patch 16Dec16

Merge pull request #301 from akohlmey/corrections-and-bugfixes
Collected corrections and bugfixes
2016-12-16 10:30:57 -07:00 · 2016-12-16 10:25:29 -07:00 · 2016-12-16 10:24:25 -07:00 · 2016-12-16 11:22:25 -05:00 · 2016-12-16 11:21:15 -05:00 · 2016-12-16 10:25:12 -05:00
806 changed files with 58854 additions and 17874 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/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="16 Dec 2016 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@ -21,7 +21,7 @@
 <H1></H1>
 LAMMPS Documentation :c,h3
-17 Nov 2016 version :c,h4
+16 Dec 2016 version :c,h4
 Version info: :h4
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@ -531,7 +531,8 @@ package"_Section_start.html#start_3.
 "dump nc"_dump_nc.html,
 "dump nc/mpiio"_dump_nc.html,
 "group2ndx"_group2ndx.html,
-"ndx2group"_group2ndx.html :tb(c=3,ea=c)
+"ndx2group"_group2ndx.html,
 "temper/grem"_temper_grem.html :tb(c=3,ea=c)
 :line
@ -632,10 +633,10 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "rigid/nve (o)"_fix_rigid.html,
 "rigid/nvt (o)"_fix_rigid.html,
 "rigid/small (o)"_fix_rigid.html,
-"rigid/small/nph"_fix_rigid.html,
+"rigid/small/nph (o)"_fix_rigid.html,
-"rigid/small/npt"_fix_rigid.html,
+"rigid/small/npt (o)"_fix_rigid.html,
-"rigid/small/nve"_fix_rigid.html,
+"rigid/small/nve (o)"_fix_rigid.html,
-"rigid/small/nvt"_fix_rigid.html,
+"rigid/small/nvt (o)"_fix_rigid.html,
 "setforce (k)"_fix_setforce.html,
 "shake"_fix_shake.html,
 "spring"_fix_spring.html,
@ -687,6 +688,7 @@ package"_Section_start.html#start_3.
 "eos/table/rx"_fix_eos_table_rx.html,
 "flow/gauss"_fix_flow_gauss.html,
 "gle"_fix_gle.html,
 "grem"_fix_grem.html,
 "imd"_fix_imd.html,
 "ipi"_fix_ipi.html,
 "langevin/drude"_fix_langevin_drude.html,
@ -765,6 +767,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "erotate/sphere"_compute_erotate_sphere.html,
 "erotate/sphere/atom"_compute_erotate_sphere_atom.html,
 "event/displace"_compute_event_displace.html,
 "global/atom"_compute_global_atom.html,
 "group/group"_compute_group_group.html,
 "gyration"_compute_gyration.html,
 "gyration/chunk"_compute_gyration_chunk.html,
@ -911,8 +914,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "coul/msm"_pair_coul.html,
 "coul/streitz"_pair_coul.html,
 "coul/wolf (ko)"_pair_coul.html,
-"dpd (o)"_pair_dpd.html,
+"dpd (go)"_pair_dpd.html,
-"dpd/tstat (o)"_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 *)
+void lammps_reset_box(void *, double *, double *, double, double, double)
-double lammps_get_thermo(void *, char *) :pre
+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
+access the variable.
-current value of a thermo keyword as a double.
+
 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
+velocities and image flags.  It uses the coords of each atom to assign
-atom to the processor that owns it.  Additional properties for the new
+it as a new atom to the processor that owns it.  This function is
-atoms can be assigned via the lammps_scatter_atoms() or
+useful to add atoms to a simulation or (in tandem with
-lammps_extract_atom() functions.
+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_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_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
--- 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
@ -310,6 +311,7 @@ compute_erotate_sphere.html
 compute_erotate_sphere_atom.html
 compute_event_displace.html
 compute_fep.html
 compute_global_atom.html
 compute_group_group.html
 compute_gyration.html
 compute_gyration_chunk.html
--- 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/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_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/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/examples/USER/misc/grem/lj-temper/0/lj.data
+++ b/examples/USER/misc/grem/lj-temper/0/lj.data
--- a/examples/USER/misc/grem/lj-temper/0/log.lammps.0
+++ b/examples/USER/misc/grem/lj-temper/0/log.lammps.0
--- a/examples/USER/misc/grem/lj-temper/1/lj.data
+++ b/examples/USER/misc/grem/lj-temper/1/lj.data
--- a/examples/USER/misc/grem/lj-temper/1/log.lammps.1
+++ b/examples/USER/misc/grem/lj-temper/1/log.lammps.1
--- a/examples/USER/misc/grem/lj-temper/2/lj.data
+++ b/examples/USER/misc/grem/lj-temper/2/lj.data
--- a/examples/USER/misc/grem/lj-temper/2/log.lammps.2
+++ b/examples/USER/misc/grem/lj-temper/2/log.lammps.2
--- a/examples/USER/misc/grem/lj-temper/3/lj.data
+++ b/examples/USER/misc/grem/lj-temper/3/lj.data
--- a/examples/USER/misc/grem/lj-temper/3/log.lammps.3
+++ b/examples/USER/misc/grem/lj-temper/3/log.lammps.3
--- a/examples/USER/misc/grem/lj-temper/in.gREM-temper
+++ b/examples/USER/misc/grem/lj-temper/in.gREM-temper
@ -0,0 +1,31 @@
 # LJ particles
 variable        lambda world 900 910 920 930
 variable        rep world 0 1 2 3 
 #variable        walker world 0 1 3 2
 variable        T0 equal 300.0
 variable        press equal 0.0
 units           real
 atom_style      full
 pair_style      lj/cut 5.0
 # LJ particles
 log             ${rep}/log.lammps.${rep}
 print           "This is replica: ${rep}"
 read_data       ${rep}/lj.data
 #dump            dump all xyz 1000 ${rep}/dump.xyz
 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 ${lambda} -.03 -30000 fxnpt
 thermo_modify   press fxgREM_press
 temper/grem            10000 100 ${lambda} fxgREM fxnpt 10294 98392 #${walker}
 #write_data      ${rep}/lj-out.data
--- a/examples/USER/smd/aluminum_strip_pull/aluminum_strip_pull.lmp
+++ b/examples/USER/smd/aluminum_strip_pull/aluminum_strip_pull.lmp
@ -103,14 +103,14 @@ fix             integration_fix tlsph smd/integrate_tlsph
 ####################################################################################################
 # SPECIFY TRAJECTORY OUTPUT
 ####################################################################################################
-compute         dt_atom all smd/tlsph_dt
+compute         dt_atom all smd/tlsph/dt
-compute 	p all smd/plastic_strain
+compute 	p all smd/plastic/strain
-compute 	epsdot all smd/plastic_strain_rate
+compute 	epsdot all smd/plastic/strain/rate
-compute 	S all smd/tlsph_stress # Cauchy stress tensor
+compute 	S all smd/tlsph/stress # Cauchy stress tensor
-compute 	D all smd/tlsph_strain_rate
+compute 	D all smd/tlsph/strain/rate
-compute 	E all smd/tlsph_strain
+compute 	E all smd/tlsph/strain
-compute 	nn all smd/tlsph_num_neighs # number of neighbors for each particle
+compute 	nn all smd/tlsph/num/neighs # number of neighbors for each particle
-compute         shape all smd/tlsph_shape
+compute         shape all smd/tlsph/shape
 compute 	damage all smd/damage
 dump 		dump_id all custom 100 dump.LAMMPS id type x y z &
 			c_S[1] c_S[2] c_S[3] c_S[4] c_S[5] c_S[6] c_S[7] c_nn c_p &
--- a/examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp
+++ b/examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp
@ -124,11 +124,11 @@ fix             integration_fix_solids solids smd/integrate_tlsph
 ####################################################################################################
 # SPECIFY TRAJECTORY OUTPUT
 ####################################################################################################
-compute         eint all smd/internal_energy
+compute         eint all smd/internal/energy
-compute         contact_radius all smd/contact_radius
+compute         contact_radius all smd/contact/radius
-compute         S solids smd/tlsph_stress
+compute         S solids smd/tlsph/stress
-compute         nn water smd/ulsph_num_neighs
+compute         nn water smd/ulsph/num/neighs
-compute         epl solids smd/plastic_strain
+compute         epl solids smd/plastic/strain
 compute         vol all smd/volume
 compute         rho all smd/rho
--- a/examples/USER/smd/funnel_flow/funnel_flow.lmp
+++ b/examples/USER/smd/funnel_flow/funnel_flow.lmp
@ -98,9 +98,9 @@ fix             integration_fix all smd/integrate_ulsph adjust_radius 1.01 10 15
 ####################################################################################################
 variable        dumpFreq equal 100
 compute 	rho all smd/rho
-compute 	nn all smd/ulsph_num_neighs # number of neighbors for each particle
+compute 	nn all smd/ulsph/num/neighs # number of neighbors for each particle
-compute         contact_radius all smd/contact_radius
+compute         contact_radius all smd/contact/radius
-compute         surface_coords surface smd/triangle_vertices
+compute         surface_coords surface smd/triangle/vertices
 dump 		dump_id water custom ${dumpFreq} dump.LAMMPS id type x y z vx vy vz &
@ -116,7 +116,7 @@ dump_modify 	surf_dump first yes
 ####################################################################################################
 # STATUS OUTPUT
 ####################################################################################################
-compute         eint all smd/internal_energy
+compute         eint all smd/internal/energy
 compute         alleint all reduce sum c_eint
 variable        etot equal pe+ke+c_alleint+f_gfix # total energy of the system
 thermo 100
--- a/examples/USER/smd/rubber_rings_3d/rubber_rings_3d.lmp
+++ b/examples/USER/smd/rubber_rings_3d/rubber_rings_3d.lmp
@ -88,11 +88,11 @@ fix             integration_fix tlsph smd/integrate_tlsph
 # SPECIFY TRAJECTORY OUTPUT
 ####################################################################################################
 variable        dumpFreq equal 30
-compute         S all smd/tlsph_stress # Cauchy stress tensor
+compute         S all smd/tlsph/stress # Cauchy stress tensor
-compute         nn all smd/tlsph_num_neighs # number of neighbors for each particle
+compute         nn all smd/tlsph/num/neighs # number of neighbors for each particle
-compute         cr all smd/contact_radius
+compute         cr all smd/contact/radius
-compute         p all smd/plastic_strain
+compute         p all smd/plastic/strain
-compute         eint all smd/internal_energy
+compute         eint all smd/internal/energy
 compute         alleint all reduce sum c_eint
 variable        etot equal c_alleint+ke+pe
--- a/examples/USER/smd/rubber_strip_pull/rubber_strip_pull.lmp
+++ b/examples/USER/smd/rubber_strip_pull/rubber_strip_pull.lmp
@ -49,7 +49,7 @@ variable        vol_one equal ${l0}^2 # volume of one particle -- assuming unit
 variable        skin equal ${h} # Verlet list range
 neighbor        ${skin} bin
 set             group all volume ${vol_one}
-set             group all smd_mass_density ${rho}
+set             group all smd/mass/density ${rho}
 set             group all diameter ${h} # set SPH kernel radius
 ####################################################################################################
@ -83,9 +83,9 @@ fix             integration_fix tlsph smd/integrate_tlsph
 ####################################################################################################
 # SPECIFY TRAJECTORY OUTPUT
 ####################################################################################################
-compute         S all smd/tlsph_stress # Cauchy stress tensor
+compute         S all smd/tlsph/stress # Cauchy stress tensor
-compute         E all smd/tlsph_strain # Green-Lagrange strain tensor
+compute         E all smd/tlsph/strain # Green-Lagrange strain tensor
-compute         nn all smd/tlsph_num_neighs # number of neighbors for each particle
+compute         nn all smd/tlsph/num/neighs # number of neighbors for each particle
 dump            dump_id all custom 10 dump.LAMMPS id type x y z vx vy vz &
                        c_S[1] c_S[2] c_S[4] c_nn &
                        c_E[1] c_E[2] c_E[4] &
--- a/python/examples/pylammps/.gitignore
+++ b/python/examples/pylammps/.gitignore
--- a/python/examples/pylammps/README
+++ b/python/examples/pylammps/README
@ -0,0 +1,28 @@
 # Compile LAMMPS as shared library
 git clone https://github.com/lammps/lammps.git
 cd lammps/src
 python Make.py -m mpi -png -s ffmpeg exceptions -a file
 make -j 4 mode=shlib auto
 cd ../..
 # Install Python package
 virtualenv testing
 source testing/bin/activate
 (testing) cd lammps/python
 (testing) python install.py
 (testing) pip install jupyter matplotlib mpi4py
 (testing) cd ../../examples
 # Launch jupter and work inside browser
 (testing) jupyter notebook
 # Use Ctrl+c to stop jupyter
 # finally exit the virtualenv
 (testing) deactivate
--- a/python/examples/pylammps/dihedrals/data.dihedral
+++ b/python/examples/pylammps/dihedrals/data.dihedral
@ -0,0 +1,34 @@
 Comment line
 4 atoms
 0 bonds
 0 angles
 1 dihedrals
 0 impropers
 1 atom types
 0 bond types
 0 angle types
 1 dihedral types
 0 improper types
 -5.0   5.0      xlo xhi
 -5.0   5.0      ylo yhi
 -5.0   5.0      zlo zhi
 0.0   0.0   0.0   xy xz yz
 Atoms # molecular
 1      1   1     -1.00000     1.00000      0.00000
 2      1   1     -0.50000     0.00000      0.00000
 3      1   1      0.50000     0.00000      0.00000
 4      1   1      1.00000     1.00000      0.00000
 Dihedral Coeffs
 1      80.0   1   2
 Dihedrals
 1      1   1  2  3  4
--- a/python/examples/pylammps/dihedrals/dihedral.ipynb
+++ b/python/examples/pylammps/dihedrals/dihedral.ipynb
--- a/python/examples/pylammps/interface_usage.ipynb
+++ b/python/examples/pylammps/interface_usage.ipynb
--- a/python/examples/pylammps/interface_usage_bonds.ipynb
+++ b/python/examples/pylammps/interface_usage_bonds.ipynb
--- a/python/examples/pylammps/montecarlo/mc.ipynb
+++ b/python/examples/pylammps/montecarlo/mc.ipynb
--- a/python/examples/pylammps/mpi4py/hello.py
+++ b/python/examples/pylammps/mpi4py/hello.py
@ -0,0 +1,4 @@
 from mpi4py import MPI
 comm=MPI.COMM_WORLD
 print("Hello from rank %d of %d" % (comm.rank, comm.size))
--- a/python/examples/pylammps/mpi4py/in.melt
+++ b/python/examples/pylammps/mpi4py/in.melt
@ -0,0 +1,33 @@
 # 3d Lennard-Jones melt
 units		lj
 atom_style	atomic
 lattice		fcc 0.8442
 region		box block 0 10 0 10 0 10
 create_box	1 box
 create_atoms	1 box
 mass		1 1.0
 velocity	all create 3.0 87287
 pair_style	lj/cut 2.5
 pair_coeff	1 1 1.0 1.0 2.5
 neighbor	0.3 bin
 neigh_modify	every 20 delay 0 check no
 fix		1 all nve
 #dump		id all atom 50 dump.melt
 #dump		2 all image 25 image.*.jpg type type &
 #		axes yes 0.8 0.02 view 60 -30
 #dump_modify	2 pad 3
 #dump		3 all movie 25 movie.mpg type type &
 #		axes yes 0.8 0.02 view 60 -30
 #dump_modify	3 pad 3
 thermo		50
 run		250
--- a/python/examples/pylammps/mpi4py/melt.py
+++ b/python/examples/pylammps/mpi4py/melt.py
@ -0,0 +1,10 @@
 from mpi4py import MPI
 from lammps import PyLammps
 L = PyLammps()
 L.file('in.melt')
 if MPI.COMM_WORLD.rank == 0:
    pe = L.eval("pe")
    print("Potential Energy:", pe)
--- a/python/examples/pylammps/simple.ipynb
+++ b/python/examples/pylammps/simple.ipynb
--- a/src/.gitignore
+++ b/src/.gitignore
@ -18,6 +18,8 @@
 /*_tally.cpp
 /*_rx.h
 /*_rx.cpp
 /*_ssa.h
 /*_ssa.cpp
 /kokkos.cpp
 /kokkos.h
@ -205,6 +207,8 @@
 /compute_pe_tally.h
 /compute_plasticity_atom.cpp
 /compute_plasticity_atom.h
 /compute_pressure_grem.cpp
 /compute_pressure_grem.h
 /compute_rigid_local.cpp
 /compute_rigid_local.h
 /compute_spec_atom.cpp
@ -343,6 +347,8 @@
 /fix_gle.h
 /fix_gpu.cpp
 /fix_gpu.h
 /fix_grem.cpp
 /fix_grem.h
 /fix_imd.cpp
 /fix_imd.h
 /fix_ipi.cpp
@ -775,6 +781,8 @@
 /pair_tersoff.h
 /pair_tersoff_mod.cpp
 /pair_tersoff_mod.h
 /pair_tersoff_mod_c.cpp
 /pair_tersoff_mod_c.h
 /pair_tersoff_table.cpp
 /pair_tersoff_table.h
 /pair_tersoff_zbl.cpp
@ -873,6 +881,8 @@
 /tad.h
 /temper.cpp
 /temper.h
 /temper_grem.cpp
 /temper_grem.h
 /thr_data.cpp
 /thr_data.h
 /verlet_split.cpp
--- a/src/KOKKOS/Install.sh
+++ b/src/KOKKOS/Install.sh
@ -105,11 +105,16 @@ action modify_kokkos.cpp
 action modify_kokkos.h
 action neigh_bond_kokkos.cpp
 action neigh_bond_kokkos.h
 action neigh_full_kokkos.h
 action neigh_list_kokkos.cpp
 action neigh_list_kokkos.h
 action neighbor_kokkos.cpp
 action neighbor_kokkos.h
 action npair_copy_kokkos.cpp
 action npair_copy_kokkos.h
 action npair_kokkos.cpp
 action npair_kokkos.h
 action nbin_kokkos.cpp
 action nbin_kokkos.h
 action math_special_kokkos.cpp
 action math_special_kokkos.h
 action pair_buck_coul_cut_kokkos.cpp
--- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
@ -125,12 +125,10 @@ void FixQEqReaxKokkos<DeviceType>::init()
      neighbor->requests[irequest]->pair = 0;
      neighbor->requests[irequest]->full = 1;
      neighbor->requests[irequest]->half = 0;
      neighbor->requests[irequest]->full_cluster = 0;
    } else { //if (neighflag == HALF || neighflag == HALFTHREAD)
      neighbor->requests[irequest]->fix = 1;
      neighbor->requests[irequest]->full = 0;
      neighbor->requests[irequest]->half = 1;
      neighbor->requests[irequest]->full_cluster = 0;
      neighbor->requests[irequest]->ghost = 1;
    }
  }
--- a/src/KOKKOS/kokkos.cpp
+++ b/src/KOKKOS/kokkos.cpp
@ -168,7 +168,6 @@ void KokkosLMP::accelerator(int narg, char **arg)
        else 
          neighflag = HALF;
      } else if (strcmp(arg[iarg+1],"n2") == 0) neighflag = N2;
      else if (strcmp(arg[iarg+1],"full/cluster") == 0) neighflag = FULLCLUSTER;
      else error->all(FLERR,"Illegal package kokkos command");
      iarg += 2;
    } else if (strcmp(arg[iarg],"binsize") == 0) {
@ -232,20 +231,6 @@ void KokkosLMP::accelerator(int narg, char **arg)
   called by Finish
 ------------------------------------------------------------------------- */
 int KokkosLMP::neigh_list_kokkos(int m)
 {
  NeighborKokkos *nk = (NeighborKokkos *) neighbor;
  if (nk->lists_host[m] && nk->lists_host[m]->d_numneigh.dimension_0())
    return 1;
  if (nk->lists_device[m] && nk->lists_device[m]->d_numneigh.dimension_0())
    return 1;
  return 0;
 }
 /* ----------------------------------------------------------------------
   called by Finish
 ------------------------------------------------------------------------- */
 int KokkosLMP::neigh_count(int m)
 {
  int inum;
@ -255,28 +240,30 @@ int KokkosLMP::neigh_count(int m)
  ArrayTypes<LMPHostType>::t_int_1d h_numneigh;
  NeighborKokkos *nk = (NeighborKokkos *) neighbor;
-  if (nk->lists_host[m]) {
+  if (nk->lists[m]->execution_space == Host) {
-    inum = nk->lists_host[m]->inum;
+    NeighListKokkos<LMPHostType>* nlistKK = (NeighListKokkos<LMPHostType>*) nk->lists[m];
    inum = nlistKK->inum;
 #ifndef KOKKOS_USE_CUDA_UVM
-    h_ilist = Kokkos::create_mirror_view(nk->lists_host[m]->d_ilist);
+    h_ilist = Kokkos::create_mirror_view(nlistKK->d_ilist);
-    h_numneigh = Kokkos::create_mirror_view(nk->lists_host[m]->d_numneigh);
+    h_numneigh = Kokkos::create_mirror_view(nlistKK->d_numneigh);
 #else
-    h_ilist = nk->lists_host[m]->d_ilist;
+    h_ilist = nlistKK->d_ilist;
-    h_numneigh = nk->lists_host[m]->d_numneigh;
+    h_numneigh = nlistKK->d_numneigh;
 #endif
-    Kokkos::deep_copy(h_ilist,nk->lists_host[m]->d_ilist);
+    Kokkos::deep_copy(h_ilist,nlistKK->d_ilist);
-    Kokkos::deep_copy(h_numneigh,nk->lists_host[m]->d_numneigh);
+    Kokkos::deep_copy(h_numneigh,nlistKK->d_numneigh);
-  } else if (nk->lists_device[m]) {
+  } else if (nk->lists[m]->execution_space == Device) {
-    inum = nk->lists_device[m]->inum;
+    NeighListKokkos<LMPDeviceType>* nlistKK = (NeighListKokkos<LMPDeviceType>*) nk->lists[m];
    inum = nlistKK->inum;
 #ifndef KOKKOS_USE_CUDA_UVM
-    h_ilist = Kokkos::create_mirror_view(nk->lists_device[m]->d_ilist);
+    h_ilist = Kokkos::create_mirror_view(nlistKK->d_ilist);
-    h_numneigh = Kokkos::create_mirror_view(nk->lists_device[m]->d_numneigh);
+    h_numneigh = Kokkos::create_mirror_view(nlistKK->d_numneigh);
 #else
-    h_ilist = nk->lists_device[m]->d_ilist;
+    h_ilist = nlistKK->d_ilist;
-    h_numneigh = nk->lists_device[m]->d_numneigh;
+    h_numneigh = nlistKK->d_numneigh;
 #endif
-    Kokkos::deep_copy(h_ilist,nk->lists_device[m]->d_ilist);
+    Kokkos::deep_copy(h_ilist,nlistKK->d_ilist);
-    Kokkos::deep_copy(h_numneigh,nk->lists_device[m]->d_numneigh);
+    Kokkos::deep_copy(h_numneigh,nlistKK->d_numneigh);
  }
  for (int i = 0; i < inum; i++) nneigh += h_numneigh[h_ilist[i]];
--- a/src/KOKKOS/kokkos.h
+++ b/src/KOKKOS/kokkos.h
@ -34,7 +34,6 @@ class KokkosLMP : protected Pointers {
  KokkosLMP(class LAMMPS *, int, char **);
  ~KokkosLMP();
  void accelerator(int, char **);
  int neigh_list_kokkos(int);
  int neigh_count(int);
 private:
  static void my_signal_handler(int);
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
Steve Plimpton	3027ac9250	patch 16Dec16	2016-12-16 10:30:57 -07:00
sjplimp	fc54ab5cea	Merge pull request #301 from akohlmey/corrections-and-bugfixes Collected corrections and bugfixes	2016-12-16 10:25:29 -07:00
Steve Plimpton	e364b80724	added length keyword to python command	2016-12-16 10:24:25 -07:00
Axel Kohlmeyer	830c9e8661	Merge branch 'USER-DPD_internal_energy' of https://github.com/timattox/lammps_USER-DPD into corrections-and-bugfixes This closes #303	2016-12-16 11:22:25 -05:00
Axel Kohlmeyer	4907b29ad2	Merge branch 'USER-DPD_bugfixes' of https://github.com/timattox/lammps_USER-DPD into corrections-and-bugfixes This closes #302	2016-12-16 11:21:15 -05:00
Tim Mattox	eff7238ff2	USER-DPD: fix_eos*: partition all internal energy into the uMech term only This makes our results more closely match a vetted serial implementation. NOTE: This does make the output different from any previous versions. Patch by Jim Larentzos. Applied by Tim Mattox.	2016-12-16 10:25:12 -05:00
Tim Mattox	126fb22e93	USER-DPD: Fix #define typo in pair_multi_lucy.h and pair_multi_lucy_rx.h	2016-12-16 10:08:30 -05:00
Tim Mattox	0a90492c44	USER-DPD: Update the header files to properly document all error statements Patch by Jim Larentzos. Applied by Tim Mattox.	2016-12-15 17:39:15 -05:00
Tim Mattox	fed629c23e	USER-DPD: Bugfix for fix_rx and fix_eos_table_rx to handle restart files. Patch by Jim Larentzos. Applied by Tim Mattox.	2016-12-15 17:10:13 -05:00
Tim Mattox	925481c3f4	USER-DPD: Fix hard-wall force interaction bug, and ensure fraction is >= 0 pair_exp6_rx.cpp patch by Jim Larentzos. Applied by Tim Mattox.	2016-12-15 16:46:25 -05:00
Axel Kohlmeyer	da2ad5b6e0	update FixIntel code for new neighbor list code	2016-12-14 15:51:12 -05:00
Axel Kohlmeyer	bfcab72268	restore change to make -DLAMMPS_MEMALIGN=64 default when USER-INTEL package is installed (which requires it)	2016-12-14 15:24:55 -05:00
Steve Plimpton	f509f133af	patch 13Dec16: neighbor refactor, Stan pppm/disp bug fix, M Brown INTEL package updates	2016-12-13 17:14:28 -07:00
sjplimp	624c57e9da	Merge pull request #185 from akohlmey/new-neighbor New neighbor list code with updates for USER-OMP and USER-DPD	2016-12-13 16:24:41 -07:00
sjplimp	f3b355bcbe	Merge pull request #298 from akohlmey/collected-small-fixes Collected small fixes	2016-12-13 16:23:23 -07:00
Steve Plimpton	ae5764beac	added functionity to lib interface	2016-12-13 16:22:17 -07:00
Axel Kohlmeyer	fda43c00fd	add deleted file in package to purge list	2016-12-12 13:22:54 -05:00
Axel Kohlmeyer	b34be30be6	Merge pull request #53 from stanmoore1/new-neighbor New neighbor Kokkos	2016-12-12 13:18:03 -05:00
Stan Moore	13b6196b82	Fixing Kokkos compile error	2016-12-12 10:47:39 -07:00
Stan Moore	baf55c90f4	Whitespace change	2016-12-12 09:25:41 -07:00
Stan Moore	770f5d0bf7	Whitespace change	2016-12-12 09:24:37 -07:00
Stan Moore	a31b00965a	Updating to master	2016-12-12 09:18:20 -07:00
Stan Moore	a5e46e3e6a	Merging	2016-12-09 16:20:42 -07:00
Stan Moore	31be0da590	Merging pull request	2016-12-09 16:17:35 -07:00
stanmoore1	0f3b2544a1	Merge pull request #1 from timattox/new-neighbor USER-DPD workaround for neighbor list issues	2016-12-09 16:08:31 -07:00
stanmoore1	586514e05c	Merge branch 'new-neighbor' into new-neighbor	2016-12-09 16:08:08 -07:00
Stan Moore	43c459ba56	More changes for Kokkos neighbor	2016-12-09 15:56:55 -07:00
Axel Kohlmeyer	b5c3d2f66c	Merge pull request #52 from timattox/new-neighbor USER-DPD workaround for neighbor list issues	2016-12-09 17:51:35 -05:00
Tim Mattox	5187cb97e5	USER-DPD: Make fix_shardlow request its own SSA-specific neighbor list, instead of having pair_dpd_fdt* make the SSA-neighbor list request for it. Forces an "extra" list to be built, but now skip lists work properly. Maybe we can detect if skip lists won't be used, and squash the extra list.	2016-12-09 15:42:27 -06:00
Tim Mattox	eff503e56c	Prevent neighbor list copies between SSA and non-SSA neighbor list requests.	2016-12-09 15:39:46 -06:00
Axel Kohlmeyer	cdcebab3bd	make the output of the %CPU/OpenMP threads line consistent with compiling in OpenMP support, not having USER-OMP installed	2016-12-09 14:43:56 -05:00
Axel Kohlmeyer	ddf678da51	make fix gcmc command overview consistent this closes #296	2016-12-09 14:30:27 -05:00
Stan Moore	435421301b	Small tweaks to Kokkos neighbor	2016-12-09 08:37:01 -07:00
Stan Moore	9b48c49f83	Removing used Kokkos file	2016-12-08 09:18:55 -07:00
Efrem Braun	d3d5ac17bf	Fixed small typos in doc	2016-12-07 19:37:51 -08:00
Stan Moore	8318c67816	Kokkos neighbor refactor	2016-12-07 13:00:27 -07:00
Axel Kohlmeyer	7c61dbf5e2	Merge branch 'new-neighbor' of github.com:akohlmey/lammps into new-neighbor	2016-12-07 13:43:04 -05:00
Axel Kohlmeyer	39a12b15d7	Merge branch 'master' into new-neighbor Resolved Conflicts: src/Purge.list src/neigh_derive.cpp	2016-12-07 13:40:14 -05:00
Steve Plimpton	fb3f597f41	30Nov16 patch	2016-11-30 14:04:41 -07:00
sjplimp	d14814ae2e	Merge pull request #289 from akohlmey/collected-updates-and-bugfixes Collected updates and bugfixes	2016-11-30 14:02:41 -07:00
Steve Plimpton	beb5a30f67	new compute global/atom command, also bug fix for descending dump sorts	2016-11-30 14:01:27 -07:00
Axel Kohlmeyer	7ddb6670c0	fix typo	2016-11-30 00:12:35 -05:00
Axel Kohlmeyer	789e62388f	simplify code	2016-11-29 09:03:53 -05:00
Jakub Krajniak	7d098bff90	update format (cherry picked from commit `2597185afb`)	2016-11-29 09:01:36 -05:00
Jakub Krajniak	1d970d3cdf	dihedral_nharmonic: added writing coefficient by write_data (cherry picked from commit `618f5c6aa5`)	2016-11-29 09:01:36 -05:00
Axel Kohlmeyer	42d430168b	fix typo in compute cluster/atom docs this closes #292	2016-11-29 07:24:09 -05:00
Axel Kohlmeyer	5ff5bc2a6c	avoid issues detected by coverity scan	2016-11-28 21:34:35 -05:00
Axel Kohlmeyer	02ae2d218a	correct broken link to USER-SMD docs PDF	2016-11-28 11:34:22 -05:00
Axel Kohlmeyer	470908fc93	explicitly disallow dynamic groups with compute rdf	2016-11-24 05:46:15 -05:00
Steve Plimpton	6759630c16	bug fix for dump sort in descending order	2016-11-23 17:08:36 -07:00
Axel Kohlmeyer	87781771ba	fix typo and USER-OMP support omission	2016-11-23 09:02:32 -05:00
Axel Kohlmeyer	df46b9aa38	rename compute pressure/grem to compute PRESSURE/GREM	2016-11-22 15:25:59 -05:00
Axel Kohlmeyer	647c6f00ce	Merge branch 'grem-feature' of https://github.com/dstelter92/lammps into collected-updates-and-bugfixes	2016-11-22 14:51:19 -05:00
dstelter92	237307eda2	small typo and changes	2016-11-22 12:16:00 -05:00
dstelter92	d58dd4f159	bugfix when parsing mpirun	2016-11-22 12:13:20 -05:00
dstelter92	ae70f1090f	added readme for grem examples	2016-11-22 12:05:14 -05:00
Steve Plimpton	59d100ab57	final prep for 22Nov patch	2016-11-22 09:23:02 -07:00
sjplimp	61e71d23ed	Merge pull request #288 from akohlmey/moltemplate-1.40 update bundled version of moltemplate to v1.40	2016-11-22 08:51:11 -07:00
sjplimp	b6f2f0e6e9	Merge pull request #287 from rbberger/pylammps/docs Created PyLammps documentation	2016-11-22 08:50:29 -07:00
sjplimp	ff0441ac16	Merge pull request #286 from akohlmey/small-fixes-and-updates Collected small fixes and updates	2016-11-22 08:49:46 -07:00
sjplimp	41907d3110	Merge pull request #285 from akohlmey/fix-ipi-update update for fix ipi from michele ceriotti	2016-11-22 08:48:27 -07:00
Steve Plimpton	b95f255af4	small changes to temper/grem commands	2016-11-22 08:47:44 -07:00
sjplimp	d7b542101a	Merge pull request #283 from akohlmey/grem-feature gREM generalized replica exchange feature for USER-MISC	2016-11-22 08:15:35 -07:00
Steve Plimpton	0ffa50f8e8	tweaked author syntax	2016-11-22 08:15:13 -07:00
Axel Kohlmeyer	7893215964	small comment/whitespace tweak	2016-11-21 12:46:43 -05:00
dstelter92	3dff9f2018	removed extra file	2016-11-21 12:05:30 -05:00
dstelter92	dab232c542	modified temper_grem name to fit conventions, re-ran example to match	2016-11-21 12:02:17 -05:00
Axel Kohlmeyer	9e9d9d5aa5	update bundled version of moltemplate to v1.40	2016-11-21 11:34:42 -05:00
Axel Kohlmeyer	c982b174a2	Merge pull request #49 from epfl-cosmo/fix-ipi i-PI interface fix	2016-11-19 19:36:13 -05:00
Michele Ceriotti	87a5a35bad	A tiny bugfix for the reset flag, and a brief explanation of the changes	2016-11-20 00:44:23 +01:00
Michele Ceriotti	fd174ce2b1	Merge branch 'fix-ipi-update' of https://github.com/akohlmey/lammps into fix-ipi	2016-11-20 00:04:56 +01:00
Michele Ceriotti	b11f376a4f	Merge branch 'master' of github.com:lammps/lammps	2016-11-19 23:25:51 +01:00
Axel Kohlmeyer	230b29eae6	correct accelerator flags for dpd styles in pair style overview	2016-11-19 11:47:12 -05:00
Richard Berger	2383c31f15	Created PyLammps documentation Based on material presented during MD Workshop at Temple University in August 2016.	2016-11-18 23:58:57 -07:00
Axel Kohlmeyer	e175a18bdb	be more thorough in initializing optional data in pair style dpd/fdt/energy	2016-11-18 16:18:47 -05:00
Axel Kohlmeyer	a5bde82e37	update .gitignore for recent addition	2016-11-18 15:38:11 -05:00
Axel Kohlmeyer	d787afcca9	also remove generated html files with 'make clean' in docs folder	2016-11-18 15:37:49 -05:00
Axel Kohlmeyer	176cde8ed3	minor cleanups	2016-11-18 15:36:38 -05:00
Axel Kohlmeyer	2862c20815	Merge branch 'master' into grem-feature	2016-11-18 14:51:46 -05:00
Axel Kohlmeyer	78e018829f	Merge branch 'grem-feature' of https://github.com/dstelter92/lammps into grem-feature	2016-11-18 14:48:47 -05:00
Axel Kohlmeyer	c78914e7b3	update for fix ipi from michele ceriotti	2016-11-18 09:21:50 -05:00
Axel Kohlmeyer	635f3ce128	synchronize USER-SMD examples with code	2016-11-18 08:09:24 -05:00
Axel Kohlmeyer	81f68e06fd	Merge branch 'master' into doc-updates	2016-11-17 20:44:07 -05:00
dstelter92	2a026c9ad8	revised temper_grem example, better file management	2016-11-17 12:53:25 -05:00
dstelter92	4a3091f844	modified temper_grem example with more exchanges	2016-11-17 11:24:29 -05:00
dstelter92	747c95c525	revised documentation, added temper_grem ref to fix_grem	2016-11-17 11:00:49 -05:00
dstelter92	5c64934bc8	added documention, re-ran temper_grem example	2016-11-17 10:40:10 -05:00
Axel Kohlmeyer	4e62e58d29	Merge pull request #47 from dstelter92/grem-feature added internal tempering in grem with example	2016-11-17 10:04:43 -05:00
dstelter92	5ac2d9532e	Re-run example with debug off	2016-11-17 09:43:44 -05:00
dstelter92	19ac9d2959	turned off dev mode by default in temper_grem	2016-11-17 09:31:07 -05:00
dstelter92	9f313aac75	shorter example	2016-11-16 20:43:41 -05:00
dstelter92	0102c5dadc	file cleanup	2016-11-16 20:38:53 -05:00
dstelter92	07e46b797a	added internal tempering in grem with example	2016-11-16 20:27:14 -05:00
Axel Kohlmeyer	b45d1e37ef	integrate fix grem docs and update to match current conventions	2016-11-16 16:46:00 -05:00
Axel Kohlmeyer	2e7fd513d4	provide fix grem example input for nvt and npt	2016-11-16 16:42:01 -05:00
Axel Kohlmeyer	82364d10e3	Merge branch 'grem-feature' of https://github.com/dstelter92/lammps into grem-feature Resolved merge conflicts and adapted logic to most recent changes in feature branch Closes #46	2016-11-16 16:11:53 -05:00
dstelter92	16c8a307e5	removed leftover tex files	2016-11-16 15:39:02 -05:00
dstelter92	94f14ab051	spell check, minor typos	2016-11-16 15:34:32 -05:00
Axel Kohlmeyer	683f514fac	simplify multi-replica run by passing per-replica parameters as variables on the command line	2016-11-16 14:22:20 -05:00
Axel Kohlmeyer	f617993944	need to apply fix_modify already in fix grem constructor	2016-11-16 13:52:27 -05:00
dstelter92	4641c9e568	Added basic documentation for grem fix	2016-11-16 13:36:13 -05:00
Axel Kohlmeyer	705f66aaee	remove superfluous code	2016-11-16 13:24:41 -05:00
Axel Kohlmeyer	e57ae1ce3f	compute scaled kinetic energy tensor without destroying the original data	2016-11-16 12:45:13 -05:00
dstelter92	950442b8b1	added check for nvt vs npt, enabled nvt simulation with fix_grem	2016-11-15 21:53:28 -05:00
Axel Kohlmeyer	1c68e42ecc	fix_modify is not longer needed	2016-11-14 13:43:28 -05:00
Axel Kohlmeyer	5f94b31806	add multi-replica example for gREM	2016-11-14 10:12:48 -05:00
Axel Kohlmeyer	fdf5d68f9f	allow to extract properties in NH integrator only when they are active	2016-11-14 09:27:33 -05:00
Axel Kohlmeyer	0c25f3b1d6	whitespace cleanup	2016-11-13 23:20:09 -05:00
Axel Kohlmeyer	14c7cf4197	retrieve target temperature and pressure from fix npt. add sanity checks.	2016-11-13 23:18:59 -05:00
Axel Kohlmeyer	26870f223d	add example for gREM	2016-11-13 23:18:14 -05:00
Axel Kohlmeyer	09544d0698	bugfix for compute pressure/grem: must make a copy of argument strings	2016-11-13 19:19:52 -05:00
Axel Kohlmeyer	b5130a3b35	avoid NaN for variance from average output	2016-11-13 18:46:55 -05:00
Axel Kohlmeyer	20daf82463	initial import of adapted gREM code by David Stelter and Edyta Malolepsza The following changes were made: - the modifications to compute pressure were transferred to a derived class compute pressure/grem - fix scaleforce was renamed to fix grem - identifying the grem fix was simplified as fix grem passes an additional argument to compute pressure/grem - dead code was removed in both files - checking of arguments was tightened	2016-11-13 18:44:10 -05:00
Axel Kohlmeyer	114926a488	Merge branch 'master' into new-neighbor	2016-10-02 00:26:56 -04:00
Axel Kohlmeyer	5eb9dd0c5d	Merge branch 'master' into new-neighbor	2016-09-29 23:14:28 -04:00
Axel Kohlmeyer	ebabc8f0bc	Merge remote-tracking branch 'lammps-rw/integration' into update-neighbor	2016-09-09 15:46:20 -04:00
Axel Kohlmeyer	232abf8534	restore locale and enforce grep option squashing	2016-09-09 15:42:14 -04:00
Axel Kohlmeyer	d22caf2658	Merge pull request #29 from timattox/new-neighbor USER-DPD: remove several files from src that came from src/USER-DPD/	2016-09-09 15:28:56 -04:00
Axel Kohlmeyer	3842aa6095	forward skip lists /omp neighbor list builds to non-omp implementations	2016-09-09 15:23:40 -04:00
Tim Mattox	32c240978a	USER-DPD: remove several files from src that came from src/USER-DPD/ These were accidentally added to git in `c9c2ae6`.	2016-09-09 15:17:42 -04:00
Axel Kohlmeyer	212c2617f6	delete a couple more files, that don't belong into src/	2016-09-09 14:56:23 -04:00
Axel Kohlmeyer	40f85c93ba	corrected mismatched free() vs. delete[]	2016-09-09 14:10:42 -04:00
Axel Kohlmeyer	2f02d98469	remove USER-DPD files that should not be where they are	2016-09-09 13:53:07 -04:00
Axel Kohlmeyer	4553881fc2	Merge pull request #28 from timattox/new-neighbor New neighbor, USER-DPD updates	2016-09-09 13:11:55 -04:00
Tim Mattox	81fcbcd99c	USER-DPD: move nstencil_ssa out of core LAMMPS into USER-DPD	2016-09-09 12:19:54 -04:00
Tim Mattox	82c6eb4675	USER-DPD: Set missing NP_HALF flag in npair_half_bin_newton_ssa.h	2016-09-09 12:19:36 -04:00
Tim Mattox	8ed3f4226e	USER-DPD: move custom binning stuff to a NBinSSA child class. Removes most SSA specific fields from class NeighList.	2016-09-09 12:19:06 -04:00
Tim Mattox	9b7a0d7e1c	Update gitignore for the new USER-DPD source files.	2016-09-09 12:18:51 -04:00
Steve Plimpton	c9c2ae6c61	new neighbor list changes	2016-09-07 13:42:58 -06:00
Michele Ceriotti	0229556b03	Merge branch 'master' of github.com:lammps/lammps	2015-07-03 15:43:29 +02:00
Michele Ceriotti	357d4517e8	Merge branch 'master' of github.com:lammps/lammps	2015-04-08 10:46:50 +02:00
Michele Ceriotti	a4a97de84f	A few GLE fixes	2015-04-08 10:45:49 +02:00