com/chunk cc1
+compute 1 all global/atom c_cc1 c_com\[1\] c_com\[2\] c_com\[3\]
+compute 1 all global/atom c_cc1 c_com\[*\] :pre
+
+:line
+
+This section explains the {index} parameter.  Note that it must
+reference per-atom values, as contrasted with the {input} values which
+must reference global values.
+
+Note that all of these options generate floating point values.  When
+they are used as an index into the specified input vectors, they
+simple rounded down to convert the value to integer indices.  The
+final values should range from 1 to N (inclusive), since they are used
+to access values from N-length vectors.
+
+If {index} begins with "c_", a compute ID must follow which has been
+previously defined in the input script.  The compute must generate
+per-atom quantities.  See the individual "compute"_compute.html doc
+page for details.  If no bracketed integer is appended, the per-atom
+vector calculated by the compute is used.  If a bracketed integer is
+appended, the Ith column of the per-atom array calculated by the
+compute is used.  Users can also write code for their own compute
+styles and "add them to LAMMPS"_Section_modify.html.  See the
+discussion above for how I can be specified with a wildcard asterisk
+to effectively specify multiple values.
+
+If {index} begins with "f_", a fix ID must follow which has been
+previously defined in the input script.  The Fix must generate
+per-atom quantities.  See the individual "fix"_fix.html doc page for
+details.  Note that some fixes only produce their values on certain
+timesteps, which must be compatible with when compute global/atom
+references the values, else an error results.  If no bracketed integer
+is appended, the per-atom vector calculated by the fix is used.  If a
+bracketed integer is appended, the Ith column of the per-atom array
+calculated by the fix is used.  Users can also write code for their
+own fix style and "add them to LAMMPS"_Section_modify.html.  See the
+discussion above for how I can be specified with a wildcard asterisk
+to effectively specify multiple values.
+
+If {index} begins with "v_", a variable name must follow which has
+been previously defined in the input script.  It must be an
+"atom-style variable"_variable.html.  Atom-style variables can
+reference thermodynamic keywords and various per-atom attributes, or
+invoke other computes, fixes, or variables when they are evaluated, so
+this is a very general means of generating per-atom quantities to use
+as {index}.
+
+:line
+
+This section explains the kinds of {input} values that can be used.
+Note that inputs reference global values, as contrasted with the
+{index} parameter which must reference per-atom values.
+
+If a value begins with "c_", a compute ID must follow which has been
+previously defined in the input script.  The compute must generate a
+global vector or array.  See the individual "compute"_compute.html doc
+page for details.  If no bracketed integer is appended, the vector
+calculated by the compute is used.  If a bracketed integer is
+appended, the Ith column of the array calculated by the compute is
+used.  Users can also write code for their own compute styles and "add
+them to LAMMPS"_Section_modify.html.  See the discussion above for how
+I can be specified with a wildcard asterisk to effectively specify
+multiple values.
+
+If a value begins with "f_", a fix ID must follow which has been
+previously defined in the input script.  The fix must generate a
+global vector or array.  See the individual "fix"_fix.html doc page
+for details.  Note that some fixes only produce their values on
+certain timesteps, which must be compatible with when compute
+global/atom references the values, else an error results.  If no
+bracketed integer is appended, the vector calculated by the fix is
+used.  If a bracketed integer is appended, the Ith column of the array
+calculated by the fix is used.  Users can also write code for their
+own fix style and "add them to LAMMPS"_Section_modify.html.  See the
+discussion above for how I can be specified with a wildcard asterisk
+to effectively specify multiple values.
+
+If a value begins with "v_", a variable name must follow which has
+been previously defined in the input script.  It must be a
+"vector-style variable"_variable.html.  Vector-style variables can
+reference thermodynamic keywords and various other attributes of
+atoms, or invoke other computes, fixes, or variables when they are
+evaluated, so this is a very general means of generating a vector of
+global quantities which the {index} parameter will reference for
+assignement of global values to atoms.
+
+:line
+
+[Output info:]
+
+If a single input is specified this compute produces a per-atom
+vector.  If multiple inputs are specified, this compute produces a
+per-atom array values, where the number of columns is equal to the
+number of inputs specified.  These values can be used by any command
+that uses per-atom vector or array values from a compute as input.
+See "Section 6.15"_Section_howto.html#howto_15 for an overview of
+LAMMPS output options.
+
+The per-atom vector or array values will be in whatever units the
+corresponsing input values are in.
+
+[Restrictions:] none
+
+[Related commands:]
+
+"compute"_compute.html, "fix"_fix.html, "variable"_variable.html,
+"compute chunk/atom"_compute_chunk_atom.html, "compute
+reduce"_compute_reduce.html
+
+[Default:] none
--- a/doc/src/compute_pressure.txt
+++ b/doc/src/compute_pressure.txt
@ -37,12 +37,18 @@ The pressure is computed by the formula

 where N is the number of atoms in the system (see discussion of DOF
 below), Kb is the Boltzmann constant, T is the temperature, d is the
-dimensionality of the system (2 or 3 for 2d/3d), V is the system
-volume (or area in 2d), and the second term is the virial, computed
-within LAMMPS for all pairwise as well as 2-body, 3-body, and 4-body,
-and long-range interactions.  "Fixes"_fix.html that impose constraints
-(e.g. the "fix shake"_fix_shake.html command) also contribute to the
-virial term.
+dimensionality of the system (2 or 3 for 2d/3d), and V is the system
+volume (or area in 2d).  The second term is the virial, equal to
+-dU/dV, computed for all pairwise as well as 2-body, 3-body, 4-body,
+manybody, and long-range interactions, where r_i and f_i are the
+position and force vector of atom i, and the black dot indicates a dot
+product.  When periodic boundary conditions are used, N' necessarily
+includes periodic image (ghost) atoms outside the central box, and the
+position and force vectors of ghost atoms are thus included in the
+summation.  When periodic boundary conditions are not used, N' = N =
+the number of atoms in the system.  "Fixes"_fix.html that impose
+constraints (e.g. the "fix shake"_fix_shake.html command) also
+contribute to the virial term.

 A symmetric pressure tensor, stored as a 6-element vector, is also
 calculated by this compute.  The 6 components of the vector are
@ -62,8 +68,9 @@ compute temperature or ke and/or the virial.  The {virial} keyword
 means include all terms except the kinetic energy {ke}.

 Details of how LAMMPS computes the virial efficiently for the entire
-system, including the effects of periodic boundary conditions is
-discussed in "(Thompson)"_#Thompson.
+system, including for manybody potentials and accounting for the
+effects of periodic boundary conditions are discussed in
+"(Thompson)"_#Thompson.

 The temperature and kinetic energy tensor is not calculated by this
 compute, but rather by the temperature compute specified with the
--- a/doc/src/compute_smd_contact_radius.txt
+++ b/doc/src/compute_smd_contact_radius.txt
@ -27,7 +27,7 @@ contact radius is used only to prevent particles belonging to
 different physical bodies from penetrating each other. It is used by
 the contact pair styles, e.g., smd/hertz and smd/tri_surface.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 The value of the contact radius will be 0.0 for particles not in the
--- a/doc/src/compute_smd_damage.txt
+++ b/doc/src/compute_smd_damage.txt
@ -24,7 +24,7 @@ compute 1 all smd/damage :pre
 Define a computation that calculates the damage status of SPH particles
 according to the damage model which is defined via the SMD SPH pair styles, e.g., the maximum plastic strain failure criterion.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.

 [Output Info:]

--- a/doc/src/compute_smd_hourglass_error.txt
+++ b/doc/src/compute_smd_hourglass_error.txt
@ -32,7 +32,7 @@ configuration.  This compute is only really useful for debugging the
 hourglass control mechanim which is part of the Total-Lagrangian SPH
 pair style.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth
 Mach Dynamics in LAMMPS.

 [Output Info:]
--- a/doc/src/compute_smd_internal_energy.txt
+++ b/doc/src/compute_smd_internal_energy.txt
@ -24,7 +24,7 @@ compute 1 all smd/internal/energy :pre
 Define a computation which outputs the per-particle enthalpy, i.e.,
 the sum of potential energy and heat.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth
 Mach Dynamics in LAMMPS.

 [Output Info:]
--- a/doc/src/compute_smd_plastic_strain.txt
+++ b/doc/src/compute_smd_plastic_strain.txt
@ -25,7 +25,7 @@ Define a computation that outputs the equivalent plastic strain per
 particle.  This command is only meaningful if a material model with
 plasticity is defined.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth
 Mach Dynamics in LAMMPS.

 [Output Info:]
--- a/doc/src/compute_smd_plastic_strain_rate.txt
+++ b/doc/src/compute_smd_plastic_strain_rate.txt
@ -25,7 +25,7 @@ Define a computation that outputs the time rate of the equivalent
 plastic strain.  This command is only meaningful if a material model
 with plasticity is defined.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth
 Mach Dynamics in LAMMPS.

 [Output Info:]
--- a/doc/src/compute_smd_rho.txt
+++ b/doc/src/compute_smd_rho.txt
@ -26,7 +26,7 @@ The mass density is the mass of a particle which is constant during
 the course of a simulation, divided by its volume, which can change
 due to mechanical deformation.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_tlsph_defgrad.txt
+++ b/doc/src/compute_smd_tlsph_defgrad.txt
@ -25,7 +25,7 @@ Define a computation that calculates the deformation gradient.  It is
 only meaningful for particles which interact according to the
 Total-Lagrangian SPH pair style.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_tlsph_dt.txt
+++ b/doc/src/compute_smd_tlsph_dt.txt
@ -30,7 +30,7 @@ time step.  This calculation is performed automatically in the
 relevant SPH pair styles and this compute only serves to make the
 stable time increment accessible for output purposes.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_tlsph_num_neighs.txt
+++ b/doc/src/compute_smd_tlsph_num_neighs.txt
@ -25,7 +25,7 @@ Define a computation that calculates the number of particles inside of
 the smoothing kernel radius for particles interacting via the
 Total-Lagrangian SPH pair style.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_tlsph_shape.txt
+++ b/doc/src/compute_smd_tlsph_shape.txt
@ -26,7 +26,7 @@ associated with a particle as a rotated ellipsoid.  It is only
 meaningful for particles which interact according to the
 Total-Lagrangian SPH pair style.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_tlsph_strain.txt
+++ b/doc/src/compute_smd_tlsph_strain.txt
@ -24,7 +24,7 @@ compute 1 all smd/tlsph/strain :pre
 Define a computation that calculates the Green-Lagrange strain tensor
 for particles interacting via the Total-Lagrangian SPH pair style.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_tlsph_strain_rate.txt
+++ b/doc/src/compute_smd_tlsph_strain_rate.txt
@ -24,7 +24,7 @@ compute 1 all smd/tlsph/strain/rate :pre
 Define a computation that calculates the rate of the strain tensor for
 particles interacting via the Total-Lagrangian SPH pair style.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_tlsph_stress.txt
+++ b/doc/src/compute_smd_tlsph_stress.txt
@ -24,7 +24,7 @@ compute 1 all smd/tlsph/stress :pre
 Define a computation that outputs the Cauchy stress tensor for
 particles interacting via the Total-Lagrangian SPH pair style.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_triangle_mesh_vertices.txt
+++ b/doc/src/compute_smd_triangle_mesh_vertices.txt
@ -25,7 +25,7 @@ Define a computation that returns the coordinates of the vertices
 corresponding to the triangle-elements of a mesh created by the "fix
 smd/wall_surface"_fix_smd_wall_surface.html.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_ulsph_num_neighs.txt
+++ b/doc/src/compute_smd_ulsph_num_neighs.txt
@ -25,7 +25,7 @@ Define a computation that returns the number of neighbor particles
 inside of the smoothing kernel radius for particles interacting via
 the updated Lagrangian SPH pair style.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_ulsph_strain.txt
+++ b/doc/src/compute_smd_ulsph_strain.txt
@ -24,7 +24,7 @@ compute 1 all smd/ulsph/strain :pre
 Define a computation that outputs the logarithmic strain tensor.  for
 particles interacting via the updated Lagrangian SPH pair style.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_ulsph_strain_rate.txt
+++ b/doc/src/compute_smd_ulsph_strain_rate.txt
@ -25,7 +25,7 @@ Define a computation that outputs the rate of the logarithmic strain
 tensor for particles interacting via the updated Lagrangian SPH pair
 style.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_ulsph_stress.txt
+++ b/doc/src/compute_smd_ulsph_stress.txt
@ -23,7 +23,7 @@ compute 1 all smd/ulsph/stress :pre

 Define a computation that outputs the Cauchy stress tensor.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_vol.txt
+++ b/doc/src/compute_smd_vol.txt
@ -24,7 +24,7 @@ compute 1 all smd/vol :pre
 Define a computation that provides the per-particle volume and the sum
 of the per-particle volumes of the group for which the fix is defined.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_stress_atom.txt
+++ b/doc/src/compute_stress_atom.txt
@ -60,7 +60,7 @@ produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3
 atoms in a Tersoff 3-body interaction) is assigned in equal portions
 to each atom in the set.  E.g. 1/4 of the dihedral virial to each of
 the 4 atoms, or 1/3 of the fix virial due to SHAKE constraints applied
-to atoms in a a water molecule via the "fix shake"_fix_shake.html
+to atoms in a water molecule via the "fix shake"_fix_shake.html
 command.

 If no extra keywords are listed, all of the terms in this formula are
--- a/doc/src/compute_temp_profile.txt
+++ b/doc/src/compute_temp_profile.txt
@ -69,8 +69,8 @@ velocity for each atom.  Note that if there is only one atom in the
 bin, its thermal velocity will thus be 0.0.

 After the spatially-averaged velocity field has been subtracted from
-each atom, the temperature is calculated by the formula KE = (dim/2 N
- dim*Nx*Ny*Nz) k T, where KE = total kinetic energy of the group of
+each atom, the temperature is calculated by the formula KE = (dim*N
+- dim*Nx*Ny*Nz) k T/2, where KE = total kinetic energy of the group of
 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
--- a/doc/src/dihedral_charmm.txt
+++ b/doc/src/dihedral_charmm.txt
@ -109,7 +109,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/dihedral_harmonic.txt
+++ b/doc/src/dihedral_harmonic.txt
@ -76,7 +76,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/dihedral_helix.txt
+++ b/doc/src/dihedral_helix.txt
@ -69,7 +69,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/dihedral_hybrid.txt
+++ b/doc/src/dihedral_hybrid.txt
@ -77,7 +77,7 @@ for specific dihedral types.
 [Restrictions:]

 This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 Unlike other dihedral styles, the hybrid dihedral style does not store
--- a/doc/src/dihedral_multi_harmonic.txt
+++ b/doc/src/dihedral_multi_harmonic.txt
@ -63,7 +63,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/dihedral_opls.txt
+++ b/doc/src/dihedral_opls.txt
@ -71,7 +71,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/dihedral_table.txt
+++ b/doc/src/dihedral_table.txt
@ -154,7 +154,7 @@ radians instead of degrees.  (Note: This changes the way the forces
 are scaled in the 4th column of the data file.)

 The optional "CHECKU" keyword is followed by a filename.  This allows
-the user to save all of the the {Ntable} different entries in the
+the user to save all of the {Ntable} different entries in the
 interpolated energy table to a file to make sure that the interpolated
 function agrees with the user's expectations.  (Note: You can
 temporarily increase the {Ntable} parameter to a high value for this
--- a/doc/src/dump_modify.txt
+++ b/doc/src/dump_modify.txt
@ -165,7 +165,7 @@ extra buffering.

 :line

-The {element} keyword applies only to the the dump {cfg}, {xyz}, and
+The {element} keyword applies only to the dump {cfg}, {xyz}, and
 {image} styles.  It associates element names (e.g. H, C, Fe) with
 LAMMPS atom types.  See the list of element names at the bottom of
 this page.
@ -574,7 +574,7 @@ e.g. its x-component of velocity if the atom-attribute "vx" was
 specified.

 The basic idea of a color map is that the atom-attribute will be
-within a range of values, and that range is associated with a a series
+within a range of values, and that range is associated with a series
 of colors (e.g. red, blue, green).  An atom's specific value (vx =
 -3.2) can then mapped to the series of colors (e.g. halfway between
 red and blue), and a specific color is determined via an interpolation
--- a/doc/src/fix_cmap.txt
+++ b/doc/src/fix_cmap.txt
@ -113,7 +113,7 @@ quantity being minimized), you MUST enable the
 [Restrictions:]

 This fix can only be used if LAMMPS was built with the MOLECULE
-package (which it is by default).  See the "Making
+package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/fix_deform.txt
+++ b/doc/src/fix_deform.txt
@ -150,7 +150,7 @@ initial box length is 100 Angstroms, and V is 10 Angstroms/psec, then
 after 10 psec, the box length will have doubled.  After 20 psec, it
 will have tripled.

-The {erate} style changes a dimension of the the box at a "constant
+The {erate} style changes a dimension of the box at a "constant
 engineering strain rate".  The units of the specified strain rate are
 1/time.  See the "units"_units.html command for the time units
 associated with different choices of simulation units,
--- a/doc/src/fix_gcmc.txt
+++ b/doc/src/fix_gcmc.txt
@ -21,7 +21,7 @@ type = atom type for inserted atoms (must be 0 if mol keyword used) :l
 seed = random # seed (positive integer) :l
 T = temperature of the ideal gas reservoir (temperature units) :l
 mu = chemical potential of the ideal gas reservoir (energy units) :l
-translate = maximum Monte Carlo translation distance (length 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}
  {mol} value = template-ID
--- a/doc/src/fix_grem.txt
+++ b/doc/src/fix_grem.txt
@ -0,0 +1,111 @@
+"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 grem command :h3
+
+[Syntax:]
+
+fix ID group-ID grem lambda eta H0 thermostat-ID :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+grem = style name of this fix command :l
+lambda = intercept parameter of linear effective temperature function :l
+eta = slope parameter of linear effective temperature function :l
+H0 = shift parameter of linear effective temperature function :l
+thermostat-ID = ID of Nose-Hoover thermostat or barostat used in simulation :l,ule
+
+[Examples:]
+
+fix             fxgREM all grem 400 -0.01 -30000 fxnpt
+thermo_modify   press fxgREM_press :pre
+
+fix             fxgREM all grem 502 -0.15 -80000 fxnvt :pre
+
+[Description:]
+
+This fix implements the molecular dynamics version of the generalized
+replica exchange method (gREM) originally developed by "(Kim)"_#Kim,
+which uses non-Boltzmann ensembles to sample over first order phase
+transitions. The is done by defining replicas with an enthalpy
+dependent effective temperature
+
+:c,image(Eqs/fix_grem.jpg)
+
+with {eta} negative and steep enough to only intersect the
+characteristic microcanonical temperature (Ts) of the system once,
+ensuring a unimodal enthalpy distribution in that replica. {Lambda} is
+the intercept and effects the generalized ensemble similar to how
+temperature effects a Boltzmann ensemble. {H0} is a reference
+enthalpy, and is typically set as the lowest desired sampled enthalpy.
+Further explanation can be found in our recent papers
+"(Malolepsza)"_#Malolepsza.
+
+This fix requires a Nose-Hoover thermostat fix reference passed to the
+grem as {thermostat-ID}. Two distinct temperatures exist in this
+generalized ensemble, the effective temperature defined above, and a
+kinetic temperature that controls the velocity distribution of
+particles as usual. Either constant volume or constant pressure
+algorithms can be used.
+
+The fix enforces a generalized ensemble in a single replica
+only. Typically, this ideaology is combined with replica exchange with
+replicas differing by {lambda} only for simplicity, but this is not
+required. A multi-replica simulation can be run within the LAMMPS
+environment using the "temper/grem"_temper_grem.html command. This
+utilizes LAMMPS partition mode and requires the number of available
+processors be on the order of the number of desired replicas. A
+100-replica simulation would require at least 100 processors (1 per
+world at minimum). If a many replicas are needed on a small number of
+processors, multi-replica runs can be run outside of LAMMPS.  An
+example of this can be found in examples/USER/misc/grem and has no
+limit on the number of replicas per processor. However, this is very
+inefficient and error prone and should be avoided if possible.
+
+In general, defining the generalized ensembles is unique for every
+system. When starting a many-replica simulation without any knowledge
+of the underlying microcanonical temperature, there are several tricks
+we have utilized to optimize the process.  Choosing a less-steep {eta}
+yields broader distributions, requiring fewer replicas to map the
+microcanonical temperature.  While this likely struggles from the same
+sampling problems gREM was built to avoid, it provides quick insight
+to Ts.  Initially using an evenly-spaced {lambda} distribution
+identifies regions where small changes in enthalpy lead to large
+temperature changes. Replicas are easily added where needed.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.
+
+The "thermo_modify"_thermo_modify.html {press} option is supported
+by this fix to add the rescaled kinetic pressure as part of 
+"thermodynamic output"_thermo_style.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.
+
+[Related commands:]
+
+"temper/grem"_temper_grem.html, "fix nvt"_fix_nh.html, "fix
+npt"_fix_nh.html, "thermo_modify"_thermo_modify.html
+
+[Default:] none
+
+:line
+
+:link(Kim)
+[(Kim)] Kim, Keyes, Straub, J Chem. Phys, 132, 224107 (2010).
+
+:link(Malolepsza)
+[(Malolepsza)] Malolepsza, Secor, Keyes, J Phys Chem B 119 (42),
+13379-13384 (2015).
--- a/doc/src/fix_ipi.txt
+++ b/doc/src/fix_ipi.txt
@ -10,18 +10,19 @@ fix ipi command :h3

 [Syntax:]

-fix ID group-ID ipi address port \[unix\] :pre
+fix ID group-ID ipi address port \[unix\] \[reset\] :pre

 ID, group-ID are documented in "fix"_fix.html command
 ipi = style name of this fix command
 address = internet address (FQDN or IP), or UNIX socket name
 port = port number (ignored for UNIX sockets)
-optional keyword = {unix}, if present uses a unix socket :ul
+optional keyword = {unix}, if present uses a unix socket
+optional keyword = {reset}, if present reset electrostatics at each call :ul

 [Examples:]

 fix 1 all ipi my.server.com 12345
-fix 1 all ipi mysocket 666 unix
+fix 1 all ipi mysocket 666 unix reset

 [Description:]

@ -57,6 +58,15 @@ input are listed in the same order as in the data file of LAMMPS. The
 initial configuration is ignored, as it will be substituted with the
 coordinates received from i-PI before forces are ever evaluated.

+A note of caution when using potentials that contain long-range 
+electrostatics, or that contain parameters that depend on box size:
+all of these options will be initialized based on the cell size in the
+LAMMPS-side initial configuration and kept constant during the run. 
+This is required to e.g. obtain reproducible and conserved forces. 
+If the cell varies too wildly, it may be advisable to reinitialize 
+these interactions at each call. This behavior can be requested by 
+setting the {reset} switch. 
+
 [Restart, fix_modify, output, run start/stop, minimize info:]

 There is no restart information associated with this fix, since all
--- a/doc/src/fix_langevin.txt
+++ b/doc/src/fix_langevin.txt
@ -237,7 +237,7 @@ described in the papers cited below, the purpose of this method is to
 enable longer timesteps to be used (up to the numerical stability
 limit of the integrator), while still producing the correct Boltzmann
 distribution of atom positions.  It is implemented within LAMMPS, by
-changing how the the random force is applied so that it is composed of
+changing how the random force is applied so that it is composed of
 the average of two random forces representing half-contributions from
 the previous and current time intervals.

--- a/doc/src/fix_lb_fluid.txt
+++ b/doc/src/fix_lb_fluid.txt
@ -233,7 +233,7 @@ present, the speed of sound squared is set equal to (1/3)*(dx/dt)^2.
 Setting a0 > (dx/dt)^2 is not allowed, as this may lead to
 instabilities.

-If the {noise} keyword is used, followed by a a positive temperature
+If the {noise} keyword is used, followed by a positive temperature
 value, and a positive integer random number seed, a thermal
 lattice-Boltzmann algorithm is used.  If {LBtype} is set equal to 1
 (i.e. the standard LB integrator is chosen), the thermal LB algorithm
--- a/doc/src/fix_reax_bonds.txt
+++ b/doc/src/fix_reax_bonds.txt
@ -8,6 +8,7 @@

 fix reax/bonds command :h3
 fix reax/c/bonds command :h3
+fix reax/c/bonds/kk command :h3

 [Syntax:]

@ -47,6 +48,31 @@ commands"_Section_howto.html#howto_15.  No parameter of this fix can
 be used with the {start/stop} keywords of the "run"_run.html command.
 This fix is not invoked during "energy minimization"_minimize.html.

+:line
+
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in "Section_accelerate"_Section_accelerate.html
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See "Section_accelerate"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:]

 The fix reax/bonds command requires that the "pair_style
--- a/doc/src/fix_reaxc_species.txt
+++ b/doc/src/fix_reaxc_species.txt
@ -7,6 +7,7 @@
 :line

 fix reax/c/species command :h3
+fix reax/c/species/kk command :h3

 [Syntax:]

@ -129,6 +130,31 @@ No parameter of this fix can be used with the {start/stop} keywords of
 the "run"_run.html command.  This fix is not invoked during "energy
 minimization"_minimize.html.

+:line
+
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in "Section_accelerate"_Section_accelerate.html
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See "Section_accelerate"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:]

 The fix species currently only works with
--- a/doc/src/fix_rx.txt
+++ b/doc/src/fix_rx.txt
@ -87,7 +87,7 @@ end of each run. A positive value N means that the diagnostics are reported once
 per N time-steps.

 The diagnostics report the average # of integrator steps and RHS function evaluations
-and run-time per ODE as well as the the average/RMS/min/max per process. If the
+and run-time per ODE as well as the average/RMS/min/max per process. If the
 reporting frequency is 1, the RMS/min/max per ODE are also reported. The per ODE
 statistics can be used to adjust the tolerance and min/max step parameters. The
 statistics per MPI process can be useful to examine any load imbalance caused by the
--- a/doc/src/fix_smd_adjust_dt.txt
+++ b/doc/src/fix_smd_adjust_dt.txt
@ -28,7 +28,7 @@ fix 1 all smd/adjust_dt 0.1 :pre
 The fix calculates a new stable time increment for use with the SMD time integrators.

 The stable time increment is based on multiple conditions. For the SPH pair styles, a
-CFL criterion (Courant, Friedrichs & Lewy, 1928) is evaluated, which determines the the speed of
+CFL criterion (Courant, Friedrichs & Lewy, 1928) is evaluated, which determines the speed of
 sound cannot propagate further than a typical spacing between particles within a single time step to ensure
 no information is lost. For the contact pair styles, a linear analysis of the pair potential determines a
 stable maximum time step.
@ -36,7 +36,7 @@ stable maximum time step.
 This fix inquires the minimum stable time increment across all particles contained in the group for which this
 fix is defined. An additional safety factor {s_fact} is applied to the time increment.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.

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

--- a/doc/src/fix_smd_integrate_tlsph.txt
+++ b/doc/src/fix_smd_integrate_tlsph.txt
@ -32,7 +32,7 @@ fix 1 all smd/integrate_tlsph limit_velocity 1000 :pre

 The fix performs explicit time integration for particles which interact according with the Total-Lagrangian SPH pair style.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.

 The {limit_velocity} keyword will control the velocity, scaling the norm of
 the velocity vector to max_vel in case it exceeds this velocity limit.
--- a/doc/src/fix_smd_integrate_ulsph.txt
+++ b/doc/src/fix_smd_integrate_ulsph.txt
@ -34,7 +34,7 @@ fix 1 all smd/integrate_ulsph limit_velocity 1000 :pre
 [Description:]

 The fix performs explicit time integration for particles which interact with the updated Lagrangian SPH pair style.
-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.

 The {adjust_radius} keyword activates dynamic adjustment of the per-particle SPH smoothing kernel radius such that the number of neighbors per particles remains
 within the interval {min_nn} to {max_nn}. The parameter {adjust_radius_factor} determines the amount of adjustment per timestep. Typical values are
--- a/doc/src/fix_smd_move_triangulated_surface.txt
+++ b/doc/src/fix_smd_move_triangulated_surface.txt
@ -55,7 +55,7 @@ specified. This style also sets the velocity of each particle to (omega cross
 Rperp) where omega is its angular velocity around the rotation axis and
 Rperp is a perpendicular vector from the rotation axis to the particle.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS.

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

--- a/doc/src/fix_smd_wall_surface.txt
+++ b/doc/src/fix_smd_wall_surface.txt
@ -37,7 +37,7 @@ It is possible to move the triangulated surface via the "smd/move_tri_surf"_fix_
 Immediately after a .STL file has been read, the simulation needs to be run for 0 timesteps in order to properly register the new particles
 in the system. See the "funnel_flow" example in the USER-SMD examples directory.

-See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
+See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.

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

--- a/doc/src/fix_srd.txt
+++ b/doc/src/fix_srd.txt
@ -101,7 +101,7 @@ particles move in the normal way via a time integration "fix"_fix.html
 with a short timestep dt.  SRD particles advect with a large timestep
 dt_SRD >= dt.

-If the {lamda} keyword is not specified, the the SRD temperature
+If the {lamda} keyword is not specified, the SRD temperature
 {Tsrd} is used in the above formula to compute lamda.  If the {lamda}
 keyword is specified, then the {Tsrd} setting is ignored and the above
 equation is used to compute the SRD temperature.
--- a/doc/src/fix_ttm.txt
+++ b/doc/src/fix_ttm.txt
@ -107,7 +107,7 @@ specified as parameters to the fix.  The other quantities are derived.
 The form of the heat diffusion equation used here is almost the same
 as that in equation 6 of "(Duffy)"_#Duffy, with the exception that the
 electronic density is explicitly reprensented, rather than being part
-of the the specific heat parameter.
+of the specific heat parameter.

 Currently, fix ttm assumes that none of the user-supplied parameters
 will vary with temperature. Note that "(Duffy)"_#Duffy used a tanh()
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@ -48,6 +48,7 @@ Fixes :h1
   fix_gld
   fix_gle
   fix_gravity
+   fix_grem
   fix_halt
   fix_heat
   fix_imd
--- a/doc/src/improper_cvff.txt
+++ b/doc/src/improper_cvff.txt
@ -77,7 +77,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This improper style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/improper_harmonic.txt
+++ b/doc/src/improper_harmonic.txt
@ -81,7 +81,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This improper style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/improper_hybrid.txt
+++ b/doc/src/improper_hybrid.txt
@ -55,7 +55,7 @@ types.
 [Restrictions:]

 This improper style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 Unlike other improper styles, the hybrid improper style does not store
--- a/doc/src/improper_style.txt
+++ b/doc/src/improper_style.txt
@ -27,7 +27,7 @@ between quadruplets of atoms, which remain in force for the duration
 of the simulation.  The list of improper quadruplets is read in by a
 "read_data"_read_data.html or "read_restart"_read_restart.html command
 from a data or restart file.  Note that the ordering of the 4 atoms in
-an improper quadruplet determines the the definition of the improper
+an improper quadruplet determines the definition of the improper
 angle used in the formula for each style.  See the doc pages of
 individual styles for details.

--- a/doc/src/improper_umbrella.txt
+++ b/doc/src/improper_umbrella.txt
@ -74,7 +74,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This improper style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/info.txt
+++ b/doc/src/info.txt
@ -14,7 +14,7 @@ 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}
     {out} values = {screen}, {log}, {append} filename, {overwrite} filename
-     {styles} values = {all}, {angle}, {atom}, {bond}, {compute}, {command}, {dump}, {dihedral}, {fix}, {improper}, {integrate}, {kspace}, {minimize}, {region} :ul
+     {styles} values = {all}, {angle}, {atom}, {bond}, {compute}, {command}, {dump}, {dihedral}, {fix}, {improper}, {integrate}, {kspace}, {minimize}, {pair}, {region} :ul

 [Examples:]

@ -70,8 +70,9 @@ The {variables} category prints a list of all currently defined
 variables, their names, styles, definition and last computed value, if
 available.

-The {styles} category prints the list of styles available in LAMMPS. It
-supports one of the following options to control what is printed out:
+The {styles} category prints the list of styles available in the
+current LAMMPS binary. It supports one of the following options
+to control which category of styles is printed out:

 all
 angle
@ -86,6 +87,7 @@ improper
 integrate
 kspace
 minimize
+pair
 region :ul

 The {time} category prints the accumulated CPU and wall time for the
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@ -59,6 +59,7 @@ dump_h5md.html
 dump_image.html
 dump_modify.html
 dump_molfile.html
+dump_nc.html
 echo.html
 fix.html
 fix_modify.html
@ -152,6 +153,7 @@ fix_colvars.html
 fix_controller.html
 fix_deform.html
 fix_deposit.html
+fix_dpd_energy.html
 fix_drag.html
 fix_drude.html
 fix_drude_transform.html
@ -170,6 +172,7 @@ fix_gcmc.html
 fix_gld.html
 fix_gle.html
 fix_gravity.html
+fix_grem.html
 fix_halt.html
 fix_heat.html
 fix_imd.html
@ -272,6 +275,7 @@ fix_viscosity.html
 fix_viscous.html
 fix_wall.html
 fix_wall_gran.html
+fix_wall_gran_region.html
 fix_wall_piston.html
 fix_wall_reflect.html
 fix_wall_region.html
@ -307,6 +311,7 @@ compute_erotate_sphere.html
 compute_erotate_sphere_atom.html
 compute_event_displace.html
 compute_fep.html
+compute_global_atom.html
 compute_group_group.html
 compute_gyration.html
 compute_gyration_chunk.html
@ -390,6 +395,7 @@ compute_voronoi_atom.html
 compute_xrd.html

 pair_adp.html
+pair_agni.html
 pair_airebo.html
 pair_awpmd.html
 pair_beck.html
@ -622,3 +628,4 @@ USER/atc/man_unfix_flux.html
 USER/atc/man_unfix_nodes.html
 USER/atc/man_write_atom_weights.html
 USER/atc/man_write_restart.html
+
--- a/doc/src/neb.txt
+++ b/doc/src/neb.txt
@ -284,7 +284,7 @@ ID2 x2 y2 z2
 ...
 IDN xN yN zN :pre

-The fields are the the atom ID, followed by the x,y,z coordinates.
+The fields are the atom ID, followed by the x,y,z coordinates.
 The lines can be listed in any order.  Additional trailing information
 on the line is OK, such as a comment.

--- a/doc/src/next.txt
+++ b/doc/src/next.txt
@ -44,7 +44,7 @@ one value from their respective list of values.  A {file}-style
 variable reads the next line from its associated file.  An
 {atomfile}-style variable reads the next set of lines (one per atom)
 from its associated file.  {String-} or {atom}- or {equal}- or
-{world}-style variables cannot be used with the the next command,
+{world}-style variables cannot be used with the next command,
 since they only store a single value.

 When any of the variables in the next command has no more values, a
--- a/doc/src/pair_adp.txt
+++ b/doc/src/pair_adp.txt
@ -168,7 +168,7 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]

 This pair style is part of the MANYBODY package.  It is only enabled
-if LAMMPS was built with that package (which it is by default).
+if LAMMPS was built with that package.

 [Related commands:]

--- a/Show More
+++ b/Show More