patch 6Jan17

enable pppm/tip4p to work with triclinic
Merge pull request #324 from ibaned/pair-table-kokkos-inherit
2017-01-06 11:14:48 -07:00 · 2017-01-06 10:38:32 -07:00 · 2017-01-06 10:10:59 -07:00 · 2017-01-06 10:10:09 -07:00 · 2017-01-06 10:03:32 -07:00 · 2017-01-06 10:03:05 -07:00
976 changed files with 64428 additions and 21263 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_new_pull_request.png
+++ b/doc/src/JPG/tutorial_new_pull_request.png
--- a/doc/src/JPG/tutorial_reverse_pull_request.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request.png
--- a/doc/src/JPG/tutorial_reverse_pull_request2.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request2.png
--- a/doc/src/JPG/tutorial_reverse_pull_request3.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request3.png
--- a/doc/src/JPG/tutorial_reverse_pull_request4.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request4.png
--- a/doc/src/JPG/tutorial_reverse_pull_request5.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request5.png
--- a/doc/src/JPG/tutorial_reverse_pull_request6.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request6.png
--- a/doc/src/JPG/tutorial_steve_assignee.png
+++ b/doc/src/JPG/tutorial_steve_assignee.png
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="17 Nov 2016 version">
+<META NAME="docnumber" CONTENT="6 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
+6 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

@ -580,7 +581,7 @@ 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,
 "msst"_fix_msst.html,
 "neb"_fix_neb.html,
@ -632,10 +633,10 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "rigid/nve (o)"_fix_rigid.html,
 "rigid/nvt (o)"_fix_rigid.html,
 "rigid/small (o)"_fix_rigid.html,
-"rigid/small/nph"_fix_rigid.html,
-"rigid/small/npt"_fix_rigid.html,
-"rigid/small/nve"_fix_rigid.html,
-"rigid/small/nvt"_fix_rigid.html,
+"rigid/small/nph (o)"_fix_rigid.html,
+"rigid/small/npt (o)"_fix_rigid.html,
+"rigid/small/nve (o)"_fix_rigid.html,
+"rigid/small/nvt (o)"_fix_rigid.html,
 "setforce (k)"_fix_setforce.html,
 "shake"_fix_shake.html,
 "spring"_fix_spring.html,
@ -687,6 +688,7 @@ package"_Section_start.html#start_3.
 "eos/table/rx"_fix_eos_table_rx.html,
 "flow/gauss"_fix_flow_gauss.html,
 "gle"_fix_gle.html,
+"grem"_fix_grem.html,
 "imd"_fix_imd.html,
 "ipi"_fix_ipi.html,
 "langevin/drude"_fix_langevin_drude.html,
@ -700,6 +702,7 @@ 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 +768,7 @@ 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,
@ -911,8 +915,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "coul/msm"_pair_coul.html,
 "coul/streitz"_pair_coul.html,
 "coul/wolf (ko)"_pair_coul.html,
-"dpd (o)"_pair_dpd.html,
-"dpd/tstat (o)"_pair_dpd.html,
+"dpd (go)"_pair_dpd.html,
+"dpd/tstat (go)"_pair_dpd.html,
 "dsmc"_pair_dsmc.html,
 "eam (gkot)"_pair_eam.html,
 "eam/alloy (gkot)"_pair_eam.html,
--- 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_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/compute_bond_local.txt
+++ b/doc/src/compute_bond_local.txt
@ -51,12 +51,12 @@ relative to the center of mass (COM) velocity of the 2 atoms in the
 bond.

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

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

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

--- a/doc/src/compute_chunk_atom.txt
+++ b/doc/src/compute_chunk_atom.txt
@ -641,7 +641,8 @@ the restarted simulation begins.

 [Related commands:]

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

 [Default:]

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

 NOTE: If you have a bonded system, then the settings of
 "special_bonds"_special_bonds.html command can remove pairwise
--- a/doc/src/compute_global_atom.txt
+++ b/doc/src/compute_global_atom.txt
@ -0,0 +1,220 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute global/atom command :h3
+
+[Syntax:]
+
+compute ID group-ID style index input1 input2 ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
+global/atom = style name of this compute command :l
+index = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l
+  c_ID = per-atom vector calculated by a compute with ID
+  c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID
+  f_ID = per-atom vector calculated by a fix with ID
+  f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID
+  v_name = per-atom vector calculated by an atom-style variable with name :pre
+one or more inputs can be listed :l
+input = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l
+  c_ID = global vector calculated by a compute with ID
+  c_ID\[I\] = Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
+  f_ID = global vector calculated by a fix with ID
+  f_ID\[I\] = Ith column of global array calculated by a fix with ID, I can include wildcard (see below)
+  v_name = global vector calculated by a vector-style variable with name :pre
+:ule
+
+[Examples:]
+
+compute 1 all global/atom c_chunk c_com\[1\\] c_com\[2\\] c_com\[3\\]
+compute 1 all global/atom c_chunk c_com\[*\\] :pre
+
+[Description:]
+
+Define a calculation that assigns global values to each atom from
+vectors or arrays of global values.  The specified {index} parameter
+is used to determine which global value is assigned to each atom.
+
+The {index} parameter must reference a per-atom vector or array from a
+"compute"_compute.html or "fix"_fix.html or the evaluation of an
+atom-style "variable"_variable.html.  Each {input} value must
+reference a global vector or array from a "compute"_compute.html or
+"fix"_fix.html or the evaluation of an vector-style
+"variable"_variable.html.  Details are given below.
+
+The {index} value for an atom is used as a index I (from 1 to N) into
+the vector associated with each of the input values.  The Ith value
+from the input vector becomes one output value for that atom.  If the
+atom is not in the specified group, or the index I < 1 or I > M, where
+M is the actual length of the input vector, then an output value of
+0.0 is assigned to the atom.
+
+An example of how this command is useful, is in the context of
+"chunks" which are static or dyanmic subsets of atoms.  The "compute
+chunk/atom"_compute_chunk_atom.html command assigns unique chunk IDs
+to each atom.  It's output can be used as the {index} parameter for
+this command.  Various other computes with "chunk" in their style
+name, such as "compute com/chunk"_compute_com_chunk.html or "compute
+msd/chunk"_compute_msd_chunk.html, calculate properties for each
+chunk.  The output of these commands are global vectors or arrays,
+with one or more values per chunk, and can be used as input values for
+this command.  This command will then assign the global chunk value to
+each atom in the chunk, producing a per-atom vector or per-atom array
+as output.  The per-atom values can then be output to a dump file or
+used by any command that uses per-atom values from a compute as input,
+as discussed in "Section 6.15"_Section_howto.html#howto_15.
+
+As a concrete example, these commands will calculate the displacement
+of each atom from the center-of-mass of the molecule it is in, and
+dump those values to a dump file.  In this case, each molecule is a
+chunk.
+
+compute cc1 all chunk/atom molecule
+compute myChunk all com/chunk cc1
+compute prop all property/atom xu yu zu
+compute glob all global/atom c_cc1 c_myChunk\[*\]
+variable dx atom c_prop\[1\]-c_glob\[1\]
+variable dy atom c_prop\[2\]-c_glob\[2\]
+variable dz atom c_prop\[3\]-c_glob\[3\]
+variable dist atom sqrt(v_dx*v_dx+v_dy*v_dy+v_dz*v_dz)
+dump 1 all custom 100 tmp.dump id xu yu zu c_glob\[1\] c_glob\[2\] c_glob\[3\] &
+     v_dx v_dy v_dz v_dist
+dump_modify 1 sort id :pre
+
+You can add these commands to the bench/in.chain script to see how
+they work.
+
+:line
+
+Note that for input values from a compute or fix, the bracketed index
+I can be specified using a wildcard asterisk with the index to
+effectively specify multiple values.  This takes the form "*" or "*n"
+or "n*" or "m*n".  If N = the size of the vector (for {mode} = scalar)
+or the number of columns in the array (for {mode} = vector), then an
+asterisk with no numeric values means all indices from 1 to N.  A
+leading asterisk means all indices from 1 to n (inclusive).  A
+trailing asterisk means all indices from n to N (inclusive).  A middle
+asterisk means all indices from m to n (inclusive).
+
+Using a wildcard is the same as if the individual columns of the array
+had been listed one by one.  E.g. these 2 compute global/atom commands
+are equivalent, since the "compute com/chunk"_compute_com_chunk.html
+command creates a global array with 3 columns:
+
+compute cc1 all chunk/atom molecule
+compute com all com/chunk cc1
+compute 1 all global/atom c_cc1 c_com\[1\] c_com\[2\] c_com\[3\]
+compute 1 all global/atom c_cc1 c_com\[*\] :pre
+
+:line
+
+This section explains the {index} parameter.  Note that it must
+reference per-atom values, as contrasted with the {input} values which
+must reference global values.
+
+Note that all of these options generate floating point values.  When
+they are used as an index into the specified input vectors, they
+simple rounded down to convert the value to integer indices.  The
+final values should range from 1 to N (inclusive), since they are used
+to access values from N-length vectors.
+
+If {index} begins with "c_", a compute ID must follow which has been
+previously defined in the input script.  The compute must generate
+per-atom quantities.  See the individual "compute"_compute.html doc
+page for details.  If no bracketed integer is appended, the per-atom
+vector calculated by the compute is used.  If a bracketed integer is
+appended, the Ith column of the per-atom array calculated by the
+compute is used.  Users can also write code for their own compute
+styles and "add them to LAMMPS"_Section_modify.html.  See the
+discussion above for how I can be specified with a wildcard asterisk
+to effectively specify multiple values.
+
+If {index} begins with "f_", a fix ID must follow which has been
+previously defined in the input script.  The Fix must generate
+per-atom quantities.  See the individual "fix"_fix.html doc page for
+details.  Note that some fixes only produce their values on certain
+timesteps, which must be compatible with when compute global/atom
+references the values, else an error results.  If no bracketed integer
+is appended, the per-atom vector calculated by the fix is used.  If a
+bracketed integer is appended, the Ith column of the per-atom array
+calculated by the fix is used.  Users can also write code for their
+own fix style and "add them to LAMMPS"_Section_modify.html.  See the
+discussion above for how I can be specified with a wildcard asterisk
+to effectively specify multiple values.
+
+If {index} begins with "v_", a variable name must follow which has
+been previously defined in the input script.  It must be an
+"atom-style variable"_variable.html.  Atom-style variables can
+reference thermodynamic keywords and various per-atom attributes, or
+invoke other computes, fixes, or variables when they are evaluated, so
+this is a very general means of generating per-atom quantities to use
+as {index}.
+
+:line
+
+This section explains the kinds of {input} values that can be used.
+Note that inputs reference global values, as contrasted with the
+{index} parameter which must reference per-atom values.
+
+If a value begins with "c_", a compute ID must follow which has been
+previously defined in the input script.  The compute must generate a
+global vector or array.  See the individual "compute"_compute.html doc
+page for details.  If no bracketed integer is appended, the vector
+calculated by the compute is used.  If a bracketed integer is
+appended, the Ith column of the array calculated by the compute is
+used.  Users can also write code for their own compute styles and "add
+them to LAMMPS"_Section_modify.html.  See the discussion above for how
+I can be specified with a wildcard asterisk to effectively specify
+multiple values.
+
+If a value begins with "f_", a fix ID must follow which has been
+previously defined in the input script.  The fix must generate a
+global vector or array.  See the individual "fix"_fix.html doc page
+for details.  Note that some fixes only produce their values on
+certain timesteps, which must be compatible with when compute
+global/atom references the values, else an error results.  If no
+bracketed integer is appended, the vector calculated by the fix is
+used.  If a bracketed integer is appended, the Ith column of the array
+calculated by the fix is used.  Users can also write code for their
+own fix style and "add them to LAMMPS"_Section_modify.html.  See the
+discussion above for how I can be specified with a wildcard asterisk
+to effectively specify multiple values.
+
+If a value begins with "v_", a variable name must follow which has
+been previously defined in the input script.  It must be a
+"vector-style variable"_variable.html.  Vector-style variables can
+reference thermodynamic keywords and various other attributes of
+atoms, or invoke other computes, fixes, or variables when they are
+evaluated, so this is a very general means of generating a vector of
+global quantities which the {index} parameter will reference for
+assignement of global values to atoms.
+
+:line
+
+[Output info:]
+
+If a single input is specified this compute produces a per-atom
+vector.  If multiple inputs are specified, this compute produces a
+per-atom array values, where the number of columns is equal to the
+number of inputs specified.  These values can be used by any command
+that uses per-atom vector or array values from a compute as input.
+See "Section 6.15"_Section_howto.html#howto_15 for an overview of
+LAMMPS output options.
+
+The per-atom vector or array values will be in whatever units the
+corresponsing input values are in.
+
+[Restrictions:] none
+
+[Related commands:]
+
+"compute"_compute.html, "fix"_fix.html, "variable"_variable.html,
+"compute chunk/atom"_compute_chunk_atom.html, "compute
+reduce"_compute_reduce.html
+
+[Default:] none
--- a/doc/src/compute_smd_contact_radius.txt
+++ b/doc/src/compute_smd_contact_radius.txt
@ -27,7 +27,7 @@ contact radius is used only to prevent particles belonging to
 different physical bodies from penetrating each other. It is used by
 the contact pair styles, e.g., smd/hertz and smd/tri_surface.

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

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

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

 [Output Info:]

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

 Define a computation that outputs the Cauchy stress tensor.

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

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

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

 [Output info:]
--- a/doc/src/fix_colvars.txt
+++ b/doc/src/fix_colvars.txt
@ -31,21 +31,19 @@ fix abf all colvars colvars.inp tstat 1 :pre

 [Description:]

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

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

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

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

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

 [Syntax:]

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

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

 [Examples:]

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

 [Description:]

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

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

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

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

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

 [Restrictions:]
--- a/doc/src/fix_gcmc.txt
+++ b/doc/src/fix_gcmc.txt
@ -21,7 +21,7 @@ type = atom type for inserted atoms (must be 0 if mol keyword used) :l
 seed = random # seed (positive integer) :l
 T = temperature of the ideal gas reservoir (temperature units) :l
 mu = chemical potential of the ideal gas reservoir (energy units) :l
-translate = maximum Monte Carlo translation distance (length units) :l
+displace = maximum Monte Carlo translation distance (length units) :l
 zero or more keyword/value pairs may be appended to args :l
 keyword = {mol}, {region}, {maxangle}, {pressure}, {fugacity_coeff}, {full_energy}, {charge}, {group}, {grouptype}, {intra_energy}, or {tfac_insert}
  {mol} value = template-ID
--- a/doc/src/fix_grem.txt
+++ b/doc/src/fix_grem.txt
@ -0,0 +1,111 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix grem command :h3
+
+[Syntax:]
+
+fix ID group-ID grem lambda eta H0 thermostat-ID :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+grem = style name of this fix command :l
+lambda = intercept parameter of linear effective temperature function :l
+eta = slope parameter of linear effective temperature function :l
+H0 = shift parameter of linear effective temperature function :l
+thermostat-ID = ID of Nose-Hoover thermostat or barostat used in simulation :l,ule
+
+[Examples:]
+
+fix             fxgREM all grem 400 -0.01 -30000 fxnpt
+thermo_modify   press fxgREM_press :pre
+
+fix             fxgREM all grem 502 -0.15 -80000 fxnvt :pre
+
+[Description:]
+
+This fix implements the molecular dynamics version of the generalized
+replica exchange method (gREM) originally developed by "(Kim)"_#Kim,
+which uses non-Boltzmann ensembles to sample over first order phase
+transitions. The is done by defining replicas with an enthalpy
+dependent effective temperature
+
+:c,image(Eqs/fix_grem.jpg)
+
+with {eta} negative and steep enough to only intersect the
+characteristic microcanonical temperature (Ts) of the system once,
+ensuring a unimodal enthalpy distribution in that replica. {Lambda} is
+the intercept and effects the generalized ensemble similar to how
+temperature effects a Boltzmann ensemble. {H0} is a reference
+enthalpy, and is typically set as the lowest desired sampled enthalpy.
+Further explanation can be found in our recent papers
+"(Malolepsza)"_#Malolepsza.
+
+This fix requires a Nose-Hoover thermostat fix reference passed to the
+grem as {thermostat-ID}. Two distinct temperatures exist in this
+generalized ensemble, the effective temperature defined above, and a
+kinetic temperature that controls the velocity distribution of
+particles as usual. Either constant volume or constant pressure
+algorithms can be used.
+
+The fix enforces a generalized ensemble in a single replica
+only. Typically, this ideaology is combined with replica exchange with
+replicas differing by {lambda} only for simplicity, but this is not
+required. A multi-replica simulation can be run within the LAMMPS
+environment using the "temper/grem"_temper_grem.html command. This
+utilizes LAMMPS partition mode and requires the number of available
+processors be on the order of the number of desired replicas. A
+100-replica simulation would require at least 100 processors (1 per
+world at minimum). If a many replicas are needed on a small number of
+processors, multi-replica runs can be run outside of LAMMPS.  An
+example of this can be found in examples/USER/misc/grem and has no
+limit on the number of replicas per processor. However, this is very
+inefficient and error prone and should be avoided if possible.
+
+In general, defining the generalized ensembles is unique for every
+system. When starting a many-replica simulation without any knowledge
+of the underlying microcanonical temperature, there are several tricks
+we have utilized to optimize the process.  Choosing a less-steep {eta}
+yields broader distributions, requiring fewer replicas to map the
+microcanonical temperature.  While this likely struggles from the same
+sampling problems gREM was built to avoid, it provides quick insight
+to Ts.  Initially using an evenly-spaced {lambda} distribution
+identifies regions where small changes in enthalpy lead to large
+temperature changes. Replicas are easily added where needed.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.
+
+The "thermo_modify"_thermo_modify.html {press} option is supported
+by this fix to add the rescaled kinetic pressure as part of 
+"thermodynamic output"_thermo_style.html.
+
+[Restrictions:]
+
+This fix is part of the USER-MISC package. It is only enabled if 
+LAMMPS was built with that package. See the "Making 
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"temper/grem"_temper_grem.html, "fix nvt"_fix_nh.html, "fix
+npt"_fix_nh.html, "thermo_modify"_thermo_modify.html
+
+[Default:] none
+
+:line
+
+:link(Kim)
+[(Kim)] Kim, Keyes, Straub, J Chem. Phys, 132, 224107 (2010).
+
+:link(Malolepsza)
+[(Malolepsza)] Malolepsza, Secor, Keyes, J Phys Chem B 119 (42),
+13379-13384 (2015).
--- a/doc/src/fix_ipi.txt
+++ b/doc/src/fix_ipi.txt
@ -10,18 +10,19 @@ fix ipi command :h3

 [Syntax:]

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

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

 [Examples:]

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

 [Description:]

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

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

 There is no restart information associated with this fix, since all
--- a/doc/src/fix_momentum.txt
+++ b/doc/src/fix_momentum.txt
@ -7,6 +7,7 @@
 :line

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

 [Syntax:]

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

+:line
+
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in "Section 5"_Section_accelerate.html
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See "Section 5"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
 [Restart, fix_modify, output, run start/stop, minimize info:]

 No information about this fix is written to "binary restart
--- a/doc/src/fix_nvk.txt
+++ b/doc/src/fix_nvk.txt
@ -0,0 +1,71 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix nvk command :h3
+
+[Syntax:]
+
+fix ID group-ID nvk :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+nvk = style name of this fix command :ul
+
+[Examples:]
+
+fix 1 all nvk :pre
+
+[Description:]
+
+Perform constant kinetic energy integration using the Gaussian
+thermostat to update position and velocity for atoms in the group each
+timestep.  V is volume; K is kinetic energy. This creates a system
+trajectory consistent with the isokinetic ensemble.
+
+The equations of motion used are those of Minary et al in
+"(Minary)"_#nvk-Minary, a variant of those initially given by Zhang in 
+"(Zhang)"_#nvk-Zhang.
+
+The kinetic energy will be held constant at its value given when fix
+nvk is initiated. If a different kinetic energy is desired, the
+"velocity"_velocity.html command should be used to change the kinetic
+energy prior to this fix.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various "output
+commands"_Section_howto.html#howto_15.  No parameter of this fix can
+be used with the {start/stop} keywords of the "run"_run.html command.
+This fix is not invoked during "energy minimization"_minimize.html.
+
+[Restrictions:]
+
+The Gaussian thermostat only works when it is applied to all atoms in
+the simulation box. Therefore, the group must be set to all.
+
+This fix has not yet been implemented to work with the RESPA integrator.
+
+This fix is part of the USER-MISC package.  It is only enabled if LAMMPS
+was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:] none
+
+[Default:] none
+
+:line
+
+:link(nvk-Minary)
+[(Minary)] Minary, Martyna, and Tuckerman, J Chem Phys, 18, 2510 (2003).
+
+:link(nvk-Zhang)
+[(Zhang)] Zhang, J Chem Phys, 106, 6102 (1997).
--- a/doc/src/fix_smd_adjust_dt.txt
+++ b/doc/src/fix_smd_adjust_dt.txt
@ -36,7 +36,7 @@ stable maximum time step.
 This fix inquires the minimum stable time increment across all particles contained in the group for which this
 fix is defined. An additional safety factor {s_fact} is applied to the time increment.

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

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

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

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

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

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

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

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

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

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

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

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

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

--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@ -48,6 +48,7 @@ Fixes :h1
   fix_gld
   fix_gle
   fix_gravity
+   fix_grem
   fix_halt
   fix_heat
   fix_imd
@ -89,6 +90,7 @@ 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
@ -172,6 +172,7 @@ fix_gcmc.html
 fix_gld.html
 fix_gle.html
 fix_gravity.html
+fix_grem.html
 fix_halt.html
 fix_heat.html
 fix_imd.html
@ -213,6 +214,7 @@ 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 +312,7 @@ 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_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/temper_grem.txt
+++ b/doc/src/temper_grem.txt
@ -0,0 +1,109 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+temper/grem command :h3
+
+[Syntax:]
+
+temper/grem N M lambda fix-ID thermostat-ID seed1 seed2 index :pre
+
+N = total # of timesteps to run
+M = attempt a tempering swap every this many steps
+lambda = initial lambda for this ensemble
+fix-ID = ID of fix_grem
+thermostat-ID = ID of the thermostat that controls kinetic temperature
+seed1 = random # seed used to decide on adjacent temperature to partner with
+seed2 = random # seed for Boltzmann factor in Metropolis swap
+index = which temperature (0 to N-1) I am simulating (optional) :ul
+
+[Examples:]
+
+temper/grem 100000 1000 ${lambda} fxgREM fxnvt 0 58728
+temper/grem 40000 100 ${lambda} fxgREM fxnpt 0 32285 ${walkers} :pre
+
+[Description:]
+
+Run a parallel tempering or replica exchange simulation in LAMMPS
+partition mode using multiple generalized replicas (ensembles) of a
+system defined by "fix grem"_fix_grem.html, which stands for the
+generalized replica exchange method (gREM) originally developed by
+"(Kim)"_#Kim.  It uses non-Boltzmann ensembles to sample over first
+order phase transitions. The is done by defining replicas with an
+enthalpy dependent effective temperature
+
+Two or more replicas must be used.  See the "temper"_temper.html
+command for an explanation of how to run replicas on multiple
+partitions of one or more processors.
+
+This command is a modification of the "temper"_temper.html command and
+has the same dependencies, restraints, and input variables which are
+discussed there in greater detail.
+
+Instead of temperature, this command performs replica exchanges in
+lambda as per the generalized ensemble enforced by "fix
+grem"_fix_grem.html.  The desired lambda is specified by {lambda},
+which is typically a variable previously set in the input script, so
+that each partition is assigned a different temperature.  See the
+"variable"_variable.html command for more details.  For example:
+
+variable lambda world 400 420 440 460
+fix fxnvt all nvt temp 300.0 300.0 100.0
+fix fxgREM all grem ${lambda} -0.05 -50000 fxnvt
+temper 100000 100 ${lambda} fxgREM fxnvt 3847 58382 :pre
+
+would define 4 lambdas with constant kinetic temperature but unique
+generalized temperature, and assign one of them to "fix
+grem"_fix_grem.html used by each replica, and to the grem command.
+
+As the gREM simulation runs for {N} timesteps, a swap between adjacent
+ensembles will be attempted every {M} timesteps.  If {seed1} is 0,
+then the swap attempts will alternate between odd and even pairings.
+If {seed1} is non-zero then it is used as a seed in a random number
+generator to randomly choose an odd or even pairing each time.  Each
+attempted swap of temperatures is either accepted or rejected based on
+a Metropolis criterion, derived for gREM by "(Kim)"_#Kim, which uses
+{seed2} in the random number generator.
+
+File management works identical to the "temper"_temper.html command.
+Dump files created by this fix contain continuous trajectories and
+require post-processing to obtain per-replica information.
+
+The last argument {index} in the grem command is optional and is used
+when restarting a run from a set of restart files (one for each
+replica) which had previously swapped to new lambda.  This is done
+using a variable. For example if the log file listed the following for
+a simulation with 5 replicas:
+
+500000 2 4 0 1 3 :pre
+
+then a setting of
+
+variable walkers world 2 4 0 1 3 :pre
+
+would be used to restart the run with a grem command like the example
+above with ${walkers} as the last argument. This functionality is
+identical to "temper"_temper.html.
+
+:line
+
+[Restrictions:]
+
+This command can only be used if LAMMPS was built with the USER-MISC
+package.  See the "Making LAMMPS"_Section_start.html#start_3 section
+for more info on packages.
+
+This command must be used with "fix grem"_fix_grem.html.
+
+[Related commands:]
+
+"fix grem"_fix_grem.html, "temper"_temper.html, "variable"_variable.html
+
+[Default:] none
+
+:link(Kim)
+[(Kim)] Kim, Keyes, Straub, J Chem Phys, 132, 224107 (2010).
--- a/doc/src/tutorial_github.txt
+++ b/doc/src/tutorial_github.txt
@ -11,10 +11,22 @@ LAMMPS GitHub tutorial :h3

 :line

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

 :line

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

 [Forking the repository]

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

 :c,image(JPG/tutorial_branch.png)

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

 :c,image(JPG/tutorial_fork.png)

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

 :line

 [Adding changes to your own fork]

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

 [Feature branches]

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

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

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

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

 :c,image(JPG/tutorial_https_block.png)

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

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

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

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

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

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

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

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

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

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

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

 $ git push :pre

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

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

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

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

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

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

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

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

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

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

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

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

 :line

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

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

 :line

 [After a merge]

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

 :c,image(JPG/tutorial_merged.png)

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

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

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

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

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

   tutorial_drude
   tutorial_github
+   tutorial_pylammps
   body
   manifolds

--- a/examples/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 
-     600     300.4791158523048011    1540.4690749004150803    1189.4551948503105905     393.2158976318902432    7852.5601875000220389    7852.9312239063838206   17288.1625038886049879     299.9832002920041987 
-     610     300.5939139841889869    1368.0565839211087678    1189.4252547652590692     393.3661258776944578    7852.5601874999574648    7852.8130977336286378   17288.1646658765384927     299.9807742697515778 
-     620     300.7674247480806002    1483.2566452708945235    1189.3941250938435132     393.5931872179773450    7852.5601875000193104    7852.6187967208716145   17288.1662965327122947     299.9766963671718258 
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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/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/examples/USER/dpd/dpdrx-shardlow/log.dpdrx-shardlow.reference
+++ b/examples/USER/dpd/dpdrx-shardlow/log.dpdrx-shardlow.reference
@ -48,7 +48,7 @@ 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
@ -69,39 +69,51 @@ dump_modify     2 sort id

 run             10
 Neighbor list info ...
-  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 18
  ghost atom cutoff = 18
-  binsize = 9 -> bins = 8 8 5
-Memory usage per processor = 6.52436 Mbytes
+  binsize = 9, bins = 8 8 5
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair dpd/fdt/energy, perpetual
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) pair exp6/rx, perpetual, copy from (1)
+      pair build: copy
+      stencil: none
+      bin: none
+  (3) fix shardlow, perpetual, ssa
+      pair build: half/bin/newton/ssa
+      stencil: half/bin/3d/newton/ssa
+      bin: ssa
+Memory usage per processor = 8.39564 Mbytes
 Step Temp Press Volume PotEng KinEng c_dpdU[1] c_dpdU[2] c_dpdU[3] v_totEnergy c_dpdU[4] 
-       0   2065.00000000   1368.17463335 179834.51777865      0.00000000    230.35385810   3841.42393279   3841.42393279      0.00000000   7682.84786557   2065.00000000 
-       1   2064.93210437   1368.12964881 179834.51777865      0.00000000    230.34628424   3841.42393279   3841.43150665      0.00000000   7682.85543943   2065.20275230 
-       2   2067.82089565   1370.04362990 179834.51777865     -0.00000000    230.66853326   3841.42393279   3841.10925763      0.00000000   7682.53319042   2065.32453473 
-       3   2070.45225169   1371.78704616 179834.51777865     -0.00000000    230.96206499   3841.42393279   3840.81572590      0.00000000   7682.23965869   2065.45336917 
-       4   2075.00241157   1374.80177416 179834.51777865     -0.00000000    231.46964217   3841.42393279   3840.30814872      0.00000000   7681.73208151   2065.52973333 
-       5   2073.96509212   1374.11449370 179834.51777865     -0.00000000    231.35392762   3841.42393279   3840.42386327      0.00000000   7681.84779605   2065.76011517 
-       6   2074.26516936   1374.31331117 179834.51777865     -0.00000000    231.38740169   3841.42393279   3840.39038920      0.00000000   7681.81432198   2065.95399323 
-       7   2071.41069700   1372.42206822 179834.51777865     -0.00000000    231.06898100   3841.42393279   3840.70880989      0.00000000   7682.13274267   2066.23407076 
-       8   2071.35844957   1372.38745146 179834.51777865     -0.00000000    231.06315272   3841.42393279   3840.71463817      0.00000000   7682.13857095   2066.43766287 
-       9   2071.35676496   1372.38633532 179834.51777865     -0.00000000    231.06296480   3841.42393279   3840.71482609      0.00000000   7682.13875887   2066.64001166 
-      10   2066.53172340   1369.18948328 179834.51777865     -0.00000000    230.52472415   3841.42393279   3841.25306673      0.00000000   7682.67699952   2066.97516855 
-Loop time of 0.289778 on 1 procs for 10 steps with 864 atoms
+       0   2065.00000000   1368.17463335 179834.51777865      0.00000000    230.35385810      0.00000000   7682.84786557      0.00000000   7682.84786557   2065.00000000 
+       1   2064.93210437   1368.12964881 179834.51777865      0.00000000    230.34628424      0.00000000   7682.85543943      0.00000000   7682.85543943   2065.20275230 
+       2   2067.82089565   1370.04362990 179834.51777865     -0.00000000    230.66853326      0.00000000   7682.53319042      0.00000000   7682.53319042   2065.32453473 
+       3   2070.45225169   1371.78704616 179834.51777865     -0.00000000    230.96206499      0.00000000   7682.23965869      0.00000000   7682.23965869   2065.45336917 
+       4   2075.00241157   1374.80177416 179834.51777865     -0.00000000    231.46964217      0.00000000   7681.73208151      0.00000000   7681.73208151   2065.52973333 
+       5   2073.96509212   1374.11449370 179834.51777865     -0.00000000    231.35392762     -0.00000000   7681.84779605      0.00000000   7681.84779605   2065.76011517 
+       6   2074.26516936   1374.31331117 179834.51777865     -0.00000000    231.38740169     -0.00000000   7681.81432198      0.00000000   7681.81432198   2065.95399323 
+       7   2071.41069700   1372.42206822 179834.51777865     -0.00000000    231.06898100     -0.00000000   7682.13274267      0.00000000   7682.13274267   2066.23407076 
+       8   2071.35844957   1372.38745146 179834.51777865     -0.00000000    231.06315272      0.00000000   7682.13857095      0.00000000   7682.13857095   2066.43766287 
+       9   2071.35676496   1372.38633532 179834.51777865     -0.00000000    231.06296480      0.00000000   7682.13875887      0.00000000   7682.13875887   2066.64001166 
+      10   2066.53172340   1369.18948328 179834.51777865     -0.00000000    230.52472415      0.00000000   7682.67699952      0.00000000   7682.67699952   2066.97516855 
+Loop time of 0.611304 on 1 procs for 10 steps with 864 atoms

-Performance: 2.982 ns/day, 8.049 hours/ns, 34.509 timesteps/s
-99.4% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 1.413 ns/day, 16.981 hours/ns, 16.358 timesteps/s
+98.2% CPU use with 1 MPI tasks x no OpenMP threads

 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.16405    | 0.16405    | 0.16405    |   0.0 | 56.61
+Pair    | 0.34177    | 0.34177    | 0.34177    |   0.0 | 55.91
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.00066328 | 0.00066328 | 0.00066328 |   0.0 |  0.23
-Output  | 0.037718   | 0.037718   | 0.037718   |   0.0 | 13.02
-Modify  | 0.087281   | 0.087281   | 0.087281   |   0.0 | 30.12
-Other   |            | 7.057e-05  |            |       |  0.02
+Comm    | 0.0013342  | 0.0013342  | 0.0013342  |   0.0 |  0.22
+Output  | 0.083583   | 0.083583   | 0.083583   |   0.0 | 13.67
+Modify  | 0.18451    | 0.18451    | 0.18451    |   0.0 | 30.18
+Other   |            | 0.0001087  |            |       |  0.02

 Nlocal:    864 ave 864 max 864 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
--- a/examples/USER/misc/grem/README
+++ b/examples/USER/misc/grem/README
@ -0,0 +1,81 @@
+Generalized Replica Exchange Method (gREM) examples
+===================================================
+
+Examples:
+---------------------------------------------------
+
+  lj-single:
+    This example is the simplest case scenario utilizing the generalized 
+    ensemble defined by fix_grem. It utilizes only 1 replica and requires 
+    the LAMMPS executable to be run as usual:
+
+    mpirun -np 4 lmp_mpi -in in.gREM-npt
+    ./lmp_serial -in in.gREM-nvt
+
+    While this does not obtain any information about Ts(H), it is most similar to 
+    a microcanonical simulation and "single-replica gREM" can be useful for 
+    studying non-equilibrium processes as well.
+
+  lj-6rep:
+    This example utilizes an external python script to handle swaps between
+    replicas. Included is run.sh, which requires the path to your LAMMPS 
+    executable. The python script is fragile as it relies on parsing output files 
+    from the LAMMPS run and moving LAMMPS data files between directories. Use 
+    caution if modifying this example further. If complied with mpi, multiple 
+    processors can be used as:
+
+    ./run.sh $NUM_PROCS
+
+    a serial run is completed simply as
+
+    ./run.sh 1
+
+    where the executable provided must be serial if "1" is provided as the number 
+    of procs. While this external replica exchange module is quite slow and
+    inefficient, it allows for many replicas to be used on a single processor. 
+    While here there are only 6 replicas, this example could be extended to >100
+    replicas while still using a serial compilation. This is also beneficial for
+    running on high performance nodes with few cores to complete a full-scale gREM
+    simulation with a large number of replicas. 
+
+    A quick note on efficiency: frequent exchanges slow down this script
+    substantially because LAMMPS is restarted every exchange attempt. The script
+    works best for large systems with infrequent exchanges.
+
+  lj-temper:
+    This is an example using the internal replica exchange module. While fast 
+    in comparison to the python version, it requires substantial resources 
+    (at least 1 proc per replica). Instead of stopping LAMMPS every exchange
+    attempt, all replicas are run concurrently, and exchanges take place 
+    internally. This requires use of LAMMPS partition mode, via the command 
+    line using the -p flag. Input files require world type variables defining 
+    the parameters of each replica. The included example with 4 replicas must 
+    run on at least 4 procs, in that case LAMMPS could be initiated as:
+
+    mpirun -np 4 lmp_mpi -p 4x1 -in in.gREM-temper 
+
+    spawning 4 partitions with 1 replica each. Multiple procs per replica could 
+    be used. In the case of a 16 system with 4 replicas, the
+    following logic could be used:
+
+    mpirun -np 16 lmp_mpi -p 4x4 -in in.gREM-temper
+
+    Once started, a universe log file will be created as well as log files for 
+    each replica. The universe (log.lammps) contains exchange information, while 
+    the replicas (*/log.lammps.*) contains the thermo_output as usual. In this
+    example, in.gREM-temper moves the log files to their respective folders.
+
+
+Closing Notes:
+---------------------------------------------------
+  
+  Of significant difference between lj-6rep and lj-temper is the format of data. 
+  In lj-6rep, data is stored as 'replicas' meaning discontinuous trajectories, as
+  files are moved between directories labeled by the 'lambda' of the replica. In 
+  lj-temper, data is stored as 'walkers' with continuous trajectories, but
+  discontinuous parameters. The later is significantly more efficient, but 
+  requires post-processing to obtain per-replica information.
+
+
+Any problems/questions should be directed to <dstelter@bu.edu>.
+
--- a/examples/USER/misc/grem/lj-6rep/400/restart.init
+++ b/examples/USER/misc/grem/lj-6rep/400/restart.init
--- a/examples/USER/misc/grem/lj-6rep/405/restart.init
+++ b/examples/USER/misc/grem/lj-6rep/405/restart.init
--- a/examples/USER/misc/grem/lj-6rep/410/restart.init
+++ b/examples/USER/misc/grem/lj-6rep/410/restart.init
--- a/examples/USER/misc/grem/lj-6rep/415/restart.init
+++ b/examples/USER/misc/grem/lj-6rep/415/restart.init
--- a/examples/USER/misc/grem/lj-6rep/420/restart.init
+++ b/examples/USER/misc/grem/lj-6rep/420/restart.init
--- a/examples/USER/misc/grem/lj-6rep/425/restart.init
+++ b/examples/USER/misc/grem/lj-6rep/425/restart.init
--- a/examples/USER/misc/grem/lj-6rep/clean.sh
+++ b/examples/USER/misc/grem/lj-6rep/clean.sh
@ -0,0 +1,15 @@
+#/bin/bash
+
+for i in $(ls -d [0-9]*)
+do
+    rm -f $i/final* 
+    rm -f $i/log*
+    rm -f $i/ent*
+    rm -f $i/output
+    cp $i/restart.init $i/restart_file
+done
+
+echo 1 > lastexchange
+cp walker.bkp lastwalker
+
+exit 0
--- a/examples/USER/misc/grem/lj-6rep/double-re-short.py
+++ b/examples/USER/misc/grem/lj-6rep/double-re-short.py
@ -0,0 +1,168 @@
+#!/usr/bin/env python2.7
+
+import os, sys
+from numpy import *
+import numpy.random
+
+### Runs replica exchange with gREM (fix grem) for unlimited number of replicas on a set number of processors. This script is inefficient, but necessary if wanting to run with hundreds of replicas on relatively few number of procs.
+
+
+### read number of processors from the command line
+nproc = int(sys.argv[1])
+
+### path to simulation directory
+path = os.getcwd()
+
+### path to LAMMPS executable
+lmp = sys.argv[2]
+
+### LAMMPS input name
+inp = sys.argv[3]
+
+### define pressure for simulations (0 if const V)
+pressure = 0
+
+### some constants for gREM, must match with LAMMPS input file!
+H = -30000
+eta = -0.01
+#kB = 0.000086173324 # eV (metal)
+kB = 0.0019872 # kcal/mol (real)
+
+### define lambdas - script assumes that there are already existing directories with all files necessary to run
+lambdas=[400,405,410,415,420,425]
+ll = len(lambdas)
+
+### define number of exchanges
+starting_ex = int(loadtxt("lastexchange"))
+how_many_ex = 5
+max_exchange = starting_ex+how_many_ex
+
+### array with walkers
+walker = loadtxt("lastwalker")
+
+### initiate array with enthalpies
+enthalpy = zeros(ll)
+aver_enthalpy = zeros(ll)
+
+for exchange in arange(starting_ex,max_exchange):
+	print "run", exchange
+	for l in range(ll):
+		#print "replica", l
+		os.chdir(path+"/%s" % lambdas[l])
+		#os.system("cp restart_file restart_file%d" % exchange)
+                if (nproc > 1):
+                    os.system("mpirun -np %d " % (nproc) + lmp + " -in ../" + inp + " -var lambda %g -var eta %g -var enthalpy %g > output" % (lambdas[l], eta, H))
+                if (nproc == 1):
+                    os.system(lmp + " -in ../" + inp + " -var lambda %g -var eta %g -var enthalpy %g > output" % (lambdas[l], eta, H))
+		os.system("grep -v '[a-zA-Z]' output | awk '{if(NF==6 && NR>19)print $0}' | awk '{print $3}' >ent")
+		enthalpy[l] = os.popen("tail -n 1 ent").read()
+		ee = loadtxt("ent")
+		aver_enthalpy[l] = mean(ee[-1])
+#		os.system("mv dump.dcd dump%d.dcd" % exchange)
+		os.system("mv log.lammps log%d.lammps" % exchange)
+		os.system("mv final_restart_file final_restart_file%d" % exchange)
+		os.system("mv ent ent%d" % exchange)
+		os.system("bzip2 log%d.lammps ent%d" % (exchange,exchange))
+		os.system("cp final_restart_file%d restart_file" % exchange)
+
+	### replicas will be exchanged based on enthalpy order, not replicas order (termostat order)
+	#entalpy_sorted_indices = enthalpy.argsort()
+	aver_entalpy_sorted_indices = aver_enthalpy.argsort()
+
+	### choose pair of replicas for exchange attempt based on enthalpy order
+	pp = random.random_integers(0,ll-2)
+	first = aver_entalpy_sorted_indices[pp]
+	second = aver_entalpy_sorted_indices[pp+1]
+	#if (first>second):
+	#	tmp = first
+	#	first = second
+	#	second = tmp
+	print "pair1:", first, second
+
+	### calculate weights for exchange criterion
+	w1 = log(lambdas[first]+eta*(enthalpy[first]-1*H))
+	w2 = log(lambdas[first]+eta*(enthalpy[second]-1*H))
+	w3 = log(lambdas[second]+eta*(enthalpy[first]-1*H))
+	w4 = log(lambdas[second]+eta*(enthalpy[second]-1*H))
+	weight = (w4-w3+w1-w2)/eta/kB
+
+	### generate randon number for exchange criterion and calc its log
+	LOGRANDNUM = log(random.random())
+
+	### wyzeruj warunki
+	compare1 = 0
+	compare2 = 0
+
+	if (weight>0):
+		compare1 = 1
+	if (weight>LOGRANDNUM):
+		compare2 = 1
+
+	### exchange restart files if exchange condition is satisfied
+	if (compare1>0 or compare2>0):
+		print "exchange1 accepted for pair", first, second, lambdas[first], lambdas[second], "with compares as", compare1, compare2, "weight as", weight, "and lograndnum", LOGRANDNUM
+		os.system("cp %s/%s/final_restart_file%d %s/%s/restart_file" % (path,lambdas[first],exchange,path,lambdas[second]))
+		os.system("cp %s/%s/final_restart_file%d %s/%s/restart_file" % (path,lambdas[second],exchange,path,lambdas[first]))
+		### update walkers
+		tmp1=walker[first]
+		tmp2=walker[second]
+		walker[first]=tmp2
+		walker[second]=tmp1
+	else:
+		print "exchange1 not accepted for pair", first, second, lambdas[first], lambdas[second], "with compares as", compare1, compare2, "weight as", weight, "and lograndnum", LOGRANDNUM
+
+	### choose again pair of replicas for exchange attempt based on enthalpy order
+	### but make sure this pair is different than the first pair
+	if_different = 0
+	while if_different<1:
+		pp2 = random.random_integers(0,ll-2)
+		third = aver_entalpy_sorted_indices[pp2]
+		fourth = aver_entalpy_sorted_indices[pp2+1]
+		if (third!=first and third!=second and third!=aver_entalpy_sorted_indices[pp-1]):
+			if_different = 1
+
+	print "pair2:", third, fourth
+
+	### calculate weights for exchange criterion
+	w1 = log(lambdas[third]+eta*(enthalpy[third]-1*H))
+	w2 = log(lambdas[third]+eta*(enthalpy[fourth]-1*H))
+	w3 = log(lambdas[fourth]+eta*(enthalpy[third]-1*H))
+	w4 = log(lambdas[fourth]+eta*(enthalpy[fourth]-1*H))
+	weight = (w4-w3+w1-w2)/eta/kB
+
+	### generate randon number for exchange criterion and calc its log
+	LOGRANDNUM = log(random.random())
+
+	### wyzeruj warunki
+	compare1 = 0
+	compare2 = 0
+
+	if (weight>0):
+		compare1 = 1
+	if (weight>LOGRANDNUM):
+		compare2 = 1
+
+	### exchange restart files if exchange condition is satisfied
+	if (compare1>0 or compare2>0):
+		print "exchange2 accepted for pair", third, fourth, lambdas[third], lambdas[fourth], "with compares as", compare1, compare2, "weight as", weight, "and lograndnum", LOGRANDNUM
+		os.system("cp %s/%s/final_restart_file%d %s/%s/restart_file" % (path,lambdas[third],exchange,path,lambdas[fourth]))
+		os.system("cp %s/%s/final_restart_file%d %s/%s/restart_file" % (path,lambdas[fourth],exchange,path,lambdas[third]))
+		### update walkers
+		tmp1=walker[third]
+		tmp2=walker[fourth]
+		walker[third]=tmp2
+		walker[fourth]=tmp1
+	else:
+		print "exchange2 not accepted for pair", third, fourth, lambdas[third], lambdas[fourth], "with compares as", compare1, compare2, "weight as", weight, "and lograndnum", LOGRANDNUM
+	#print "walkers:", walker
+	print "".join(["%d " % x for x in walker])
+	sys.stdout.flush()
+
+	lastwalker = open(path + "/lastwalker", "w")
+	lastwalker.write("".join(["%d " % w for w in walker]))
+	lastwalker.close()
+
+	lastexchange = open(path + "/lastexchange", "w")
+	lastexchange.write("%d" % (exchange+1))
+	lastexchange.close()
+
--- a/examples/USER/misc/grem/lj-6rep/in.gREM
+++ b/examples/USER/misc/grem/lj-6rep/in.gREM
@ -0,0 +1,25 @@
+# LJ particles
+variable        T0 index 300.0
+variable        press index 0.0
+variable        lambda index 400.0
+variable        eta index -0.01
+variable        enthalpy index -30000.0
+
+units           real
+atom_style      full
+pair_style      lj/cut 5.0
+
+read_data       "restart_file"
+
+thermo          10
+thermo_style    custom step temp pe etotal press vol
+
+velocity        all create ${T0} 12427
+timestep        1.0
+
+fix             fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0 
+fix             fxgREM all grem ${lambda} ${eta} ${enthalpy} fxnvt
+thermo_modify   press fxgREM_press
+run             10000
+
+write_data      final_restart_file
--- a/examples/USER/misc/grem/lj-6rep/run.sh
+++ b/examples/USER/misc/grem/lj-6rep/run.sh
@ -0,0 +1,12 @@
+#!/bin/sh
+
+NPROCS=1
+if [ $# -gt 0 ]; then
+  NPROCS=$1
+fi
+
+bash ./clean.sh
+
+python ./double-re-short.py $NPROCS $HOME/compile/lammps-icms/src/lmp_omp in.gREM > total_output.$NPROCS
+
+exit 0
--- a/examples/USER/misc/grem/lj-6rep/walker.bkp
+++ b/examples/USER/misc/grem/lj-6rep/walker.bkp
@ -0,0 +1 @@
+0 1 2 3 4 5
--- a/examples/USER/misc/grem/lj-single/in.gREM-npt
+++ b/examples/USER/misc/grem/lj-single/in.gREM-npt
@ -0,0 +1,21 @@
+# LJ particles
+variable        T0 equal 300.0
+variable        press equal 0.0
+
+units           real
+atom_style      full
+pair_style      lj/cut 5.0
+
+read_data       "lj.data"
+
+thermo          10
+thermo_style    custom step temp pe etotal press vol
+
+timestep        1.0
+
+fix             fxnpt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0 
+fix             fxgREM all grem 400 -.01 -30000 fxnpt
+thermo_modify   press fxgREM_press
+run             1000
+
+#write_data      lj-out.data
--- a/examples/USER/misc/grem/lj-single/in.gREM-nvt
+++ b/examples/USER/misc/grem/lj-single/in.gREM-nvt
@ -0,0 +1,20 @@
+# LJ particles
+variable        T0 equal 300.0
+variable        press equal 0.0
+
+units           real
+atom_style      full
+pair_style      lj/cut 5.0
+
+read_data       "lj.data"
+
+thermo          10
+thermo_style    custom step temp pe etotal press vol
+
+timestep        1.0
+
+fix             fxnvt all nvt temp ${T0} ${T0} 1000.0
+fix             fxgREM all grem 400 -.01 -30000 fxnvt
+run             1000
+
+#write_data      lj-out.data
--- a/examples/USER/misc/grem/lj-single/lj.data
+++ b/examples/USER/misc/grem/lj-single/lj.data
--- a/examples/USER/misc/grem/lj-single/log.gREM-npt.9Nov16.g++.1
+++ b/examples/USER/misc/grem/lj-single/log.gREM-npt.9Nov16.g++.1
@ -0,0 +1,176 @@
+LAMMPS (9 Nov 2016)
+  using 1 OpenMP thread(s) per MPI task
+# LJ particles
+variable        T0 equal 300.0
+variable        press equal 0.0
+
+units           real
+atom_style      full
+pair_style      lj/cut 5.0
+
+read_data       "lj.data"
+  orthogonal box = (1.06874 1.06874 1.06874) to (23.9313 23.9313 23.9313)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  500 atoms
+  reading velocities ...
+  500 velocities
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+
+thermo          10
+thermo_style    custom step temp pe etotal press vol
+
+timestep        1.0
+
+fix             fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
+fix             fxnvt all npt temp 300 ${T0} 1000.0 iso ${press} ${press} 10000.0
+fix             fxnvt all npt temp 300 300 1000.0 iso ${press} ${press} 10000.0
+fix             fxnvt all npt temp 300 300 1000.0 iso 0 ${press} 10000.0
+fix             fxnvt all npt temp 300 300 1000.0 iso 0 0 10000.0
+fix             fxgREM all grem 400 -.01 -30000 fxnvt
+thermo_modify   press fxgREM_press
+run             1000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7
+  ghost atom cutoff = 7
+  binsize = 3.5 -> bins = 7 7 7
+Memory usage per processor = 5.37943 Mbytes
+Step Temp PotEng TotEng Press Volume 
+       0    305.69499   -3177.6423   -2722.9442   -91.741776    11950.115 
+      10    312.30124   -3182.2257   -2717.7013   -203.95075    11950.113 
+      20    314.94567    -3186.456   -2717.9982   -265.56737    11950.108 
+      30      312.229   -3183.7641   -2719.3472   -196.90499    11950.097 
+      40    305.94068   -3180.7085   -2725.6449   -92.562221    11950.083 
+      50    300.42281   -3176.5838   -2729.7277    10.896769    11950.066 
+      60    299.16747   -3174.1939    -2729.205    50.094171     11950.05 
+      70    301.65965   -3176.0918    -2727.396  0.096901939    11950.035 
+      80    304.77876   -3178.2699   -2724.9346   -64.001022    11950.019 
+      90    305.60598   -3178.9517    -2724.386   -93.672879    11950.003 
+     100     303.8005   -3177.5156   -2725.6354   -74.516709    11949.985 
+     110    300.86776   -3175.4773   -2727.9593    -34.22655    11949.965 
+     120    298.70177   -3175.6488   -2731.3526   -19.014898    11949.944 
+     130    298.39686   -3176.3792   -2732.5365   -21.293245    11949.923 
+     140    300.00669   -3177.7032    -2731.466   -40.992937    11949.902 
+     150    301.85665   -3178.1312   -2729.1423   -45.715505     11949.88 
+     160    301.20597   -3177.3218   -2729.3007   -10.104082    11949.857 
+     170    297.01134   -3172.7462   -2730.9643    99.298381    11949.833 
+     180      291.279   -3168.3513   -2735.0958    219.47549    11949.812 
+     190    287.13954   -3165.1287   -2738.0304    309.36947    11949.796 
+     200    286.57735   -3165.2951    -2739.033    323.96954    11949.786 
+     210    289.83941   -3167.8245   -2736.7103    271.77305    11949.783 
+     220    296.12858   -3171.8054   -2731.3366     172.4056    11949.785 
+     230    303.82424   -3176.3108   -2724.3952    56.711479    11949.791 
+     240    309.95738   -3180.9789   -2719.9408   -40.992898    11949.798 
+     250     312.0405   -3182.3473   -2718.2107   -57.591676    11949.805 
+     260    309.65444   -3181.0587   -2720.4712    3.3540332     11949.81 
+     270    304.40001   -3176.5798   -2723.8078    130.77028    11949.816 
+     280    298.65985   -3174.1505   -2729.9166    237.63562    11949.825 
+     290    294.78709   -3170.9701   -2732.4966    326.94924    11949.838 
+     300    294.03216   -3169.9567   -2732.6062    349.85486    11949.859 
+     310    296.44397   -3172.8519    -2731.914    284.80897    11949.886 
+     320    301.41027   -3175.9697   -2727.6447     179.4647     11949.92 
+     330    307.88911   -3181.2615   -2723.2998    24.702414    11949.957 
+     340    314.73138   -3186.0047   -2717.8656    -132.6263    11949.995 
+     350    320.55591   -3187.8509   -2711.0483   -245.88468    11950.031 
+     360    323.50274   -3188.9994   -2707.8136   -314.73676    11950.062 
+     370    321.61539   -3187.1233   -2708.7448   -293.17446    11950.086 
+     380    314.37275    -3181.484   -2713.8784   -169.00448    11950.104 
+     390    303.54884   -3174.1675   -2722.6616    12.923999    11950.119 
+     400    293.40432   -3167.0348   -2730.6181     187.6624    11950.135 
+     410    288.46351    -3165.273   -2736.2054    252.20051    11950.154 
+     420    290.31387    -3168.604   -2736.7841    193.73816    11950.178 
+     430    296.35519     -3173.09   -2732.2841    81.521847    11950.207 
+     440    301.92973   -3175.4344   -2726.3368   -1.8329439    11950.237 
+     450    303.76205    -3176.777   -2724.9539   -35.002096    11950.267 
+     460    301.71619   -3174.2731   -2725.4932    14.977875    11950.296 
+     470    298.92404   -3172.9921   -2728.3652    64.224747    11950.326 
+     480    298.80164   -3172.5329   -2728.0881    82.781347    11950.358 
+     490    302.71589   -3175.3703   -2725.1034    27.223049     11950.39 
+     500    309.10665   -3179.3013   -2719.5285   -65.460658    11950.424 
+     510    314.36408   -3183.2854   -2715.6927   -151.19245    11950.456 
+     520    315.71154   -3183.5328   -2713.9358   -163.19151    11950.485 
+     530    313.31886   -3182.2521    -2716.214    -125.5741    11950.511 
+     540    309.81847   -3178.9358   -2718.1043    -55.55841    11950.534 
+     550    308.29687    -3177.837   -2719.2688    -24.39371    11950.556 
+     560    308.75927   -3176.3265   -2717.0705   0.93689833    11950.578 
+     570    307.52811   -3175.8145   -2718.3897    35.502429      11950.6 
+     580    301.75074   -3173.1208   -2724.2894    136.29625    11950.622 
+     590    292.37743   -3165.5806   -2730.6913    319.75957    11950.648 
+     600    283.57627   -3159.8617   -2738.0635    471.28045     11950.68 
+     610    279.85172   -3157.4557   -2741.1975    530.72699    11950.722 
+     620    283.40879   -3160.5911    -2739.042    455.28104    11950.775 
+     630    292.53718   -3166.3125   -2731.1856    296.63465    11950.838 
+     640    302.81112   -3173.3096    -2722.901    113.80844    11950.907 
+     650    309.83321   -3179.3684    -2718.515   -26.499431    11950.978 
+     660     312.1283   -3182.7335   -2718.4663   -89.363745    11951.049 
+     670    311.16363    -3181.867   -2719.0347   -69.370989    11951.118 
+     680    308.51041   -3180.6869    -2721.801   -25.972987    11951.186 
+     690    304.64393   -3176.8751   -2723.7403    56.592367    11951.254 
+     700    300.24456   -3175.4797   -2728.8887    112.34442    11951.323 
+     710    296.35785   -3172.9705   -2732.1607    168.18009    11951.394 
+     720    293.78145   -3172.1065   -2735.1289    182.81082    11951.468 
+     730    293.25707   -3170.8715   -2734.6738    171.04236    11951.547 
+     740    295.33219   -3172.9109   -2733.6266    91.351362    11951.629 
+     750    299.69136   -3175.2574   -2729.4892   -16.266404    11951.713 
+     760     305.2281   -3177.9836   -2723.9799   -137.30615    11951.796 
+     770    310.59309   -3182.7053   -2720.7216   -272.72961    11951.877 
+     780    314.65573   -3183.4212   -2715.3947     -341.231    11951.952 
+     790    316.48606     -3185.44    -2714.691   -388.53602     11952.02 
+     800    315.15897    -3186.846   -2718.0709   -384.28316     11952.08 
+     810    310.43559   -3183.6648   -2721.9154   -282.61999    11952.133 
+     820    303.22265    -3178.464   -2727.4433   -121.47565    11952.179 
+     830    295.36843   -3175.4771   -2736.1389    33.066504    11952.223 
+     840    288.69698   -3169.5813   -2740.1664    216.10697    11952.268 
+     850    283.82649   -3165.7822   -2743.6118    359.56896    11952.317 
+     860    280.04102   -3162.8228    -2746.283    475.61942    11952.374 
+     870    277.10059   -3159.6212   -2747.4551     572.5432    11952.441 
+     880    275.76549   -3158.2545   -2748.0743    616.43304     11952.52 
+     890    276.82327   -3158.9703   -2747.2166    596.08147    11952.612 
+     900    280.72135   -3162.0637   -2744.5119    506.33695    11952.716 
+     910     287.1035   -3167.4388   -2740.3941    356.68688    11952.831 
+     920    294.28041   -3171.6218    -2733.902    206.06394    11952.953 
+     930    300.36009   -3173.9046   -2727.1418    88.047911     11953.08 
+     940    303.86761   -3175.5599   -2723.5798    7.6846808    11953.209 
+     950    304.42957   -3176.0831   -2723.2672    -25.15496    11953.339 
+     960    303.13982   -3176.0534   -2725.1559   -28.715178    11953.467 
+     970    302.30166   -3176.9758    -2727.325   -43.264668    11953.596 
+     980    303.93331   -3178.9891   -2726.9114   -88.434034    11953.723 
+     990    307.36223   -3180.7316   -2723.5535   -145.46208    11953.849 
+    1000    310.09574    -3181.101   -2719.8571   -180.39125    11953.972 
+Loop time of 0.307225 on 1 procs for 1000 steps with 500 atoms
+
+Performance: 281.227 ns/day, 0.085 hours/ns, 3254.944 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.25351    | 0.25351    | 0.25351    |   0.0 | 82.52
+Bond    | 7.1526e-05 | 7.1526e-05 | 7.1526e-05 |   0.0 |  0.02
+Neigh   | 0.0042093  | 0.0042093  | 0.0042093  |   0.0 |  1.37
+Comm    | 0.010211   | 0.010211   | 0.010211   |   0.0 |  3.32
+Output  | 0.0013611  | 0.0013611  | 0.0013611  |   0.0 |  0.44
+Modify  | 0.033891   | 0.033891   | 0.033891   |   0.0 | 11.03
+Other   |            | 0.003969   |            |       |  1.29
+
+Nlocal:    500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1610 ave 1610 max 1610 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    14765 ave 14765 max 14765 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 14765
+Ave neighs/atom = 29.53
+Ave special neighs/atom = 0
+Neighbor list builds = 5
+Dangerous builds = 0
+
+#write_data      lj-out.data
+Total wall time: 0:00:00
--- a/examples/USER/misc/grem/lj-single/log.gREM-npt.9Nov16.g++.4
+++ b/examples/USER/misc/grem/lj-single/log.gREM-npt.9Nov16.g++.4
@ -0,0 +1,176 @@
+LAMMPS (9 Nov 2016)
+  using 1 OpenMP thread(s) per MPI task
+# LJ particles
+variable        T0 equal 300.0
+variable        press equal 0.0
+
+units           real
+atom_style      full
+pair_style      lj/cut 5.0
+
+read_data       "lj.data"
+  orthogonal box = (1.06874 1.06874 1.06874) to (23.9313 23.9313 23.9313)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  500 atoms
+  reading velocities ...
+  500 velocities
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+
+thermo          10
+thermo_style    custom step temp pe etotal press vol
+
+timestep        1.0
+
+fix             fxnvt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0
+fix             fxnvt all npt temp 300 ${T0} 1000.0 iso ${press} ${press} 10000.0
+fix             fxnvt all npt temp 300 300 1000.0 iso ${press} ${press} 10000.0
+fix             fxnvt all npt temp 300 300 1000.0 iso 0 ${press} 10000.0
+fix             fxnvt all npt temp 300 300 1000.0 iso 0 0 10000.0
+fix             fxgREM all grem 400 -.01 -30000 fxnvt
+thermo_modify   press fxgREM_press
+run             1000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7
+  ghost atom cutoff = 7
+  binsize = 3.5 -> bins = 7 7 7
+Memory usage per processor = 5.34276 Mbytes
+Step Temp PotEng TotEng Press Volume 
+       0    305.69499   -3177.6423   -2722.9442   -91.741776    11950.115 
+      10    312.30124   -3182.2257   -2717.7013   -203.95075    11950.113 
+      20    314.94567    -3186.456   -2717.9982   -265.56737    11950.108 
+      30      312.229   -3183.7641   -2719.3472   -196.90499    11950.097 
+      40    305.94068   -3180.7085   -2725.6449   -92.562221    11950.083 
+      50    300.42281   -3176.5838   -2729.7277    10.896769    11950.066 
+      60    299.16747   -3174.1939    -2729.205    50.094171     11950.05 
+      70    301.65965   -3176.0918    -2727.396  0.096901939    11950.035 
+      80    304.77876   -3178.2699   -2724.9346   -64.001022    11950.019 
+      90    305.60598   -3178.9517    -2724.386   -93.672879    11950.003 
+     100     303.8005   -3177.5156   -2725.6354   -74.516709    11949.985 
+     110    300.86776   -3175.4773   -2727.9593    -34.22655    11949.965 
+     120    298.70177   -3175.6488   -2731.3526   -19.014898    11949.944 
+     130    298.39686   -3176.3792   -2732.5365   -21.293245    11949.923 
+     140    300.00669   -3177.7032    -2731.466   -40.992937    11949.902 
+     150    301.85665   -3178.1312   -2729.1423   -45.715505     11949.88 
+     160    301.20597   -3177.3218   -2729.3007   -10.104082    11949.857 
+     170    297.01134   -3172.7462   -2730.9643    99.298381    11949.833 
+     180      291.279   -3168.3513   -2735.0958    219.47549    11949.812 
+     190    287.13954   -3165.1287   -2738.0304    309.36947    11949.796 
+     200    286.57735   -3165.2951    -2739.033    323.96954    11949.786 
+     210    289.83941   -3167.8245   -2736.7103    271.77305    11949.783 
+     220    296.12858   -3171.8054   -2731.3366     172.4056    11949.785 
+     230    303.82424   -3176.3108   -2724.3952    56.711479    11949.791 
+     240    309.95738   -3180.9789   -2719.9408   -40.992898    11949.798 
+     250     312.0405   -3182.3473   -2718.2107   -57.591676    11949.805 
+     260    309.65444   -3181.0587   -2720.4712    3.3540332     11949.81 
+     270    304.40001   -3176.5798   -2723.8078    130.77028    11949.816 
+     280    298.65985   -3174.1505   -2729.9166    237.63562    11949.825 
+     290    294.78709   -3170.9701   -2732.4966    326.94924    11949.838 
+     300    294.03216   -3169.9567   -2732.6062    349.85486    11949.859 
+     310    296.44397   -3172.8519    -2731.914    284.80897    11949.886 
+     320    301.41027   -3175.9697   -2727.6447     179.4647     11949.92 
+     330    307.88911   -3181.2615   -2723.2998    24.702414    11949.957 
+     340    314.73138   -3186.0047   -2717.8656    -132.6263    11949.995 
+     350    320.55591   -3187.8509   -2711.0483   -245.88468    11950.031 
+     360    323.50274   -3188.9994   -2707.8136   -314.73676    11950.062 
+     370    321.61539   -3187.1233   -2708.7448   -293.17446    11950.086 
+     380    314.37275    -3181.484   -2713.8784   -169.00448    11950.104 
+     390    303.54884   -3174.1675   -2722.6616    12.923999    11950.119 
+     400    293.40432   -3167.0348   -2730.6181     187.6624    11950.135 
+     410    288.46351    -3165.273   -2736.2054    252.20051    11950.154 
+     420    290.31387    -3168.604   -2736.7841    193.73816    11950.178 
+     430    296.35519     -3173.09   -2732.2841    81.521847    11950.207 
+     440    301.92973   -3175.4344   -2726.3368   -1.8329439    11950.237 
+     450    303.76205    -3176.777   -2724.9539   -35.002096    11950.267 
+     460    301.71619   -3174.2731   -2725.4932    14.977875    11950.296 
+     470    298.92404   -3172.9921   -2728.3652    64.224747    11950.326 
+     480    298.80164   -3172.5329   -2728.0881    82.781347    11950.358 
+     490    302.71589   -3175.3703   -2725.1034    27.223049     11950.39 
+     500    309.10665   -3179.3013   -2719.5285   -65.460658    11950.424 
+     510    314.36408   -3183.2854   -2715.6927   -151.19245    11950.456 
+     520    315.71154   -3183.5328   -2713.9358   -163.19151    11950.485 
+     530    313.31886   -3182.2521    -2716.214    -125.5741    11950.511 
+     540    309.81847   -3178.9358   -2718.1043    -55.55841    11950.534 
+     550    308.29687    -3177.837   -2719.2688    -24.39371    11950.556 
+     560    308.75927   -3176.3265   -2717.0705   0.93689833    11950.578 
+     570    307.52811   -3175.8145   -2718.3897    35.502429      11950.6 
+     580    301.75074   -3173.1208   -2724.2894    136.29625    11950.622 
+     590    292.37743   -3165.5806   -2730.6913    319.75957    11950.648 
+     600    283.57627   -3159.8617   -2738.0635    471.28045     11950.68 
+     610    279.85172   -3157.4557   -2741.1975    530.72699    11950.722 
+     620    283.40879   -3160.5911    -2739.042    455.28104    11950.775 
+     630    292.53718   -3166.3125   -2731.1856    296.63465    11950.838 
+     640    302.81112   -3173.3096    -2722.901    113.80844    11950.907 
+     650    309.83321   -3179.3684    -2718.515   -26.499431    11950.978 
+     660     312.1283   -3182.7335   -2718.4663   -89.363745    11951.049 
+     670    311.16363    -3181.867   -2719.0347   -69.370989    11951.118 
+     680    308.51041   -3180.6869    -2721.801   -25.972987    11951.186 
+     690    304.64393   -3176.8751   -2723.7403    56.592367    11951.254 
+     700    300.24456   -3175.4797   -2728.8887    112.34442    11951.323 
+     710    296.35785   -3172.9705   -2732.1607    168.18009    11951.394 
+     720    293.78145   -3172.1065   -2735.1289    182.81082    11951.468 
+     730    293.25707   -3170.8715   -2734.6738    171.04236    11951.547 
+     740    295.33219   -3172.9109   -2733.6266    91.351362    11951.629 
+     750    299.69136   -3175.2574   -2729.4892   -16.266404    11951.713 
+     760     305.2281   -3177.9836   -2723.9799   -137.30615    11951.796 
+     770    310.59309   -3182.7053   -2720.7216   -272.72961    11951.877 
+     780    314.65573   -3183.4212   -2715.3947     -341.231    11951.952 
+     790    316.48606     -3185.44    -2714.691   -388.53602     11952.02 
+     800    315.15897    -3186.846   -2718.0709   -384.28316     11952.08 
+     810    310.43559   -3183.6648   -2721.9154   -282.61999    11952.133 
+     820    303.22265    -3178.464   -2727.4433   -121.47565    11952.179 
+     830    295.36843   -3175.4771   -2736.1389    33.066504    11952.223 
+     840    288.69698   -3169.5813   -2740.1664    216.10697    11952.268 
+     850    283.82649   -3165.7822   -2743.6118    359.56896    11952.317 
+     860    280.04102   -3162.8228    -2746.283    475.61942    11952.374 
+     870    277.10059   -3159.6212   -2747.4551     572.5432    11952.441 
+     880    275.76549   -3158.2545   -2748.0743    616.43304     11952.52 
+     890    276.82327   -3158.9703   -2747.2166    596.08147    11952.612 
+     900    280.72135   -3162.0637   -2744.5119    506.33695    11952.716 
+     910     287.1035   -3167.4388   -2740.3941    356.68688    11952.831 
+     920    294.28041   -3171.6218    -2733.902    206.06394    11952.953 
+     930    300.36009   -3173.9046   -2727.1418    88.047911     11953.08 
+     940    303.86761   -3175.5599   -2723.5798    7.6846808    11953.209 
+     950    304.42957   -3176.0831   -2723.2672    -25.15496    11953.339 
+     960    303.13982   -3176.0534   -2725.1559   -28.715178    11953.467 
+     970    302.30166   -3176.9758    -2727.325   -43.264668    11953.596 
+     980    303.93331   -3178.9891   -2726.9114   -88.434034    11953.723 
+     990    307.36223   -3180.7316   -2723.5535   -145.46208    11953.849 
+    1000    310.09574    -3181.101   -2719.8571   -180.39125    11953.972 
+Loop time of 0.154208 on 4 procs for 1000 steps with 500 atoms
+
+Performance: 560.281 ns/day, 0.043 hours/ns, 6484.730 timesteps/s
+98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.072079   | 0.074846   | 0.079666   |   1.1 | 48.54
+Bond    | 5.7936e-05 | 6.634e-05  | 8.1062e-05 |   0.1 |  0.04
+Neigh   | 0.0010812  | 0.0012064  | 0.0012748  |   0.2 |  0.78
+Comm    | 0.032452   | 0.037544   | 0.04076    |   1.6 | 24.35
+Output  | 0.0018461  | 0.0020589  | 0.0026393  |   0.7 |  1.34
+Modify  | 0.032085   | 0.032688   | 0.033361   |   0.3 | 21.20
+Other   |            | 0.005799   |            |       |  3.76
+
+Nlocal:    125 ave 127 max 123 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost:    870.5 ave 882 max 862 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+Neighs:    3691.25 ave 3807 max 3563 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+
+Total # of neighbors = 14765
+Ave neighs/atom = 29.53
+Ave special neighs/atom = 0
+Neighbor list builds = 5
+Dangerous builds = 0
+
+#write_data      lj-out.data
+Total wall time: 0:00:00
--- a/examples/USER/misc/grem/lj-single/log.gREM-nvt.9Nov16.g++.1
+++ b/examples/USER/misc/grem/lj-single/log.gREM-nvt.9Nov16.g++.1
@ -0,0 +1,173 @@
+LAMMPS (9 Nov 2016)
+  using 1 OpenMP thread(s) per MPI task
+# LJ particles
+variable        T0 equal 300.0
+variable        press equal 0.0
+
+units           real
+atom_style      full
+pair_style      lj/cut 5.0
+
+read_data       "lj.data"
+  orthogonal box = (1.06874 1.06874 1.06874) to (23.9313 23.9313 23.9313)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  500 atoms
+  reading velocities ...
+  500 velocities
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+
+thermo          10
+thermo_style    custom step temp pe etotal press vol
+
+timestep        1.0
+
+fix             fxnvt all nvt temp ${T0} ${T0} 1000.0
+fix             fxnvt all nvt temp 300 ${T0} 1000.0
+fix             fxnvt all nvt temp 300 300 1000.0
+fix             fxgREM all grem 400 -.01 -30000 fxnvt
+run             1000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7
+  ghost atom cutoff = 7
+  binsize = 3.5 -> bins = 7 7 7
+Memory usage per processor = 5.37943 Mbytes
+Step Temp PotEng TotEng Press Volume 
+       0    305.69499   -3177.6423   -2722.9442    883.58369    11950.115 
+      10    312.30121   -3182.2257   -2717.7013    793.47811    11950.115 
+      20    314.94553   -3186.4559   -2717.9983    738.74091    11950.115 
+      30    312.22861   -3183.7638   -2719.3474    797.47978    11950.115 
+      40    305.93987   -3180.7079   -2725.6455    881.30806    11950.115 
+      50    300.42132   -3176.5828   -2729.7288    967.92042    11950.115 
+      60    299.16487   -3174.1921   -2729.2071     1004.247    11950.115 
+      70    301.65565   -3176.0891   -2727.3992    962.58134    11950.115 
+      80    304.77334   -3178.2663    -2724.939     907.8946    11950.115 
+      90    305.59929   -3178.9472   -2724.3914    879.91629    11950.115 
+     100    303.79263   -3177.5103   -2725.6418    892.67631    11950.115 
+     110    300.85863   -3175.4711   -2727.9667    923.44924    11950.115 
+     120    298.69083   -3175.6415   -2731.3615    931.87518    11950.115 
+     130    298.38415   -3176.3706   -2732.5468    928.88286    11950.115 
+     140    299.99129   -3177.6935   -2731.4792    914.36783    11950.115 
+     150    301.83869    -3178.121   -2729.1588    915.01407    11950.115 
+     160    301.18834   -3177.3117   -2729.3169    947.45228    11950.115 
+     170    296.99406   -3172.7363   -2730.9801    1042.6928    11950.115 
+     180    291.25952   -3168.3407   -2735.1142    1144.5436    11950.115 
+     190     287.1178   -3164.9847   -2737.9187    1223.4003    11950.115 
+     200      286.552   -3165.2799   -2739.0555    1235.6703    11950.115 
+     210    289.81033   -3167.8062   -2736.7353    1194.6672    11950.115 
+     220    296.09616   -3171.7847   -2731.3641    1115.8799    11950.115 
+     230    303.79176   -3176.2893   -2724.4221    1024.6471    11950.115 
+     240     309.9273   -3180.9591   -2719.9657    945.55045    11950.115 
+     250     312.0159   -3182.3307   -2718.2306    934.36956    11950.115 
+     260    309.63264   -3181.0452   -2720.4901    986.77385    11950.115 
+     270    304.38172    -3176.568   -2723.8233     1097.264    11950.115 
+     280    298.64188   -3174.1384   -2729.9313    1186.2239    11950.115 
+     290    294.76686   -3170.9562   -2732.5128     1264.247    11950.115 
+     300    294.00805   -3169.8091   -2732.4944    1287.4001    11950.115 
+     310    296.41801    -3172.834   -2731.9347    1229.5624    11950.115 
+     320    301.38477   -3175.9514   -2727.6644    1140.8664    11950.115 
+     330    307.86584   -3181.2442   -2723.3171    1007.1545    11950.115 
+     340     314.7103   -3185.9891   -2717.8814    871.74528    11950.115 
+     350    320.53954   -3187.8385   -2711.0602    776.85994    11950.115 
+     360    323.49505   -3188.9927   -2707.8184    716.58062    11950.115 
+     370    321.62077   -3187.1246   -2708.7381    731.01909    11950.115 
+     380    314.39049   -3181.4931   -2713.8611    831.21057    11950.115 
+     390    303.57079   -3174.1804   -2722.6419    978.62645    11950.115 
+     400    293.42165   -3167.0452   -2730.6027    1122.3558    11950.115 
+     410    288.46838   -3165.4071   -2736.3322    1171.8087    11950.115 
+     420    290.30766   -3168.5988   -2736.7882    1122.5413    11950.115 
+     430    296.34338   -3173.0824   -2732.2941    1030.2769    11950.115 
+     440    301.92394   -3175.4307   -2726.3417    964.25387    11950.115 
+     450    303.76745   -3176.9122   -2725.0811    934.49176    11950.115 
+     460    301.72985   -3174.2821   -2725.4818    979.07605    11950.115 
+     470    298.93736   -3173.0014   -2728.3548    1020.0482    11950.115 
+     480    298.80912    -3172.803   -2728.3471    1036.6531    11950.115 
+     490    302.72217   -3175.3764   -2725.1001    997.71146    11950.115 
+     500    309.11393   -3179.3088   -2719.5253    925.81108    11950.115 
+     510    314.37612   -3183.2961   -2715.6855    856.23748    11950.115 
+     520    315.72767    -3183.547    -2713.926    847.70543    11950.115 
+     530    313.34173   -3182.2695   -2716.1974    877.30842    11950.115 
+     540    309.84312   -3178.9553   -2718.0871    936.69244    11950.115 
+     550     308.3251   -3177.8582    -2719.248    963.93032    11950.115 
+     560    308.79192   -3176.4834   -2717.1788    989.67643    11950.115 
+     570    307.57194   -3175.8464   -2718.3565    1021.0494    11950.115 
+     580     301.8035   -3173.1582   -2724.2483    1102.4893    11950.115 
+     590    292.43425    -3165.751   -2730.7772    1254.7815    11950.115 
+     600    283.62905   -3159.8987    -2738.022    1381.0608    11950.115 
+     610    279.90122     -3157.49   -2741.1581    1431.0028    11950.115 
+     620     283.4582    -3160.756   -2739.1334    1367.7385    11950.115 
+     630    292.58866   -3166.3469   -2731.1435    1241.1194    11950.115 
+     640    302.86585   -3173.4778   -2722.9878    1089.7342    11950.115 
+     650    309.89252   -3179.4078   -2718.4662     972.6359    11950.115 
+     660    312.19165   -3182.7754    -2718.414    916.62037    11950.115 
+     670     311.2287   -3181.9102   -2718.9811    933.79804    11950.115 
+     680    308.57852   -3180.7312   -2721.7441    969.24936    11950.115 
+     690    304.71609   -3176.9196   -2723.6775    1040.2699    11950.115 
+     700    300.31995   -3175.5245   -2728.8213     1082.845    11950.115 
+     710    296.43537   -3173.0166   -2732.0915    1127.4487    11950.115 
+     720    293.86692   -3172.1582   -2735.0535    1135.0215    11950.115 
+     730    293.35611   -3170.9335   -2734.5885    1122.9143    11950.115 
+     740    295.44861   -3172.9862   -2733.5288     1050.995    11950.115 
+     750    299.82732   -3175.3467   -2729.3763    958.31462    11950.115 
+     760    305.37987    -3178.216   -2723.9866     854.1946    11950.115 
+     770    310.75394   -3182.8127   -2720.5898    737.72668    11950.115 
+     780    314.81395   -3183.7905   -2715.5286    679.74198    11950.115 
+     790    316.63339   -3185.8028   -2714.8346    638.48871    11950.115 
+     800     315.2894   -3186.9345   -2717.9654    641.53256    11950.115 
+     810    310.54289   -3183.7383   -2721.8293    728.51241    11950.115 
+     820    303.31439   -3178.7897   -2727.6326    864.45674    11950.115 
+     830    295.46125   -3175.5387   -2736.0625    997.72969    11950.115 
+     840      288.802   -3169.6502   -2740.0791    1160.6622    11950.115 
+     850    283.94785   -3165.8605   -2743.5096      1289.55    11950.115 
+     860    280.17501   -3163.0381    -2746.299    1392.8854    11950.115 
+     870     277.2456   -3159.8429   -2747.4611    1481.3899    11950.115 
+     880    275.93123   -3158.3584   -2747.9316    1523.5374    11950.115 
+     890     277.0215   -3159.2285     -2747.18    1506.1558    11950.115 
+     900    280.96237    -3162.483   -2744.5728    1428.4183    11950.115 
+     910    287.37962   -3167.6183   -2740.1628    1303.0268    11950.115 
+     920    294.56731   -3171.6765   -2733.5299     1177.748    11950.115 
+     930    300.63273   -3174.0842   -2726.9158    1078.7393    11950.115 
+     940    304.10943   -3175.9847    -2723.645    1007.7154    11950.115 
+     950    304.64845   -3176.6263   -2723.4848    976.37917    11950.115 
+     960    303.36343   -3176.4694   -2725.2393    971.40749    11950.115 
+     970    302.57138   -3177.5541   -2727.5021    954.01115    11950.115 
+     980     304.2593   -3179.2101   -2726.6475    919.74949    11950.115 
+     990    307.69959   -3180.9631   -2723.2833     874.9594    11950.115 
+    1000     310.3971   -3181.9675   -2720.2753    842.81184    11950.115 
+Loop time of 0.279202 on 1 procs for 1000 steps with 500 atoms
+
+Performance: 309.453 ns/day, 0.078 hours/ns, 3581.633 timesteps/s
+99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.24196    | 0.24196    | 0.24196    |   0.0 | 86.66
+Bond    | 6.628e-05  | 6.628e-05  | 6.628e-05  |   0.0 |  0.02
+Neigh   | 0.0043204  | 0.0043204  | 0.0043204  |   0.0 |  1.55
+Comm    | 0.010242   | 0.010242   | 0.010242   |   0.0 |  3.67
+Output  | 0.0012252  | 0.0012252  | 0.0012252  |   0.0 |  0.44
+Modify  | 0.017572   | 0.017572   | 0.017572   |   0.0 |  6.29
+Other   |            | 0.003811   |            |       |  1.37
+
+Nlocal:    500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1610 ave 1610 max 1610 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    14767 ave 14767 max 14767 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 14767
+Ave neighs/atom = 29.534
+Ave special neighs/atom = 0
+Neighbor list builds = 5
+Dangerous builds = 0
+
+#write_data      lj-out.data
+Total wall time: 0:00:00
--- a/examples/USER/misc/grem/lj-single/log.gREM-nvt.9Nov16.g++.4
+++ b/examples/USER/misc/grem/lj-single/log.gREM-nvt.9Nov16.g++.4
@ -0,0 +1,173 @@
+LAMMPS (9 Nov 2016)
+  using 1 OpenMP thread(s) per MPI task
+# LJ particles
+variable        T0 equal 300.0
+variable        press equal 0.0
+
+units           real
+atom_style      full
+pair_style      lj/cut 5.0
+
+read_data       "lj.data"
+  orthogonal box = (1.06874 1.06874 1.06874) to (23.9313 23.9313 23.9313)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  500 atoms
+  reading velocities ...
+  500 velocities
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+
+thermo          10
+thermo_style    custom step temp pe etotal press vol
+
+timestep        1.0
+
+fix             fxnvt all nvt temp ${T0} ${T0} 1000.0
+fix             fxnvt all nvt temp 300 ${T0} 1000.0
+fix             fxnvt all nvt temp 300 300 1000.0
+fix             fxgREM all grem 400 -.01 -30000 fxnvt
+run             1000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7
+  ghost atom cutoff = 7
+  binsize = 3.5 -> bins = 7 7 7
+Memory usage per processor = 5.34276 Mbytes
+Step Temp PotEng TotEng Press Volume 
+       0    305.69499   -3177.6423   -2722.9442    883.58369    11950.115 
+      10    312.30121   -3182.2257   -2717.7013    793.47811    11950.115 
+      20    314.94553   -3186.4559   -2717.9983    738.74091    11950.115 
+      30    312.22861   -3183.7638   -2719.3474    797.47978    11950.115 
+      40    305.93987   -3180.7079   -2725.6455    881.30806    11950.115 
+      50    300.42132   -3176.5828   -2729.7288    967.92042    11950.115 
+      60    299.16487   -3174.1921   -2729.2071     1004.247    11950.115 
+      70    301.65565   -3176.0891   -2727.3992    962.58134    11950.115 
+      80    304.77334   -3178.2663    -2724.939     907.8946    11950.115 
+      90    305.59929   -3178.9472   -2724.3914    879.91629    11950.115 
+     100    303.79263   -3177.5103   -2725.6418    892.67631    11950.115 
+     110    300.85863   -3175.4711   -2727.9667    923.44924    11950.115 
+     120    298.69083   -3175.6415   -2731.3615    931.87518    11950.115 
+     130    298.38415   -3176.3706   -2732.5468    928.88286    11950.115 
+     140    299.99129   -3177.6935   -2731.4792    914.36783    11950.115 
+     150    301.83869    -3178.121   -2729.1588    915.01407    11950.115 
+     160    301.18834   -3177.3117   -2729.3169    947.45228    11950.115 
+     170    296.99406   -3172.7363   -2730.9801    1042.6928    11950.115 
+     180    291.25952   -3168.3407   -2735.1142    1144.5436    11950.115 
+     190     287.1178   -3164.9847   -2737.9187    1223.4003    11950.115 
+     200      286.552   -3165.2799   -2739.0555    1235.6703    11950.115 
+     210    289.81033   -3167.8062   -2736.7353    1194.6672    11950.115 
+     220    296.09616   -3171.7847   -2731.3641    1115.8799    11950.115 
+     230    303.79176   -3176.2893   -2724.4221    1024.6471    11950.115 
+     240     309.9273   -3180.9591   -2719.9657    945.55045    11950.115 
+     250     312.0159   -3182.3307   -2718.2306    934.36956    11950.115 
+     260    309.63264   -3181.0452   -2720.4901    986.77385    11950.115 
+     270    304.38172    -3176.568   -2723.8233     1097.264    11950.115 
+     280    298.64188   -3174.1384   -2729.9313    1186.2239    11950.115 
+     290    294.76686   -3170.9562   -2732.5128     1264.247    11950.115 
+     300    294.00805   -3169.8091   -2732.4944    1287.4001    11950.115 
+     310    296.41801    -3172.834   -2731.9347    1229.5624    11950.115 
+     320    301.38477   -3175.9514   -2727.6644    1140.8664    11950.115 
+     330    307.86584   -3181.2442   -2723.3171    1007.1545    11950.115 
+     340     314.7103   -3185.9891   -2717.8814    871.74528    11950.115 
+     350    320.53954   -3187.8385   -2711.0602    776.85994    11950.115 
+     360    323.49505   -3188.9927   -2707.8184    716.58062    11950.115 
+     370    321.62077   -3187.1246   -2708.7381    731.01909    11950.115 
+     380    314.39049   -3181.4931   -2713.8611    831.21057    11950.115 
+     390    303.57079   -3174.1804   -2722.6419    978.62645    11950.115 
+     400    293.42165   -3167.0452   -2730.6027    1122.3558    11950.115 
+     410    288.46838   -3165.4071   -2736.3322    1171.8087    11950.115 
+     420    290.30766   -3168.5988   -2736.7882    1122.5413    11950.115 
+     430    296.34338   -3173.0824   -2732.2941    1030.2769    11950.115 
+     440    301.92394   -3175.4307   -2726.3417    964.25387    11950.115 
+     450    303.76745   -3176.9122   -2725.0811    934.49176    11950.115 
+     460    301.72985   -3174.2821   -2725.4818    979.07605    11950.115 
+     470    298.93736   -3173.0014   -2728.3548    1020.0482    11950.115 
+     480    298.80912    -3172.803   -2728.3471    1036.6531    11950.115 
+     490    302.72217   -3175.3764   -2725.1001    997.71146    11950.115 
+     500    309.11393   -3179.3088   -2719.5253    925.81108    11950.115 
+     510    314.37612   -3183.2961   -2715.6855    856.23748    11950.115 
+     520    315.72767    -3183.547    -2713.926    847.70543    11950.115 
+     530    313.34173   -3182.2695   -2716.1974    877.30842    11950.115 
+     540    309.84312   -3178.9553   -2718.0871    936.69244    11950.115 
+     550     308.3251   -3177.8582    -2719.248    963.93032    11950.115 
+     560    308.79192   -3176.4834   -2717.1788    989.67643    11950.115 
+     570    307.57194   -3175.8464   -2718.3565    1021.0494    11950.115 
+     580     301.8035   -3173.1582   -2724.2483    1102.4893    11950.115 
+     590    292.43425    -3165.751   -2730.7772    1254.7815    11950.115 
+     600    283.62905   -3159.8987    -2738.022    1381.0608    11950.115 
+     610    279.90122     -3157.49   -2741.1581    1431.0028    11950.115 
+     620     283.4582    -3160.756   -2739.1334    1367.7385    11950.115 
+     630    292.58866   -3166.3469   -2731.1435    1241.1194    11950.115 
+     640    302.86585   -3173.4778   -2722.9878    1089.7342    11950.115 
+     650    309.89252   -3179.4078   -2718.4662     972.6359    11950.115 
+     660    312.19165   -3182.7754    -2718.414    916.62037    11950.115 
+     670     311.2287   -3181.9102   -2718.9811    933.79804    11950.115 
+     680    308.57852   -3180.7312   -2721.7441    969.24936    11950.115 
+     690    304.71609   -3176.9196   -2723.6775    1040.2699    11950.115 
+     700    300.31995   -3175.5245   -2728.8213     1082.845    11950.115 
+     710    296.43537   -3173.0166   -2732.0915    1127.4487    11950.115 
+     720    293.86692   -3172.1582   -2735.0535    1135.0215    11950.115 
+     730    293.35611   -3170.9335   -2734.5885    1122.9143    11950.115 
+     740    295.44861   -3172.9862   -2733.5288     1050.995    11950.115 
+     750    299.82732   -3175.3467   -2729.3763    958.31462    11950.115 
+     760    305.37987    -3178.216   -2723.9866     854.1946    11950.115 
+     770    310.75394   -3182.8127   -2720.5898    737.72668    11950.115 
+     780    314.81395   -3183.7905   -2715.5286    679.74198    11950.115 
+     790    316.63339   -3185.8028   -2714.8346    638.48871    11950.115 
+     800     315.2894   -3186.9345   -2717.9654    641.53256    11950.115 
+     810    310.54289   -3183.7383   -2721.8293    728.51241    11950.115 
+     820    303.31439   -3178.7897   -2727.6326    864.45674    11950.115 
+     830    295.46125   -3175.5387   -2736.0625    997.72969    11950.115 
+     840      288.802   -3169.6502   -2740.0791    1160.6622    11950.115 
+     850    283.94785   -3165.8605   -2743.5096      1289.55    11950.115 
+     860    280.17501   -3163.0381    -2746.299    1392.8854    11950.115 
+     870     277.2456   -3159.8429   -2747.4611    1481.3899    11950.115 
+     880    275.93123   -3158.3584   -2747.9316    1523.5374    11950.115 
+     890     277.0215   -3159.2285     -2747.18    1506.1558    11950.115 
+     900    280.96237    -3162.483   -2744.5728    1428.4183    11950.115 
+     910    287.37962   -3167.6183   -2740.1628    1303.0268    11950.115 
+     920    294.56731   -3171.6765   -2733.5299     1177.748    11950.115 
+     930    300.63273   -3174.0842   -2726.9158    1078.7393    11950.115 
+     940    304.10943   -3175.9847    -2723.645    1007.7154    11950.115 
+     950    304.64845   -3176.6263   -2723.4848    976.37917    11950.115 
+     960    303.36343   -3176.4694   -2725.2393    971.40749    11950.115 
+     970    302.57138   -3177.5541   -2727.5021    954.01115    11950.115 
+     980     304.2593   -3179.2101   -2726.6475    919.74949    11950.115 
+     990    307.69959   -3180.9631   -2723.2833     874.9594    11950.115 
+    1000     310.3971   -3181.9675   -2720.2753    842.81184    11950.115 
+Loop time of 0.133894 on 4 procs for 1000 steps with 500 atoms
+
+Performance: 645.285 ns/day, 0.037 hours/ns, 7468.580 timesteps/s
+98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.065271   | 0.071043   | 0.07818    |   1.9 | 53.06
+Bond    | 5.6505e-05 | 6.5565e-05 | 7.7724e-05 |   0.1 |  0.05
+Neigh   | 0.0011396  | 0.0012607  | 0.0013669  |   0.2 |  0.94
+Comm    | 0.033866   | 0.040269   | 0.045386   |   2.6 | 30.08
+Output  | 0.0019252  | 0.0020776  | 0.0023642  |   0.4 |  1.55
+Modify  | 0.012141   | 0.013629   | 0.01486    |   0.9 | 10.18
+Other   |            | 0.005549   |            |       |  4.14
+
+Nlocal:    125 ave 127 max 123 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost:    871.25 ave 882 max 863 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs:    3691.75 ave 3808 max 3563 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+
+Total # of neighbors = 14767
+Ave neighs/atom = 29.534
+Ave special neighs/atom = 0
+Neighbor list builds = 5
+Dangerous builds = 0
+
+#write_data      lj-out.data
+Total wall time: 0:00:00
--- a/Show More
+++ b/Show More