final prep for 22Nov patch

Merge pull request #288 from akohlmey/moltemplate-1.40
update bundled version of moltemplate to v1.40
2016-11-22 09:23:02 -07:00 · 2016-11-22 08:51:11 -07:00 · 2016-11-22 08:50:29 -07:00 · 2016-11-22 08:49:46 -07:00 · 2016-11-22 08:48:27 -07:00 · 2016-11-22 08:47:44 -07:00
570 changed files with 40813 additions and 1574 deletions
--- a/doc/Makefile
+++ b/doc/Makefile
@ -43,7 +43,7 @@ clean-all:
 	rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe

 clean:
-	rm -rf $(RSTDIR)
+	rm -rf $(RSTDIR) html

 html: $(OBJECTS)
 	@(\
--- a/doc/src/Eqs/fix_grem.jpg
+++ b/doc/src/Eqs/fix_grem.jpg
--- a/doc/src/Eqs/fix_grem.tex
+++ b/doc/src/Eqs/fix_grem.tex
@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+  T_{eff} = \lambda + \eta (H - H_0)
+$$
+
+\end{document}
--- a/doc/src/Eqs/pair_agni.jpg
+++ b/doc/src/Eqs/pair_agni.jpg
--- a/doc/src/Eqs/pair_tersoff_mod_c.jpg
+++ b/doc/src/Eqs/pair_tersoff_mod_c.jpg
--- a/doc/src/Eqs/pair_tersoff_mod_c.tex
+++ b/doc/src/Eqs/pair_tersoff_mod_c.tex
@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+
+\begin{document}
+
+\begin{eqnarray*}
+  V_{ij}  & =  & f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) + c_0 \right]
+\end{eqnarray*}
+
+\end{document}
--- a/doc/src/Eqs/pressure.jpg
+++ b/doc/src/Eqs/pressure.jpg
--- a/doc/src/Eqs/pressure.tex
+++ b/doc/src/Eqs/pressure.tex
@ -3,7 +3,7 @@
 \begin{document}

 $$
-   P = \frac{N k_B T}{V} + \frac{\sum_{i}^{N} r_i \bullet f_i}{dV}
+   P = \frac{N k_B T}{V} + \frac{\sum_{i}^{N'} r_i \bullet f_i}{dV}
 $$

 \end{document}
--- a/doc/src/Eqs/pressure_tensor.jpg
+++ b/doc/src/Eqs/pressure_tensor.jpg
--- a/doc/src/Eqs/pressure_tensor.tex
+++ b/doc/src/Eqs/pressure_tensor.tex
@ -4,7 +4,7 @@

 $$
   P_{IJ} = \frac{\sum_{k}^{N} m_k v_{k_I} v_{k_J}}{V} + 
-   \frac{\sum_{k}^{N} r_{k_I} f_{k_J}}{V}
+   \frac{\sum_{k}^{N'} r_{k_I} f_{k_J}}{V}
 $$

 \end{document}
--- a/doc/src/JPG/pylammps_dihedral.jpg
+++ b/doc/src/JPG/pylammps_dihedral.jpg
--- a/doc/src/JPG/pylammps_mc_disordered.jpg
+++ b/doc/src/JPG/pylammps_mc_disordered.jpg
--- a/doc/src/JPG/pylammps_mc_energies_plot.jpg
+++ b/doc/src/JPG/pylammps_mc_energies_plot.jpg
--- a/doc/src/JPG/pylammps_mc_minimum.jpg
+++ b/doc/src/JPG/pylammps_mc_minimum.jpg
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="27 Oct 2016 version">
+<META NAME="docnumber" CONTENT="22 Nov 2016 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@ -21,7 +21,7 @@
 <H1></H1>

 LAMMPS Documentation :c,h3
-27 Oct 2016 version :c,h4
+22 Nov 2016 version :c,h4

 Version info: :h4

--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@ -531,7 +531,8 @@ package"_Section_start.html#start_3.
 "dump nc"_dump_nc.html,
 "dump nc/mpiio"_dump_nc.html,
 "group2ndx"_group2ndx.html,
-"ndx2group"_group2ndx.html :tb(c=3,ea=c)
+"ndx2group"_group2ndx.html,
+"temper/grem"_temper_grem.html :tb(c=3,ea=c)

 :line

@ -631,7 +632,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "rigid/npt (o)"_fix_rigid.html,
 "rigid/nve (o)"_fix_rigid.html,
 "rigid/nvt (o)"_fix_rigid.html,
-"rigid/small (o)"_fix_rigid.html,
+<"rigid/small (o)"_fix_rigid.html,
 "rigid/small/nph"_fix_rigid.html,
 "rigid/small/npt"_fix_rigid.html,
 "rigid/small/nve"_fix_rigid.html,
@ -687,6 +688,7 @@ package"_Section_start.html#start_3.
 "eos/table/rx"_fix_eos_table_rx.html,
 "flow/gauss"_fix_flow_gauss.html,
 "gle"_fix_gle.html,
+"grem"_fix_grem.html,
 "imd"_fix_imd.html,
 "ipi"_fix_ipi.html,
 "langevin/drude"_fix_langevin_drude.html,
@ -886,6 +888,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "body"_pair_body.html,
 "bop"_pair_bop.html,
 "born (go)"_pair_born.html,
+"born/coul/dsf"_pair_born.html,
+"born/coul/dsf/cs"_pair_born.html,
 "born/coul/long (go)"_pair_born.html,
 "born/coul/long/cs"_pair_born.html,
 "born/coul/msm (o)"_pair_born.html,
@ -909,8 +913,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "coul/msm"_pair_coul.html,
 "coul/streitz"_pair_coul.html,
 "coul/wolf (ko)"_pair_coul.html,
-"dpd (o)"_pair_dpd.html,
-"dpd/tstat (o)"_pair_dpd.html,
+"dpd (go)"_pair_dpd.html,
+"dpd/tstat (go)"_pair_dpd.html,
 "dsmc"_pair_dsmc.html,
 "eam (gkot)"_pair_eam.html,
 "eam/alloy (gkot)"_pair_eam.html,
@ -979,11 +983,12 @@ KOKKOS, o = USER-OMP, t = OPT.
 "table (gko)"_pair_table.html,
 "tersoff (gkio)"_pair_tersoff.html,
 "tersoff/mod (gko)"_pair_tersoff_mod.html,
+"tersoff/mod/c (o)"_pair_tersoff_mod.html,
 "tersoff/zbl (gko)"_pair_tersoff_zbl.html,
 "tip4p/cut (o)"_pair_coul.html,
 "tip4p/long (o)"_pair_coul.html,
 "tri/lj"_pair_tri_lj.html,
-"vashishta (o)"_pair_vashishta.html,
+"vashishta (ko)"_pair_vashishta.html,
 "vashishta/table (o)"_pair_vashishta.html,
 "yukawa (go)"_pair_yukawa.html,
 "yukawa/colloid (go)"_pair_yukawa_colloid.html,
@ -993,6 +998,7 @@ These are additional pair styles in USER packages, which can be used
 if "LAMMPS is built with the appropriate
 package"_Section_start.html#start_3.

+"agni (o)"_pair_agni.html,
 "awpmd/cut"_pair_awpmd.html,
 "buck/mdf"_pair_mdf.html,
 "coul/cut/soft (o)"_pair_lj_soft.html,
--- a/doc/src/Section_intro.txt
+++ b/doc/src/Section_intro.txt
@ -366,11 +366,11 @@ complementary modeling tasks.
 "DL_POLY"_dlpoly
 "Tinker"_tinker :ul

-:link(charmm,http://www.scripps.edu/brooks)
-:link(amber,http://amber.scripps.edu)
+:link(charmm,http://www.charmm.org)
+:link(amber,http://ambermd.org)
 :link(namd,http://www.ks.uiuc.edu/Research/namd/)
 :link(nwchem,http://www.emsl.pnl.gov/docs/nwchem/nwchem.html)
-:link(dlpoly,http://www.cse.clrc.ac.uk/msi/software/DL_POLY)
+:link(dlpoly,http://www.ccp5.ac.uk/DL_POLY_CLASSIC)
 :link(tinker,http://dasher.wustl.edu/tinker)

 CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for
--- a/doc/src/Section_python.txt
+++ b/doc/src/Section_python.txt
@ -8,19 +8,26 @@

 11. Python interface to LAMMPS :h3

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

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

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

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

 If you are not familiar with it, "Python"_http://www.python.org is a
 powerful scripting and programming language which can essentially do
@ -824,3 +832,7 @@ different visualization package options.  Click to see larger images:
 :image(JPG/screenshot_atomeye_small.jpg,JPG/screenshot_atomeye.jpg)
 :image(JPG/screenshot_pymol_small.jpg,JPG/screenshot_pymol.jpg)
 :image(JPG/screenshot_vmd_small.jpg,JPG/screenshot_vmd.jpg)
+
+11.9 PyLammps interface :link(py_9),h4
+
+Please see the "PyLammps Tutorial"_tutorial_pylammps.html.
--- a/doc/src/compute_pressure.txt
+++ b/doc/src/compute_pressure.txt
@ -37,12 +37,18 @@ The pressure is computed by the formula

 where N is the number of atoms in the system (see discussion of DOF
 below), Kb is the Boltzmann constant, T is the temperature, d is the
-dimensionality of the system (2 or 3 for 2d/3d), V is the system
-volume (or area in 2d), and the second term is the virial, computed
-within LAMMPS for all pairwise as well as 2-body, 3-body, and 4-body,
-and long-range interactions.  "Fixes"_fix.html that impose constraints
-(e.g. the "fix shake"_fix_shake.html command) also contribute to the
-virial term.
+dimensionality of the system (2 or 3 for 2d/3d), and V is the system
+volume (or area in 2d).  The second term is the virial, equal to
+-dU/dV, computed for all pairwise as well as 2-body, 3-body, 4-body,
+manybody, and long-range interactions, where r_i and f_i are the
+position and force vector of atom i, and the black dot indicates a dot
+product.  When periodic boundary conditions are used, N' necessarily
+includes periodic image (ghost) atoms outside the central box, and the
+position and force vectors of ghost atoms are thus included in the
+summation.  When periodic boundary conditions are not used, N' = N =
+the number of atoms in the system.  "Fixes"_fix.html that impose
+constraints (e.g. the "fix shake"_fix_shake.html command) also
+contribute to the virial term.

 A symmetric pressure tensor, stored as a 6-element vector, is also
 calculated by this compute.  The 6 components of the vector are
@ -62,8 +68,9 @@ compute temperature or ke and/or the virial.  The {virial} keyword
 means include all terms except the kinetic energy {ke}.

 Details of how LAMMPS computes the virial efficiently for the entire
-system, including the effects of periodic boundary conditions is
-discussed in "(Thompson)"_#Thompson.
+system, including for manybody potentials and accounting for the
+effects of periodic boundary conditions are discussed in
+"(Thompson)"_#Thompson.

 The temperature and kinetic energy tensor is not calculated by this
 compute, but rather by the temperature compute specified with the
--- a/doc/src/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/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/info.txt
+++ b/doc/src/info.txt
@ -14,7 +14,7 @@ info args :pre

 args = one or more of the following keywords: {out}, {all}, {system}, {communication}, {computes}, {dumps}, {fixes}, {groups}, {regions}, {variables}, {styles}, {time}, or {configuration}
     {out} values = {screen}, {log}, {append} filename, {overwrite} filename
-     {styles} values = {all}, {angle}, {atom}, {bond}, {compute}, {command}, {dump}, {dihedral}, {fix}, {improper}, {integrate}, {kspace}, {minimize}, {region} :ul
+     {styles} values = {all}, {angle}, {atom}, {bond}, {compute}, {command}, {dump}, {dihedral}, {fix}, {improper}, {integrate}, {kspace}, {minimize}, {pair}, {region} :ul

 [Examples:]

@ -70,8 +70,9 @@ The {variables} category prints a list of all currently defined
 variables, their names, styles, definition and last computed value, if
 available.

-The {styles} category prints the list of styles available in LAMMPS. It
-supports one of the following options to control what is printed out:
+The {styles} category prints the list of styles available in the
+current LAMMPS binary. It supports one of the following options
+to control which category of styles is printed out:

 all
 angle
@ -86,6 +87,7 @@ improper
 integrate
 kspace
 minimize
+pair
 region :ul

 The {time} category prints the accumulated CPU and wall time for the
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@ -59,6 +59,7 @@ dump_h5md.html
 dump_image.html
 dump_modify.html
 dump_molfile.html
+dump_nc.html
 echo.html
 fix.html
 fix_modify.html
@ -152,6 +153,7 @@ fix_colvars.html
 fix_controller.html
 fix_deform.html
 fix_deposit.html
+fix_dpd_energy.html
 fix_drag.html
 fix_drude.html
 fix_drude_transform.html
@ -170,6 +172,7 @@ fix_gcmc.html
 fix_gld.html
 fix_gle.html
 fix_gravity.html
+fix_grem.html
 fix_halt.html
 fix_heat.html
 fix_imd.html
@ -272,6 +275,7 @@ fix_viscosity.html
 fix_viscous.html
 fix_wall.html
 fix_wall_gran.html
+fix_wall_gran_region.html
 fix_wall_piston.html
 fix_wall_reflect.html
 fix_wall_region.html
@ -390,6 +394,7 @@ compute_voronoi_atom.html
 compute_xrd.html

 pair_adp.html
+pair_agni.html
 pair_airebo.html
 pair_awpmd.html
 pair_beck.html
@ -622,3 +627,4 @@ USER/atc/man_unfix_flux.html
 USER/atc/man_unfix_nodes.html
 USER/atc/man_write_atom_weights.html
 USER/atc/man_write_restart.html
+
--- a/doc/src/pair_agni.txt
+++ b/doc/src/pair_agni.txt
@ -0,0 +1,128 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+pair_style agni command :h3
+pair_style agni/omp command :h3
+
+[Syntax:]
+
+pair_style agni :pre
+
+[Examples:]
+pair_style      agni
+pair_coeff      * * Al.agni Al
+
+[Description:]
+
+Style {agni} style computes the manybody vectorial force components for
+an atom as
+
+:c,image(Eqs/pair_agni.jpg)
+
+{u} labels the individual components, i.e. x, y or z, and {V} is the
+corresponding atomic fingerprint. {d} is the Euclidean distance between
+any two atomic fingerprints. A total of N_t reference atomic
+environments are considered to construct the force field file. {alpha_t}
+and {l} are the weight coefficients and length scale parameter of the
+non-linear regression model.
+
+The method implements the recently proposed machine learning access to
+atomic forces as discussed extensively in the following publications -
+"(Botu1)"_#Botu2015adaptive and "(Botu2)"_#Botu2015learning. The premise
+of the method is to map the atomic enviornment numerically into a
+fingerprint, and use machine learning methods to create a mapping to the
+vectorial atomic forces.
+
+Only a single pair_coeff command is used with the {agni} style which
+specifies an AGNI potential file containing the parameters of the
+force field for the needed elements. These are mapped to LAMMPS atom 
+types by specifying N additional arguments after the filename in the 
+pair_coeff command, where N is the number of LAMMPS atom types:
+
+filename
+N element names = mapping of AGNI elements to atom types :ul
+
+See the "pair_coeff"_pair_coeff.html doc page for alternate ways
+to specify the path for the force field file.
+
+An AGNI force field is fully specified by the filename which contains the
+parameters of the force field, i.e., the reference training environments
+used to construct the machine learning force field. Example force field 
+and input files are provided in the examples/USER/misc/agni directory. 
+
+:line
+
+Styles with {omp} suffix is functionally the same as the corresponding 
+style without the suffix. They have been optimized to run faster, depending 
+on your available hardware, as discussed in "Section 5"_Section_accelerate.html
+of the manual.  The accelerated style takes the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+The accelerated style is part of the USER-OMP.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated style explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See "Section 5"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+This pair style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+This pair style does not write its information to "binary restart
+files"_restart.html, since it is stored in potential files.  Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the {pair} keyword of the
+"run_style respa"_run_style.html command.  It does not support the
+{inner}, {middle}, {outer} keywords.
+
+:line
+
+[Restrictions:]
+
+Currently, only elemental systems are implemented. Also, the method only
+provides access to the forces and not energies or stresses. However, one
+can access the energy via thermodynamic integration of the forces as
+discussed in "(Botu3)"_#Botu2016construct.  This pair style is part
+of the USER-MISC package. It is only enabled if LAMMPS was built with
+that package. See the "Making LAMMPS"_Section_start.html#start_3 section
+for more info.
+
+The AGNI force field files provided with LAMMPS (see the
+potentials directory) are parameterized for metal "units"_units.html.
+You can use the AGNI potential with any LAMMPS units, but you would need
+to create your own AGNI potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+
+[Default:] none
+
+:line
+
+:link(Botu2015adaptive)
+[(Botu1)] V. Botu and R. Ramprasad, Int. J. Quant. Chem., 115(16), 1074 (2015).
+
+:link(Botu2015learning)
+[(Botu2)] V. Botu and R. Ramprasad, Phys. Rev. B, 92(9), 094306 (2015).
+
+:link(Botu2016construct)
+[(Botu3)] V. Botu, R. Batra, J. Chapman and R. Ramprasad, https://arxiv.org/abs/1610.02098 (2016).
--- a/doc/src/pair_born.txt
+++ b/doc/src/pair_born.txt
@ -19,6 +19,8 @@ pair_style born/coul/msm/omp command :h3
 pair_style born/coul/wolf command :h3
 pair_style born/coul/wolf/gpu command :h3
 pair_style born/coul/wolf/omp command :h3
+pair_style born/coul/dsf command :h3
+pair_style born/coul/dsf/cs command :h3

 [Syntax:]

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

 [Examples:]

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

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

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

+The {born/coul/dsf} style computes the Coulomb contribution with the
+damped shifted force model as in the "coul/dsf"_pair_coul.html style.
+
 Style {born/coul/long/cs} is identical to {born/coul/long} except that
 a term is added for the "core/shell model"_Section_howto.html#howto_25
 to allow charges on core and shell particles to be separated by r =
-0.0.
+0.0. The same correction is introduced for {born/coul/dsf/cs} style
+which is identical to {born/coul/dsf}.

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

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

 :line

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

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

 [Syntax:]

 pair_style style args :pre

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

 [Examples:]

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

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

 These pair styles are designed to be used with the adiabatic
@ -39,7 +48,7 @@ core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham.  See
 "Section 6.25"_Section_howto.html#howto_25 of the manual for an
 overview of the model as implemented in LAMMPS.

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

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

 These pair styles are part of the CORESHELL package.  They are only
--- a/doc/src/pair_snap.txt
+++ b/doc/src/pair_snap.txt
@ -15,7 +15,7 @@ pair_style snap :pre
 [Examples:]

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

 [Description:]

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

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

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

 :link(Bartok2010)
 [(Bartok2010)] Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
--- a/doc/src/pair_tersoff_mod.txt
+++ b/doc/src/pair_tersoff_mod.txt
@ -7,32 +7,43 @@
 :line

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

 [Syntax:]

 pair_style tersoff/mod :pre

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

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

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

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

 :c,image(Eqs/pair_tersoff_mod.jpg)

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

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

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

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

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

 The Tersoff/MOD potential file must contain entries for all the elements
 listed in the pair_coeff command.  It can also contain entries for
--- a/doc/src/pair_vashishta.txt
+++ b/doc/src/pair_vashishta.txt
@ -8,6 +8,7 @@

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

--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@ -6,6 +6,7 @@ Pair Styles :h1
   :maxdepth: 1

   pair_adp
+   pair_agni
   pair_airebo
   pair_awpmd
   pair_beck
--- a/doc/src/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/addtorque/in.addtorque
+++ b/examples/USER/misc/addtorque/in.addtorque
@ -0,0 +1,64 @@
+
+units           lj
+lattice         fcc 0.8442
+boundary        f f f
+
+region          ball   sphere   0.0 0.0 0.0 5.0
+region          box    block  -10 10 -10 10 -10 10
+region          half   block  -10  0 -10 10 -10 10
+
+# add molecule ids so we can use chunk/atom
+fix             0   all property/atom mol ghost yes
+
+create_box      2  box
+create_atoms    1  region ball
+
+pair_style      lj/cut 4.0
+pair_coeff      * *  1.0 1.0
+mass            *    1.0
+set             group all mol 1
+
+# label half the sphere with a different type for better visualization
+set             region half   type 2
+
+# use a dynamic group (may require a patch to fix addtorque with older versions of LAMMPS)
+group           ball   dynamic all   region ball
+
+neigh_modify    delay 2  every 1  check yes
+
+minimize        0.0  0.0    1000  10000
+reset_timestep  0
+
+velocity        all create 1.2 12351235
+
+fix             1   all  nve
+fix             2   all  wall/reflect  xlo EDGE xhi EDGE ylo EDGE yhi EDGE zlo EDGE zhi EDGE
+
+compute 1 all chunk/atom molecule
+compute 2 ball omega/chunk 1
+compute 3 ball inertia/chunk 1
+
+# compute rotational kinetic energy: 1/2 * I * omega**2
+variable r_ke_x equal c_2[1][1]*c_2[1][1]*c_3[1][1]*0.5
+variable r_ke_y equal c_2[1][2]*c_2[1][2]*c_3[1][2]*0.5
+variable r_ke_z equal c_2[1][3]*c_2[1][3]*c_3[1][3]*0.5
+
+# output moments of inertia for x,y,z and angular velocity as well as rotational kinertic energy
+
+thermo_style custom step ke pe c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
+thermo 500
+
+# dump 1 all atom 100 dump.lammpstrj
+
+# dump 2 all movie 10 ball.mp4 type mass
+
+# equilibration w/o torque added
+run 1000 post no
+
+# start spinning the ball. rotation around z should increase and Erot_z should grow
+fix 4 ball addtorque 0.0 0.0 200.0
+run 10000 upto  post no
+
+# continue without adding more torque. rotation continues at fixed speed
+unfix 4
+run 5000
--- a/examples/USER/misc/addtorque/log.9Nov16.addtorque.g++.1
+++ b/examples/USER/misc/addtorque/log.9Nov16.addtorque.g++.1
@ -0,0 +1,202 @@
+LAMMPS (9 Nov 2016)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+
+units           lj
+lattice         fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+boundary        f f f
+
+region          ball   sphere   0.0 0.0 0.0 5.0
+region          box    block  -10 10 -10 10 -10 10
+region          half   block  -10  0 -10 10 -10 10
+
+# add molecule ids so we can use chunk/atom
+fix             0   all property/atom mol ghost yes
+
+create_box      2  box
+Created orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1  region ball
+Created 2123 atoms
+
+pair_style      lj/cut 4.0
+pair_coeff      * *  1.0 1.0
+mass            *    1.0
+set             group all mol 1
+  2123 settings made for mol
+
+# label half the sphere with a different type for better visualization
+set             region half   type 2
+  1142 settings made for type
+
+# use a dynamic group (may require a patch to fix addtorque with older versions of LAMMPS)
+group           ball   dynamic all   region ball
+dynamic group ball defined
+
+neigh_modify    delay 2  every 1  check yes
+
+minimize        0.0  0.0    1000  10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.3
+  ghost atom cutoff = 4.3
+  binsize = 2.15 -> bins = 16 16 16
+Memory usage per processor = 3.68322 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -6.2285099            0   -6.2285099  -0.38871568 
+    1000            0   -7.3616908            0   -7.3616908 -9.1828951e-16 
+Loop time of 12.4181 on 1 procs for 1000 steps with 2123 atoms
+
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+  Stopping criterion = max iterations
+  Energy initial, next-to-last, final = 
+        -6.22850993032     -7.36169083402     -7.36169083402
+  Force two-norm initial, final = 197.762 3.3539e-12
+  Force max component initial, final = 7.88704 1.52475e-13
+  Final line search alpha, max atom move = 1 1.52475e-13
+  Iterations, force evaluations = 1000 1994
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 12.282     | 12.282     | 12.282     |   0.0 | 98.91
+Neigh   | 0.06315    | 0.06315    | 0.06315    |   0.0 |  0.51
+Comm    | 0.000443   | 0.000443   | 0.000443   |   0.0 |  0.00
+Output  | 2.7e-05    | 2.7e-05    | 2.7e-05    |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.07231    |            |       |  0.58
+
+Nlocal:    2123 ave 2123 max 2123 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    270799 ave 270799 max 270799 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 270799
+Ave neighs/atom = 127.555
+Neighbor list builds = 11
+Dangerous builds = 0
+reset_timestep  0
+
+velocity        all create 1.2 12351235
+
+fix             1   all  nve
+fix             2   all  wall/reflect  xlo EDGE xhi EDGE ylo EDGE yhi EDGE zlo EDGE zhi EDGE
+
+compute 1 all chunk/atom molecule
+compute 2 ball omega/chunk 1
+compute 3 ball inertia/chunk 1
+
+# compute rotational kinetic energy: 1/2 * I * omega**2
+variable r_ke_x equal c_2[1][1]*c_2[1][1]*c_3[1][1]*0.5
+variable r_ke_y equal c_2[1][2]*c_2[1][2]*c_3[1][2]*0.5
+variable r_ke_z equal c_2[1][3]*c_2[1][3]*c_3[1][3]*0.5
+
+# output moments of inertia for x,y,z and angular velocity as well as rotational kinertic energy
+
+thermo_style custom step ke pe c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
+thermo 500
+
+# dump 1 all atom 100 dump.lammpstrj
+
+# dump 2 all movie 10 ball.mp4 type mass
+
+# equilibration w/o torque added
+run 1000 post no
+WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 2 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.3
+  ghost atom cutoff = 4.3
+  binsize = 2.15 -> bins = 16 16 16
+Memory usage per processor = 2.68359 Mbytes
+Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z 
+       0    1.7991521   -7.3616908    51125.265    51125.265    51125.265 0.0034331372 -0.0045852283 0.0091015032   0.30129221   0.53743693     2.117541 
+     500    0.8882476     -6.43927    52585.112    52205.936    52112.109 0.0033058719 -0.0043753253 0.0089502237    0.2873458   0.49970143    2.0872595 
+    1000   0.79407357    -6.337372    53754.145    54093.977    53787.624 0.0033214912 -0.0042125031 0.0090171557   0.29651603   0.47995375    2.1867116 
+Loop time of 4.26119 on 1 procs for 1000 steps with 2123 atoms
+
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+# start spinning the ball. rotation around z should increase and Erot_z should grow
+fix 4 ball addtorque 0.0 0.0 200.0
+run 10000 upto  post no
+WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
+Memory usage per processor = 2.68359 Mbytes
+Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z 
+    1000   0.79407357    -6.337372    53754.145    54093.977    53787.624 0.0033214912 -0.0042125031 0.0090171557   0.29651603   0.47995375    2.1867116 
+    1500   0.68685306   -6.2226287    55026.889    54809.958    55224.858 0.0026096779 -0.0039390202   0.01797948   0.18737807   0.42521238    8.9260406 
+    2000   0.65370325   -6.1832475    54914.897    55655.542    55405.781 0.0029310978 -0.0040761978  0.025816421   0.23589612   0.46236922    18.463634 
+    2500   0.69337585   -6.2170462     54604.66    54800.001    54488.865 0.0028821313 -0.0045216915  0.035781895   0.22679174   0.56021203    34.882245 
+    3000   0.76778067   -6.2850756    53423.198    53620.349    53692.133  0.004088872 -0.004451787  0.044703139   0.44658786   0.53133496     53.64839 
+    3500   0.79707238   -6.3044974    53055.225    53071.129    52927.537 0.0036751739 -0.0037584362  0.054889715    0.3583059    0.3748372    79.732181 
+    4000   0.80746429   -6.3010044    53519.853    53643.284    54058.105  0.003813517 -0.0041637733  0.062983015   0.38916725   0.46500703    107.22047 
+    4500   0.81206394   -6.2884719    53371.354    53883.202    53854.559   0.00385001 -0.003643712  0.072544638   0.39555051   0.35769386    141.71085 
+    5000   0.81648687   -6.2737414    53776.764    54233.367    53762.425 0.0024484228 -0.0043310965  0.080673643   0.16118978   0.50866551    174.94929 
+    5500   0.81888245   -6.2572796     53908.22    53502.342    54717.506 0.0037110524  -0.00327586  0.088836946   0.37120958   0.28707375    215.91536 
+    6000   0.86533749   -6.2804248    53687.533    53571.135    53536.171 0.0025223465 -0.0047753224  0.099646475   0.17078626   0.61081016    265.79156 
+    6500   0.88029206   -6.2719195     53344.67    53291.068    53298.665  0.003937416 -0.0033910578   0.10778737   0.41350774   0.30640427    309.61504 
+    7000    0.9066019   -6.2714707    53928.646    53524.142    54003.175 0.0028500736 -0.0039730774   0.11855069   0.21902903    0.4224485     379.4875 
+    7500   0.94601421   -6.2819912    53534.525    53547.598    53851.344 0.0028610722 -0.0049440438   0.12716472   0.21910969    0.6544472    435.41142 
+    8000    0.9562253   -6.2626222    53486.577    53033.175    53858.803 0.0025501008 -0.0048075887   0.13526164   0.17391198   0.61287549    492.69254 
+    8500   0.99679401   -6.2691139    53566.766    53721.523    53831.283 0.0034137155   -0.0039265   0.14392854    0.3121189   0.41412316    557.56894 
+    9000    1.0371056   -6.2761647    53415.879    53605.078     53985.02 0.0029321914 -0.0046362889    0.1518846    0.2296281   0.57612526     622.6884 
+    9500    1.0598491     -6.26216    53493.003    53049.859    53699.774 0.0032127038 -0.0050624912   0.16002437   0.27606311   0.67980256    687.56651 
+   10000    1.1014855   -6.2654945     53418.49    53251.964     53867.56 0.0037330249 -0.0056278017   0.17103133   0.37220602   0.84330216    787.85924 
+Loop time of 43.025 on 1 procs for 9000 steps with 2123 atoms
+
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+# continue without adding more torque. rotation continues at fixed speed
+unfix 4
+run 5000
+WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
+Memory usage per processor = 2.68359 Mbytes
+Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z 
+   10000    1.1014855   -6.2654945     53418.49    53251.964     53867.56 0.0037330249 -0.0056278017   0.17103133   0.37220602   0.84330216    787.85924 
+   10500      1.07259   -6.2363698    52825.233    52896.327    55753.551 0.0035928335 -0.0050843805   0.16344484   0.34094601   0.68370948    744.70621 
+   11000    1.0644214   -6.2282099    52016.795    51950.497    54922.101 0.0047316668 -0.0050149935   0.16196531   0.58229343   0.65328165    720.37919 
+   11500    1.0887339   -6.2525622    52602.789    52903.594     54461.53 0.0044295697 -0.0046710153   0.16698036   0.51606197   0.57713546    759.26022 
+   12000    1.0707466    -6.234719    52785.654    52997.192    54943.066 0.0057389353 -0.0030340721   0.16553451   0.86925773    0.2439353    752.76594 
+   12500    1.0758302   -6.2397291    52375.734    52783.309    55011.986 0.0047029783 -0.0023526884   0.16493895   0.57922337   0.14608158    748.29657 
+   13000    1.0716957   -6.2354221    52711.183    52788.224    55234.737 0.0034033406  -0.00206283   0.16427569   0.30526962   0.11231401    745.29615 
+   13500     1.083667   -6.2475953    52698.902    52203.324    55102.881 0.0032012254 -0.0021366488   0.16381832   0.27002507   0.11916109    739.38261 
+   14000     1.085106   -6.2490655    52767.613    52353.974    55225.438 0.0025647931 -0.0022235227    0.1636534   0.17355699   0.12942041    739.53587 
+   14500    1.0838261   -6.2477856    52292.343    51995.567    54735.836  0.001794954 -0.0029396951   0.16409339  0.084239299   0.22466783    736.92607 
+   15000    1.0827419   -6.2468971    51917.584    51388.833    54481.681 0.0017979486 -0.0025793756   0.16196568  0.083914884   0.17094953    714.60575 
+Loop time of 22.7848 on 1 procs for 5000 steps with 2123 atoms
+
+Performance: 94800.138 tau/day, 219.445 timesteps/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 18.891     | 18.891     | 18.891     |   0.0 | 82.91
+Neigh   | 3.5735     | 3.5735     | 3.5735     |   0.0 | 15.68
+Comm    | 0.005778   | 0.005778   | 0.005778   |   0.0 |  0.03
+Output  | 0.001862   | 0.001862   | 0.001862   |   0.0 |  0.01
+Modify  | 0.27476    | 0.27476    | 0.27476    |   0.0 |  1.21
+Other   |            | 0.0379     |            |       |  0.17
+
+Nlocal:    2123 ave 2123 max 2123 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    242472 ave 242472 max 242472 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 242472
+Ave neighs/atom = 114.212
+Neighbor list builds = 560
+Dangerous builds = 0
+Total wall time: 0:01:22
--- a/examples/USER/misc/addtorque/log.9Nov16.addtorque.g++.4
+++ b/examples/USER/misc/addtorque/log.9Nov16.addtorque.g++.4
@ -0,0 +1,202 @@
+LAMMPS (9 Nov 2016)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+
+units           lj
+lattice         fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+boundary        f f f
+
+region          ball   sphere   0.0 0.0 0.0 5.0
+region          box    block  -10 10 -10 10 -10 10
+region          half   block  -10  0 -10 10 -10 10
+
+# add molecule ids so we can use chunk/atom
+fix             0   all property/atom mol ghost yes
+
+create_box      2  box
+Created orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
+  1 by 2 by 2 MPI processor grid
+create_atoms    1  region ball
+Created 2123 atoms
+
+pair_style      lj/cut 4.0
+pair_coeff      * *  1.0 1.0
+mass            *    1.0
+set             group all mol 1
+  2123 settings made for mol
+
+# label half the sphere with a different type for better visualization
+set             region half   type 2
+  1142 settings made for type
+
+# use a dynamic group (may require a patch to fix addtorque with older versions of LAMMPS)
+group           ball   dynamic all   region ball
+dynamic group ball defined
+
+neigh_modify    delay 2  every 1  check yes
+
+minimize        0.0  0.0    1000  10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.3
+  ghost atom cutoff = 4.3
+  binsize = 2.15 -> bins = 16 16 16
+Memory usage per processor = 3.77014 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -6.2285099            0   -6.2285099  -0.38871568 
+    1000            0   -7.3616908            0   -7.3616908 -9.7399049e-16 
+Loop time of 8.29581 on 4 procs for 1000 steps with 2123 atoms
+
+89.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+  Stopping criterion = max iterations
+  Energy initial, next-to-last, final = 
+        -6.22850993032     -7.36169083402     -7.36169083402
+  Force two-norm initial, final = 197.762 3.40861e-12
+  Force max component initial, final = 7.88704 1.60379e-13
+  Final line search alpha, max atom move = 1 1.60379e-13
+  Iterations, force evaluations = 1000 1994
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.8462     | 6.8198     | 8.0872     |  34.0 | 82.21
+Neigh   | 0.021211   | 0.028936   | 0.035891   |   3.8 |  0.35
+Comm    | 0.10672    | 1.3842     | 2.3694     |  76.2 | 16.69
+Output  | 2.8e-05    | 3.35e-05   | 5e-05      |   0.2 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.0629     |            |       |  0.76
+
+Nlocal:    530.75 ave 543 max 514 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Nghost:    1058.25 ave 1075 max 1046 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+Neighs:    67699.8 ave 82013 max 55681 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 270799
+Ave neighs/atom = 127.555
+Neighbor list builds = 11
+Dangerous builds = 0
+reset_timestep  0
+
+velocity        all create 1.2 12351235
+
+fix             1   all  nve
+fix             2   all  wall/reflect  xlo EDGE xhi EDGE ylo EDGE yhi EDGE zlo EDGE zhi EDGE
+
+compute 1 all chunk/atom molecule
+compute 2 ball omega/chunk 1
+compute 3 ball inertia/chunk 1
+
+# compute rotational kinetic energy: 1/2 * I * omega**2
+variable r_ke_x equal c_2[1][1]*c_2[1][1]*c_3[1][1]*0.5
+variable r_ke_y equal c_2[1][2]*c_2[1][2]*c_3[1][2]*0.5
+variable r_ke_z equal c_2[1][3]*c_2[1][3]*c_3[1][3]*0.5
+
+# output moments of inertia for x,y,z and angular velocity as well as rotational kinertic energy
+
+thermo_style custom step ke pe c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
+thermo 500
+
+# dump 1 all atom 100 dump.lammpstrj
+
+# dump 2 all movie 10 ball.mp4 type mass
+
+# equilibration w/o torque added
+run 1000 post no
+WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 2 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.3
+  ghost atom cutoff = 4.3
+  binsize = 2.15 -> bins = 16 16 16
+Memory usage per processor = 2.77052 Mbytes
+Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z 
+       0    1.7991521   -7.3616908    51125.265    51125.265    51125.265 0.0040198435 -0.0024237256 0.0011306245    0.4130702   0.15016629  0.032677011 
+     500   0.90968729   -6.4603004    52559.075    52593.598    52370.876 0.0039073429 -0.0023505431 0.0011032256   0.40121833   0.14529121  0.031870471 
+    1000   0.80269935   -6.3456699    53966.859     54192.03    54298.931 0.0040875347 -0.0023098179 0.00077010445   0.45083753   0.14456425  0.016101285 
+Loop time of 2.3842 on 4 procs for 1000 steps with 2123 atoms
+
+89.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+# start spinning the ball. rotation around z should increase and Erot_z should grow
+fix 4 ball addtorque 0.0 0.0 200.0
+run 10000 upto  post no
+WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
+Memory usage per processor = 2.77052 Mbytes
+Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z 
+    1000   0.80269935   -6.3456699    53966.859     54192.03    54298.931 0.0040875347 -0.0023098179 0.00077010445   0.45083753   0.14456425  0.016101285 
+    1500   0.68922642   -6.2266953    54966.109    54681.607    54947.256 0.0038798951 -0.0016325797 0.0099837591   0.41371853  0.072871893    2.7384461 
+    2000   0.64105167   -6.1739656    54782.995    54570.486    54910.316 0.0034645832 -0.0027243304  0.017763588   0.32878936   0.20251043    8.6633395 
+    2500   0.69929409   -6.2287557     54307.47    53952.925    54538.409 0.0035199565 -0.0022538001  0.028279733   0.33643732   0.13703004    21.808363 
+    3000   0.77013056   -6.2945597    53916.743     53801.81    53955.863 0.0039732989 -0.0024543292  0.037182149   0.42559463   0.16204384    37.297319 
+    3500   0.80807105   -6.3246605    53451.163    53387.178    53474.789 0.0043137676 -0.0020556348  0.047270147   0.49732542   0.11279735    59.743821 
+    4000   0.81007199   -6.3142362    53334.317    53243.089    53685.963 0.0038548696 -0.0031009535  0.055811043    0.3962745   0.25599044    83.612467 
+    4500    0.7850954   -6.2735818    53738.002    53682.367    53639.471 0.0033046861 -0.0018472801  0.065975851   0.29343502  0.091594032    116.74129 
+    5000   0.77992741   -6.2508277    53864.644    53804.867    53877.025 0.0038258186 -0.0028703189  0.073848203   0.39420539    0.2216419    146.91071 
+    5500   0.79428302   -6.2467907    54353.329    53987.578    54234.062 0.0034715133 -0.0030161617  0.082746129   0.32751699   0.24556875    185.66819 
+    6000   0.82211943   -6.2549436    54273.545    53195.299    54061.645 0.0030929934 -0.0031282112  0.090458895   0.25960687   0.26027676    221.18813 
+    6500   0.87630771   -6.2870988    54042.229    53505.982    54492.239 0.0026486452 -0.0024783378   0.10046947   0.18956181    0.1643211    275.02546 
+    7000   0.88614639   -6.2727488    53701.993    52682.206    53948.142 0.0035384498 -0.0035905797   0.11030427   0.33619131   0.33959641    328.19439 
+    7500   0.92102182   -6.2787281    53410.068    52577.853    53132.511 0.0033084315 -0.0031776605   0.11973875    0.2923058   0.26545312     380.8902 
+    8000   0.94010525   -6.2697758    53732.562    53384.271    53795.933 0.0046460009 -0.0032755993   0.12803006    0.5799174   0.28639462    440.90328 
+    8500   0.95359399    -6.252319    53444.305    53558.444    53789.691 0.0037919474 -0.0035729209   0.13616177   0.38423423   0.34185722    498.63117 
+    9000   0.98631627     -6.25197     53115.01    54017.327    53955.578 0.0045084495 -0.0034368377   0.14488919   0.53981096   0.31902236    566.34143 
+    9500    1.0328238   -6.2632597    53287.675    53682.978    53769.692 0.0044595175 -0.0025931203   0.15416363    0.5298739    0.1804895    638.95665 
+   10000    1.0741755   -6.2667785    53103.657    53319.569    53601.523 0.0059237675 -0.0019561182   0.16445664   0.93173079   0.10201096    724.85302 
+Loop time of 21.8398 on 4 procs for 9000 steps with 2123 atoms
+
+90.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+# continue without adding more torque. rotation continues at fixed speed
+unfix 4
+run 5000
+WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
+Memory usage per processor = 2.77052 Mbytes
+Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z 
+   10000    1.0741755   -6.2667785    53103.657    53319.569    53601.523 0.0059237675 -0.0019561182   0.16445664   0.93173079   0.10201096    724.85302 
+   10500    1.0588571   -6.2509381    52374.303    52131.544    55020.367 0.0048843769 -0.0018716797   0.15729531   0.62475047  0.091313217    680.65188 
+   11000    1.0554911   -6.2471863    52803.345    52177.891    55200.756 0.0042073234 -0.0024283269   0.15742315   0.46735107   0.15384055    683.99392 
+   11500    1.0559499   -6.2469955    54031.351    52919.728     54882.35 0.0046703444 -0.0016225764   0.15994353   0.58926908   0.06966232    701.99832 
+   12000    1.0311805   -6.2224471     52812.51     52444.13    55356.101 0.0044986993 -0.0019225732   0.15672327   0.53441759  0.096924293    679.83334 
+   12500    1.0423882   -6.2339087    52000.562    52043.013    55003.272 0.0038688875 -0.0022935053    0.1548654   0.38917977   0.13687746    659.57977 
+   13000    1.0548857   -6.2465445    52196.499    52869.024    54622.553 0.0036650563 -0.0025542156    0.1590498   0.35056832   0.17245921    690.88895 
+   13500    1.0443009   -6.2360149    51921.746    53124.078    54750.325 0.0052756473 -0.0011658069   0.15689119   0.72255483  0.036100621    673.83538 
+   14000    1.0505583    -6.241923    51861.696    52153.234    54321.531 0.0037119391 -0.00045576703   0.15738082   0.35728798 0.0054167284    672.73745 
+   14500     1.040343   -6.2316147    52035.588    51680.479    54443.305 0.0026177168 -0.0014795729   0.15428968    0.1782854  0.056567797    648.01978 
+   15000    1.0404962   -6.2322338    52376.795    51327.453    54677.693 0.0025711787 -0.0021695312   0.15403509   0.17313044   0.12079571    648.66363 
+Loop time of 11.9695 on 4 procs for 5000 steps with 2123 atoms
+
+Performance: 180458.440 tau/day, 417.728 timesteps/s
+89.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.0313     | 8.4017     | 9.6932     |  35.5 | 70.19
+Neigh   | 0.97886    | 1.3633     | 1.7406     |  26.8 | 11.39
+Comm    | 0.34002    | 2.0227     | 3.7911     |  94.9 | 16.90
+Output  | 0.001198   | 0.0015522  | 0.002578   |   1.5 |  0.01
+Modify  | 0.12841    | 0.131      | 0.13336    |   0.5 |  1.09
+Other   |            | 0.04924    |            |       |  0.41
+
+Nlocal:    530.75 ave 534 max 529 min
+Histogram: 1 0 2 0 0 0 0 0 0 1
+Nghost:    1038 ave 1048 max 1029 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Neighs:    60482.5 ave 72547 max 49124 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+
+Total # of neighbors = 241930
+Ave neighs/atom = 113.957
+Neighbor list builds = 555
+Dangerous builds = 0
+Total wall time: 0:00:44
--- a/examples/USER/misc/agni/Al_prb.agni
+++ b/examples/USER/misc/agni/Al_prb.agni
--- a/examples/USER/misc/agni/adatom.data
+++ b/examples/USER/misc/agni/adatom.data
@ -0,0 +1,197 @@
+Data File created from VASP POSCAR
+
+181 atoms
+1 atom types
+
+0 17.121440767 xlo xhi
+0 14.8276026536 ylo yhi
+0 39.3197318979 zlo zhi
+
+Masses
+
+1 26.982
+
+Atoms
+
+1 1 0.0 1.64751140595 15.0
+2 1 2.85357346116 1.64751140595 15.0
+3 1 5.70714692232 1.64751140595 15.0
+4 1 8.56072038348 1.64751140595 15.0
+5 1 11.4142938446 1.64751140595 15.0
+6 1 14.2678673058 1.64751140595 15.0
+7 1 1.42678673058 4.11877851488 15.0
+8 1 4.28036019174 4.11877851488 15.0
+9 1 7.1339336529 4.11877851488 15.0
+10 1 9.98750711406 4.11877851488 15.0
+11 1 12.8410805752 4.11877851488 15.0
+12 1 15.6946540364 4.11877851488 15.0
+13 1 0.0 6.59004562381 15.0
+14 1 2.85357346116 6.59004562381 15.0
+15 1 5.70714692232 6.59004562381 15.0
+16 1 8.56072038348 6.59004562381 15.0
+17 1 11.4142938446 6.59004562381 15.0
+18 1 14.2678673058 6.59004562381 15.0
+19 1 1.42678673058 9.06131273274 15.0
+20 1 4.28036019174 9.06131273274 15.0
+21 1 7.1339336529 9.06131273274 15.0
+22 1 9.98750711406 9.06131273274 15.0
+23 1 12.8410805752 9.06131273274 15.0
+24 1 15.6946540364 9.06131273274 15.0
+25 1 0.0 11.5325798417 15.0
+26 1 2.85357346116 11.5325798417 15.0
+27 1 5.70714692232 11.5325798417 15.0
+28 1 8.56072038348 11.5325798417 15.0
+29 1 11.4142938446 11.5325798417 15.0
+30 1 14.2678673058 11.5325798417 15.0
+31 1 1.42678673058 14.0038469506 15.0
+32 1 4.28036019174 14.0038469506 15.0
+33 1 7.1339336529 14.0038469506 15.0
+34 1 9.98750711406 14.0038469506 15.0
+35 1 12.8410805752 14.0038469506 15.0
+36 1 15.6946540364 14.0038469506 15.0
+37 1 0.0 0.0 17.3299329745
+38 1 2.85357346116 0.0 17.3299329745
+39 1 5.70714692232 0.0 17.3299329745
+40 1 8.56072038348 0.0 17.3299329745
+41 1 11.4142938446 0.0 17.3299329745
+42 1 14.2678673058 0.0 17.3299329745
+43 1 1.42678673058 2.47126710893 17.3299329745
+44 1 4.28036019174 2.47126710893 17.3299329745
+45 1 7.1339336529 2.47126710893 17.3299329745
+46 1 9.98750711406 2.47126710893 17.3299329745
+47 1 12.8410805752 2.47126710893 17.3299329745
+48 1 15.6946540364 2.47126710893 17.3299329745
+49 1 0.0 4.94253421786 17.3299329745
+50 1 2.85357346116 4.94253421786 17.3299329745
+51 1 5.70714692232 4.94253421786 17.3299329745
+52 1 8.56072038348 4.94253421786 17.3299329745
+53 1 11.4142938446 4.94253421786 17.3299329745
+54 1 14.2678673058 4.94253421786 17.3299329745
+55 1 1.42678673058 7.41380132679 17.3299329745
+56 1 4.28036019174 7.41380132679 17.3299329745
+57 1 7.1339336529 7.41380132679 17.3299329745
+58 1 9.98750711406 7.41380132679 17.3299329745
+59 1 12.8410805752 7.41380132679 17.3299329745
+60 1 15.6946540364 7.41380132679 17.3299329745
+61 1 0.0 9.88506843572 17.3299329745
+62 1 2.85357346116 9.88506843572 17.3299329745
+63 1 5.70714692232 9.88506843572 17.3299329745
+64 1 8.56072038348 9.88506843572 17.3299329745
+65 1 11.4142938446 9.88506843572 17.3299329745
+66 1 14.2678673058 9.88506843572 17.3299329745
+67 1 1.42678673058 12.3563355446 17.3299329745
+68 1 4.28036019174 12.3563355446 17.3299329745
+69 1 7.1339336529 12.3563355446 17.3299329745
+70 1 9.98750711406 12.3563355446 17.3299329745
+71 1 12.8410805752 12.3563355446 17.3299329745
+72 1 15.6946540364 12.3563355446 17.3299329745
+73 1 1.42678673058 0.823755702976 19.6598659489
+74 1 4.28036019174 0.823755702976 19.6598659489
+75 1 7.1339336529 0.823755702976 19.6598659489
+76 1 9.98750711406 0.823755702976 19.6598659489
+77 1 12.8410805752 0.823755702976 19.6598659489
+78 1 15.6946540364 0.823755702976 19.6598659489
+79 1 0.0 3.29502281191 19.6598659489
+80 1 2.85357346116 3.29502281191 19.6598659489
+81 1 5.70714692232 3.29502281191 19.6598659489
+82 1 8.56072038348 3.29502281191 19.6598659489
+83 1 11.4142938446 3.29502281191 19.6598659489
+84 1 14.2678673058 3.29502281191 19.6598659489
+85 1 1.42678673058 5.76628992084 19.6598659489
+86 1 4.28036019174 5.76628992084 19.6598659489
+87 1 7.1339336529 5.76628992084 19.6598659489
+88 1 9.98750711406 5.76628992084 19.6598659489
+89 1 12.8410805752 5.76628992084 19.6598659489
+90 1 15.6946540364 5.76628992084 19.6598659489
+91 1 0.0 8.23755702976 19.6598659489
+92 1 2.85357346116 8.23755702976 19.6598659489
+93 1 5.70714692232 8.23755702976 19.6598659489
+94 1 8.56072038348 8.23755702976 19.6598659489
+95 1 11.4142938446 8.23755702976 19.6598659489
+96 1 14.2678673058 8.23755702976 19.6598659489
+97 1 1.42678673058 10.7088241387 19.6598659489
+98 1 4.28036019174 10.7088241387 19.6598659489
+99 1 7.1339336529 10.7088241387 19.6598659489
+100 1 9.98750711406 10.7088241387 19.6598659489
+101 1 12.8410805752 10.7088241387 19.6598659489
+102 1 15.6946540364 10.7088241387 19.6598659489
+103 1 0.0 13.1800912476 19.6598659489
+104 1 2.85357346116 13.1800912476 19.6598659489
+105 1 5.70714692232 13.1800912476 19.6598659489
+106 1 8.56072038348 13.1800912476 19.6598659489
+107 1 11.4142938446 13.1800912476 19.6598659489
+108 1 14.2678673058 13.1800912476 19.6598659489
+109 1 0.0 1.64751140595 21.9897989234
+110 1 2.85357346116 1.64751140595 21.9897989234
+111 1 5.70714692232 1.64751140595 21.9897989234
+112 1 8.56072038348 1.64751140595 21.9897989234
+113 1 11.4142938446 1.64751140595 21.9897989234
+114 1 14.2678673058 1.64751140595 21.9897989234
+115 1 1.42678673058 4.11877851488 21.9897989234
+116 1 4.28036019174 4.11877851488 21.9897989234
+117 1 7.1339336529 4.11877851488 21.9897989234
+118 1 9.98750711406 4.11877851488 21.9897989234
+119 1 12.8410805752 4.11877851488 21.9897989234
+120 1 15.6946540364 4.11877851488 21.9897989234
+121 1 0.0 6.59004562381 21.9897989234
+122 1 2.85357346116 6.59004562381 21.9897989234
+123 1 5.70714692232 6.59004562381 21.9897989234
+124 1 8.56072038348 6.59004562381 21.9897989234
+125 1 11.4142938446 6.59004562381 21.9897989234
+126 1 14.2678673058 6.59004562381 21.9897989234
+127 1 1.42678673058 9.06131273274 21.9897989234
+128 1 4.28036019174 9.06131273274 21.9897989234
+129 1 7.1339336529 9.06131273274 21.9897989234
+130 1 9.98750711406 9.06131273274 21.9897989234
+131 1 12.8410805752 9.06131273274 21.9897989234
+132 1 15.6946540364 9.06131273274 21.9897989234
+133 1 0.0 11.5325798417 21.9897989234
+134 1 2.85357346116 11.5325798417 21.9897989234
+135 1 5.70714692232 11.5325798417 21.9897989234
+136 1 8.56072038348 11.5325798417 21.9897989234
+137 1 11.4142938446 11.5325798417 21.9897989234
+138 1 14.2678673058 11.5325798417 21.9897989234
+139 1 1.42678673058 14.0038469506 21.9897989234
+140 1 4.28036019174 14.0038469506 21.9897989234
+141 1 7.1339336529 14.0038469506 21.9897989234
+142 1 9.98750711406 14.0038469506 21.9897989234
+143 1 12.8410805752 14.0038469506 21.9897989234
+144 1 15.6946540364 14.0038469506 21.9897989234
+145 1 0.0 0.0 24.3197318979
+146 1 2.85357346116 0.0 24.3197318979
+147 1 5.70714692232 0.0 24.3197318979
+148 1 8.56072038348 0.0 24.3197318979
+149 1 11.4142938446 0.0 24.3197318979
+150 1 14.2678673058 0.0 24.3197318979
+151 1 1.42678673058 2.47126710893 24.3197318979
+152 1 4.28036019174 2.47126710893 24.3197318979
+153 1 7.1339336529 2.47126710893 24.3197318979
+154 1 9.98750711406 2.47126710893 24.3197318979
+155 1 12.8410805752 2.47126710893 24.3197318979
+156 1 15.6946540364 2.47126710893 24.3197318979
+157 1 0.0 4.94253421786 24.3197318979
+158 1 2.85357346116 4.94253421786 24.3197318979
+159 1 5.70714692232 4.94253421786 24.3197318979
+160 1 8.56072038348 4.94253421786 24.3197318979
+161 1 11.4142938446 4.94253421786 24.3197318979
+162 1 14.2678673058 4.94253421786 24.3197318979
+163 1 1.42678673058 7.41380132679 24.3197318979
+164 1 4.28036019174 7.41380132679 24.3197318979
+165 1 7.1339336529 7.41380132679 24.3197318979
+166 1 9.98750711406 7.41380132679 24.3197318979
+167 1 12.8410805752 7.41380132679 24.3197318979
+168 1 15.6946540364 7.41380132679 24.3197318979
+169 1 0.0 9.88506843572 24.3197318979
+170 1 2.85357346116 9.88506843572 24.3197318979
+171 1 5.70714692232 9.88506843572 24.3197318979
+172 1 8.56072038348 9.88506843572 24.3197318979
+173 1 11.4142938446 9.88506843572 24.3197318979
+174 1 14.2678673058 9.88506843572 24.3197318979
+175 1 1.42678673058 12.3563355446 24.3197318979
+176 1 4.28036019174 12.3563355446 24.3197318979
+177 1 7.1339336529 12.3563355446 24.3197318979
+178 1 9.98750711406 12.3563355446 24.3197318979
+179 1 12.8410805752 12.3563355446 24.3197318979
+180 1 15.6946540364 12.3563355446 24.3197318979
+181 1 7.1339336529 4.11877851488 26.7197318979
+
--- a/examples/USER/misc/agni/in.adatom
+++ b/examples/USER/misc/agni/in.adatom
@ -0,0 +1,23 @@
+
+processors * * 1
+units metal
+boundary p p f
+read_data adatom.data
+
+pair_style agni
+pair_coeff * * Al_prb.agni Al
+
+neighbor 0.3 bin 
+neigh_modify delay 2 check yes 
+
+timestep 0.0005
+velocity all create 500 12345
+fix 1 all nvt temp 250 250 0.2 
+fix 5 all momentum 1 linear 1 1 1
+
+thermo 100
+thermo_style custom step ke temp
+
+# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
+
+run 1000
--- a/examples/USER/misc/agni/in.vacancy
+++ b/examples/USER/misc/agni/in.vacancy
@ -0,0 +1,23 @@
+
+units metal
+boundary p p p
+read_data vacancy.data
+
+pair_style agni
+pair_coeff * * Al_prb.agni Al
+neighbor 0.3 bin 
+neigh_modify delay 2 check yes 
+
+
+timestep 0.0005
+velocity all create 1000 12345
+fix 1 all nvt temp 900 900 200
+fix 5 all momentum 1 linear 1 1 1
+
+
+thermo 100
+thermo_style custom step ke etotal temp
+
+# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
+
+run 1000
--- a/examples/USER/misc/agni/log.9Nov16.adatom.g++.1
+++ b/examples/USER/misc/agni/log.9Nov16.adatom.g++.1
@ -0,0 +1,82 @@
+LAMMPS (9 Nov 2016)
+  using 1 OpenMP thread(s) per MPI task
+
+processors * * 1
+units metal
+boundary p p f
+read_data adatom.data
+  orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  181 atoms
+
+pair_style agni
+pair_coeff * * Al_prb.agni Al
+Reading potential file Al_prb.agni with DATE: 2016-11-11
+
+neighbor 0.3 bin
+neigh_modify delay 2 check yes
+
+timestep 0.0005
+velocity all create 500 12345
+fix 1 all nvt temp 250 250 0.2
+fix 5 all momentum 1 linear 1 1 1
+
+thermo 100
+thermo_style custom step ke temp
+
+# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
+
+run 1000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 2 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.3
+  ghost atom cutoff = 8.3
+  binsize = 4.15 -> bins = 5 4 10
+Memory usage per processor = 2.37049 Mbytes
+Step KinEng Temp 
+       0    11.633413          500 
+     100     4.049974    174.06646 
+     200    5.8983472    253.50889 
+     300    5.3667309    230.66021 
+     400    4.9343935     212.0785 
+     500    5.4054496    232.32432 
+     600    6.1779127    265.52452 
+     700    6.3749266     273.9921 
+     800    6.0701481    260.89283 
+     900    6.4582394    277.57286 
+    1000    6.4047444    275.27366 
+Loop time of 20.8273 on 1 procs for 1000 steps with 181 atoms
+
+Performance: 2.074 ns/day, 11.571 hours/ns, 48.014 timesteps/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 20.79      | 20.79      | 20.79      |   0.0 | 99.82
+Neigh   | 0.022742   | 0.022742   | 0.022742   |   0.0 |  0.11
+Comm    | 0.0040836  | 0.0040836  | 0.0040836  |   0.0 |  0.02
+Output  | 0.00011086 | 0.00011086 | 0.00011086 |   0.0 |  0.00
+Modify  | 0.0089345  | 0.0089345  | 0.0089345  |   0.0 |  0.04
+Other   |            | 0.001819   |            |       |  0.01
+
+Nlocal:    181 ave 181 max 181 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    562 ave 562 max 562 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  18810 ave 18810 max 18810 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18810
+Ave neighs/atom = 103.923
+Neighbor list builds = 33
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:20
--- a/examples/USER/misc/agni/log.9Nov16.adatom.g++.4
+++ b/examples/USER/misc/agni/log.9Nov16.adatom.g++.4
@ -0,0 +1,82 @@
+LAMMPS (9 Nov 2016)
+  using 1 OpenMP thread(s) per MPI task
+
+processors * * 1
+units metal
+boundary p p f
+read_data adatom.data
+  orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  181 atoms
+
+pair_style agni
+pair_coeff * * Al_prb.agni Al
+Reading potential file Al_prb.agni with DATE: 2016-11-11
+
+neighbor 0.3 bin
+neigh_modify delay 2 check yes
+
+timestep 0.0005
+velocity all create 500 12345
+fix 1 all nvt temp 250 250 0.2
+fix 5 all momentum 1 linear 1 1 1
+
+thermo 100
+thermo_style custom step ke temp
+
+# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
+
+run 1000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 2 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.3
+  ghost atom cutoff = 8.3
+  binsize = 4.15 -> bins = 5 4 10
+Memory usage per processor = 2.48695 Mbytes
+Step KinEng Temp 
+       0    11.633413          500 
+     100     4.049974    174.06646 
+     200    5.8983472    253.50889 
+     300    5.3667309    230.66021 
+     400    4.9343935     212.0785 
+     500    5.4054496    232.32432 
+     600    6.1779127    265.52451 
+     700    6.3749266     273.9921 
+     800    6.0701481    260.89283 
+     900    6.4582394    277.57286 
+    1000    6.4047444    275.27366 
+Loop time of 5.96868 on 4 procs for 1000 steps with 181 atoms
+
+Performance: 7.238 ns/day, 3.316 hours/ns, 167.541 timesteps/s
+99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.4176     | 5.4602     | 5.5505     |   2.3 | 91.48
+Neigh   | 0.0056074  | 0.0060464  | 0.0062635  |   0.3 |  0.10
+Comm    | 0.39544    | 0.48696    | 0.53111    |   7.9 |  8.16
+Output  | 0.0001545  | 0.00015736 | 0.0001595  |   0.0 |  0.00
+Modify  | 0.010492   | 0.011565   | 0.012588   |   0.9 |  0.19
+Other   |            | 0.003794   |            |       |  0.06
+
+Nlocal:    45.25 ave 47 max 42 min
+Histogram: 1 0 0 0 0 0 0 0 2 1
+Nghost:    374.75 ave 380 max 373 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  4702.5 ave 4868 max 4389 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+
+Total # of neighbors = 18810
+Ave neighs/atom = 103.923
+Neighbor list builds = 33
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:05
--- a/examples/USER/misc/agni/log.9Nov16.vacancy.g++.1
+++ b/examples/USER/misc/agni/log.9Nov16.vacancy.g++.1
@ -0,0 +1,82 @@
+LAMMPS (9 Nov 2016)
+  using 1 OpenMP thread(s) per MPI task
+
+units metal
+boundary p p p
+read_data vac.data
+  orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  31 atoms
+
+pair_style agni
+pair_coeff * * Al_prb.agni Al
+Reading potential file Al_prb.agni with DATE: 2016-11-11
+neighbor 0.3 bin
+neigh_modify delay 2 check yes
+
+
+timestep 0.0005
+velocity all create 1000 12345
+fix 1 all nvt temp 900 900 200
+fix 5 all momentum 1 linear 1 1 1
+
+
+thermo 100
+thermo_style custom step ke etotal temp
+
+# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
+
+run 1000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 2 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.3
+  ghost atom cutoff = 8.3
+  binsize = 4.15 -> bins = 2 2 2
+Memory usage per processor = 2.40842 Mbytes
+Step KinEng TotEng Temp 
+       0    3.8778043    3.8778043         1000 
+     100    2.8126642    2.8126642    725.32391 
+     200    3.7110413    3.7110413     956.9955 
+     300    3.2361084    3.2361084    834.52081 
+     400    3.4625769    3.4625769    892.92201 
+     500    3.4563307    3.4563307    891.31126 
+     600    2.8486344    2.8486344    734.59982 
+     700    3.1183057    3.1183057    804.14208 
+     800    2.9164818    2.9164818    752.09618 
+     900     3.464416     3.464416    893.39629 
+    1000    3.5954546    3.5954546    927.18825 
+Loop time of 3.86777 on 1 procs for 1000 steps with 31 atoms
+
+Performance: 11.169 ns/day, 2.149 hours/ns, 258.547 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.8463     | 3.8463     | 3.8463     |   0.0 | 99.44
+Neigh   | 0.011294   | 0.011294   | 0.011294   |   0.0 |  0.29
+Comm    | 0.0057271  | 0.0057271  | 0.0057271  |   0.0 |  0.15
+Output  | 0.00014257 | 0.00014257 | 0.00014257 |   0.0 |  0.00
+Modify  | 0.0029459  | 0.0029459  | 0.0029459  |   0.0 |  0.08
+Other   |            | 0.001395   |            |       |  0.04
+
+Nlocal:    31 ave 31 max 31 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    878 ave 878 max 878 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  4334 ave 4334 max 4334 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 4334
+Ave neighs/atom = 139.806
+Neighbor list builds = 51
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03
--- a/examples/USER/misc/agni/log.9Nov16.vacancy.g++.4
+++ b/examples/USER/misc/agni/log.9Nov16.vacancy.g++.4
@ -0,0 +1,82 @@
+LAMMPS (9 Nov 2016)
+  using 1 OpenMP thread(s) per MPI task
+
+units metal
+boundary p p p
+read_data vac.data
+  orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  31 atoms
+
+pair_style agni
+pair_coeff * * Al_prb.agni Al
+Reading potential file Al_prb.agni with DATE: 2016-11-11
+neighbor 0.3 bin
+neigh_modify delay 2 check yes
+
+
+timestep 0.0005
+velocity all create 1000 12345
+fix 1 all nvt temp 900 900 200
+fix 5 all momentum 1 linear 1 1 1
+
+
+thermo 100
+thermo_style custom step ke etotal temp
+
+# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
+
+run 1000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 2 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.3
+  ghost atom cutoff = 8.3
+  binsize = 4.15 -> bins = 2 2 2
+Memory usage per processor = 2.3974 Mbytes
+Step KinEng TotEng Temp 
+       0    3.8778044    3.8778044         1000 
+     100    2.8126642    2.8126642    725.32391 
+     200    3.7110413    3.7110413    956.99549 
+     300    3.2361084    3.2361084    834.52081 
+     400    3.4625769    3.4625769    892.92201 
+     500    3.4563307    3.4563307    891.31126 
+     600    2.8486343    2.8486343    734.59981 
+     700    3.1183057    3.1183057    804.14208 
+     800    2.9164819    2.9164819    752.09618 
+     900    3.4644161    3.4644161    893.39631 
+    1000    3.5954546    3.5954546    927.18824 
+Loop time of 1.11007 on 4 procs for 1000 steps with 31 atoms
+
+Performance: 38.916 ns/day, 0.617 hours/ns, 900.843 timesteps/s
+99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.906      | 0.99469    | 1.0291     |   5.1 | 89.61
+Neigh   | 0.0026186  | 0.0027665  | 0.0028622  |   0.2 |  0.25
+Comm    | 0.066125   | 0.10079    | 0.1896     |  16.2 |  9.08
+Output  | 0.00012875 | 0.00014615 | 0.00018787 |   0.2 |  0.01
+Modify  | 0.0080338  | 0.0083079  | 0.00861    |   0.2 |  0.75
+Other   |            | 0.003372   |            |       |  0.30
+
+Nlocal:    7.75 ave 8 max 7 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Nghost:    623.5 ave 630 max 616 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  1083.5 ave 1131 max 988 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+
+Total # of neighbors = 4334
+Ave neighs/atom = 139.806
+Neighbor list builds = 51
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:01
--- a/examples/USER/misc/agni/vacancy.data
+++ b/examples/USER/misc/agni/vacancy.data
@ -0,0 +1,46 @@
+Data File created from VASP POSCAR
+
+31 atoms
+1 atom types
+
+0 8.071125 xlo xhi
+0 8.071125 ylo yhi
+0 8.071125 zlo zhi
+
+Masses
+
+1 26.9815
+
+Atoms
+
+1 1 8.05711986217 3.20498589607 7.09652861184
+2 1 8.05262255028 3.62006786258 3.16719841667
+3 1 2.08891866821 1.38430927213 3.14852514324
+4 1 4.25446836692 3.27689661974 3.35678388118
+5 1 7.92524269451 7.20500664579 3.03232792051
+6 1 6.04056771113 7.24499020906 1.11223380379
+7 1 2.32585852889 5.29910389395 7.31500292009
+8 1 2.09613190567 1.27658214906 7.44277603054
+9 1 3.96852985867 7.2805082905 3.37568009522
+10 1 0.0773420461671 1.29964047903 5.27451616984
+11 1 7.96501442334 1.24471347504 1.17853896176
+12 1 2.13035246804 5.36148411996 3.3817805118
+13 1 2.06211525033 7.25482811482 1.52039033766
+14 1 3.99735704234 7.4099829467 7.05753768668
+15 1 3.84113228596 5.1855444403 1.41642147402
+16 1 0.231862769544 5.38528175164 5.51171817022
+17 1 0.12718452785 5.35814065671 1.11669573581
+18 1 8.05303937039 7.38861123542 7.41398359808
+19 1 1.88506066609 3.17578974033 1.20929473631
+20 1 4.33739926831 1.37976783613 5.28141762358
+21 1 2.23200994743 3.12419127088 5.36881641316
+22 1 6.22871004896 1.34968648416 7.24032447626
+23 1 6.08380394159 1.16222146146 3.30535465675
+24 1 6.16629028099 5.22806528503 3.7675179617
+25 1 4.30194966153 1.14526017671 1.45054175732
+26 1 6.24221620153 5.05377575942 7.17573714759
+27 1 3.92820642281 2.9627641757 7.71515743722
+28 1 4.33686872315 4.73096617728 5.57649231331
+29 1 6.05033104136 3.51389714904 1.34127903322
+30 1 6.27311587476 7.19257797516 5.46814369382
+31 1 1.81274009101 7.47392095028 5.35484578074
--- 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 +1,169 @@
+#!/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 " + lmp + " -in ../" + inp + " -var lambda %g -var eta %g -var enthalpy %g > output" % (nproc, 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("rm output")
+		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 	p all smd/plastic_strain
-compute 	epsdot all smd/plastic_strain_rate
-compute 	S all smd/tlsph_stress # Cauchy stress tensor
-compute 	D all smd/tlsph_strain_rate
-compute 	E all smd/tlsph_strain
-compute 	nn all smd/tlsph_num_neighs # number of neighbors for each particle
-compute         shape all smd/tlsph_shape
+compute         dt_atom all smd/tlsph/dt
+compute 	p all smd/plastic/strain
+compute 	epsdot all smd/plastic/strain/rate
+compute 	S all smd/tlsph/stress # Cauchy stress tensor
+compute 	D all smd/tlsph/strain/rate
+compute 	E all smd/tlsph/strain
+compute 	nn all smd/tlsph/num/neighs # number of neighbors for each particle
+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         contact_radius all smd/contact_radius
-compute         S solids smd/tlsph_stress
-compute         nn water smd/ulsph_num_neighs
-compute         epl solids smd/plastic_strain
+compute         eint all smd/internal/energy
+compute         contact_radius all smd/contact/radius
+compute         S solids smd/tlsph/stress
+compute         nn water smd/ulsph/num/neighs
+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         contact_radius all smd/contact_radius
-compute         surface_coords surface smd/triangle_vertices
+compute 	nn all smd/ulsph/num/neighs # number of neighbors for each particle
+compute         contact_radius all smd/contact/radius
+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         nn all smd/tlsph_num_neighs # number of neighbors for each particle
-compute         cr all smd/contact_radius
-compute         p all smd/plastic_strain
-compute         eint all smd/internal_energy
+compute         S all smd/tlsph/stress # Cauchy stress tensor
+compute         nn all smd/tlsph/num/neighs # number of neighbors for each particle
+compute         cr all smd/contact/radius
+compute         p all smd/plastic/strain
+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         E all smd/tlsph_strain # Green-Lagrange strain tensor
-compute         nn all smd/tlsph_num_neighs # number of neighbors for each particle
+compute         S all smd/tlsph/stress # Cauchy stress tensor
+compute         E all smd/tlsph/strain # Green-Lagrange strain tensor
+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/examples/coreshell/in.coreshell.dsf
+++ b/examples/coreshell/in.coreshell.dsf
@ -0,0 +1,71 @@
+# Testsystem for core-shell model compared to Mitchel and Finchham
+# Hendrik Heenen, June 2014
+
+# ------------------------ INITIALIZATION ----------------------------
+
+units 		metal
+dimension	3
+boundary	p	p	p
+atom_style	full
+
+# ----------------------- ATOM DEFINITION ----------------------------
+
+fix csinfo all property/atom i_CSID
+read_data data.coreshell fix csinfo NULL CS-Info
+
+group cores type 1 2
+group shells type 3 4
+
+neighbor 2.0 bin
+comm_modify vel yes
+
+# ------------------------ FORCE FIELDS ------------------------------
+
+pair_style   born/coul/dsf/cs 0.1 20.0 20.0    # A, rho, sigma=0, C, D 
+pair_coeff   * *      0.0 1.000   0.00  0.00   0.00
+pair_coeff   3 3    487.0 0.23768 0.00  1.05   0.50 #Na-Na
+pair_coeff   3 4 145134.0 0.23768 0.00  6.99   8.70 #Na-Cl
+pair_coeff   4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
+
+bond_style harmonic
+bond_coeff 1 63.014 0.0
+bond_coeff 2 25.724 0.0
+
+# ------------------------ Equilibration Run -------------------------------
+
+reset_timestep 0
+
+thermo 50
+thermo_style custom step etotal pe ke temp press &
+             epair evdwl ecoul elong ebond fnorm fmax vol
+
+compute CSequ all temp/cs cores shells 
+
+# output via chunk method
+
+#compute prop all property/atom i_CSID
+#compute cs_chunk all chunk/atom c_prop
+#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
+#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector 
+
+thermo_modify temp CSequ
+
+# velocity bias option
+
+velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
+velocity all scale 1427 temp CSequ
+
+fix thermoberendsen all temp/berendsen 1427 1427 0.4
+fix nve all nve
+fix_modify thermoberendsen temp CSequ
+
+# 2 fmsec timestep
+
+timestep 0.002
+run 500
+
+unfix thermoberendsen
+
+# ------------------------ Dynamic Run -------------------------------
+
+run 1000
--- a/examples/coreshell/log.9Nov16.coreshell.dsf.1
+++ b/examples/coreshell/log.9Nov16.coreshell.dsf.1
@ -0,0 +1,185 @@
+LAMMPS (27 Oct 2016)
+# Testsystem for core-shell model compared to Mitchel and Finchham
+# Hendrik Heenen, June 2014
+
+# ------------------------ INITIALIZATION ----------------------------
+
+units 		metal
+dimension	3
+boundary	p	p	p
+atom_style	full
+
+# ----------------------- ATOM DEFINITION ----------------------------
+
+fix csinfo all property/atom i_CSID
+read_data data.coreshell fix csinfo NULL CS-Info
+  orthogonal box = (0 0 0) to (24.096 24.096 24.096)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  432 atoms
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  216 bonds
+  1 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+
+group cores type 1 2
+216 atoms in group cores
+group shells type 3 4
+216 atoms in group shells
+
+neighbor 2.0 bin
+comm_modify vel yes
+
+# ------------------------ FORCE FIELDS ------------------------------
+
+pair_style   born/coul/dsf/cs 0.1 20.0 20.0    # A, rho, sigma=0, C, D
+pair_coeff   * *      0.0 1.000   0.00  0.00   0.00
+pair_coeff   3 3    487.0 0.23768 0.00  1.05   0.50 #Na-Na
+pair_coeff   3 4 145134.0 0.23768 0.00  6.99   8.70 #Na-Cl
+pair_coeff   4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
+
+bond_style harmonic
+bond_coeff 1 63.014 0.0
+bond_coeff 2 25.724 0.0
+
+# ------------------------ Equilibration Run -------------------------------
+
+reset_timestep 0
+
+thermo 50
+thermo_style custom step etotal pe ke temp press              epair evdwl ecoul elong ebond fnorm fmax vol
+
+compute CSequ all temp/cs cores shells
+
+# output via chunk method
+
+#compute prop all property/atom i_CSID
+#compute cs_chunk all chunk/atom c_prop
+#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
+#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
+
+thermo_modify temp CSequ
+
+# velocity bias option
+
+velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
+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 = 22
+  ghost atom cutoff = 22
+  binsize = 11 -> bins = 3 3 3
+velocity all scale 1427 temp CSequ
+
+fix thermoberendsen all temp/berendsen 1427 1427 0.4
+fix nve all nve
+fix_modify thermoberendsen temp CSequ
+
+# 2 fmsec timestep
+
+timestep 0.002
+run 500
+Memory usage per processor = 7.04355 Mbytes
+Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume 
+       0   -635.80596   -675.46362    39.657659         1427   -21302.622   -675.46362    1.6320365   -677.09565            0            0 1.3517686e-14 2.942091e-15      13990.5 
+      50    -633.9898   -666.02679     32.03699    1152.7858   -4578.5681   -668.50431    37.800204   -706.30452            0    2.4775226    14.568073    4.3012389      13990.5 
+     100   -631.89604   -661.96148    30.065442    1081.8436   -3536.6738   -664.61798     39.18583   -703.80381            0    2.6564973    14.677968    3.9051029      13990.5 
+     150   -630.08723   -662.95879    32.871559     1182.816   -109.19506   -665.76772    46.247821   -712.01554            0    2.8089226    15.270039    2.9328953      13990.5 
+     200   -628.55895   -663.97376    35.414806    1274.3296     -1748.35   -666.58439    41.738552   -708.32294            0    2.6106349    14.148282    3.1047826      13990.5 
+     250   -627.28761   -661.92274    34.635123    1246.2743   -1280.4899     -664.917    43.045475   -707.96247            0    2.9942594    14.248617    2.4694705      13990.5 
+     300    -626.6163   -663.65651    37.040209    1332.8164   -1887.9043   -666.35215     40.84964   -707.20179            0    2.6956373    13.142643    1.9263242      13990.5 
+     350   -625.76781   -664.66441    38.896607    1399.6151    -1839.482   -667.47659    40.999206   -708.47579            0    2.8121749    13.601238    1.9262698      13990.5 
+     400   -625.02586   -661.46042    36.434568    1311.0236    -868.2031   -664.40231     43.21398   -707.61629            0    2.9418875    14.945389    2.7493413      13990.5 
+     450    -624.3278   -660.50844    36.180639    1301.8865   -2203.3944   -663.49896    40.008669   -703.50763            0    2.9905179    14.158866    1.7299899      13990.5 
+     500   -623.56254   -661.33839    37.775849    1359.2869   -810.50736   -664.11652    42.993999   -707.11052            0    2.7781274     13.68709    2.9115277      13990.5 
+Loop time of 10.7162 on 1 procs for 500 steps with 432 atoms
+
+Performance: 8.063 ns/day, 2.977 hours/ns, 46.658 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 10.478     | 10.478     | 10.478     |   0.0 | 97.78
+Bond    | 0.0029511  | 0.0029511  | 0.0029511  |   0.0 |  0.03
+Neigh   | 0.14159    | 0.14159    | 0.14159    |   0.0 |  1.32
+Comm    | 0.074382   | 0.074382   | 0.074382   |   0.0 |  0.69
+Output  | 0.00054097 | 0.00054097 | 0.00054097 |   0.0 |  0.01
+Modify  | 0.010588   | 0.010588   | 0.010588   |   0.0 |  0.10
+Other   |            | 0.007748   |            |       |  0.07
+
+Nlocal:    432 ave 432 max 432 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    9280 ave 9280 max 9280 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    297636 ave 297636 max 297636 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 297636
+Ave neighs/atom = 688.972
+Ave special neighs/atom = 1
+Neighbor list builds = 20
+Dangerous builds = 0
+
+unfix thermoberendsen
+
+# ------------------------ Dynamic Run -------------------------------
+
+run 1000
+Memory usage per processor = 7.04355 Mbytes
+Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume 
+     500   -623.56254   -661.33839    37.775849    1359.2869   -810.50736   -664.11652    42.993999   -707.11052            0    2.7781274     13.68709    2.9115277      13990.5 
+     550    -623.5004   -660.74472    37.244326    1340.1611   -1413.4326   -663.99669    41.875014    -705.8717            0    3.2519651    15.097948     2.278405      13990.5 
+     600   -623.46963   -659.61729    36.147655    1300.6997   -521.50578   -662.54994    43.956071   -706.50601            0    2.9326492     14.99649    2.6334959      13990.5 
+     650   -623.49291   -661.50698    38.014069    1367.8588   -1230.0925   -664.21074    42.027844   -706.23859            0    2.7037578    13.982308    1.6247207      13990.5 
+     700    -623.4913   -660.11564     36.62434    1317.8522   -727.89052   -663.24921    43.413397   -706.66261            0    3.1335699    15.009937    2.0563966      13990.5 
+     750   -623.50292   -657.95982      34.4569    1239.8613    636.46644   -661.16971    46.539267   -707.70898            0    3.2098934     15.25993    2.1864622      13990.5 
+     800    -623.5176   -659.92032    36.402711    1309.8773   -912.75799   -662.84989    42.668309    -705.5182            0    2.9295708    13.577516    2.0006099      13990.5 
+     850   -623.44098   -660.92727    37.486295    1348.8679   -550.40358   -664.08308    43.667245   -707.75033            0    3.1558098    14.836208     2.279198      13990.5 
+     900   -623.46361   -661.21737    37.753765    1358.4923    1267.8647   -664.52195     47.67284   -712.19479            0    3.3045765    15.058502     1.886141      13990.5 
+     950   -623.50114   -660.58464    37.083492    1334.3739    1754.7359   -663.48186     48.70363   -712.18549            0     2.897226    15.519042    2.2654928      13990.5 
+    1000   -623.50161   -660.02915    36.527539     1314.369    228.76104   -663.31152    45.374099   -708.68562            0    3.2823685    14.783709    2.4201134      13990.5 
+    1050   -623.45985   -660.57417    37.114321    1335.4832    -1490.604   -663.75391    41.258878   -705.01279            0    3.1797391    14.250262    2.3153255      13990.5 
+    1100   -623.51051   -661.20338    37.692871    1356.3011    1791.7899   -664.01042    48.626451   -712.63687            0     2.807039    15.559872     3.184101      13990.5 
+    1150   -623.51067   -663.19545    39.684776    1427.9758    1023.0584   -666.07723      46.5628   -712.64003            0    2.8817804    13.895322    2.3950292      13990.5 
+    1200   -623.49625    -659.6715    36.175253    1301.6927    1600.2805   -662.62259    48.522365   -711.14495            0    2.9510854    15.567834    2.1677651      13990.5 
+    1250   -623.48282   -660.56735    37.084533    1334.4113   -871.67341   -663.86673    42.560699   -706.42743            0    3.2993759    14.569539    2.0093709      13990.5 
+    1300   -623.47744   -663.63125    40.153811     1444.853    1343.7147   -666.39564    47.104842   -713.50048            0    2.7643857    14.186019    1.4599359      13990.5 
+    1350   -623.49121   -661.42731    37.936096    1365.0531    589.73669   -664.46099    45.947687   -710.40867            0    3.0336821    14.801223    2.7486556      13990.5 
+    1400   -623.50803   -660.03912     36.53109    1314.4968    362.97431   -663.24909    45.772904   -709.02199            0    3.2099708    14.566488    1.9170714      13990.5 
+    1450   -623.51243   -659.65548    36.143052     1300.534    2853.0755    -663.0534    51.355353   -714.40875            0    3.3979157    15.890282    2.5251359      13990.5 
+    1500   -623.51621   -661.87741    38.361201    1380.3496    740.04973   -665.00896    46.208742    -711.2177            0    3.1315492    15.168927    2.4710846      13990.5 
+Loop time of 22.2766 on 1 procs for 1000 steps with 432 atoms
+
+Performance: 7.757 ns/day, 3.094 hours/ns, 44.890 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 21.8       | 21.8       | 21.8       |   0.0 | 97.86
+Bond    | 0.005852   | 0.005852   | 0.005852   |   0.0 |  0.03
+Neigh   | 0.30423    | 0.30423    | 0.30423    |   0.0 |  1.37
+Comm    | 0.14388    | 0.14388    | 0.14388    |   0.0 |  0.65
+Output  | 0.0010855  | 0.0010855  | 0.0010855  |   0.0 |  0.00
+Modify  | 0.0064189  | 0.0064189  | 0.0064189  |   0.0 |  0.03
+Other   |            | 0.01527    |            |       |  0.07
+
+Nlocal:    432 ave 432 max 432 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    9318 ave 9318 max 9318 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    297131 ave 297131 max 297131 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 297131
+Ave neighs/atom = 687.803
+Ave special neighs/atom = 1
+Neighbor list builds = 44
+Dangerous builds = 0
+Total wall time: 0:00:33
--- a/examples/threebody/in.threebody
+++ b/examples/threebody/in.threebody
@ -114,3 +114,35 @@ neighbor        1.0 bin
 neigh_modify    every 1 delay 10 check yes
 run             100

+# Test Tersoff/Mod model for Si
+
+clear
+read_restart	restart.equil
+
+pair_style      tersoff/mod
+pair_coeff 	* * Si.tersoff.mod Si Si Si Si Si Si Si Si
+
+thermo          10
+fix             1 all nvt temp $t $t 0.1
+fix_modify 	1 energy yes
+timestep        1.0e-3
+neighbor        1.0 bin
+neigh_modify    every 1 delay 10 check yes
+run             100
+
+# Test Tersoff/Mod/C model for Si
+
+clear
+read_restart	restart.equil
+
+pair_style      tersoff/mod/c
+pair_coeff 	* * Si.tersoff.modc Si Si Si Si Si Si Si Si
+
+thermo          10
+fix             1 all nvt temp $t $t 0.1
+fix_modify 	1 energy yes
+timestep        1.0e-3
+neighbor        1.0 bin
+neigh_modify    every 1 delay 10 check yes
+run             100
+
--- a/potentials/Al_prb.agni
+++ b/potentials/Al_prb.agni
--- a/potentials/Si.tersoff.modc
+++ b/potentials/Si.tersoff.modc
@ -0,0 +1,10 @@
+# DATE: 2016-11-09 CONTRIBUTOR: Ganga P Purja Pun (George Mason University, Fairfax) CITATION: Unknown
+#
+# Format:
+# element1 element2 element3
+# beta alpha h eta
+# beta_ters lam2 B R D lam1 A
+# n c1 c2 c3 c4 c5 C
+Si Si Si 3.00000000 1.80536502 -0.38136087 2.16152496
+1 1.39343356 117.78072440 2.87478837 0.33090566 3.18011795 3198.51383127
+1.98633876 0.20123243 614230.04310619 996439.09714140 3.33560562 25.20963770 -0.00592042
--- 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
@ -205,6 +205,8 @@
 /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 +345,8 @@
 /fix_gle.h
 /fix_gpu.cpp
 /fix_gpu.h
+/fix_grem.cpp
+/fix_grem.h
 /fix_imd.cpp
 /fix_imd.h
 /fix_ipi.cpp
@ -539,6 +543,8 @@

 /pair_adp.cpp
 /pair_adp.h
+/pair_agni.cpp
+/pair_agni.h
 /pair_airebo.cpp
 /pair_airebo.h
 /pair_airebo_morse.cpp
@ -773,6 +779,8 @@
 /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
@ -871,6 +879,8 @@
 /tad.h
 /temper.cpp
 /temper.h
+/temper_grem.cpp
+/temper_grem.h
 /thr_data.cpp
 /thr_data.h
 /verlet_split.cpp
@ -976,6 +986,8 @@
 /fix_ttm_mod.h
 /pair_born_coul_long_cs.cpp
 /pair_born_coul_long_cs.h
+/pair_born_coul_dsf_cs.cpp
+/pair_born_coul_dsf_cs.h
 /pair_buck_coul_long_cs.cpp
 /pair_buck_coul_long_cs.h
 /pair_coul_long_cs.cpp
--- a/src/ASPHERE/compute_temp_asphere.cpp
+++ b/src/ASPHERE/compute_temp_asphere.cpp
@ -38,7 +38,8 @@ enum{ROTATE,ALL};
 /* ---------------------------------------------------------------------- */

 ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg)
+  Compute(lmp, narg, arg),
+  id_bias(NULL), tbias(NULL), avec(NULL)
 {
  if (narg < 3) error->all(FLERR,"Illegal compute temp/asphere command");

--- a/src/BODY/body_nparticle.cpp
+++ b/src/BODY/body_nparticle.cpp
@ -28,7 +28,7 @@ enum{SPHERE,LINE,TRI};           // also in DumpImage
 /* ---------------------------------------------------------------------- */

 BodyNparticle::BodyNparticle(LAMMPS *lmp, int narg, char **arg) :
-  Body(lmp, narg, arg)
+  Body(lmp, narg, arg), imflag(NULL), imdata(NULL)
 {
  if (narg != 3) error->all(FLERR,"Invalid body nparticle command");

--- a/src/BODY/compute_body_local.cpp
+++ b/src/BODY/compute_body_local.cpp
@ -33,7 +33,7 @@ enum{ID,TYPE,INDEX};
 /* ---------------------------------------------------------------------- */

 ComputeBodyLocal::ComputeBodyLocal(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg)
+  Compute(lmp, narg, arg), which(NULL), index(NULL), avec(NULL), bptr(NULL)
 {
  if (narg < 4) error->all(FLERR,"Illegal compute body/local command");

--- a/src/BODY/compute_temp_body.cpp
+++ b/src/BODY/compute_temp_body.cpp
@ -37,7 +37,7 @@ enum{ROTATE,ALL};
 /* ---------------------------------------------------------------------- */

 ComputeTempBody::ComputeTempBody(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg)
+  Compute(lmp, narg, arg), id_bias(NULL), tbias(NULL), avec(NULL)
 {
  if (narg < 3) error->all(FLERR,"Illegal compute temp/body command");

--- a/src/CORESHELL/Install.sh
+++ b/src/CORESHELL/Install.sh
@ -31,8 +31,10 @@ action () {
 action compute_temp_cs.cpp
 action compute_temp_cs.h
 action pair_born_coul_long_cs.cpp pair_born_coul_long.cpp
+action pair_born_coul_dsf_cs.cpp pair_born_coul_dsf.cpp
 action pair_buck_coul_long_cs.cpp pair_buck_coul_long.cpp
 action pair_born_coul_long_cs.h pair_born_coul_long.h
+action pair_born_coul_dsf_cs.h pair_born_coul_dsf.h
 action pair_buck_coul_long_cs.h pair_buck_coul_long.h
 action pair_coul_long_cs.cpp pair_coul_long.cpp
 action pair_coul_long_cs.h pair_coul_long.h
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
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
Steve Plimpton	4b51719e67	new 17Nov16 patch and stable	2016-11-17 16:51:35 -07:00
Steve Plimpton	25d7be5f3d	compute pressure doc change	2016-11-17 16:11:30 -07:00
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
sjplimp	74c0e4dd5c	Merge pull request #278 from akohlmey/pair-agni Implementation of the AGNI manybody potential	2016-11-17 09:04:31 -07:00
sjplimp	073e8a0524	Merge pull request #276 from akohlmey/doc-updates Small bugfixes and updates	2016-11-17 09:02:27 -07:00
sjplimp	5320bbf585	Merge pull request #275 from andeplane/IP_VORONOI Initializing pointers in VORONOI	2016-11-17 09:01:46 -07:00
sjplimp	4448819824	Merge pull request #274 from andeplane/IP_POEMS Initialize pointers in POEMS	2016-11-17 09:01:37 -07:00
sjplimp	300ac30332	Merge pull request #273 from akohlmey/auto-memalign turn on -DLAMMPS_MEMALIGN=64 automatically when USER-INTEL is installed	2016-11-17 09:01:27 -07:00
sjplimp	2535e44991	Merge pull request #271 from akohlmey/tersoff-modc pair style tersoff/mod/c	2016-11-17 09:00:52 -07:00
dstelter92	747c95c525	revised documentation, added temper_grem ref to fix_grem	2016-11-17 11:00:49 -05:00
sjplimp	cdae794383	Merge pull request #242 from andeplane/vashishta_kokkos Added KOKKOS vashishta	2016-11-17 09:00:03 -07:00
Steve Plimpton	8756a1017d	Kokkos updates by Stan	2016-11-17 08:58:22 -07:00
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	22d93fe8fb	add restrict to CCFLAGS for makefiles intended for intel compilers	2016-11-16 14:31:10 -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	57124b9b25	update documentation metadata files for recent changes	2016-11-12 09:18:21 -05:00
Axel Kohlmeyer	03b3834fe3	add documentation for pair style agni	2016-11-12 09:07:42 -05:00
Axel Kohlmeyer	d0124eac95	optimized data access and using approximate exponential for USER-OMP version	2016-11-12 08:36:27 -05:00
Axel Kohlmeyer	5685131fe2	add USER-OMP version of pair style agni	2016-11-11 19:08:01 -05:00
Axel Kohlmeyer	22fc92f9d8	use special ev_tally() function suitable for this kind of force compute	2016-11-11 18:32:55 -05:00
Axel Kohlmeyer	b9770766a8	add adatom and vacancy examples for AGNI pair style	2016-11-11 18:19:29 -05:00
Axel Kohlmeyer	9cc0c8badd	error exit when requested element is not in potential file	2016-11-11 18:10:57 -05:00
Axel Kohlmeyer	6e1492a86c	add potential file for pair style AGNI	2016-11-11 18:10:26 -05:00
Axel Kohlmeyer	9b0987d8c4	first complete implementation of AGNI pair style	2016-11-11 17:32:47 -05:00
Axel Kohlmeyer	e453adaf81	implemented parser for 1 element potential files	2016-11-11 15:53:37 -05:00
Axel Kohlmeyer	8e0fd88697	add example demonstrating the use of fix addtorque	2016-11-11 10:52:50 -05:00
Axel Kohlmeyer	fdcabd7d1d	fix addtorque is compatible with dynamic groups	2016-11-11 09:01:18 -05:00
Axel Kohlmeyer	c5c8c50e97	initialize 'nper'	2016-11-11 07:47:42 -05:00
Axel Kohlmeyer	72b0841b28	Merge branch 'doc-updates' of github.com:akohlmey/lammps into doc-updates	2016-11-11 07:44:44 -05:00
Axel Kohlmeyer	801111a7ab	dummy framework implementation for AGNI pair style	2016-11-10 15:00:36 -05:00
Axel Kohlmeyer	bfc478c320	simpler variant of the segfault workaround, that does not offend Clang c++.	2016-11-10 14:12:02 -05:00
Axel Kohlmeyer	2b75ee761d	avoid segmentation fault, when creating a LAMMPS instance from the library interface. arg[] may be NULL.	2016-11-10 13:28:32 -05:00
Axel Kohlmeyer	352e177fcd	Merge branch 'master' into small-fixes-and-updates	2016-11-10 13:26:00 -05:00
Anders Hafreager	c20ee34c7b	Initializing pointers in VORONOI	2016-11-10 09:30:07 +01:00
Anders Hafreager	95a7f7160e	Initialize pointers in POEMS	2016-11-10 09:26:52 +01:00
Axel Kohlmeyer	1f38e1a771	Merge branch 'master' into doc-updates	2016-11-09 18:18:05 -05:00
Steve Plimpton	9806da69f3	Stan bug fixes for fix reaxc/bonds/kk	2016-11-09 15:47:50 -07:00
Axel Kohlmeyer	fec87c070d	simplify compiling USER-INTEL package, by defaulting to -DLAMMPS_MEMALIGN=64 in case it is not set	2016-11-09 16:53:39 -05:00
Axel Kohlmeyer	3d3a99c082	added missing potential for tersoff/mod/c	2016-11-09 16:50:34 -05:00
Axel Kohlmeyer	3e36ec3754	remove unused class member	2016-11-09 16:17:46 -05:00
Axel Kohlmeyer	9ed5c4f0fa	Merge branch 'master' into kokkos-vashishta	2016-11-09 15:15:10 -05:00
Axel Kohlmeyer	c55fd502e0	correct typo in formula	2016-11-09 15:04:24 -05:00
Axel Kohlmeyer	71ee2ecaa1	integrate pair style tersoff/mod/c contributed by Ganga P Purja Pun (GMU) This includes docs, added testing and inclusion of USER-OMP support.	2016-11-09 14:52:39 -05:00
sjplimp	bfea3dce7d	Merge pull request #268 from arielzn/born_dsf pair styles born/coul/dsf and born/coul/dsf/cs added	2016-11-09 11:57:09 -07:00
sjplimp	eef862ee1c	Merge pull request #267 from akohlmey/pager-help use pager for help message, if connected to stdout	2016-11-09 11:53:43 -07:00
sjplimp	0cc2fbf1d6	Merge pull request #266 from andeplane/IP_USER_OMP Initializing pointers in USER-OMP	2016-11-09 11:52:05 -07:00
sjplimp	ae00666994	Merge pull request #265 from andeplane/IP_DIFF_DPD Initializing pointers in USER-DIFFRACTION and USER-DPD	2016-11-09 11:51:53 -07:00
sjplimp	51b3b5fb35	Merge pull request #264 from andeplane/IP_SNAP_SRD Initialize pointers in SNAP and SRD	2016-11-09 11:51:44 -07:00
sjplimp	176f2c3aa1	Merge pull request #263 from andeplane/IP_RIGID_SHOCK Initialize pointers in RIGID and SHOCK	2016-11-09 11:51:36 -07:00
sjplimp	3f71bfb185	Merge pull request #262 from andeplane/IP_PERI_QEQ_REPLICA Initializing pointers in PERI, QEQ and REPLICA	2016-11-09 11:51:25 -07:00
sjplimp	cf3ab51679	Merge pull request #261 from andeplane/IP_MISC_MOLECULE Initialized pointers in MISC and MOLECULE	2016-11-09 11:51:09 -07:00
sjplimp	59922f894b	Merge pull request #260 from andeplane/IP_MANYBODY_MC Initialize pointers in MANYBODY and MC	2016-11-09 11:51:01 -07:00
sjplimp	5e2b9d8bf3	Merge pull request #259 from andeplane/IP_KSPACE Initialize pointers in KSPACE	2016-11-09 11:50:50 -07:00
sjplimp	2d132cad6b	Merge pull request #258 from andeplane/IP_GRANULAR Initialize pointers in GRANULAR	2016-11-09 11:50:41 -07:00
sjplimp	ef6801f8bf	Merge pull request #257 from andeplane/IP_CORESHELL Initialize pointers in CORESHELL	2016-11-09 11:50:31 -07:00
sjplimp	c81a723642	Merge pull request #256 from andeplane/IP_BODY Initialized pointers in BODY	2016-11-09 11:50:23 -07:00
sjplimp	f9eb2a99ce	Merge pull request #255 from andeplane/IP_ASPHERE Initialize pointers in ASPHERE	2016-11-09 11:50:11 -07:00
sjplimp	16a02ef27d	Merge pull request #254 from andeplane/IP_root Initialized pointers in src folder	2016-11-09 11:47:21 -07:00
Steve Plimpton	2c801320c2	fixed links in Section_intro.txt	2016-11-09 11:46:10 -07:00
Anders Hafreager	d20b32092e	Building correct shortlists and removed rsq test in force loops	2016-11-08 18:57:27 +01:00
arielzn	9de1a2a08f	added input using born/coul/dsf/cs to examples/coreshell	2016-11-08 18:27:44 +01:00
arielzn	cdb5d47e9f	add FLERR argument to force->bounds() in born/coul/dsf	2016-11-08 18:24:54 +01:00
Steve Plimpton	a23b287a7a	sync with SVN for creation of stable release	2016-11-08 09:05:50 -07:00
Steve Plimpton	31204aab6a	sync with SVN	2016-11-08 08:57:51 -07:00
arielzn	25e7d074cf	documentation added for born/coul/dsf and born/coul/dsf/cs styles	2016-11-08 16:51:54 +01:00
arielzn	667f4dfe28	pair style born/coul/dsf added with its coreshell version	2016-11-08 11:32:38 +01:00
Axel Kohlmeyer	21694ca3a8	improve help and it through a pager, when screen == stdout	2016-11-07 17:10:12 -05:00
Axel Kohlmeyer	9b910d5511	make name of the actual executable (i.e. arg[0]) accessible	2016-11-07 17:07:40 -05:00
Anders Hafreager	054ab6bff3	Initializing pointers in USER-OMP	2016-11-07 21:07:10 +01:00
Anders Hafreager	616420cda8	Initializing pointers in USER-DIFFRACTION and USER-DPD	2016-11-07 20:51:36 +01:00
Anders Hafreager	fb3ac9afba	Initialize pointers in SNAP and SRD	2016-11-07 20:30:38 +01:00
Anders Hafreager	7cd7cda2d4	Initialize pointers in RIGID and SHOCK	2016-11-07 20:22:04 +01:00
Anders Hafreager	db0524278a	Initializing pointers in PERI, QEQ and REPLICA	2016-11-07 19:58:27 +01:00
Anders Hafreager	1ff75eaba2	Initialized pointers in MISC and MOLECULE	2016-11-07 17:15:48 +01:00
Anders Hafreager	30dede867a	Initialize pointers in MANYBODY and MC	2016-11-07 17:02:32 +01:00
Anders Hafreager	a5c6104d64	Initialize pointers in KSPACE	2016-11-07 16:54:59 +01:00
Anders Hafreager	c5869bdee2	Initialize pointers in GRANULAR	2016-11-07 16:33:50 +01:00
Anders Hafreager	e7a2c6b5d1	Initialize pointers in CORESHELL	2016-11-07 16:26:16 +01:00
Anders Hafreager	06959a9c59	Initialized pointers in BODY	2016-11-07 16:21:08 +01:00
Anders Hafreager	cd65d44d95	Initialize pointers in ASPHERE	2016-11-07 16:15:39 +01:00
Anders Hafreager	45f2e86dd6	NULLed ptrs in files	2016-11-07 16:07:37 +01:00
Anders Hafreager	f8226e8ae5	NULL ptrs in dump_custom and dump_image	2016-11-07 15:56:47 +01:00
Anders Hafreager	b221b15d24	NULLing ptrs in comm_brick and dump*.cpp	2016-11-07 15:50:18 +01:00
Axel Kohlmeyer	3a3d96b877	info styles also prints out pair styles	2016-11-04 18:18:40 -04:00
Anders Hafreager	f333d659c2	Using short neighborlists in neigh full	2016-10-29 22:54:43 +02:00
Anders Hafreager	51e2313fac	Using short neighbor lists	2016-10-29 22:35:29 +02:00
Anders Hafreager	e37d2b5c94	Calculating short neighbor lists	2016-10-29 22:20:37 +02:00
Axel Kohlmeyer	3870780894	Merge branch 'master' into kokkos-vashishta	2016-10-28 10:43:05 -04:00
stamoor	21619f6a2f	Recommitting reverted change git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15794 f3b2605a-c512-4ea7-a41b-209d697bcdaa (cherry picked from commit `c0b98f5299`)	2016-10-25 15:25:39 -04:00
Anders Hafreager	039bda9b61	Added updated vashishta for KOKKOS support (cherry picked from commit 96089a42547f625e70aa2ac3933d248d2731b731)	2016-10-25 15:07:10 -04:00
Anders Hafreager	6929603eef	Added KOKKOS vashishta (cherry picked from commit 5edc474bf0be574ddba96d00bb63894edf400ddb)	2016-10-25 15:07:10 -04:00
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