add fix mscg command, example, lib

patch 6Jan17
enable pppm/tip4p to work with triclinic
2017-01-09 13:36:40 -07:00 · 2017-01-06 11:14:48 -07:00 · 2017-01-06 10:38:32 -07:00 · 2017-01-06 10:10:59 -07:00 · 2017-01-06 10:10:09 -07:00 · 2017-01-06 10:03:32 -07:00
1156 changed files with 95389 additions and 21687 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/JPG/tutorial_additional_changes.png
+++ b/doc/src/JPG/tutorial_additional_changes.png
--- a/doc/src/JPG/tutorial_automated_checks.png
+++ b/doc/src/JPG/tutorial_automated_checks.png
--- a/doc/src/JPG/tutorial_automated_checks_passed.png
+++ b/doc/src/JPG/tutorial_automated_checks_passed.png
--- a/doc/src/JPG/tutorial_branch.png
+++ b/doc/src/JPG/tutorial_branch.png
--- a/doc/src/JPG/tutorial_changes_others.png
+++ b/doc/src/JPG/tutorial_changes_others.png
--- a/doc/src/JPG/tutorial_create_new_pull_request1.png
+++ b/doc/src/JPG/tutorial_create_new_pull_request1.png
--- a/doc/src/JPG/tutorial_create_new_pull_request2.png
+++ b/doc/src/JPG/tutorial_create_new_pull_request2.png
--- a/doc/src/JPG/tutorial_edits_maintainers.png
+++ b/doc/src/JPG/tutorial_edits_maintainers.png
--- a/doc/src/JPG/tutorial_fork.png
+++ b/doc/src/JPG/tutorial_fork.png
--- a/doc/src/JPG/tutorial_https_block.png
+++ b/doc/src/JPG/tutorial_https_block.png
--- a/doc/src/JPG/tutorial_new_pull_request.png
+++ b/doc/src/JPG/tutorial_new_pull_request.png
--- a/doc/src/JPG/tutorial_reverse_pull_request.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request.png
--- a/doc/src/JPG/tutorial_reverse_pull_request2.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request2.png
--- a/doc/src/JPG/tutorial_reverse_pull_request3.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request3.png
--- a/doc/src/JPG/tutorial_reverse_pull_request4.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request4.png
--- a/doc/src/JPG/tutorial_reverse_pull_request5.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request5.png
--- a/doc/src/JPG/tutorial_reverse_pull_request6.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request6.png
--- a/doc/src/JPG/tutorial_steve_assignee.png
+++ b/doc/src/JPG/tutorial_steve_assignee.png
--- 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="9 Jan 2017 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@ -21,7 +21,7 @@
 <H1></H1>

 LAMMPS Documentation :c,h3
-27 Oct 2016 version :c,h4
+9 Jan 2017 version :c,h4

 Version info: :h4

--- a/doc/src/PDF/colvars-refman-lammps.pdf
+++ b/doc/src/PDF/colvars-refman-lammps.pdf
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@ -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

@ -580,8 +581,9 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "indent"_fix_indent.html,
 "langevin (k)"_fix_langevin.html,
 "lineforce"_fix_lineforce.html,
-"momentum"_fix_momentum.html,
+"momentum (k)"_fix_momentum.html,
 "move"_fix_move.html,
+"mscg"_fix_mscg.html,
 "msst"_fix_msst.html,
 "neb"_fix_neb.html,
 "nph (ko)"_fix_nh.html,
@ -632,10 +634,10 @@ 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 +689,7 @@ 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,
@ -700,6 +703,7 @@ package"_Section_start.html#start_3.
 "manifoldforce"_fix_manifoldforce.html,
 "meso/stationary"_fix_meso_stationary.html,
 "nve/manifold/rattle"_fix_nve_manifold_rattle.html,
+"nvk"_fix_nvk.html,
 "nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
 "nph/eff"_fix_nh_eff.html,
 "npt/eff"_fix_nh_eff.html,
@ -765,6 +769,7 @@ 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 +891,8 @@ 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,
@ -909,10 +916,10 @@ 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 (gkiot)"_pair_eam.html,
 "eam/alloy (gkot)"_pair_eam.html,
 "eam/fs (gkot)"_pair_eam.html,
 "eim (o)"_pair_eim.html,
@ -979,11 +986,12 @@ 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 +1001,7 @@ 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
--- 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/accelerate_intel.txt
+++ b/doc/src/accelerate_intel.txt
@ -29,7 +29,7 @@ Bond Styles: fene, harmonic :l
 Dihedral Styles: charmm, harmonic, opls :l
 Fixes: nve, npt, nvt, nvt/sllod :l
 Improper Styles: cvff, harmonic :l
-Pair Styles: buck/coul/cut, buck/coul/long, buck, gayberne,
+Pair Styles: buck/coul/cut, buck/coul/long, buck, eam, gayberne,
 charmm/coul/long, lj/cut, lj/cut/coul/long, sw, tersoff :l
 K-Space Styles: pppm :l
 :ule
--- 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_chunk_atom.txt
+++ b/doc/src/compute_chunk_atom.txt
@ -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/fix_colvars.txt
+++ b/doc/src/fix_colvars.txt
@ -31,21 +31,19 @@ fix abf all colvars colvars.inp tstat 1 :pre

 [Description:]

-This fix interfaces LAMMPS to a "collective variables" or "colvars"
-module library which allows to calculate potentials of mean force
+This fix interfaces LAMMPS to the collective variables "Colvars"
+library, which allows to calculate potentials of mean force
 (PMFs) for any set of colvars, using different sampling methods:
 currently implemented are the Adaptive Biasing Force (ABF) method,
 metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling
-(US) via a flexible harmonic restraint bias. The colvars library is
-hosted at "http://colvars.github.io/"_http://colvars.github.io/
+(US) via a flexible harmonic restraint bias.

 This documentation describes only the fix colvars command itself and
 LAMMPS specific parts of the code.  The full documentation of the
 colvars library is available as "this supplementary PDF document"_PDF/colvars-refman-lammps.pdf

-A detailed discussion of the implementation of the portable collective
-variable library is in "(Fiorin)"_#Fiorin. Additional information can
-be found in "(Henin)"_#Henin.
+The Colvars library is developed at "https://github.com/colvars/colvars"_https://github.com/colvars/colvars
+A detailed discussion of its implementation is in "(Fiorin)"_#Fiorin.

 There are some example scripts for using this package with LAMMPS in the
 examples/USER/colvars directory.
@ -129,8 +127,3 @@ and tstat = NULL.

 :link(Fiorin)
 [(Fiorin)] Fiorin , Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594
-
-:link(Henin)
-[(Henin)] Henin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6,
-35-47 (2010)
-
--- a/doc/src/fix_eos_table_rx.txt
+++ b/doc/src/fix_eos_table_rx.txt
@ -10,7 +10,7 @@ fix eos/table/rx command :h3

 [Syntax:]

-fix ID group-ID eos/table/rx style file1 N keyword file2 :pre
+fix ID group-ID eos/table/rx style file1 N keyword ... :pre

 ID, group-ID are documented in "fix"_fix.html command
 eos/table/rx = style name of this fix command
@ -18,11 +18,16 @@ style = {linear} = method of interpolation
 file1 = filename containing the tabulated equation of state
 N = use N values in {linear} tables
 keyword = name of table keyword correponding to table file
-file2 = filename containing the heats of formation of each species :ul
+file2 = filename containing the heats of formation of each species (optional)
+deltaHf = heat of formation for a single species in energy units (optional)
+energyCorr = energy correction in energy units (optional)
+tempCorrCoeff = temperature correction coefficient (optional) :ul

 [Examples:]

-fix 1 all eos/table/rx linear eos.table 10000 KEYWORD thermo.table :pre
+fix 1 all eos/table/rx linear eos.table 10000 KEYWORD thermo.table
+fix 1 all eos/table/rx linear eos.table 10000 KEYWORD 1.5
+fix 1 all eos/table/rx linear eos.table 10000 KEYWORD 1.5 0.025 0.0 :pre

 [Description:]

@ -39,7 +44,15 @@ where {m} is the number of species, {c_i,j} is the concentration of
 species {j} in particle {i}, {u_j} is the internal energy of species j,
 {DeltaH_f,j} is the heat of formation of species {j}, N is the number of
 molecules represented by the coarse-grained particle, kb is the
-Boltzmann constant, and T is the temperature of the system.
+Boltzmann constant, and T is the temperature of the system.  Additionally,
+it is possible to modify the concentration-dependent particle internal 
+energy relation by adding an energy correction, temperature-dependent 
+correction, and/or a molecule-dependent correction.  An energy correction can
+be specified as a constant (in energy units).  A temperature correction can be 
+specified by multiplying a temperature correction coefficient by the 
+internal temperature.  A molecular correction can be specified by 
+by multiplying a molecule correction coefficient by the average number of 
+product gas particles in the coarse-grain particle. 

 Fix {eos/table/rx} creates interpolation tables of length {N} from {m}
 internal energy values of each species {u_j} listed in a file as a
@ -58,6 +71,14 @@ file is described below.
 The second filename specifies a file containing heat of formation
 {DeltaH_f,j} for each species.

+In cases where the coarse-grain particle represents a single molecular
+species (i.e., no reactions occur and fix {rx} is not present in the input file), 
+fix {eos/table/rx} can be applied in a similar manner to fix {eos/table} 
+within a non-reactive DPD simulation.  In this case, the heat of formation 
+filename is replaced with the heat of formation value for the single species.
+Additionally, the energy correction and temperature correction coefficients may 
+also be specified as fix arguments.  
+
 :line

 The format of a tabulated file is as follows (without the
@ -116,6 +137,19 @@ Note that the species can be listed in any order.  The tag that is
 used as the species name must correspond with the tags used to define
 the reactions with the "fix rx"_fix_rx.html command.

+Alternatively, corrections to the EOS can be included by specifying
+three additional columns that correspond to the energy correction, 
+the temperature correction coefficient and molecule correction 
+coefficient.  In this case, the format of the file is as follows:
+
+# HEAT OF FORMATION TABLE     (one or more comment or blank lines) :pre
+                              (blank)
+h2      0.00 1.23 0.025  0.0  (species name, heat of formation, energy correction, temperature correction coefficient, molecule correction coefficient)
+no2     0.34 0.00 0.000 -1.76
+n2      0.00 0.00 0.000 -1.76
+...
+no      0.93 0.00 0.000 -1.76 :pre
+
 :line

 [Restrictions:]
--- 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_momentum.txt
+++ b/doc/src/fix_momentum.txt
@ -7,6 +7,7 @@
 :line

 fix momentum command :h3
+fix momentum/kk command :h3

 [Syntax:]

@ -55,6 +56,29 @@ of atoms by rescaling the velocities after the momentum was removed.
 Note that the "velocity"_velocity.html command can be used to create
 initial velocities with zero aggregate linear and/or angular momentum.

+: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 5"_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 5"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
 [Restart, fix_modify, output, run start/stop, minimize info:]

 No information about this fix is written to "binary restart
--- a/doc/src/fix_mscg.txt
+++ b/doc/src/fix_mscg.txt
@ -0,0 +1,130 @@
+"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 mscg command :h3
+
+[Syntax:]
+
+fix ID group-ID mscg N keyword args ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+mscg = style name of this fix command :l
+N = envoke this fix every this many timesteps :l
+zero or more keyword/value pairs may be appended :l
+keyword = {range} or {name} or {max} :l
+  {range} arg = {on} or {off}
+    {on} = range finding functionality is performed
+    {off} = force matching functionality is performed
+  {name} args = name1 ... nameN
+    name1,...,nameN = string names for each atom type (1-Ntype)
+  {max} args = maxb maxa maxd
+    maxb,maxa,maxd = maximum bonds/angles/dihedrals per atom :pre
+:ule
+
+[Examples:]
+
+fix 1 all mscg 1
+fix 1 all mscg 1 range name A B
+fix 1 all mscg 1 max 4 8 20 :pre
+
+[Description:]
+
+This fix applies the Multi-Scale Coarse-Graining (MSCG) method to
+snapshots from a dump file to generate potentials for coarse-grained
+simulations from all-atom simulations, using a force-matching
+technique ("Izvekov"_#Izvekov, "Noid"_#Noid).
+
+It makes use of the MS-CG library, written and maintained by Greg
+Voth's group at the University of Chicago, which is freely available
+on their "MS-CG GitHub
+site"_https://github.com/uchicago-voth/MSCG-release.  See instructions
+on obtaining and installing the MS-CG library in the src/MSCG/README
+file, which must be done before you build LAMMPS with this fix command
+and use the command in a LAMMPS input script.
+
+An example script using this fix is provided the examples/mscg
+directory.
+
+The general workflow for using LAMMPS in conjunction with the MS-CG
+library to create a coarse-grained model and run coarse-grained
+simulations is as follows:
+
+Perform all-atom simulations on the system to be coarse grained.
+Generate a trajectory mapped to the coarse-grained model.
+Create input files for the MS-CG library.
+Run the range finder functionality of the MS-CG library.  
+Run the force matching functionality of the MS-CG library.
+Check the results of the force matching.
+Run coarse-grained simulations using the new coarse-grained potentials. :ol
+
+This fix can perform the range finding and force matching steps 4 and
+5 of the above workflow when used in conjunction with the
+"rerun"_rerun.html command.  It does not perform steps 1-3 and 6-7.
+
+Step 2 can be performed using a Python script (what is the name?)
+provided with the MS-CG library which defines the coarse-grained model
+and converts a standard LAMMPS dump file for an all-atom simulation
+(step 1) into a LAMMPS dump file which has the positions of and forces
+on the coarse-grained beads.  
+
+In step 3, an input file named "control.in" is needed by the MS-CG
+library which sets parameters for the range finding and force matching
+functionalities.  See the examples/mscg/control.in file as an example.
+And see the documentation provided with the MS-CG library for more
+info on this file.
+
+When this fix is used to perform steps 4 and 5, the MS-CG library also
+produces additional output files.  The range finder functionality
+(step 4) outputs files defining pair and bonded interaction ranges.
+The force matching functionality (step 5) outputs tabulated force
+files for every interaction in the system. Other diagnostic files can
+also be output depending on the paramters in the MS-CG library input
+script.  Again, see the documentation provided with the MS-CG library
+for more info.
+
+:line
+
+The {range} keyword specifies which MS-CG library functionality should
+be invoked. If {on}, the step 4 range finder functionality is invoked.
+{off}, the step 5 force matching functionality is invoked.
+
+If the {name} keyword is used, string names are defined to associate
+with the integer atom types in LAMMPS.  {Ntype} names must be
+provided, one for each atom type (1-Ntype).
+
+The {max} keyword specifies the maximum number of bonds, angles, and
+dihedrals a bead can have in the coarse-grained model.
+
+[Restrictions:]
+
+This fix is part of the MSCG 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 MS-CG library uses C++11, which may not be supported by older
+compilers. The MS-CG library also has some additional numeric library
+dependencies, which are describd in its documentation.
+
+Currently, the MS-CG library is not setup to run in parallel with MPI,
+so this fix can only be used in a serial LAMMPS build and run
+on a single processor.
+
+[Related commands:] none
+
+[Default:]
+
+The default keyword settings are range off, max 4 12 36.
+
+:line
+
+:link(Izvekov)
+[(Izvekov)] Izvekov, Voth, J Chem Phys 123, 134105 (2005).
+
+:link(Noid)
+[(Noid)] Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J
+Chem Phys 128, 134105 (2008).
--- a/doc/src/fix_nvk.txt
+++ b/doc/src/fix_nvk.txt
@ -0,0 +1,71 @@
+"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 nvk command :h3
+
+[Syntax:]
+
+fix ID group-ID nvk :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+nvk = style name of this fix command :ul
+
+[Examples:]
+
+fix 1 all nvk :pre
+
+[Description:]
+
+Perform constant kinetic energy integration using the Gaussian
+thermostat to update position and velocity for atoms in the group each
+timestep.  V is volume; K is kinetic energy. This creates a system
+trajectory consistent with the isokinetic ensemble.
+
+The equations of motion used are those of Minary et al in
+"(Minary)"_#nvk-Minary, a variant of those initially given by Zhang in 
+"(Zhang)"_#nvk-Zhang.
+
+The kinetic energy will be held constant at its value given when fix
+nvk is initiated. If a different kinetic energy is desired, the
+"velocity"_velocity.html command should be used to change the kinetic
+energy prior to this fix.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various "output
+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.
+
+[Restrictions:]
+
+The Gaussian thermostat only works when it is applied to all atoms in
+the simulation box. Therefore, the group must be set to all.
+
+This fix has not yet been implemented to work with the RESPA integrator.
+
+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:] none
+
+[Default:] none
+
+:line
+
+:link(nvk-Minary)
+[(Minary)] Minary, Martyna, and Tuckerman, J Chem Phys, 18, 2510 (2003).
+
+:link(nvk-Zhang)
+[(Zhang)] Zhang, J Chem Phys, 106, 6102 (1997).
--- a/doc/src/fix_smd_adjust_dt.txt
+++ b/doc/src/fix_smd_adjust_dt.txt
@ -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/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
@ -67,6 +68,7 @@ Fixes :h1
   fix_meso_stationary
   fix_momentum
   fix_move
+   fix_mscg
   fix_msst
   fix_neb
   fix_nh
@ -89,6 +91,7 @@ Fixes :h1
   fix_nve_noforce
   fix_nve_sphere
   fix_nve_tri
+   fix_nvk
   fix_nvt_asphere
   fix_nvt_body
   fix_nvt_manifold_rattle
--- 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
@ -189,6 +192,7 @@ fix_meso.html
 fix_meso_stationary.html
 fix_momentum.html
 fix_move.html
+fix_mscg.html
 fix_msst.html
 fix_neb.html
 fix_nh.html
@ -211,6 +215,7 @@ fix_nve_manifold_rattle.html
 fix_nve_noforce.html
 fix_nve_sphere.html
 fix_nve_tri.html
+fix_nvk.html
 fix_nvt_asphere.html
 fix_nvt_body.html
 fix_nvt_manifold_rattle.html
@ -272,6 +277,7 @@ 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 +313,7 @@ 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 +397,7 @@ compute_voronoi_atom.html
 compute_xrd.html

 pair_adp.html
+pair_agni.html
 pair_airebo.html
 pair_awpmd.html
 pair_beck.html
@ -622,3 +630,4 @@ 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/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_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

--- 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
@ -8,6 +8,7 @@

 pair_style eam command :h3
 pair_style eam/gpu command :h3
+pair_style eam/intel command :h3
 pair_style eam/kk command :h3
 pair_style eam/omp command :h3
 pair_style eam/opt command :h3
--- a/doc/src/pair_exp6_rx.txt
+++ b/doc/src/pair_exp6_rx.txt
@ -10,16 +10,21 @@ pair_style exp6/rx command :h3

 [Syntax:]

-pair_style exp6/rx cutoff :pre
+pair_style exp6/rx cutoff ... :pre

-cutoff = global cutoff for DPD interactions (distance units) :ul
+cutoff = global cutoff for DPD interactions (distance units)
+weighting = fractional or molecular (optional) :ul

 [Examples:]

 pair_style exp6/rx 10.0
-pair_coeff * * exp6.params h2o h2o 1.0 1.0 10.0
-pair_coeff * * exp6.params h2o 1fluid 1.0 1.0 10.0
-pair_coeff * * exp6.params 1fluid 1fluid 1.0 1.0 10.0 :pre
+pair_style exp6/rx 10.0 fractional
+pair_style exp6/rx 10.0 molecular
+pair_coeff * * exp6.params h2o h2o exponent 1.0 1.0 10.0
+pair_coeff * * exp6.params h2o 1fluid exponent 1.0 1.0 10.0
+pair_coeff * * exp6.params 1fluid 1fluid exponent 1.0 1.0 10.0
+pair_coeff * * exp6.params 1fluid 1fluid none 10.0
+pair_coeff * * exp6.params 1fluid 1fluid polynomial filename 10.0 :pre

 [Description:]

@ -50,14 +55,36 @@ defined in the reaction kinetics files specified with the "fix
 rx"_fix_rx.html command or they must correspond to the tag "1fluid",
 signifying interaction with a product species mixture determined
 through a one-fluid approximation.  The interaction potential is
-weighted by the geometric average of the concentrations of the two
-species.  The coarse-grained potential is stored before and after the
+weighted by the geometric average of either the mole fraction concentrations 
+or the number of molecules associated with the interacting coarse-grained 
+particles (see the {fractional} or {molecular} weighting pair style options). 
+The coarse-grained potential is stored before and after the
 reaction kinetics solver is applied, where the difference is defined
 to be the internal chemical energy (uChem).

-The fourth and fifth arguments specify the {Rm} and {epsilon} scaling exponents.
+The fourth argument specifies the type of scaling that will be used 
+to scale the EXP-6 paramters as reactions occur.  Currently, there
+are three scaling options:  {exponent}, {polynomial} and {none}.

-The final argument specifies the interaction cutoff.
+Exponent scaling requires two additional arguments for scaling 
+the {Rm} and {epsilon} parameters, respectively.  The scaling factor
+is computed by phi^exponent, where phi is the number of molecules  
+represented by the coarse-grain particle and exponent is specified 
+as a pair coefficient argument for {Rm} and {epsilon}, respectively.
+The {Rm} and {epsilon} parameters are multiplied by the scaling 
+factor to give the scaled interaction paramters for the CG particle.
+
+Polynomial scaling requires a filename to be specified as a pair 
+coeff argument.  The file contains the coefficients to a fifth order
+polynomial for the {alpha}, {epsilon} and {Rm} parameters that depend 
+upon phi (the number of molecules represented by the CG particle). 
+The format of a polynomial file is provided below.
+
+The {none} option to the scaling does not have any additional pair coeff
+arguments.  This is equivalent to specifying the {exponent} option with 
+{Rm} and {epsilon} exponents of 0.0 and 0.0, respectively.
+
+The final argument specifies the interaction cutoff (optional).

 :line

@ -70,6 +97,19 @@ no2  exp6  13.60 0.01 3.70
 ...
 co2  exp6  13.00 0.03 3.20 :pre

+The format of the polynomial scaling file as follows (without the
+parenthesized comments):
+
+# POLYNOMIAL FILE          (one or more comment or blank lines) :pre
+#  General Functional Form:
+#  A*phi^5 + B*phi^4 + C*phi^3 + D*phi^2 + E*phi + F 
+#
+#  Parameter  A        B         C        D         E        F
+                           (blank)
+alpha        0.0000   0.00000   0.00008  0.04955  -0.73804  13.63201
+epsilon      0.0000   0.00478  -0.06283  0.24486  -0.33737   2.60097
+rm           0.0001  -0.00118  -0.00253  0.05812  -0.00509   1.50106 :pre
+
 A section begins with a non-blank line whose 1st character is not a
 "#"; blank lines or lines starting with "#" can be used as comments
 between sections.
@ -117,4 +157,4 @@ LAMMPS"_Section_start.html#start_3 section for more info.

 "pair_coeff"_pair_coeff.html

-[Default:] none
+[Default:] fractional weighting
--- a/doc/src/pair_multi_lucy_rx.txt
+++ b/doc/src/pair_multi_lucy_rx.txt
@ -13,11 +13,14 @@ pair_style multi/lucy/rx command :h3
 pair_style multi/lucy/rx style N keyword ... :pre

 style = {lookup} or {linear} = method of interpolation
-N = use N values in {lookup}, {linear} tables :ul
+N = use N values in {lookup}, {linear} tables
+weighting = fractional or molecular (optional) :ul

 [Examples:]

 pair_style multi/lucy/rx linear 1000
+pair_style multi/lucy/rx linear 1000 fractional
+pair_style multi/lucy/rx linear 1000 molecular
 pair_coeff * * multibody.table ENTRY1 h2o h2o 7.0
 pair_coeff * * multibody.table ENTRY1 h2o 1fluid 7.0 :pre

@ -94,8 +97,10 @@ tags must either correspond to the species defined in the reaction
 kinetics files specified with the "fix rx"_fix_rx.html command or they
 must correspond to the tag "1fluid", signifying interaction with a
 product species mixture determined through a one-fluid approximation.
-The interaction potential is weighted by the geometric average of the
-concentrations of the two species.  The coarse-grained potential is
+The interaction potential is weighted by the geometric average of 
+either the mole fraction concentrations or the number of molecules 
+associated with the interacting coarse-grained particles (see the 
+{fractional} or {molecular} weighting pair style options). The coarse-grained potential is
 stored before and after the reaction kinetics solver is applied, where
 the difference is defined to be the internal chemical energy (uChem).

@ -205,7 +210,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.

 "pair_coeff"_pair_coeff.html

-[Default:] none
+[Default:] fractional weighting

 :line

--- a/doc/src/pair_smd_tlsph.txt
+++ b/doc/src/pair_smd_tlsph.txt
@ -39,7 +39,7 @@ invocation of the {tlsph} for a solid body would consist of an equation of state
 the pressure (the diagonal components of the stress tensor), and a material model to compute shear
 stresses (the off-diagonal components of the stress tensor). Damage and failure models can also be added.

-Please see the "SMD user guide"_USER/smd/SMD_LAMMPS_userguide.pdf for a complete listing of the possible keywords and material models.
+Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a complete listing of the possible keywords and material models.

 :line

--- a/doc/src/pair_smd_ulsph.txt
+++ b/doc/src/pair_smd_ulsph.txt
@ -43,7 +43,7 @@ stresses (the off-diagonal components of the stress tensor).

 Note that the use of *GRADIENT_CORRECTION can lead to severe numerical instabilities. For a general fluid simulation, *NO_GRADIENT_CORRECTION is recommended.

-Please see the "SMD user guide"_USER/smd/SMD_LAMMPS_userguide.pdf for a complete listing of the possible keywords and material models.
+Please see the "SMD user guide"_PDF/SMD_LAMMPS_userguide.pdf for a complete listing of the possible keywords and material models.

 :line

--- 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_table_rx.txt
+++ b/doc/src/pair_table_rx.txt
@ -10,16 +10,17 @@ pair_style table/rx command :h3

 [Syntax:]

-pair_style table style N :pre
+pair_style table style N ... :pre

 style = {lookup} or {linear} or {spline} or {bitmap} = method of interpolation
 N = use N values in {lookup}, {linear}, {spline} tables
-N = use 2^N values in {bitmap} tables
+weighting = fractional or molecular (optional) :ul

 [Examples:]

 pair_style table/rx linear 1000
-pair_style table/rx bitmap 12
+pair_style table/rx linear 1000 fractional
+pair_style table/rx linear 1000 molecular
 pair_coeff * * rxn.table ENTRY1 h2o h2o 10.0
 pair_coeff * * rxn.table ENTRY1 1fluid 1fluid 10.0
 pair_coeff * 3 rxn.table ENTRY1 h2o no2 10.0 :pre
@ -84,8 +85,10 @@ tags must either correspond to the species defined in the reaction
 kinetics files specified with the "fix rx"_fix_rx.html command or they
 must correspond to the tag "1fluid", signifying interaction with a
 product species mixture determined through a one-fluid approximation.
-The interaction potential is weighted by the geometric average of the
-concentrations of the two species.  The coarse-grained potential is
+The interaction potential is weighted by the geometric average of 
+either the mole fraction concentrations or the number of molecules 
+associated with the interacting coarse-grained particles (see the 
+{fractional} or {molecular} weighting pair style options). The coarse-grained potential is
 stored before and after the reaction kinetics solver is applied, where
 the difference is defined to be the internal chemical energy (uChem).

@ -230,7 +233,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.

 "pair_coeff"_pair_coeff.html

-[Default:] none
+[Default:] fractional weighting

 :line

--- 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
--- 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

--- 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/python.txt
+++ b/doc/src/python.txt
@ -14,7 +14,7 @@ python func keyword args ... :pre

 func = name of Python function :ulb,l
 one or more keyword/args pairs must be appended :l
-keyword = {invoke} or {input} or {return} or {format} or {file} or {here} or {exists}
+keyword = {invoke} or {input} or {return} or {format} or {length} or {file} or {here} or {exists}
  {invoke} arg = none = invoke the previously defined Python function
  {input} args = N i1 i2 ... iN
    N = # of inputs to function
@ -29,6 +29,8 @@ keyword = {invoke} or {input} or {return} or {format} or {file} or {here} or {ex
    M = N+1 if there is a return value
    fstring = each character (i,f,s,p) corresponds in order to an input or return value
    'i' = integer, 'f' = floating point, 's' = string, 'p' = SELF
+  {length} arg = Nlen
+    Nlen = max length of string returned from Python function
  {file} arg = filename
    filename = file of Python code, which defines func
  {here} arg = inline
@ -165,6 +167,17 @@ equal-style variable as an argument, but only if the output of the
 Python function is flagged as a numeric value ("i" or "f") via the
 {format} keyword.

+If the {return} keyword is used and the {format} keyword specifies the
+output as a string, then the default maximum length of that string is
+63 characters (64-1 for the string terminator).  If you want to return
+a longer string, the {length} keyword can be specified with its {Nlen}
+value set to a larger number (the code allocates space for Nlen+1 to
+include the string terminator).  If the Python function generates a
+string longer than the default 63 or the specified {Nlen}, it will be
+trunctated.
+
+:line
+
 Either the {file}, {here}, or {exists} keyword must be used, but only
 one of them.  These keywords specify what Python code to load into the
 Python interpreter.  The {file} keyword gives the name of a file,
--- a/doc/src/read_dump.txt
+++ b/doc/src/read_dump.txt
@ -15,11 +15,12 @@ read_dump file Nstep field1 field2 ... keyword values ... :pre
 file = name of dump file to read :ulb,l
 Nstep = snapshot timestep to read from file :l
 one or more fields may be appended :l
-field = {x} or {y} or {z} or {vx} or {vy} or {vz} or {q} or {ix} or {iy} or {iz}
+field = {x} or {y} or {z} or {vx} or {vy} or {vz} or {q} or {ix} or {iy} or {iz} or {fx} or {fy} or {fz}
  {x},{y},{z} = atom coordinates
  {vx},{vy},{vz} = velocity components
  {q} = charge
-  {ix},{iy},{iz} = image flags in each dimension :pre
+  {ix},{iy},{iz} = image flags in each dimension
+  {fx},{fy},{fz} = force components :pre
 zero or more keyword/value pairs may be appended :l
 keyword = {box} or {replace} or {purge} or {trim} or {add} or {label} or {scaled} or {wrapped} or {format} :l
  {box} value = {yes} or {no} = replace simulation box with dump box
--- 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_github.txt
+++ b/doc/src/tutorial_github.txt
@ -11,10 +11,22 @@ LAMMPS GitHub tutorial :h3

 :line

-This document briefly describes how to use GitHub to merge changes you
-make into LAMMPS, using GitHub. It assumes that you are familiar with
-git. You may want to have a look at the "Git
-book"_http://git-scm.com/book/ to reacquaint yourself.
+This document describes the process of how to use GitHub to integrate
+changes or additions you have made to LAMMPS into the official LAMMPS
+distribution.  It uses the process of updating this very tutorial as
+an example to describe the individual steps and options.  You need to
+be familiar with git and you may want to have a look at the
+"Git book"_http://git-scm.com/book/ to reacquaint yourself with some
+of the more advanced git features used below.
+
+As of fall 2016, submitting contributions to LAMMPS via pull requests
+on GitHub is the preferred option for integrating contributed features
+or improvements to LAMMPS, as it significantly reduces the amount of
+work required by the LAMMPS developers. Consequently, creating a pull
+request will increase your chances to have your contribution included
+and will reduce the time until the integration is complete. For more
+information on the requirements to have your code included into LAMMPS
+please see "Section 10.15"_Section_modify.html#mod_15

 :line

@ -30,106 +42,121 @@ username or e-mail address and password.

 [Forking the repository]

-To get changes into LAMMPS, you need to first fork the repository. At
-the time of writing, LAMMPS-ICMS is the preferred fork. Go to "LAMMPS
-on GitHub"_https://github.com/lammps/lammps and make sure branch is
-set to "lammps-icms", see the figure below.
+To get changes into LAMMPS, you need to first fork the `lammps/lammps`
+repository on GitHub. At the time of writing, {master} is the preferred
+target branch. Thus go to "LAMMPS on GitHub"_https://github.com/lammps/lammps
+and make sure branch is set to "master", as shown in the figure below.

 :c,image(JPG/tutorial_branch.png)

-Now, click on fork in the top right corner:
+If it is not, use the button to change it to {master}. Once it is, use the
+fork button to create a fork.

 :c,image(JPG/tutorial_fork.png)

-This will create your own fork of the LAMMPS repository. You can make
-changes in this fork and later file {pull requests} to allow the
-upstream repository to merge changes from your own fork into the one
-we just forked from. At the same time, you can set things up, so you
-can include changes from upstream into your repository.
+
+This will create a fork (which is essentially a copy, but uses less
+resources) of the LAMMPS repository under your own GitHub account. You
+can make changes in this fork and later file {pull requests} to allow
+the upstream repository to merge changes from your own fork into the one
+we just forked from (or others that were forked from the same repository).
+At the same time, you can set things up, so you can include changes from
+upstream into your repository and thus keep it in sync with the ongoing
+LAMMPS development.

 :line

 [Adding changes to your own fork]

-Before adding changes, it is better to first create a new branch that
-will contain these changes, a so-called feature branch.
+Additions to the upstream version of LAMMPS are handled using {feature
+branches}.  For every new feature, a so-called feature branch is
+created, which contains only those modification relevant to one specific
+feature. For example, adding a single fix would consist of creating a
+branch with only the fix header and source file and nothing else.  It is
+explained in more detail here: "feature branch
+workflow"_https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow.

 [Feature branches]

-Since LAMMPS is such a big project and most user contributions come in
-small portions, the most ideal workflow for LAMMPS is the so-called
-"Feature branch" workflow. It is explained in great detail here:
-"feature branch
-workflow"_https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow.
+First of all, create a clone of your version on github on your local
+machine via HTTPS:

-The idea is that every new feature for LAMMPS gets its own
-branch. This way, it is fairly painless to incorporate new features
-into the upstream repository. I will explain briefly here how to do
-it. In this feature branch, I will add a USER-package.
+  $ git clone https://github.com/<your user name>/lammps.git <some name> :pre

-I assume that git is installed on the local machine and you know how
-to use a command line.
+or, if you have set up your GitHub account for using SSH keys, via SSH:

-First of all, you need to clone your own fork of LAMMPS:
-
-  $ git clone https://github.com/<your user name>/lammps.git :pre
-
-You can find the proper url to the right of the "HTTPS" block, see figure.
+  $ git clone git@github.com:<your user name>/lammps.git :pre
+  
+You can find the proper URL by clicking the "Clone or download"-button:

 :c,image(JPG/tutorial_https_block.png)

 The above command copies ("clones") the git repository to your local
-machine. You can use this local clone to make changes and test them
-without interfering with the repository on github. First, however, it
-is recommended to make a new branch for a particular feature you would
-like added to LAMMPS. In this example, I will try adding a new
-USER-package called USER-MANIFOLD.
+machine to a directory with the name you chose. If none is given, it will
+default to "lammps". Typical names are "mylammps" or something similar.

-To create a new branch, run the following git command in your repository:
+You can use this local clone to make changes and
+test them without interfering with the repository on Github.

-$ git checkout -b add-user-manifold :pre
+To pull changes from upstream into this copy, you can go to the directory
+and use git pull:

-The name of this new branch is "add-user-manifold" in my case. Just
-name it after something that resembles the feature you want added to
-LAMMPS.
+  $ cd mylammps
+  $ git checkout master
+  $ git pull https://github.com/lammps/lammps :pre

-Now that you've changed branches, you can edit the files as you see
-fit, add new files, and commit as much as you would like. Just
-remember that if halfway you decide to add another, unrelated feature,
-you should switch branches!
+You can also add this URL as a remote:
+
+  $ git remote add lammps_upstream https://www.github.com/lammps/lammps :pre
+
+At this point, you typically make a feature branch from the updated master
+branch for the feature you want to work on. This tutorial contains the
+workflow that updated this tutorial, and hence we will call the branch
+"github-tutorial-update":
+
+ $ git checkout -b github-tutorial-update master :pre
+
+Now that we have changed branches, we can make our changes to our local
+repository. Just remember that if you want to start working on another,
+unrelated feature, you should switch branches!
+
+[After changes are made]

 After everything is done, add the files to the branch and commit them:

-  $ git add src/USER-MANIFOLD examples/USER/manifold/
-  $ git add doc/fix_nv\{t,e\}_manifold_rattle.txt
-  $ git add doc/fix_manifoldforce.txt doc/user_manifolds.txt :pre
+ $ git add doc/src/tutorial_github.txt
+ $ git add doc/src/JPG/tutorial*.png :pre

-After the files are added, the change should be comitted:
+IMPORTANT NOTE: Do not use {git commit -a} (or {git add -A}).  The -a
+flag (or -A flag) will automatically include _all_ modified or new files
+and that is rarely the behavior you want.  It can easily lead to
+accidentally adding unrelated and unwanted changes into the repository.
+Instead it is preferable to explicitly use {git add}, {git rm}, {git mv}
+for adding, removing, renaming individual files, respectively, and then
+{git commit} to finalize the commit.  Carefully check all pending
+changes with {git status} before committing them.  If you find doing
+this on the command line too tedious, consider using a GUI, for example
+the one included in git distributions written in Tk, i.e. use {git gui}
+(on some Linux distributions it may be required to install an additional
+package to use it).

-  $ git commit -m 'Added user-manifold package' :pre
+After adding all files, the change set can be committed with some
+useful message that explains the change.

-The "-m" switch is used to add a message to the commit. Use this to
-indicate what type of change was commited.
-
-[Wisdom by Axel]
-
-{"Do not use "git commit -a".  the -a flag will automatically include
-*all* modified or new files.  mercurial does that and it find it
-hugely annoying and often leading to accidental commits of files you
-don't want.  use git add, git rm, git mv for adding, removing,
-renaming and then git commit to finalize the commit.  personally, i
-find it very convenient to use the bundled gui for commits, i.e. git
-gui.  typically, i will do git add and other operations, but then
-verify and review them with git gui.  git gui also allows to do
-line-by-line unstaging and other convenient operations."}
+  $ git commit -m 'Finally updated the github tutorial' :pre

 After the commit, the changes can be pushed to the same branch on GitHub:

 $ git push :pre

 Git will ask you for your user name and password on GitHub if you have
-not configured anything. If you correctly type your user name and
-password, the change should be added to your fork on GitHub.
+not configured anything. If your local branch is not present on Github yet,
+it will ask you to add it by running
+
+  $ git push --set-upstream origin github-tutorial-update :pre
+
+If you correctly type your user name and
+password, the feature branch should be added to your fork on GitHub.

 If you want to make really sure you push to the right repository
 (which is good practice), you can provide it explicitly:
@ -140,16 +167,20 @@ or using an explicit URL:

 $ git push git@github.com:Pakketeretet2/lammps.git :pre

-After that, you can file a new pull request based on this
-branch. GitHub will now look like this:
+:line

-:c,image(JPG/tutorial_pull_request_feature_branch1.png)
+[Filing a pull request]
+
+Up to this point in the tutorial, all changes were to {your} clones of
+LAMMPS.  Eventually, however, you want this feature to be included into
+the official LAMMPS version.  To do this, you will want to file a pull
+request by clicking on the "New pull request" button:
+
+:c,image(JPG/tutorial_new_pull_request.png)

 Make sure that the current branch is set to the correct one, which, in
-this case, is "add-user-manifold". Now click "New pull request". If
-done correctly, the only changes you will see are those that were made
-on this branch, so in my case, I will see nothing related to
-$\mathrm{pair\_dzugatov}.$
+this case, is "github-tutorial-update". If done correctly, the only
+changes you will see are those that were made on this branch.

 This will open up a new window that lists changes made to the
 repository. If you are just adding new files, there is not much to do,
@ -158,36 +189,159 @@ changes in existing files. If all changes can automatically be merged,
 green text at the top will say so and you can click the "Create pull
 request" button, see image.

-:c,image(JPG/tutorial_pull_request2.png)
+:c,image(JPG/tutorial_create_new_pull_request1.png)

-After this you have to specify a short title and a comment with
-details about your pull request. I guess here you write what your
-modifications do and why they should be incorporated upstream. After
-that, click the "Create pull request" button, see image below.
+Before creating the pull request, make sure the short title is accurate
+and add a comment with details about your pull request.  Here you write
+what your modifications do and why they should be incorporated upstream.

-:c,image(JPG/tutorial_pull_request3.png)
+Note the checkbox that says "Allow edits from maintainers".
+This is checked by default checkbox (although in my version of Firefox, only the checkmark is visible):

-Now just write some nice comments, click "Comment", and that is it. It
-is now up to the maintainer(s) of the upstream repository to
-incorporate the changes into the repository and to close the pull
-request.
+:c,image(JPG/tutorial_edits_maintainers.png)

-:c,image(JPG/tutorial_pull_request4.png)
+If it is checked, maintainers can immediately add their own edits to the
+pull request.  This helps the inclusion of your branch significantly, as
+simple/trivial changes can be added directly to your pull request branch
+by the LAMMPS maintainers.  The alternative would be that they make
+changes on their own version of the branch and file a reverse pull
+request to you.  Just leave this box checked unless you have a very good
+reason not to.
+
+Now just write some nice comments and click on "Create pull request".
+
+:c,image(JPG/tutorial_create_new_pull_request2.png)

 :line

+[After filing a pull request]
+
+NOTE: When you submit a pull request (or ask for a pull request) for the
+first time, you will receive an invitation to become a LAMMPS project
+collaborator. Please accept this invite as being a collaborator will
+simplify certain administrative tasks and will probably speed up the
+merging of your feature, too.
+
+You will notice that after filing the pull request, some checks are
+performed automatically:
+
+:c,image(JPG/tutorial_automated_checks.png)
+
+If all is fine, you will see this:
+
+:c,image(JPG/tutorial_automated_checks_passed.png)
+
+If any of the checks are failing, your pull request will not be
+processed, as your changes may break compilation for certain
+configurations or may not merge cleanly. It is your responsibility
+to remove the reason(s) for the failed test(s). If you need help
+with this, please contact the LAMMPS developers by adding a comment
+explaining your problems with resolving the failed tests.
+
+A few further interesting things (can) happen to pull requests before
+they are included.
+
 [Additional changes]

-Before the pull request is accepted, any additional changes you push
-into your repository will automatically become part of the pull
-request.
+First of all, any additional changes you push into your branch in your
+repository will automatically become part of the pull request:
+
+:c,image(JPG/tutorial_additional_changes.png)
+
+This means you can add changes that should be part of the feature after
+filing the pull request, which is useful in case you have forgotten
+them, or if a developer has requested that something needs to be changed
+before the feature can be accepted into the official LAMMPS version.
+After each push, the automated checks are run again.
+
+[Assignees]
+
+There is an assignee label for pull requests. If the request has not
+been reviewed by any developer yet, it is not assigned to anyone. After
+revision, a developer can choose to assign it to either a) you, b) a
+LAMMPS developer (including him/herself) or c) Steve Plimpton (sjplimp).
+
+Case a) happens if changes are required on your part :ulb,l
+Case b) means that at the moment, it is being tested and reviewed by a
+LAMMPS developer with the expectation that some changes would be required.
+After the review, the developer can choose to implement changes directly
+or suggest them to you. :l
+Case c) means that the pull request has been assigned to the lead
+developer Steve Plimpton and means it is considered ready for merging. :ule,l
+
+In this case, Axel assigned the tutorial to Steve:
+
+:c,image(JPG/tutorial_steve_assignee.png)
+
+[Edits from LAMMPS maintainers]
+
+If you allowed edits from maintainers (the default), any LAMMPS
+maintainer can add changes to your pull request.  In this case, both
+Axel and Richard made changes to the tutorial:
+
+:c,image(JPG/tutorial_changes_others.png)
+
+[Reverse pull requests]
+
+Sometimes, however, you might not feel comfortable having other people
+push changes into your own branch, or maybe the maintainers are not sure
+their idea was the right one.  In such a case, they can make changes,
+reassign you as the assignee, and file a "reverse pull request", i.e.
+file a pull request in your GitHub repository to include changes in the
+branch, that you have submitted as a pull request yourself.  In that
+case, you can choose to merge their changes back into your branch,
+possibly make additional changes or corrections and proceed from there.
+It looks something like this:
+
+:c,image(JPG/tutorial_reverse_pull_request.png)
+
+For some reason, the highlighted button didn't work in my case, but I
+can go to my own repository and merge the pull request from there:
+
+:c,image(JPG/tutorial_reverse_pull_request2.png)
+
+Be sure to check the changes to see if you agree with them by clicking
+on the tab button:
+
+:c,image(JPG/tutorial_reverse_pull_request3.png)
+
+In this case, most of it is changes in the markup and a short rewrite of
+Axel's explanation of the "git gui" and "git add" commands.
+
+:c,image(JPG/tutorial_reverse_pull_request4.png)
+
+Because the changes are OK with us, we are going to merge by clicking on
+"Merge pull request".  After a merge it looks like this:
+
+:c,image(JPG/tutorial_reverse_pull_request5.png)
+
+Now, since in the meantime our local text for the tutorial also changed,
+we need to pull Axel's change back into our branch, and merge them:
+
+ $ git add tutorial_github.txt
+ $ git add JPG/tutorial_reverse_pull_request*.png
+ $ git commit -m "Updated text and images on reverse pull requests"
+ $ git pull :pre
+
+In this case, the merge was painless because git could auto-merge:
+
+:c,image(JPG/tutorial_reverse_pull_request6.png)
+
+With Axel's changes merged in and some final text updates, our feature
+branch is now perfect as far as we are concerned, so we are going to
+commit and push again:
+
+ $ git add tutorial_github.txt
+ $ git add JPG/tutorial_reverse_pull_request6.png
+ $ git commit -m "Merged Axel's suggestions and updated text"
+ $ git push git@github.com:Pakketeretet2/lammps :pre
+

 :line

 [After a merge]

-When everything is fine the feature branch is merged into the LAMMPS
-repositories:
+When everything is fine, the feature branch is merged into the master branch.

 :c,image(JPG/tutorial_merged.png)

@ -198,17 +352,29 @@ It is in principle safe to delete them from your own fork. This helps
 keep it a bit more tidy. Note that you first have to switch to another
 branch!

-$ git checkout lammps-icms
-$ git pull lammps-icms
-$ git branch -d add-user-manifold :pre
+$ git checkout master
+$ git pull master
+$ git branch -d github-tutorial-update :pre

 If you do not pull first, it is not really a problem but git will warn
 you at the next statement that you are deleting a local branch that
 was not yet fully merged into HEAD. This is because git does not yet
-know your branch just got merged into lammps-icms upstream. If you
+know your branch just got merged into LAMMPS upstream. If you
 first delete and then pull, everything should still be fine.

 Finally, if you delete the branch locally, you might want to push this
 to your remote(s) as well:

-$ git push origin :add-user-manifold :pre
+$ git push origin :github-tutorial-update :pre
+
+[Recent changes in the workflow]
+
+Some changes to the workflow are not captured in this tutorial.  For
+example, in addition to the master branch, to which all new features
+should be submitted, there is now also an "unstable" and a "stable"
+branch; these have the same content as "master", but are only updated
+after a patch release or stable release was made.
+Furthermore, the naming of the patches now follow the pattern
+"patch_<Day><Month><Year>" to simplify comparisons between releases.
+Finally, all patches and submissions are subject to automatic testing
+and code checks to make sure they at the very least compile.
--- a/doc/src/tutorial_pylammps.txt
+++ b/doc/src/tutorial_pylammps.txt
@ -0,0 +1,462 @@
+"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
+
+PyLammps Tutorial :h1
+
+<!-- RST
+.. contents::
+END_RST -->
+
+Overview :h2
+
+PyLammps is a Python wrapper class which can be created on its own or use an
+existing lammps Python object. It creates a simpler, Python-like interface to
+common LAMMPS functionality. Unlike the original flat C-types interface, it
+exposes a discoverable API. It no longer requires knowledge of the underlying
+C++ code implementation.  Finally, the IPyLammps wrapper builds on top of
+PyLammps and adds some additional features for IPython integration into IPython
+notebooks, e.g. for embedded visualization output from dump/image.
+
+Comparison of lammps and PyLammps interfaces :h3
+
+lammps.lammps :h4
+
+uses C-Types
+direct memory access to native C++ data
+provides functions to send and receive data to LAMMPS
+requires knowledge of how LAMMPS internally works (C pointers, etc) :ul
+
+lammps.PyLammps :h4
+
+higher-level abstraction built on top of original C-Types interface
+manipulation of Python objects
+communication with LAMMPS is hidden from API user 
+shorter, more concise Python
+better IPython integration, designed for quick prototyping :ul
+
+
+Quick Start :h2
+
+System-wide Installation :h3
+
+Step 1: Building LAMMPS as a shared library :h4
+
+To use LAMMPS inside of Python it has to be compiled as shared library. This
+library is then loaded by the Python interface. In this example, we use the
+Make.py utility to create a Makefile with C++ exceptions, PNG, JPEG and FFMPEG
+output support enabled. Finally, we also enable the MOLECULE package and compile
+using the generated {auto} Makefile.
+
+cd $LAMMPS_DIR/src :pre
+
+# generate custom Makefile
+python2 Make.py -jpg -png -s ffmpeg exceptions -m mpi -a file :pre
+
+# add packages if necessary
+make yes-MOLECULE :pre
+
+# compile shared library using Makefile
+make mode=shlib auto :pre
+
+Step 2: Installing the LAMMPS Python package :h4
+
+PyLammps is part of the lammps Python package. To install it simply install
+that package into your current Python installation.
+
+cd $LAMMPS_DIR/python
+python install.py :pre
+
+NOTE: Recompiling the shared library requires reinstalling the Python package
+
+
+Installation inside of a virtualenv :h3
+
+You can use virtualenv to create a custom Python environment specifically tuned
+for your workflow.
+
+Benefits of using a virtualenv :h4
+
+isolation of your system Python installation from your development installation
+installation can happen in your user directory without root access (useful for HPC clusters)
+installing packages through pip allows you to get newer versions of packages than e.g., through apt-get or yum package managers (and without root access)
+you can even install specific old versions of a package if necessary :ul
+
+[Prerequisite (e.g. on Ubuntu)]
+
+apt-get install python-virtualenv :pre
+
+Creating a virtualenv with lammps installed :h4
+
+# create virtualenv name 'testing' :pre
+
+# activate 'testing' environment
+source testing/bin/activate :pre
+
+# install LAMMPS package in virtualenv
+(testing) cd $LAMMPS_DIR/python
+(testing) python install.py :pre
+
+# install other useful packages
+(testing) pip install matplotlib jupyter mpi4py :pre
+
+... :pre
+
+# return to original shell
+(testing) deactivate :pre
+
+
+Creating a new instance of PyLammps :h2
+
+To create a PyLammps object you need to first import the class from the lammps
+module. By using the default constructor, a new {lammps} instance is created.
+
+from lammps import PyLammps
+L = PyLammps() :pre
+
+You can also initialize PyLammps on top of this existing {lammps} object:
+
+from lammps import lammps, PyLammps
+lmp = lammps()
+L = PyLammps(ptr=lmp) :pre
+
+Commands :h2
+
+Sending a LAMMPS command with the existing library interfaces is done using
+the command method of the lammps object instance.
+
+For instance, let's take the following LAMMPS command:
+
+region box block 0 10 0 5 -0.5 0.5 :pre
+
+In the original interface this command can be executed with the following
+Python code if {L} was a lammps instance:
+
+L.command("region box block 0 10 0 5 -0.5 0.5") :pre
+
+With the PyLammps interface, any command can be split up into arbitrary parts
+separated by whitespace, passed as individual arguments to a region method.
+
+L.region("box block", 0, 10, 0, 5, -0.5, 0.5) :pre
+
+Note that each parameter is set as Python literal floating-point number. In the
+PyLammps interface, each command takes an arbitrary parameter list and transparently
+merges it to a single command string, separating individual parameters by whitespace.
+
+The benefit of this approach is avoiding redundant command calls and easier
+parameterization. In the original interface parametrization needed to be done
+manually by creating formatted strings.
+
+L.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi)) :pre
+
+In contrast, methods of PyLammps accept parameters directly and will convert
+them automatically to a final command string.
+
+L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi) :pre
+
+System state :h2
+
+In addition to dispatching commands directly through the PyLammps object, it
+also provides several properties which allow you to query the system state.
+
+:dlb
+
+L.system :dt
+
+Is a dictionary describing the system such as the bounding box or number of atoms :dd
+
+L.system.xlo, L.system.xhi :dt
+
+bounding box limits along x-axis :dd
+
+L.system.ylo, L.system.yhi :dt
+
+bounding box limits along y-axis :dd
+
+L.system.zlo, L.system.zhi :dt
+
+bounding box limits along z-axis :dd
+
+L.communication :dt
+
+configuration of communication subsystem, such as the number of threads or processors :dd
+
+L.communication.nthreads :dt
+
+number of threads used by each LAMMPS process :dd
+
+L.communication.nprocs :dt
+
+number of MPI processes used by LAMMPS :dd
+
+L.fixes :dt
+
+List of fixes in the current system :dd
+
+L.computes :dt
+
+List of active computes in the current system :dd
+
+L.dump :dt
+
+List of active dumps in the current system :dd
+
+L.groups :dt
+
+List of groups present in the current system :dd
+
+:dle
+
+Working with LAMMPS variables :h2
+
+LAMMPS variables can be both defined and accessed via the PyLammps interface.
+
+To define a variable you can use the "variable"_variable.html command:
+
+L.variable("a index 2") :pre
+
+A dictionary of all variables is returned by L.variables
+
+you can access an individual variable by retrieving a variable object from the
+L.variables dictionary by name
+
+a = L.variables\['a'\] :pre
+
+The variable value can then be easily read and written by accessing the value
+property of this object.
+
+print(a.value)
+a.value = 4 :pre
+
+Retrieving the value of an arbitrary LAMMPS expressions :h2
+
+LAMMPS expressions can be immediately evaluated by using the eval method. The
+passed string parameter can be any expression containing global thermo values,
+variables, compute or fix data.
+
+result = L.eval("ke") # kinetic energy
+result = L.eval("pe") # potential energy :pre
+
+result = L.eval("v_t/2.0") :pre
+
+Accessing atom data :h2
+
+All atoms in the current simulation can be accessed by using the L.atoms list.
+Each element of this list is an object which exposes its properties (id, type,
+position, velocity, force, etc.).
+
+# access first atom
+L.atoms\[0\].id
+L.atoms\[0\].type :pre
+
+# access second atom
+L.atoms\[1\].position
+L.atoms\[1\].velocity
+L.atoms\[1\].force :pre
+
+Some properties can also be used to set:
+
+# set position in 2D simulation
+L.atoms\[0\].position = (1.0, 0.0) :pre
+
+# set position in 3D simulation
+L.atoms\[0\].position = (1.0, 0.0, 1.) :pre
+
+Evaluating thermo data :h2
+
+Each simulation run usually produces thermo output based on system state,
+computes, fixes or variables. The trajectories of these values can be queried
+after a run via the L.runs list. This list contains a growing list of run data.
+The first element is the output of the first run, the second element that of
+the second run.
+
+L.run(1000)
+L.runs\[0\] # data of first 1000 time steps :pre
+
+L.run(1000)
+L.runs\[1\] # data of second 1000 time steps :pre
+
+Each run contains a dictionary of all trajectories. Each trajectory is
+accessible through its thermo name:
+
+L.runs\[0\].step # list of time steps in first run
+L.runs\[0\].ke   # list of kinetic energy values in first run :pre
+
+Together with matplotlib plotting data out of LAMMPS becomes simple:
+
+import matplotlib.plot as plt
+
+steps = L.runs\[0\].step
+ke    = L.runs\[0\].ke
+plt.plot(steps, ke) :pre
+
+Error handling with PyLammps :h2
+
+Compiling the shared library with C++ exception support provides a better error
+handling experience.  Without exceptions the LAMMPS code will terminate the
+current Python process with an error message.  C++ exceptions allow capturing
+them on the C++ side and rethrowing them on the Python side. This way you
+can handle LAMMPS errors through the Python exception handling mechanism.
+
+IMPORTANT NOTE: Capturing a LAMMPS exception in Python can still mean that the
+current LAMMPS process is in an illegal state and must be terminated. It is
+advised to save your data and terminate the Python instance as quickly as
+possible.
+
+Using PyLammps in IPython notebooks and Jupyter :h2
+
+If the LAMMPS Python package is installed for the same Python interpreter as
+IPython, you can use PyLammps directly inside of an IPython notebook inside of
+Jupyter. Jupyter is a powerful integrated development environment (IDE) for
+many dynamic languages like Python, Julia and others, which operates inside of
+any web browser. Besides auto-completion and syntax highlighting it allows you
+to create formatted documents using Markup, mathematical formulas, graphics and
+animations intermixed with executable Python code. It is a great format for
+tutorials and showcasing your latest research.
+
+To launch an instance of Jupyter simply run the following command inside your
+Python environment (this assumes you followed the Quick Start instructions):
+
+jupyter notebook :pre
+
+IPyLammps Examples :h2
+
+Examples of IPython notebooks can be found in the python/examples/pylammps
+subdirectory. To open these notebooks launch {jupyter notebook} inside this
+directory and navigate to one of them. If you compiled and installed 
+a LAMMPS shared library with execeptions, PNG, JPEG and FFMPEG support
+you should be able to rerun all of these notebooks.
+
+Validating a dihedral potential :h3
+
+This example showcases how an IPython Notebook can be used to compare a simple
+LAMMPS simulation of a harmonic dihedral potential to its analytical solution.
+Four atoms are placed in the simulation and the dihedral potential is applied on
+them using a datafile. Then one of the atoms is rotated along the central axis by
+setting its position from Python, which changes the dihedral angle.
+
+phi = \[d * math.pi / 180 for d in range(360)\] :pre
+
+pos = \[(1.0, math.cos(p), math.sin(p)) for p in phi\] :pre
+
+pe = \[\]
+for p in pos:
+    L.atoms\[3\].position = p
+    L.run(0)
+    pe.append(L.eval("pe")) :pre
+
+By evaluating the potential energy for each position we can verify that
+trajectory with the analytical formula.  To compare both solutions, we plot
+both trajectories over each other using matplotlib, which embeds the generated
+plot inside the IPython notebook.
+
+:c,image(JPG/pylammps_dihedral.jpg)
+
+Running a Monte Carlo relaxation :h3
+
+This second example shows how to use PyLammps to create a 2D Monte Carlo Relaxation
+simulation, computing and plotting energy terms and even embedding video output.
+
+Initially, a 2D system is created in a state with minimal energy.
+
+:c,image(JPG/pylammps_mc_minimum.jpg)
+
+It is then disordered by moving each atom by a random delta.
+
+random.seed(27848)
+deltaperturb = 0.2 :pre
+
+for i in range(L.system.natoms):
+    x, y = L.atoms\[i\].position
+    dx = deltaperturb * random.uniform(-1, 1)
+    dy = deltaperturb * random.uniform(-1, 1)
+    L.atoms\[i\].position  = (x+dx, y+dy) :pre
+
+L.run(0) :pre
+
+:c,image(JPG/pylammps_mc_disordered.jpg)
+
+Finally, the Monte Carlo algorithm is implemented in Python. It continuously
+moves random atoms by a random delta and only accepts certain moves.
+
+estart = L.eval("pe")
+elast = estart :pre
+
+naccept = 0
+energies = \[estart\] :pre
+
+niterations = 3000
+deltamove = 0.1
+kT = 0.05 :pre
+
+natoms = L.system.natoms :pre
+
+for i in range(niterations):
+    iatom = random.randrange(0, natoms)
+    current_atom = L.atoms\[iatom\] :pre
+    
+    x0, y0 = current_atom.position :pre
+    
+    dx = deltamove * random.uniform(-1, 1)
+    dy = deltamove * random.uniform(-1, 1) :pre
+    
+    current_atom.position = (x0+dx, y0+dy) :pre
+    
+    L.run(1, "pre no post no") :pre
+    
+    e = L.eval("pe")
+    energies.append(e) :pre
+    
+    if e <= elast:
+        naccept += 1
+        elast = e
+    elif random.random() <= math.exp(natoms*(elast-e)/kT):
+        naccept += 1
+        elast = e
+    else:
+        current_atom.position = (x0, y0) :pre
+
+The energies of each iteration are collected in a Python list and finally plotted using matplotlib.
+
+:c,image(JPG/pylammps_mc_energies_plot.jpg)
+
+The IPython notebook also shows how to use dump commands and embed video files
+inside of the IPython notebook.
+
+Using PyLammps and mpi4py (Experimental) :h2
+
+PyLammps can be run in parallel using mpi4py. This python package can be installed using
+
+pip install mpi4py :pre
+
+The following is a short example which reads in an existing LAMMPS input file and
+executes it in parallel.  You can find in.melt in the examples/melt folder.
+
+from mpi4py import MPI
+from lammps import PyLammps :pre
+
+L = PyLammps()
+L.file("in.melt") :pre
+
+if MPI.COMM_WORLD.rank == 0:
+    print("Potential energy: ", L.eval("pe")) :pre
+
+MPI.Finalize() :pre
+
+To run this script (melt.py) in parallel using 4 MPI processes we invoke the
+following mpirun command:
+
+mpirun -np 4 python melt.py :pre
+
+IMPORTANT NOTE: Any command must be executed by all MPI processes. However, evaluations and querying the system state is only available on rank 0.
+
+Feedback and Contributing :h2
+
+If you find this Python interface useful, please feel free to provide feedback
+and ideas on how to improve it to Richard Berger (richard.berger@temple.edu). We also
+want to encourage people to write tutorial style IPython notebooks showcasing LAMMPS usage
+and maybe their latest research results. 
--- a/doc/src/tutorials.txt
+++ b/doc/src/tutorials.txt
@ -7,6 +7,7 @@ Tutorials :h1

   tutorial_drude
   tutorial_github
+   tutorial_pylammps
   body
   manifolds

--- a/examples/README
+++ b/examples/README
@ -82,6 +82,7 @@ meam:	  MEAM test for SiC and shear (same as shear examples)
 melt:	  rapid melt of 3d LJ system
 micelle:  self-assembly of small lipid-like molecules into 2d bilayers
 min:	  energy minimization of 2d LJ melt
+mscg:     parameterize a multi-scale coarse-graining (MSCG) model
 msst:	  MSST shock dynamics
 nb3b:     use of nonbonded 3-body harmonic pair style
 neb:	  nudged elastic band (NEB) calculation for barrier finding
--- a/Show More
+++ b/Show More