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Merge pull request #354 from stanmoore1/kokkos_bugfixes
Kokkos bugfixes
2017-01-26 14:06:43 -07:00 · 2017-01-26 13:51:47 -07:00 · 2017-01-26 13:50:13 -07:00 · 2017-01-26 13:49:56 -07:00 · 2017-01-26 13:47:12 -07:00 · 2017-01-26 13:45:45 -07:00
762 changed files with 63792 additions and 31989 deletions
--- a/doc/src/Eqs/bond_oxdna_fene.jpg
+++ b/doc/src/Eqs/bond_oxdna_fene.jpg
--- a/doc/src/Eqs/bond_oxdna_fene.tex
+++ b/doc/src/Eqs/bond_oxdna_fene.tex
@ -0,0 +1,10 @@
 \documentclass[12pt]{article}
 \pagestyle{empty}
 \begin{document}
 $$ 
  E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r0}{\Delta}\right)^2\right]
 $$
 \end{document}
--- a/doc/src/JPG/tutorial_additional_changes.png
+++ b/doc/src/JPG/tutorial_additional_changes.png
--- a/doc/src/JPG/tutorial_automated_checks.png
+++ b/doc/src/JPG/tutorial_automated_checks.png
--- a/doc/src/JPG/tutorial_automated_checks_passed.png
+++ b/doc/src/JPG/tutorial_automated_checks_passed.png
--- a/doc/src/JPG/tutorial_branch.png
+++ b/doc/src/JPG/tutorial_branch.png
--- a/doc/src/JPG/tutorial_changes_others.png
+++ b/doc/src/JPG/tutorial_changes_others.png
--- a/doc/src/JPG/tutorial_create_new_pull_request1.png
+++ b/doc/src/JPG/tutorial_create_new_pull_request1.png
--- a/doc/src/JPG/tutorial_create_new_pull_request2.png
+++ b/doc/src/JPG/tutorial_create_new_pull_request2.png
--- a/doc/src/JPG/tutorial_edits_maintainers.png
+++ b/doc/src/JPG/tutorial_edits_maintainers.png
--- a/doc/src/JPG/tutorial_fork.png
+++ b/doc/src/JPG/tutorial_fork.png
--- a/doc/src/JPG/tutorial_https_block.png
+++ b/doc/src/JPG/tutorial_https_block.png
--- a/doc/src/JPG/tutorial_merged.png
+++ b/doc/src/JPG/tutorial_merged.png
--- a/doc/src/JPG/tutorial_new_pull_request.png
+++ b/doc/src/JPG/tutorial_new_pull_request.png
--- a/doc/src/JPG/tutorial_reverse_pull_request.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request.png
--- a/doc/src/JPG/tutorial_reverse_pull_request2.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request2.png
--- a/doc/src/JPG/tutorial_reverse_pull_request3.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request3.png
--- a/doc/src/JPG/tutorial_reverse_pull_request4.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request4.png
--- a/doc/src/JPG/tutorial_reverse_pull_request5.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request5.png
--- a/doc/src/JPG/tutorial_reverse_pull_request6.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request6.png
--- a/doc/src/JPG/tutorial_reverse_pull_request7.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request7.png
--- a/doc/src/JPG/tutorial_steve_assignee.png
+++ b/doc/src/JPG/tutorial_steve_assignee.png
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="13 Dec 2016 version">
+<META NAME="docnumber" CONTENT="26 Jan 2017 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@ -21,7 +21,7 @@
 <H1></H1>
 LAMMPS Documentation :c,h3
-13 Dec 2016 version :c,h4
+26 Jan 2017 version :c,h4
 Version info: :h4
--- a/doc/src/PDF/USER-CGDNA-overview.pdf
+++ b/doc/src/PDF/USER-CGDNA-overview.pdf
--- a/doc/src/PDF/colvars-refman-lammps.pdf
+++ b/doc/src/PDF/colvars-refman-lammps.pdf
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@ -581,8 +581,9 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "indent"_fix_indent.html,
 "langevin (k)"_fix_langevin.html,
 "lineforce"_fix_lineforce.html,
-"momentum"_fix_momentum.html,
+"momentum (k)"_fix_momentum.html,
 "move"_fix_move.html,
 "mscg"_fix_mscg.html,
 "msst"_fix_msst.html,
 "neb"_fix_neb.html,
 "nph (ko)"_fix_nh.html,
@ -701,7 +702,10 @@ package"_Section_start.html#start_3.
 "meso"_fix_meso.html,
 "manifoldforce"_fix_manifoldforce.html,
 "meso/stationary"_fix_meso_stationary.html,
 "nve/dot"_fix_nve_dot.html,
 "nve/dotc/langevin"_fix_nve_dotc_langevin.html,
 "nve/manifold/rattle"_fix_nve_manifold_rattle.html,
 "nvk"_fix_nvk.html,
 "nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
 "nph/eff"_fix_nh_eff.html,
 "npt/eff"_fix_nh_eff.html,
@ -917,7 +921,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "dpd (go)"_pair_dpd.html,
 "dpd/tstat (go)"_pair_dpd.html,
 "dsmc"_pair_dsmc.html,
-"eam (gkot)"_pair_eam.html,
+"eam (gkiot)"_pair_eam.html,
 "eam/alloy (gkot)"_pair_eam.html,
 "eam/fs (gkot)"_pair_eam.html,
 "eim (o)"_pair_eim.html,
@ -1033,6 +1037,11 @@ package"_Section_start.html#start_3.
 "morse/soft"_pair_morse.html,
 "multi/lucy"_pair_multi_lucy.html,
 "multi/lucy/rx"_pair_multi_lucy_rx.html,
 "oxdna/coaxstk"_pair_oxdna.html,
 "oxdna/excv"_pair_oxdna.html,
 "oxdna/hbond"_pair_oxdna.html,
 "oxdna/stk"_pair_oxdna.html,
 "oxdna/xstk"_pair_oxdna.html,
 "quip"_pair_quip.html,
 "reax/c (k)"_pair_reax_c.html,
 "smd/hertz"_pair_smd_hertz.html,
@ -1081,7 +1090,8 @@ if "LAMMPS is built with the appropriate
 package"_Section_start.html#start_3.
 "harmonic/shift (o)"_bond_harmonic_shift.html,
-"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html :tb(c=4,ea=c)
+"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
 "oxdna/fene"_bond_oxdna_fene.html :tb(c=4,ea=c)
 :line
--- a/doc/src/Section_errors.txt
+++ b/doc/src/Section_errors.txt
@ -55,12 +55,13 @@ LAMMPS errors are detected at setup time; others like a bond
 stretching too far may not occur until the middle of a run.
 LAMMPS tries to flag errors and print informative error messages so
-you can fix the problem.  Of course, LAMMPS cannot figure out your
+you can fix the problem.  For most errors it will also print the last
-physics or numerical mistakes, like choosing too big a timestep,
+input script command that it was processing.  Of course, LAMMPS cannot
-specifying erroneous force field coefficients, or putting 2 atoms on
+figure out your physics or numerical mistakes, like choosing too big a
-top of each other!  If you run into errors that LAMMPS doesn't catch
+timestep, specifying erroneous force field coefficients, or putting 2
-that you think it should flag, please send an email to the
+atoms on top of each other!  If you run into errors that LAMMPS
-"developers"_http://lammps.sandia.gov/authors.html.
+doesn't catch that you think it should flag, please send an email to
 the "developers"_http://lammps.sandia.gov/authors.html.
 If you get an error message about an invalid command in your input
 script, you can determine what command is causing the problem by
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@ -84,7 +84,7 @@ Package, Description, Author(s), Doc page, Example, Library
 "PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
 "POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
 "PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python
-"REAX"_#REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax,  lib/reax
+"REAX"_#REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax, lib/reax
 "REPLICA"_#REPLICA, multi-replica methods, -, "Section 6.6.5"_Section_howto.html#howto_5, tad, -
 "RIGID"_#RIGID, rigid bodies, -, "fix rigid"_fix_rigid.html, rigid, -
 "SHOCK"_#SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
@ -1140,6 +1140,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
 "USER-ATC"_#USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (1), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
 "USER-AWPMD"_#USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
 "USER-CG-CMM"_#USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
 "USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, Oliver Henrich (U Edinburgh), src/USER-CGDNA/README, USER/cgdna, -, -
 "USER-COLVARS"_#USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
 "USER-DIFFRACTION"_#USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -
 "USER-DPD"_#USER-DPD, reactive dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, -
@ -1153,7 +1154,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
 "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
 "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -
 "USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
-"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc, dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
+"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc / dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
 "USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, -
 "USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
 "USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
@ -1284,6 +1285,31 @@ him directly if you have questions.
 :line
 USER-CGDNA package :link(USER-CGDNA),h5
 Contents: The CGDNA package implements coarse-grained force fields for
 single- and double-stranded DNA. This is at the moment mainly the
 oxDNA model, developed by Doye, Louis and Ouldridge at the University
 of Oxford.  The package also contains Langevin-type rigid-body
 integrators with improved stability.
 See these doc pages to get started:
 "bond_style oxdna_fene"_bond_oxdna_fene.html
 "pair_style oxdna_excv"_pair_oxdna_excv.html
 "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul
 Supporting info: /src/USER-CGDNA/README, "bond_style
 oxdna_fene"_bond_oxdna_fene.html, "pair_style
 oxdna_excv"_pair_oxdna_excv.html, "fix
 nve/dotc/langevin"_fix_nve_dotc_langevin.html
 Author: Oliver Henrich at the University of Edinburgh, UK (o.henrich
 at epcc.ed.ac.uk or ohenrich at ph.ed.ac.uk).  Contact him directly if
 you have any questions.
 :line
 USER-COLVARS package :link(USER-COLVARS),h5
 Contents: COLVARS stands for collective variables which can be used to
@ -1610,11 +1636,12 @@ and a "dump nc/mpiio"_dump_nc.html command to output LAMMPS snapshots
 in this format.  See src/USER-NC-DUMP/README for more details.
 NetCDF files can be directly visualized with the following tools:
 Ovito (http://www.ovito.org/). Ovito supports the AMBER convention
-  and all of the above extensions. :ulb,l
+and all of the above extensions. :ulb,l
 VMD (http://www.ks.uiuc.edu/Research/vmd/) :l
 AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains
-  a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule
+a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule
 The person who created these files is Lars Pastewka at
 Karlsruhe Institute of Technology (lars.pastewka at kit.edu).
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@ -1727,7 +1727,7 @@ thermodynamic state and a total run time for the simulation.  It then
 appends statistics about the CPU time and storage requirements for the
 simulation.  An example set of statistics is shown here:
-Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
+Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms :pre
 Performance: 18.436 ns/day  1.302 hours/ns  106.689 timesteps/s
 97.0% CPU use with 4 MPI tasks x no OpenMP threads :pre
@ -1757,14 +1757,14 @@ Ave special neighs/atom = 2.34032
 Neighbor list builds = 26
 Dangerous builds = 0 :pre
-The first section provides a global loop timing summary. The loop time
+The first section provides a global loop timing summary. The {loop time}
 is the total wall time for the section.  The {Performance} line is
 provided for convenience to help predicting the number of loop
-continuations required and for comparing performance with other
+continuations required and for comparing performance with other,
-similar MD codes.  The CPU use line provides the CPU utilzation per
+similar MD codes.  The {CPU use} line provides the CPU utilzation per
 MPI task; it should be close to 100% times the number of OpenMP
-threads (or 1). Lower numbers correspond to delays due to file I/O or
+threads (or 1 of no OpenMP). Lower numbers correspond to delays due
-insufficient thread utilization.
+to file I/O or insufficient thread utilization.
 The MPI task section gives the breakdown of the CPU run time (in
 seconds) into major categories:
@ -1791,7 +1791,7 @@ is present that also prints the CPU utilization in percent. In
 addition, when using {timer full} and the "package omp"_package.html
 command are active, a similar timing summary of time spent in threaded
 regions to monitor thread utilization and load balance is provided. A
-new entry is the {Reduce} section, which lists the time spend in
+new entry is the {Reduce} section, which lists the time spent in
 reducing the per-thread data elements to the storage for non-threaded
 computation. These thread timings are taking from the first MPI rank
 only and and thus, as the breakdown for MPI tasks can change from MPI
--- a/doc/src/accelerate_intel.txt
+++ b/doc/src/accelerate_intel.txt
@ -29,7 +29,7 @@ Bond Styles: fene, harmonic :l
 Dihedral Styles: charmm, harmonic, opls :l
 Fixes: nve, npt, nvt, nvt/sllod :l
 Improper Styles: cvff, harmonic :l
-Pair Styles: buck/coul/cut, buck/coul/long, buck, gayberne,
+Pair Styles: buck/coul/cut, buck/coul/long, buck, eam, gayberne,
 charmm/coul/long, lj/cut, lj/cut/coul/long, sw, tersoff :l
 K-Space Styles: pppm :l
 :ule
--- a/doc/src/accelerate_kokkos.txt
+++ b/doc/src/accelerate_kokkos.txt
@ -110,14 +110,14 @@ mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj   # ditto on 8 Phis :p
 [Required hardware/software:]
 Kokkos support within LAMMPS must be built with a C++11 compatible
-compiler.  If using gcc, version 4.8.1 or later is required.
+compiler.  If using gcc, version 4.7.2 or later is required.
 To build with Kokkos support for CPUs, your compiler must support the
 OpenMP interface.  You should have one or more multi-core CPUs so that
 multiple threads can be launched by each MPI task running on a CPU.
 To build with Kokkos support for NVIDIA GPUs, NVIDIA Cuda software
-version 6.5 or later must be installed on your system.  See the
+version 7.5 or later must be installed on your system.  See the
 discussion for the "GPU"_accelerate_gpu.html package for details of
 how to check and do this.
--- a/doc/src/bond_oxdna_fene.txt
+++ b/doc/src/bond_oxdna_fene.txt
@ -0,0 +1,70 @@
 "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
 bond_style oxdna_fene command :h3
 [Syntax:]
 bond_style oxdna_fene :pre
 [Examples:]
 bond_style oxdna_fene
 bond_coeff * 2.0 0.25 0.7525 :pre
 [Description:]
 The {oxdna_fene} bond style uses the potential
 :c,image(Eqs/bond_oxdna_fene.jpg)
 to define a modified finite extensible nonlinear elastic (FENE) potential
 "(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone
 in the oxDNA force field for coarse-grained modelling of DNA. 
 The following coefficients must be defined for the bond type via the
 "bond_coeff"_bond_coeff.html command as given in the above example, or in
 the data file or restart files read by the "read_data"_read_data.html
 or "read_restart"_read_restart.html commands:
 epsilon (energy)
 Delta (distance)
 r0 (distance) :ul
 NOTE: This bond style has to be used together with the corresponding oxDNA pair styles
 for excluded volume interaction {oxdna_excv}, stacking {oxdna_stk}, cross-stacking {oxdna_xstk}
 and coaxial stacking interaction {oxdna_coaxstk} as well as hydrogen-bonding interaction {oxdna_hbond} (see also documentation of 
 "pair_style oxdna_excv"_pair_oxdna_excv.html). The coefficients 
 in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
 Example input and data files can be found in /examples/USER/cgdna/examples/duplex1/ and /duplex2/.
 A simple python setup tool which creates single straight or helical DNA strands,
 DNA duplexes or arrays of DNA duplexes can be found in /examples/USER/cgdna/util/.
 A technical report with more information on the model, the structure of the input file,
 the setup tool and the performance of the LAMMPS-implementation of oxDNA
 can be found "here"_PDF/USER-CGDNA-overview.pdf.
 :line
 [Restrictions:]
 This bond style can only be used if LAMMPS was built with the
 USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 [Related commands:]
 "pair_style oxdna_excv"_pair_oxdna_excv.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html 
 [Default:] none
 :line
 :link(oxdna_fene)
 [(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
--- a/doc/src/bonds.txt
+++ b/doc/src/bonds.txt
@ -15,6 +15,7 @@ Bond Styles :h1
   bond_morse
   bond_none
   bond_nonlinear
   bond_oxdna_fene
   bond_quartic
   bond_table
   bond_zero
--- a/doc/src/commands.txt
+++ b/doc/src/commands.txt
@ -91,6 +91,7 @@ Commands :h1
   suffix
   tad
   temper
   temper_grem
   thermo
   thermo_modify
   thermo_style
--- a/doc/src/compute_coord_atom.txt
+++ b/doc/src/compute_coord_atom.txt
@ -10,34 +10,43 @@ compute coord/atom command :h3
 [Syntax:]
-compute ID group-ID coord/atom cutoff type1 type2 ... :pre
+compute ID group-ID coord/atom cstyle args ... :pre
-ID, group-ID are documented in "compute"_compute.html command
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
-coord/atom = style name of this compute command
+coord/atom = style name of this compute command :l
-cutoff = distance within which to count coordination neighbors (distance units)
+cstyle = {cutoff} or {orientorder} :l
-typeN = atom type for Nth coordination count (see asterisk form below) :ul
+  {cutoff} args = cutoff typeN
    cutoff = distance within which to count coordination neighbors (distance units)
    typeN = atom type for Nth coordination count (see asterisk form below)
  {orientorder} args = orientorderID threshold
    orientorderID = ID of an orientorder/atom compute
    threshold = minimum value of the product of two "connected" atoms :pre
 :ule
 [Examples:]
-compute 1 all coord/atom 2.0
+compute 1 all coord/atom cutoff 2.0
-compute 1 all coord/atom 6.0 1 2
+compute 1 all coord/atom cutoff 6.0 1 2
-compute 1 all coord/atom 6.0 2*4 5*8 * :pre
+compute 1 all coord/atom cutoff 6.0 2*4 5*8 *
 compute 1 all coord/atom orientorder 2 0.5 :pre
 [Description:]
-Define a computation that calculates one or more coordination numbers
+This compute performs calculations between neighboring atoms to
-for each atom in a group.
+determine a coordination value.  The specific calculation and the
 meaning of the resulting value depend on the {cstyle} keyword used.
-A coordination number is defined as the number of neighbor atoms with
+The {cutoff} cstyle calculates one or more traditional coordination
-specified atom type(s) that are within the specified cutoff distance
+numbers for each atom.  A coordination number is defined as the number
-from the central atom.  Atoms not in the group are included in a
+of neighbor atoms with specified atom type(s) that are within the
-coordination number of atoms in the group.
+specified cutoff distance from the central atom.  Atoms not in the
 specified group are included in the coordination number tally.
-The {typeN} keywords allow you to specify which atom types contribute
+The {typeN} keywords allow specification of which atom types
-to each coordination number.  One coordination number is computed for
+contribute to each coordination number.  One coordination number is
-each of the {typeN} keywords listed.  If no {typeN} keywords are
+computed for each of the {typeN} keywords listed.  If no {typeN}
-listed, a single coordination number is calculated, which includes
+keywords are listed, a single coordination number is calculated, which
-atoms of all types (same as the "*" format, see below).
+includes atoms of all types (same as the "*" format, see below).
 The {typeN} keywords can be specified in one of two ways.  An explicit
 numeric value can be used, as in the 2nd example above.  Or a
@ -49,8 +58,27 @@ from 1 to N.  A leading asterisk means all types from 1 to n
 (inclusive).  A middle asterisk means all types from m to n
 (inclusive).
-The value of all coordination numbers will be 0.0 for atoms not in the
+The {orientorder} cstyle calculates the number of "connected" neighbor
-specified compute group.
+atoms J around each central atom I.  For this {cstyle}, connected is
 defined by the orientational order parameter calculated by the
 "compute orientorder/atom"_compute_orientorder_atom.html command.
 This {cstyle} thus allows one to apply the ten Wolde's criterion to
 identify crystal-like atoms in a system, as discussed in "ten
 Wolde"_#tenWolde.
 The ID of the previously specified "compute
 orientorder/atom"_compute_orientorder/atom command is specified as
 {orientorderID}.  The compute must invoke its {components} option to
 calculate components of the {Ybar_lm} vector for each atoms, as
 described in its documenation.  Note that orientorder/atom compute
 defines its own criteria for identifying neighboring atoms.  If the
 scalar product ({Ybar_lm(i)},{Ybar_lm(j)}), calculated by the
 orientorder/atom compute is larger than the specified {threshold},
 then I and J are connected, and the coordination value of I is
 incremented by one.
 For all {cstyle} settings, all coordination values will be 0.0 for
 atoms not in the specified compute group.
 The neighbor list needed to compute this quantity is constructed each
 time the calculation is performed (i.e. each time a snapshot of atoms
@ -72,11 +100,16 @@ the neighbor list.
 [Output info:]
-If single {type1} keyword is specified (or if none are specified),
+For {cstyle} cutoff, this compute can calculate a per-atom vector or
-this compute calculates a per-atom vector.  If multiple {typeN}
+array.  If single {type1} keyword is specified (or if none are
-keywords are specified, this compute calculates a per-atom array, with
+specified), this compute calculates a per-atom vector.  If multiple
-N columns.  These values can be accessed by any command that uses
+{typeN} keywords are specified, this compute calculates a per-atom
-per-atom values from a compute as input.  See "Section
+array, with N columns.
 For {cstyle} orientorder, this compute calculates a per-atom vector.
 These values can be accessed by any command that uses per-atom values
 from a compute as input.  See "Section
 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
 options.
@ -88,5 +121,12 @@ explained above.
 [Related commands:]
 "compute cluster/atom"_compute_cluster_atom.html
 "compute orientorder/atom"_compute_orientorder_atom.html
 [Default:] none
 :line
 :link(tenWolde)
 [(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
 J. Chem. Phys. 104, 9932 (1996).
--- a/doc/src/compute_orientorder_atom.txt
+++ b/doc/src/compute_orientorder_atom.txt
@ -15,17 +15,19 @@ compute ID group-ID orientorder/atom keyword values ... :pre
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 orientorder/atom = style name of this compute command :l
 one or more keyword/value pairs may be appended :l
-keyword = {cutoff} or {nnn} or {degrees}
+keyword = {cutoff} or {nnn} or {degrees} or {components}
  {cutoff} value = distance cutoff
  {nnn} value = number of nearest neighbors
-  {degrees} values = nlvalues, l1, l2,...  :pre
+  {degrees} values = nlvalues, l1, l2,...
  {components} value = ldegree  :pre
 :ule
 [Examples:]
 compute 1 all orientorder/atom
-compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5 :pre
+compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5
 compute 1 all orientorder/atom degrees 4 6 components 6 nnn NULL cutoff 3.0 :pre
 [Description:]
@ -62,14 +64,21 @@ specified distance cutoff are used.
 The optional keyword {degrees} defines the list of order parameters to
 be computed.  The first argument {nlvalues} is the number of order
 parameters. This is followed by that number of integers giving the
-degree of each order parameter. Because {Q}2 and all odd-degree
+degree of each order parameter. Because {Q}2 and all odd-degree order
-order parameters are zero for atoms in cubic crystals
+parameters are zero for atoms in cubic crystals (see
-(see "Steinhardt"_#Steinhardt), the default order parameters
+"Steinhardt"_#Steinhardt), the default order parameters are {Q}4,
-are {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12. For the
+{Q}6, {Q}8, {Q}10, and {Q}12. For the FCC crystal with {nnn}=12, {Q}4
-FCC crystal with {nnn}=12, {Q}4 = sqrt(7/3)/8 = 0.19094....
+= sqrt(7/3)/8 = 0.19094....  The numerical values of all order
-The numerical values of all order parameters up to {Q}12
+parameters up to {Q}12 for a range of commonly encountered
-for a range of commonly encountered high-symmetry structures are given
+high-symmetry structures are given in Table I of "Mickel et
-in Table I of "Mickel et al."_#Mickel.
+al."_#Mickel.
 The optional keyword {components} will output the components of the
 normalized complex vector {Ybar_lm} of degree {ldegree}, which must be
 explicitly included in the keyword {degrees}. This option can be used
 in conjunction with "compute coord_atom"_compute_coord_atom.html to
 calculate the ten Wolde's criterion to identify crystal-like
 particles, as discussed in "ten Wolde"_#tenWolde.
 The value of {Ql} is set to zero for atoms not in the
 specified compute group, as well as for atoms that have less than
@ -95,8 +104,16 @@ the neighbor list.
 [Output info:]
-This compute calculates a per-atom array with {nlvalues} columns, giving the
+This compute calculates a per-atom array with {nlvalues} columns,
-{Ql} values for each atom, which are real numbers on the range 0 <= {Ql} <= 1.
+giving the {Ql} values for each atom, which are real numbers on the
 range 0 <= {Ql} <= 1.
 If the keyword {components} is set, then the real and imaginary parts
 of each component of (normalized) {Ybar_lm} will be added to the
 output array in the following order: Re({Ybar_-m}) Im({Ybar_-m})
 Re({Ybar_-m+1}) Im({Ybar_-m+1}) ... Re({Ybar_m}) Im({Ybar_m}).  This
 way, the per-atom array will have a total of {nlvalues}+2*(2{l}+1)
 columns.
 These values can be accessed by any command that uses
 per-atom values from a compute as input.  See "Section
@ -107,15 +124,25 @@ options.
 [Related commands:]
-"compute coord/atom"_compute_coord_atom.html, "compute centro/atom"_compute_centro_atom.html, "compute hexorder/atom"_compute_hexorder_atom.html
+"compute coord/atom"_compute_coord_atom.html, "compute
 centro/atom"_compute_centro_atom.html, "compute
 hexorder/atom"_compute_hexorder_atom.html
 [Default:]
-The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, {degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.
+The option defaults are {cutoff} = pair style cutoff, {nnn} = 12,
 {degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.
 :line
 :link(Steinhardt)
-[(Steinhardt)] P. Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).
+[(Steinhardt)] P. Steinhardt, D. Nelson, and M. Ronchetti,
 Phys. Rev. B 28, 784 (1983).
 :link(Mickel)
-[(Mickel)] W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013).
+[(Mickel)] W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke,
 J. Chem. Phys. 138, 044501 (2013).
 :link(tenWolde)
 [(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
 J. Chem. Phys. 104, 9932 (1996).
--- a/doc/src/computes.txt
+++ b/doc/src/computes.txt
@ -35,6 +35,7 @@ Computes :h1
   compute_erotate_sphere_atom
   compute_event_displace
   compute_fep
   compute_global_atom
   compute_group_group
   compute_gyration
   compute_gyration_chunk
--- a/doc/src/fix_colvars.txt
+++ b/doc/src/fix_colvars.txt
@ -31,21 +31,19 @@ fix abf all colvars colvars.inp tstat 1 :pre
 [Description:]
-This fix interfaces LAMMPS to a "collective variables" or "colvars"
+This fix interfaces LAMMPS to the collective variables "Colvars"
-module library which allows to calculate potentials of mean force
+library, which allows to calculate potentials of mean force
 (PMFs) for any set of colvars, using different sampling methods:
 currently implemented are the Adaptive Biasing Force (ABF) method,
 metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling
-(US) via a flexible harmonic restraint bias. The colvars library is
+(US) via a flexible harmonic restraint bias.
 hosted at "http://colvars.github.io/"_http://colvars.github.io/
 This documentation describes only the fix colvars command itself and
 LAMMPS specific parts of the code.  The full documentation of the
 colvars library is available as "this supplementary PDF document"_PDF/colvars-refman-lammps.pdf
-A detailed discussion of the implementation of the portable collective
+The Colvars library is developed at "https://github.com/colvars/colvars"_https://github.com/colvars/colvars
-variable library is in "(Fiorin)"_#Fiorin. Additional information can
+A detailed discussion of its implementation is in "(Fiorin)"_#Fiorin.
 be found in "(Henin)"_#Henin.
 There are some example scripts for using this package with LAMMPS in the
 examples/USER/colvars directory.
@ -129,8 +127,3 @@ and tstat = NULL.
 :link(Fiorin)
 [(Fiorin)] Fiorin , Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594
 :link(Henin)
 [(Henin)] Henin, Fiorin, Chipot, Klein, J. Chem. Theory Comput., 6,
 35-47 (2010)
--- a/doc/src/fix_eos_table_rx.txt
+++ b/doc/src/fix_eos_table_rx.txt
@ -10,7 +10,7 @@ fix eos/table/rx command :h3
 [Syntax:]
-fix ID group-ID eos/table/rx style file1 N keyword file2 :pre
+fix ID group-ID eos/table/rx style file1 N keyword ... :pre
 ID, group-ID are documented in "fix"_fix.html command
 eos/table/rx = style name of this fix command
@ -18,11 +18,16 @@ style = {linear} = method of interpolation
 file1 = filename containing the tabulated equation of state
 N = use N values in {linear} tables
 keyword = name of table keyword correponding to table file
-file2 = filename containing the heats of formation of each species :ul
+file2 = filename containing the heats of formation of each species (optional)
 deltaHf = heat of formation for a single species in energy units (optional)
 energyCorr = energy correction in energy units (optional)
 tempCorrCoeff = temperature correction coefficient (optional) :ul
 [Examples:]
-fix 1 all eos/table/rx linear eos.table 10000 KEYWORD thermo.table :pre
+fix 1 all eos/table/rx linear eos.table 10000 KEYWORD thermo.table
 fix 1 all eos/table/rx linear eos.table 10000 KEYWORD 1.5
 fix 1 all eos/table/rx linear eos.table 10000 KEYWORD 1.5 0.025 0.0 :pre
 [Description:]
@ -39,7 +44,15 @@ where {m} is the number of species, {c_i,j} is the concentration of
 species {j} in particle {i}, {u_j} is the internal energy of species j,
 {DeltaH_f,j} is the heat of formation of species {j}, N is the number of
 molecules represented by the coarse-grained particle, kb is the
-Boltzmann constant, and T is the temperature of the system.
+Boltzmann constant, and T is the temperature of the system.  Additionally,
 it is possible to modify the concentration-dependent particle internal 
 energy relation by adding an energy correction, temperature-dependent 
 correction, and/or a molecule-dependent correction.  An energy correction can
 be specified as a constant (in energy units).  A temperature correction can be 
 specified by multiplying a temperature correction coefficient by the 
 internal temperature.  A molecular correction can be specified by 
 by multiplying a molecule correction coefficient by the average number of 
 product gas particles in the coarse-grain particle. 
 Fix {eos/table/rx} creates interpolation tables of length {N} from {m}
 internal energy values of each species {u_j} listed in a file as a
@ -58,6 +71,14 @@ file is described below.
 The second filename specifies a file containing heat of formation
 {DeltaH_f,j} for each species.
 In cases where the coarse-grain particle represents a single molecular
 species (i.e., no reactions occur and fix {rx} is not present in the input file), 
 fix {eos/table/rx} can be applied in a similar manner to fix {eos/table} 
 within a non-reactive DPD simulation.  In this case, the heat of formation 
 filename is replaced with the heat of formation value for the single species.
 Additionally, the energy correction and temperature correction coefficients may 
 also be specified as fix arguments.  
 :line
 The format of a tabulated file is as follows (without the
@ -116,6 +137,19 @@ Note that the species can be listed in any order.  The tag that is
 used as the species name must correspond with the tags used to define
 the reactions with the "fix rx"_fix_rx.html command.
 Alternatively, corrections to the EOS can be included by specifying
 three additional columns that correspond to the energy correction, 
 the temperature correction coefficient and molecule correction 
 coefficient.  In this case, the format of the file is as follows:
 # HEAT OF FORMATION TABLE     (one or more comment or blank lines) :pre
                              (blank)
 h2      0.00 1.23 0.025  0.0  (species name, heat of formation, energy correction, temperature correction coefficient, molecule correction coefficient)
 no2     0.34 0.00 0.000 -1.76
 n2      0.00 0.00 0.000 -1.76
 ...
 no      0.93 0.00 0.000 -1.76 :pre
 :line
 [Restrictions:]
--- a/doc/src/fix_flow_gauss.txt
+++ b/doc/src/fix_flow_gauss.txt
@ -151,7 +151,7 @@ The option default for the {energy} keyword is energy = no.
 :line
 :link(Strong)
-[(Strong)] Strong and Eaves, J. Phys. Chem. Lett. 7, 1907 (2016).
+[(Strong)] Strong and Eaves, J. Phys. Chem. B 121, 189 (2017).
 :link(Evans)
 [(Evans)] Evans and Morriss, Phys. Rev. Lett. 56, 2172 (1986).
--- a/doc/src/fix_grem.txt
+++ b/doc/src/fix_grem.txt
@ -29,7 +29,7 @@ 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,
+replica exchange method (gREM) originally developed by "(Kim)"_#Kim2010,
 which uses non-Boltzmann ensembles to sample over first order phase
 transitions. The is done by defining replicas with an enthalpy
 dependent effective temperature
@ -103,7 +103,7 @@ npt"_fix_nh.html, "thermo_modify"_thermo_modify.html
 :line
-:link(Kim)
+:link(Kim2010)
 [(Kim)] Kim, Keyes, Straub, J Chem. Phys, 132, 224107 (2010).
 :link(Malolepsza)
--- a/doc/src/fix_momentum.txt
+++ b/doc/src/fix_momentum.txt
@ -7,6 +7,7 @@
 :line
 fix momentum command :h3
 fix momentum/kk command :h3
 [Syntax:]
@ -55,6 +56,29 @@ of atoms by rescaling the velocities after the momentum was removed.
 Note that the "velocity"_velocity.html command can be used to create
 initial velocities with zero aggregate linear and/or angular momentum.
 :line
 Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
 hardware, as discussed in "Section 5"_Section_accelerate.html
 of the manual.  The accelerated styles take the same arguments and
 should produce the same results, except for round-off and precision
 issues.
 These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
 USER-OMP and OPT packages, respectively.  They are only enabled if
 LAMMPS was built with those packages.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the "-suffix command-line
 switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 See "Section 5"_Section_accelerate.html of the manual for
 more instructions on how to use the accelerated styles effectively.
 [Restart, fix_modify, output, run start/stop, minimize info:]
 No information about this fix is written to "binary restart
--- a/doc/src/fix_mscg.txt
+++ b/doc/src/fix_mscg.txt
@ -0,0 +1,130 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Section_commands.html#comm)
 :line
 fix mscg command :h3
 [Syntax:]
 fix ID group-ID mscg N keyword args ... :pre
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 mscg = style name of this fix command :l
 N = envoke this fix every this many timesteps :l
 zero or more keyword/value pairs may be appended :l
 keyword = {range} or {name} or {max} :l
  {range} arg = {on} or {off}
    {on} = range finding functionality is performed
    {off} = force matching functionality is performed
  {name} args = name1 ... nameN
    name1,...,nameN = string names for each atom type (1-Ntype)
  {max} args = maxb maxa maxd
    maxb,maxa,maxd = maximum bonds/angles/dihedrals per atom :pre
 :ule
 [Examples:]
 fix 1 all mscg 1
 fix 1 all mscg 1 range name A B
 fix 1 all mscg 1 max 4 8 20 :pre
 [Description:]
 This fix applies the Multi-Scale Coarse-Graining (MSCG) method to
 snapshots from a dump file to generate potentials for coarse-grained
 simulations from all-atom simulations, using a force-matching
 technique ("Izvekov"_#Izvekov, "Noid"_#Noid).
 It makes use of the MS-CG library, written and maintained by Greg
 Voth's group at the University of Chicago, which is freely available
 on their "MS-CG GitHub
 site"_https://github.com/uchicago-voth/MSCG-release.  See instructions
 on obtaining and installing the MS-CG library in the src/MSCG/README
 file, which must be done before you build LAMMPS with this fix command
 and use the command in a LAMMPS input script.
 An example script using this fix is provided the examples/mscg
 directory.
 The general workflow for using LAMMPS in conjunction with the MS-CG
 library to create a coarse-grained model and run coarse-grained
 simulations is as follows:
 Perform all-atom simulations on the system to be coarse grained.
 Generate a trajectory mapped to the coarse-grained model.
 Create input files for the MS-CG library.
 Run the range finder functionality of the MS-CG library.  
 Run the force matching functionality of the MS-CG library.
 Check the results of the force matching.
 Run coarse-grained simulations using the new coarse-grained potentials. :ol
 This fix can perform the range finding and force matching steps 4 and
 5 of the above workflow when used in conjunction with the
 "rerun"_rerun.html command.  It does not perform steps 1-3 and 6-7.
 Step 2 can be performed using a Python script (what is the name?)
 provided with the MS-CG library which defines the coarse-grained model
 and converts a standard LAMMPS dump file for an all-atom simulation
 (step 1) into a LAMMPS dump file which has the positions of and forces
 on the coarse-grained beads.  
 In step 3, an input file named "control.in" is needed by the MS-CG
 library which sets parameters for the range finding and force matching
 functionalities.  See the examples/mscg/control.in file as an example.
 And see the documentation provided with the MS-CG library for more
 info on this file.
 When this fix is used to perform steps 4 and 5, the MS-CG library also
 produces additional output files.  The range finder functionality
 (step 4) outputs files defining pair and bonded interaction ranges.
 The force matching functionality (step 5) outputs tabulated force
 files for every interaction in the system. Other diagnostic files can
 also be output depending on the paramters in the MS-CG library input
 script.  Again, see the documentation provided with the MS-CG library
 for more info.
 :line
 The {range} keyword specifies which MS-CG library functionality should
 be invoked. If {on}, the step 4 range finder functionality is invoked.
 {off}, the step 5 force matching functionality is invoked.
 If the {name} keyword is used, string names are defined to associate
 with the integer atom types in LAMMPS.  {Ntype} names must be
 provided, one for each atom type (1-Ntype).
 The {max} keyword specifies the maximum number of bonds, angles, and
 dihedrals a bead can have in the coarse-grained model.
 [Restrictions:]
 This fix is part of the MSCG package. It is only enabled if LAMMPS was
 built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 The MS-CG library uses C++11, which may not be supported by older
 compilers. The MS-CG library also has some additional numeric library
 dependencies, which are describd in its documentation.
 Currently, the MS-CG library is not setup to run in parallel with MPI,
 so this fix can only be used in a serial LAMMPS build and run
 on a single processor.
 [Related commands:] none
 [Default:]
 The default keyword settings are range off, max 4 12 36.
 :line
 :link(Izvekov)
 [(Izvekov)] Izvekov, Voth, J Chem Phys 123, 134105 (2005).
 :link(Noid)
 [(Noid)] Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J
 Chem Phys 128, 134105 (2008).
--- a/doc/src/fix_nve_dot.txt
+++ b/doc/src/fix_nve_dot.txt
@ -0,0 +1,61 @@
 "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 nve/dot command :h3
 [Syntax:]
 fix ID group-ID nve/dot :pre
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 nve/dot = style name of this fix command :l
 :ule
 [Examples:]
 fix 1 all nve/dot :pre
 [Description:]
 Apply a rigid-body integrator as described in "(Davidchack)"_#Davidchack
 to a group of atoms, but without Langevin dynamics. 
 This command performs Molecular dynamics (MD)
 via a velocity-Verlet algorithm and an evolution operator that rotates 
 the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller. 
 This command is the equivalent of the "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
 without damping and noise and can be used to determine the stability range 
 in a NVE ensemble prior to using the Langevin-type DOTC-integrator
 (see also "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html).
 The command is equivalent to the "fix nve"_fix_nve.html.
 The particles are always considered to have a finite size.
 An example input file can be found in /examples/USER/cgdna/examples/duplex1/.
 A technical report with more information on this integrator can be found
 "here"_PDF/USER-CGDNA-overview.pdf.
 :line
 [Restrictions:]
 These pair styles can only be used if LAMMPS was built with the
 USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 [Related commands:]
 "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "fix nve"_fix_nve.html
 [Default:] none
 :line
 :link(Davidchack)
 [(Davidchack)] R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
 :link(Miller)
 [(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
--- a/doc/src/fix_nve_dotc_langevin.txt
+++ b/doc/src/fix_nve_dotc_langevin.txt
@ -0,0 +1,134 @@
 "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 nve/dotc/langevin command :h3
 [Syntax:]
 fix ID group-ID nve/dotc/langevin Tstart Tstop damp seed keyword value :pre
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 nve/dotc/langevin = style name of this fix command :l
 Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
 damp = damping parameter (time units) :l
 seed = random number seed to use for white noise (positive integer) :l
 keyword = {angmom} :l
  {angmom} value = factor
    factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below :pre
 :ule
 [Examples:]
 fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 :pre
 [Description:]
 Apply a rigid-body Langevin-type integrator of the kind "Langevin C" 
 as described in "(Davidchack)"_#Davidchack
 to a group of atoms, which models an interaction with an implicit background
 solvent.  This command performs Brownian dynamics (BD)
 via a technique that splits the integration into a deterministic Hamiltonian 
 part and the Ornstein-Uhlenbeck process for noise and damping. 
 The quaternion degrees of freedom are updated though an evolution
 operator which performs a rotation in quaternion space, preserves
 the quaternion norm and is akin to "(Miller)"_#Miller.
 In terms of syntax this command has been closely modelled on the 
 "fix langevin"_fix_langevin.html and its {angmom} option. But it combines 
 the "fix nve"_fix_nve.html and the "fix langevin"_fix_langevin.html in 
 one single command. The main feature is improved stability 
 over the standard integrator, permitting slightly larger timestep sizes.
 NOTE: Unlike the "fix langevin"_fix_langevin.html this command performs
 also time integration of the translational and quaternion degrees of freedom.
 The total force on each atom will have the form:
 F = Fc + Ff + Fr
 Ff = - (m / damp) v
 Fr is proportional to sqrt(Kb T m / (dt damp)) :pre
 Fc is the conservative force computed via the usual inter-particle
 interactions ("pair_style"_pair_style.html,
 "bond_style"_bond_style.html, etc).
 The Ff and Fr terms are implicitly taken into account by this fix 
 on a per-particle basis.
 Ff is a frictional drag or viscous damping term proportional to the
 particle's velocity.  The proportionality constant for each atom is
 computed as m/damp, where m is the mass of the particle and damp is
 the damping factor specified by the user.
 Fr is a force due to solvent atoms at a temperature T randomly bumping
 into the particle.  As derived from the fluctuation/dissipation
 theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
 dt damp), where Kb is the Boltzmann constant, T is the desired
 temperature, m is the mass of the particle, dt is the timestep size,
 and damp is the damping factor.  Random numbers are used to randomize
 the direction and magnitude of this force as described in
 "(Dunweg)"_#Dunweg, where a uniform random number is used (instead of
 a Gaussian random number) for speed.
 :line
 {Tstart} and {Tstop} have to be constant values, i.e. they cannot 
 be variables.
 The {damp} parameter is specified in time units and determines how
 rapidly the temperature is relaxed.  For example, a value of 0.03
 means to relax the temperature in a timespan of (roughly) 0.03 time
 units tau (see the "units"_units.html command).
 The damp factor can be thought of as inversely related to the
 viscosity of the solvent, i.e. a small relaxation time implies a
 hi-viscosity solvent and vice versa.  See the discussion about gamma
 and viscosity in the documentation for the "fix
 viscous"_fix_viscous.html command for more details.
 The random # {seed} must be a positive integer. A Marsaglia random
 number generator is used.  Each processor uses the input seed to
 generate its own unique seed and its own stream of random numbers.
 Thus the dynamics of the system will not be identical on two runs on
 different numbers of processors.
 The keyword/value option has to be used in the following way:
 This fix has to be used together with the {angmom} keyword. The 
 particles are always considered to have a finite size. 
 The keyword {angmom} enables thermostatting of the rotational degrees of 
 freedom in addition to the usual translational degrees of freedom. 
 The scale factor after the {angmom} keyword gives the ratio of the rotational to 
 the translational friction coefficient.
 An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
 A technical report with more information on this integrator can be found 
 "here"_PDF/USER-CGDNA-overview.pdf.
 :line
 [Restrictions:]
 These pair styles can only be used if LAMMPS was built with the
 USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 [Related commands:]
 "fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html,  
 [Default:] none
 :line
 :link(Davidchack)
 [(Davidchack)] R.L Davidchack, T.E. Ouldridge, M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
 :link(Miller)
 [(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
 :link(Dunweg)
 [(Dunweg)] B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991).
--- a/doc/src/fix_nvk.txt
+++ b/doc/src/fix_nvk.txt
@ -0,0 +1,71 @@
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
 :link(ld,Manual.html)
 :link(lc,Section_commands.html#comm)
 :line
 fix nvk command :h3
 [Syntax:]
 fix ID group-ID nvk :pre
 ID, group-ID are documented in "fix"_fix.html command
 nvk = style name of this fix command :ul
 [Examples:]
 fix 1 all nvk :pre
 [Description:]
 Perform constant kinetic energy integration using the Gaussian
 thermostat to update position and velocity for atoms in the group each
 timestep.  V is volume; K is kinetic energy. This creates a system
 trajectory consistent with the isokinetic ensemble.
 The equations of motion used are those of Minary et al in
 "(Minary)"_#nvk-Minary, a variant of those initially given by Zhang in 
 "(Zhang)"_#nvk-Zhang.
 The kinetic energy will be held constant at its value given when fix
 nvk is initiated. If a different kinetic energy is desired, the
 "velocity"_velocity.html command should be used to change the kinetic
 energy prior to this fix.
 :line
 [Restart, fix_modify, output, run start/stop, minimize info:]
 No information about this fix is written to "binary restart
 files"_restart.html.  None of the "fix_modify"_fix_modify.html options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various "output
 commands"_Section_howto.html#howto_15.  No parameter of this fix can
 be used with the {start/stop} keywords of the "run"_run.html command.
 This fix is not invoked during "energy minimization"_minimize.html.
 [Restrictions:]
 The Gaussian thermostat only works when it is applied to all atoms in
 the simulation box. Therefore, the group must be set to all.
 This fix has not yet been implemented to work with the RESPA integrator.
 This fix is part of the USER-MISC package.  It is only enabled if LAMMPS
 was built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 [Related commands:] none
 [Default:] none
 :line
 :link(nvk-Minary)
 [(Minary)] Minary, Martyna, and Tuckerman, J Chem Phys, 18, 2510 (2003).
 :link(nvk-Zhang)
 [(Zhang)] Zhang, J Chem Phys, 106, 6102 (1997).
--- a/doc/src/fix_spring.txt
+++ b/doc/src/fix_spring.txt
@ -89,11 +89,7 @@ NOTE: The center of mass of a group of atoms is calculated in
 group can straddle a periodic boundary.  See the "dump"_dump.html doc
 page for a discussion of unwrapped coordinates.  It also means that a
 spring connecting two groups or a group and the tether point can cross
-a periodic boundary and its length be calculated correctly.  One
+a periodic boundary and its length be calculated correctly.  
 exception is for rigid bodies, which should not be used with the fix
 spring command, if the rigid body will cross a periodic boundary.
 This is because image flags for rigid bodies are used in a different
 way, as explained on the "fix rigid"_fix_rigid.html doc page.
 [Restart, fix_modify, output, run start/stop, minimize info:]
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@ -68,6 +68,7 @@ Fixes :h1
   fix_meso_stationary
   fix_momentum
   fix_move
   fix_mscg
   fix_msst
   fix_neb
   fix_nh
@ -83,6 +84,8 @@ Fixes :h1
   fix_nve_asphere
   fix_nve_asphere_noforce
   fix_nve_body
   fix_nve_dot
   fix_nve_dotc_langevin
   fix_nve_eff
   fix_nve_limit
   fix_nve_line
@ -90,6 +93,7 @@ Fixes :h1
   fix_nve_noforce
   fix_nve_sphere
   fix_nve_tri
   fix_nvk
   fix_nvt_asphere
   fix_nvt_body
   fix_nvt_manifold_rattle
--- a/doc/src/kspace_style.txt
+++ b/doc/src/kspace_style.txt
@ -229,11 +229,16 @@ dramatically in z.  For example, for a triclinic system with all three
 tilt factors set to the maximum limit, the PPPM grid should be
 increased roughly by a factor of 1.5 in the y direction and 2.0 in the
 z direction as compared to the same system using a cubic orthogonal
-simulation cell. One way to ensure the accuracy requirement is being
+simulation cell.  One way to handle this issue if you have a long
-met is to run a short simulation at the maximum expected tilt or
+simulation where the box size changes dramatically, is to break it
-length, note the required grid size, and then use the
+into shorter simulations (multiple "run"_run.html commands).  This
 works because the grid size is re-computed at the beginning of each
 run.  Another way to ensure the descired accuracy requirement is met
 is to run a short simulation at the maximum expected tilt or length,
 note the required grid size, and then use the
 "kspace_modify"_kspace_modify.html {mesh} command to manually set the
-PPPM grid size to this value.
+PPPM grid size to this value for the long run.  The simulation then
 will be "too accurate" for some portion of the run.
 RMS force errors in real space for {ewald} and {pppm} are estimated
 using equation 18 of "(Kolafa)"_#Kolafa, which is also referenced as
@ -285,6 +290,8 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 See "Section 5"_Section_accelerate.html of the manual for
 more instructions on how to use the accelerated styles effectively.
 :line
 [Restrictions:]
 Note that the long-range electrostatic solvers in LAMMPS assume conducting
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@ -23,6 +23,7 @@ Section_history.html
 tutorial_drude.html
 tutorial_github.html
 tutorial_pylammps.html
 body.html
 manifolds.html
@ -113,6 +114,7 @@ special_bonds.html
 suffix.html
 tad.html
 temper.html
 temper_grem.html
 thermo.html
 thermo_modify.html
 thermo_style.html
@ -207,6 +209,8 @@ fix_nve.html
 fix_nve_asphere.html
 fix_nve_asphere_noforce.html
 fix_nve_body.html
 fix_nve_dot.html
 fix_nve_dotc_langevin.html
 fix_nve_eff.html
 fix_nve_limit.html
 fix_nve_line.html
@ -454,6 +458,7 @@ pair_multi_lucy_rx.html
 pair_nb3b_harmonic.html
 pair_nm.html
 pair_none.html
 pair_oxdna_excv.html
 pair_peri.html
 pair_polymorphic.html
 pair_quip.html
@ -492,6 +497,7 @@ pair_zero.html
 bond_class2.html
 bond_fene.html
 bond_fene_expand.html
 bond_oxdna_fene.html
 bond_harmonic.html
 bond_harmonic_shift.html
 bond_harmonic_shift_cut.html
--- a/doc/src/pair_eam.txt
+++ b/doc/src/pair_eam.txt
@ -8,6 +8,7 @@
 pair_style eam command :h3
 pair_style eam/gpu command :h3
 pair_style eam/intel command :h3
 pair_style eam/kk command :h3
 pair_style eam/omp command :h3
 pair_style eam/opt command :h3
--- a/doc/src/pair_exp6_rx.txt
+++ b/doc/src/pair_exp6_rx.txt
@ -10,16 +10,21 @@ pair_style exp6/rx command :h3
 [Syntax:]
-pair_style exp6/rx cutoff :pre
+pair_style exp6/rx cutoff ... :pre
-cutoff = global cutoff for DPD interactions (distance units) :ul
+cutoff = global cutoff for DPD interactions (distance units)
 weighting = fractional or molecular (optional) :ul
 [Examples:]
 pair_style exp6/rx 10.0
-pair_coeff * * exp6.params h2o h2o 1.0 1.0 10.0
+pair_style exp6/rx 10.0 fractional
-pair_coeff * * exp6.params h2o 1fluid 1.0 1.0 10.0
+pair_style exp6/rx 10.0 molecular
-pair_coeff * * exp6.params 1fluid 1fluid 1.0 1.0 10.0 :pre
+pair_coeff * * exp6.params h2o h2o exponent 1.0 1.0 10.0
 pair_coeff * * exp6.params h2o 1fluid exponent 1.0 1.0 10.0
 pair_coeff * * exp6.params 1fluid 1fluid exponent 1.0 1.0 10.0
 pair_coeff * * exp6.params 1fluid 1fluid none 10.0
 pair_coeff * * exp6.params 1fluid 1fluid polynomial filename 10.0 :pre
 [Description:]
@ -50,14 +55,36 @@ defined in the reaction kinetics files specified with the "fix
 rx"_fix_rx.html command or they must correspond to the tag "1fluid",
 signifying interaction with a product species mixture determined
 through a one-fluid approximation.  The interaction potential is
-weighted by the geometric average of the concentrations of the two
+weighted by the geometric average of either the mole fraction concentrations 
-species.  The coarse-grained potential is stored before and after the
+or the number of molecules associated with the interacting coarse-grained 
 particles (see the {fractional} or {molecular} weighting pair style options). 
 The coarse-grained potential is stored before and after the
 reaction kinetics solver is applied, where the difference is defined
 to be the internal chemical energy (uChem).
-The fourth and fifth arguments specify the {Rm} and {epsilon} scaling exponents.
+The fourth argument specifies the type of scaling that will be used 
 to scale the EXP-6 paramters as reactions occur.  Currently, there
 are three scaling options:  {exponent}, {polynomial} and {none}.
-The final argument specifies the interaction cutoff.
+Exponent scaling requires two additional arguments for scaling 
 the {Rm} and {epsilon} parameters, respectively.  The scaling factor
 is computed by phi^exponent, where phi is the number of molecules  
 represented by the coarse-grain particle and exponent is specified 
 as a pair coefficient argument for {Rm} and {epsilon}, respectively.
 The {Rm} and {epsilon} parameters are multiplied by the scaling 
 factor to give the scaled interaction paramters for the CG particle.
 Polynomial scaling requires a filename to be specified as a pair 
 coeff argument.  The file contains the coefficients to a fifth order
 polynomial for the {alpha}, {epsilon} and {Rm} parameters that depend 
 upon phi (the number of molecules represented by the CG particle). 
 The format of a polynomial file is provided below.
 The {none} option to the scaling does not have any additional pair coeff
 arguments.  This is equivalent to specifying the {exponent} option with 
 {Rm} and {epsilon} exponents of 0.0 and 0.0, respectively.
 The final argument specifies the interaction cutoff (optional).
 :line
@ -70,6 +97,19 @@ no2  exp6  13.60 0.01 3.70
 ...
 co2  exp6  13.00 0.03 3.20 :pre
 The format of the polynomial scaling file as follows (without the
 parenthesized comments):
 # POLYNOMIAL FILE          (one or more comment or blank lines) :pre
 #  General Functional Form:
 #  A*phi^5 + B*phi^4 + C*phi^3 + D*phi^2 + E*phi + F 
 #
 #  Parameter  A        B         C        D         E        F
                           (blank)
 alpha        0.0000   0.00000   0.00008  0.04955  -0.73804  13.63201
 epsilon      0.0000   0.00478  -0.06283  0.24486  -0.33737   2.60097
 rm           0.0001  -0.00118  -0.00253  0.05812  -0.00509   1.50106 :pre
 A section begins with a non-blank line whose 1st character is not a
 "#"; blank lines or lines starting with "#" can be used as comments
 between sections.
@ -117,4 +157,4 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 "pair_coeff"_pair_coeff.html
-[Default:] none
+[Default:] fractional weighting
--- a/doc/src/pair_multi_lucy_rx.txt
+++ b/doc/src/pair_multi_lucy_rx.txt
@ -13,11 +13,14 @@ pair_style multi/lucy/rx command :h3
 pair_style multi/lucy/rx style N keyword ... :pre
 style = {lookup} or {linear} = method of interpolation
-N = use N values in {lookup}, {linear} tables :ul
+N = use N values in {lookup}, {linear} tables
 weighting = fractional or molecular (optional) :ul
 [Examples:]
 pair_style multi/lucy/rx linear 1000
 pair_style multi/lucy/rx linear 1000 fractional
 pair_style multi/lucy/rx linear 1000 molecular
 pair_coeff * * multibody.table ENTRY1 h2o h2o 7.0
 pair_coeff * * multibody.table ENTRY1 h2o 1fluid 7.0 :pre
@ -94,8 +97,10 @@ tags must either correspond to the species defined in the reaction
 kinetics files specified with the "fix rx"_fix_rx.html command or they
 must correspond to the tag "1fluid", signifying interaction with a
 product species mixture determined through a one-fluid approximation.
-The interaction potential is weighted by the geometric average of the
+The interaction potential is weighted by the geometric average of 
-concentrations of the two species.  The coarse-grained potential is
+either the mole fraction concentrations or the number of molecules 
 associated with the interacting coarse-grained particles (see the 
 {fractional} or {molecular} weighting pair style options). The coarse-grained potential is
 stored before and after the reaction kinetics solver is applied, where
 the difference is defined to be the internal chemical energy (uChem).
@ -205,7 +210,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 "pair_coeff"_pair_coeff.html
-[Default:] none
+[Default:] fractional weighting
 :line
--- a/doc/src/pair_oxdna_excv.txt
+++ b/doc/src/pair_oxdna_excv.txt
@ -0,0 +1,80 @@
 "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 oxdna_excv command :h3
 pair_style oxdna_stk command :h3
 pair_style oxdna_hbond command :h3
 pair_style oxdna_xstk command :h3
 pair_style oxdna_coaxstk command :h3
 [Syntax:]
 pair_style style :pre
 style = {hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk} :ul
 [Examples:]
 pair_style hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk
 pair_coeff * * oxdna_excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
 pair_coeff * * oxdna_stk     1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
 pair_coeff * * oxdna_hbond   0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 1 4 oxdna_hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 2 3 oxdna_hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna_xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna_coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 :pre
 [Description:]
 The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field 
 for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the 
 excluded volume interaction {oxdna_excv}, the stacking {oxdna_stk}, cross-stacking {oxdna_xstk}
 and coaxial stacking interaction {oxdna_coaxstk} as well
 as the hydrogen-bonding interaction {oxdna_hbond} between complementary pairs of nucleotides on
 opposite strands.
 The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients 
 in the above example. The individual potentials consist of products of modulation factors, 
 which themselves are constructed from a number of more basic potentials 
 (Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. 
 We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil and "(Ouldridge)"_#Ouldridge
 for a detailed description of the oxDNA force field.
 NOTE: These pair styles have to be used together with the related oxDNA bond style
 {oxdna_fene} for the connectivity of the phosphate backbone (see also documentation of
 "bond_style oxdna_fene"_bond_oxdna_fene.html). The coefficients
 in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
 Example input and data files can be found in /examples/USER/cgdna/examples/duplex1/ and /duplex2/.
 A simple python setup tool which creates single straight or helical DNA strands, 
 DNA duplexes or arrays of DNA duplexes can be found in /examples/USER/cgdna/util/.
 A technical report with more information on the model, the structure of the input file,
 the setup tool and the performance of the LAMMPS-implementation of oxDNA 
 can be found "here"_PDF/USER-CGDNA-overview.pdf.
 :line
 [Restrictions:]
 These pair styles can only be used if LAMMPS was built with the
 USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 [Related commands:]
 "bond_style oxdna_fene"_bond_oxdna_fene.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html 
 [Default:] none
 :line
 :link(Ouldridge-DPhil)
 [(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
 :link(Ouldridge)
 [(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
--- a/doc/src/pair_table_rx.txt
+++ b/doc/src/pair_table_rx.txt
@ -10,16 +10,17 @@ pair_style table/rx command :h3
 [Syntax:]
-pair_style table style N :pre
+pair_style table style N ... :pre
 style = {lookup} or {linear} or {spline} or {bitmap} = method of interpolation
 N = use N values in {lookup}, {linear}, {spline} tables
-N = use 2^N values in {bitmap} tables
+weighting = fractional or molecular (optional) :ul
 [Examples:]
 pair_style table/rx linear 1000
-pair_style table/rx bitmap 12
+pair_style table/rx linear 1000 fractional
 pair_style table/rx linear 1000 molecular
 pair_coeff * * rxn.table ENTRY1 h2o h2o 10.0
 pair_coeff * * rxn.table ENTRY1 1fluid 1fluid 10.0
 pair_coeff * 3 rxn.table ENTRY1 h2o no2 10.0 :pre
@ -84,8 +85,10 @@ tags must either correspond to the species defined in the reaction
 kinetics files specified with the "fix rx"_fix_rx.html command or they
 must correspond to the tag "1fluid", signifying interaction with a
 product species mixture determined through a one-fluid approximation.
-The interaction potential is weighted by the geometric average of the
+The interaction potential is weighted by the geometric average of 
-concentrations of the two species.  The coarse-grained potential is
+either the mole fraction concentrations or the number of molecules 
 associated with the interacting coarse-grained particles (see the 
 {fractional} or {molecular} weighting pair style options). The coarse-grained potential is
 stored before and after the reaction kinetics solver is applied, where
 the difference is defined to be the internal chemical energy (uChem).
@ -230,7 +233,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 "pair_coeff"_pair_coeff.html
-[Default:] none
+[Default:] fractional weighting
 :line
--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@ -65,6 +65,7 @@ Pair Styles :h1
   pair_nb3b_harmonic
   pair_nm
   pair_none
   pair_oxdna_excv
   pair_peri
   pair_polymorphic
   pair_quip
--- a/doc/src/python.txt
+++ b/doc/src/python.txt
@ -14,7 +14,7 @@ python func keyword args ... :pre
 func = name of Python function :ulb,l
 one or more keyword/args pairs must be appended :l
-keyword = {invoke} or {input} or {return} or {format} or {file} or {here} or {exists}
+keyword = {invoke} or {input} or {return} or {format} or {length} or {file} or {here} or {exists}
  {invoke} arg = none = invoke the previously defined Python function
  {input} args = N i1 i2 ... iN
    N = # of inputs to function
@ -29,6 +29,8 @@ keyword = {invoke} or {input} or {return} or {format} or {file} or {here} or {ex
    M = N+1 if there is a return value
    fstring = each character (i,f,s,p) corresponds in order to an input or return value
    'i' = integer, 'f' = floating point, 's' = string, 'p' = SELF
  {length} arg = Nlen
    Nlen = max length of string returned from Python function
  {file} arg = filename
    filename = file of Python code, which defines func
  {here} arg = inline
@ -165,6 +167,17 @@ equal-style variable as an argument, but only if the output of the
 Python function is flagged as a numeric value ("i" or "f") via the
 {format} keyword.
 If the {return} keyword is used and the {format} keyword specifies the
 output as a string, then the default maximum length of that string is
 63 characters (64-1 for the string terminator).  If you want to return
 a longer string, the {length} keyword can be specified with its {Nlen}
 value set to a larger number (the code allocates space for Nlen+1 to
 include the string terminator).  If the Python function generates a
 string longer than the default 63 or the specified {Nlen}, it will be
 trunctated.
 :line
 Either the {file}, {here}, or {exists} keyword must be used, but only
 one of them.  These keywords specify what Python code to load into the
 Python interpreter.  The {file} keyword gives the name of a file,
--- a/doc/src/read_dump.txt
+++ b/doc/src/read_dump.txt
@ -15,11 +15,12 @@ read_dump file Nstep field1 field2 ... keyword values ... :pre
 file = name of dump file to read :ulb,l
 Nstep = snapshot timestep to read from file :l
 one or more fields may be appended :l
-field = {x} or {y} or {z} or {vx} or {vy} or {vz} or {q} or {ix} or {iy} or {iz}
+field = {x} or {y} or {z} or {vx} or {vy} or {vz} or {q} or {ix} or {iy} or {iz} or {fx} or {fy} or {fz}
  {x},{y},{z} = atom coordinates
  {vx},{vy},{vz} = velocity components
  {q} = charge
-  {ix},{iy},{iz} = image flags in each dimension :pre
+  {ix},{iy},{iz} = image flags in each dimension
  {fx},{fy},{fz} = force components :pre
 zero or more keyword/value pairs may be appended :l
 keyword = {box} or {replace} or {purge} or {trim} or {add} or {label} or {scaled} or {wrapped} or {format} :l
  {box} value = {yes} or {no} = replace simulation box with dump box
--- a/doc/src/temper_grem.txt
+++ b/doc/src/temper_grem.txt
@ -32,7 +32,7 @@ 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
+"(Kim)"_#KimStraub.  It uses non-Boltzmann ensembles to sample over first
 order phase transitions. The is done by defining replicas with an
 enthalpy dependent effective temperature
@ -105,5 +105,5 @@ This command must be used with "fix grem"_fix_grem.html.
 [Default:] none
-:link(Kim)
+:link(KimStraub)
 [(Kim)] Kim, Keyes, Straub, J Chem Phys, 132, 224107 (2010).
--- a/doc/src/timer.txt
+++ b/doc/src/timer.txt
@ -33,14 +33,14 @@ timer loop :pre
 Select the level of detail at which LAMMPS performs its CPU timings.
 Multiple keywords can be specified with the {timer} command.  For
 keywords that are mutually exclusive, the last one specified takes
-effect.
+precedence.
 During a simulation run LAMMPS collects information about how much
 time is spent in different sections of the code and thus can provide
 information for determining performance and load imbalance problems.
 This can be done at different levels of detail and accuracy.  For more
 information about the timing output, see this "discussion of screen
-output"_Section_start.html#start_8.
+output in Section 2.8"_Section_start.html#start_8.
 The {off} setting will turn all time measurements off. The {loop}
 setting will only measure the total time for a run and not collect any
@ -52,20 +52,22 @@ procsessors.  The {full} setting adds information about CPU
 utilization and thread utilization, when multi-threading is enabled.
 With the {sync} setting, all MPI tasks are synchronized at each timer
-call which meaures load imbalance more accuractly, though it can also
+call which measures load imbalance for each section more accuractly,
-slow down the simulation.  Using the {nosync} setting (which is the
+though it can also slow down the simulation by prohibiting overlapping
-default) turns off this synchronization.
+independent computations on different MPI ranks  Using the {nosync}
 setting (which is the default) turns this synchronization off.
-With the {timeout} keyword a walltime limit can be imposed that
+With the {timeout} keyword a walltime limit can be imposed, that
 affects the "run"_run.html and "minimize"_minimize.html commands.
-This can be convenient when runs have to confirm to time limits,
+This can be convenient when calculations have to comply with execution
-e.g. when running under a batch system and you want to maximize
+time limits, e.g. when running under a batch system when you want to
-the utilization of the batch time slot, especially when the time
+maximize the utilization of the batch time slot, especially for runs
-per timestep varies and is thus difficult to predict how many
+where the time per timestep varies much and thus it becomes difficult
-steps a simulation can perform, or for difficult to converge
+to predict how many steps a simulation can perform for a given walltime
-minimizations. The timeout {elapse} value should be somewhat smaller
+limit. This also applies for difficult to converge minimizations.
-than the time requested from the batch system, as there is usually
+The timeout {elapse} value should be somewhat smaller than the maximum
-some overhead to launch jobs, and it may be advisable to write
+wall time requested from the batch system, as there is usually
 some overhead to launch jobs, and it is advisable to write
 out a restart after terminating a run due to a timeout.
 The timeout timer starts when the command is issued. When the time
--- a/doc/src/tutorial_github.txt
+++ b/doc/src/tutorial_github.txt
@ -11,10 +11,22 @@ LAMMPS GitHub tutorial :h3
 :line
-This document briefly describes how to use GitHub to merge changes you
+This document describes the process of how to use GitHub to integrate
-make into LAMMPS, using GitHub. It assumes that you are familiar with
+changes or additions you have made to LAMMPS into the official LAMMPS
-git. You may want to have a look at the "Git
+distribution.  It uses the process of updating this very tutorial as
-book"_http://git-scm.com/book/ to reacquaint yourself.
+an example to describe the individual steps and options.  You need to
 be familiar with git and you may want to have a look at the
 "Git book"_http://git-scm.com/book/ to reacquaint yourself with some
 of the more advanced git features used below.
 As of fall 2016, submitting contributions to LAMMPS via pull requests
 on GitHub is the preferred option for integrating contributed features
 or improvements to LAMMPS, as it significantly reduces the amount of
 work required by the LAMMPS developers. Consequently, creating a pull
 request will increase your chances to have your contribution included
 and will reduce the time until the integration is complete. For more
 information on the requirements to have your code included into LAMMPS
 please see "Section 10.15"_Section_modify.html#mod_15
 :line
@ -30,106 +42,121 @@ username or e-mail address and password.
 [Forking the repository]
-To get changes into LAMMPS, you need to first fork the repository. At
+To get changes into LAMMPS, you need to first fork the `lammps/lammps`
-the time of writing, LAMMPS-ICMS is the preferred fork. Go to "LAMMPS
+repository on GitHub. At the time of writing, {master} is the preferred
-on GitHub"_https://github.com/lammps/lammps and make sure branch is
+target branch. Thus go to "LAMMPS on GitHub"_https://github.com/lammps/lammps
-set to "lammps-icms", see the figure below.
+and make sure branch is set to "master", as shown in the figure below.
 :c,image(JPG/tutorial_branch.png)
-Now, click on fork in the top right corner:
+If it is not, use the button to change it to {master}. Once it is, use the
 fork button to create a fork.
 :c,image(JPG/tutorial_fork.png)
-This will create your own fork of the LAMMPS repository. You can make
+
-changes in this fork and later file {pull requests} to allow the
+This will create a fork (which is essentially a copy, but uses less
-upstream repository to merge changes from your own fork into the one
+resources) of the LAMMPS repository under your own GitHub account. You
-we just forked from. At the same time, you can set things up, so you
+can make changes in this fork and later file {pull requests} to allow
-can include changes from upstream into your repository.
+the upstream repository to merge changes from your own fork into the one
 we just forked from (or others that were forked from the same repository).
 At the same time, you can set things up, so you can include changes from
 upstream into your repository and thus keep it in sync with the ongoing
 LAMMPS development.
 :line
 [Adding changes to your own fork]
-Before adding changes, it is better to first create a new branch that
+Additions to the upstream version of LAMMPS are handled using {feature
-will contain these changes, a so-called feature branch.
+branches}.  For every new feature, a so-called feature branch is
 created, which contains only those modification relevant to one specific
 feature. For example, adding a single fix would consist of creating a
 branch with only the fix header and source file and nothing else.  It is
 explained in more detail here: "feature branch
 workflow"_https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow.
 [Feature branches]
-Since LAMMPS is such a big project and most user contributions come in
+First of all, create a clone of your version on github on your local
-small portions, the most ideal workflow for LAMMPS is the so-called
+machine via HTTPS:
 "Feature branch" workflow. It is explained in great detail here:
 "feature branch
 workflow"_https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow.
-The idea is that every new feature for LAMMPS gets its own
+  $ git clone https://github.com/<your user name>/lammps.git <some name> :pre
 branch. This way, it is fairly painless to incorporate new features
 into the upstream repository. I will explain briefly here how to do
 it. In this feature branch, I will add a USER-package.
-I assume that git is installed on the local machine and you know how
+or, if you have set up your GitHub account for using SSH keys, via SSH:
 to use a command line.
-First of all, you need to clone your own fork of LAMMPS:
+  $ git clone git@github.com:<your user name>/lammps.git :pre
-
+  
-  $ git clone https://github.com/<your user name>/lammps.git :pre
+You can find the proper URL by clicking the "Clone or download"-button:
 You can find the proper url to the right of the "HTTPS" block, see figure.
 :c,image(JPG/tutorial_https_block.png)
 The above command copies ("clones") the git repository to your local
-machine. You can use this local clone to make changes and test them
+machine to a directory with the name you chose. If none is given, it will
-without interfering with the repository on github. First, however, it
+default to "lammps". Typical names are "mylammps" or something similar.
 is recommended to make a new branch for a particular feature you would
 like added to LAMMPS. In this example, I will try adding a new
 USER-package called USER-MANIFOLD.
-To create a new branch, run the following git command in your repository:
+You can use this local clone to make changes and
 test them without interfering with the repository on Github.
-$ git checkout -b add-user-manifold :pre
+To pull changes from upstream into this copy, you can go to the directory
 and use git pull:
-The name of this new branch is "add-user-manifold" in my case. Just
+  $ cd mylammps
-name it after something that resembles the feature you want added to
+  $ git checkout master
-LAMMPS.
+  $ git pull https://github.com/lammps/lammps :pre
-Now that you've changed branches, you can edit the files as you see
+You can also add this URL as a remote:
-fit, add new files, and commit as much as you would like. Just
+
-remember that if halfway you decide to add another, unrelated feature,
+  $ git remote add lammps_upstream https://www.github.com/lammps/lammps :pre
-you should switch branches!
+
 At this point, you typically make a feature branch from the updated master
 branch for the feature you want to work on. This tutorial contains the
 workflow that updated this tutorial, and hence we will call the branch
 "github-tutorial-update":
 $ git checkout -b github-tutorial-update master :pre
 Now that we have changed branches, we can make our changes to our local
 repository. Just remember that if you want to start working on another,
 unrelated feature, you should switch branches!
 [After changes are made]
 After everything is done, add the files to the branch and commit them:
-  $ git add src/USER-MANIFOLD examples/USER/manifold/
+ $ git add doc/src/tutorial_github.txt
-  $ git add doc/fix_nv\{t,e\}_manifold_rattle.txt
+ $ git add doc/src/JPG/tutorial*.png :pre
  $ git add doc/fix_manifoldforce.txt doc/user_manifolds.txt :pre
-After the files are added, the change should be comitted:
+IMPORTANT NOTE: Do not use {git commit -a} (or {git add -A}).  The -a
 flag (or -A flag) will automatically include _all_ modified or new files
 and that is rarely the behavior you want.  It can easily lead to
 accidentally adding unrelated and unwanted changes into the repository.
 Instead it is preferable to explicitly use {git add}, {git rm}, {git mv}
 for adding, removing, renaming individual files, respectively, and then
 {git commit} to finalize the commit.  Carefully check all pending
 changes with {git status} before committing them.  If you find doing
 this on the command line too tedious, consider using a GUI, for example
 the one included in git distributions written in Tk, i.e. use {git gui}
 (on some Linux distributions it may be required to install an additional
 package to use it).
-  $ git commit -m 'Added user-manifold package' :pre
+After adding all files, the change set can be committed with some
 useful message that explains the change.
-The "-m" switch is used to add a message to the commit. Use this to
+  $ git commit -m 'Finally updated the github tutorial' :pre
 indicate what type of change was commited.
 [Wisdom by Axel]
 {"Do not use "git commit -a".  the -a flag will automatically include
 *all* modified or new files.  mercurial does that and it find it
 hugely annoying and often leading to accidental commits of files you
 don't want.  use git add, git rm, git mv for adding, removing,
 renaming and then git commit to finalize the commit.  personally, i
 find it very convenient to use the bundled gui for commits, i.e. git
 gui.  typically, i will do git add and other operations, but then
 verify and review them with git gui.  git gui also allows to do
 line-by-line unstaging and other convenient operations."}
 After the commit, the changes can be pushed to the same branch on GitHub:
 $ git push :pre
 Git will ask you for your user name and password on GitHub if you have
-not configured anything. If you correctly type your user name and
+not configured anything. If your local branch is not present on Github yet,
-password, the change should be added to your fork on GitHub.
+it will ask you to add it by running
  $ git push --set-upstream origin github-tutorial-update :pre
 If you correctly type your user name and
 password, the feature branch should be added to your fork on GitHub.
 If you want to make really sure you push to the right repository
 (which is good practice), you can provide it explicitly:
@ -140,16 +167,20 @@ or using an explicit URL:
 $ git push git@github.com:Pakketeretet2/lammps.git :pre
-After that, you can file a new pull request based on this
+:line
 branch. GitHub will now look like this:
-:c,image(JPG/tutorial_pull_request_feature_branch1.png)
+[Filing a pull request]
 Up to this point in the tutorial, all changes were to {your} clones of
 LAMMPS.  Eventually, however, you want this feature to be included into
 the official LAMMPS version.  To do this, you will want to file a pull
 request by clicking on the "New pull request" button:
 :c,image(JPG/tutorial_new_pull_request.png)
 Make sure that the current branch is set to the correct one, which, in
-this case, is "add-user-manifold". Now click "New pull request". If
+this case, is "github-tutorial-update". If done correctly, the only
-done correctly, the only changes you will see are those that were made
+changes you will see are those that were made on this branch.
 on this branch, so in my case, I will see nothing related to
 $\mathrm{pair\_dzugatov}.$
 This will open up a new window that lists changes made to the
 repository. If you are just adding new files, there is not much to do,
@ -158,36 +189,162 @@ changes in existing files. If all changes can automatically be merged,
 green text at the top will say so and you can click the "Create pull
 request" button, see image.
-:c,image(JPG/tutorial_pull_request2.png)
+:c,image(JPG/tutorial_create_new_pull_request1.png)
-After this you have to specify a short title and a comment with
+Before creating the pull request, make sure the short title is accurate
-details about your pull request. I guess here you write what your
+and add a comment with details about your pull request.  Here you write
-modifications do and why they should be incorporated upstream. After
+what your modifications do and why they should be incorporated upstream.
 that, click the "Create pull request" button, see image below.
-:c,image(JPG/tutorial_pull_request3.png)
+Note the checkbox that says "Allow edits from maintainers".
 This is checked by default checkbox (although in my version of Firefox, only the checkmark is visible):
-Now just write some nice comments, click "Comment", and that is it. It
+:c,image(JPG/tutorial_edits_maintainers.png)
 is now up to the maintainer(s) of the upstream repository to
 incorporate the changes into the repository and to close the pull
 request.
-:c,image(JPG/tutorial_pull_request4.png)
+If it is checked, maintainers can immediately add their own edits to the
 pull request.  This helps the inclusion of your branch significantly, as
 simple/trivial changes can be added directly to your pull request branch
 by the LAMMPS maintainers.  The alternative would be that they make
 changes on their own version of the branch and file a reverse pull
 request to you.  Just leave this box checked unless you have a very good
 reason not to.
 Now just write some nice comments and click on "Create pull request".
 :c,image(JPG/tutorial_create_new_pull_request2.png)
 :line
 [After filing a pull request]
 NOTE: When you submit a pull request (or ask for a pull request) for the
 first time, you will receive an invitation to become a LAMMPS project
 collaborator. Please accept this invite as being a collaborator will
 simplify certain administrative tasks and will probably speed up the
 merging of your feature, too.
 You will notice that after filing the pull request, some checks are
 performed automatically:
 :c,image(JPG/tutorial_automated_checks.png)
 If all is fine, you will see this:
 :c,image(JPG/tutorial_automated_checks_passed.png)
 If any of the checks are failing, your pull request will not be
 processed, as your changes may break compilation for certain
 configurations or may not merge cleanly. It is your responsibility
 to remove the reason(s) for the failed test(s). If you need help
 with this, please contact the LAMMPS developers by adding a comment
 explaining your problems with resolving the failed tests.
 A few further interesting things (can) happen to pull requests before
 they are included.
 [Additional changes]
-Before the pull request is accepted, any additional changes you push
+First of all, any additional changes you push into your branch in your
-into your repository will automatically become part of the pull
+repository will automatically become part of the pull request:
-request.
+
 :c,image(JPG/tutorial_additional_changes.png)
 This means you can add changes that should be part of the feature after
 filing the pull request, which is useful in case you have forgotten
 them, or if a developer has requested that something needs to be changed
 before the feature can be accepted into the official LAMMPS version.
 After each push, the automated checks are run again.
 [Assignees]
 There is an assignee label for pull requests. If the request has not
 been reviewed by any developer yet, it is not assigned to anyone. After
 revision, a developer can choose to assign it to either a) you, b) a
 LAMMPS developer (including him/herself) or c) Steve Plimpton (sjplimp).
 Case a) happens if changes are required on your part :ulb,l
 Case b) means that at the moment, it is being tested and reviewed by a
 LAMMPS developer with the expectation that some changes would be required.
 After the review, the developer can choose to implement changes directly
 or suggest them to you. :l
 Case c) means that the pull request has been assigned to the lead
 developer Steve Plimpton and means it is considered ready for merging. :ule,l
 In this case, Axel assigned the tutorial to Steve:
 :c,image(JPG/tutorial_steve_assignee.png)
 [Edits from LAMMPS maintainers]
 If you allowed edits from maintainers (the default), any LAMMPS
 maintainer can add changes to your pull request.  In this case, both
 Axel and Richard made changes to the tutorial:
 :c,image(JPG/tutorial_changes_others.png)
 [Reverse pull requests]
 Sometimes, however, you might not feel comfortable having other people
 push changes into your own branch, or maybe the maintainers are not sure
 their idea was the right one.  In such a case, they can make changes,
 reassign you as the assignee, and file a "reverse pull request", i.e.
 file a pull request in your GitHub repository to include changes in the
 branch, that you have submitted as a pull request yourself.  In that
 case, you can choose to merge their changes back into your branch,
 possibly make additional changes or corrections and proceed from there.
 It looks something like this:
 :c,image(JPG/tutorial_reverse_pull_request.png)
 For some reason, the highlighted button didn't work in my case, but I
 can go to my own repository and merge the pull request from there:
 :c,image(JPG/tutorial_reverse_pull_request2.png)
 Be sure to check the changes to see if you agree with them by clicking
 on the tab button:
 :c,image(JPG/tutorial_reverse_pull_request3.png)
 In this case, most of it is changes in the markup and a short rewrite of
 Axel's explanation of the "git gui" and "git add" commands.
 :c,image(JPG/tutorial_reverse_pull_request4.png)
 Because the changes are OK with us, we are going to merge by clicking on
 "Merge pull request".  After a merge it looks like this:
 :c,image(JPG/tutorial_reverse_pull_request5.png)
 Now, since in the meantime our local text for the tutorial also changed,
 we need to pull Axel's change back into our branch, and merge them:
 $ git add tutorial_github.txt
 $ git add JPG/tutorial_reverse_pull_request*.png
 $ git commit -m "Updated text and images on reverse pull requests"
 $ git pull :pre
 In this case, the merge was painless because git could auto-merge:
 :c,image(JPG/tutorial_reverse_pull_request6.png)
 With Axel's changes merged in and some final text updates, our feature
 branch is now perfect as far as we are concerned, so we are going to
 commit and push again:
 $ git add tutorial_github.txt
 $ git add JPG/tutorial_reverse_pull_request6.png
 $ git commit -m "Merged Axel's suggestions and updated text"
 $ git push git@github.com:Pakketeretet2/lammps :pre
 This merge also shows up on the lammps Github page:
 :c,image(JPG/tutorial_reverse_pull_request7.png)
 :line
 [After a merge]
-When everything is fine the feature branch is merged into the LAMMPS
+When everything is fine, the feature branch is merged into the master branch:
 repositories:
 :c,image(JPG/tutorial_merged.png)
@ -198,17 +355,29 @@ It is in principle safe to delete them from your own fork. This helps
 keep it a bit more tidy. Note that you first have to switch to another
 branch!
-$ git checkout lammps-icms
+$ git checkout master
-$ git pull lammps-icms
+$ git pull master
-$ git branch -d add-user-manifold :pre
+$ git branch -d github-tutorial-update :pre
 If you do not pull first, it is not really a problem but git will warn
 you at the next statement that you are deleting a local branch that
 was not yet fully merged into HEAD. This is because git does not yet
-know your branch just got merged into lammps-icms upstream. If you
+know your branch just got merged into LAMMPS upstream. If you
 first delete and then pull, everything should still be fine.
 Finally, if you delete the branch locally, you might want to push this
 to your remote(s) as well:
-$ git push origin :add-user-manifold :pre
+$ git push origin :github-tutorial-update :pre
 [Recent changes in the workflow]
 Some changes to the workflow are not captured in this tutorial.  For
 example, in addition to the master branch, to which all new features
 should be submitted, there is now also an "unstable" and a "stable"
 branch; these have the same content as "master", but are only updated
 after a patch release or stable release was made.
 Furthermore, the naming of the patches now follow the pattern
 "patch_<Day><Month><Year>" to simplify comparisons between releases.
 Finally, all patches and submissions are subject to automatic testing
 and code checks to make sure they at the very least compile.
--- a/examples/README
+++ b/examples/README
@ -82,6 +82,7 @@ meam:	  MEAM test for SiC and shear (same as shear examples)
 melt:	  rapid melt of 3d LJ system
 micelle:  self-assembly of small lipid-like molecules into 2d bilayers
 min:	  energy minimization of 2d LJ melt
 mscg:     parameterize a multi-scale coarse-graining (MSCG) model
 msst:	  MSST shock dynamics
 nb3b:     use of nonbonded 3-body harmonic pair style
 neb:	  nudged elastic band (NEB) calculation for barrier finding
--- a/examples/USER/cgdna/README
+++ b/examples/USER/cgdna/README
@ -0,0 +1,28 @@
 This directory contains example data and input files 
 and utility scripts for the oxDNA coarse-grained model 
 for DNA.
 /examples/duplex1:
 Input, data and log files for a DNA duplex (double-stranded DNA) 
 consisiting of 5 base pairs. The duplex contains two strands with 
 complementary base pairs. The topology is
 A - A - A - A - A
 |   |   |   |   |
 T - T - T - T - T     
 /examples/duplex2:
 Input, data and log files for a nicked DNA duplex (double-stranded DNA) 
 consisiting of 8 base pairs. The duplex contains strands with 
 complementary base pairs, but the backbone on one side is not continuous: 
 two individual strands on one side form a duplex with a longer single 
 strand on the other side. The topology is
 A - A - A - A - A - A - A - A
 |   |   |   |   |   |   |   |
 T - T - T   T - T - T - T - T
 /util:
 This directory contains a simple python setup tool which creates 
 single straight or helical DNA strands, DNA duplexes or arrays of DNA 
 duplexes.
--- a/examples/USER/cgdna/examples/duplex1/data.duplex1
+++ b/examples/USER/cgdna/examples/duplex1/data.duplex1
@ -0,0 +1,74 @@
 # LAMMPS data file
 10 atoms
 10 ellipsoids
 8 bonds
 4 atom types
 1 bond types
 # System size
 -20.000000 20.000000 xlo xhi
 -20.000000 20.000000 ylo yhi
 -20.000000 20.000000 zlo zhi
 # Atom masses for each atom type
 Masses
 1 3.1575
 2 3.1575
 3 3.1575
 4 3.1575
 # Atom-ID, type, position, molecule-ID, ellipsoid flag, density
 Atoms
 1 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 1 1 1
 2 1 1.3274493266864451e-01 -4.2912827978022683e-01 3.7506163469402809e-01 1 1 1
 3 1 4.8460810659772807e-01 -7.0834970533509178e-01 7.5012326938805618e-01 1 1 1
 4 1 9.3267359196674593e-01 -7.4012419946742802e-01 1.1251849040820843e+00 1 1 1
 5 1 1.3204192238113461e+00 -5.1335201721887447e-01 1.5002465387761124e+00 1 1 1
 6 4 1.9958077618865377e-01 5.1335201721887447e-01 1.5002465387761124e+00 1 1 1
 7 4 5.8732640803325409e-01 7.4012419946742802e-01 1.1251849040820843e+00 1 1 1
 8 4 1.0353918934022719e+00 7.0834970533509178e-01 7.5012326938805618e-01 1 1 1
 9 4 1.3872550673313555e+00 4.2912827978022683e-01 3.7506163469402809e-01 1 1 1
 10 4 1.5200000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 1 1 1
 # Atom-ID, translational, rotational velocity
 Velocities
 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
 2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
 3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
 4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
 5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
 6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
 7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
 8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
 9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
 10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
 # Atom-ID, shape, quaternion
 Ellipsoids
 1 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
 2 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 9.5533648912560598e-01 0.0000000000000000e+00 0.0000000000000000e+00 2.9552020666133955e-01
 3 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 8.2533561490967822e-01 0.0000000000000000e+00 0.0000000000000000e+00 5.6464247339503526e-01
 4 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 6.2160996827066439e-01 0.0000000000000000e+00 0.0000000000000000e+00 7.8332690962748319e-01
 5 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 3.6235775447667351e-01 0.0000000000000000e+00 0.0000000000000000e+00 9.3203908596722607e-01
 6 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 9.3203908596722607e-01 -3.6235775447667351e-01 0.0000000000000000e+00
 7 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 7.8332690962748319e-01 -6.2160996827066439e-01 0.0000000000000000e+00
 8 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 5.6464247339503526e-01 -8.2533561490967822e-01 0.0000000000000000e+00
 9 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 2.9552020666133955e-01 -9.5533648912560598e-01 0.0000000000000000e+00
 10 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00
 # Bond topology
 Bonds
 1 1 1 2
 2 1 2 3
 3 1 3 4
 4 1 4 5
 5 1 6 7
 6 1 7 8
 7 1 8 9
 8 1 9 10
--- a/examples/USER/cgdna/examples/duplex1/input.duplex1
+++ b/examples/USER/cgdna/examples/duplex1/input.duplex1
@ -0,0 +1,75 @@
 variable number	equal 1
 variable ofreq	equal 1000
 variable efreq	equal 1000
 units lj
 dimension 3
 newton off
 boundary  p p p
 atom_style hybrid bond ellipsoid
 atom_modify sort 0 1.0
 # Pair interactions require lists of neighbours to be calculated
 neighbor 1.0 bin
 neigh_modify every 1 delay 0 check yes
 read_data data.duplex1
 set atom * mass 3.1575
 group all type 1 4
 # oxDNA bond interactions - FENE backbone
 bond_style oxdna_fene
 bond_coeff * 2.0 0.25 0.7525
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk
 pair_coeff * * oxdna_excv   2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
 pair_coeff * * oxdna_stk    1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
 pair_coeff * * oxdna_hbond  0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 1 4 oxdna_hbond  1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 2 3 oxdna_hbond  1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna_xstk   47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna_coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
 # NVE ensemble
 #fix 1 all   nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
 fix 1 all   nve/dot
 timestep 1e-5
 #comm_style tiled
 #fix 3 all balance 10000 1.1 rcb
 #compute mol all chunk/atom molecule
 #compute mychunk all vcm/chunk mol
 #fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
 dump pos all xyz ${ofreq} traj.${number}.xyz
 compute quat all property/atom quatw quati quatj quatk
 dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
 dump_modify quat sort id
 dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
 compute erot all erotate/asphere
 compute ekin all ke
 compute epot all pe
 variable erot equal c_erot
 variable ekin equal c_ekin
 variable epot equal c_epot
 variable etot equal c_erot+c_ekin+c_epot
 fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
 dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
 dump_modify out sort id
 dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
 run 1000000
 #write_restart config.${number}.*
--- a/examples/USER/cgdna/examples/duplex1/log.9Jan17.duplex1.g++.1
+++ b/examples/USER/cgdna/examples/duplex1/log.9Jan17.duplex1.g++.1
--- a/examples/USER/cgdna/examples/duplex1/log.9Jan17.duplex1.g++.4
+++ b/examples/USER/cgdna/examples/duplex1/log.9Jan17.duplex1.g++.4
--- a/examples/USER/cgdna/examples/duplex2/data.duplex2
+++ b/examples/USER/cgdna/examples/duplex2/data.duplex2
@ -0,0 +1,97 @@
 # LAMMPS data file
 16 atoms
 16 ellipsoids
 13 bonds
 4 atom types
 1 bond types
 # System size
 -20.0 20.0 xlo xhi
 -20.0 20.0 ylo yhi
 -20.0 20.0 zlo zhi
 # Atom masses for each atom type
 Masses
 1 3.1575
 2 3.1575
 3 3.1575
 4 3.1575
 # Atom-ID, type, position, molecule-ID, ellipsoid flag, density
 Atoms
 1  1  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  1 1 1
 2  1  1.327449326686445e-01 -4.291282797802268e-01  3.750616346940281e-01  1 1 1
 3  1  4.846081065977281e-01 -7.083497053350921e-01  7.501232693880562e-01  1 1 1
 4  1  9.326735919667459e-01 -7.401241994674285e-01  1.125184904082084e+00  1 1 1
 5  1  1.320419223811347e+00 -5.133520172188747e-01  1.500246538776112e+00  1 1 1
 6  1  1.512394297416339e+00 -1.072512061254991e-01  1.875308173470140e+00  1 1 1
 7  1  1.441536396413952e+00  3.363155369040876e-01  2.250369808164169e+00  1 1 1
 8  1  1.132598224218932e+00  6.623975870343269e-01  2.625431442858197e+00  1 1 1
 9  4  5.873264080332541e-01  7.401241994674285e-01  1.125184904082084e+00  1 1 1
 10 4  1.035391893402272e+00  7.083497053350921e-01  7.501232693880562e-01  1 1 1
 11 4  1.387255067331356e+00  4.291282797802267e-01  3.750616346940281e-01  1 1 1
 12 4  1.520000000000000e+00  1.260981291332700e-33  0.000000000000000e+00  1 1 1
 13 4  3.874017757810680e-01 -6.623975870343268e-01  2.625431442858197e+00  1 1 1
 14 4  7.846360358604798e-02 -3.363155369040874e-01  2.250369808164169e+00  1 1 1
 15 4  7.605702583661333e-03  1.072512061254995e-01  1.875308173470140e+00  1 1 1
 16 4  1.995807761886533e-01  5.133520172188748e-01  1.500246538776112e+00  1 1 1
 # Atom-ID, translational, rotational velocity
 Velocities
 1  0.0  0.0  0.0  0.0  0.0  0.0 
 2  0.0  0.0  0.0  0.0  0.0  0.0 
 3  0.0  0.0  0.0  0.0  0.0  0.0 
 4  0.0  0.0  0.0  0.0  0.0  0.0 
 5  0.0  0.0  0.0  0.0  0.0  0.0 
 6  0.0  0.0  0.0  0.0  0.0  0.0 
 7  0.0  0.0  0.0  0.0  0.0  0.0 
 8  0.0  0.0  0.0  0.0  0.0  0.0 
 9  0.0  0.0  0.0  0.0  0.0  0.0 
 10 0.0  0.0  0.0  0.0  0.0  0.0 
 11 0.0  0.0  0.0  0.0  0.0  0.0 
 12 0.0  0.0  0.0  0.0  0.0  0.0 
 13 0.0  0.0  0.0  0.0  0.0  0.0 
 14 0.0  0.0  0.0  0.0  0.0  0.0 
 15 0.0  0.0  0.0  0.0  0.0  0.0 
 16 0.0  0.0  0.0  0.0  0.0  0.0 
 # Atom-ID, shape, quaternion
 Ellipsoids
 1   1.1739845031423408 1.1739845031423408 1.1739845031423408  1.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
 2   1.1739845031423408 1.1739845031423408 1.1739845031423408  9.553364891256060e-01  0.000000000000000e+00  0.000000000000000e+00  2.955202066613395e-01 
 3   1.1739845031423408 1.1739845031423408 1.1739845031423408  8.253356149096783e-01  0.000000000000000e+00  0.000000000000000e+00  5.646424733950354e-01 
 4   1.1739845031423408 1.1739845031423408 1.1739845031423408  6.216099682706646e-01  0.000000000000000e+00  0.000000000000000e+00  7.833269096274833e-01 
 5   1.1739845031423408 1.1739845031423408 1.1739845031423408  3.623577544766736e-01  0.000000000000000e+00  0.000000000000000e+00  9.320390859672263e-01 
 6   1.1739845031423408 1.1739845031423408 1.1739845031423408  7.073720166770291e-02  0.000000000000000e+00  0.000000000000000e+00  9.974949866040544e-01 
 7   1.1739845031423408 1.1739845031423408 1.1739845031423408 -2.272020946930869e-01 -0.000000000000000e+00  0.000000000000000e+00  9.738476308781953e-01 
 8   1.1739845031423408 1.1739845031423408 1.1739845031423408 -5.048461045998575e-01 -0.000000000000000e+00  0.000000000000000e+00  8.632093666488738e-01 
 9   1.1739845031423408 1.1739845031423408 1.1739845031423408  4.796493962806427e-17  7.833269096274833e-01 -6.216099682706646e-01  3.806263289803786e-17 
 10  1.1739845031423408 1.1739845031423408 1.1739845031423408  5.707093416549944e-17  5.646424733950354e-01 -8.253356149096784e-01  2.218801320830406e-17 
 11  1.1739845031423408 1.1739845031423408 1.1739845031423408  6.107895212550935e-17  2.955202066613394e-01 -9.553364891256061e-01  4.331404380149668e-18 
 12  1.1739845031423408 1.1739845031423408 1.1739845031423408  5.963096920061075e-17  0.000000000000000e+00 -1.000000000000000e+00 -1.391211590127312e-17 
 13  1.1739845031423408 1.1739845031423408 1.1739845031423408  5.285632939302787e-17  8.632093666488739e-01  5.048461045998572e-01 -3.091290830301125e-17 
 14  1.1739845031423408 1.1739845031423408 1.1739845031423408  4.136019110019290e-17  9.738476308781953e-01  2.272020946930868e-01 -4.515234267244800e-17 
 15  1.1739845031423408 1.1739845031423408 1.1739845031423408  2.616947011741696e-17  9.974949866040544e-01 -7.073720166770313e-02 -5.535845274597425e-17 
 16  1.1739845031423408 1.1739845031423408 1.1739845031423408  8.641108308308281e-18  9.320390859672264e-01 -3.623577544766736e-01 -6.061955710708163e-17 
 # Bond-ID, type, atom pairs
 Bonds
 1	1	1	2
 2	1	2	3
 3	1	3	4
 4	1	4	5
 5	1	5	6
 6	1	6	7
 7	1	7	8
 8	1	13	14
 9	1	14	15
 10	1	15	16
 11	1	9	10
 12	1	10	11
 13	1	11	12
--- a/examples/USER/cgdna/examples/duplex2/input.duplex2
+++ b/examples/USER/cgdna/examples/duplex2/input.duplex2
@ -0,0 +1,75 @@
 variable number	equal 2
 variable ofreq	equal 1000
 variable efreq	equal 1000
 units lj
 dimension 3
 newton off
 boundary  p p p
 atom_style hybrid bond ellipsoid
 atom_modify sort 0 1.0
 # Pair interactions require lists of neighbours to be calculated
 neighbor 1.0 bin
 neigh_modify every 1 delay 0 check yes
 read_data data.duplex2
 set atom * mass 3.1575
 group all type 1 4
 # oxDNA bond interactions - FENE backbone
 bond_style oxdna_fene
 bond_coeff * 2.0 0.25 0.7525
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk
 pair_coeff * * oxdna_excv   2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
 pair_coeff * * oxdna_stk    1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65   
 pair_coeff * * oxdna_hbond  0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 1 4 oxdna_hbond  1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 2 3 oxdna_hbond  1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna_xstk   47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 
 pair_coeff * * oxdna_coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
 # NVE ensemble
 fix 1 all   nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
 #fix 1 all   nve/dot
 timestep 1e-5 
 #comm_style tiled
 #fix 3 all balance 10000 1.1 rcb
 #compute mol all chunk/atom molecule
 #compute mychunk all vcm/chunk mol
 #fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
 dump pos all xyz ${ofreq} traj.${number}.xyz
 compute quat all property/atom quatw quati quatj quatk
 dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
 dump_modify quat sort id
 dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
 compute erot all erotate/asphere
 compute ekin all ke
 compute epot all pe
 variable erot equal c_erot
 variable ekin equal c_ekin
 variable epot equal c_epot
 variable etot equal c_erot+c_ekin+c_epot
 fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
 dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
 dump_modify out sort id
 dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
 run 1000000
 #write_restart config.${number}.*
--- a/examples/USER/cgdna/examples/duplex2/log.9Jan17.duplex2.g++.1
+++ b/examples/USER/cgdna/examples/duplex2/log.9Jan17.duplex2.g++.1
--- a/examples/USER/cgdna/examples/duplex2/log.9Jan17.duplex2.g++.4
+++ b/examples/USER/cgdna/examples/duplex2/log.9Jan17.duplex2.g++.4
--- a/examples/USER/cgdna/util/generate_input.py
+++ b/examples/USER/cgdna/util/generate_input.py
@ -0,0 +1,388 @@
 # Setup tool for oxDNA input in LAMMPS format.
 import math,numpy as np,sys,os
 # system size
 lxmin = -115.0
 lxmax = +115.0
 lymin = -115.0
 lymax = +115.0
 lzmin = -115.0
 lzmax = +115.0
 # rise in z-direction
 r0 = 0.7
 # definition of single untwisted strand
 def single():
  strand = inp[1].split(':')
  com_start=strand[0].split(',')
  posx=float(com_start[0])
  posy=float(com_start[1])
  posz=float(com_start[2])
  risex=0
  risey=0
  risez=r0
  strandstart=len(nucleotide)+1
  for letter in strand[2]:
    temp=[]
    temp.append(nt2num[letter])
    temp.append([posx,posy,posz])
    vel=[0,0,0,0,0,0]
    temp.append(vel)
    temp.append(shape)
    quat=[1,0,0,0]
    temp.append(quat)
    posx=posx+risex
    posy=posy+risey
    posz=posz+risez
    if (len(nucleotide)+1 > strandstart):
      topology.append([1,len(nucleotide),len(nucleotide)+1])
    nucleotide.append(temp)
  return
 # definition of single twisted strand
 def single_helix():
  strand = inp[1].split(':')
  com_start=strand[0].split(',')
  twist=float(strand[1])
  posx = float(com_start[0])
  posy = float(com_start[1])
  posz = float(com_start[2])
  risex=0
  risey=0
  risez=math.sqrt(r0**2-4.0*math.sin(0.5*twist)**2) 
  dcomh=0.76
  axisx=dcomh + posx
  axisy=posy
  strandstart=len(nucleotide)+1
  quat=[1,0,0,0]
  qrot0=math.cos(0.5*twist)
  qrot1=0
  qrot2=0
  qrot3=math.sin(0.5*twist)
  for letter in strand[2]:
    temp=[]
    temp.append(nt2num[letter])
    temp.append([posx,posy,posz])
    vel=[0,0,0,0,0,0]
    temp.append(vel)
    temp.append(shape)
    temp.append(quat)
    quat0 = quat[0]*qrot0 - quat[1]*qrot1 - quat[2]*qrot2 - quat[3]*qrot3 
    quat1 = quat[0]*qrot1 + quat[1]*qrot0 + quat[2]*qrot3 - quat[3]*qrot2 
    quat2 = quat[0]*qrot2 + quat[2]*qrot0 + quat[3]*qrot1 - quat[1]*qrot3 
    quat3 = quat[0]*qrot3 + quat[3]*qrot0 + quat[1]*qrot2 + quat[2]*qrot1 
    quat = [quat0,quat1,quat2,quat3]
    posx=axisx - dcomh*(quat[0]**2+quat[1]**2-quat[2]**2-quat[3]**2)
    posy=axisy - dcomh*(2*(quat[1]*quat[2]+quat[0]*quat[3]))
    posz=posz+risez
    if (len(nucleotide)+1 > strandstart):
      topology.append([1,len(nucleotide),len(nucleotide)+1])
    nucleotide.append(temp)
  return
 # definition of twisted duplex  
 def duplex():
  strand = inp[1].split(':')
  com_start=strand[0].split(',')
  twist=float(strand[1])
  compstrand=[]
  comptopo=[]
  posx1 = float(com_start[0])
  posy1 = float(com_start[1])
  posz1 = float(com_start[2])
  risex=0
  risey=0
  risez=math.sqrt(r0**2-4.0*math.sin(0.5*twist)**2) 
  dcomh=0.76
  axisx=dcomh + posx1
  axisy=posy1
  posx2 = axisx + dcomh  
  posy2 = posy1
  posz2 = posz1
  strandstart=len(nucleotide)+1
  quat1=[1,0,0,0]
  quat2=[0,0,-1,0]
  qrot0=math.cos(0.5*twist)
  qrot1=0
  qrot2=0
  qrot3=math.sin(0.5*twist)
  for letter in strand[2]:
    temp1=[]
    temp2=[]
    temp1.append(nt2num[letter])
    temp2.append(compnt2num[letter])
    temp1.append([posx1,posy1,posz1])
    temp2.append([posx2,posy2,posz2])
    vel=[0,0,0,0,0,0]
    temp1.append(vel)
    temp2.append(vel)
    temp1.append(shape)
    temp2.append(shape)
    temp1.append(quat1)
    temp2.append(quat2)
    quat1_0 = quat1[0]*qrot0 - quat1[1]*qrot1 - quat1[2]*qrot2 - quat1[3]*qrot3 
    quat1_1 = quat1[0]*qrot1 + quat1[1]*qrot0 + quat1[2]*qrot3 - quat1[3]*qrot2 
    quat1_2 = quat1[0]*qrot2 + quat1[2]*qrot0 + quat1[3]*qrot1 - quat1[1]*qrot3 
    quat1_3 = quat1[0]*qrot3 + quat1[3]*qrot0 + quat1[1]*qrot2 + quat1[2]*qrot1 
    quat1 = [quat1_0,quat1_1,quat1_2,quat1_3]
    posx1=axisx - dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
    posy1=axisy - dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
    posz1=posz1+risez
    quat2_0 = quat2[0]*qrot0 - quat2[1]*qrot1 - quat2[2]*qrot2 + quat2[3]*qrot3 
    quat2_1 = quat2[0]*qrot1 + quat2[1]*qrot0 - quat2[2]*qrot3 - quat2[3]*qrot2 
    quat2_2 = quat2[0]*qrot2 + quat2[2]*qrot0 + quat2[3]*qrot1 + quat2[1]*qrot3 
    quat2_3 =-quat2[0]*qrot3 + quat2[3]*qrot0 + quat2[1]*qrot2 + quat2[2]*qrot1 
    quat2 = [quat2_0,quat2_1,quat2_2,quat2_3]
    posx2=axisx + dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
    posy2=axisy + dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
    posz2=posz1
    if (len(nucleotide)+1 > strandstart):
      topology.append([1,len(nucleotide),len(nucleotide)+1])
      comptopo.append([1,len(nucleotide)+len(strand[2]),len(nucleotide)+len(strand[2])+1])
    nucleotide.append(temp1)
    compstrand.append(temp2)
  for ib in range(len(compstrand)):
    nucleotide.append(compstrand[len(compstrand)-1-ib])
  for ib in range(len(comptopo)):
    topology.append(comptopo[ib])
  return
 # definition of array of duplexes  
 def duplex_array():
  strand = inp[1].split(':')
  number=strand[0].split(',')
  posz1_0 = float(strand[1])
  twist=float(strand[2])
  nx = int(number[0])
  ny = int(number[1])
  dx = (lxmax-lxmin)/nx
  dy = (lymax-lymin)/ny
  risex=0
  risey=0
  risez=math.sqrt(r0**2-4.0*math.sin(0.5*twist)**2) 
  dcomh=0.76
  for ix in range(nx):
    axisx=lxmin + dx/2 + ix * dx
    for iy in range(ny):
      axisy=lymin + dy/2 + iy * dy
      compstrand=[]
      comptopo=[]
      posx1 = axisx - dcomh
      posy1 = axisy
      posz1 = posz1_0
      posx2 = axisx + dcomh  
      posy2 = posy1
      posz2 = posz1
      strandstart=len(nucleotide)+1
      quat1=[1,0,0,0]
      quat2=[0,0,-1,0]
      qrot0=math.cos(0.5*twist)
      qrot1=0
      qrot2=0
      qrot3=math.sin(0.5*twist)
      for letter in strand[3]:
 	temp1=[]
 	temp2=[]
 	temp1.append(nt2num[letter])
 	temp2.append(compnt2num[letter])
 	temp1.append([posx1,posy1,posz1])
 	temp2.append([posx2,posy2,posz2])
 	vel=[0,0,0,0,0,0]
 	temp1.append(vel)
 	temp2.append(vel)
 	temp1.append(shape)
 	temp2.append(shape)
 	temp1.append(quat1)
 	temp2.append(quat2)
 	quat1_0 = quat1[0]*qrot0 - quat1[1]*qrot1 - quat1[2]*qrot2 - quat1[3]*qrot3 
 	quat1_1 = quat1[0]*qrot1 + quat1[1]*qrot0 + quat1[2]*qrot3 - quat1[3]*qrot2 
 	quat1_2 = quat1[0]*qrot2 + quat1[2]*qrot0 + quat1[3]*qrot1 - quat1[1]*qrot3 
 	quat1_3 = quat1[0]*qrot3 + quat1[3]*qrot0 + quat1[1]*qrot2 + quat1[2]*qrot1 
 	quat1 = [quat1_0,quat1_1,quat1_2,quat1_3]
 	posx1=axisx - dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
 	posy1=axisy - dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
 	posz1=posz1+risez
 	quat2_0 = quat2[0]*qrot0 - quat2[1]*qrot1 - quat2[2]*qrot2 + quat2[3]*qrot3 
 	quat2_1 = quat2[0]*qrot1 + quat2[1]*qrot0 - quat2[2]*qrot3 - quat2[3]*qrot2 
 	quat2_2 = quat2[0]*qrot2 + quat2[2]*qrot0 + quat2[3]*qrot1 + quat2[1]*qrot3 
 	quat2_3 =-quat2[0]*qrot3 + quat2[3]*qrot0 + quat2[1]*qrot2 + quat2[2]*qrot1 
 	quat2 = [quat2_0,quat2_1,quat2_2,quat2_3]
 	posx2=axisx + dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
 	posy2=axisy + dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
 	posz2=posz1
 	if (len(nucleotide)+1 > strandstart):
 	  topology.append([1,len(nucleotide),len(nucleotide)+1])
 	  comptopo.append([1,len(nucleotide)+len(strand[3]),len(nucleotide)+len(strand[3])+1])
 	nucleotide.append(temp1)
 	compstrand.append(temp2)
      for ib in range(len(compstrand)):
 	nucleotide.append(compstrand[len(compstrand)-1-ib])
      for ib in range(len(comptopo)):
 	topology.append(comptopo[ib])
  return
 # main part
 nt2num = {'A':1, 'C':2, 'G':3, 'T':4}
 compnt2num = {'T':1, 'G':2, 'C':3, 'A':4}
 shape = [1.1739845031423408,1.1739845031423408,1.1739845031423408]
 nucleotide=[]
 topology=[]
 seqfile = open(sys.argv[1],'r')
 # process sequence file line by line
 for line in seqfile:
  inp = line.split()
  if inp[0] == 'single':
    single()
  if inp[0] == 'single_helix':
    single_helix()
  if inp[0] == 'duplex':
    duplex()
  if inp[0] == 'duplex_array':
    duplex_array()
 # output atom data in LAMMPS format
 out = open(sys.argv[2],'w')
 out.write('# LAMMPS data file\n')
 out.write('%d atoms\n' % len(nucleotide))
 out.write('%d ellipsoids\n' % len(nucleotide))
 out.write('%d bonds\n' % len(topology))
 out.write('\n')
 out.write('4 atom types\n')
 out.write('1 bond types\n')
 out.write('\n')
 out.write('# System size\n')
 out.write('%f %f xlo xhi\n' % (lxmin,lxmax))
 out.write('%f %f ylo yhi\n' % (lymin,lymax))
 out.write('%f %f zlo zhi\n' % (lzmin,lzmax))
 out.write('\n')
 out.write('Masses\n')
 out.write('\n')
 out.write('1 3.1575\n')
 out.write('2 3.1575\n')
 out.write('3 3.1575\n')
 out.write('4 3.1575\n')
 out.write('\n')
 out.write('# Atom-ID, type, position, molecule-ID, ellipsoid flag, density\n')
 out.write('Atoms\n')
 out.write('\n')
 for ib in range(len(nucleotide)):
  out.write("%d %d %22.16le %22.16le %22.16le 1 1 1\n" % (ib+1,nucleotide[ib][0],nucleotide[ib][1][0],nucleotide[ib][1][1],nucleotide[ib][1][2]))
 out.write('\n')
 out.write('# Atom-ID, translational, rotational velocity\n')
 out.write('Velocities\n')
 out.write('\n')
 for ib in range(len(nucleotide)):
  out.write("%d %22.16le %22.16le %22.16le %22.16le %22.16le %22.16le\n" % (ib+1,nucleotide[ib][2][0],nucleotide[ib][2][1],nucleotide[ib][2][2],nucleotide[ib][2][3],nucleotide[ib][2][4],nucleotide[ib][2][5]))
 out.write('\n')
 out.write('# Atom-ID, shape, quaternion\n')
 out.write('Ellipsoids\n')
 out.write('\n')
 for ib in range(len(nucleotide)):
  out.write("%d %22.16le %22.16le %22.16le %22.16le %22.16le %22.16le %22.16le\n" % (ib+1,nucleotide[ib][3][0],nucleotide[ib][3][1],nucleotide[ib][3][2],nucleotide[ib][4][0],nucleotide[ib][4][1],nucleotide[ib][4][2],nucleotide[ib][4][3]))
 out.write('\n')
 out.write('# Bond topology\n')
 out.write('Bonds\n')
 out.write('\n')
 for ib in range(len(topology)):
  out.write("%d %d %d %d\n" % (ib+1,topology[ib][0],topology[ib][1],topology[ib][2]))
 out.close() 
 seqfile.close()
 sys.exit(0)
--- a/examples/USER/cgdna/util/input.ref
+++ b/examples/USER/cgdna/util/input.ref
@ -0,0 +1,77 @@
 variable number	equal 8
 variable ofreq	equal 1000
 variable efreq	equal 1000
 units lj
 dimension 3
 newton off
 processors 1 1 1
 boundary  p p p
 atom_style hybrid bond ellipsoid
 atom_modify sort 0 1.0
 # Pair interactions require lists of neighbours to be calculated
 neighbor 1.0 bin
 neigh_modify every 1 delay 0 check yes
 read_data data.duplex2
 set atom * mass 3.1575
 group all type 1 4
 # oxDNA bond interactions - FENE backbone
 bond_style oxdna_fene
 bond_coeff * 2.0 0.25 0.7525
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk
 pair_coeff * * oxdna_excv   2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
 pair_coeff * * oxdna_stk    1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65   
 pair_coeff * * oxdna_hbond  0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 1 4 oxdna_hbond  1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 2 3 oxdna_hbond  1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna_xstk   47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 
 pair_coeff * * oxdna_coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
 # NVE ensemble
 #fix 1 all   nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
 fix 1 all   nve/dot
 timestep 1e-5 
 #comm_style tiled
 #fix 3 all balance 10000 1.1 rcb
 #compute mol all chunk/atom molecule
 #compute mychunk all vcm/chunk mol
 #fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
 #dump pos all xyz ${ofreq} traj.${number}.xyz
 #compute quat all property/atom quatw quati quatj quatk
 #dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
 #dump_modify quat sort id
 #dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
 compute erot all erotate/asphere
 compute ekin all ke
 compute epot all pe
 variable erot equal c_erot
 variable ekin equal c_ekin
 variable epot equal c_epot
 variable etot equal c_erot+c_ekin+c_epot
 fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
 dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
 dump_modify out sort id
 dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
 run 1000000
 #write_restart config.${number}.*
--- a/examples/USER/cgdna/util/sequence.txt
+++ b/examples/USER/cgdna/util/sequence.txt
@ -0,0 +1,4 @@
 single 0,0,0:0.6:AAAAA
 single_helix 0,0,0:0.6:AAAAA
 duplex 0,0,0:0.6:AAAAA
 duplex_array 10,10:-112.0:0.6:AAAAA
--- a/examples/USER/dpd/dpde-vv/log.dpde-vv.reference
+++ b/examples/USER/dpd/dpde-vv/log.dpde-vv.reference
@ -35,129 +35,133 @@ thermo_modify   format float %24.16f
 run             1000
 Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check no
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10.6
  ghost atom cutoff = 10.6
-  binsize = 5.3 -> bins = 25 25 25
+  binsize = 5.3, bins = 25 25 25
-Memory usage per processor = 3.36353 Mbytes
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair dpd/fdt/energy, perpetual
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
 Memory usage per processor = 4.28221 Mbytes
 Step Temp Press PotEng KinEng c_dpdU[1] c_dpdU[2] v_totEnergy c_dpdU[4] 
-       0     301.4391322267262012    1636.1776395935085020    1188.6488072196075336     394.4722035796053206    7852.5601874986105031    7852.5601874986105031   17288.2413857964347699     299.9999999999841407 
+       0     301.4391322267262012    1636.1776395935080473    1188.6488072196075336     394.4722035796053206       0.0000000000000000   15705.1203749972210062   17288.2413857964347699     299.9999999999841407 
-      10     301.4791572483523510    1486.4422375141198245    1188.7147620806101713     394.5245815119678241    7852.5601874999802021    7852.3731942333779443   17288.1727253259377903     299.9960221120699089 
+      10     301.4791572483523510    1486.4422375141214161    1188.7147620806101713     394.5245815119678241       0.0000000000000000   15704.9333817333845218   17288.1727253259632562     299.9960221120699089 
-      20     301.4275643919337426    1677.9356110821624952    1188.7839634625399867     394.4570655673388728    7852.5601874999938445    7852.3711851933012440   17288.1724017231754260     299.9955485734552099 
+      20     301.4275643919337995    1677.9356110821622678    1188.7839634625399867     394.4570655673389865      -0.0000000000000000   15704.9313726932996360   17288.1724017231790640     299.9955485734552667 
-      30     301.2240988054542186    1452.7304951528931269    1188.8550809767796181     394.1908044563202225    7852.5601875000002110    7852.5679666239848302   17288.1740395570850524     299.9988968405210130 
+      30     301.2240988054542186    1452.7304951528922174    1188.8550809767796181     394.1908044563202225      -0.0000000000000000   15705.1281541239713988   17288.1740395570705005     299.9988968405209562 
-      40     301.1023506886409677    1527.9758363521380033    1188.9264527568634549     394.0314812537677653    7852.5601874999947540    7852.6574764573806533   17288.1755979680056043     300.0001694462812338 
+      40     301.1023506886409109    1527.9758363521384581    1188.9264527568634549     394.0314812537677085      -0.0000000000000000   15705.2176639573335706   17288.1755979679655866     300.0001694462812907 
-      50     301.0409654880461972    1597.1737251233498682    1188.9944523606982330     393.9511507566391515    7852.5601875000029395    7852.6700547249911324   17288.1758453423317405     299.9999653064982681 
+      50     301.0409654880461972    1597.1737251233505503    1188.9944523606984603     393.9511507566391515      -0.0000000000000000   15705.2302422249904339   17288.1758453423281026     299.9999653064982112 
-      60     301.2904978886139133    1610.8630327676828529    1189.0651026961211301     394.2776962691256131    7852.5601874999829306    7852.2734988976435488   17288.1764853628737910     299.9919857290491905 
+      60     301.2904978886138565    1610.8630327676828529    1189.0651026961211301     394.2776962691255562      -0.0000000000000000   15704.8336863976528548   17288.1764853628992569     299.9919857290491905 
-      70     300.8575037843163500    1489.3259312130880971    1189.1295686642290548     393.7110673208616731    7852.5601874999856591    7852.7707182199101226   17288.1715417049854295     300.0010992278233175 
+      70     300.8575037843164068    1489.3259312130892340    1189.1295686642290548     393.7110673208617300       0.0000000000000000   15705.3309057198275696   17288.1715417049199459     300.0010992278232607 
-      80     300.5955830326474825    1449.3896097889587509    1189.1880764967559116     393.3683100440913449    7852.5601875000411383    7853.0484238882281716   17288.1649979291178170     300.0059513551503301 
+      80     300.5955830326474825    1449.3896097889576140    1189.1880764967559116     393.3683100440913449      -0.0000000000000000   15705.6086113882302016   17288.1649979290777992     300.0059513551502164 
-      90     301.0092332775843147    1553.9266324350364812    1189.2470037925052111     393.9096250433288446    7852.5601875000420478    7852.4452067113825251   17288.1620230472581170     299.9940347326859182 
+      90     301.0092332775843147    1553.9266324350371633    1189.2470037925056658     393.9096250433288446      -0.0000000000000000   15705.0053942113881931   17288.1620230472217372     299.9940347326859182 
-     100     301.0478004479094238    1539.2270336322194453    1189.3010269201699884     393.9600951881690207    7852.5601875000074870    7852.3416236045995902   17288.1629332129450631     299.9916385566916119 
+     100     301.0478004479094238    1539.2270336322201274    1189.3010269201699884     393.9600951881690207      -0.0000000000000000   15704.9018111045588739   17288.1629332128977694     299.9916385566916119 
-     110     300.9609384905550087    1500.0429484565006533    1189.3524514939088021     393.8464250502817663    7852.5601874999983920    7852.4114980357189779   17288.1705620799075405     299.9925626482005327 
+     110     300.9609384905550655    1500.0429484565015628    1189.3524514939088021     393.8464250502818231      -0.0000000000000000   15704.9716855356964516   17288.1705620798857126     299.9925626482006464 
-     120     300.9625536631411933    1630.5065919443034090    1189.4006029528841282     393.8485387131115658    7852.5601875000575092    7852.3600810123671181   17288.1694101784196391     299.9911580775880680 
+     120     300.9625536631413070    1630.5065919443020448    1189.4006029528841282     393.8485387131116795       0.0000000000000000   15704.9202685123345873   17288.1694101783286897     299.9911580775880680 
-     130     301.0373750247310340    1539.2267307640183844    1189.4426173625224692     393.9464521696795032    7852.5601874999993015    7852.2178388309775983   17288.1670958631802932     299.9879581026651749 
+     130     301.0373750247309772    1539.2267307640188392    1189.4426173625224692     393.9464521696794463      -0.0000000000000000   15704.7780263310032751   17288.1670958632057591     299.9879581026650044 
-     140     300.7465104415114752    1550.8353679735087098    1189.4887352231000932     393.5658181350791551    7852.5601874999920256    7852.5559582333216895   17288.1706990914935886     299.9939749909034958 
+     140     300.7465104415114183    1550.8353679735089372    1189.4887352231000932     393.5658181350790983       0.0000000000000000   15705.1161457332873397   17288.1706990914681228     299.9939749909034958 
-     150     300.6667173911141617    1634.8987162883277051    1189.5368575067818711     393.4613985788388959    7852.5601874999920256    7852.6079668015609059   17288.1664103871735279     299.9946423938895350 
+     150     300.6667173911142186    1634.8987162883267956    1189.5368575067818711     393.4613985788390096       0.0000000000000000   15705.1681543015274656   17288.1664103871480620     299.9946423938894213 
-     160     300.4684731724562425    1462.9400882126803936    1189.5825022927965620     393.2019703048678707    7852.5601874999847496    7852.8265187980177870   17288.1711788956672535     299.9983600613423960 
+     160     300.4684731724561857    1462.9400882126797114    1189.5825022927965620     393.2019703048678139       0.0000000000000000   15705.3867062980680203   17288.1711788957327371     299.9983600613422254 
-     170     300.1439323338466920    1510.2352578813552100    1189.6305700279478970     392.7772665220106774    7852.5601874999802021    7853.2009671047335360   17288.1689911546709482     300.0051118582463232 
+     170     300.1439323338466920    1510.2352578813547552    1189.6305700279476696     392.7772665220106774      -0.0000000000000000   15705.7611546046609874   17288.1689911546200165     300.0051118582463232 
-     180     300.1074244553407198    1529.6307083879951279    1189.6764977580119194     392.7294912276224181    7852.5601874999729262    7853.2047509722533505   17288.1709274578606710     300.0047089238623812 
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-    1000     301.3195135766228532    1562.6587211933920116    1187.8034267774903583     394.3156670604516307    7852.5601874999356369    7853.5372636956635688   17288.2165450335414789     299.9807651637231629 
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-Loop time of 21.3308 on 1 procs for 1000 steps with 10125 atoms
+Loop time of 17.0881 on 1 procs for 1000 steps with 10125 atoms
-Performance: 4.050 ns/day, 5.925 hours/ns, 46.880 timesteps/s
+Performance: 5.056 ns/day, 4.747 hours/ns, 58.520 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 10.099     | 10.099     | 10.099     |   0.0 | 47.34
+Pair    | 8.0541     | 8.0541     | 8.0541     |   0.0 | 47.13
-Neigh   | 10.145     | 10.145     | 10.145     |   0.0 | 47.56
+Neigh   | 8.1306     | 8.1306     | 8.1306     |   0.0 | 47.58
-Comm    | 0.49807    | 0.49807    | 0.49807    |   0.0 |  2.33
+Comm    | 0.39415    | 0.39415    | 0.39415    |   0.0 |  2.31
-Output  | 0.011203   | 0.011203   | 0.011203   |   0.0 |  0.05
+Output  | 0.01103    | 0.01103    | 0.01103    |   0.0 |  0.06
-Modify  | 0.28296    | 0.28296    | 0.28296    |   0.0 |  1.33
+Modify  | 0.24061    | 0.24061    | 0.24061    |   0.0 |  1.41
-Other   |            | 0.295      |            |       |  1.38
+Other   |            | 0.2576     |            |       |  1.51
 Nlocal:    10125 ave 10125 max 10125 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -170,4 +174,4 @@ Total # of neighbors = 114682
 Ave neighs/atom = 11.3266
 Neighbor list builds = 1000
 Dangerous builds not checked
-Total wall time: 0:00:21
+Total wall time: 0:00:17
--- a/examples/USER/dpd/dpdh-shardlow/in.dpdh-shardlow
+++ b/examples/USER/dpd/dpdh-shardlow/in.dpdh-shardlow
@ -18,7 +18,7 @@ neigh_modify    every 1 delay 0 check no once no
 timestep        0.001
 compute         dpdU all dpd
-variable        totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[1]+press*vol
+variable        totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[2]+press*vol
 thermo          1
 thermo_style    custom step temp press vol pe ke v_totEnergy cella cellb cellc
--- a/examples/USER/dpd/dpdh-shardlow/log.dpdh-shardlow.reference
+++ b/examples/USER/dpd/dpdh-shardlow/log.dpdh-shardlow.reference
@ -22,7 +22,7 @@ neigh_modify    every 1 delay 0 check no once no
 timestep        0.001
 compute         dpdU all dpd
-variable        totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[1]+press*vol
+variable        totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[2]+press*vol
 thermo          1
 thermo_style    custom step temp press vol pe ke v_totEnergy cella cellb cellc
@ -34,129 +34,137 @@ fix             2 all eos/cv 0.0005
 run             100
 Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check no
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
-  binsize = 6 -> bins = 22 22 22
+  binsize = 6, bins = 22 22 22
-Memory usage per processor = 6.48143 Mbytes
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair dpd/fdt/energy, perpetual
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
  (2) fix shardlow, perpetual, ssa
      pair build: half/bin/newton/ssa
      stencil: half/bin/3d/newton/ssa
      bin: ssa
 Memory usage per processor = 8.55503 Mbytes
 Step Temp Press Volume PotEng KinEng v_totEnergy Cella Cellb Cellc 
-       0  239.4274282976 2817.4421750949 2146689.0000000000 2639.8225470740  313.3218455755 6048176597.3066043854  129.0000000000  129.0000000000  129.0000000000 
+       0  239.4274282976 2817.4421750949 2146689.0000000000 2639.8225470740  313.3218455755 6048176597.3066034317  129.0000000000  129.0000000000  129.0000000000 
-       1  239.4771405316 2817.4798146419 2146689.0000581890 2639.8304543632  313.3869004818 6048257397.9450111389  129.0000000012  129.0000000012  129.0000000012 
+       1  239.4771405316 2817.4798146419 2146689.0000581890 2639.8304543632  313.3869004818 6048257397.8720483780  129.0000000012  129.0000000012  129.0000000012 
-       2  239.5643955010 2817.5423194969 2146689.0002327557 2639.8379071907  313.5010849268 6048391577.0431985855  129.0000000047  129.0000000047  129.0000000047 
+       2  239.5643955010 2817.5423194969 2146689.0002327557 2639.8379071907  313.5010849268 6048391576.8485937119  129.0000000047  129.0000000047  129.0000000047 
-       3  239.6633839196 2817.6123662396 2146689.0005237064 2639.8445238058  313.6306241122 6048541946.5712032318  129.0000000105  129.0000000105  129.0000000105 
+       3  239.6633839196 2817.6123662396 2146689.0005237064 2639.8445238058  313.6306241122 6048541946.2404479980  129.0000000105  129.0000000105  129.0000000105 
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-      62  242.9276177041 2819.8088790098 2146689.2237249981 2639.4201279058  317.9022974164 6053257809.6067762375  129.0000044814  129.0000044814  129.0000044814 
+      62  242.9276177041 2819.8088790098 2146689.2237249981 2639.4201279058  317.9022974164 6053257805.4283437729  129.0000044814  129.0000044814  129.0000044814 
-      63  243.0465445938 2819.8814758895 2146689.2310012528 2639.3991657500  318.0579286774 6053413673.1989650726  129.0000046272  129.0000046272  129.0000046272 
+      63  243.0465445938 2819.8814758895 2146689.2310012528 2639.3991657500  318.0579286774 6053413668.8858547211  129.0000046272  129.0000046272  129.0000046272 
-      64  242.9890585501 2819.8387587817 2146689.2383939880 2639.3781767844  317.9827007328 6053321993.5937871933  129.0000047752  129.0000047752  129.0000047752 
+      64  242.9890585501 2819.8387587817 2146689.2383939880 2639.3781767844  317.9827007328 6053321989.3768787384  129.0000047752  129.0000047752  129.0000047752 
-      65  242.9653746583 2819.8180104181 2146689.2459031967 2639.3568184374  317.9517072884 6053277474.4272727966  129.0000049256  129.0000049256  129.0000049256 
+      65  242.9653746583 2819.8180104181 2146689.2459031967 2639.3568184374  317.9517072884 6053277470.2627182007  129.0000049256  129.0000049256  129.0000049256 
-      66  243.0259297024 2819.8514334947 2146689.2535288804 2639.3352568621  318.0309514181 6053349244.9473772049  129.0000050784  129.0000050784  129.0000050784 
+      66  243.0259297024 2819.8514334947 2146689.2535288804 2639.3352568621  318.0309514181 6053349240.7251205444  129.0000050784  129.0000050784  129.0000050784 
-      67  242.9638979697 2819.8046112742 2146689.2612710390 2639.3134547096  317.9497748498 6053248753.9180717468  129.0000052335  129.0000052335  129.0000052335 
+      67  242.9638979697 2819.8046112742 2146689.2612710390 2639.3134547096  317.9497748498 6053248749.7987766266  129.0000052335  129.0000052335  129.0000052335 
-      68  243.0283540775 2819.8395632725 2146689.2691296688 2639.2912303374  318.0341240273 6053323807.2197017670  129.0000053909  129.0000053909  129.0000053909 
+      68  243.0283540775 2819.8395632725 2146689.2691296688 2639.2912303374  318.0341240273 6053323803.0382738113  129.0000053909  129.0000053909  129.0000053909 
-      69  243.2256418664 2819.9609646019 2146689.2771047787 2639.2684509205  318.2923006889 6053584440.8757400513  129.0000055506  129.0000055506  129.0000055506 
+      69  243.2256418664 2819.9609646019 2146689.2771047787 2639.2684509205  318.2923006889 6053584436.4588871002  129.0000055506  129.0000055506  129.0000055506 
-      70  243.2507495334 2819.9706145524 2146689.2851963686 2639.2450126010  318.3251573278 6053605179.1483964920  129.0000057127  129.0000057127  129.0000057127 
+      70  243.2507495334 2819.9706145524 2146689.2851963686 2639.2450126010  318.3251573278 6053605174.7221174240  129.0000057127  129.0000057127  129.0000057127 
-      71  243.4287155518 2820.0794853386 2146689.2934044413 2639.2213699915  318.5580489464 6053838914.2552747726  129.0000058771  129.0000058771  129.0000058771 
+      71  243.4287155518 2820.0794853386 2146689.2934044413 2639.2213699915  318.5580489464 6053838909.6197280884  129.0000058771  129.0000058771  129.0000058771 
-      72  243.5097518574 2820.1249498194 2146689.3017290002 2639.1971212009  318.6640954635 6053936535.9274711609  129.0000060439  129.0000060439  129.0000060439 
+      72  243.5097518574 2820.1249498194 2146689.3017290002 2639.1971212009  318.6640954635 6053936531.2101163864  129.0000060439  129.0000060439  129.0000060439 
-      73  243.5356790969 2820.1337977544 2146689.3101700447 2639.1723394661  318.6980246193 6053955553.5090074539  129.0000062130  129.0000062130  129.0000062130 
+      73  243.5356790969 2820.1337977544 2146689.3101700447 2639.1723394661  318.6980246193 6053955548.7824945450  129.0000062130  129.0000062130  129.0000062130 
-      74  243.5479180498 2820.1331964183 2146689.3187275808 2639.1473868749  318.7140408766 6053954286.7515821457  129.0000063844  129.0000063844  129.0000063844 
+      74  243.5479180498 2820.1331964183 2146689.3187275808 2639.1473868749  318.7140408766 6053954282.0339813232  129.0000063844  129.0000063844  129.0000063844 
-      75  243.7115573025 2820.2314361523 2146689.3274016059 2639.1220411207  318.9281840641 6054165201.5909118652  129.0000065581  129.0000065581  129.0000065581 
+      75  243.7115573025 2820.2314361523 2146689.3274016059 2639.1220411207  318.9281840641 6054165196.6845111847  129.0000065581  129.0000065581  129.0000065581 
-      76  243.7457279618 2820.2454531429 2146689.3361921217 2639.0963868224  318.9729008040 6054195316.5254154205  129.0000067342  129.0000067342  129.0000067342 
+      76  243.7457279618 2820.2454531429 2146689.3361921217 2639.0963868224  318.9729008040 6054195311.5999307632  129.0000067342  129.0000067342  129.0000067342 
-      77  243.8345031069 2820.2948644965 2146689.3450991292 2639.0700900389  319.0890745962 6054301412.5615310669  129.0000069126  129.0000069126  129.0000069126 
+      77  243.8345031069 2820.2948644965 2146689.3450991292 2639.0700900389  319.0890745962 6054301407.5461502075  129.0000069126  129.0000069126  129.0000069126 
-      78  244.0193931195 2820.4067881628 2146689.3541226317 2639.0435094409  319.3310271594 6054541703.5689058304  129.0000070934  129.0000070934  129.0000070934 
+      78  244.0193931195 2820.4067881628 2146689.3541226317 2639.0435094409  319.3310271594 6054541698.3381366730  129.0000070934  129.0000070934  129.0000070934 
-      79  243.9919100078 2820.3799166166 2146689.3632626338 2639.0164249037  319.2950619430 6054484044.4218587875  129.0000072765  129.0000072765  129.0000072765 
+      79  243.9919100078 2820.3799166166 2146689.3632626338 2639.0164249037  319.2950619430 6054484039.2541246414  129.0000072765  129.0000072765  129.0000072765 
-      80  244.0965612207 2820.4387335935 2146689.3725191355 2638.9888176882  319.4320116291 6054610332.4174261093  129.0000074619  129.0000074619  129.0000074619 
+      80  244.0965612207 2820.4387335935 2146689.3725191355 2638.9888176882  319.4320116291 6054610327.1403293610  129.0000074619  129.0000074619  129.0000074619 
-      81  244.1334315951 2820.4535208568 2146689.3818921377 2638.9608330195  319.4802612965 6054642102.5347270966  129.0000076496  129.0000076496  129.0000076496 
+      81  244.1334315951 2820.4535208568 2146689.3818921377 2638.9608330195  319.4802612965 6054642097.2373485565  129.0000076496  129.0000076496  129.0000076496 
-      82  244.3029520408 2820.5543485196 2146689.3913816395 2638.9318525796  319.7021007878 6054858575.1664342880  129.0000078397  129.0000078397  129.0000078397 
+      82  244.3029520408 2820.5543485196 2146689.3913816395 2638.9318525796  319.7021007878 6054858569.6761827469  129.0000078397  129.0000078397  129.0000078397 
-      83  244.3445761189 2820.5713690935 2146689.4009876498 2638.9021684795  319.7565712929 6054895140.1710596085  129.0000080321  129.0000080321  129.0000080321 
+      83  244.3445761189 2820.5713690935 2146689.4009876498 2638.9021684795  319.7565712929 6054895134.6560049057  129.0000080321  129.0000080321  129.0000080321 
-      84  244.2696671559 2820.5125763350 2146689.4107101629 2638.8720941742  319.6585431986 6054768957.6739044189  129.0000082269  129.0000082269  129.0000082269 
+      84  244.2696671559 2820.5125763350 2146689.4107101629 2638.8720941742  319.6585431986 6054768952.2869329453  129.0000082269  129.0000082269  129.0000082269 
-      85  244.5161919319 2820.6629431352 2146689.4205491822 2638.8415194387  319.9811528443 6055091776.5361995697  129.0000084240  129.0000084240  129.0000084240 
+      85  244.5161919319 2820.6629431352 2146689.4205491822 2638.8415194387  319.9811528443 6055091770.8571672440  129.0000084240  129.0000084240  129.0000084240 
-      86  244.5641090282 2820.6838080201 2146689.4305047127 2638.8103612394  320.0438585800 6055136595.0767974854  129.0000086234  129.0000086234  129.0000086234 
+      86  244.5641090282 2820.6838080201 2146689.4305047127 2638.8103612394  320.0438585800 6055136589.3662166595  129.0000086234  129.0000086234  129.0000086234 
-      87  244.5348240638 2820.6541129118 2146689.4405767513 2638.7789728309  320.0055354056 6055072877.2416200638  129.0000088251  129.0000088251  129.0000088251 
+      87  244.5348240638 2820.6541129118 2146689.4405767513 2638.7789728309  320.0055354056 6055072871.6007261276  129.0000088251  129.0000088251  129.0000088251 
-      88  244.6939431427 2820.7468233396 2146689.4507653015 2638.7470269267  320.2137633592 6055271926.6536149979  129.0000090292  129.0000090292  129.0000090292 
+      88  244.6939431427 2820.7468233396 2146689.4507653015 2638.7470269267  320.2137633592 6055271920.8364210129  129.0000090292  129.0000090292  129.0000090292 
-      89  244.8800201091 2820.8567117003 2146689.4610703662 2638.7147520097  320.4572692055 6055507852.1186332703  129.0000092356  129.0000092356  129.0000092356 
+      89  244.8800201091 2820.8567117003 2146689.4610703662 2638.7147520097  320.4572692055 6055507846.0901927948  129.0000092356  129.0000092356  129.0000092356 
-      90  244.8804280382 2820.8451141876 2146689.4714919478 2638.6820441173  320.4578030336 6055482985.2258749008  129.0000094444  129.0000094444  129.0000094444 
+      90  244.8804280382 2820.8451141876 2146689.4714919478 2638.6820441173  320.4578030336 6055482979.2295818329  129.0000094444  129.0000094444  129.0000094444 
-      91  244.9558851986 2820.8815975090 2146689.4820300462 2638.6491836104  320.5565485155 6055561333.3803453445  129.0000096555  129.0000096555  129.0000096555 
+      91  244.9558851986 2820.8815975090 2146689.4820300462 2638.6491836104  320.5565485155 6055561327.3181543350  129.0000096555  129.0000096555  129.0000096555 
-      92  244.9965893140 2820.8949614294 2146689.4926846647 2638.6159817170  320.6098151301 6055590051.6433181763  129.0000098689  129.0000098689  129.0000098689 
+      92  244.9965893140 2820.8949614294 2146689.4926846647 2638.6159817170  320.6098151301 6055590045.5610351562  129.0000098689  129.0000098689  129.0000098689 
-      93  245.1381056687 2820.9732811388 2146689.5034558061 2638.5824451870  320.7950076360 6055758210.2774200439  129.0000100846  129.0000100846  129.0000100846 
+      93  245.1381056687 2820.9732811388 2146689.5034558061 2638.5824451870  320.7950076360 6055758204.0434722900  129.0000100846  129.0000100846  129.0000100846 
-      94  245.2954807041 2821.0619342131 2146689.5143434699 2638.5485198222  321.0009532826 6055948551.7882709503  129.0000103027  129.0000103027  129.0000103027 
+      94  245.2954807041 2821.0619342131 2146689.5143434699 2638.5485198222  321.0009532826 6055948545.3822879791  129.0000103027  129.0000103027  129.0000103027 
-      95  245.3535822199 2821.0860553731 2146689.5253476589 2638.5144817512  321.0769866522 6056000363.5151576996  129.0000105232  129.0000105232  129.0000105232 
+      95  245.3535822199 2821.0860553731 2146689.5253476589 2638.5144817512  321.0769866522 6056000357.0671482086  129.0000105232  129.0000105232  129.0000105232 
-      96  245.5013476026 2821.1682908185 2146689.5364683764 2638.4801107361  321.2703568219 6056176929.0169925690  129.0000107459  129.0000107459  129.0000107459 
+      96  245.5013476026 2821.1682908185 2146689.5364683764 2638.4801107361  321.2703568219 6056176922.4099712372  129.0000107459  129.0000107459  129.0000107459 
-      97  245.4166531417 2821.0989038023 2146689.5477056229 2638.4453663061  321.1595231342 6056028008.1910057068  129.0000109710  129.0000109710  129.0000109710 
+      97  245.4166531417 2821.0989038023 2146689.5477056229 2638.4453663061  321.1595231342 6056028001.7295455933  129.0000109710  129.0000109710  129.0000109710 
-      98  245.4121937790 2821.0817490953 2146689.5590593945 2638.4097762390  321.1536874797 6055991214.3494396210  129.0000111984  129.0000111984  129.0000111984 
+      98  245.4121937790 2821.0817490953 2146689.5590593945 2638.4097762390  321.1536874797 6055991207.9293851852  129.0000111984  129.0000111984  129.0000111984 
-      99  245.4532592994 2821.0946353191 2146689.5705296928 2638.3738037546  321.2074270397 6056018909.4480972290  129.0000114282  129.0000114282  129.0000114282 
+      99  245.4532592994 2821.0946353191 2146689.5705296928 2638.3738037546  321.2074270397 6056018903.0102539062  129.0000114282  129.0000114282  129.0000114282 
-     100  245.7500657390 2821.2735939427 2146689.5821165247 2638.3375549051  321.5958367642 6056403111.1006488800  129.0000116603  129.0000116603  129.0000116603 
+     100  245.7500657390 2821.2735939427 2146689.5821165247 2638.3375549051  321.5958367642 6056403104.3106222153  129.0000116603  129.0000116603  129.0000116603 
-Loop time of 4.05006 on 1 procs for 100 steps with 10125 atoms
+Loop time of 5.22601 on 1 procs for 100 steps with 10125 atoms
-Performance: 2.133 ns/day, 11.250 hours/ns, 24.691 timesteps/s
+Performance: 1.653 ns/day, 14.517 hours/ns, 19.135 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
+99.7% CPU use with 1 MPI tasks x no OpenMP threads
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.46587    | 0.46587    | 0.46587    |   0.0 | 11.50
+Pair    | 0.44045    | 0.44045    | 0.44045    |   0.0 |  8.43
-Neigh   | 1.4713     | 1.4713     | 1.4713     |   0.0 | 36.33
+Neigh   | 2.669      | 2.669      | 2.669      |   0.0 | 51.07
-Comm    | 0.05567    | 0.05567    | 0.05567    |   0.0 |  1.37
+Comm    | 0.056143   | 0.056143   | 0.056143   |   0.0 |  1.07
-Output  | 0.011364   | 0.011364   | 0.011364   |   0.0 |  0.28
+Output  | 0.012469   | 0.012469   | 0.012469   |   0.0 |  0.24
-Modify  | 2.0158     | 2.0158     | 2.0158     |   0.0 | 49.77
+Modify  | 2.0163     | 2.0163     | 2.0163     |   0.0 | 38.58
-Other   |            | 0.03004    |            |       |  0.74
+Other   |            | 0.03168    |            |       |  0.61
 Nlocal:    10125 ave 10125 max 10125 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -172,4 +180,4 @@ Dangerous builds not checked
 Please see the log.cite file for references relevant to this simulation
-Total wall time: 0:00:04
+Total wall time: 0:00:05
--- a/examples/USER/dpd/dpdrx-shardlow/in.dpdrx-shardlow
+++ b/examples/USER/dpd/dpdrx-shardlow/in.dpdrx-shardlow
@ -37,7 +37,7 @@ timestep        0.001
 pair_style      hybrid/overlay dpd/fdt/energy 16.00 234324 exp6/rx 16.00
 pair_coeff      * * dpd/fdt/energy 0.0 0.05 10.0 16.00
-pair_coeff      * * exp6/rx params.exp6 1fluid 1fluid 1.0 1.0 16.00
+pair_coeff      * * exp6/rx params.exp6 1fluid 1fluid exponent 1.0 1.0 16.00
 fix             1 all shardlow
 fix             2 all nve
--- a/examples/USER/dpd/dpdrx-shardlow/log.dpdrx-shardlow.reference
+++ b/examples/USER/dpd/dpdrx-shardlow/log.dpdrx-shardlow.reference
@ -48,7 +48,7 @@ timestep        0.001
 pair_style      hybrid/overlay dpd/fdt/energy 16.00 234324 exp6/rx 16.00
 pair_coeff      * * dpd/fdt/energy 0.0 0.05 10.0 16.00
-pair_coeff      * * exp6/rx params.exp6 1fluid 1fluid 1.0 1.0 16.00
+pair_coeff      * * exp6/rx params.exp6 1fluid 1fluid exponent 1.0 1.0 16.00
 fix             1 all shardlow
 fix             2 all nve
@ -69,39 +69,51 @@ dump_modify     2 sort id
 run             10
 Neighbor list info ...
  2 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 18
  ghost atom cutoff = 18
-  binsize = 9 -> bins = 8 8 5
+  binsize = 9, bins = 8 8 5
-Memory usage per processor = 6.52436 Mbytes
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
  (1) pair dpd/fdt/energy, perpetual
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
  (2) pair exp6/rx, perpetual, copy from (1)
      pair build: copy
      stencil: none
      bin: none
  (3) fix shardlow, perpetual, ssa
      pair build: half/bin/newton/ssa
      stencil: half/bin/3d/newton/ssa
      bin: ssa
 Memory usage per processor = 8.39564 Mbytes
 Step Temp Press Volume PotEng KinEng c_dpdU[1] c_dpdU[2] c_dpdU[3] v_totEnergy c_dpdU[4] 
-       0   2065.00000000   1368.17463335 179834.51777865      0.00000000    230.35385810   3841.42393279   3841.42393279      0.00000000   7682.84786557   2065.00000000 
+       0   2065.00000000   1368.17463335 179834.51777865      0.00000000    230.35385810      0.00000000   7682.84786557      0.00000000   7682.84786557   2065.00000000 
-       1   2064.93210437   1368.12964881 179834.51777865      0.00000000    230.34628424   3841.42393279   3841.43150665      0.00000000   7682.85543943   2065.20275230 
+       1   2064.93210437   1368.12964881 179834.51777865      0.00000000    230.34628424      0.00000000   7682.85543943      0.00000000   7682.85543943   2065.20275230 
-       2   2067.82089565   1370.04362990 179834.51777865     -0.00000000    230.66853326   3841.42393279   3841.10925763      0.00000000   7682.53319042   2065.32453473 
+       2   2067.82089565   1370.04362990 179834.51777865     -0.00000000    230.66853326      0.00000000   7682.53319042      0.00000000   7682.53319042   2065.32453473 
-       3   2070.45225169   1371.78704616 179834.51777865     -0.00000000    230.96206499   3841.42393279   3840.81572590      0.00000000   7682.23965869   2065.45336917 
+       3   2070.45225169   1371.78704616 179834.51777865     -0.00000000    230.96206499      0.00000000   7682.23965869      0.00000000   7682.23965869   2065.45336917 
-       4   2075.00241157   1374.80177416 179834.51777865     -0.00000000    231.46964217   3841.42393279   3840.30814872      0.00000000   7681.73208151   2065.52973333 
+       4   2075.00241157   1374.80177416 179834.51777865     -0.00000000    231.46964217      0.00000000   7681.73208151      0.00000000   7681.73208151   2065.52973333 
-       5   2073.96509212   1374.11449370 179834.51777865     -0.00000000    231.35392762   3841.42393279   3840.42386327      0.00000000   7681.84779605   2065.76011517 
+       5   2073.96509212   1374.11449370 179834.51777865     -0.00000000    231.35392762     -0.00000000   7681.84779605      0.00000000   7681.84779605   2065.76011517 
-       6   2074.26516936   1374.31331117 179834.51777865     -0.00000000    231.38740169   3841.42393279   3840.39038920      0.00000000   7681.81432198   2065.95399323 
+       6   2074.26516936   1374.31331117 179834.51777865     -0.00000000    231.38740169     -0.00000000   7681.81432198      0.00000000   7681.81432198   2065.95399323 
-       7   2071.41069700   1372.42206822 179834.51777865     -0.00000000    231.06898100   3841.42393279   3840.70880989      0.00000000   7682.13274267   2066.23407076 
+       7   2071.41069700   1372.42206822 179834.51777865     -0.00000000    231.06898100     -0.00000000   7682.13274267      0.00000000   7682.13274267   2066.23407076 
-       8   2071.35844957   1372.38745146 179834.51777865     -0.00000000    231.06315272   3841.42393279   3840.71463817      0.00000000   7682.13857095   2066.43766287 
+       8   2071.35844957   1372.38745146 179834.51777865     -0.00000000    231.06315272      0.00000000   7682.13857095      0.00000000   7682.13857095   2066.43766287 
-       9   2071.35676496   1372.38633532 179834.51777865     -0.00000000    231.06296480   3841.42393279   3840.71482609      0.00000000   7682.13875887   2066.64001166 
+       9   2071.35676496   1372.38633532 179834.51777865     -0.00000000    231.06296480      0.00000000   7682.13875887      0.00000000   7682.13875887   2066.64001166 
-      10   2066.53172340   1369.18948328 179834.51777865     -0.00000000    230.52472415   3841.42393279   3841.25306673      0.00000000   7682.67699952   2066.97516855 
+      10   2066.53172340   1369.18948328 179834.51777865     -0.00000000    230.52472415      0.00000000   7682.67699952      0.00000000   7682.67699952   2066.97516855 
-Loop time of 0.289778 on 1 procs for 10 steps with 864 atoms
+Loop time of 0.611304 on 1 procs for 10 steps with 864 atoms
-Performance: 2.982 ns/day, 8.049 hours/ns, 34.509 timesteps/s
+Performance: 1.413 ns/day, 16.981 hours/ns, 16.358 timesteps/s
-99.4% CPU use with 1 MPI tasks x no OpenMP threads
+98.2% CPU use with 1 MPI tasks x no OpenMP threads
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.16405    | 0.16405    | 0.16405    |   0.0 | 56.61
+Pair    | 0.34177    | 0.34177    | 0.34177    |   0.0 | 55.91
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.00066328 | 0.00066328 | 0.00066328 |   0.0 |  0.23
+Comm    | 0.0013342  | 0.0013342  | 0.0013342  |   0.0 |  0.22
-Output  | 0.037718   | 0.037718   | 0.037718   |   0.0 | 13.02
+Output  | 0.083583   | 0.083583   | 0.083583   |   0.0 | 13.67
-Modify  | 0.087281   | 0.087281   | 0.087281   |   0.0 | 30.12
+Modify  | 0.18451    | 0.18451    | 0.18451    |   0.0 | 30.18
-Other   |            | 7.057e-05  |            |       |  0.02
+Other   |            | 0.0001087  |            |       |  0.02
 Nlocal:    864 ave 864 max 864 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
--- a/examples/USER/misc/basal/in.basal
+++ b/examples/USER/misc/basal/in.basal
@ -1,163 +1,163 @@
-############################################################################
+############################################################################
-# Input file for investigating twinning nucleation under uniaxial loading with basal plane vector analysis
+# Input file for investigating twinning nucleation under uniaxial loading with basal plane vector analysis
-# Christopher Barrett, March 2013
+# Christopher Barrett, March 2013
-# This script requires a Mg pair potential file to be in the same directory.
+# This script requires a Mg pair potential file to be in the same directory.
-
+
-# fname is the file name.  It is necessary for loops to work correctly. (See jump command)
+# fname is the file name.  It is necessary for loops to work correctly. (See jump command)
-variable fname index in.basal
+variable fname index in.basal
-
+
-######################################
+######################################
-# POTENTIAL VARIABLES
+# POTENTIAL VARIABLES
-# lattice parameters and the minimum energy per atom which should be obtained with the current pair potential and homogeneous lattice
+# lattice parameters and the minimum energy per atom which should be obtained with the current pair potential and homogeneous lattice
-variable lx equal 3.181269601 
+variable lx equal 3.181269601 
-variable b equal sqrt(3)
+variable b equal sqrt(3)
-variable c equal sqrt(8/3)
+variable c equal sqrt(8/3)
-variable ly equal ${b}*${lx}
+variable ly equal ${b}*${lx}
-variable lz equal ${c}*${lx}
+variable lz equal ${c}*${lx}
-variable pairlocation index almg.liu
+variable pairlocation index almg.liu
-variable pairstyle index eam/alloy/opt
+variable pairstyle index eam/alloy/opt
-
+
-######################################
+######################################
-# EQUILIBRATION/DEFORMATION VARIABLES
+# EQUILIBRATION/DEFORMATION VARIABLES
-# eqpress = 10 bar = 1 MPa
+# eqpress = 10 bar = 1 MPa
-# tstep (the timestep) is set to a default value of 0.001 (1 fs) 
+# tstep (the timestep) is set to a default value of 0.001 (1 fs) 
-# seed randomizes the velocity
+# seed randomizes the velocity
-# srate is the rate of strain in 1/s
+# srate is the rate of strain in 1/s
-# Ndump is the number of timesteps in between each dump of the atom coordinates
+# Ndump is the number of timesteps in between each dump of the atom coordinates
-variable tstep equal 0.001
+variable tstep equal 0.001
-variable seed equal 95812384
+variable seed equal 95812384
-variable srate equal 1e9
+variable srate equal 1e9
-
+
-######################################
+######################################
-# INITIALIZATION
+# INITIALIZATION
-units 		metal
+units 		metal
-dimension		3
+dimension		3
-boundary		s	s	s
+boundary		s	s	s
-atom_style		atomic
+atom_style		atomic
-
+
-######################################
+######################################
-# ATOM BUILD
+# ATOM BUILD
-atom_modify map array
+atom_modify map array
-
+
-# lattice custom scale a1 "coordinates of a1" a2 "coordinates of a2" a3 "coordinates of a3" basis "atom1 coordinates" basis "atom2 coordinates" basis "atom3 coordinates" basis "atom4 coordinates" orient x "crystallagraphic orientation of x axis" orient y "crystallagraphic orientation of y axis" z "crystallagraphic orientation of z axis"
+# lattice custom scale a1 "coordinates of a1" a2 "coordinates of a2" a3 "coordinates of a3" basis "atom1 coordinates" basis "atom2 coordinates" basis "atom3 coordinates" basis "atom4 coordinates" orient x "crystallagraphic orientation of x axis" orient y "crystallagraphic orientation of y axis" z "crystallagraphic orientation of z axis"
-lattice custom 3.181269601 a1 1 0 0 a2 0 1.732050808 0 a3 0 0 1.632993162 basis 0.0 0.0 0.0 basis 0.5 0.5 0 basis 0 0.3333333 0.5 basis 0.5 0.833333 0.5 orient x 0 1 1 orient y 1 0 0 orient z 0 1 -1
+lattice custom 3.181269601 a1 1 0 0 a2 0 1.732050808 0 a3 0 0 1.632993162 basis 0.0 0.0 0.0 basis 0.5 0.5 0 basis 0 0.3333333 0.5 basis 0.5 0.833333 0.5 orient x 0 1 1 orient y 1 0 0 orient z 0 1 -1
-variable multiple equal 20
+variable multiple equal 20
-variable mx equal "v_lx*v_multiple"
+variable mx equal "v_lx*v_multiple"
-variable my equal "v_ly*v_multiple"
+variable my equal "v_ly*v_multiple"
-variable mz equal "v_lz*v_multiple"
+variable mz equal "v_lz*v_multiple"
-
+
-# the simulation region should be from 0 to a multiple of the periodic boundary in x, y and z.
+# the simulation region should be from 0 to a multiple of the periodic boundary in x, y and z.
-region		whole block 0 ${mz} 0 ${mx} 0 ${my} units box 
+region		whole block 0 ${mz} 0 ${mx} 0 ${my} units box 
-create_box		2 whole
+create_box		2 whole
-create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 1 
+create_atoms 1 box basis 1 1 basis 2 1 basis 3 1 basis 4 1 
-
+
-region fixed1 block INF INF INF INF INF 10 units box
+region fixed1 block INF INF INF INF INF 10 units box
-region fixed2 block INF INF INF INF  100 INF units box
+region fixed2 block INF INF INF INF  100 INF units box
-group lower region fixed1
+group lower region fixed1
-group upper region fixed2
+group upper region fixed2
-group boundary union upper lower
+group boundary union upper lower
-group mobile subtract all boundary
+group mobile subtract all boundary
-
+
-variable natoms equal "count(all)"
+variable natoms equal "count(all)"
-print "# of atoms are: ${natoms}"
+print "# of atoms are: ${natoms}"
-
+
-######################################
+######################################
-# INTERATOMIC POTENTIAL
+# INTERATOMIC POTENTIAL
-pair_style	${pairstyle}
+pair_style	${pairstyle}
-pair_coeff	* * ${pairlocation} Mg Mg
+pair_coeff	* * ${pairlocation} Mg Mg
-
+
-######################################
+######################################
-# COMPUTES REQUIRED
+# COMPUTES REQUIRED
-compute csym all centro/atom 12
+compute csym all centro/atom 12
-compute eng all pe/atom
+compute eng all pe/atom
-compute eatoms all reduce sum c_eng
+compute eatoms all reduce sum c_eng
-compute basal all basal/atom
+compute basal all basal/atom
-
+
-######################################
+######################################
-# MINIMIZATION
+# MINIMIZATION
-# Primarily adjusts the c/a ratio to value predicted by EAM potential
+# Primarily adjusts the c/a ratio to value predicted by EAM potential
-reset_timestep	0
+reset_timestep	0
-thermo 1
+thermo 1
-thermo_style custom step pe c_eatoms
+thermo_style custom step pe c_eatoms
-min_style cg
+min_style cg
-minimize	1e-15 1e-15 1000 2000
+minimize	1e-15 1e-15 1000 2000
-variable eminimum equal "c_eatoms / count(all)"
+variable eminimum equal "c_eatoms / count(all)"
-print "%%e(it,1)=${eminimum}"
+print "%%e(it,1)=${eminimum}"
-
+
-######################################
+######################################
-# EQUILIBRATION
+# EQUILIBRATION
-reset_timestep	0
+reset_timestep	0
-timestep ${tstep}
+timestep ${tstep}
-# atoms are given a random velocity based on a temperature of 100K.
+# atoms are given a random velocity based on a temperature of 100K.
-velocity all create 100 ${seed} mom yes rot no
+velocity all create 100 ${seed} mom yes rot no
-
+
-# temperature and pressure are set to 100 and 0
+# temperature and pressure are set to 100 and 0
-fix 1 all nve
+fix 1 all nve
-
+
-# Set thermo output
+# Set thermo output
-thermo 100
+thermo 100
-thermo_style custom step lx ly lz press pxx pyy pzz pe temp
+thermo_style custom step lx ly lz press pxx pyy pzz pe temp
-
+
-# Run for at least 2 picosecond (assuming 1 fs timestep)
+# Run for at least 2 picosecond (assuming 1 fs timestep)
-run 2000
+run 2000
-
+
-# Loop to run until pressure is below the variable eqpress (defined at beginning of file)
+# Loop to run until pressure is below the variable eqpress (defined at beginning of file)
-label loopeq 
+label loopeq 
-variable eq loop 100 
+variable eq loop 100 
-run 250
+run 250
-variable converge equal press
+variable converge equal press
-if "${converge} <= 0" then "variable converge equal -press" else "variable converge equal press" 
+if "${converge} <= 0" then "variable converge equal -press" else "variable converge equal press" 
-if "${converge} <= 50" then "jump ${fname} breakeq" 
+if "${converge} <= 50" then "jump ${fname} breakeq" 
-next eq 
+next eq 
-jump ${fname} loopeq 
+jump ${fname} loopeq 
-label breakeq 
+label breakeq 
-
+
-# Store length for strain rate calculations
+# Store length for strain rate calculations
-variable tmp equal "lx"
+variable tmp equal "lx"
-variable L0 equal ${tmp}
+variable L0 equal ${tmp}
-print "Initial Length, L0: ${L0}"
+print "Initial Length, L0: ${L0}"
-unfix 1
+unfix 1
-
+
-######################################
+######################################
-# DEFORMATION
+# DEFORMATION
-reset_timestep	0
+reset_timestep	0
-timestep ${tstep}
+timestep ${tstep}
-
+
-# Impose constant strain rate 
+# Impose constant strain rate 
-variable srate1 equal "v_srate / 1.0e10"
+variable srate1 equal "v_srate / 1.0e10"
-velocity	upper set 0.0 NULL 0.0 units box
+velocity	upper set 0.0 NULL 0.0 units box
-velocity        lower set 0.0 NULL 0.0 units box
+velocity        lower set 0.0 NULL 0.0 units box
-
+
-fix 2 upper setforce 0.0 NULL 0.0
+fix 2 upper setforce 0.0 NULL 0.0
-fix 3 lower setforce 0.0 NULL 0.0
+fix 3 lower setforce 0.0 NULL 0.0
-fix 1 all nve
+fix 1 all nve
-
+
-# Output strain and stress info to file
+# Output strain and stress info to file
-# for units metal, pressure is in [bars] = 100 [kPa] = 1/10000 [GPa]
+# for units metal, pressure is in [bars] = 100 [kPa] = 1/10000 [GPa]
-# p2 is in GPa
+# p2 is in GPa
-variable strain equal "(lx - v_L0)/v_L0"
+variable strain equal "(lx - v_L0)/v_L0"
-variable p1 equal "v_strain"
+variable p1 equal "v_strain"
-variable p2 equal "-pxz/10000"
+variable p2 equal "-pxz/10000"
-variable p3 equal "lx"
+variable p3 equal "lx"
-variable p4 equal "temp"
+variable p4 equal "temp"
-variable p5 equal "pe"
+variable p5 equal "pe"
-variable p6 equal "ke"
+variable p6 equal "ke"
-fix def1 all print 100 "${p1} ${p2} ${p3} ${p4} ${p5} ${p6}" file output.def1.txt screen no
+fix def1 all print 100 "${p1} ${p2} ${p3} ${p4} ${p5} ${p6}" file output.def1.txt screen no
-# Dump coordinates to file (for void size calculations)
+# Dump coordinates to file (for void size calculations)
-dump 		1 all custom 1000 output.dump.* id x y z c_basal[1] c_basal[2] c_basal[3]
+dump 		1 all custom 1000 output.dump.* id x y z c_basal[1] c_basal[2] c_basal[3]
-
+
-# Display thermo
+# Display thermo
-thermo_style	custom step v_strain pxz lx temp pe ke
+thermo_style	custom step v_strain pxz lx temp pe ke
-restart 50000 output.restart
+restart 50000 output.restart
-
+
-# run deformation for 100000 timesteps (10% strain assuming 1 fs timestep and 1e9/s strainrate)
+# run deformation for 100000 timesteps (10% strain assuming 1 fs timestep and 1e9/s strainrate)
-variable runtime equal 0
+variable runtime equal 0
-label loop
+label loop
-displace_atoms	all ramp x 0.0 ${srate1} z 10 100 units box
+displace_atoms	all ramp x 0.0 ${srate1} z 10 100 units box
-run		100
+run		100
-variable runtime equal ${runtime}+100
+variable runtime equal ${runtime}+100
-if "${runtime} < 100000" then "jump ${fname} loop"
+if "${runtime} < 100000" then "jump ${fname} loop"
-
+
-######################################
+######################################
-# SIMULATION DONE
+# SIMULATION DONE
-print "All done"
+print "All done"
--- a/examples/USER/misc/srp/in.srp
+++ b/examples/USER/misc/srp/in.srp
@ -15,6 +15,7 @@ bond_style      harmonic
 bond_coeff      * 225.0 0.85
 comm_modify vel yes
 comm_modify cutoff 3.6
 # must use pair hybrid, since srp bond particles
 # do not interact with other atoms types
--- a/examples/mscg/README
+++ b/examples/mscg/README
@ -0,0 +1,10 @@
 Running this example requires that LAMMPS be built with the MSCG
 package and its fix mscg command.  The fix uses the Multi-Scale
 Coarse-Graining (MS-CG) library, freely available at
 https://github.com/uchicago-voth/MSCG-release, to compute optimized
 coarse-grained force field parameters.  The MS-CG library was
 developed by Jacob Wagner in Greg Voth's group at the University of
 Chicago.
 See the lib/mscg/README file for instructions on how to download and
 install the MS-CG library for use with LAMMPS.
--- a/examples/mscg/control.in
+++ b/examples/mscg/control.in
@ -0,0 +1,12 @@
 block_size 1
 start_frame 1
 n_frames 19
 nonbonded_cutoff 10.0
 basis_type 0
 primary_output_style 0
 output_solution_flag 1
 output_spline_coeffs_flag 1
 pair_nonbonded_bspline_basis_order 6
 pair_nonbonded_basis_set_resolution 0.7
 pair_nonbonded_output_binwidth 0.1
 matrix_type 0
--- a/examples/mscg/data.meoh
+++ b/examples/mscg/data.meoh
--- a/examples/mscg/dump.meoh
+++ b/examples/mscg/dump.meoh
--- a/examples/mscg/in.mscg
+++ b/examples/mscg/in.mscg
@ -0,0 +1,22 @@
 units real
 atom_style full
 pair_style zero 10.0
 read_data data.meoh
 pair_coeff * *
 thermo 1
 thermo_style custom step
 # Test 1a: range finder functionality
 fix 1 all mscg 1 range on
 rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
 print "TEST_1a mscg range finder"
 unfix 1
 # Test 1b: force matching functionality
 fix 1 all mscg 1
 rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
 print "TEST_1b mscg force matching"
 print TEST_DONE
--- a/examples/mscg/output_9Jan17/1_1.dat
+++ b/examples/mscg/output_9Jan17/1_1.dat
@ -0,0 +1,77 @@
 2.500000 5.670970817963099e+02
 2.600000 2.404059283529051e+02
 2.700000 9.157060823529977e+01
 2.800000 3.428273061369140e+01
 2.900000 1.619868149395266e+01
 3.000000 1.039607214301755e+01
 3.100000 6.830187514267188e+00
 3.200000 3.861970842349535e+00
 3.300000 1.645948643278161e+00
 3.400000 2.395428971623918e-01
 3.500000 -4.276763637833773e-01
 3.600000 -5.132022977965877e-01
 3.700000 -2.208024961234051e-01
 3.800000 2.402697744243800e-01
 3.900000 6.956064296165573e-01
 4.000000 1.034070044257954e+00
 4.100000 1.205997975111669e+00
 4.200000 1.209501102128581e+00
 4.300000 1.076304670380924e+00
 4.400000 8.575891319958883e-01
 4.500000 6.098309880892070e-01
 4.600000 3.807992942746473e-01
 4.700000 1.995994191469442e-01
 4.800000 7.699059877424269e-02
 4.900000 9.750744163981299e-03
 5.000000 -1.480308769532222e-02
 5.100000 -1.429422279228416e-02
 5.200000 -6.765899050869768e-03
 5.300000 -6.214398421078919e-03
 5.400000 -1.951586041390797e-02
 5.500000 -4.689090237947263e-02
 5.600000 -8.376292122940529e-02
 5.700000 -1.226699982917263e-01
 5.800000 -1.551768041657136e-01
 5.900000 -1.737865035767736e-01
 6.000000 -1.738272491408507e-01
 6.100000 -1.546779867768825e-01
 6.200000 -1.193171291488982e-01
 6.300000 -7.321054075616322e-02
 6.400000 -2.317411193286228e-02
 6.500000 2.376366715221714e-02
 6.600000 6.149913249600215e-02
 6.700000 8.597538938112201e-02
 6.800000 9.590170060736655e-02
 6.900000 9.245100462148878e-02
 7.000000 7.855487875847664e-02
 7.100000 5.818301960249692e-02
 7.200000 3.562272334783877e-02
 7.300000 1.475836615985744e-02
 7.400000 -1.639617536128255e-03
 7.500000 -1.237881063914745e-02
 7.600000 -1.768202571195587e-02
 7.700000 -1.877757119362295e-02
 7.800000 -1.748001968416543e-02
 7.900000 -1.577097622918088e-02
 8.000000 -1.537984660448136e-02
 8.100000 -1.737044400054951e-02
 8.200000 -2.187939410237979e-02
 8.300000 -2.823987455760605e-02
 8.400000 -3.525715284001425e-02
 8.500000 -4.148996251287761e-02
 8.600000 -4.553187949229211e-02
 8.700000 -4.629269831051163e-02
 8.800000 -4.327548798226762e-02
 8.900000 -3.674131754868225e-02
 9.000000 -2.758883541814894e-02
 9.100000 -1.712151838480657e-02
 9.200000 -6.810600249997737e-03
 9.300000 1.941999556272785e-03
 9.400000 8.040747353879739e-03
 9.500000 1.092691524686838e-02
 9.600000 1.063606620723048e-02
 9.700000 7.416550438142138e-03
 9.800000 1.175066786686231e-03
 9.900000 -9.084427187675534e-03
 10.000000 -2.582180514463068e-02
 10.100000 -5.352186189454393e-02
--- a/examples/mscg/output_9Jan17/1_1.table
+++ b/examples/mscg/output_9Jan17/1_1.table
@ -0,0 +1,82 @@
 # Header information on force file
 1_1
 N 77 R 2.500000 10.100000
 1 2.500000 69.428523 567.097082
 2 2.600000 29.053372 240.405928
 3 2.700000 12.454545 91.570608
 4 2.800000 6.161878 34.282731
 5 2.900000 3.637808 16.198681
 6 3.000000 2.308070 10.396072
 7 3.100000 1.446757 6.830188
 8 3.200000 0.912149 3.861971
 9 3.300000 0.636753 1.645949
 10 3.400000 0.542478 0.239543
 11 3.500000 0.551885 -0.427676
 12 3.600000 0.598929 -0.513202
 13 3.700000 0.635629 -0.220802
 14 3.800000 0.634656 0.240270
 15 3.900000 0.587862 0.695606
 16 4.000000 0.501378 1.034070
 17 4.100000 0.389375 1.205998
 18 4.200000 0.268600 1.209501
 19 4.300000 0.154310 1.076305
 20 4.400000 0.057615 0.857589
 21 4.500000 -0.015756 0.609831
 22 4.600000 -0.065288 0.380799
 23 4.700000 -0.094307 0.199599
 24 4.800000 -0.108137 0.076991
 25 4.900000 -0.112474 0.009751
 26 5.000000 -0.112221 -0.014803
 27 5.100000 -0.110767 -0.014294
 28 5.200000 -0.109714 -0.006766
 29 5.300000 -0.109065 -0.006214
 30 5.400000 -0.107778 -0.019516
 31 5.500000 -0.104458 -0.046891
 32 5.600000 -0.097925 -0.083763
 33 5.700000 -0.087603 -0.122670
 34 5.800000 -0.073711 -0.155177
 35 5.900000 -0.057263 -0.173787
 36 6.000000 -0.039882 -0.173827
 37 6.100000 -0.023457 -0.154678
 38 6.200000 -0.009757 -0.119317
 39 6.300000 -0.000131 -0.073211
 40 6.400000 0.004688 -0.023174
 41 6.500000 0.004659 0.023764
 42 6.600000 0.000396 0.061499
 43 6.700000 -0.006978 0.085975
 44 6.800000 -0.016072 0.095902
 45 6.900000 -0.025489 0.092451
 46 7.000000 -0.034040 0.078555
 47 7.100000 -0.040877 0.058183
 48 7.200000 -0.045567 0.035623
 49 7.300000 -0.048086 0.014758
 50 7.400000 -0.048742 -0.001640
 51 7.500000 -0.048041 -0.012379
 52 7.600000 -0.046538 -0.017682
 53 7.700000 -0.044715 -0.018778
 54 7.800000 -0.042902 -0.017480
 55 7.900000 -0.041239 -0.015771
 56 8.000000 -0.039682 -0.015380
 57 8.100000 -0.038044 -0.017370
 58 8.200000 -0.036082 -0.021879
 59 8.300000 -0.033576 -0.028240
 60 8.400000 -0.030401 -0.035257
 61 8.500000 -0.026564 -0.041490
 62 8.600000 -0.022213 -0.045532
 63 8.700000 -0.017621 -0.046293
 64 8.800000 -0.013143 -0.043275
 65 8.900000 -0.009142 -0.036741
 66 9.000000 -0.005926 -0.027589
 67 9.100000 -0.003690 -0.017122
 68 9.200000 -0.002494 -0.006811
 69 9.300000 -0.002250 0.001942
 70 9.400000 -0.002749 0.008041
 71 9.500000 -0.003698 0.010927
 72 9.600000 -0.004776 0.010636
 73 9.700000 -0.005678 0.007417
 74 9.800000 -0.006108 0.001175
 75 9.900000 -0.005712 -0.009084
 76 10.000000 -0.003967 -0.025822
 77 10.100000 0.000000 -0.053522
--- a/examples/mscg/output_9Jan17/b-spline.out
+++ b/examples/mscg/output_9Jan17/b-spline.out
@ -0,0 +1,2 @@
 n: 1 1 6 12 2.400000000000002e+00 1.010000000000000e+01
 1.200460787805587e+03 2.169623423326193e+01 2.388396964379328e+01 -1.197754948555067e+01 6.472482422420378e+00 -1.483711824891365e+00 7.768139601662113e-01 -7.869494711740244e-01 4.830820182054661e-01 -1.892989444995645e-01 1.021275453070386e-01 -1.637649039972671e-01 5.570978712841167e-02 7.637188693695119e-03 -4.109175461195019e-03 -5.352186189455146e-02 
--- a/examples/mscg/output_9Jan17/rmin.in
+++ b/examples/mscg/output_9Jan17/rmin.in
@ -0,0 +1 @@
 1 1 2.852369 10.000000 fm
--- a/examples/mscg/output_9Jan17/rmin_b.in
+++ b/examples/mscg/output_9Jan17/rmin_b.in
--- a/examples/mscg/output_9Jan17/sol_info.out
+++ b/examples/mscg/output_9Jan17/sol_info.out
@ -0,0 +1,18 @@
 fm_matrix_rows:3000; fm_matrix_columns:16;
 Singular vector:
 2.442317e+00
 2.105009e+00
 1.433251e+00
 1.184602e+00
 9.739627e-01
 6.944898e-01
 5.376709e-01
 4.616070e-01
 3.257062e-01
 2.683729e-01
 1.530153e-01
 9.336288e-02
 5.042150e-02
 2.126912e-02
 1.446682e-02
 4.167763e-05
--- a/examples/mscg/output_9Jan17/x.out
+++ b/examples/mscg/output_9Jan17/x.out
@ -0,0 +1 @@
 <EFBFBD>-<2D><><EFBFBD><EFBFBD><EFBFBD>@47h<<3C>5@<40><><EFBFBD><EFBFBD>K<EFBFBD>7@<40>R<EFBFBD>]<5D><>'<27><><EFBFBD><EFBFBD>n<EFBFBD><6E>@݌I<DD8C>H<EFBFBD><48><EFBFBD><19>?<3F><><EFBFBD><EFBFBD>?r<>I<EFBFBD><49>.<2E><><11>^<5E><><EFBFBD><EFBFBD>?W<57><7F><EFBFBD>:ȿ(O<1D>%<25>?<3F>Ns<4E>?<3F>Ŀ<EFBFBD>:<3A>C<EFBFBD><43><EFBFBD>?<3F><><EFBFBD>:,H?<3F>}<7D>c<EFBFBD><63>p<EFBFBD><70><EFBFBD><EFBFBD><EFBFBD>7g<37><67>
--- a/examples/prd/in.prd
+++ b/examples/prd/in.prd
@ -78,7 +78,7 @@ run             100
 # only output atoms near vacancy
-compute coord all coord/atom $r
+compute coord all coord/atom cutoff $r
 #dump events all custom 1 dump.prd id type x y z
 #dump_modify events thresh c_coord != 4
--- a/examples/tad/in.tad
+++ b/examples/tad/in.tad
@ -80,7 +80,7 @@ velocity all zero linear
 # only output atoms near vacancy
-compute coord all coord/atom $r
+compute coord all coord/atom cutoff $r
 #dump events all custom 1 dump.prd id type x y z
 #dump_modify events thresh c_coord != 4
--- a/examples/voronoi/README
+++ b/examples/voronoi/README
@ -0,0 +1,10 @@
 Running this example requires that LAMMPS be built with the VORONOI
 package and its compute voronoi command.  The compute uses the Voro++
 library, freely available at http://math.lbl.gov/voro++, to compute
 the Voronoi tesselation locally on each processor.  Voro++ was
 developed by Chris H. Rycroft while at UC Berkeley / Lawrence Berkeley
 Laboratory.
 See the lib/voronoi/README file for instructions on how to download
 and install the Voro++ library for use with LAMMPS.
--- a/lib/README
+++ b/lib/README
@ -39,6 +39,8 @@ meam	      modified embedded atom method (MEAM) potential, MEAM package
                from Greg Wagner (Sandia)
 molfile       hooks to VMD molfile plugins, used by the USER-MOLFILE package
                from Axel Kohlmeyer (Temple U) and the VMD development team
 mscg          hooks to the MSCG library, used by fix_mscg command
                from Jacob Wagner and Greg Voth group (U Chicago)
 python        hooks to the system Python library, used by the PYTHON package
                from the LAMMPS development team
 qmmm	      quantum mechanics/molecular mechanics coupling interface
--- a/lib/colvars/Makefile.colvars
+++ b/lib/colvars/Makefile.colvars
@ -0,0 +1,119 @@
 # library build -*- makefile -*- for colvars module
 # which file will be copied to Makefile.lammps
 EXTRAMAKE = Makefile.lammps.empty
 # ------ SETTINGS ------
 CXX =		g++
 CXXFLAGS =	-O2 -g -Wall -fPIC -funroll-loops # -DCOLVARS_DEBUG
 ARCHIVE =	ar
 ARCHFLAG =	-rscv
 SHELL =		/bin/sh
 # ------ DEFINITIONS ------
 SRC = colvaratoms.cpp colvarbias_abf.cpp colvarbias_alb.cpp colvarbias.cpp  \
 colvarbias_histogram.cpp colvarbias_meta.cpp colvarbias_restraint.cpp      \
 colvarcomp_angles.cpp colvarcomp_coordnums.cpp colvarcomp.cpp              \
 colvarcomp_distances.cpp colvarcomp_protein.cpp colvarcomp_rotations.cpp   \
 colvardeps.cpp colvar.cpp colvargrid.cpp colvarmodule.cpp colvarparse.cpp  \
 colvarscript.cpp colvartypes.cpp colvarvalue.cpp
 LIB = libcolvars.a
 OBJ = $(SRC:.cpp=.o)
 EXE = #colvars_standalone
 # ------ MAKE PROCEDURE ------
 default: $(LIB) $(EXE) Makefile.lammps
 Makefile.lammps:
 	@cp $(EXTRAMAKE) Makefile.lammps
 $(LIB):	$(OBJ)
 	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
 colvars_standalone: colvars_main.o colvarproxy_standalone.o $(LIB)
 	$(CXX) -o $@ $(CXXFLAGS) $^
 # ------ MAKE FLAGS ------
 .SUFFIXES:
 .SUFFIXES: .cpp .o
 .PHONY: default clean
 # ------ COMPILE RULES ------
 .cpp.o:
 	$(CXX) $(CXXFLAGS) -c $<
 # ------ DEPENDENCIES ------
 #
 colvaratoms.o: colvaratoms.cpp colvarmodule.h colvartypes.h colvarproxy.h \
 colvarvalue.h colvarparse.h colvardeps.h colvaratoms.h
 colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h colvartypes.h \
 colvarproxy.h colvarvalue.h colvar.h colvarparse.h colvardeps.h \
 colvarbias_abf.h colvarbias.h colvargrid.h
 colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h colvartypes.h \
 colvarproxy.h colvarvalue.h colvarbias_alb.h colvar.h colvarparse.h \
 colvardeps.h colvarbias_restraint.h colvarbias.h
 colvarbias.o: colvarbias.cpp colvarmodule.h colvartypes.h colvarproxy.h \
 colvarvalue.h colvarbias.h colvar.h colvarparse.h colvardeps.h
 colvarbias_histogram.o: colvarbias_histogram.cpp colvarmodule.h \
 colvartypes.h colvarproxy.h colvarvalue.h colvar.h colvarparse.h \
 colvardeps.h colvarbias_histogram.h colvarbias.h colvargrid.h
 colvarbias_meta.o: colvarbias_meta.cpp colvar.h colvarmodule.h \
 colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
 colvarbias_meta.h colvarbias.h colvargrid.h
 colvarbias_restraint.o: colvarbias_restraint.cpp colvarmodule.h \
 colvartypes.h colvarproxy.h colvarvalue.h colvarbias_restraint.h \
 colvarbias.h colvar.h colvarparse.h colvardeps.h
 colvarcomp_angles.o: colvarcomp_angles.cpp colvarmodule.h colvartypes.h \
 colvarproxy.h colvarvalue.h colvar.h colvarparse.h colvardeps.h \
 colvarcomp.h colvaratoms.h
 colvarcomp_coordnums.o: colvarcomp_coordnums.cpp colvarmodule.h \
 colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
 colvaratoms.h colvar.h colvarcomp.h
 colvarcomp.o: colvarcomp.cpp colvarmodule.h colvartypes.h colvarproxy.h \
 colvarvalue.h colvar.h colvarparse.h colvardeps.h colvarcomp.h \
 colvaratoms.h
 colvarcomp_distances.o: colvarcomp_distances.cpp colvarmodule.h \
 colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
 colvar.h colvarcomp.h colvaratoms.h
 colvarcomp_protein.o: colvarcomp_protein.cpp colvarmodule.h colvartypes.h \
 colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h colvar.h \
 colvarcomp.h colvaratoms.h
 colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
 colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \
 colvar.h colvarcomp.h colvaratoms.h
 colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
 colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
 colvaratoms.h colvarscript.h colvarbias.h
 colvardeps.o: colvardeps.cpp colvardeps.h colvarmodule.h colvartypes.h \
 colvarproxy.h colvarvalue.h colvarparse.h
 colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
 colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
 colvaratoms.h colvargrid.h
 colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h \
 colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h colvar.h \
 colvarbias.h colvarbias_abf.h colvargrid.h colvarbias_alb.h \
 colvarbias_restraint.h colvarbias_histogram.h colvarbias_meta.h \
 colvarscript.h
 colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
 colvarvalue.h colvarparse.h
 colvarscript.o: colvarscript.cpp colvarscript.h colvarmodule.h \
 colvartypes.h colvarproxy.h colvarvalue.h colvarbias.h colvar.h \
 colvarparse.h colvardeps.h
 colvartypes.o: colvartypes.cpp colvarmodule.h colvartypes.h colvarproxy.h \
 colvarvalue.h colvarparse.h
 colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
 colvarvalue.h
 # ------ CLEAN ------
 clean:
 	-rm *.o *~ $(LIB)
--- a/lib/colvars/colvar.cpp
+++ b/lib/colvars/colvar.cpp
@ -1,5 +1,12 @@
 // -*- c++ -*-
 // This file is part of the Collective Variables module (Colvars).
 // The original version of Colvars and its updates are located at:
 // https://github.com/colvars/colvars
 // Please update all Colvars source files before making any changes.
 // If you wish to distribute your changes, please submit them to the
 // Colvars repository at GitHub.
 #include "colvarmodule.h"
 #include "colvarvalue.h"
 #include "colvarparse.h"
@ -163,38 +170,38 @@ colvar::colvar(std::string const &conf)
    }
    feature_states[f_cv_homogeneous]->enabled = homogeneous;
  }
-  // Colvar is deemed periodic iff:
+
  // Colvar is deemed periodic if:
  // - it is homogeneous
  // - all cvcs are periodic
  // - all cvcs have the same period
-
+  if (cvcs[0]->b_periodic) { // TODO make this a CVC feature
-  b_periodic = cvcs[0]->b_periodic && is_enabled(f_cv_homogeneous);
+    bool b_periodic = true;
-  period = cvcs[0]->period;
+    period = cvcs[0]->period;
-  for (i = 1; i < cvcs.size(); i++) {
+    for (i = 1; i < cvcs.size(); i++) {
-    if (!cvcs[i]->b_periodic || cvcs[i]->period != period) {
+      if (!cvcs[i]->b_periodic || cvcs[i]->period != period) {
-      b_periodic = false;
+        b_periodic = false;
-      period = 0.0;
+        period = 0.0;
        cvm::log("Warning: although one component is periodic, this colvar will "
                 "not be treated as periodic, either because the exponent is not "
                 "1, or because components of different periodicity are defined.  "
                 "Make sure that you know what you are doing!");
      }
    }
    feature_states[f_cv_periodic]->enabled = b_periodic;
  }
  feature_states[f_cv_periodic]->enabled = b_periodic;
  // check that cvcs are compatible
  for (i = 0; i < cvcs.size(); i++) {
    if ((cvcs[i])->b_periodic && !b_periodic) {
        cvm::log("Warning: although this component is periodic, the colvar will "
                  "not be treated as periodic, either because the exponent is not "
                  "1, or because multiple components are present. Make sure that "
                  "you know what you are doing!");
    }
    // components may have different types only for scripted functions
    if (!is_enabled(f_cv_scripted) && (colvarvalue::check_types(cvcs[i]->value(),
-                                                           cvcs[0]->value())) ) {
+                                                                cvcs[0]->value())) ) {
      cvm::error("ERROR: you are definining this collective variable "
                 "by using components of different types. "
                 "You must use the same type in order to "
-                 " sum them together.\n", INPUT_ERROR);
+                 "sum them together.\n", INPUT_ERROR);
      return;
    }
  }
@ -207,16 +214,15 @@ colvar::colvar(std::string const &conf)
  // at this point, the colvar's type is defined
  f.type(value());
  f_accumulated.type(value());
-  fb.type(value());
+
  reset_bias_force();
  get_keyval(conf, "width", width, 1.0);
  if (width <= 0.0) {
    cvm::error("Error: \"width\" must be positive.\n", INPUT_ERROR);
    return;
  }
  // NOTE: not porting wall stuff to new deps, as this will change to a separate bias
  // the grid functions will wait a little as well
  lower_boundary.type(value());
  lower_wall.type(value());
@ -308,6 +314,9 @@ colvar::colvar(std::string const &conf)
      enable(f_cv_extended_Lagrangian);
      provide(f_cv_Langevin);
      // The extended mass will apply forces
      enable(f_cv_gradient);
      xr.type(value());
      vr.type(value());
      fr.type(value());
@ -400,6 +409,9 @@ colvar::colvar(std::string const &conf)
  f_old.type(value());
  f_old.reset();
  x_restart.type(value());
  after_restart = false;
  if (cvm::b_analysis)
    parse_analysis(conf);
@ -761,9 +773,13 @@ int colvar::calc_cvcs(int first_cvc, size_t num_cvcs)
    return error_code;
  }
  if (cvm::step_relative() > 0) {
    // Total force depends on Jacobian derivative from previous timestep
    error_code |= calc_cvc_total_force(first_cvc, num_cvcs);
  }
  // atom coordinates are updated by the next line
  error_code |= calc_cvc_values(first_cvc, num_cvcs);
  error_code |= calc_cvc_gradients(first_cvc, num_cvcs);
  error_code |= calc_cvc_total_force(first_cvc, num_cvcs);
  error_code |= calc_cvc_Jacobians(first_cvc, num_cvcs);
  if (cvm::debug())
@ -780,9 +796,12 @@ int colvar::collect_cvc_data()
  int error_code = COLVARS_OK;
  if (cvm::step_relative() > 0) {
    // Total force depends on Jacobian derivative from previous timestep
    error_code |= collect_cvc_total_forces();
  }
  error_code |= collect_cvc_values();
  error_code |= collect_cvc_gradients();
  error_code |= collect_cvc_total_forces();
  error_code |= collect_cvc_Jacobians();
  error_code |= calc_colvar_properties();
@ -872,6 +891,22 @@ int colvar::collect_cvc_values()
    cvm::log("Colvar \""+this->name+"\" has value "+
              cvm::to_str(x, cvm::cv_width, cvm::cv_prec)+".\n");
  if (after_restart) {
    after_restart = false;
    if (cvm::proxy->simulation_running()) {
      cvm::real const jump2 = dist2(x, x_restart) / (width*width);
      if (jump2 > 0.25) {
        cvm::error("Error: the calculated value of colvar \""+name+
                   "\":\n"+cvm::to_str(x)+"\n differs greatly from the value "
                   "last read from the state file:\n"+cvm::to_str(x_restart)+
                   "\nPossible causes are changes in configuration, "
                   "wrong state file, or how PBC wrapping is handled.\n",
                   INPUT_ERROR);
        return INPUT_ERROR;
      }
    }
  }
  return COLVARS_OK;
 }
@ -979,22 +1014,17 @@ int colvar::calc_cvc_total_force(int first_cvc, size_t num_cvcs)
    if (cvm::debug())
      cvm::log("Calculating total force of colvar \""+this->name+"\".\n");
-    // if (!tasks[task_extended_lagrangian] && (cvm::step_relative() > 0)) {
+    cvm::increase_depth();
   // Disabled check to allow for explicit total force calculation
    // even with extended Lagrangian
-    if (cvm::step_relative() > 0) {
+    for (i = first_cvc, cvc_count = 0;
-      cvm::increase_depth();
+        (i < cvcs.size()) && (cvc_count < cvc_max_count);
-      // get from the cvcs the total forces from the PREVIOUS step
+        i++) {
-      for (i = first_cvc, cvc_count = 0;
+      if (!cvcs[i]->is_enabled()) continue;
-          (i < cvcs.size()) && (cvc_count < cvc_max_count);
+      cvc_count++;
-          i++) {
+      (cvcs[i])->calc_force_invgrads();
        if (!cvcs[i]->is_enabled()) continue;
        cvc_count++;
        (cvcs[i])->calc_force_invgrads();
      }
      cvm::decrease_depth();
    }
    cvm::decrease_depth();
    if (cvm::debug())
      cvm::log("Done calculating total force of colvar \""+this->name+"\".\n");
@ -1013,6 +1043,11 @@ int colvar::collect_cvc_total_forces()
      // get from the cvcs the total forces from the PREVIOUS step
      for (size_t i = 0; i < cvcs.size();  i++) {
        if (!cvcs[i]->is_enabled()) continue;
            if (cvm::debug())
            cvm::log("Colvar component no. "+cvm::to_str(i+1)+
                " within colvar \""+this->name+"\" has total force "+
                cvm::to_str((cvcs[i])->total_force(),
                cvm::cv_width, cvm::cv_prec)+".\n");
        // linear combination is assumed
        ft += (cvcs[i])->total_force() * (cvcs[i])->sup_coeff / active_cvc_square_norm;
      }
@ -1056,6 +1091,11 @@ int colvar::collect_cvc_Jacobians()
    fj.reset();
    for (size_t i = 0; i < cvcs.size(); i++) {
      if (!cvcs[i]->is_enabled()) continue;
        if (cvm::debug())
          cvm::log("Colvar component no. "+cvm::to_str(i+1)+
            " within colvar \""+this->name+"\" has Jacobian derivative"+
            cvm::to_str((cvcs[i])->Jacobian_derivative(),
            cvm::cv_width, cvm::cv_prec)+".\n");
      // linear combination is assumed
      fj += (cvcs[i])->Jacobian_derivative() * (cvcs[i])->sup_coeff / active_cvc_square_norm;
    }
@ -1085,7 +1125,7 @@ int colvar::calc_colvar_properties()
    // TODO: put it in the restart information
    if (cvm::step_relative() == 0) {
      xr = x;
-      vr = 0.0; // (already 0; added for clarity)
+      vr.reset(); // (already 0; added for clarity)
    }
    // report the restraint center as "value"
@ -1128,15 +1168,16 @@ cvm::real colvar::update_forces_energy()
  if (is_enabled(f_cv_Jacobian)) {
    // the instantaneous Jacobian force was not included in the reported total force;
    // instead, it is subtracted from the applied force (silent Jacobian correction)
    // This requires the Jacobian term for the *current* timestep
    if (is_enabled(f_cv_hide_Jacobian))
      f -= fj;
  }
-  if (is_enabled(f_cv_lower_wall) || is_enabled(f_cv_upper_wall)) {
+  // Wall force
  colvarvalue fw(x);
  fw.reset();
-    // Wall force
+  if (is_enabled(f_cv_lower_wall) || is_enabled(f_cv_upper_wall)) {
    colvarvalue fw(x);
    fw.reset();
    if (cvm::debug())
      cvm::log("Calculating wall forces for colvar \""+this->name+"\".\n");
@ -1144,12 +1185,11 @@ cvm::real colvar::update_forces_energy()
    // For a periodic colvar, both walls may be applicable at the same time
    // in which case we pick the closer one
    if ( (!is_enabled(f_cv_upper_wall)) ||
-         (this->dist2(x_reported, lower_wall) < this->dist2(x_reported, upper_wall)) ) {
+         (this->dist2(x, lower_wall) < this->dist2(x, upper_wall)) ) {
-      cvm::real const grad = this->dist2_lgrad(x_reported, lower_wall);
+      cvm::real const grad = this->dist2_lgrad(x, lower_wall);
      if (grad < 0.0) {
        fw = -0.5 * lower_wall_k * grad;
        f += fw;
        if (cvm::debug())
          cvm::log("Applying a lower wall force("+
                    cvm::to_str(fw)+") to \""+this->name+"\".\n");
@ -1157,10 +1197,9 @@ cvm::real colvar::update_forces_energy()
    } else {
-      cvm::real const grad = this->dist2_lgrad(x_reported, upper_wall);
+      cvm::real const grad = this->dist2_lgrad(x, upper_wall);
      if (grad > 0.0) {
        fw = -0.5 * upper_wall_k * grad;
        f += fw;
        if (cvm::debug())
          cvm::log("Applying an upper wall force("+
                    cvm::to_str(fw)+") to \""+this->name+"\".\n");
@ -1168,17 +1207,26 @@ cvm::real colvar::update_forces_energy()
    }
  }
  // At this point f is the force f from external biases that will be applied to the
  // extended variable if there is one
  if (is_enabled(f_cv_extended_Lagrangian)) {
    if (cvm::debug()) {
      cvm::log("Updating extended-Lagrangian degrees of freedom.\n");
    }
    cvm::real dt = cvm::dt();
-    cvm::real f_ext;
+    colvarvalue f_ext(fr.type());
    f_ext.reset();
    // the total force is applied to the fictitious mass, while the
-    // atoms only feel the harmonic force
+    // atoms only feel the harmonic force + wall force
    // fr: bias force on extended variable (without harmonic spring), for output in trajectory
    // f_ext: total force on extended variable (including harmonic spring)
-    // f: - initially, external biasing force (including wall forces)
+    // f: - initially, external biasing force
-    //    - after this code block, colvar force to be applied to atomic coordinates, ie. spring force
+    //    - after this code block, colvar force to be applied to atomic coordinates
    //      ie. spring force + wall force
    fr    = f;
    f_ext = f + (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
    f     =     (-0.5 * ext_force_k) * this->dist2_rgrad(xr, x);
@ -1200,15 +1248,24 @@ cvm::real colvar::update_forces_energy()
    potential_energy = 0.5 * ext_force_k * this->dist2(xr, x);
    // leap to v_(i+1/2)
    if (is_enabled(f_cv_Langevin)) {
-      vr -= dt * ext_gamma * vr.real_value;
+      vr -= dt * ext_gamma * vr;
-      vr += dt * ext_sigma * cvm::rand_gaussian() / ext_mass;
+      colvarvalue rnd(x);
      rnd.set_random();
      vr += dt * ext_sigma * rnd / ext_mass;
    }
    vr  += (0.5 * dt) * f_ext / ext_mass;
    xr  += dt * vr;
    xr.apply_constraints();
-    if (this->b_periodic) this->wrap(xr);
+    if (this->is_enabled(f_cv_periodic)) this->wrap(xr);
  }
  // TODO remove the wall force
  f += fw;
  // Now adding the force on the actual colvar (for those biases who
  // bypass the extended Lagrangian mass)
  f += fb_actual;
  // Store force to be applied, possibly summed over several timesteps
  f_accumulated += f;
  if (is_enabled(f_cv_fdiff_velocity)) {
@ -1425,14 +1482,15 @@ std::istream & colvar::read_restart(std::istream &is)
    }
  }
-  if ( !(get_keyval(conf, "x", x,
+  if ( !(get_keyval(conf, "x", x, x, colvarparse::parse_silent)) ) {
                    colvarvalue(x.type()), colvarparse::parse_silent)) ) {
    cvm::log("Error: restart file does not contain "
             "the value of the colvar \""+
             name+"\" .\n");
  } else {
    cvm::log("Restarting collective variable \""+name+"\" from value: "+
             cvm::to_str(x)+"\n");
    x_restart = x;
    after_restart = true;
  }
  if (is_enabled(f_cv_extended_Lagrangian)) {
--- a/lib/colvars/colvar.h
+++ b/lib/colvars/colvar.h
@ -1,5 +1,12 @@
 // -*- c++ -*-
 // This file is part of the Collective Variables module (Colvars).
 // The original version of Colvars and its updates are located at:
 // https://github.com/colvars/colvars
 // Please update all Colvars source files before making any changes.
 // If you wish to distribute your changes, please submit them to the
 // Colvars repository at GitHub.
 #ifndef COLVAR_H
 #define COLVAR_H
@ -170,6 +177,9 @@ public:
  /// the biases are updated
  colvarvalue fb;
  /// \brief Bias force to the actual value (only useful with extended Lagrangian)
  colvarvalue fb_actual;
  /// \brief Total \em applied force; fr (if extended_lagrangian
  /// is defined), fb (if biases are applied) and the walls' forces
  /// (if defined) contribute to it
@ -183,13 +193,9 @@ public:
  colvarvalue ft;
-  /// Period, if it is a constant
+  /// Period, if this variable is periodic
  cvm::real period;
  /// \brief Same as above, but also takes into account components
  /// with a variable period, such as distanceZ
  bool b_periodic;
  /// \brief Expand the boundaries of multiples of width, to keep the
  /// value always within range
@ -290,6 +296,9 @@ public:
  /// Add to the total force from biases
  void add_bias_force(colvarvalue const &force);
  /// Apply a force to the actual value (only meaningful with extended Lagrangian)
  void add_bias_force_actual_value(colvarvalue const &force);
  /// \brief Collect all forces on this colvar, integrate internal
  /// equations of motion of internal degrees of freedom; see also
  /// colvar::communicate_forces()
@ -386,6 +395,12 @@ protected:
  /// Previous value (to calculate velocities during analysis)
  colvarvalue            x_old;
  /// Value read from the most recent state file (if any)
  colvarvalue            x_restart;
  /// True if a state file was just read
  bool                   after_restart;
  /// Time series of values and velocities used in correlation
  /// functions
  std::list< std::list<colvarvalue> > acf_x_history, acf_v_history;
@ -577,9 +592,20 @@ inline void colvar::add_bias_force(colvarvalue const &force)
 }
 inline void colvar::add_bias_force_actual_value(colvarvalue const &force)
 {
  if (cvm::debug()) {
    cvm::log("Adding biasing force "+cvm::to_str(force)+" to colvar \""+name+"\".\n");
  }
  fb_actual += force;
 }
 inline void colvar::reset_bias_force() {
  fb.type(value());
  fb.reset();
  fb_actual.type(value());
  fb_actual.reset();
 }
 #endif
--- a/Show More
+++ b/Show More
		`@ -0,0 +1,2 @@`
							`n: 1 1 6 12 2.400000000000002e+00 1.010000000000000e+01`
							`1.200460787805587e+03 2.169623423326193e+01 2.388396964379328e+01 -1.197754948555067e+01 6.472482422420378e+00 -1.483711824891365e+00 7.768139601662113e-01 -7.869494711740244e-01 4.830820182054661e-01 -1.892989444995645e-01 1.021275453070386e-01 -1.637649039972671e-01 5.570978712841167e-02 7.637188693695119e-03 -4.109175461195019e-03 -5.352186189455146e-02`
		`@ -0,0 +1 @@`
							`<EFBFBD>-<2D><><EFBFBD><EFBFBD><EFBFBD>@47h<<3C>5@<40><><EFBFBD><EFBFBD>K<EFBFBD>7@<40>R<EFBFBD>]<5D><>'<27><><EFBFBD><EFBFBD>n<EFBFBD><6E>@݌I<DD8C>H<EFBFBD><48><EFBFBD><19>?<3F><><EFBFBD><EFBFBD>?r<>I<EFBFBD><49>.<2E><><11>^<5E><><EFBFBD><EFBFBD>?W<57><7F><EFBFBD>:ȿ(O<1D>%<25>?<3F>Ns<4E>?<3F>Ŀ<EFBFBD>:<3A>C<EFBFBD><43><EFBFBD>?<3F><><EFBFBD>:,H?<3F>}<7D>c<EFBFBD><63>p<EFBFBD><70><EFBFBD><EFBFBD><EFBFBD>7g<37><67>`