patch 17Jan17

Merge pull request #339 from akohlmey/fixes-for-srp-example
Fixes for srp example
2017-01-17 10:14:53 -07:00 · 2017-01-17 09:36:28 -07:00 · 2017-01-17 09:33:25 -07:00 · 2017-01-17 09:14:03 -07:00 · 2017-01-17 09:13:47 -07:00 · 2017-01-17 09:13:27 -07:00
1418 changed files with 108760 additions and 49536 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/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_merged.png
+++ b/doc/src/JPG/tutorial_merged.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_reverse_pull_request7.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request7.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="17 Nov 2016 version">
+<META NAME="docnumber" CONTENT="17 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
-17 Nov 2016 version :c,h4
+17 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,
@ -911,10 +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,
--- a/doc/src/Section_errors.txt
+++ b/doc/src/Section_errors.txt
@ -55,12 +55,13 @@ LAMMPS errors are detected at setup time; others like a bond
 stretching too far may not occur until the middle of a run.

 LAMMPS tries to flag errors and print informative error messages so
-you can fix the problem.  Of course, LAMMPS cannot figure out your
-physics or numerical mistakes, like choosing too big a timestep,
-specifying erroneous force field coefficients, or putting 2 atoms on
-top of each other!  If you run into errors that LAMMPS doesn't catch
-that you think it should flag, please send an email to the
-"developers"_http://lammps.sandia.gov/authors.html.
+you can fix the problem.  For most errors it will also print the last
+input script command that it was processing.  Of course, LAMMPS cannot
+figure out your physics or numerical mistakes, like choosing too big a
+timestep, specifying erroneous force field coefficients, or putting 2
+atoms on top of each other!  If you run into errors that LAMMPS
+doesn't catch that you think it should flag, please send an email to
+the "developers"_http://lammps.sandia.gov/authors.html.

 If you get an error message about an invalid command in your input
 script, you can determine what command is causing the problem by
--- 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_packages.txt
+++ b/doc/src/Section_packages.txt
@ -1153,7 +1153,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
 "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
 "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -
 "USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
-"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc, dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
+"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc / dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
 "USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, -
 "USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
 "USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
@ -1610,11 +1610,12 @@ and a "dump nc/mpiio"_dump_nc.html command to output LAMMPS snapshots
 in this format.  See src/USER-NC-DUMP/README for more details.

 NetCDF files can be directly visualized with the following tools:
+
 Ovito (http://www.ovito.org/). Ovito supports the AMBER convention
-  and all of the above extensions. :ulb,l
+and all of the above extensions. :ulb,l
 VMD (http://www.ks.uiuc.edu/Research/vmd/) :l
 AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains
-  a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule
+a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule

 The person who created these files is Lars Pastewka at
 Karlsruhe Institute of Technology (lars.pastewka at kit.edu).
--- a/doc/src/Section_python.txt
+++ b/doc/src/Section_python.txt
@ -8,19 +8,26 @@

 11. Python interface to LAMMPS :h3

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

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

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

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

 If you are not familiar with it, "Python"_http://www.python.org is a
 powerful scripting and programming language which can essentially do
@ -824,3 +832,7 @@ different visualization package options.  Click to see larger images:
 :image(JPG/screenshot_atomeye_small.jpg,JPG/screenshot_atomeye.jpg)
 :image(JPG/screenshot_pymol_small.jpg,JPG/screenshot_pymol.jpg)
 :image(JPG/screenshot_vmd_small.jpg,JPG/screenshot_vmd.jpg)
+
+11.9 PyLammps interface :link(py_9),h4
+
+Please see the "PyLammps Tutorial"_tutorial_pylammps.html.
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@ -1727,7 +1727,7 @@ thermodynamic state and a total run time for the simulation.  It then
 appends statistics about the CPU time and storage requirements for the
 simulation.  An example set of statistics is shown here:

-Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
+Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms :pre

 Performance: 18.436 ns/day  1.302 hours/ns  106.689 timesteps/s
 97.0% CPU use with 4 MPI tasks x no OpenMP threads :pre
@ -1757,14 +1757,14 @@ Ave special neighs/atom = 2.34032
 Neighbor list builds = 26
 Dangerous builds = 0 :pre

-The first section provides a global loop timing summary. The loop time
+The first section provides a global loop timing summary. The {loop time}
 is the total wall time for the section.  The {Performance} line is
 provided for convenience to help predicting the number of loop
-continuations required and for comparing performance with other
-similar MD codes.  The CPU use line provides the CPU utilzation per
+continuations required and for comparing performance with other,
+similar MD codes.  The {CPU use} line provides the CPU utilzation per
 MPI task; it should be close to 100% times the number of OpenMP
-threads (or 1). Lower numbers correspond to delays due to file I/O or
-insufficient thread utilization.
+threads (or 1 of no OpenMP). Lower numbers correspond to delays due
+to file I/O or insufficient thread utilization.

 The MPI task section gives the breakdown of the CPU run time (in
 seconds) into major categories:
@ -1791,7 +1791,7 @@ is present that also prints the CPU utilization in percent. In
 addition, when using {timer full} and the "package omp"_package.html
 command are active, a similar timing summary of time spent in threaded
 regions to monitor thread utilization and load balance is provided. A
-new entry is the {Reduce} section, which lists the time spend in
+new entry is the {Reduce} section, which lists the time spent in
 reducing the per-thread data elements to the storage for non-threaded
 computation. These thread timings are taking from the first MPI rank
 only and and thus, as the breakdown for MPI tasks can change from MPI
--- 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/accelerate_kokkos.txt
+++ b/doc/src/accelerate_kokkos.txt
@ -110,14 +110,14 @@ mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj   # ditto on 8 Phis :p
 [Required hardware/software:]

 Kokkos support within LAMMPS must be built with a C++11 compatible
-compiler.  If using gcc, version 4.8.1 or later is required.
+compiler.  If using gcc, version 4.7.2 or later is required.

 To build with Kokkos support for CPUs, your compiler must support the
 OpenMP interface.  You should have one or more multi-core CPUs so that
 multiple threads can be launched by each MPI task running on a CPU.

 To build with Kokkos support for NVIDIA GPUs, NVIDIA Cuda software
-version 6.5 or later must be installed on your system.  See the
+version 7.5 or later must be installed on your system.  See the
 discussion for the "GPU"_accelerate_gpu.html package for details of
 how to check and do this.

--- a/doc/src/commands.txt
+++ b/doc/src/commands.txt
@ -91,6 +91,7 @@ Commands :h1
   suffix
   tad
   temper
+   temper_grem
   thermo
   thermo_modify
   thermo_style
--- 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_coord_atom.txt
+++ b/doc/src/compute_coord_atom.txt
@ -10,22 +10,34 @@ compute coord/atom command :h3

 [Syntax:]

-compute ID group-ID coord/atom cutoff type1 type2 ... :pre
+compute ID group-ID coord/atom cstyle args ... :pre

 ID, group-ID are documented in "compute"_compute.html command
 coord/atom = style name of this compute command
-cutoff = distance within which to count coordination neighbors (distance units)
-typeN = atom type for Nth coordination count (see asterisk form below) :ul
+one cstyle must be appended :ul
+
+cstyle = {cutoff} or {orientorder}
+
+{cutoff} args = cutoff typeN
+  cutoff = distance within which to count coordination neighbors (distance units)
+  typeN = atom type for Nth coordination count (see asterisk form below) :pre
+
+{orientorder} args = orientorderID threshold
+  orientorderID = ID of a previously defined orientorder/atom compute
+  threshold = minimum value of the scalar product between two 'connected' atoms (see text for explanation) :pre

 [Examples:]

-compute 1 all coord/atom 2.0
-compute 1 all coord/atom 6.0 1 2
-compute 1 all coord/atom 6.0 2*4 5*8 * :pre
+compute 1 all coord/atom cutoff 2.0
+compute 1 all coord/atom cutoff 6.0 1 2
+compute 1 all coord/atom cutoff 6.0 2*4 5*8 *
+compute 1 all coord/atom orientorder 2 0.5 :pre

 [Description:]

-Define a computation that calculates one or more coordination numbers
+This compute performs generic calculations between neighboring atoms. So far,
+there are two cstyles implemented: {cutoff} and {orientorder}.
+The {cutoff} cstyle calculates one or more coordination numbers
 for each atom in a group.

 A coordination number is defined as the number of neighbor atoms with
@ -49,6 +61,14 @@ from 1 to N.  A leading asterisk means all types from 1 to n
 (inclusive).  A middle asterisk means all types from m to n
 (inclusive).

+The {orientorder} cstyle calculates the number of 'connected' atoms j 
+around each atom i. The atom j is connected to i if the scalar product
+({Ybar_lm(i)},{Ybar_lm(j)}) is larger than {threshold}. Thus, this cstyle
+will work only if a "compute orientorder/atom"_compute_orientorder_atom.html
+has been previously defined. This cstyle allows one to apply the 
+ten Wolde's criterion to identify cristal-like atoms in a system 
+(see "ten Wolde et al."_#tenWolde).
+
 The value of all coordination numbers will be 0.0 for atoms not in the
 specified compute group.

@ -83,10 +103,19 @@ options.
 The per-atom vector or array values will be a number >= 0.0, as
 explained above.

-[Restrictions:] none
+[Restrictions:]
+The cstyle {orientorder} can only be used if a 
+"compute orientorder/atom"_compute_orientorder_atom.html command
+was previously defined. Otherwise, an error message will be issued.

 [Related commands:]

 "compute cluster/atom"_compute_cluster_atom.html
+"compute orientorder/atom"_compute_orientorder_atom.html

 [Default:] none
+
+:line
+
+:link(tenWolde)
+[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
--- 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_orientorder_atom.txt
+++ b/doc/src/compute_orientorder_atom.txt
@ -15,17 +15,19 @@ compute ID group-ID orientorder/atom keyword values ... :pre
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 orientorder/atom = style name of this compute command :l
 one or more keyword/value pairs may be appended :l
-keyword = {cutoff} or {nnn} or {degrees}
+keyword = {cutoff} or {nnn} or {degrees} or {components}
  {cutoff} value = distance cutoff
  {nnn} value = number of nearest neighbors
-  {degrees} values = nlvalues, l1, l2,...  :pre
+  {degrees} values = nlvalues, l1, l2,...
+  {components} value = l  :pre

 :ule

 [Examples:]

 compute 1 all orientorder/atom
-compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5 :pre
+compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5
+compute 1 all orientorder/atom degrees 4 6 components 6 nnn NULL cutoff 3.0 :pre

 [Description:]

@ -71,6 +73,13 @@ The numerical values of all order parameters up to {Q}12
 for a range of commonly encountered high-symmetry structures are given
 in Table I of "Mickel et al."_#Mickel.

+The optional keyword {components} will output the components of
+the normalized complex vector {Ybar_lm} of degree {l}, which must be
+explicitly included in the keyword {degrees}. This option can be used
+in conjunction with "compute coord_atom"_compute_coord_atom.html to
+calculate the ten Wolde's criterion to identify crystal-like particles
+(see "ten Wolde et al."_#tenWolde96).
+
 The value of {Ql} is set to zero for atoms not in the
 specified compute group, as well as for atoms that have less than
 {nnn} neighbors within the distance cutoff.
@ -98,6 +107,12 @@ the neighbor list.
 This compute calculates a per-atom array with {nlvalues} columns, giving the
 {Ql} values for each atom, which are real numbers on the range 0 <= {Ql} <= 1.

+If the keyword {components} is set, then the real and imaginary parts of each
+component of (normalized) {Ybar_lm} will be added to the output array in the
+following order:
+Re({Ybar_-m}) Im({Ybar_-m}) Re({Ybar_-m+1}) Im({Ybar_-m+1}) ... Re({Ybar_m}) Im({Ybar_m}).
+This way, the per-atom array will have a total of {nlvalues}+2*(2{l}+1) columns.
+
 These values can be accessed by any command that uses
 per-atom values from a compute as input.  See "Section
 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
@ -117,5 +132,9 @@ The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, {degrees} = 5

 :link(Steinhardt)
 [(Steinhardt)] P. Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).
+
 :link(Mickel)
 [(Mickel)] W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013).
+
+:link(tenWolde96)
+[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
--- 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/computes.txt
+++ b/doc/src/computes.txt
@ -35,6 +35,7 @@ Computes :h1
   compute_erotate_sphere_atom
   compute_event_displace
   compute_fep
+   compute_global_atom
   compute_group_group
   compute_gyration
   compute_gyration_chunk
--- 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_flow_gauss.txt
+++ b/doc/src/fix_flow_gauss.txt
@ -151,7 +151,7 @@ The option default for the {energy} keyword is energy = no.
 :line

 :link(Strong)
-[(Strong)] Strong and Eaves, J. Phys. Chem. Lett. 7, 1907 (2016).
+[(Strong)] Strong and Eaves, J. Phys. Chem. B 121, 189 (2017).

 :link(Evans)
 [(Evans)] Evans and Morriss, Phys. Rev. Lett. 56, 2172 (1986).
--- 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)"_#Kim2010,
+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(Kim2010)
+[(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/fix_spring.txt
+++ b/doc/src/fix_spring.txt
@ -89,11 +89,7 @@ NOTE: The center of mass of a group of atoms is calculated in
 group can straddle a periodic boundary.  See the "dump"_dump.html doc
 page for a discussion of unwrapped coordinates.  It also means that a
 spring connecting two groups or a group and the tether point can cross
-a periodic boundary and its length be calculated correctly.  One
-exception is for rigid bodies, which should not be used with the fix
-spring command, if the rigid body will cross a periodic boundary.
-This is because image flags for rigid bodies are used in a different
-way, as explained on the "fix rigid"_fix_rigid.html doc page.
+a periodic boundary and its length be calculated correctly.  

 [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/lammps.book
+++ b/doc/src/lammps.book
@ -23,6 +23,7 @@ Section_history.html

 tutorial_drude.html
 tutorial_github.html
+tutorial_pylammps.html

 body.html
 manifolds.html
@ -113,6 +114,7 @@ special_bonds.html
 suffix.html
 tad.html
 temper.html
+temper_grem.html
 thermo.html
 thermo_modify.html
 thermo_style.html
@ -172,6 +174,7 @@ fix_gcmc.html
 fix_gld.html
 fix_gle.html
 fix_gravity.html
+fix_grem.html
 fix_halt.html
 fix_heat.html
 fix_imd.html
@ -191,6 +194,7 @@ 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
@ -213,6 +217,7 @@ 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
@ -310,6 +315,7 @@ 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
--- 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_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/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)"_#KimStraub.  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(KimStraub)
+[(Kim)] Kim, Keyes, Straub, J Chem Phys, 132, 224107 (2010).
--- a/doc/src/timer.txt
+++ b/doc/src/timer.txt
@ -33,14 +33,14 @@ timer loop :pre
 Select the level of detail at which LAMMPS performs its CPU timings.
 Multiple keywords can be specified with the {timer} command.  For
 keywords that are mutually exclusive, the last one specified takes
-effect.
+precedence.

 During a simulation run LAMMPS collects information about how much
 time is spent in different sections of the code and thus can provide
 information for determining performance and load imbalance problems.
 This can be done at different levels of detail and accuracy.  For more
 information about the timing output, see this "discussion of screen
-output"_Section_start.html#start_8.
+output in Section 2.8"_Section_start.html#start_8.

 The {off} setting will turn all time measurements off. The {loop}
 setting will only measure the total time for a run and not collect any
@ -52,20 +52,22 @@ procsessors.  The {full} setting adds information about CPU
 utilization and thread utilization, when multi-threading is enabled.

 With the {sync} setting, all MPI tasks are synchronized at each timer
-call which meaures load imbalance more accuractly, though it can also
-slow down the simulation.  Using the {nosync} setting (which is the
-default) turns off this synchronization.
+call which measures load imbalance for each section more accuractly,
+though it can also slow down the simulation by prohibiting overlapping
+independent computations on different MPI ranks  Using the {nosync}
+setting (which is the default) turns this synchronization off.

-With the {timeout} keyword a walltime limit can be imposed that
+With the {timeout} keyword a walltime limit can be imposed, that
 affects the "run"_run.html and "minimize"_minimize.html commands.
-This can be convenient when runs have to confirm to time limits,
-e.g. when running under a batch system and you want to maximize
-the utilization of the batch time slot, especially when the time
-per timestep varies and is thus difficult to predict how many
-steps a simulation can perform, or for difficult to converge
-minimizations. The timeout {elapse} value should be somewhat smaller
-than the time requested from the batch system, as there is usually
-some overhead to launch jobs, and it may be advisable to write
+This can be convenient when calculations have to comply with execution
+time limits, e.g. when running under a batch system when you want to
+maximize the utilization of the batch time slot, especially for runs
+where the time per timestep varies much and thus it becomes difficult
+to predict how many steps a simulation can perform for a given walltime
+limit. This also applies for difficult to converge minimizations.
+The timeout {elapse} value should be somewhat smaller than the maximum
+wall time requested from the batch system, as there is usually
+some overhead to launch jobs, and it is advisable to write
 out a restart after terminating a run due to a timeout.

 The timeout timer starts when the command is issued. When the time
--- 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 +189,162 @@ 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
+
+This merge also shows up on the lammps Github page:
+
+:c,image(JPG/tutorial_reverse_pull_request7.png)

 :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 +355,29 @@ 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/examples/USER/dpd/dpde-vv/log.dpde-vv.reference
+++ b/examples/USER/dpd/dpde-vv/log.dpde-vv.reference
@ -35,129 +35,133 @@ thermo_modify   format float %24.16f

 run             1000
 Neighbor list info ...
-  1 neighbor list requests
  update every 1 steps, delay 0 steps, check no
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10.6
  ghost atom cutoff = 10.6
-  binsize = 5.3 -> bins = 25 25 25
-Memory usage per processor = 3.36353 Mbytes
+  binsize = 5.3, bins = 25 25 25
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair dpd/fdt/energy, perpetual
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Memory usage per processor = 4.28221 Mbytes
 Step Temp Press PotEng KinEng c_dpdU[1] c_dpdU[2] v_totEnergy c_dpdU[4] 
-       0     301.4391322267262012    1636.1776395935085020    1188.6488072196075336     394.4722035796053206    7852.5601874986105031    7852.5601874986105031   17288.2413857964347699     299.9999999999841407 
-      10     301.4791572483523510    1486.4422375141198245    1188.7147620806101713     394.5245815119678241    7852.5601874999802021    7852.3731942333779443   17288.1727253259377903     299.9960221120699089 
-      20     301.4275643919337426    1677.9356110821624952    1188.7839634625399867     394.4570655673388728    7852.5601874999938445    7852.3711851933012440   17288.1724017231754260     299.9955485734552099 
-      30     301.2240988054542186    1452.7304951528931269    1188.8550809767796181     394.1908044563202225    7852.5601875000002110    7852.5679666239848302   17288.1740395570850524     299.9988968405210130 
-      40     301.1023506886409677    1527.9758363521380033    1188.9264527568634549     394.0314812537677653    7852.5601874999947540    7852.6574764573806533   17288.1755979680056043     300.0001694462812338 
-      50     301.0409654880461972    1597.1737251233498682    1188.9944523606982330     393.9511507566391515    7852.5601875000029395    7852.6700547249911324   17288.1758453423317405     299.9999653064982681 
-      60     301.2904978886139133    1610.8630327676828529    1189.0651026961211301     394.2776962691256131    7852.5601874999829306    7852.2734988976435488   17288.1764853628737910     299.9919857290491905 
-      70     300.8575037843163500    1489.3259312130880971    1189.1295686642290548     393.7110673208616731    7852.5601874999856591    7852.7707182199101226   17288.1715417049854295     300.0010992278233175 
-      80     300.5955830326474825    1449.3896097889587509    1189.1880764967559116     393.3683100440913449    7852.5601875000411383    7853.0484238882281716   17288.1649979291178170     300.0059513551503301 
-      90     301.0092332775843147    1553.9266324350364812    1189.2470037925052111     393.9096250433288446    7852.5601875000420478    7852.4452067113825251   17288.1620230472581170     299.9940347326859182 
-     100     301.0478004479094238    1539.2270336322194453    1189.3010269201699884     393.9600951881690207    7852.5601875000074870    7852.3416236045995902   17288.1629332129450631     299.9916385566916119 
-     110     300.9609384905550087    1500.0429484565006533    1189.3524514939088021     393.8464250502817663    7852.5601874999983920    7852.4114980357189779   17288.1705620799075405     299.9925626482005327 
-     120     300.9625536631411933    1630.5065919443034090    1189.4006029528841282     393.8485387131115658    7852.5601875000575092    7852.3600810123671181   17288.1694101784196391     299.9911580775880680 
-     130     301.0373750247310340    1539.2267307640183844    1189.4426173625224692     393.9464521696795032    7852.5601874999993015    7852.2178388309775983   17288.1670958631802932     299.9879581026651749 
-     140     300.7465104415114752    1550.8353679735087098    1189.4887352231000932     393.5658181350791551    7852.5601874999920256    7852.5559582333216895   17288.1706990914935886     299.9939749909034958 
-     150     300.6667173911141617    1634.8987162883277051    1189.5368575067818711     393.4613985788388959    7852.5601874999920256    7852.6079668015609059   17288.1664103871735279     299.9946423938895350 
-     160     300.4684731724562425    1462.9400882126803936    1189.5825022927965620     393.2019703048678707    7852.5601874999847496    7852.8265187980177870   17288.1711788956672535     299.9983600613423960 
-     170     300.1439323338466920    1510.2352578813552100    1189.6305700279478970     392.7772665220106774    7852.5601874999802021    7853.2009671047335360   17288.1689911546709482     300.0051118582463232 
-     180     300.1074244553407198    1529.6307083879951279    1189.6764977580119194     392.7294912276224181    7852.5601874999729262    7853.2047509722533505   17288.1709274578606710     300.0047089238623812 
-     190     300.4193298066089142    1546.3205495807171701    1189.7172820166240399     393.1376598363699486    7852.5601874999847496    7852.7461854379371289   17288.1613147909156396     299.9954451643528728 
-     200     300.3353919251508728    1532.5496449337254035    1189.7600175880224924     393.0278162310690391    7852.5601874999683787    7852.8107089913455638   17288.1587303104060993     299.9962707550171785 
-     210     300.3276568499739483    1504.8178651700843602    1189.7998299597820733     393.0176938818990493    7852.5601875000156724    7852.7810130200659842   17288.1587243617614149     299.9953436245502871 
-     220     300.5768315696971626    1592.5896084568344122    1189.8391466344742184     393.3437713226064716    7852.5601875000329528    7852.4205574703573802   17288.1636629274726147     299.9880321846658831 
-     230     300.6587445618569063    1672.3049358942289473    1189.8766340798690635     393.4509650976162334    7852.5601874999847496    7852.2733199687863817   17288.1611066462573945     299.9848228571166828 
-     240     300.7517707836825025    1527.1722267937811921    1189.9126240081129708     393.5727019751183207    7852.5601875000065775    7852.1160682173085661   17288.1615817005440476     299.9814952182625802 
-     250     300.8473715548367409    1589.1847713095248764    1189.9441342461948352     393.6978079843565865    7852.5601875000047585    7851.9625847797888127   17288.1647145103452203     299.9782210858571148 
-     260     300.8450266408960942    1623.1896863377055524    1189.9636161513917614     393.6947393603111891    7852.5601874999820211    7851.9471828473988353   17288.1657258590821584     299.9775302202895659 
-     270     300.6663619570709898    1564.5160171187899323    1189.9764081239700317     393.4609334472908131    7852.5601875000193104    7852.1708276117251444   17288.1683566830033669     299.9812899253168439 
-     280     300.7668534205726019    1618.5400526904263643    1189.9872008155405183     393.5924395618274048    7852.5601875000184009    7852.0271568534708422   17288.1669847308585304     299.9781169783826158 
-     290     300.8462727198648849    1562.6765776748122789    1189.9918265985252219     393.6963700162682471    7852.5601875000211294    7851.9189772084127981   17288.1673613232269417     299.9756806168044250 
-     300     300.8095414073812890    1525.1785808192844343    1189.9873922767767453     393.6483023295390922    7852.5601875000020300    7851.9657301693578120   17288.1616122756749974     299.9761279889730758 
-     310     300.9496330741350221    1566.5597234051326723    1189.9752299662607129     393.8316304464934774    7852.5601875000056680    7851.7898117189633922   17288.1568596317229094     299.9723726900590464 
-     320     301.2370566356515837    1513.6869483705047514    1189.9626455872523820     394.2077614578674343    7852.5601874999929350    7851.4248466706330873   17288.1554412157456682     299.9650543775110236 
-     330     301.3279721508968692    1549.0667862452519330    1189.9513389477854162     394.3267362020337146    7852.5601874999929350    7851.3129955581916875   17288.1512582080031279     299.9625537201162615 
-     340     301.1145736537583844    1414.7930515101759283    1189.9408691169965095     394.0474765890400590    7852.5601874999993015    7851.6028846074832472   17288.1514178135184920     299.9677356565828745 
-     350     301.1651600907370039    1529.8016115175887535    1189.9314470205476937     394.1136755032911196    7852.5601874999929350    7851.5441417268757505   17288.1494517507089768     299.9662576716461331 
-     360     301.0550563185083206    1536.7721716375504002    1189.9200519814730796     393.9695904359920178    7852.5601875000074870    7851.7101209691463737   17288.1599508866202086     299.9690811750865009 
-     370     301.1008976932964742    1522.3385843459479929    1189.9109162496640693     394.0295798208944120    7852.5601875000211294    7851.6603423306560217   17288.1610259012340975     299.9677565060027860 
-     380     301.1656898730700505    1505.0548721701993600    1189.9005648244351505     394.1143687921909304    7852.5601875000056680    7851.5816827598300733   17288.1568038764598896     299.9659906785156522 
-     390     300.8379322662876802    1740.9151205755624687    1189.8851457594087151     393.6854554509390596    7852.5601875000238579    7852.0268864110385039   17288.1576751214088290     299.9741278188615752 
-     400     300.8663790447546376    1564.9461156870302148    1189.8690133470408909     393.7226817503372445    7852.5601875000411383    7852.0043792319993372   17288.1562618294192362     299.9732593416579789 
-     410     300.6263441860635908    1564.2840871092373618    1189.8566574093877080     393.4085650033033517    7852.5601874999892971    7852.3284491703725507   17288.1538590830532485     299.9792095875052951 
-     420     300.5302259436974168    1438.1569922368764765    1189.8406936554465574     393.2827818158641549    7852.5601875000302243    7852.4696075433648730   17288.1532705147074012     299.9815165752025337 
-     430     300.5877786105220935    1503.3641639033023694    1189.8251514530138593     393.3580969454444016    7852.5601874999802021    7852.4023373559457468   17288.1457732543858583     299.9798346272511935 
-     440     300.7289160804472772    1689.2527029957295781    1189.8035410609209066     393.5427936314976591    7852.5601875000029395    7852.2436462415198548   17288.1501684339418716     299.9764596782897570 
-     450     300.9487198282456575    1497.3668092174791582    1189.7808137689632986     393.8304353457919547    7852.5601874999938445    7851.9788323927432430   17288.1502690074921702     299.9710227473042323 
-     460     300.9359942496024587    1625.1573864018491804    1189.7615359247627111     393.8137822755282400    7852.5601875000147629    7852.0165192783370003   17288.1520249786408385     299.9713565393226986 
-     470     301.0000133856357252    1486.1561922844011860    1189.7439269526955741     393.8975596188205941    7852.5601874999656502    7851.9561324572268859   17288.1578065287103527     299.9697143418395626 
-     480     300.8568627175957886    1535.6080526199095857    1189.7237810071801505     393.7102284019063063    7852.5601874999601932    7852.1697010727630186   17288.1638979818089865     299.9732503057674080 
-     490     301.0608040775520067    1497.3221544489886128    1189.7062242497636362     393.9771121242308709    7852.5601874999974825    7851.9258988739011329   17288.1694227478947141     299.9682362511933320 
-     500     301.0232592587148019    1517.5854528541199215    1189.6911287485861521     393.9279798589197981    7852.5601875000247674    7851.9823225510326665   17288.1616186585633841     299.9690333355835037 
-     510     300.7038579923685120    1420.2615974401142012    1189.6747661513456933     393.5100018730125839    7852.5601874999674692    7852.4114869568047652   17288.1564424811294884     299.9768186576545759 
-     520     300.5917863355052759    1537.4862082427132464    1189.6604754398756540     393.3633415734188361    7852.5601875000029395    7852.5789017095057716   17288.1629062228021212     299.9795694302102333 
-     530     300.4751352158502868    1481.1071694751799441    1189.6453243069925065     393.2106884527691477    7852.5601874999811116    7852.7451655714066874   17288.1613658311471227     299.9823181268525900 
-     540     300.5380123640739498    1547.3461372766389559    1189.6261485232855648     393.2929713568877332    7852.5601875000375003    7852.6850583598352387   17288.1643657400454686     299.9808112190538623 
-     550     300.4253885005187499    1544.3485889749692888    1189.6033595464525661     393.1455884232119047    7852.5601874999756546    7852.8598718466746504   17288.1690073163154011     299.9835860164698147 
-     560     300.3263552442093101    1556.5150300058251105    1189.5759163336824713     393.0159905619273673    7852.5601875000111249    7853.0148613782675966   17288.1669557738860021     299.9861837797674866 
-     570     300.1977324643196425    1511.2320626303917379    1189.5441090918316149     392.8476709710407704    7852.5601875000102154    7853.2098259401755058   17288.1617935030590161     299.9896761688499964 
-     580     300.3543631005173893    1588.9566243200433746    1189.5094471319721379     393.0526424747489500    7852.5601875000156724    7853.0374555421631158   17288.1597326488990802     299.9859298211933378 
-     590     300.5019108864805730    1504.4406939723214691    1189.4809412920112663     393.2457278908070748    7852.5601874999874781    7852.8704277855340479   17288.1572844683396397     299.9823573257917815 
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-Loop time of 21.3308 on 1 procs for 1000 steps with 10125 atoms
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+Loop time of 17.0881 on 1 procs for 1000 steps with 10125 atoms

-Performance: 4.050 ns/day, 5.925 hours/ns, 46.880 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 5.056 ns/day, 4.747 hours/ns, 58.520 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads

 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 10.099     | 10.099     | 10.099     |   0.0 | 47.34
-Neigh   | 10.145     | 10.145     | 10.145     |   0.0 | 47.56
-Comm    | 0.49807    | 0.49807    | 0.49807    |   0.0 |  2.33
-Output  | 0.011203   | 0.011203   | 0.011203   |   0.0 |  0.05
-Modify  | 0.28296    | 0.28296    | 0.28296    |   0.0 |  1.33
-Other   |            | 0.295      |            |       |  1.38
+Pair    | 8.0541     | 8.0541     | 8.0541     |   0.0 | 47.13
+Neigh   | 8.1306     | 8.1306     | 8.1306     |   0.0 | 47.58
+Comm    | 0.39415    | 0.39415    | 0.39415    |   0.0 |  2.31
+Output  | 0.01103    | 0.01103    | 0.01103    |   0.0 |  0.06
+Modify  | 0.24061    | 0.24061    | 0.24061    |   0.0 |  1.41
+Other   |            | 0.2576     |            |       |  1.51

 Nlocal:    10125 ave 10125 max 10125 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -170,4 +174,4 @@ Total # of neighbors = 114682
 Ave neighs/atom = 11.3266
 Neighbor list builds = 1000
 Dangerous builds not checked
-Total wall time: 0:00:21
+Total wall time: 0:00:17
--- a/examples/USER/dpd/dpdh-shardlow/in.dpdh-shardlow
+++ b/examples/USER/dpd/dpdh-shardlow/in.dpdh-shardlow
@ -18,7 +18,7 @@ neigh_modify    every 1 delay 0 check no once no
 timestep        0.001

 compute         dpdU all dpd
-variable        totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[1]+press*vol
+variable        totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[2]+press*vol

 thermo          1
 thermo_style    custom step temp press vol pe ke v_totEnergy cella cellb cellc
--- a/examples/USER/dpd/dpdh-shardlow/log.dpdh-shardlow.reference
+++ b/examples/USER/dpd/dpdh-shardlow/log.dpdh-shardlow.reference
@ -22,7 +22,7 @@ neigh_modify    every 1 delay 0 check no once no
 timestep        0.001

 compute         dpdU all dpd
-variable        totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[1]+press*vol
+variable        totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[2]+press*vol

 thermo          1
 thermo_style    custom step temp press vol pe ke v_totEnergy cella cellb cellc
@ -34,129 +34,137 @@ fix             2 all eos/cv 0.0005

 run             100
 Neighbor list info ...
-  1 neighbor list requests
  update every 1 steps, delay 0 steps, check no
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
-  binsize = 6 -> bins = 22 22 22
-Memory usage per processor = 6.48143 Mbytes
+  binsize = 6, bins = 22 22 22
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair dpd/fdt/energy, perpetual
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix shardlow, perpetual, ssa
+      pair build: half/bin/newton/ssa
+      stencil: half/bin/3d/newton/ssa
+      bin: ssa
+Memory usage per processor = 8.55503 Mbytes
 Step Temp Press Volume PotEng KinEng v_totEnergy Cella Cellb Cellc 
-       0  239.4274282976 2817.4421750949 2146689.0000000000 2639.8225470740  313.3218455755 6048176597.3066043854  129.0000000000  129.0000000000  129.0000000000 
-       1  239.4771405316 2817.4798146419 2146689.0000581890 2639.8304543632  313.3869004818 6048257397.9450111389  129.0000000012  129.0000000012  129.0000000012 
-       2  239.5643955010 2817.5423194969 2146689.0002327557 2639.8379071907  313.5010849268 6048391577.0431985855  129.0000000047  129.0000000047  129.0000000047 
-       3  239.6633839196 2817.6123662396 2146689.0005237064 2639.8445238058  313.6306241122 6048541946.5712032318  129.0000000105  129.0000000105  129.0000000105 
-       4  239.5371222027 2817.5355424336 2146689.0009310376 2639.8505035043  313.4653942786 6048377030.7404460907  129.0000000186  129.0000000186  129.0000000186 
-       5  239.6512678169 2817.6153097076 2146689.0014547524 2639.8561498340  313.6147686202 6048548267.9007377625  129.0000000291  129.0000000291  129.0000000291 
-       6  239.5617886781 2817.5624195435 2146689.0020948485 2639.8617493725  313.4976735610 6048434730.8592004776  129.0000000420  129.0000000420  129.0000000420 
-       7  239.5228587856 2817.5420009502 2146689.0028513218 2639.8666590407  313.4467287471 6048390900.5748577118  129.0000000571  129.0000000571  129.0000000571 
-       8  239.6066877934 2817.6008649264 2146689.0037241788 2639.8710757645  313.5564298772 6048517265.7987136841  129.0000000746  129.0000000746  129.0000000746 
-       9  239.5719861485 2817.5823530300 2146689.0047134170 2639.8752557893  313.5110182737 6048477529.2603597641  129.0000000944  129.0000000944  129.0000000944 
-      10  239.5800176776 2817.5915671176 2146689.0058190385 2639.8793778438  313.5215285712 6048497312.1706552505  129.0000001166  129.0000001166  129.0000001166 
-      11  239.6299830954 2817.6281223139 2146689.0070410441 2639.8829762049  313.5869148014 6048575788.3208351135  129.0000001410  129.0000001410  129.0000001410 
-      12  239.6011995911 2817.6132377273 2146689.0083794324 2639.8860704236  313.5492478526 6048543839.4788360596  129.0000001678  129.0000001678  129.0000001678 
-      13  239.6407681166 2817.6427924824 2146689.0098342048 2639.8889816934  313.6010284005 6048607288.5005025864  129.0000001970  129.0000001970  129.0000001970 
-      14  239.6981172055 2817.6844100046 2146689.0114053637 2639.8913405110  313.6760771219 6048696632.8825626373  129.0000002285  129.0000002285  129.0000002285 
-      15  239.8563971968 2817.7922519039 2146689.0130929090 2639.8934358481  313.8832070208 6048928140.8671455383  129.0000002623  129.0000002623  129.0000002623 
-      16  239.8561894618 2817.7971208197 2146689.0148968464 2639.8950496967  313.8829351726 6048938597.9994916916  129.0000002984  129.0000002984  129.0000002984 
-      17  239.8816520361 2817.8185621543 2146689.0168171758 2639.8961257823  313.9162562538 6048984631.3226108551  129.0000003369  129.0000003369  129.0000003369 
-      18  239.9099966096 2817.8417368960 2146689.0188538977 2639.8965743204  313.9533488047 6049034386.0627622604  129.0000003777  129.0000003777  129.0000003777 
-      19  240.0514024347 2817.9389205774 2146689.0210070144 2639.8966103811  314.1383966683 6049243015.4568052292  129.0000004208  129.0000004208  129.0000004208 
-      20  239.8802541140 2817.8327386176 2146689.0232765260 2639.8962085210  313.9144268914 6049015081.9802341461  129.0000004662  129.0000004662  129.0000004662 
-      21  239.8462621903 2817.8160306167 2146689.0256624296 2639.8953174755  313.8699440502 6048979221.7758703232  129.0000005140  129.0000005140  129.0000005140 
-      22  240.0487944678 2817.9533849157 2146689.0281647225 2639.8938590354  314.1349838054 6049274086.0571212769  129.0000005642  129.0000005642  129.0000005642 
-      23  240.0966314441 2817.9897873787 2146689.0307834130 2639.8918104774  314.1975846937 6049352238.2649183273  129.0000006166  129.0000006166  129.0000006166 
-      24  240.1765312516 2818.0463843765 2146689.0335185044 2639.8891292321  314.3021439554 6049473742.2287187576  129.0000006714  129.0000006714  129.0000006714 
-      25  240.1500705973 2818.0336048048 2146689.0363699966 2639.8858785483  314.2675167572 6049446316.4600162506  129.0000007285  129.0000007285  129.0000007285 
-      26  240.2681423500 2818.1151708195 2146689.0393378921 2639.8825176506  314.4220289603 6049621421.8445177078  129.0000007880  129.0000007880  129.0000007880 
-      27  240.4728815247 2818.2527327079 2146689.0424221945 2639.8784158747  314.6899567267 6049916733.3989181519  129.0000008498  129.0000008498  129.0000008498 
-      28  240.4793027032 2818.2613348477 2146689.0456229053 2639.8736089473  314.6983596717 6049935208.5421981812  129.0000009139  129.0000009139  129.0000009139 
-      29  240.5020619198 2818.2805472685 2146689.0489400285 2639.8681043704  314.7281430587 6049976461.0082206726  129.0000009803  129.0000009803  129.0000009803 
-      30  240.5513721776 2818.3167157263 2146689.0523735629 2639.8623484053  314.7926719270 6050054113.1760177612  129.0000010491  129.0000010491  129.0000010491 
-      31  240.7340393104 2818.4391703712 2146689.0559235099 2639.8563442170  315.0317155636 6050316995.4599781036  129.0000011202  129.0000011202  129.0000011202 
-      32  240.8254719483 2818.5014640740 2146689.0595898777 2639.8498122053  315.1513670299 6050450731.1168394089  129.0000011936  129.0000011936  129.0000011936 
-      33  240.9681573541 2818.5965480750 2146689.0633726656 2639.8425779528  315.3380893908 6050654857.7432861328  129.0000012694  129.0000012694  129.0000012694 
-      34  241.0039494187 2818.6217008564 2146689.0672718794 2639.8347174393  315.3849279499 6050708863.9733209610  129.0000013475  129.0000013475  129.0000013475 
-      35  241.0314566197 2818.6411150538 2146689.0712875174 2639.8262983643  315.4209246902 6050750551.5649127960  129.0000014279  129.0000014279  129.0000014279 
-      36  241.0829173424 2818.6763455617 2146689.0754195810 2639.8174397481  315.4882677207 6050826192.2165899277  129.0000015107  129.0000015107  129.0000015107 
-      37  241.2845682012 2818.8087982181 2146689.0796680767 2639.8080129872  315.7521540252 6051110539.1171846390  129.0000015958  129.0000015958  129.0000015958 
-      38  241.3214712920 2818.8336260248 2146689.0840330068 2639.7981963574  315.8004465062 6051163849.0412235260  129.0000016833  129.0000016833  129.0000016833 
-      39  241.3392127125 2818.8456991528 2146689.0885143690 2639.7879618658  315.8236634561 6051189778.9386901855  129.0000017730  129.0000017730  129.0000017730 
-      40  241.5383770555 2818.9753950055 2146689.0931121684 2639.7769824244  316.0842958321 6051468208.8210506439  129.0000018651  129.0000018651  129.0000018651 
-      41  241.5059730674 2818.9543817992 2146689.0978264087 2639.7656512498  316.0418910106 6051423113.2358427048  129.0000019595  129.0000019595  129.0000019595 
-      42  241.3907605672 2818.8793800508 2146689.1026570834 2639.7541331920  315.8911205101 6051262121.2551422119  129.0000020563  129.0000020563  129.0000020563 
-      43  241.5095917610 2818.9559595711 2146689.1076041958 2639.7424355740  316.0466265406 6051426527.7663059235  129.0000021554  129.0000021554  129.0000021554 
-      44  241.6271631762 2819.0312325531 2146689.1126677482 2639.7297705654  316.2004839873 6051588129.8722610474  129.0000022568  129.0000022568  129.0000022568 
-      45  241.5702411838 2818.9923790176 2146689.1178477411 2639.7163554760  316.1259941770 6051504737.9250564575  129.0000023606  129.0000023606  129.0000023606 
-      46  241.7029985068 2819.0771124986 2146689.1231441777 2639.7024246704  316.2997243538 6051686649.4576120377  129.0000024667  129.0000024667  129.0000024667 
-      47  241.7966144965 2819.1357830868 2146689.1285570571 2639.6882106593  316.4222330191 6051812612.3391046524  129.0000025751  129.0000025751  129.0000025751 
-      48  241.8573480255 2819.1726205120 2146689.1340863821 2639.6735287925  316.5017107195 6051891706.4921989441  129.0000026859  129.0000026859  129.0000026859 
-      49  241.9611147338 2819.2374095379 2146689.1397321564 2639.6583357477  316.6375029166 6052030804.4275226593  129.0000027990  129.0000027990  129.0000027990 
-      50  242.1023518806 2819.3259059811 2146689.1454943856 2639.6424863169  316.8223300428 6052220795.1955394745  129.0000029144  129.0000029144  129.0000029144 
-      51  242.1174105473 2819.3319633044 2146689.1513730693 2639.6264141131  316.8420362613 6052233814.9634265900  129.0000030321  129.0000030321  129.0000030321 
-      52  242.2534914901 2819.4164594322 2146689.1573682069 2639.6098392670  317.0201158259 6052415218.9485445023  129.0000031522  129.0000031522  129.0000031522 
-      53  242.3504633236 2819.4754119996 2146689.1634798055 2639.5930076506  317.1470160479 6052541789.1274013519  129.0000032746  129.0000032746  129.0000032746 
-      54  242.2982323323 2819.4368568264 2146689.1697078613 2639.5756353782  317.0786650211 6052459040.6286897659  129.0000033994  129.0000033994  129.0000033994 
-      55  242.3452896272 2819.4623310219 2146689.1760523771 2639.5575918586  317.1402455951 6052513743.7400159836  129.0000035265  129.0000035265  129.0000035265 
-      56  242.4181903333 2819.5048897011 2146689.1825133534 2639.5390347547  317.2356456249 6052605122.2894439697  129.0000036559  129.0000036559  129.0000036559 
-      57  242.5317091656 2819.5739975787 2146689.1890907930 2639.5199828249  317.3841997413 6052753494.0979280472  129.0000037876  129.0000037876  129.0000037876 
-      58  242.5478978740 2819.5796954935 2146689.1957846982 2639.5006137388  317.4053847660 6052765744.6257629395  129.0000039217  129.0000039217  129.0000039217 
-      59  242.6655316466 2819.6519225743 2146689.2025950695 2639.4808234811  317.5593238156 6052920813.0568208694  129.0000040582  129.0000040582  129.0000040582 
-      60  242.8126131177 2819.7431588157 2146689.2095219092 2639.4607996998  317.7517989980 6053116688.6155729294  129.0000041969  129.0000041969  129.0000041969 
-      61  242.7957124913 2819.7275989047 2146689.2165652174 2639.4406312730  317.7296823362 6053083306.1403274536  129.0000043380  129.0000043380  129.0000043380 
-      62  242.9276177041 2819.8088790098 2146689.2237249981 2639.4201279058  317.9022974164 6053257809.6067762375  129.0000044814  129.0000044814  129.0000044814 
-      63  243.0465445938 2819.8814758895 2146689.2310012528 2639.3991657500  318.0579286774 6053413673.1989650726  129.0000046272  129.0000046272  129.0000046272 
-      64  242.9890585501 2819.8387587817 2146689.2383939880 2639.3781767844  317.9827007328 6053321993.5937871933  129.0000047752  129.0000047752  129.0000047752 
-      65  242.9653746583 2819.8180104181 2146689.2459031967 2639.3568184374  317.9517072884 6053277474.4272727966  129.0000049256  129.0000049256  129.0000049256 
-      66  243.0259297024 2819.8514334947 2146689.2535288804 2639.3352568621  318.0309514181 6053349244.9473772049  129.0000050784  129.0000050784  129.0000050784 
-      67  242.9638979697 2819.8046112742 2146689.2612710390 2639.3134547096  317.9497748498 6053248753.9180717468  129.0000052335  129.0000052335  129.0000052335 
-      68  243.0283540775 2819.8395632725 2146689.2691296688 2639.2912303374  318.0341240273 6053323807.2197017670  129.0000053909  129.0000053909  129.0000053909 
-      69  243.2256418664 2819.9609646019 2146689.2771047787 2639.2684509205  318.2923006889 6053584440.8757400513  129.0000055506  129.0000055506  129.0000055506 
-      70  243.2507495334 2819.9706145524 2146689.2851963686 2639.2450126010  318.3251573278 6053605179.1483964920  129.0000057127  129.0000057127  129.0000057127 
-      71  243.4287155518 2820.0794853386 2146689.2934044413 2639.2213699915  318.5580489464 6053838914.2552747726  129.0000058771  129.0000058771  129.0000058771 
-      72  243.5097518574 2820.1249498194 2146689.3017290002 2639.1971212009  318.6640954635 6053936535.9274711609  129.0000060439  129.0000060439  129.0000060439 
-      73  243.5356790969 2820.1337977544 2146689.3101700447 2639.1723394661  318.6980246193 6053955553.5090074539  129.0000062130  129.0000062130  129.0000062130 
-      74  243.5479180498 2820.1331964183 2146689.3187275808 2639.1473868749  318.7140408766 6053954286.7515821457  129.0000063844  129.0000063844  129.0000063844 
-      75  243.7115573025 2820.2314361523 2146689.3274016059 2639.1220411207  318.9281840641 6054165201.5909118652  129.0000065581  129.0000065581  129.0000065581 
-      76  243.7457279618 2820.2454531429 2146689.3361921217 2639.0963868224  318.9729008040 6054195316.5254154205  129.0000067342  129.0000067342  129.0000067342 
-      77  243.8345031069 2820.2948644965 2146689.3450991292 2639.0700900389  319.0890745962 6054301412.5615310669  129.0000069126  129.0000069126  129.0000069126 
-      78  244.0193931195 2820.4067881628 2146689.3541226317 2639.0435094409  319.3310271594 6054541703.5689058304  129.0000070934  129.0000070934  129.0000070934 
-      79  243.9919100078 2820.3799166166 2146689.3632626338 2639.0164249037  319.2950619430 6054484044.4218587875  129.0000072765  129.0000072765  129.0000072765 
-      80  244.0965612207 2820.4387335935 2146689.3725191355 2638.9888176882  319.4320116291 6054610332.4174261093  129.0000074619  129.0000074619  129.0000074619 
-      81  244.1334315951 2820.4535208568 2146689.3818921377 2638.9608330195  319.4802612965 6054642102.5347270966  129.0000076496  129.0000076496  129.0000076496 
-      82  244.3029520408 2820.5543485196 2146689.3913816395 2638.9318525796  319.7021007878 6054858575.1664342880  129.0000078397  129.0000078397  129.0000078397 
-      83  244.3445761189 2820.5713690935 2146689.4009876498 2638.9021684795  319.7565712929 6054895140.1710596085  129.0000080321  129.0000080321  129.0000080321 
-      84  244.2696671559 2820.5125763350 2146689.4107101629 2638.8720941742  319.6585431986 6054768957.6739044189  129.0000082269  129.0000082269  129.0000082269 
-      85  244.5161919319 2820.6629431352 2146689.4205491822 2638.8415194387  319.9811528443 6055091776.5361995697  129.0000084240  129.0000084240  129.0000084240 
-      86  244.5641090282 2820.6838080201 2146689.4305047127 2638.8103612394  320.0438585800 6055136595.0767974854  129.0000086234  129.0000086234  129.0000086234 
-      87  244.5348240638 2820.6541129118 2146689.4405767513 2638.7789728309  320.0055354056 6055072877.2416200638  129.0000088251  129.0000088251  129.0000088251 
-      88  244.6939431427 2820.7468233396 2146689.4507653015 2638.7470269267  320.2137633592 6055271926.6536149979  129.0000090292  129.0000090292  129.0000090292 
-      89  244.8800201091 2820.8567117003 2146689.4610703662 2638.7147520097  320.4572692055 6055507852.1186332703  129.0000092356  129.0000092356  129.0000092356 
-      90  244.8804280382 2820.8451141876 2146689.4714919478 2638.6820441173  320.4578030336 6055482985.2258749008  129.0000094444  129.0000094444  129.0000094444 
-      91  244.9558851986 2820.8815975090 2146689.4820300462 2638.6491836104  320.5565485155 6055561333.3803453445  129.0000096555  129.0000096555  129.0000096555 
-      92  244.9965893140 2820.8949614294 2146689.4926846647 2638.6159817170  320.6098151301 6055590051.6433181763  129.0000098689  129.0000098689  129.0000098689 
-      93  245.1381056687 2820.9732811388 2146689.5034558061 2638.5824451870  320.7950076360 6055758210.2774200439  129.0000100846  129.0000100846  129.0000100846 
-      94  245.2954807041 2821.0619342131 2146689.5143434699 2638.5485198222  321.0009532826 6055948551.7882709503  129.0000103027  129.0000103027  129.0000103027 
-      95  245.3535822199 2821.0860553731 2146689.5253476589 2638.5144817512  321.0769866522 6056000363.5151576996  129.0000105232  129.0000105232  129.0000105232 
-      96  245.5013476026 2821.1682908185 2146689.5364683764 2638.4801107361  321.2703568219 6056176929.0169925690  129.0000107459  129.0000107459  129.0000107459 
-      97  245.4166531417 2821.0989038023 2146689.5477056229 2638.4453663061  321.1595231342 6056028008.1910057068  129.0000109710  129.0000109710  129.0000109710 
-      98  245.4121937790 2821.0817490953 2146689.5590593945 2638.4097762390  321.1536874797 6055991214.3494396210  129.0000111984  129.0000111984  129.0000111984 
-      99  245.4532592994 2821.0946353191 2146689.5705296928 2638.3738037546  321.2074270397 6056018909.4480972290  129.0000114282  129.0000114282  129.0000114282 
-     100  245.7500657390 2821.2735939427 2146689.5821165247 2638.3375549051  321.5958367642 6056403111.1006488800  129.0000116603  129.0000116603  129.0000116603 
-Loop time of 4.05006 on 1 procs for 100 steps with 10125 atoms
+       0  239.4274282976 2817.4421750949 2146689.0000000000 2639.8225470740  313.3218455755 6048176597.3066034317  129.0000000000  129.0000000000  129.0000000000 
+       1  239.4771405316 2817.4798146419 2146689.0000581890 2639.8304543632  313.3869004818 6048257397.8720483780  129.0000000012  129.0000000012  129.0000000012 
+       2  239.5643955010 2817.5423194969 2146689.0002327557 2639.8379071907  313.5010849268 6048391576.8485937119  129.0000000047  129.0000000047  129.0000000047 
+       3  239.6633839196 2817.6123662396 2146689.0005237064 2639.8445238058  313.6306241122 6048541946.2404479980  129.0000000105  129.0000000105  129.0000000105 
+       4  239.5371222027 2817.5355424336 2146689.0009310376 2639.8505035043  313.4653942786 6048377030.5689325333  129.0000000186  129.0000000186  129.0000000186 
+       5  239.6512678169 2817.6153097076 2146689.0014547524 2639.8561498340  313.6147686202 6048548267.5742130280  129.0000000291  129.0000000291  129.0000000291 
+       6  239.5617886781 2817.5624195435 2146689.0020948485 2639.8617493725  313.4976735610 6048434730.6441593170  129.0000000420  129.0000000420  129.0000000420 
+       7  239.5228587856 2817.5420009502 2146689.0028513218 2639.8666590407  313.4467287471 6048390900.4058599472  129.0000000571  129.0000000571  129.0000000571 
+       8  239.6066877934 2817.6008649264 2146689.0037241788 2639.8710757645  313.5564298772 6048517265.5155982971  129.0000000746  129.0000000746  129.0000000746 
+       9  239.5719861485 2817.5823530300 2146689.0047134170 2639.8752557893  313.5110182737 6048477529.0184717178  129.0000000944  129.0000000944  129.0000000944 
+      10  239.5800176776 2817.5915671176 2146689.0058190385 2639.8793778438  313.5215285712 6048497311.9141387939  129.0000001166  129.0000001166  129.0000001166 
+      11  239.6299830954 2817.6281223139 2146689.0070410441 2639.8829762049  313.5869148014 6048575787.9953098297  129.0000001410  129.0000001410  129.0000001410 
+      12  239.6011995911 2817.6132377273 2146689.0083794324 2639.8860704236  313.5492478526 6048543839.1878814697  129.0000001678  129.0000001678  129.0000001678 
+      13  239.6407681166 2817.6427924824 2146689.0098342048 2639.8889816934  313.6010284005 6048607288.1548709869  129.0000001970  129.0000001970  129.0000001970 
+      14  239.6981172055 2817.6844100046 2146689.0114053637 2639.8913405110  313.6760771219 6048696632.4595127106  129.0000002285  129.0000002285  129.0000002285 
+      15  239.8563971968 2817.7922519039 2146689.0130929090 2639.8934358481  313.8832070208 6048928140.2348766327  129.0000002623  129.0000002623  129.0000002623 
+      16  239.8561894618 2817.7971208196 2146689.0148968464 2639.8950496967  313.8829351726 6048938597.3658657074  129.0000002984  129.0000002984  129.0000002984 
+      17  239.8816520361 2817.8185621543 2146689.0168171758 2639.8961257823  313.9162562538 6048984630.6545839310  129.0000003369  129.0000003369  129.0000003369 
+      18  239.9099966096 2817.8417368960 2146689.0188538977 2639.8965743204  313.9533488047 6049034385.3571958542  129.0000003777  129.0000003777  129.0000003777 
+      19  240.0514024347 2817.9389205774 2146689.0210070144 2639.8966103811  314.1383966683 6049243014.5661621094  129.0000004208  129.0000004208  129.0000004208 
+      20  239.8802541140 2817.8327386176 2146689.0232765260 2639.8962085210  313.9144268914 6049015081.3139505386  129.0000004662  129.0000004662  129.0000004662 
+      21  239.8462621903 2817.8160306167 2146689.0256624296 2639.8953174755  313.8699440502 6048979221.1549577713  129.0000005140  129.0000005140  129.0000005140 
+      22  240.0487944678 2817.9533849157 2146689.0281647225 2639.8938590354  314.1349838054 6049274085.1726217270  129.0000005642  129.0000005642  129.0000005642 
+      23  240.0966314441 2817.9897873787 2146689.0307834130 2639.8918104774  314.1975846937 6049352237.3198652267  129.0000006166  129.0000006166  129.0000006166 
+      24  240.1765312516 2818.0463843765 2146689.0335185044 2639.8891292321  314.3021439554 6049473741.1817827225  129.0000006714  129.0000006714  129.0000006714 
+      25  240.1500705973 2818.0336048048 2146689.0363699966 2639.8858785483  314.2675167572 6049446315.4509468079  129.0000007285  129.0000007285  129.0000007285 
+      26  240.2681423500 2818.1151708195 2146689.0393378921 2639.8825176506  314.4220289603 6049621420.6842966080  129.0000007880  129.0000007880  129.0000007880 
+      27  240.4728815247 2818.2527327079 2146689.0424221945 2639.8784158747  314.6899567267 6049916731.9748563766  129.0000008498  129.0000008498  129.0000008498 
+      28  240.4793027032 2818.2613348477 2146689.0456229053 2639.8736089473  314.6983596717 6049935207.1145420074  129.0000009139  129.0000009139  129.0000009139 
+      29  240.5020619198 2818.2805472685 2146689.0489400285 2639.8681043704  314.7281430587 6049976459.5562763214  129.0000009803  129.0000009803  129.0000009803 
+      30  240.5513721776 2818.3167157263 2146689.0523735629 2639.8623484053  314.7926719270 6050054111.6652946472  129.0000010491  129.0000010491  129.0000010491 
+      31  240.7340393104 2818.4391703712 2146689.0559235099 2639.8563442170  315.0317155636 6050316993.7162160873  129.0000011202  129.0000011202  129.0000011202 
+      32  240.8254719483 2818.5014640740 2146689.0595898777 2639.8498122053  315.1513670299 6050450729.2599506378  129.0000011936  129.0000011936  129.0000011936 
+      33  240.9681573541 2818.5965480750 2146689.0633726656 2639.8425779528  315.3380893908 6050654855.7068986893  129.0000012694  129.0000012694  129.0000012694 
+      34  241.0039494187 2818.6217008564 2146689.0672718794 2639.8347174393  315.3849279499 6050708861.8979463577  129.0000013475  129.0000013475  129.0000013475 
+      35  241.0314566197 2818.6411150538 2146689.0712875174 2639.8262983643  315.4209246902 6050750549.4619541168  129.0000014279  129.0000014279  129.0000014279 
+      36  241.0829173424 2818.6763455617 2146689.0754195810 2639.8174397481  315.4882677207 6050826190.0551443100  129.0000015107  129.0000015107  129.0000015107 
+      37  241.2845682012 2818.8087982181 2146689.0796680767 2639.8080129872  315.7521540252 6051110536.7012710571  129.0000015958  129.0000015958  129.0000015958 
+      38  241.3214712920 2818.8336260248 2146689.0840330068 2639.7981963574  315.8004465062 6051163846.5868301392  129.0000016833  129.0000016833  129.0000016833 
+      39  241.3392127125 2818.8456991528 2146689.0885143690 2639.7879618658  315.8236634561 6051189776.4712991714  129.0000017730  129.0000017730  129.0000017730 
+      40  241.5383770555 2818.9753950055 2146689.0931121684 2639.7769824244  316.0842958321 6051468206.1039972305  129.0000018651  129.0000018651  129.0000018651 
+      41  241.5059730674 2818.9543817992 2146689.0978264087 2639.7656512498  316.0418910106 6051423110.5725250244  129.0000019595  129.0000019595  129.0000019595 
+      42  241.3907605672 2818.8793800508 2146689.1026570834 2639.7541331920  315.8911205101 6051262118.7541017532  129.0000020563  129.0000020563  129.0000020563 
+      43  241.5095917610 2818.9559595711 2146689.1076041958 2639.7424355740  316.0466265406 6051426525.1214485168  129.0000021554  129.0000021554  129.0000021554 
+      44  241.6271631762 2819.0312325531 2146689.1126677482 2639.7297705654  316.2004839873 6051588127.0861988068  129.0000022568  129.0000022568  129.0000022568 
+      45  241.5702411838 2818.9923790176 2146689.1178477411 2639.7163554760  316.1259941770 6051504735.2269029617  129.0000023606  129.0000023606  129.0000023606 
+      46  241.7029985068 2819.0771124986 2146689.1231441777 2639.7024246704  316.2997243538 6051686646.5996389389  129.0000024667  129.0000024667  129.0000024667 
+      47  241.7966144965 2819.1357830868 2146689.1285570571 2639.6882106593  316.4222330191 6051812609.3728218079  129.0000025751  129.0000025751  129.0000025751 
+      48  241.8573480255 2819.1726205120 2146689.1340863821 2639.6735287925  316.5017107195 6051891703.4611186981  129.0000026859  129.0000026859  129.0000026859 
+      49  241.9611147338 2819.2374095379 2146689.1397321564 2639.6583357477  316.6375029166 6052030801.2758235931  129.0000027990  129.0000027990  129.0000027990 
+      50  242.1023518806 2819.3259059811 2146689.1454943856 2639.6424863169  316.8223300428 6052220791.8748512268  129.0000029144  129.0000029144  129.0000029144 
+      51  242.1174105473 2819.3319633044 2146689.1513730693 2639.6264141131  316.8420362613 6052233811.6391019821  129.0000030321  129.0000030321  129.0000030321 
+      52  242.2534914901 2819.4164594322 2146689.1573682069 2639.6098392671  317.0201158259 6052415215.4627037048  129.0000031522  129.0000031522  129.0000031522 
+      53  242.3504633236 2819.4754119996 2146689.1634798055 2639.5930076506  317.1470160479 6052541785.5314817429  129.0000032746  129.0000032746  129.0000032746 
+      54  242.2982323323 2819.4368568264 2146689.1697078613 2639.5756353782  317.0786650211 6052459037.1184797287  129.0000033994  129.0000033994  129.0000033994 
+      55  242.3452896272 2819.4623310219 2146689.1760523771 2639.5575918586  317.1402455951 6052513740.1862611771  129.0000035265  129.0000035265  129.0000035265 
+      56  242.4181903333 2819.5048897011 2146689.1825133534 2639.5390347547  317.2356456249 6052605118.6588287354  129.0000036559  129.0000036559  129.0000036559 
+      57  242.5317091656 2819.5739975787 2146689.1890907930 2639.5199828249  317.3841997413 6052753490.3378009796  129.0000037876  129.0000037876  129.0000037876 
+      58  242.5478978740 2819.5796954935 2146689.1957846982 2639.5006137388  317.4053847660 6052765740.8638200760  129.0000039217  129.0000039217  129.0000039217 
+      59  242.6655316466 2819.6519225743 2146689.2025950695 2639.4808234811  317.5593238156 6052920809.1607065201  129.0000040582  129.0000040582  129.0000040582 
+      60  242.8126131177 2819.7431588157 2146689.2095219092 2639.4607996998  317.7517989980 6053116684.5470046997  129.0000041969  129.0000041969  129.0000041969 
+      61  242.7957124913 2819.7275989047 2146689.2165652174 2639.4406312730  317.7296823362 6053083302.1140241623  129.0000043380  129.0000043380  129.0000043380 
+      62  242.9276177041 2819.8088790098 2146689.2237249981 2639.4201279058  317.9022974164 6053257805.4283437729  129.0000044814  129.0000044814  129.0000044814 
+      63  243.0465445938 2819.8814758895 2146689.2310012528 2639.3991657500  318.0579286774 6053413668.8858547211  129.0000046272  129.0000046272  129.0000046272 
+      64  242.9890585501 2819.8387587817 2146689.2383939880 2639.3781767844  317.9827007328 6053321989.3768787384  129.0000047752  129.0000047752  129.0000047752 
+      65  242.9653746583 2819.8180104181 2146689.2459031967 2639.3568184374  317.9517072884 6053277470.2627182007  129.0000049256  129.0000049256  129.0000049256 
+      66  243.0259297024 2819.8514334947 2146689.2535288804 2639.3352568621  318.0309514181 6053349240.7251205444  129.0000050784  129.0000050784  129.0000050784 
+      67  242.9638979697 2819.8046112742 2146689.2612710390 2639.3134547096  317.9497748498 6053248749.7987766266  129.0000052335  129.0000052335  129.0000052335 
+      68  243.0283540775 2819.8395632725 2146689.2691296688 2639.2912303374  318.0341240273 6053323803.0382738113  129.0000053909  129.0000053909  129.0000053909 
+      69  243.2256418664 2819.9609646019 2146689.2771047787 2639.2684509205  318.2923006889 6053584436.4588871002  129.0000055506  129.0000055506  129.0000055506 
+      70  243.2507495334 2819.9706145524 2146689.2851963686 2639.2450126010  318.3251573278 6053605174.7221174240  129.0000057127  129.0000057127  129.0000057127 
+      71  243.4287155518 2820.0794853386 2146689.2934044413 2639.2213699915  318.5580489464 6053838909.6197280884  129.0000058771  129.0000058771  129.0000058771 
+      72  243.5097518574 2820.1249498194 2146689.3017290002 2639.1971212009  318.6640954635 6053936531.2101163864  129.0000060439  129.0000060439  129.0000060439 
+      73  243.5356790969 2820.1337977544 2146689.3101700447 2639.1723394661  318.6980246193 6053955548.7824945450  129.0000062130  129.0000062130  129.0000062130 
+      74  243.5479180498 2820.1331964183 2146689.3187275808 2639.1473868749  318.7140408766 6053954282.0339813232  129.0000063844  129.0000063844  129.0000063844 
+      75  243.7115573025 2820.2314361523 2146689.3274016059 2639.1220411207  318.9281840641 6054165196.6845111847  129.0000065581  129.0000065581  129.0000065581 
+      76  243.7457279618 2820.2454531429 2146689.3361921217 2639.0963868224  318.9729008040 6054195311.5999307632  129.0000067342  129.0000067342  129.0000067342 
+      77  243.8345031069 2820.2948644965 2146689.3450991292 2639.0700900389  319.0890745962 6054301407.5461502075  129.0000069126  129.0000069126  129.0000069126 
+      78  244.0193931195 2820.4067881628 2146689.3541226317 2639.0435094409  319.3310271594 6054541698.3381366730  129.0000070934  129.0000070934  129.0000070934 
+      79  243.9919100078 2820.3799166166 2146689.3632626338 2639.0164249037  319.2950619430 6054484039.2541246414  129.0000072765  129.0000072765  129.0000072765 
+      80  244.0965612207 2820.4387335935 2146689.3725191355 2638.9888176882  319.4320116291 6054610327.1403293610  129.0000074619  129.0000074619  129.0000074619 
+      81  244.1334315951 2820.4535208568 2146689.3818921377 2638.9608330195  319.4802612965 6054642097.2373485565  129.0000076496  129.0000076496  129.0000076496 
+      82  244.3029520408 2820.5543485196 2146689.3913816395 2638.9318525796  319.7021007878 6054858569.6761827469  129.0000078397  129.0000078397  129.0000078397 
+      83  244.3445761189 2820.5713690935 2146689.4009876498 2638.9021684795  319.7565712929 6054895134.6560049057  129.0000080321  129.0000080321  129.0000080321 
+      84  244.2696671559 2820.5125763350 2146689.4107101629 2638.8720941742  319.6585431986 6054768952.2869329453  129.0000082269  129.0000082269  129.0000082269 
+      85  244.5161919319 2820.6629431352 2146689.4205491822 2638.8415194387  319.9811528443 6055091770.8571672440  129.0000084240  129.0000084240  129.0000084240 
+      86  244.5641090282 2820.6838080201 2146689.4305047127 2638.8103612394  320.0438585800 6055136589.3662166595  129.0000086234  129.0000086234  129.0000086234 
+      87  244.5348240638 2820.6541129118 2146689.4405767513 2638.7789728309  320.0055354056 6055072871.6007261276  129.0000088251  129.0000088251  129.0000088251 
+      88  244.6939431427 2820.7468233396 2146689.4507653015 2638.7470269267  320.2137633592 6055271920.8364210129  129.0000090292  129.0000090292  129.0000090292 
+      89  244.8800201091 2820.8567117003 2146689.4610703662 2638.7147520097  320.4572692055 6055507846.0901927948  129.0000092356  129.0000092356  129.0000092356 
+      90  244.8804280382 2820.8451141876 2146689.4714919478 2638.6820441173  320.4578030336 6055482979.2295818329  129.0000094444  129.0000094444  129.0000094444 
+      91  244.9558851986 2820.8815975090 2146689.4820300462 2638.6491836104  320.5565485155 6055561327.3181543350  129.0000096555  129.0000096555  129.0000096555 
+      92  244.9965893140 2820.8949614294 2146689.4926846647 2638.6159817170  320.6098151301 6055590045.5610351562  129.0000098689  129.0000098689  129.0000098689 
+      93  245.1381056687 2820.9732811388 2146689.5034558061 2638.5824451870  320.7950076360 6055758204.0434722900  129.0000100846  129.0000100846  129.0000100846 
+      94  245.2954807041 2821.0619342131 2146689.5143434699 2638.5485198222  321.0009532826 6055948545.3822879791  129.0000103027  129.0000103027  129.0000103027 
+      95  245.3535822199 2821.0860553731 2146689.5253476589 2638.5144817512  321.0769866522 6056000357.0671482086  129.0000105232  129.0000105232  129.0000105232 
+      96  245.5013476026 2821.1682908185 2146689.5364683764 2638.4801107361  321.2703568219 6056176922.4099712372  129.0000107459  129.0000107459  129.0000107459 
+      97  245.4166531417 2821.0989038023 2146689.5477056229 2638.4453663061  321.1595231342 6056028001.7295455933  129.0000109710  129.0000109710  129.0000109710 
+      98  245.4121937790 2821.0817490953 2146689.5590593945 2638.4097762390  321.1536874797 6055991207.9293851852  129.0000111984  129.0000111984  129.0000111984 
+      99  245.4532592994 2821.0946353191 2146689.5705296928 2638.3738037546  321.2074270397 6056018903.0102539062  129.0000114282  129.0000114282  129.0000114282 
+     100  245.7500657390 2821.2735939427 2146689.5821165247 2638.3375549051  321.5958367642 6056403104.3106222153  129.0000116603  129.0000116603  129.0000116603 
+Loop time of 5.22601 on 1 procs for 100 steps with 10125 atoms

-Performance: 2.133 ns/day, 11.250 hours/ns, 24.691 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 1.653 ns/day, 14.517 hours/ns, 19.135 timesteps/s
+99.7% CPU use with 1 MPI tasks x no OpenMP threads

 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.46587    | 0.46587    | 0.46587    |   0.0 | 11.50
-Neigh   | 1.4713     | 1.4713     | 1.4713     |   0.0 | 36.33
-Comm    | 0.05567    | 0.05567    | 0.05567    |   0.0 |  1.37
-Output  | 0.011364   | 0.011364   | 0.011364   |   0.0 |  0.28
-Modify  | 2.0158     | 2.0158     | 2.0158     |   0.0 | 49.77
-Other   |            | 0.03004    |            |       |  0.74
+Pair    | 0.44045    | 0.44045    | 0.44045    |   0.0 |  8.43
+Neigh   | 2.669      | 2.669      | 2.669      |   0.0 | 51.07
+Comm    | 0.056143   | 0.056143   | 0.056143   |   0.0 |  1.07
+Output  | 0.012469   | 0.012469   | 0.012469   |   0.0 |  0.24
+Modify  | 2.0163     | 2.0163     | 2.0163     |   0.0 | 38.58
+Other   |            | 0.03168    |            |       |  0.61

 Nlocal:    10125 ave 10125 max 10125 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -172,4 +180,4 @@ Dangerous builds not checked

 Please see the log.cite file for references relevant to this simulation

-Total wall time: 0:00:04
+Total wall time: 0:00:05
--- a/examples/USER/dpd/dpdrx-shardlow/in.dpdrx-shardlow
+++ b/examples/USER/dpd/dpdrx-shardlow/in.dpdrx-shardlow
@ -37,7 +37,7 @@ timestep        0.001

 pair_style      hybrid/overlay dpd/fdt/energy 16.00 234324 exp6/rx 16.00
 pair_coeff      * * dpd/fdt/energy 0.0 0.05 10.0 16.00
-pair_coeff      * * exp6/rx params.exp6 1fluid 1fluid 1.0 1.0 16.00
+pair_coeff      * * exp6/rx params.exp6 1fluid 1fluid exponent 1.0 1.0 16.00

 fix             1 all shardlow
 fix             2 all nve
--- a/Show More
+++ b/Show More