final prep for 22Nov patch

Merge pull request #288 from akohlmey/moltemplate-1.40
update bundled version of moltemplate to v1.40
2016-11-22 09:23:02 -07:00 · 2016-11-22 08:51:11 -07:00 · 2016-11-22 08:50:29 -07:00 · 2016-11-22 08:49:46 -07:00 · 2016-11-22 08:48:27 -07:00 · 2016-11-22 08:47:44 -07:00
878 changed files with 42831 additions and 2612 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="22 Nov 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
+22 Nov 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

@ -631,7 +632,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "rigid/npt (o)"_fix_rigid.html,
 "rigid/nve (o)"_fix_rigid.html,
 "rigid/nvt (o)"_fix_rigid.html,
-"rigid/small (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,
@ -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,
@ -886,6 +888,8 @@ 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 +913,8 @@ 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 +983,12 @@ 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 +998,7 @@ 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
@ -2729,7 +2729,7 @@ 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 +2830,7 @@ 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_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
--- 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_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_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.
--- 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
@ -390,6 +394,7 @@ compute_voronoi_atom.html
 compute_xrd.html

 pair_adp.html
+pair_agni.html
 pair_airebo.html
 pair_awpmd.html
 pair_beck.html
@ -622,3 +627,4 @@ 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/doc/src/pair_agni.txt
+++ b/doc/src/pair_agni.txt
@ -0,0 +1,128 @@
+"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
+
+pair_style agni command :h3
+pair_style agni/omp command :h3
+
+[Syntax:]
+
+pair_style agni :pre
+
+[Examples:]
+pair_style      agni
+pair_coeff      * * Al.agni Al
+
+[Description:]
+
+Style {agni} style computes the manybody vectorial force components for
+an atom as
+
+:c,image(Eqs/pair_agni.jpg)
+
+{u} labels the individual components, i.e. x, y or z, and {V} is the
+corresponding atomic fingerprint. {d} is the Euclidean distance between
+any two atomic fingerprints. A total of N_t reference atomic
+environments are considered to construct the force field file. {alpha_t}
+and {l} are the weight coefficients and length scale parameter of the
+non-linear regression model.
+
+The method implements the recently proposed machine learning access to
+atomic forces as discussed extensively in the following publications -
+"(Botu1)"_#Botu2015adaptive and "(Botu2)"_#Botu2015learning. The premise
+of the method is to map the atomic enviornment numerically into a
+fingerprint, and use machine learning methods to create a mapping to the
+vectorial atomic forces.
+
+Only a single pair_coeff command is used with the {agni} style which
+specifies an AGNI potential file containing the parameters of the
+force field for the needed elements. These are mapped to LAMMPS atom 
+types by specifying N additional arguments after the filename in the 
+pair_coeff command, where N is the number of LAMMPS atom types:
+
+filename
+N element names = mapping of AGNI elements to atom types :ul
+
+See the "pair_coeff"_pair_coeff.html doc page for alternate ways
+to specify the path for the force field file.
+
+An AGNI force field is fully specified by the filename which contains the
+parameters of the force field, i.e., the reference training environments
+used to construct the machine learning force field. Example force field 
+and input files are provided in the examples/USER/misc/agni directory. 
+
+:line
+
+Styles with {omp} suffix is 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 5"_Section_accelerate.html
+of the manual.  The accelerated style takes the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+The accelerated style is part of the USER-OMP.  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 style 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 5"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+This pair style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+This pair style does not write its information to "binary restart
+files"_restart.html, since it is stored in potential files.  Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the {pair} keyword of the
+"run_style respa"_run_style.html command.  It does not support the
+{inner}, {middle}, {outer} keywords.
+
+:line
+
+[Restrictions:]
+
+Currently, only elemental systems are implemented. Also, the method only
+provides access to the forces and not energies or stresses. However, one
+can access the energy via thermodynamic integration of the forces as
+discussed in "(Botu3)"_#Botu2016construct.  This pair style 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.
+
+The AGNI force field files provided with LAMMPS (see the
+potentials directory) are parameterized for metal "units"_units.html.
+You can use the AGNI potential with any LAMMPS units, but you would need
+to create your own AGNI potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+
+[Default:] none
+
+:line
+
+:link(Botu2015adaptive)
+[(Botu1)] V. Botu and R. Ramprasad, Int. J. Quant. Chem., 115(16), 1074 (2015).
+
+:link(Botu2015learning)
+[(Botu2)] V. Botu and R. Ramprasad, Phys. Rev. B, 92(9), 094306 (2015).
+
+:link(Botu2016construct)
+[(Botu3)] V. Botu, R. Batra, J. Chapman and R. Ramprasad, https://arxiv.org/abs/1610.02098 (2016).
--- a/doc/src/pair_airebo.txt
+++ b/doc/src/pair_airebo.txt
@ -203,9 +203,8 @@ These pair styles can only be used via the {pair} keyword of the
 [Restrictions:]

 These pair styles are part of the MANYBODY package.  They are only
-enabled if LAMMPS was built with that package (which it is by
-default).  See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
+enabled if LAMMPS was built with that package.  See the
+"Making LAMMPS"_Section_start.html#start_3 section for more info.

 These pair potentials require the "newton"_newton.html setting to be
 "on" for pair interactions.
--- a/doc/src/pair_bop.txt
+++ b/doc/src/pair_bop.txt
@ -382,7 +382,7 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]

 These pair styles are part of the MANYBODY package.  They are only
-enabled if LAMMPS was built with that package (which it is by default).
+enabled if LAMMPS was built with that package.
 See the "Making LAMMPS"_Section_start.html#start_3 section for more
 info.

--- a/doc/src/pair_born.txt
+++ b/doc/src/pair_born.txt
@ -19,6 +19,8 @@ pair_style born/coul/msm/omp command :h3
 pair_style born/coul/wolf command :h3
 pair_style born/coul/wolf/gpu command :h3
 pair_style born/coul/wolf/omp command :h3
+pair_style born/coul/dsf command :h3
+pair_style born/coul/dsf/cs command :h3

 [Syntax:]

@ -37,7 +39,11 @@ args = list of arguments for a particular style :ul
  {born/coul/wolf} args = alpha cutoff (cutoff2)
    alpha = damping parameter (inverse distance units)
    cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
+    cutoff2 = global cutoff for Coulombic (optional) (distance units)
+  {born/coul/dsf} or {born/coul/dsf/cs} args = alpha cutoff (cutoff2)
+    alpha = damping parameter (inverse distance units)
+    cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
+    cutoff2 = global cutoff for Coulombic (distance units) :pre

 [Examples:]

@ -62,6 +68,10 @@ pair_style born/coul/wolf 0.25 10.0 9.0
 pair_coeff * * 6.08 0.317 2.340 24.18 11.51
 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre

+pair_style born/coul/dsf 0.1 10.0 12.0
+pair_coeff * *   0.0 1.00 0.00 0.00 0.00
+pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre
+
 [Description:]

 The {born} style computes the Born-Mayer-Huggins or Tosi/Fumi
@ -90,10 +100,14 @@ term.
 The {born/coul/wolf} style adds a Coulombic term as described for the
 Wolf potential in the "coul/wolf"_pair_coul.html pair style.

+The {born/coul/dsf} style computes the Coulomb contribution with the
+damped shifted force model as in the "coul/dsf"_pair_coul.html style.
+
 Style {born/coul/long/cs} is identical to {born/coul/long} except that
 a term is 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.
+0.0. The same correction is introduced for {born/coul/dsf/cs} style
+which is identical to {born/coul/dsf}.

 Note that these potentials are related to the "Buckingham
 potential"_pair_buck.html.
@ -116,9 +130,10 @@ The second coefficient, rho, must be greater than zero.
 The last coefficient is optional.  If not specified, the global A,C,D
 cutoff specified in the pair_style command is used.

-For {born/coul/long} and {born/coul/wolf} no Coulombic cutoff can be
-specified for an individual I,J type pair.  All type pairs use the
-same global Coulombic cutoff specified in the pair_style command.
+For {born/coul/long}, {born/coul/wolf} and {born/coul/dsf} no
+Coulombic cutoff can be specified for an individual I,J type pair.
+All type pairs use the same global Coulombic cutoff specified in the
+pair_style command.

 :line

@ -174,9 +189,8 @@ respa"_run_style.html command.  They do not support the {inner},
 [Restrictions:]

 The {born/coul/long} style is part of the KSPACE package.  It is only
-enabled if LAMMPS was built with that package (which it is by
-default).  See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
+enabled if LAMMPS was built with that package.  See the
+"Making LAMMPS"_Section_start.html#start_3 section for more info.

 [Related commands:]

--- a/doc/src/pair_buck.txt
+++ b/doc/src/pair_buck.txt
@ -186,9 +186,8 @@ respa"_run_style.html command.  They do not support the {inner},

 The {buck/coul/long} style is part of the KSPACE package.  The
 {buck/coul/long/cs} style is part of the CORESHELL package.  They are
-only enabled if LAMMPS was built with that package (which it is by
-default).  See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
+only enabled if LAMMPS was built with that package.  See the
+"Making LAMMPS"_Section_start.html#start_3 section for more info.

 [Related commands:]

--- a/doc/src/pair_comb.txt
+++ b/doc/src/pair_comb.txt
@ -156,7 +156,7 @@ These pair styles can only be used via the {pair} keyword of the
 [Restrictions:]

 These pair styles are part of the MANYBODY package.  It is only enabled
-if LAMMPS was built with that package (which it is by default).  See
+if LAMMPS was built with that package.  See
 the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 These pair styles requires the "newton"_newton.html setting to be "on"
--- a/doc/src/pair_coul.txt
+++ b/doc/src/pair_coul.txt
@ -313,9 +313,8 @@ This pair style can only be used via the {pair} keyword of the

 The {coul/long}, {coul/msm} and {tip4p/long} styles are part of the
 KSPACE package.  The {coul/long/cs} style is part of the CORESHELL
-package.  They are only enabled if LAMMPS was built with that package
-(which it is by default).  See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+package.  They are only enabled if LAMMPS was built with that package.
+See the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 [Related commands:]

--- a/doc/src/pair_cs.txt
+++ b/doc/src/pair_cs.txt
@ -8,19 +8,24 @@

 pair_style born/coul/long/cs command :h3
 pair_style buck/coul/long/cs command :h3
+pair_style born/coul/dsf/cs command :h3

 [Syntax:]

 pair_style style args :pre

-style = {born/coul/long/cs} or {buck/coul/long/cs}
+style = {born/coul/long/cs} or {buck/coul/long/cs} or {born/coul/dsf/cs}
 args = list of arguments for a particular style :ul
  {born/coul/long/cs} args = cutoff (cutoff2)
    cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
    cutoff2 = global cutoff for Coulombic (optional) (distance units)
  {buck/coul/long/cs} args = cutoff (cutoff2)
    cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
+    cutoff2 = global cutoff for Coulombic (optional) (distance units)
+  {born/coul/dsf/cs} args = alpha cutoff (cutoff2)
+    alpha = damping parameter (inverse distance units)
+    cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
+    cutoff2 = global cutoff for Coulombic (distance units) :pre

 [Examples:]

@ -32,6 +37,10 @@ pair_style buck/coul/long/cs 10.0 8.0
 pair_coeff * * 100.0 1.5 200.0
 pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre

+pair_style born/coul/dsf/cs 0.1 10.0 12.0
+pair_coeff * *   0.0 1.00 0.00 0.00 0.00
+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
@ -39,7 +48,7 @@ core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham.  See
 "Section 6.25"_Section_howto.html#howto_25 of the manual for an
 overview of the model as implemented in LAMMPS.

-These pair styles are identical to the "pair_style
+The styles with a {coul/long} term are identical to the "pair_style
 born/coul/long"_pair_born.html and "pair_style
 buck/coul/long"_pair_buck.html styles, except they correctly treat the
 special case where the distance between two charged core and shell
@ -63,6 +72,14 @@ where C is an energy-conversion constant, Qi and Qj are the charges on
 the core and shell, epsilon is the dielectric constant and r_min is the
 minimal distance.

+The pair style {born/coul/dsf/cs} is identical to the
+"pair_style born/coul/dsf"_pair_born.html style, which uses the
+the damped shifted force model as in "coul/dsf"_pair_coul.html
+to compute the Coulomb contribution. This approach does not require
+a long-range solver, thus the only correction is the addition of a
+minimal distance to avoid the possible r = 0.0 case for a
+core/shell pair.
+
 [Restrictions:]

 These pair styles are part of the CORESHELL package.  They are only
--- a/doc/src/pair_eam.txt
+++ b/doc/src/pair_eam.txt
@ -412,9 +412,8 @@ The eam pair styles can only be used via the {pair} keyword of the
 [Restrictions:]

 All of these styles except the {eam/cd} style are part of the MANYBODY
-package.  They are only enabled if LAMMPS was built with that package
-(which it is by default).  See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+package.  They are only enabled if LAMMPS was built with that package.
+See the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 The {eam/cd} style is part of the USER-MISC package and also requires
 the MANYBODY package.  It is only enabled if LAMMPS was built with
--- a/doc/src/pair_eim.txt
+++ b/doc/src/pair_eim.txt
@ -159,7 +159,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

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

 [Related commands:]

--- a/doc/src/pair_lcbop.txt
+++ b/doc/src/pair_lcbop.txt
@ -72,7 +72,7 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]

 This pair styles is part of the MANYBODY package.  It is only enabled
-if LAMMPS was built with that package (which it is by default).  See
+if LAMMPS was built with that package.  See
 the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 This pair potential requires the "newton"_newton.html setting to be
--- a/doc/src/pair_nb3b_harmonic.txt
+++ b/doc/src/pair_nb3b_harmonic.txt
@ -113,7 +113,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This pair style can only be used if LAMMPS was built with the MANYBODY
-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/pair_polymorphic.txt
+++ b/doc/src/pair_polymorphic.txt
@ -191,7 +191,7 @@ input script. If using read_data, atomic masses must be defined in the
 atomic structure data file.

 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). See the
+LAMMPS was built with that package. See the
 "Making LAMMPS"_Section_start.html#start_3 section for more info.

 This pair potential requires the "newtion"_newton.html setting to be
--- a/doc/src/pair_snap.txt
+++ b/doc/src/pair_snap.txt
@ -15,7 +15,7 @@ pair_style snap :pre
 [Examples:]

 pair_style snap
-pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P :pre
+pair_coeff * * InP.snapcoeff In P InP.snapparam In In P P :pre

 [Description:]

@ -27,9 +27,9 @@ it uses bispectrum components
 to characterize the local neighborhood of each atom
 in a very general way. The mathematical definition of the
 bispectrum calculation used by SNAP is identical
-to that used of "compute sna/atom"_compute_sna_atom.html.
+to that used by "compute sna/atom"_compute_sna_atom.html.
 In SNAP, the total energy is decomposed into a sum over
-atom energies. The energy of atom {i} is
+atom energies. The energy of atom {i } is
 expressed as a weighted sum over bispectrum components.

 :c,image(Eqs/pair_snap.jpg)
@ -183,8 +183,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 :line

 :link(Thompson2014)
-[(Thompson)] Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint
-available at "arXiv:1409.3880"_http://arxiv.org/abs/1409.3880
+[(Thompson)] Thompson, Swiler, Trott, Foiles, Tucker, J Comp Phys, 285, 316 (2015).

 :link(Bartok2010)
 [(Bartok2010)] Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
--- a/doc/src/pair_srp.txt
+++ b/doc/src/pair_srp.txt
@ -99,7 +99,7 @@ The optional {exclude} keyword determines if forces are computed
 between first neighbor (directly connected) bonds.  For a setting of
 {no}, first neighbor forces are computed; for {yes} they are not
 computed. A setting of {no} cannot be used with the {min} option for
-distance calculation because the the minimum distance between directly
+distance calculation because the minimum distance between directly
 connected bonds is zero.

 Pair style {srp} turns off normalization of thermodynamic properties
--- a/doc/src/pair_sw.txt
+++ b/doc/src/pair_sw.txt
@ -192,7 +192,7 @@ 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).  See
+if LAMMPS was built with that package.  See
 the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 This pair style requires the "newton"_newton.html setting to be "on"
--- a/doc/src/pair_tersoff.txt
+++ b/doc/src/pair_tersoff.txt
@ -222,7 +222,7 @@ 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).  See
+if LAMMPS was built with that package.  See
 the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 This pair style requires the "newton"_newton.html setting to be "on"
--- a/doc/src/pair_tersoff_mod.txt
+++ b/doc/src/pair_tersoff_mod.txt
@ -7,32 +7,43 @@
 :line

 pair_style tersoff/mod command :h3
+pair_style tersoff/mod/c command :h3
 pair_style tersoff/mod/gpu command :h3
 pair_style tersoff/mod/kk command :h3
 pair_style tersoff/mod/omp command :h3
+pair_style tersoff/mod/c/omp command :h3

 [Syntax:]

 pair_style tersoff/mod :pre

+pair_style tersoff/mod/c :pre
+
 [Examples:]

 pair_style tersoff/mod
 pair_coeff * * Si.tersoff.mod Si Si :pre

+pair_style tersoff/mod/c
+pair_coeff * * Si.tersoff.modc Si Si :pre
+
 [Description:]

-The {tersoff/mod} style computes a bond-order type interatomic
-potential "(Kumagai)"_#Kumagai based on a 3-body Tersoff potential
-"(Tersoff_1)"_#Tersoff_1, "(Tersoff_2)"_#Tersoff_2 with modified
-cutoff function and angular-dependent term, giving the energy E of a
-system of atoms as
+The {tersoff/mod} and {tersoff/mod/c} styles computes a bond-order type
+interatomic potential "(Kumagai)"_#Kumagai based on a 3-body Tersoff
+potential "(Tersoff_1)"_#Tersoff_1, "(Tersoff_2)"_#Tersoff_2 with
+modified cutoff function and angular-dependent term, giving the energy
+E of a system of atoms as

 :c,image(Eqs/pair_tersoff_mod.jpg)

 where f_R is a two-body term and f_A includes three-body interactions.
 The summations in the formula are over all neighbors J and K of atom I
 within a cutoff distance = R + D.
+The {tersoff/mod/c} style differs from {tersoff/mod} only in the
+formulation of the V_ij term, where it contains an additional c0 term.
+
+:c,image(Eqs/pair_tersoff_mod_c.jpg)

 The modified cutoff function f_C proposed by "(Murty)"_#Murty and
 having a continuous second-order differential is employed. The
@ -69,10 +80,11 @@ are placeholders for atom types that will be used with other
 potentials.

 Tersoff/MOD file in the {potentials} directory of the LAMMPS
-distribution have a ".tersoff.mod" suffix.  Lines that are not blank
-or comments (starting with #) define parameters for a triplet of
-elements.  The parameters in a single entry correspond to coefficients
-in the formula above:
+distribution have a ".tersoff.mod" suffix. Potential files for the
+{tersoff/mod/c} style have the suffix ".tersoff.modc". Lines that are
+not blank or comments (starting with #) define parameters for a triplet
+of elements.  The parameters in a single entry correspond to
+coefficients in the formulae above:

 element 1 (the center atom in a 3-body interaction)
 element 2 (the atom bonded to the center atom)
@ -93,13 +105,15 @@ c1
 c2
 c3
 c4
-c5 :ul
+c5
+c0 (energy units, tersoff/mod/c only):ul

 The n, eta, lambda2, B, lambda1, and A parameters are only used for
 two-body interactions.  The beta, alpha, c1, c2, c3, c4, c5, h
 parameters are only used for three-body interactions. The R and D
-parameters are used for both two-body and three-body interactions. The
-non-annotated parameters are unitless.
+parameters are used for both two-body and three-body interactions.
+The c0 term applies to {tersoff/mod/c} only. The non-annotated
+parameters are unitless.

 The Tersoff/MOD potential file must contain entries for all the elements
 listed in the pair_coeff command.  It can also contain entries for
@ -156,7 +170,7 @@ 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).  See
+if LAMMPS was built with that package.  See
 the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 This pair style requires the "newton"_newton.html setting to be "on"
--- a/doc/src/pair_tersoff_zbl.txt
+++ b/doc/src/pair_tersoff_zbl.txt
@ -232,7 +232,7 @@ 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).  See
+if LAMMPS was built with that package.  See
 the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 This pair style requires the "newton"_newton.html setting to be "on"
--- a/doc/src/pair_vashishta.txt
+++ b/doc/src/pair_vashishta.txt
@ -8,6 +8,7 @@

 pair_style vashishta command :h3
 pair_style vashishta/omp command :h3
+pair_style vashishta/kk command :h3
 pair_style vashishta/table command :h3
 pair_style vashishta/table/omp command :h3

@ -212,9 +213,8 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]

 These pair style are part of the MANYBODY package.  They is only
-enabled if LAMMPS was built with that package (which it is by
-default).  See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
+enabled if LAMMPS was built with that package.  See the
+"Making LAMMPS"_Section_start.html#start_3 section for more info.

 These pair styles requires the "newton"_newton.html setting to be "on"
 for pair interactions.
--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@ -6,6 +6,7 @@ Pair Styles :h1
   :maxdepth: 1

   pair_adp
+   pair_agni
   pair_airebo
   pair_awpmd
   pair_beck
--- a/doc/src/prd.txt
+++ b/doc/src/prd.txt
@ -214,7 +214,7 @@ when a correlated event occurs during the third stage of the loop
 listed above, i.e. when only one replica is running dynamics.

 When more than one replica detects an event at the end of the same
-event check (every {t_event} steps) during the the second stage, then
+event check (every {t_event} steps) during the second stage, then
 one of them is chosen at random.  The number of coincident events is
 the number of replicas that detected an event.  Normally, this value
 should be 1.  If it is often greater than 1, then either the number of
@ -241,7 +241,7 @@ time was spent in each stage (dephasing, dynamics, quenching, etc).

 Any "dump files"_dump.html defined in the input script, will be
 written to during a PRD run at timesteps corresponding to both
-uncorrelated and correlated events.  This means the the requested dump
+uncorrelated and correlated events.  This means the requested dump
 frequency in the "dump"_dump.html command is ignored.  There will be
 one dump file (per dump command) created for all partitions.

--- a/doc/src/python.txt
+++ b/doc/src/python.txt
@ -188,7 +188,7 @@ is assumed to have been previously loaded by another python command.

 Note that the Python code that is loaded and run must contain a
 function with the specified {func} name.  To operate properly when
-later invoked, the the function code must match the {input} and
+later invoked, the function code must match the {input} and
 {return} and {format} keywords specified by the python command.
 Otherwise Python will generate an error.

--- a/doc/src/read_dump.txt
+++ b/doc/src/read_dump.txt
@ -185,7 +185,7 @@ For dump files in {xyz} format, only the {x}, {y}, and {z} fields are
 supported.  The dump file does not store atom IDs, so these are
 assigned consecutively to the atoms as they appear in the dump file,
 starting from 1.  Thus you should insure that order of atoms is
-consistent from snapshot to snapshot in the the XYZ dump file.  See
+consistent from snapshot to snapshot in the XYZ dump file.  See
 the "dump_modify sort"_dump_modify.html command if the XYZ dump file
 was written by LAMMPS.

@ -195,7 +195,7 @@ velocities, or their respective plugins may not support reading of
 velocities.  The molfile dump files do not store atom IDs, so these
 are assigned consecutively to the atoms as they appear in the dump
 file, starting from 1.  Thus you should insure that order of atoms are
-consistent from snapshot to snapshot in the the molfile dump file.
+consistent from snapshot to snapshot in the molfile dump file.
 See the "dump_modify sort"_dump_modify.html command if the dump file
 was written by LAMMPS.

--- a/doc/src/suffix.txt
+++ b/doc/src/suffix.txt
@ -94,6 +94,13 @@ Of course this is also possible by not using any suffix commands, and
 explictly appending or not appending the suffix to the relevant
 commands in your input script.

+NOTE: The default "run_style"_run_style.html verlet is invoked prior to
+reading the input script and is therefore not affected by a suffix command
+in the input script. The KOKKOS package requires "run_style verlet/kk",
+so when using the KOKKOS package it is necessary to either use the command
+line "-sf kk" command or add an explicit "run_style verlet" command to the
+input script.
+
 [Restrictions:] none

 [Related commands:]
--- a/doc/src/tad.txt
+++ b/doc/src/tad.txt
@ -231,7 +231,7 @@ time was spent in each stage (NEB, dynamics, quenching, etc).

 Any "dump files"_dump.html defined in the input script will be written
 to during a TAD run at timesteps when an event is executed.  This
-means the the requested dump frequency in the "dump"_dump.html command
+means the requested dump frequency in the "dump"_dump.html command
 is ignored.  There will be one dump file (per dump command) created
 for all partitions.  The atom coordinates of the dump snapshot are
 those of the minimum energy configuration resulting from quenching
--- a/doc/src/temper_grem.txt
+++ b/doc/src/temper_grem.txt
@ -0,0 +1,109 @@
+"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
+
+temper/grem command :h3
+
+[Syntax:]
+
+temper/grem N M lambda fix-ID thermostat-ID seed1 seed2 index :pre
+
+N = total # of timesteps to run
+M = attempt a tempering swap every this many steps
+lambda = initial lambda for this ensemble
+fix-ID = ID of fix_grem
+thermostat-ID = ID of the thermostat that controls kinetic temperature
+seed1 = random # seed used to decide on adjacent temperature to partner with
+seed2 = random # seed for Boltzmann factor in Metropolis swap
+index = which temperature (0 to N-1) I am simulating (optional) :ul
+
+[Examples:]
+
+temper/grem 100000 1000 ${lambda} fxgREM fxnvt 0 58728
+temper/grem 40000 100 ${lambda} fxgREM fxnpt 0 32285 ${walkers} :pre
+
+[Description:]
+
+Run a parallel tempering or replica exchange simulation in LAMMPS
+partition mode using multiple generalized replicas (ensembles) of a
+system defined by "fix grem"_fix_grem.html, which stands for the
+generalized replica exchange method (gREM) originally developed by
+"(Kim)"_#Kim.  It uses non-Boltzmann ensembles to sample over first
+order phase transitions. The is done by defining replicas with an
+enthalpy dependent effective temperature
+
+Two or more replicas must be used.  See the "temper"_temper.html
+command for an explanation of how to run replicas on multiple
+partitions of one or more processors.
+
+This command is a modification of the "temper"_temper.html command and
+has the same dependencies, restraints, and input variables which are
+discussed there in greater detail.
+
+Instead of temperature, this command performs replica exchanges in
+lambda as per the generalized ensemble enforced by "fix
+grem"_fix_grem.html.  The desired lambda is specified by {lambda},
+which is typically a variable previously set in the input script, so
+that each partition is assigned a different temperature.  See the
+"variable"_variable.html command for more details.  For example:
+
+variable lambda world 400 420 440 460
+fix fxnvt all nvt temp 300.0 300.0 100.0
+fix fxgREM all grem ${lambda} -0.05 -50000 fxnvt
+temper 100000 100 ${lambda} fxgREM fxnvt 3847 58382 :pre
+
+would define 4 lambdas with constant kinetic temperature but unique
+generalized temperature, and assign one of them to "fix
+grem"_fix_grem.html used by each replica, and to the grem command.
+
+As the gREM simulation runs for {N} timesteps, a swap between adjacent
+ensembles will be attempted every {M} timesteps.  If {seed1} is 0,
+then the swap attempts will alternate between odd and even pairings.
+If {seed1} is non-zero then it is used as a seed in a random number
+generator to randomly choose an odd or even pairing each time.  Each
+attempted swap of temperatures is either accepted or rejected based on
+a Metropolis criterion, derived for gREM by "(Kim)"_#Kim, which uses
+{seed2} in the random number generator.
+
+File management works identical to the "temper"_temper.html command.
+Dump files created by this fix contain continuous trajectories and
+require post-processing to obtain per-replica information.
+
+The last argument {index} in the grem command is optional and is used
+when restarting a run from a set of restart files (one for each
+replica) which had previously swapped to new lambda.  This is done
+using a variable. For example if the log file listed the following for
+a simulation with 5 replicas:
+
+500000 2 4 0 1 3 :pre
+
+then a setting of
+
+variable walkers world 2 4 0 1 3 :pre
+
+would be used to restart the run with a grem command like the example
+above with ${walkers} as the last argument. This functionality is
+identical to "temper"_temper.html.
+
+:line
+
+[Restrictions:]
+
+This command can only be used if LAMMPS was built with the USER-MISC
+package.  See the "Making LAMMPS"_Section_start.html#start_3 section
+for more info on packages.
+
+This command must be used with "fix grem"_fix_grem.html.
+
+[Related commands:]
+
+"fix grem"_fix_grem.html, "temper"_temper.html, "variable"_variable.html
+
+[Default:] none
+
+:link(Kim)
+[(Kim)] Kim, Keyes, Straub, J Chem Phys, 132, 224107 (2010).
--- a/doc/src/tutorial_drude.txt
+++ b/doc/src/tutorial_drude.txt
@ -33,7 +33,7 @@ created by the surrounding particles.  Drude oscillators represent
 these dipoles by two fixed charges: the core (DC) and the Drude
 particle (DP) bound by a harmonic potential. The Drude particle can be
 thought of as the electron cloud whose center can be displaced from
-the position of the the corresponding nucleus.
+the position of the corresponding nucleus.

 The sum of the masses of a core-Drude pair should be the mass of the
 initial (unsplit) atom, \(m_C + m_D = m\).  The sum of their charges
--- a/Show More
+++ b/Show More