patch 13Apr17

Merge pull request #450 from rbberger/python_destruction_fix
Prevent segfault if Python was never initialized
2017-04-13 11:19:48 -06:00 · 2017-04-12 13:58:23 -06:00 · 2017-04-12 11:17:15 -04:00 · 2017-04-11 09:00:37 -06:00 · 2017-04-11 08:35:09 -06:00 · 2017-04-11 08:27:53 -06:00
186 changed files with 14095 additions and 6282 deletions
--- a/doc/src/Eqs/fix_gcmc1.jpg
+++ b/doc/src/Eqs/fix_gcmc1.jpg
--- a/doc/src/Eqs/fix_gcmc1.tex
+++ b/doc/src/Eqs/fix_gcmc1.tex
@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\mu &=&\mu^{id} + \mu^{ex}
+\end{eqnarray*}
+
+\end{document}
--- a/doc/src/Eqs/fix_gcmc2.jpg
+++ b/doc/src/Eqs/fix_gcmc2.jpg
--- a/doc/src/Eqs/fix_gcmc2.tex
+++ b/doc/src/Eqs/fix_gcmc2.tex
@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\mu^{id} &=& k T \ln{\rho \Lambda^3} \\
+&=& k T \ln{\frac{\phi P \Lambda^3}{k T}} 
+\end{eqnarray*}
+
+\end{document}
--- a/doc/src/Eqs/fix_gcmc3.jpg
+++ b/doc/src/Eqs/fix_gcmc3.jpg
--- a/doc/src/Eqs/fix_gcmc3.tex
+++ b/doc/src/Eqs/fix_gcmc3.tex
@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+\Lambda &=& \sqrt{ \frac{h^2}{2 \pi m k T}}
+\end{eqnarray*}
+
+\end{document}
--- 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="24 Mar 2017 version">
+<META NAME="docnumber" CONTENT="13 Apr 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
-24 Mar 2017 version :c,h4
+13 Apr 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/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@ -1047,6 +1047,10 @@ package"_Section_start.html#start_3.
 "oxdna/hbond"_pair_oxdna.html,
 "oxdna/stk"_pair_oxdna.html,
 "oxdna/xstk"_pair_oxdna.html,
+"oxdna2/coaxstk"_pair_oxdna2.html,
+"oxdna2/dh"_pair_oxdna2.html,
+"oxdna2/excv"_pair_oxdna2.html,
+"oxdna2/stk"_pair_oxdna2.html,
 "quip"_pair_quip.html,
 "reax/c (k)"_pair_reax_c.html,
 "smd/hertz"_pair_smd_hertz.html,
@ -1096,7 +1100,8 @@ package"_Section_start.html#start_3.

 "harmonic/shift (o)"_bond_harmonic_shift.html,
 "harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
-"oxdna/fene"_bond_oxdna.html :tb(c=4,ea=c)
+"oxdna/fene"_bond_oxdna.html,
+"oxdna2/fene"_bond_oxdna.html :tb(c=4,ea=c)

 :line

@ -1150,7 +1155,7 @@ USER-OMP, t = OPT.
 "zero"_dihedral_zero.html,
 "hybrid"_dihedral_hybrid.html,
 "charmm (ko)"_dihedral_charmm.html,
-"charmmfsh"_dihedral_charmm.html,
+"charmmfsw"_dihedral_charmm.html,
 "class2 (ko)"_dihedral_class2.html,
 "harmonic (io)"_dihedral_harmonic.html,
 "helix (o)"_dihedral_helix.html,
--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@ -215,7 +215,7 @@ documentation for the formula it computes.
 "special_bonds"_special_bonds.html charmm
 "special_bonds"_special_bonds.html amber :ul

-NOTE: For CHARMM, the newer {charmmfsw} or {charmmfsh} styles were
+NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were
 released in March 2017.  We recommend they be used instead of the
 older {charmm} styles.  See discussion of the differences on the "pair
 charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
@ -759,23 +759,14 @@ LAMMPS itself does not do visualization, but snapshots from LAMMPS
 simulations can be visualized (and analyzed) in a variety of ways.

 LAMMPS snapshots are created by the "dump"_dump.html command which can
-create files in several formats.  The native LAMMPS dump format is a
+create files in several formats. The native LAMMPS dump format is a
 text file (see "dump atom" or "dump custom") which can be visualized
-by the "xmovie"_Section_tools.html#xmovie program, included with the
-LAMMPS package.  This produces simple, fast 2d projections of 3d
-systems, and can be useful for rapid debugging of simulation geometry
-and atom trajectories.
-
+by several popular visualization tools. The "dump image"_dump_image.html
+and "dump movie"_dump_image.html styles can output internally rendered
+images and convert a sequence of them to a movie during the MD run.
 Several programs included with LAMMPS as auxiliary tools can convert
-native LAMMPS dump files to other formats.  See the
-"Section 9"_Section_tools.html doc page for details.  The first is
-the "ch2lmp tool"_Section_tools.html#charmm, which contains a
-lammps2pdb Perl script which converts LAMMPS dump files into PDB
-files.  The second is the "lmp2arc tool"_Section_tools.html#arc which
-converts LAMMPS dump files into Accelrys' Insight MD program files.
-The third is the "lmp2cfg tool"_Section_tools.html#cfg which converts
-LAMMPS dump files into CFG files which can be read into the
-"AtomEye"_atomeye visualizer.
+between LAMMPS format files and other formats.
+See the "Section 9"_Section_tools.html doc page for details.

 A Python-based toolkit distributed by our group can read native LAMMPS
 dump files, including custom dump files with additional columns of
@ -788,22 +779,7 @@ RasMol visualization programs.  Pizza.py has tools that do interactive
 3d OpenGL visualization and one that creates SVG images of dump file
 snapshots.

-LAMMPS can create XYZ files directly (via "dump xyz") which is a
-simple text-based file format used by many visualization programs
-including "VMD"_vmd.
-
-LAMMPS can create DCD files directly (via "dump dcd") which can be
-read by "VMD"_vmd in conjunction with a CHARMM PSF file.  Using this
-form of output avoids the need to convert LAMMPS snapshots to PDB
-files.  See the "dump"_dump.html command for more information on DCD
-files.
-
-LAMMPS can create XTC files directly (via "dump xtc") which is GROMACS
-file format which can also be read by "VMD"_vmd for visualization.
-See the "dump"_dump.html command for more information on XTC files.
-
 :link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
-:link(vmd,http://www.ks.uiuc.edu/Research/vmd)
 :link(ensight,http://www.ensight.com)
 :link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)

@ -1710,7 +1686,7 @@ nph) and Berendsen:
 The "fix npt"_fix_nh.html commands include a Nose-Hoover thermostat
 and barostat.  "Fix nph"_fix_nh.html is just a Nose/Hoover barostat;
 it does no thermostatting.  Both "fix nph"_fix_nh.html and "fix
-press/bernendsen"_fix_press_berendsen.html can be used in conjunction
+press/berendsen"_fix_press_berendsen.html can be used in conjunction
 with any of the thermostatting fixes.

 As with the thermostats, "fix npt"_fix_nh.html and "fix
@ -2013,6 +1989,11 @@ Both methods are thus a means to extract or assign (overwrite) any
 peratom quantities within LAMMPS.  See the extract() method in the
 src/atom.cpp file for a list of valid per-atom properties.  New names
 could easily be added if the property you want is not listed.
+A special treatment is applied for accessing image flags via the
+"image" property. Image flags are stored in a packed format with all
+three image flags stored in a single integer. When signaling to access
+the image flags as 3 individual values per atom instead of 1, the data
+is transparently packed or unpacked by the library interface.

 The lammps_create_atoms() function takes a list of N atoms as input
 with atom types and coords (required), an optionally atom IDs and
--- a/doc/src/Section_intro.txt
+++ b/doc/src/Section_intro.txt
@ -338,15 +338,13 @@ dynamics timestepping, particularly if the computations are not
 parallel, so it is often better to leave such analysis to
 post-processing codes.

-A very simple (yet fast) visualizer is provided with the LAMMPS
-package - see the "xmovie"_Section_tools.html#xmovie tool in "this
-section"_Section_tools.html.  It creates xyz projection views of
-atomic coordinates and animates them.  We find it very useful for
-debugging purposes.  For high-quality visualization we recommend the
+For high-quality visualization we recommend the
 following packages:

 "VMD"_http://www.ks.uiuc.edu/Research/vmd
 "AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A
+"OVITO"_http://www.ovito.org/
+"ParaView"_http://www.paraview.org/
 "PyMol"_http://www.pymol.org
 "Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html
 "RasMol"_http://www.openrasmol.org :ul
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@ -1140,7 +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-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, Oliver Henrich (U Strathclyde Glasgow), 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, -, -
@ -1288,25 +1288,29 @@ him directly if you have questions.
 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
+single- and double-stranded DNA. These are at the moment mainly the
+oxDNA and oxDNA2 models, 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.html
+"bond_style oxdna2/fene"_bond_oxdna.html
 "pair_style oxdna/..."_pair_oxdna.html
+"pair_style oxdna2/..."_pair_oxdna2.html
 "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul

 Supporting info: /src/USER-CGDNA/README, "bond_style
-oxdna/fene"_bond_oxdna.html, "pair_style
-oxdna/..."_pair_oxdna.html, "fix
+oxdna/fene"_bond_oxdna.html, "bond_style
+oxdna2/fene"_bond_oxdna.html, "pair_style
+oxdna/..."_pair_oxdna.html, "pair_style
+oxdna2/..."_pair_oxdna2.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.
+Author: Oliver Henrich at the University of Strathclyde, Glasgow 
+(oliver.henrich at strath.ac.uk, also ohenrich at ph.ed.ac.uk). 
+Contact him directly if you have any questions.

 :line

--- a/doc/src/Section_python.txt
+++ b/doc/src/Section_python.txt
@ -698,7 +698,12 @@ method in the src/atom.cpp file for a list of valid names.  Again, new
 names could easily be added if the property you want is missing.  The
 vector can be used via normal Python subscripting.  If atom IDs are
 not consecutively ordered within LAMMPS, a None is returned as
-indication of an error.
+indication of an error. A special treatment is applied for image flags
+stored in the "image" property. All three image flags are stored in
+a packed format in a single integer, so count would be 1 to retrieve
+that integer, however also a count value of 3 can be used and then
+the image flags will be unpacked into 3 individual integers, ordered
+in a similar fashion as coordinates. 

 Note that the data structure gather_atoms("x") returns is different
 from the data structure returned by extract_atom("x") in four ways.
@ -727,6 +732,10 @@ corresponding properties for each atom inside LAMMPS.  This requires
 LAMMPS to have its "map" option enabled; see the
 "atom_modify"_atom_modify.html command for details.  If it is not, or
 if atom IDs are not consecutively ordered, no coordinates are reset.
+Similar as for gather_atoms() a special treatment is applied for image
+flags, which can be provided in packed (count = 1) or unpacked (count = 3)
+format and in the latter case, they will be packed before applied to
+atoms.

 The array of coordinates passed to scatter_atoms() must be a ctypes
 vector of ints or doubles, allocated and initialized something like
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@ -455,8 +455,7 @@ and related PPPM operations are somewhat insensitive to floating point
 truncation errors and thus do not always need to be performed in
 double precision.  Using the -DFFT_SINGLE setting trades off a little
 accuracy for reduced memory use and parallel communication costs for
-transposing 3d FFT data.  Note that single precision FFTs have only
-been tested with the FFTW3, FFTW2, MKL, and KISS FFT options.
+transposing 3d FFT data.

 Step 7 :h6

--- a/doc/src/bond_oxdna.txt
+++ b/doc/src/bond_oxdna.txt
@ -7,19 +7,24 @@
 :line

 bond_style oxdna/fene command :h3
+bond_style oxdna2/fene command :h3

 [Syntax:]

 bond_style oxdna/fene :pre
+bond_style oxdna2/fene :pre

 [Examples:]

 bond_style oxdna/fene
 bond_coeff * 2.0 0.25 0.7525 :pre

+bond_style oxdna2/fene
+bond_coeff * 2.0 0.25 0.7564 :pre
+
 [Description:]

-The {oxdna/fene} bond style uses the potential
+The {oxdna/fene} and {oxdna2/fene} bond styles use the potential

 :c,image(Eqs/bond_oxdna_fene.jpg)

@ -36,13 +41,14 @@ epsilon (energy)
 Delta (distance)
 r0 (distance) :ul

-NOTE: This bond style has to be used together with the corresponding oxDNA pair styles
+NOTE: The oxDNA 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.html). The coefficients 
-in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
+"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair 
+style {oxdna2/dh} have to be defined.
+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/.
+Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
 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,
@ -60,7 +66,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]

-"pair_style oxdna/excv"_pair_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html 
+"pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html 

 [Default:] none

@ -68,3 +74,6 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.

 :link(oxdna_fene)
 [(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
+
+:link(oxdna2)
+[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
--- a/doc/src/bonds.txt
+++ b/doc/src/bonds.txt
@ -16,6 +16,7 @@ Bond Styles :h1
   bond_none
   bond_nonlinear
   bond_oxdna
+   bond_oxdna2
   bond_quartic
   bond_table
   bond_zero
--- a/doc/src/compute_modify.txt
+++ b/doc/src/compute_modify.txt
@ -54,7 +54,7 @@ adding atoms or molecules to the system (see the "fix
 pour"_fix_pour.html, "fix deposit"_fix_deposit.html, and "fix
 gcmc"_fix_gcmc.html commands) or expect atoms or molecules to be lost
 (e.g. due to exiting the simulation box or via "fix
-evaporation"_fix_evaporation.html), then this option should be used to
+evaporate"_fix_evaporate.html), then this option should be used to
 insure the temperature is correctly normalized.

 NOTE: The {extra} and {dynamic} keywords should not be used as they
--- a/doc/src/dihedral_charmm.txt
+++ b/doc/src/dihedral_charmm.txt
@ -10,25 +10,25 @@ dihedral_style charmm command :h3
 dihedral_style charmm/intel command :h3
 dihedral_style charmm/kk command :h3
 dihedral_style charmm/omp command :h3
-dihedral_style charmmfsh command :h3
+dihedral_style charmmfsw command :h3

 [Syntax:]

 dihedral_style style :pre

-style = {charmm} or {charmmfsh} :ul
+style = {charmm} or {charmmfsw} :ul

 [Examples:]

 dihedral_style charmm
-dihedral_style charmmfsh
+dihedral_style charmmfsw
 dihedral_coeff  1 0.2 1 180 1.0
 dihedral_coeff  2 1.8 1   0 1.0
 dihedral_coeff  1 3.1 2 180 0.5 :pre

 [Description:]

-The {charmm} and {charmmfsh} dihedral styles use the potential
+The {charmm} and {charmmfsw} dihedral styles use the potential

 :c,image(Eqs/dihedral_charmm.jpg)

@ -38,10 +38,15 @@ field (see comment on weighting factors below).  See
 "(Cornell)"_#dihedral-Cornell for a description of the AMBER force
 field.

-NOTE: The newer {charmmfsh} style was released in March 2017.  We
+NOTE: The newer {charmmfsw} style was released in March 2017.  We
 recommend it be used instead of the older {charmm} style when running
-a simulation with the CHARMM force field.  See the discussion below
-and more details on the "pair_style charmm"_pair_charmm.html doc page.
+a simulation with the CHARMM force field, either with long-range
+Coulombics or a Coulomb cutoff, via the "pair_style
+lj/charmmfsw/coul/long"_pair_charmm.html and "pair_style
+lj/charmmfsw/coul/charmmfsh"_pair_charmm.html commands respectively.
+Otherwise the older {charmm} style is fine to use.  See the discussion
+below and more details on the "pair_style charmm"_pair_charmm.html doc
+page.

 The following coefficients must be defined for each dihedral type via the
 "dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
@ -82,13 +87,19 @@ special_bonds 1-4 scaling factor to 0.0 (which is the
 default). Otherwise 1-4 non-bonded interactions in dihedrals will be
 computed twice.

-For simulations using the CHARMM force field, the difference between
-the {charmm} and {charmmfsh} styles is in the computation of the 1-4
-non-bond interactions, if the distance between the two atoms is within
-the switching distance of the pairwise potential defined by the
-corresponding CHARMM pair style, i.e. between the inner and outer
-cutoffs specified for the pair style.  See the discussion on the
-"CHARMM pair_style"_pair_charmm.html doc page for details.
+For simulations using the CHARMM force field with a Coulomb cutoff,
+the difference between the {charmm} and {charmmfsw} styles is in the
+computation of the 1-4 non-bond interactions, though only if the
+distance between the two atoms is within the switching region of the
+pairwise potential defined by the corresponding CHARMM pair style,
+i.e. within the outer cutoff specified for the pair style.  The
+{charmmfsw} style should only be used when using the corresponding
+"pair_style lj/charmmfsw/coul/charmmfsw"_pair_charmm.html or
+"pair_style lj/charmmfsw/coul/long"_pair_charmm.html commands.  Use
+the {charmm} style with the older "pair_style"_pair_charmm.html
+commands that have just "charmm" in their style name.  See the
+discussion on the "CHARMM pair_style"_pair_charmm.html doc page for
+details.

 Note that for AMBER force fields, which use pair styles with "lj/cut",
 the special_bonds 1-4 scaling factor should be set to the AMBER
@ -96,7 +107,7 @@ defaults (1/2 and 5/6) and all the dihedral weighting factors (4th
 coeff above) must be set to 0.0. In this case, you can use any pair
 style you wish, since the dihedral does not need any Lennard-Jones
 parameter information and will not compute any 1-4 non-bonded
-interactions.  Likewise the {charmm} or {charmmfsh} styles are
+interactions.  Likewise the {charmm} or {charmmfsw} styles are
 identical in this case since no 1-4 non-bonded interactions are
 computed.

--- a/doc/src/dump.txt
+++ b/doc/src/dump.txt
@ -331,10 +331,7 @@ bonds and colors.

 Note that {atom}, {custom}, {dcd}, {xtc}, and {xyz} style dump files
 can be read directly by "VMD"_http://www.ks.uiuc.edu/Research/vmd, a
-popular molecular viewing program.  See
-"Section 9"_Section_tools.html#vmd of the manual and the
-tools/lmp2vmd/README.txt file for more information about support in
-VMD for reading and visualizing LAMMPS dump files.
+popular molecular viewing program.

 :line

--- a/doc/src/dump_custom_vtk.txt
+++ b/doc/src/dump_custom_vtk.txt
@ -26,7 +26,6 @@ args = list of arguments for a particular style :l
                          q, mux, muy, muz, mu,
                          radius, diameter, omegax, omegay, omegaz,
                          angmomx, angmomy, angmomz, tqx, tqy, tqz,
-                          spin, eradius, ervel, erforce,
                          c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre

      id = atom ID
@ -51,17 +50,18 @@ args = list of arguments for a particular style :l
      angmomx,angmomy,angmomz = angular momentum of aspherical particle
      tqx,tqy,tqz = torque on finite-size particles
      c_ID = per-atom vector calculated by a compute with ID
-      c_ID\[N\] = Nth column of per-atom array calculated by a compute with ID
+      c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
      f_ID = per-atom vector calculated by a fix with ID
-      f_ID\[N\] = Nth column of per-atom array calculated by a fix with ID
-      v_name = per-atom vector calculated by an atom-style variable with name :pre
+      f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
+      v_name = per-atom vector calculated by an atom-style variable with name
+      d_name = per-atom floating point vector with name, managed by fix property/atom
+      i_name = per-atom integer vector with name, managed by fix property/atom :pre
 :ule

 [Examples:]

 dump dmpvtk all custom/vtk 100 dump*.myforce.vtk id type vx fx
-dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD\[1\] c_myD\[2\] c_myD\[3\] v_ke
-dump e_data all custom/vtk 100 dump*.vtu id type spin eradius fx fy fz eforce :pre
+dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD\[1\] c_myD\[2\] c_myD\[3\] v_ke :pre

 The style {custom/vtk} is similar to the "custom"_dump.html style but
 uses the VTK library to write data to VTK simple legacy or XML format
@ -199,32 +199,38 @@ part of the {custom/vtk} style.
 The {id}, {mol}, {proc}, {procp1}, {type}, {element}, {mass}, {vx},
 {vy}, {vz}, {fx}, {fy}, {fz}, {q} attributes are self-explanatory.

-{id} is the atom ID.  {mol} is the molecule ID, included in the data
-file for molecular systems.  {type} is the atom type.  {element} is
-typically the chemical name of an element, which you must assign to
-each type via the "dump_modify element"_dump_modify.html command.
-More generally, it can be any string you wish to associate with an
-atom type.  {mass} is the atom mass.  {vx}, {vy}, {vz}, {fx}, {fy},
-{fz}, and {q} are components of atom velocity and force and atomic
-charge.
+{Id} is the atom ID.  {Mol} is the molecule ID, included in the data
+file for molecular systems.  {Proc} is the ID of the processor (0 to
+Nprocs-1) that currently owns the atom.  {Procp1} is the proc ID+1,
+which can be convenient in place of a {type} attribute (1 to Ntypes)
+for coloring atoms in a visualization program.  {Type} is the atom
+type (1 to Ntypes).  {Element} is typically the chemical name of an
+element, which you must assign to each type via the "dump_modify
+element"_dump_modify.html command.  More generally, it can be any
+string you wish to associated with an atom type.  {Mass} is the atom
+mass.  {Vx}, {vy}, {vz}, {fx}, {fy}, {fz}, and {q} are components of
+atom velocity and force and atomic charge.

 There are several options for outputting atom coordinates.  The {x},
-{y}, {z} attributes are used to write atom coordinates "unscaled", in
-the appropriate distance "units"_units.html (Angstroms, sigma, etc).
-Additionally, you can use {xs}, {ys}, {zs} if you want to also save the
-coordinates "scaled" to the box size, so that each value is 0.0 to
-1.0.  If the simulation box is triclinic (tilted), then all atom
-coords will still be between 0.0 and 1.0.  Use {xu}, {yu}, {zu} if you
-want the coordinates "unwrapped" by the image flags for each atom.
-Unwrapped means that if the atom has passed through a periodic
-boundary one or more times, the value is printed for what the
-coordinate would be if it had not been wrapped back into the periodic
-box.  Note that using {xu}, {yu}, {zu} means that the coordinate
-values may be far outside the box bounds printed with the snapshot.
-Using {xsu}, {ysu}, {zsu} is similar to using {xu}, {yu}, {zu}, except
-that the unwrapped coordinates are scaled by the box size. Atoms that
-have passed through a periodic boundary will have the corresponding
-coordinate increased or decreased by 1.0.
+{y}, {z} attributes write atom coordinates "unscaled", in the
+appropriate distance "units"_units.html (Angstroms, sigma, etc).  Use
+{xs}, {ys}, {zs} if you want the coordinates "scaled" to the box size,
+so that each value is 0.0 to 1.0.  If the simulation box is triclinic
+(tilted), then all atom coords will still be between 0.0 and 1.0.
+I.e. actual unscaled (x,y,z) = xs*A + ys*B + zs*C, where (A,B,C) are
+the non-orthogonal vectors of the simulation box edges, as discussed
+in "Section 6.12"_Section_howto.html#howto_12.
+
+Use {xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the
+image flags for each atom.  Unwrapped means that if the atom has
+passed thru a periodic boundary one or more times, the value is
+printed for what the coordinate would be if it had not been wrapped
+back into the periodic box.  Note that using {xu}, {yu}, {zu} means
+that the coordinate values may be far outside the box bounds printed
+with the snapshot.  Using {xsu}, {ysu}, {zsu} is similar to using
+{xu}, {yu}, {zu}, except that the unwrapped coordinates are scaled by
+the box size. Atoms that have passed through a periodic boundary will
+have the corresponding coordinate increased or decreased by 1.0.

 The image flags can be printed directly using the {ix}, {iy}, {iz}
 attributes.  For periodic dimensions, they specify which image of the
@ -255,13 +261,7 @@ The {tqx}, {tqy}, {tqz} attributes are for finite-size particles that
 can sustain a rotational torque due to interactions with other
 particles.

-The {spin}, {eradius}, {ervel}, and {erforce} attributes are for
-particles that represent nuclei and electrons modeled with the
-electronic force field (EFF).  See "atom_style
-electron"_atom_style.html and "pair_style eff"_pair_eff.html for more
-details.
-
-The {c_ID} and {c_ID\[N\]} attributes allow per-atom vectors or arrays
+The {c_ID} and {c_ID\[I\]} attributes allow per-atom vectors or arrays
 calculated by a "compute"_compute.html to be output.  The ID in the
 attribute should be replaced by the actual ID of the compute that has
 been defined previously in the input script.  See the
@ -275,12 +275,14 @@ command.  Instead, global quantities can be output by the
 "thermo_style custom"_thermo_style.html command, and local quantities
 can be output by the dump local command.

-If {c_ID} is used as an attribute, then the per-atom vector calculated
-by the compute is printed.  If {c_ID\[N\]} is used, then N must be in
-the range from 1-M, which will print the Nth column of the M-length
-per-atom array calculated by the compute.
+If {c_ID} is used as a attribute, then the per-atom vector calculated
+by the compute is printed.  If {c_ID\[I\]} is used, then I must be in
+the range from 1-M, which will print the Ith column of the per-atom
+array with M columns calculated by the compute.  See the discussion
+above for how I can be specified with a wildcard asterisk to
+effectively specify multiple values.

-The {f_ID} and {f_ID\[N\]} attributes allow vector or array per-atom
+The {f_ID} and {f_ID\[I\]} attributes allow vector or array per-atom
 quantities calculated by a "fix"_fix.html to be output.  The ID in the
 attribute should be replaced by the actual ID of the fix that has been
 defined previously in the input script.  The "fix
@ -291,9 +293,11 @@ any "compute"_compute.html, "fix"_fix.html, or atom-style
 be written to a dump file.

 If {f_ID} is used as a attribute, then the per-atom vector calculated
-by the fix is printed.  If {f_ID\[N\]} is used, then N must be in the
-range from 1-M, which will print the Nth column of the M-length
-per-atom array calculated by the fix.
+by the fix is printed.  If {f_ID\[I\]} is used, then I must be in the
+range from 1-M, which will print the Ith column of the per-atom array
+with M columns calculated by the fix.  See the discussion above for
+how I can be specified with a wildcard asterisk to effectively specify
+multiple values.

 The {v_name} attribute allows per-atom vectors calculated by a
 "variable"_variable.html to be output.  The name in the attribute
@ -306,6 +310,10 @@ invoke other computes, fixes, or variables when they are evaluated, so
 this is a very general means of creating quantities to output to a
 dump file.

+The {d_name} and {i_name} attributes allow to output custom per atom
+floating point or integer properties that are managed by
+"fix property/atom"_fix_property_atom.html.
+
 See "Section 10"_Section_modify.html of the manual for information
 on how to add new compute and fix styles to LAMMPS to calculate
 per-atom quantities which could then be output into dump files.
--- a/doc/src/fix_adapt.txt
+++ b/doc/src/fix_adapt.txt
@ -22,6 +22,11 @@ attribute = {pair} or {kspace} or {atom} :l
    pparam = parameter to adapt over time
    I,J = type pair(s) to set parameter for
    v_name = variable with name that calculates value of pparam
+  {bond} args = bstyle bparam I v_name
+    bstyle = bond style name, e.g. harmonic
+    bparam = parameter to adapt over time
+    I = type bond to set parameter for
+    v_name = variable with name that calculates value of bparam
  {kspace} arg = v_name
    v_name = variable with name that calculates scale factor on K-space terms
  {atom} args = aparam v_name
@ -42,7 +47,10 @@ keyword = {scale} or {reset} :l
 fix 1 all adapt 1 pair soft a 1 1 v_prefactor
 fix 1 all adapt 1 pair soft a 2* 3 v_prefactor
 fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
-fix 1 all adapt 10 atom diameter v_size :pre
+fix 1 all adapt 10 atom diameter v_size
+
+variable ramp_up equal "ramp(0.01,0.5)"
+fix stretch all adapt 1 bond harmonic r0 1 v_ramp_up :pre

 [Description:]

@ -192,6 +200,19 @@ fix 1 all adapt 1 pair soft a * * v_prefactor :pre

 :line

+The {bond} keyword uses the specified variable to change the value of
+a bond coefficient over time, very similar to how the {pair} keyword
+operates. The only difference is that now a bond coefficient for a
+given bond type is adapted.
+
+Currently {bond} does not support bond_style hybrid nor bond_style
+hybrid/overlay as bond styles. The only bonds that currently are
+working with fix_adapt are
+
+"harmonic"_bond_harmonic.html: k,r0: type bonds :tb(c=3,s=:)
+
+:line
+
 The {kspace} keyword used the specified variable as a scale factor on
 the energy, forces, virial calculated by whatever K-Space solver is
 defined by the "kspace_style"_kspace_style.html command.  If the
--- a/doc/src/fix_cmap.txt
+++ b/doc/src/fix_cmap.txt
@ -27,7 +27,7 @@ fix_modify     myCMAP energy yes :pre
 This command enables CMAP crossterms to be added to simulations which
 use the CHARMM force field.  These are relevant for any CHARMM model
 of a peptide or protein sequences that is 3 or more amino-acid
-residues long; see "(Buck)"_#Buck and "(Brooks)"_#Brooks for details,
+residues long; see "(Buck)"_#Buck and "(Brooks)"_#Brooks2 for details,
 including the analytic energy expressions for CMAP interactions.  The
 CMAP crossterms add additional potential energy contributions to pairs
 of overlapping phi-psi dihedrals of amino-acids, which are important
@ -128,5 +128,5 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 [(Buck)] Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36
 (2006).

-:link(Brooks)
+:link(Brooks2)
 [(Brooks)] Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009).
--- a/doc/src/fix_gcmc.txt
+++ b/doc/src/fix_gcmc.txt
@ -56,26 +56,25 @@ fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk :pre
 [Description:]

 This fix performs grand canonical Monte Carlo (GCMC) exchanges of
-atoms or molecules of the given type with an imaginary ideal gas reservoir at
-the specified T and chemical potential (mu) as discussed in
-"(Frenkel)"_#Frenkel. If used with the "fix nvt"_fix_nh.html command,
-simulations in the grand canonical ensemble (muVT, constant chemical
-potential, constant volume, and constant temperature) can be
+atoms or molecules of the given type with an imaginary ideal gas
+reservoir at the specified T and chemical potential (mu) as discussed
+in "(Frenkel)"_#Frenkel. If used with the "fix nvt"_fix_nh.html
+command, simulations in the grand canonical ensemble (muVT, constant
+chemical potential, constant volume, and constant temperature) can be
 performed.  Specific uses include computing isotherms in microporous
 materials, or computing vapor-liquid coexistence curves.

-Every N timesteps the fix attempts a number of GCMC exchanges (insertions
-or deletions) of gas atoms or molecules of
-the given type between the simulation cell and the imaginary
-reservoir. It also attempts a number of Monte Carlo
-moves (translations and molecule rotations) of gas of the given type
-within the simulation cell or region.  The average number of
-attempted GCMC exchanges is X. The average number of attempted MC moves is M.
-M should typically be chosen to be
-approximately equal to the expected number of gas atoms or molecules
-of the given type within the simulation cell or region,
-which will result in roughly one
-MC translation per atom or molecule per MC cycle.
+Every N timesteps the fix attempts a number of GCMC exchanges
+(insertions or deletions) of gas atoms or molecules of the given type
+between the simulation cell and the imaginary reservoir. It also
+attempts a number of Monte Carlo moves (translations and molecule
+rotations) of gas of the given type within the simulation cell or
+region.  The average number of attempted GCMC exchanges is X. The
+average number of attempted MC moves is M.  M should typically be
+chosen to be approximately equal to the expected number of gas atoms
+or molecules of the given type within the simulation cell or region,
+which will result in roughly one MC translation per atom or molecule
+per MC cycle.

 For MC moves of molecular gasses, rotations and translations are each
 attempted with 50% probability. For MC moves of atomic gasses,
@ -83,50 +82,50 @@ translations are attempted 100% of the time. For MC exchanges of
 either molecular or atomic gasses, deletions and insertions are each
 attempted with 50% probability.

-All inserted particles are always assigned to two groups: the default group
-"all" and the group specified in the fix gcmc command (which can also
-be "all"). In addition, particles are also added to any groups specified
-by the {group} and {grouptype} keywords.
-If inserted particles are individual atoms, they are
-assigned the atom type given by the type argument.  If they are molecules,
-the type argument has no effect and must be set to zero. Instead,
-the type of each atom in the inserted molecule is specified
-in the file read by the "molecule"_molecule.html command.
+All inserted particles are always assigned to two groups: the default
+group "all" and the group specified in the fix gcmc command (which can
+also be "all"). In addition, particles are also added to any groups
+specified by the {group} and {grouptype} keywords.  If inserted
+particles are individual atoms, they are assigned the atom type given
+by the type argument.  If they are molecules, the type argument has no
+effect and must be set to zero. Instead, the type of each atom in the
+inserted molecule is specified in the file read by the
+"molecule"_molecule.html command.

 This fix cannot be used to perform MC insertions of gas atoms or
 molecules other than the exchanged type, but MC deletions,
 translations, and rotations can be performed on any atom/molecule in
 the fix group.  All atoms in the simulation cell can be moved using
-regular time integration translations, e.g. via
-"fix nvt"_fix_nh.html, resulting in a hybrid GCMC+MD simulation. A
-smaller-than-usual timestep size may be needed when running such a
-hybrid simulation, especially if the inserted molecules are not well
-equilibrated.
+regular time integration translations, e.g. via "fix nvt"_fix_nh.html,
+resulting in a hybrid GCMC+MD simulation. A smaller-than-usual
+timestep size may be needed when running such a hybrid simulation,
+especially if the inserted molecules are not well equilibrated.

 This command may optionally use the {region} keyword to define an
 exchange and move volume.  The specified region must have been
 previously defined with a "region"_region.html command.  It must be
 defined with side = {in}.  Insertion attempts occur only within the
-specified region. For non-rectangular regions, random trial
-points are generated within the rectangular bounding box until a point is found
-that lies inside the region. If no valid point is generated after 1000 trials,
-no insertion is performed, but it is counted as an attempted insertion.
-Move and deletion attempt candidates are selected
-from gas atoms or molecules within the region. If there are no candidates,
-no move or deletion is performed, but it is counted as an attempt move
-or deletion. If an attempted move places the atom or molecule center-of-mass outside
-the specified region, a new attempted move is generated. This process is repeated
-until the atom or molecule center-of-mass is inside the specified region.
+specified region. For non-rectangular regions, random trial points are
+generated within the rectangular bounding box until a point is found
+that lies inside the region. If no valid point is generated after 1000
+trials, no insertion is performed, but it is counted as an attempted
+insertion.  Move and deletion attempt candidates are selected from gas
+atoms or molecules within the region. If there are no candidates, no
+move or deletion is performed, but it is counted as an attempt move or
+deletion. If an attempted move places the atom or molecule
+center-of-mass outside the specified region, a new attempted move is
+generated. This process is repeated until the atom or molecule
+center-of-mass is inside the specified region.

 If used with "fix nvt"_fix_nh.html, the temperature of the imaginary
 reservoir, T, should be set to be equivalent to the target temperature
-used in fix nvt. Otherwise, the imaginary reservoir
-will not be in thermal equilibrium with the simulation cell. Also,
-it is important that the temperature used by fix nvt be dynamic,
-which can be achieved as follows:
+used in fix nvt. Otherwise, the imaginary reservoir will not be in
+thermal equilibrium with the simulation cell. Also, it is important
+that the temperature used by fix nvt be dynamic/dof, which can be
+achieved as follows:

 compute mdtemp mdatoms temp
-compute_modify mdtemp dynamic yes
+compute_modify mdtemp dynamic/dof yes
 fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
 fix_modify mdnvt temp mdtemp :pre

@ -137,16 +136,16 @@ interactions. Specifically, avoid performing so many MC translations
 per timestep that atoms can move beyond the neighbor list skin
 distance. See the "neighbor"_neighbor.html command for details.

-When an atom or molecule is to be inserted, its
-coordinates are chosen at a random position within the current
-simulation cell or region, and new atom velocities are randomly chosen from
-the specified temperature distribution given by T. The effective
-temperature for new atom velocities can be increased or decreased
-using the optional keyword {tfac_insert} (see below). Relative
-coordinates for atoms in a molecule are taken from the template
-molecule provided by the user. The center of mass of the molecule
-is placed at the insertion point. The orientation of the molecule
-is chosen at random by rotating about this point.
+When an atom or molecule is to be inserted, its coordinates are chosen
+at a random position within the current simulation cell or region, and
+new atom velocities are randomly chosen from the specified temperature
+distribution given by T. The effective temperature for new atom
+velocities can be increased or decreased using the optional keyword
+{tfac_insert} (see below). Relative coordinates for atoms in a
+molecule are taken from the template molecule provided by the
+user. The center of mass of the molecule is placed at the insertion
+point. The orientation of the molecule is chosen at random by rotating
+about this point.

 Individual atoms are inserted, unless the {mol} keyword is used.  It
 specifies a {template-ID} previously defined using the
@ -158,15 +157,15 @@ command for details.  The only settings required to be in this file
 are the coordinates and types of atoms in the molecule.

 When not using the {mol} keyword, you should ensure you do not delete
-atoms that are bonded to other atoms, or LAMMPS will
-soon generate an error when it tries to find bonded neighbors.  LAMMPS will
-warn you if any of the atoms eligible for deletion have a non-zero
-molecule ID, but does not check for this at the time of deletion.
+atoms that are bonded to other atoms, or LAMMPS will soon generate an
+error when it tries to find bonded neighbors.  LAMMPS will warn you if
+any of the atoms eligible for deletion have a non-zero molecule ID,
+but does not check for this at the time of deletion.

 If you wish to insert molecules via the {mol} keyword, that will be
 treated as rigid bodies, use the {rigid} keyword, specifying as its
-value the ID of a separate "fix rigid/small"_fix_rigid.html
-command which also appears in your input script.
+value the ID of a separate "fix rigid/small"_fix_rigid.html command
+which also appears in your input script.

 NOTE: If you wish the new rigid molecules (and other rigid molecules)
 to be thermostatted correctly via "fix rigid/small/nvt"_fix_rigid.html
@ -179,43 +178,76 @@ their bonds or angles constrained via SHAKE, use the {shake} keyword,
 specifying as its value the ID of a separate "fix
 shake"_fix_shake.html command which also appears in your input script.

-Optionally, users may specify the maximum rotation angle for
-molecular rotations using the {maxangle} keyword and specifying
-the angle in degrees. Rotations are performed by generating a random
-point on the unit sphere and a random rotation angle on the
-range \[0,maxangle). The molecule is then rotated by that angle about an
+Optionally, users may specify the maximum rotation angle for molecular
+rotations using the {maxangle} keyword and specifying the angle in
+degrees. Rotations are performed by generating a random point on the
+unit sphere and a random rotation angle on the range
+\[0,maxangle). The molecule is then rotated by that angle about an
 axis passing through the molecule center of mass. The axis is parallel
-to the unit vector defined by the point on the unit sphere.
-The same procedure is used for randomly rotating molecules when they
-are inserted, except that the maximum angle is 360 degrees.
+to the unit vector defined by the point on the unit sphere.  The same
+procedure is used for randomly rotating molecules when they are
+inserted, except that the maximum angle is 360 degrees.

-Note that fix GCMC does not use configurational bias
-MC or any other kind of sampling of intramolecular degrees of freedom.
-Inserted molecules can have different orientations, but they will all
-have the same intramolecular configuration,
-which was specified in the molecule command input.
+Note that fix GCMC does not use configurational bias MC or any other
+kind of sampling of intramolecular degrees of freedom.  Inserted
+molecules can have different orientations, but they will all have the
+same intramolecular configuration, which was specified in the molecule
+command input.

 For atomic gasses, inserted atoms have the specified atom type, but
-deleted atoms are any atoms that have been inserted or that belong
-to the user-specified fix group. For molecular gasses, exchanged
-molecules use the same atom types as in the template molecule
-supplied by the user.  In both cases, exchanged
-atoms/molecules are assigned to two groups: the default group "all"
-and the group specified in the fix gcmc command (which can also be
-"all").
+deleted atoms are any atoms that have been inserted or that belong to
+the user-specified fix group. For molecular gasses, exchanged
+molecules use the same atom types as in the template molecule supplied
+by the user.  In both cases, exchanged atoms/molecules are assigned to
+two groups: the default group "all" and the group specified in the fix
+gcmc command (which can also be "all").

-The gas reservoir pressure can be specified using the {pressure}
-keyword, in which case the user-specified chemical potential is
-ignored. For non-ideal gas reservoirs, the user may also specify the
-fugacity coefficient using the {fugacity_coeff} keyword.
+The chemical potential is a user-specified input parameter defined
+as:
+
+:c,image(Eqs/fix_gcmc1.jpg)
+
+The second term mu_ex is the excess chemical potential due to
+energetic interactions and is formally zero for the fictitious gas
+reservoir but is non-zero for interacting systems. So, while the
+chemical potential of the reservoir and the simulation cell are equal,
+mu_ex is not, and as a result, the densities of the two are generally
+quite different.  The first term mu_id is the ideal gas contribution
+to the chemical potential.  mu_id can be related to the density or
+pressure of the fictitious gas reservoir by:
+
+:c,image(Eqs/fix_gcmc2.jpg)
+
+where k is Boltzman's constant,
+T is the user-specified temperature, rho is the number density,
+P is the pressure, and phi is the fugacity coefficient.
+The constant Lambda is required for dimensional consistency.
+For all unit styles except {lj} it is defined as the thermal
+de Broglie wavelength
+
+:c,image(Eqs/fix_gcmc3.jpg)
+
+where h is Planck's constant, and m is the mass of the exchanged atom
+or molecule.  For unit style {lj}, Lambda is simply set to the
+unity. Note that prior to March 2017, lambda for unit style {lj} was
+calculated using the above formula with h set to the rather specific
+value of 0.18292026.  Chemical potential under the old definition can
+be converted to an equivalent value under the new definition by
+subtracting 3kTln(Lambda_old).
+
+As an alternative to specifying mu directly, the ideal gas reservoir
+can be defined by its pressure P using the {pressure} keyword, in
+which case the user-specified chemical potential is ignored. The user
+may also specify the fugacity coefficient phi using the
+{fugacity_coeff} keyword, which defaults to unity.

 The {full_energy} option means that fix GCMC will compute the total
 potential energy of the entire simulated system. The total system
 energy before and after the proposed GCMC move is then used in the
 Metropolis criterion to determine whether or not to accept the
-proposed GCMC move. By default, this option is off, in which case
-only partial energies are computed to determine the difference in
-energy that would be caused by the proposed GCMC move.
+proposed GCMC move. By default, this option is off, in which case only
+partial energies are computed to determine the difference in energy
+that would be caused by the proposed GCMC move.

 The {full_energy} option is needed for systems with complicated
 potential energy calculations, including the following:
@ -224,7 +256,7 @@ potential energy calculations, including the following:
  many-body pair styles
  hybrid pair styles
  eam pair styles
-  triclinic systems
+  tail corrections
  need to include potential energy contributions from other fixes :ul

 In these cases, LAMMPS will automatically apply the {full_energy}
@ -233,42 +265,43 @@ keyword and issue a warning message.
 When the {mol} keyword is used, the {full_energy} option also includes
 the intramolecular energy of inserted and deleted molecules. If this
 is not desired, the {intra_energy} keyword can be used to define an
-amount of energy that is subtracted from the final energy when a molecule
-is inserted, and added to the initial energy when a molecule is
-deleted. For molecules that have a non-zero intramolecular energy, this
-will ensure roughly the same behavior whether or not the {full_energy}
-option is used.
+amount of energy that is subtracted from the final energy when a
+molecule is inserted, and added to the initial energy when a molecule
+is deleted. For molecules that have a non-zero intramolecular energy,
+this will ensure roughly the same behavior whether or not the
+{full_energy} option is used.

-Inserted atoms and molecules are assigned random velocities based on the
-specified temperature T. Because the relative velocity of
-all atoms in the molecule is zero, this may result in inserted molecules
-that are systematically too cold. In addition, the intramolecular potential
-energy of the inserted molecule may cause the kinetic energy
-of the molecule to quickly increase or decrease after insertion.
-The {tfac_insert} keyword allows the user to counteract these effects
-by changing the temperature used to assign velocities to
-inserted atoms and molecules by a constant factor. For a
-particular application, some experimentation may be required
-to find a value of {tfac_insert} that results in inserted molecules that
-equilibrate quickly to the correct temperature.
+Inserted atoms and molecules are assigned random velocities based on
+the specified temperature T. Because the relative velocity of all
+atoms in the molecule is zero, this may result in inserted molecules
+that are systematically too cold. In addition, the intramolecular
+potential energy of the inserted molecule may cause the kinetic energy
+of the molecule to quickly increase or decrease after insertion.  The
+{tfac_insert} keyword allows the user to counteract these effects by
+changing the temperature used to assign velocities to inserted atoms
+and molecules by a constant factor. For a particular application, some
+experimentation may be required to find a value of {tfac_insert} that
+results in inserted molecules that equilibrate quickly to the correct
+temperature.

 Some fixes have an associated potential energy. Examples of such fixes
 include: "efield"_fix_efield.html, "gravity"_fix_gravity.html,
 "addforce"_fix_addforce.html, "langevin"_fix_langevin.html,
-"restrain"_fix_restrain.html, "temp/berendsen"_fix_temp_berendsen.html,
+"restrain"_fix_restrain.html,
+"temp/berendsen"_fix_temp_berendsen.html,
 "temp/rescale"_fix_temp_rescale.html, and "wall fixes"_fix_wall.html.
 For that energy to be included in the total potential energy of the
-system (the quantity used when performing GCMC moves),
-you MUST enable the "fix_modify"_fix_modify.html {energy} option for
-that fix.  The doc pages for individual "fix"_fix.html commands
-specify if this should be done.
+system (the quantity used when performing GCMC moves), you MUST enable
+the "fix_modify"_fix_modify.html {energy} option for that fix.  The
+doc pages for individual "fix"_fix.html commands specify if this
+should be done.

 Use the {charge} option to insert atoms with a user-specified point
-charge. Note that doing so will cause the system to become non-neutral.
-LAMMPS issues a warning when using long-range electrostatics (kspace)
-with non-neutral systems. See the
-"compute group/group"_compute_group_group.html documentation for more
-details about simulating non-neutral systems with kspace on.
+charge. Note that doing so will cause the system to become
+non-neutral.  LAMMPS issues a warning when using long-range
+electrostatics (kspace) with non-neutral systems. See the "compute
+group/group"_compute_group_group.html documentation for more details
+about simulating non-neutral systems with kspace on.

 Use of this fix typically will cause the number of atoms to fluctuate,
 therefore, you will want to use the
@ -276,16 +309,23 @@ therefore, you will want to use the
 current number of atoms is used as a normalizing factor each time
 temperature is computed.  Here is the necessary command:

+NOTE: If the density of the cell is initially very small or zero, and
+increases to a much larger density after a period of equilibration,
+then certain quantities that are only calculated once at the start
+(kspace parameters, tail corrections) may no longer be accurate.  The
+solution is to start a new simulation after the equilibrium density
+has been reached.
+
 With some pair_styles, such as "Buckingham"_pair_buck.html,
-"Born-Mayer-Huggins"_pair_born.html and "ReaxFF"_pair_reax_c.html,
-two atoms placed close to each other may have an arbitrary large, 
-negative potential energy due to the functional form of the potential.
-While these unphysical configurations are inaccessible
-to typical dynamical trajectories,
-they can be generated by Monte Carlo moves. The {overlap_cutoff}
-keyword suppresses these moves by effectively assigning an 
-infinite positive energy to all new configurations that place any
-pair of atoms closer than the specified overlap cutoff distance.
+"Born-Mayer-Huggins"_pair_born.html and "ReaxFF"_pair_reax_c.html, two
+atoms placed close to each other may have an arbitrary large, negative
+potential energy due to the functional form of the potential.  While
+these unphysical configurations are inaccessible to typical dynamical
+trajectories, they can be generated by Monte Carlo moves. The
+{overlap_cutoff} keyword suppresses these moves by effectively
+assigning an infinite positive energy to all new configurations that
+place any pair of atoms closer than the specified overlap cutoff
+distance.

 compute_modify thermo_temp dynamic yes :pre

@ -295,10 +335,10 @@ derived from LJ parameters for argon, where h* = h/sqrt(sigma^2 *
 epsilon * mass), sigma = 3.429 angstroms, epsilon/k = 121.85 K, and
 mass = 39.948 amu.

-The {group} keyword assigns all inserted atoms to the "group"_group.html
-of the group-ID value. The {grouptype} keyword assigns all
-inserted atoms of the specified type to the "group"_group.html
-of the group-ID value.
+The {group} keyword assigns all inserted atoms to the
+"group"_group.html of the group-ID value. The {grouptype} keyword
+assigns all inserted atoms of the specified type to the
+"group"_group.html of the group-ID value.

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

@ -346,15 +386,15 @@ well in parallel. Only usable for 3D simulations.
 Note that very lengthy simulations involving insertions/deletions of
 billions of gas molecules may run out of atom or molecule IDs and
 trigger an error, so it is better to run multiple shorter-duration
-simulations. Likewise, very large molecules have not been tested
-and may turn out to be problematic.
+simulations. Likewise, very large molecules have not been tested and
+may turn out to be problematic.

 Use of multiple fix gcmc commands in the same input script can be
 problematic if using a template molecule. The issue is that the
-user-referenced template molecule in the second fix gcmc command
-may no longer exist since it might have been deleted by the first
-fix gcmc command. An existing template molecule will need to be
-referenced by the user for each subsequent fix gcmc command.
+user-referenced template molecule in the second fix gcmc command may
+no longer exist since it might have been deleted by the first fix gcmc
+command. An existing template molecule will need to be referenced by
+the user for each subsequent fix gcmc command.

 [Related commands:]

@ -366,7 +406,7 @@ referenced by the user for each subsequent fix gcmc command.
 [Default:]

 The option defaults are mol = no, maxangle = 10, overlap_cutoff = 0.0,
-and full_energy = no,
+fugacity_coeff = 1, and full_energy = no, 
 except for the situations where full_energy is required, as
 listed above.

--- a/doc/src/fix_modify.txt
+++ b/doc/src/fix_modify.txt
@ -91,7 +91,7 @@ their DOF are assumed to be constant.  If you are adding atoms or
 molecules to the system (see the "fix pour"_fix_pour.html, "fix
 deposit"_fix_deposit.html, and "fix gcmc"_fix_gcmc.html commands) or
 expect atoms or molecules to be lost (e.g. due to exiting the
-simulation box or via "fix evaporation"_fix_evaporation.html), then
+simulation box or via "fix evaporate"_fix_evaporate.html), then
 this option should be used to insure the temperature is correctly
 normalized.

--- a/doc/src/kspace_modify.txt
+++ b/doc/src/kspace_modify.txt
@ -290,9 +290,10 @@ to be specified using the {gewald/disp}, {mesh/disp},
 {force/disp/real} or {force/disp/kspace} keywords, or
 the code will stop with an error message. When this option is set to
 {yes}, the error message will not appear and the simulation will start.
-For a typical application, using the automatic parameter generation will provide
-simulations that are either inaccurate or slow. Using this option is thus not
-recommended. For guidelines on how to obtain good parameters, see the "How-To"_Section_howto.html#howto_23 discussion.
+For a typical application, using the automatic parameter generation
+will provide simulations that are either inaccurate or slow. Using this
+option is thus not recommended. For guidelines on how to obtain good
+parameters, see the "How-To"_Section_howto.html#howto_24 discussion.

 [Restrictions:] none

--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@ -464,6 +464,7 @@ pair_nb3b_harmonic.html
 pair_nm.html
 pair_none.html
 pair_oxdna.html
+pair_oxdna2.html
 pair_peri.html
 pair_polymorphic.html
 pair_quip.html
--- a/doc/src/pair_buck.txt
+++ b/doc/src/pair_buck.txt
@ -75,7 +75,7 @@ Lennard-Jones 12/6) given by
 :c,image(Eqs/pair_buck.jpg)

 where rho is an ionic-pair dependent length parameter, and Rc is the
-cutoff on both terms.
+cutoff on both terms. 

 The styles with {coul/cut} or {coul/long} or {coul/msm} add a
 Coulombic term as described for the "lj/cut"_pair_lj.html pair styles.
@ -120,6 +120,9 @@ cutoff (distance units)
 cutoff2 (distance units) :ul

 The second coefficient, rho, must be greater than zero.
+The coefficients A, rho, and C can be written as analytical expressions
+of epsilon and sigma, in analogy to the Lennard-Jones potential
+"(Khrapak)"_#Khrapak.

 The latter 2 coefficients are optional.  If not specified, the global
 A,C and Coulombic cutoffs are used.  If only one cutoff is specified,
@ -127,7 +130,6 @@ it is used as the cutoff for both A,C and Coulombic interactions for
 this type pair.  If both coefficients are specified, they are used as
 the A,C and Coulombic cutoffs for this type pair.  You cannot specify
 2 cutoffs for style {buck}, since it has no Coulombic terms.
-
 For {buck/coul/long} only the LJ cutoff can be specified since a
 Coulombic cutoff cannot be specified for an individual I,J type pair.
 All type pairs use the same global Coulombic cutoff specified in the
@ -194,3 +196,6 @@ only enabled if LAMMPS was built with that package.  See the
 "pair_coeff"_pair_coeff.html, "pair_style born"_pair_born.html

 [Default:] none
+
+:link(Khrapak)
+[(Khrapak)] Khrapak, Chaudhuri, and Morfill, J Chem Phys, 134, 054120 (2011).
--- a/doc/src/pair_charmm.txt
+++ b/doc/src/pair_charmm.txt
@ -49,8 +49,8 @@ args = list of arguments for a particular style :ul

 pair_style lj/charmm/coul/charmm 8.0 10.0
 pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
-pair_style lj/charmmfsw/coul/charmmfsh 8.0 10.0 
-pair_style lj/charmmfsw/coul/charmmfsh 8.0 10.0 7.0 9.0
+pair_style lj/charmmfsw/coul/charmmfsh 10.0 12.0
+pair_style lj/charmmfsw/coul/charmmfsh 10.0 12.0 9.0
 pair_coeff * * 100.0 2.0
 pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre

@ -84,9 +84,9 @@ CHARMM force field.
 The styles with {charmm} (not {charmmfsw} or {charmmfsh}) in their
 name are the older, original LAMMPS implementations.  They compute the
 LJ and Coulombic interactions with an energy switching function (esw,
-a cubic polynomial, shown in the formula below), which ramps the
-energy smoothly to zero between the inner and outer cutoff.  This can
-cause irregularities in pair-wise forces (due to the discontinuous 2nd
+shown in the formula below as S(r)), which ramps the energy smoothly
+to zero between the inner and outer cutoff.  This can cause
+irregularities in pair-wise forces (due to the discontinuous 2nd
 derivative of energy at the boundaries of the switching region), which
 in some cases can result in detectable artifacts in an MD simulation.

@ -94,14 +94,15 @@ The newer styles with {charmmfsw} or {charmmfsh} in their name replace
 the energy switching with force switching (fsw) and force shifting
 (fsh) functions, for LJ and Coulombic interactions respectively.
 These follow the formulas and description given in
-"(Steinbach)"_#Steinbach and "(Brooks)"_#Brooks to minimize these
+"(Steinbach)"_#Steinbach and "(Brooks)"_#Brooks1 to minimize these
 artifacts.

 NOTE: The newer {charmmfsw} or {charmmfsh} styles were released in
 March 2017.  We recommend they be used instead of the older {charmm}
-styles.  Eventually code from the new styles will propagate into the
-related pair styles (e.g. implicit, accelerator, free energy
-variants).
+styles.  This includes the newer "dihedral_style
+charmmfsw"_dihedral_charmm.html command.  Eventually code from the new
+styles will propagate into the related pair styles (e.g. implicit,
+accelerator, free energy variants).

 The general CHARMM formulas are as follows

@ -248,7 +249,7 @@ the MOLECULE and KSPACE packages are installed by default.

 :line

-:link(Brooks)
+:link(Brooks1)
 [(Brooks)] Brooks, et al, J Comput Chem, 30, 1545 (2009).

 :link(pair-MacKerell)
--- a/doc/src/pair_oxdna.txt
+++ b/doc/src/pair_oxdna.txt
@ -14,15 +14,23 @@ pair_style oxdna/coaxstk command :h3

 [Syntax:]

-pair_style style :pre
+pair_style style1 :pre

-style = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk} :ul
+pair_coeff * * style2 args :pre
+
+style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk} :ul
+
+style2 = {oxdna/stk}
+args = list of arguments for these two particular styles :ul
+
+  {oxdna2/stk} args = T 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
+    T = temperature (oxDNA units, 0.1 = 300 K) :pre

 [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/stk     0.1 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
@ -42,19 +50,23 @@ The exact functional form of the pair styles is rather complex, which manifests
 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
+We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil1 and "(Ouldridge)"_#Ouldridge1
 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.html). The coefficients
+"bond_style oxdna/fene"_bond_oxdna.html). With one exception the coefficients
 in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
+The exception is the first coefficient after {oxdna/stk} (T=0.1 in the above example).  
+When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html 
+or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
+the temperature coefficients have to be matched to the one used in the fix.

-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, 
+Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
+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 
+the setup tool and the performance of the LAMMPS-implementation of oxDNA
 can be found "here"_PDF/USER-CGDNA-overview.pdf.

 :line
@ -67,14 +79,14 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]

-"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html 
+"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html, 
+"bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html

 [Default:] none

 :line

-:link(Ouldridge-DPhil)
+:link(Ouldridge-DPhil1)
 [(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
-
-:link(Ouldridge)
+:link(Ouldridge1)
 [(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
--- a/doc/src/pair_oxdna2.txt
+++ b/doc/src/pair_oxdna2.txt
@ -0,0 +1,102 @@
+"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 oxdna2/excv command :h3
+pair_style oxdna2/stk command :h3
+pair_style oxdna2/hbond command :h3
+pair_style oxdna2/xstk command :h3
+pair_style oxdna2/coaxstk command :h3
+pair_style oxdna2/dh command :h3
+
+[Syntax:]
+
+pair_style style1 :pre
+
+pair_coeff * * style2 args :pre
+
+style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh} :ul
+
+style2 = {oxdna2/stk} or {oxdna2/dh}
+args = list of arguments for these two particular styles :ul
+
+  {oxdna2/stk} args = T 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
+    T = temperature (oxDNA units, 0.1 = 300 K)
+  {oxdna2/dh} args = T rhos qeff
+    T = temperature (oxDNA units, 0.1 = 300 K)
+    rhos = salt concentration (mole per litre)
+    qeff = effective charge (elementary charges) :pre
+
+[Examples:]
+
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
+pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna2/stk     0.1 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 * * oxdna2/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 oxdna2/hbond   1.0678 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 oxdna2/hbond   1.0678 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 * * oxdna2/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 * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      0.1 1.0 0.815 :pre
+
+[Description:]
+
+The {oxdna2} 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 {oxdna2/excv}, the stacking {oxdna2/stk}, cross-stacking {oxdna2/xstk}
+and coaxial stacking interaction {oxdna2/coaxstk}, electrostatic Debye-Hueckel interaction {oxdna2/dh}
+as well as the hydrogen-bonding interaction {oxdna2/hbond} between complementary pairs of nucleotides on
+opposite strands.
+
+The exact functional form of the pair styles is rather complex. 
+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 "(Snodin)"_#Snodin and the original oxDNA publications "(Ouldridge-DPhil)"_#Ouldridge-DPhil2
+and  "(Ouldridge)"_#Ouldridge2 for a detailed description of the oxDNA2 force field.
+
+NOTE: These pair styles have to be used together with the related oxDNA2 bond style
+{oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of
+"bond_style oxdna2/fene"_bond_oxdna.html). Almost all coefficients
+in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
+Exceptions are the first coefficient after {oxdna2/stk} (T=0.1 in the above example) and the coefficients 
+after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
+e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
+the temperature coefficients have to be matched to the one used in the fix.
+
+Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
+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 oxdna2/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html,
+"bond_style oxdna/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html 
+
+[Default:] none
+
+:line
+
+:link(Snodin)
+[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
+
+:link(Ouldridge-DPhil2)
+[(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
+
+:link(Ouldridge2)
+[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@ -68,6 +68,7 @@ Pair Styles :h1
   pair_nm
   pair_none
   pair_oxdna
+   pair_oxdna2
   pair_peri
   pair_polymorphic
   pair_quip
--- a/examples/USER/cgdna/README
+++ b/examples/USER/cgdna/README
@ -7,9 +7,9 @@ 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
+A - C - G - T - A
 |   |   |   |   |
-T - T - T - T - T     
+T - G - C - A - T     

 /examples/duplex2:
 Input, data and log files for a nicked DNA duplex (double-stranded DNA) 
@ -18,9 +18,9 @@ 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
+A - C - G - T - A - C - G - T
 |   |   |   |   |   |   |   |
-T - T - T   T - T - T - T - T
+T - G - C - A   T - G - C - A

 /util:
 This directory contains a simple python setup tool which creates 
--- a/examples/USER/cgdna/examples/duplex1/data.duplex1
+++ b/examples/USER/cgdna/examples/duplex1/data.duplex1
@ -1,74 +0,0 @@
-# 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
@ -1,75 +0,0 @@
-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
@ -1,97 +0,0 @@
-# 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
@ -1,75 +0,0 @@
-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/examples/oxDNA/duplex1/data.duplex1
+++ b/examples/USER/cgdna/examples/oxDNA/duplex1/data.duplex1
@ -0,0 +1,73 @@
+# 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
+
+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 -6.000000000000001e-01  0.000000000000000e+00  0.000000000000000e+00 1 1 1
+2 2 -4.860249842674776e-01 -3.518234140414736e-01  3.897628551303122e-01 1 1 1
+3 3 -1.874009511073395e-01 -5.699832309147915e-01  7.795257102606244e-01 1 1 1
+4 4  1.824198365552941e-01 -5.715968887521518e-01  1.169288565390937e+00 1 1 1
+5 1  4.829362784135484e-01 -3.560513319622209e-01  1.559051420521249e+00 1 1 1
+6 4 -4.829362784135484e-01  3.560513319622209e-01  1.559051420521249e+00 2 1 1
+7 1 -1.824198365552941e-01  5.715968887521516e-01  1.169288565390937e+00 2 1 1
+8 2  1.874009511073395e-01  5.699832309147913e-01  7.795257102606243e-01 2 1 1
+9 3  4.860249842674775e-01  3.518234140414733e-01  3.897628551303121e-01 2 1 1
+10 4  5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1
+
+# Atom-ID, translational, rotational velocity
+Velocities
+
+1  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+2  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+3  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+4  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+5  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+6  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+7  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+8  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+9  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+10  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+
+# Atom-ID, shape, quaternion
+Ellipsoids
+
+1  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  1.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+2  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.513258223252946e-01  0.000000000000000e+00  0.000000000000000e+00  3.081869234362515e-01
+3  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  8.100416404457962e-01  0.000000000000000e+00  0.000000000000000e+00  5.863723567357894e-01
+4  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  5.899012371043606e-01  0.000000000000000e+00  0.000000000000000e+00  8.074754054847398e-01
+5  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  3.123349185122326e-01  0.000000000000000e+00  0.000000000000000e+00  9.499720515246527e-01
+6  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.499720515246527e-01 -3.123349185122326e-01 -0.000000000000000e+00
+7  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  8.074754054847401e-01 -5.899012371043604e-01  0.000000000000000e+00
+8  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  5.863723567357896e-01 -8.100416404457959e-01  0.000000000000000e+00
+9  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01  9.513258223252947e-01  0.000000000000000e+00
+10  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00  1.110223024625157e-16  1.000000000000000e+00 -0.000000000000000e+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/oxDNA/duplex1/input.duplex1
+++ b/examples/USER/cgdna/examples/oxDNA/duplex1/input.duplex1
@ -0,0 +1,77 @@
+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     0.1 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/dot
+#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+#fix 1 all nve/asphere
+#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
+
+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/oxDNA/duplex1/log.24Mar17.duplex1.g++.1
+++ b/examples/USER/cgdna/examples/oxDNA/duplex1/log.24Mar17.duplex1.g++.1
--- a/examples/USER/cgdna/examples/oxDNA/duplex1/log.24Mar17.duplex1.g++.4
+++ b/examples/USER/cgdna/examples/oxDNA/duplex1/log.24Mar17.duplex1.g++.4
--- a/examples/USER/cgdna/examples/oxDNA/duplex2/data.duplex2
+++ b/examples/USER/cgdna/examples/oxDNA/duplex2/data.duplex2
@ -0,0 +1,96 @@
+# LAMMPS data file
+16 atoms
+16 ellipsoids
+13 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
+
+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 -6.000000000000001e-01  0.000000000000000e+00  0.000000000000000e+00 1 1 1
+2 2 -4.860249842674776e-01 -3.518234140414736e-01  3.897628551303122e-01 1 1 1
+3 3 -1.874009511073395e-01 -5.699832309147915e-01  7.795257102606244e-01 1 1 1
+4 4  1.824198365552941e-01 -5.715968887521518e-01  1.169288565390937e+00 1 1 1
+5 1  4.829362784135484e-01 -3.560513319622209e-01  1.559051420521249e+00 1 1 1
+6 2  5.999771538385027e-01 -5.235921299024461e-03  1.948814275651561e+00 1 1 1
+7 3  4.890766774371325e-01  3.475687034056071e-01  2.338577130781873e+00 1 1 1
+8 4  1.923677943514057e-01  5.683261666476170e-01  2.728339985912185e+00 1 1 1
+9 1 -1.923677943514057e-01 -5.683261666476170e-01  2.728339985912185e+00 2 1 1
+10 2 -4.890766774371324e-01 -3.475687034056071e-01  2.338577130781873e+00 2 1 1
+11 3 -5.999771538385025e-01  5.235921299024461e-03  1.948814275651561e+00 2 1 1
+12 4 -4.829362784135481e-01  3.560513319622207e-01  1.559051420521249e+00 2 1 1
+13 1 -1.824198365552940e-01  5.715968887521514e-01  1.169288565390936e+00 2 1 1
+14 2  1.874009511073395e-01  5.699832309147912e-01  7.795257102606241e-01 2 1 1
+15 3  4.860249842674773e-01  3.518234140414733e-01  3.897628551303119e-01 2 1 1
+16 4  5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1
+
+# Atom-ID, translational, rotational velocity
+Velocities
+
+1  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+2  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+3  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+4  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+5  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+6  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+7  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+8  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+9  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+10  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+11  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+12  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+13  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+14  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+15  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+16  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+
+# Atom-ID, shape, quaternion
+Ellipsoids
+
+1  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  1.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+2  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.513258223252946e-01  0.000000000000000e+00  0.000000000000000e+00  3.081869234362515e-01
+3  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  8.100416404457962e-01  0.000000000000000e+00  0.000000000000000e+00  5.863723567357894e-01
+4  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  5.899012371043606e-01  0.000000000000000e+00  0.000000000000000e+00  8.074754054847398e-01
+5  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  3.123349185122326e-01  0.000000000000000e+00  0.000000000000000e+00  9.499720515246527e-01
+6  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  4.363309284746654e-03  0.000000000000000e+00  0.000000000000000e+00  9.999904807207346e-01
+7  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -3.040330609254902e-01  0.000000000000000e+00  0.000000000000000e+00  9.526614812535865e-01
+8  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  5.828323126827837e-01  0.000000000000000e+00  0.000000000000000e+00 -8.125924533816677e-01
+9  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  8.125924533816681e-01  5.828323126827832e-01 -0.000000000000000e+00
+10  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.526614812535864e-01  3.040330609254902e-01  0.000000000000000e+00
+11  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.999904807207346e-01 -4.363309284746654e-03  0.000000000000000e+00
+12  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.499720515246526e-01 -3.123349185122325e-01  0.000000000000000e+00
+13  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  8.074754054847402e-01 -5.899012371043603e-01  0.000000000000000e+00
+14  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  5.863723567357898e-01 -8.100416404457959e-01  0.000000000000000e+00
+15  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01  9.513258223252948e-01  0.000000000000000e+00
+16  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00  2.775557561562893e-17  1.000000000000000e+00 -0.000000000000000e+00
+
+# Bond topology
+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  9  10
+9  1  10  11
+10  1  11  12
+11  1  13  14
+12  1  14  15
+13  1  15  16
--- a/examples/USER/cgdna/examples/oxDNA/duplex2/input.duplex2
+++ b/examples/USER/cgdna/examples/oxDNA/duplex2/input.duplex2
@ -0,0 +1,77 @@
+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     0.1 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/dot
+fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+#fix 1 all nve/asphere
+#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
+
+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/oxDNA/duplex2/log.24Mar17.duplex2.g++.1
+++ b/examples/USER/cgdna/examples/oxDNA/duplex2/log.24Mar17.duplex2.g++.1
--- a/examples/USER/cgdna/examples/oxDNA/duplex2/log.24Mar17.duplex2.g++.4
+++ b/examples/USER/cgdna/examples/oxDNA/duplex2/log.24Mar17.duplex2.g++.4
--- a/examples/USER/cgdna/examples/oxDNA2/duplex1/data.duplex1
+++ b/examples/USER/cgdna/examples/oxDNA2/duplex1/data.duplex1
@ -0,0 +1,73 @@
+# 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
+
+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 -6.000000000000001e-01  0.000000000000000e+00  0.000000000000000e+00 1 1 1
+2 2 -4.860249842674776e-01 -3.518234140414736e-01  3.897628551303122e-01 1 1 1
+3 3 -1.874009511073395e-01 -5.699832309147915e-01  7.795257102606244e-01 1 1 1
+4 4  1.824198365552941e-01 -5.715968887521518e-01  1.169288565390937e+00 1 1 1
+5 1  4.829362784135484e-01 -3.560513319622209e-01  1.559051420521249e+00 1 1 1
+6 4 -4.829362784135484e-01  3.560513319622209e-01  1.559051420521249e+00 2 1 1
+7 1 -1.824198365552941e-01  5.715968887521516e-01  1.169288565390937e+00 2 1 1
+8 2  1.874009511073395e-01  5.699832309147913e-01  7.795257102606243e-01 2 1 1
+9 3  4.860249842674775e-01  3.518234140414733e-01  3.897628551303121e-01 2 1 1
+10 4  5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1
+
+# Atom-ID, translational, rotational velocity
+Velocities
+
+1  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+2  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+3  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+4  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+5  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+6  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+7  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+8  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+9  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+10  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+
+# Atom-ID, shape, quaternion
+Ellipsoids
+
+1  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  1.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+2  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.513258223252946e-01  0.000000000000000e+00  0.000000000000000e+00  3.081869234362515e-01
+3  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  8.100416404457962e-01  0.000000000000000e+00  0.000000000000000e+00  5.863723567357894e-01
+4  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  5.899012371043606e-01  0.000000000000000e+00  0.000000000000000e+00  8.074754054847398e-01
+5  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  3.123349185122326e-01  0.000000000000000e+00  0.000000000000000e+00  9.499720515246527e-01
+6  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.499720515246527e-01 -3.123349185122326e-01 -0.000000000000000e+00
+7  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  8.074754054847401e-01 -5.899012371043604e-01  0.000000000000000e+00
+8  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  5.863723567357896e-01 -8.100416404457959e-01  0.000000000000000e+00
+9  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01  9.513258223252947e-01  0.000000000000000e+00
+10  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00  1.110223024625157e-16  1.000000000000000e+00 -0.000000000000000e+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/oxDNA2/duplex1/input.duplex1
+++ b/examples/USER/cgdna/examples/oxDNA2/duplex1/input.duplex1
@ -0,0 +1,78 @@
+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 oxdna2/fene
+bond_coeff * 2.0 0.25 0.7564
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
+pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna2/stk     0.1 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 * * oxdna2/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 oxdna2/hbond   1.0678 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 oxdna2/hbond   1.0678 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 * * oxdna2/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 * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      0.1 1.0 0.815
+
+# NVE ensemble
+fix 1 all nve/dot
+#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+#fix 1 all nve/asphere
+#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
+
+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/oxDNA2/duplex1/log.24Mar17.duplex1.g++.1
+++ b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.24Mar17.duplex1.g++.1
--- a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.24Mar17.duplex1.g++.4
+++ b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.24Mar17.duplex1.g++.4
--- a/examples/USER/cgdna/examples/oxDNA2/duplex2/data.duplex2
+++ b/examples/USER/cgdna/examples/oxDNA2/duplex2/data.duplex2
@ -0,0 +1,96 @@
+# LAMMPS data file
+16 atoms
+16 ellipsoids
+13 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
+
+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 -6.000000000000001e-01  0.000000000000000e+00  0.000000000000000e+00 1 1 1
+2 2 -4.860249842674776e-01 -3.518234140414736e-01  3.897628551303122e-01 1 1 1
+3 3 -1.874009511073395e-01 -5.699832309147915e-01  7.795257102606244e-01 1 1 1
+4 4  1.824198365552941e-01 -5.715968887521518e-01  1.169288565390937e+00 1 1 1
+5 1  4.829362784135484e-01 -3.560513319622209e-01  1.559051420521249e+00 1 1 1
+6 2  5.999771538385027e-01 -5.235921299024461e-03  1.948814275651561e+00 1 1 1
+7 3  4.890766774371325e-01  3.475687034056071e-01  2.338577130781873e+00 1 1 1
+8 4  1.923677943514057e-01  5.683261666476170e-01  2.728339985912185e+00 1 1 1
+9 1 -1.923677943514057e-01 -5.683261666476170e-01  2.728339985912185e+00 2 1 1
+10 2 -4.890766774371324e-01 -3.475687034056071e-01  2.338577130781873e+00 2 1 1
+11 3 -5.999771538385025e-01  5.235921299024461e-03  1.948814275651561e+00 2 1 1
+12 4 -4.829362784135481e-01  3.560513319622207e-01  1.559051420521249e+00 2 1 1
+13 1 -1.824198365552940e-01  5.715968887521514e-01  1.169288565390936e+00 2 1 1
+14 2  1.874009511073395e-01  5.699832309147912e-01  7.795257102606241e-01 2 1 1
+15 3  4.860249842674773e-01  3.518234140414733e-01  3.897628551303119e-01 2 1 1
+16 4  5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1
+
+# Atom-ID, translational, rotational velocity
+Velocities
+
+1  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+2  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+3  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+4  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+5  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+6  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+7  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+8  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+9  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+10  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+11  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+12  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+13  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+14  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+15  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+16  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+
+# Atom-ID, shape, quaternion
+Ellipsoids
+
+1  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  1.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00  0.000000000000000e+00
+2  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  9.513258223252946e-01  0.000000000000000e+00  0.000000000000000e+00  3.081869234362515e-01
+3  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  8.100416404457962e-01  0.000000000000000e+00  0.000000000000000e+00  5.863723567357894e-01
+4  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  5.899012371043606e-01  0.000000000000000e+00  0.000000000000000e+00  8.074754054847398e-01
+5  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  3.123349185122326e-01  0.000000000000000e+00  0.000000000000000e+00  9.499720515246527e-01
+6  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  4.363309284746654e-03  0.000000000000000e+00  0.000000000000000e+00  9.999904807207346e-01
+7  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -3.040330609254902e-01  0.000000000000000e+00  0.000000000000000e+00  9.526614812535865e-01
+8  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  5.828323126827837e-01  0.000000000000000e+00  0.000000000000000e+00 -8.125924533816677e-01
+9  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  8.125924533816681e-01  5.828323126827832e-01 -0.000000000000000e+00
+10  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.526614812535864e-01  3.040330609254902e-01  0.000000000000000e+00
+11  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.999904807207346e-01 -4.363309284746654e-03  0.000000000000000e+00
+12  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  9.499720515246526e-01 -3.123349185122325e-01  0.000000000000000e+00
+13  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  8.074754054847402e-01 -5.899012371043603e-01  0.000000000000000e+00
+14  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00  0.000000000000000e+00  5.863723567357898e-01 -8.100416404457959e-01  0.000000000000000e+00
+15  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00 -3.081869234362514e-01  9.513258223252948e-01  0.000000000000000e+00
+16  1.173984503142341e+00  1.173984503142341e+00  1.173984503142341e+00 -0.000000000000000e+00  2.775557561562893e-17  1.000000000000000e+00 -0.000000000000000e+00
+
+# Bond topology
+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  9  10
+9  1  10  11
+10  1  11  12
+11  1  13  14
+12  1  14  15
+13  1  15  16
--- a/examples/USER/cgdna/examples/oxDNA2/duplex2/input.duplex2
+++ b/examples/USER/cgdna/examples/oxDNA2/duplex2/input.duplex2
@ -0,0 +1,78 @@
+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 oxdna2/fene
+bond_coeff * 2.0 0.25 0.7564
+
+# oxDNA pair interactions
+pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
+pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
+pair_coeff * * oxdna2/stk     0.1 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 * * oxdna2/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 oxdna2/hbond   1.0678 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 oxdna2/hbond   1.0678 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 * * oxdna2/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 * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
+pair_coeff * * oxdna2/dh      0.1 1.0 0.815
+
+# NVE ensemble
+#fix 1 all nve/dot
+fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
+#fix 1 all nve/asphere
+#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
+
+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/oxDNA2/duplex2/log.24Mar17.duplex2.g++.1
+++ b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.24Mar17.duplex2.g++.1
--- a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.24Mar17.duplex2.g++.4
+++ b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.24Mar17.duplex2.g++.4
--- a/examples/USER/cgdna/util/sequence_simple.txt
+++ b/examples/USER/cgdna/util/sequence_simple.txt
@ -1,4 +1,4 @@
-single 0,0,0:AAAAA
-single_helix 0,0,0:AAAAA
-duplex 0,0,0:AAAAA
-duplex_array 10,10:-112.0:AAAAA
+single 0,0,0:ACGTA
+single_helix 0,0,0:ACGTA
+duplex 0,0,0:ACGTA
+duplex_array 10,10:-112.0:ACGTA
--- a/examples/cmap/in.cmap
+++ b/examples/cmap/in.cmap
@ -9,11 +9,10 @@ boundary        p p p
 atom_style      full
 bond_style      harmonic
 angle_style     charmm
-dihedral_style  charmm
+dihedral_style  charmmfsw
 improper_style  harmonic

-pair_style      lj/charmm/coul/charmm 8 12
-#pair_style      lj/charmmfsw/coul/charmmfsh 8 12
+pair_style      lj/charmmfsw/coul/charmmfsh 8 12
 pair_modify     mix arithmetic

 fix             cmap all cmap charmm22.cmap
--- a/examples/cmap/log.11Apr17.cmap.g++.1
+++ b/examples/cmap/log.11Apr17.cmap.g++.1
@ -0,0 +1,205 @@
+LAMMPS (31 Mar 2017)
+# Created by charmm2lammps v1.8.2.6 beta on Thu Mar  3 20:56:57 EST 2016
+
+units           real
+neigh_modify    delay 2 every 1
+#newton          off
+
+boundary        p p p
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmmfsw
+improper_style  harmonic
+
+pair_style      lj/charmmfsw/coul/charmmfsh 8 12
+pair_modify     mix arithmetic
+
+fix             cmap all cmap charmm22.cmap
+Reading potential file charmm22.cmap with DATE: 2016-09-26
+fix_modify      cmap energy yes
+
+read_data       gagg.data fix cmap crossterm CMAP
+  orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  34 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  12 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  33 bonds
+  reading angles ...
+  57 angles
+  reading dihedrals ...
+  75 dihedrals
+  reading impropers ...
+  7 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  13 = max # of 1-4 neighbors
+  16 = max # of special neighbors
+
+special_bonds   charmm
+fix             1 all nve
+
+#fix             1 all nvt temp 300 300 100.0
+#fix             2 all shake 1e-9 500 0 m 1.0
+
+velocity        all create 0.0 12345678 dist uniform
+
+thermo          1000
+thermo_style    custom step ecoul evdwl ebond eangle edihed f_cmap eimp
+timestep        2.0
+
+run             100000
+Neighbor list info ...
+  update every 1 steps, delay 2 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7, bins = 12 12 12
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmmfsw/coul/charmmfsh, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 14.96 | 14.96 | 14.96 Mbytes
+Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro 
+       0    16.287573  -0.85933785    1.2470497    4.8441789    4.5432816    -1.473352   0.10453023 
+    1000    18.816462  -0.84379243   0.78931817    2.7554247    4.4371421   -2.7762038   0.12697656 
+    2000    18.091571    -1.045888   0.72306589    3.0951524    4.6725102   -2.3580092   0.22712496 
+    3000    17.835596   -1.2171641   0.72666403    2.6696491    5.4373798   -2.0737041  0.075101693 
+    4000    16.211232  -0.42713611   0.99472642    3.8961462    5.2009895   -2.5626866   0.17356243 
+    5000     17.72183  -0.57081189   0.90733068    3.4376382    4.5457582   -2.3727543   0.12354518 
+    6000    18.753977   -1.5772499   0.81468321    2.9236782    4.6033216   -2.3380859   0.12835782 
+    7000    18.186024  -0.84205608   0.58996182    3.0329585    4.7221473   -2.5733243   0.10047631 
+    8000    18.214306   -1.1360938   0.72597611    3.7493028    4.7319958   -2.8957969    0.2006046 
+    9000    17.248408  -0.48641993   0.90266229    2.9721743    4.7651056   -2.1473354    0.1302043 
+   10000    17.760655   -1.2968444   0.92384663    3.7007455    4.7378947   -2.2147779   0.06940579 
+   11000    17.633929  -0.57368413   0.84872849    3.4277114     4.285393    -2.236944   0.17204973 
+   12000    18.305835   -1.0675148   0.75879532    2.8853173     4.685027    -2.409087  0.087538866 
+   13000    17.391558   -0.9975291   0.66671947    3.8065638    5.2285578   -2.4198822   0.06253594 
+   14000    17.483387  -0.67727643   0.91966477    3.7317031    4.7770445   -2.6080027   0.11487095 
+   15000    18.131749   -1.1918751    1.0025684    3.1238131     4.789742   -2.2546745   0.13782813 
+   16000    16.972343  -0.43926531   0.60644597    3.7551592    4.8658618   -2.2627659   0.12353145 
+   17000    18.080785   -1.2073565    0.7867072    3.5671106      4.43754   -2.5092904   0.17429146 
+   18000    17.474576  -0.97836065    0.8678524    3.7961537    4.3409032   -1.8922572     0.134048 
+   19000    17.000911   -1.2286864   0.83615834    3.9322908    4.9319492   -2.3281576  0.056689619 
+   20000    17.043286   -0.8506561   0.80966589    3.5087339    4.8603878   -2.3365263  0.096794824 
+   21000    17.314495   -1.1430889   0.95363892    4.2446032    4.2756745   -2.1829483   0.17119518 
+   22000    18.954881    -0.998673   0.58688334      2.71536    4.6634319   -2.6862804   0.20328442 
+   23000    17.160427  -0.97803282   0.86894041    4.0897736    4.3146238   -2.1962289  0.075339092 
+   24000    17.602026   -1.0833323   0.94888776    3.7341878    4.3084335   -2.1640414  0.081493681 
+   25000    17.845584   -1.3432612   0.93497086    3.8911043     4.468032   -2.3475883  0.093204333 
+   26000    17.833261   -1.1020534   0.77931087    3.7628141     4.512381   -2.3134761   0.15568465 
+   27000     17.68607   -1.3222026    1.1985872    3.5817624    4.6360755   -2.3492774   0.08427906 
+   28000    18.326649   -1.2669291   0.74809075    3.2624429    4.4698564   -2.3679076   0.14677293 
+   29000    17.720933   -1.0773886   0.83099482    3.7652834    4.6584594   -2.8255303   0.23092596 
+   30000    18.201999   -1.0168706    1.0637455     3.453095    4.3738593   -2.8063214   0.18658217 
+   31000    17.823502   -1.2685768   0.84805585    3.8600661    4.2195821   -2.1169716   0.12517101 
+   32000    16.883133  -0.62062648   0.84434922    3.5042683    5.1264906   -2.2674699  0.030138165 
+   33000    17.805715    -1.679553    1.2430372     4.314677    4.2523894   -2.3008321   0.18591872 
+   34000    16.723767  -0.54189072    1.1282827    3.8542159    4.3026559   -2.2186336   0.05392425 
+   35000    17.976909  -0.72092075    0.5876319    2.9726396    5.0881439    -2.491692   0.17356291 
+   36000    18.782492    -1.514246   0.63237955    3.2777164    4.6077164    -2.502574  0.082537318 
+   37000    17.247716   -0.6344626   0.79885976     3.452491    4.7618281   -2.3902444   0.11450271 
+   38000    17.996494   -1.6712877    1.0111769    4.1689136      4.46963   -2.4076725   0.11875756 
+   39000    17.586857  -0.74508086   0.95970486    3.7395038    4.6011357   -2.9854953   0.30143284 
+   40000    17.494879  -0.30772446   0.72047991    3.2604877    4.7283734   -2.3812495   0.16399034 
+   41000    15.855772  -0.49642605   0.82496448    4.5139653      4.76884    -2.214141   0.10899661 
+   42000    17.898568   -1.3078863    1.1505144    4.0429873    4.3889581   -2.8696559   0.23336417 
+   43000    19.014372   -1.6325979    1.1553166    3.5660772    4.4047997   -2.9302044   0.13672127 
+   44000    18.250782  -0.97211613   0.72714301    3.2258362    4.7257298   -2.5533613   0.11968073 
+   45000    17.335174   0.24746331    1.0415866    3.3220992    4.5251095   -3.0415216   0.24453084 
+   46000     17.72846   -0.9541418   0.88153841    3.7893452    4.5251883   -2.4003613  0.051809816 
+   47000    18.226762  -0.67057787   0.84352989    3.0609522    4.5449078   -2.4694254  0.073703949 
+   48000    17.838074  -0.88768441    1.3812262    3.5890492    4.5827868   -3.0137515   0.21417113 
+   49000    17.973733  -0.75118705   0.69667886    3.3989025    4.7058886   -2.8243945   0.26665792 
+   50000    17.461583  -0.65040016   0.68943524    2.9374743    5.6971777   -2.4438011    0.1697603 
+   51000     16.79766 -0.010684434   0.89795555     3.959039      4.56763   -2.5101098   0.15048853 
+   52000    17.566543   -0.7262764   0.74354418    3.3423185    4.8426523   -2.4187649   0.16908776 
+   53000    17.964274   -0.9270914     1.065952    3.0397181    4.4682262   -2.2179503   0.07873406 
+   54000    17.941256   -0.5807578   0.76516121    3.7262371    4.6975126    -3.179899   0.24433708 
+   55000    17.079478  -0.48559832   0.95364453    3.0414645    5.2811414   -2.7064882   0.30102814 
+   56000    17.632179  -0.75403299   0.97577942    3.3672363    4.4851336   -2.3683659  0.051117638 
+   57000     16.17128  -0.44699325   0.76341543     4.267716    5.0881056   -2.4122329   0.16671692 
+   58000    16.899276  -0.76481024    1.0400825     3.973493    4.8823309   -2.4270284  0.048716383 
+   59000    18.145412  -0.84968335   0.71698306    3.2024358    4.6115739   -2.2520353   0.19466966 
+   60000    17.578258   -1.0067331   0.72822527    3.5375208    4.9110255   -2.2319607   0.11922362 
+   61000    17.434762   -1.0244393   0.90593099    3.8446915    4.8571191   -2.6228357   0.23259208 
+   62000    17.580489   -1.1135917   0.79577432    3.7043524    4.6058114    -2.351492  0.042904152 
+   63000    18.207335   -1.1512268   0.82684507    3.4114738     4.351069   -2.1878441  0.082922105 
+   64000    18.333083   -1.1182287   0.74058959    3.6905164    4.3226172   -2.7110393   0.14721704 
+   65000    16.271579   -0.7122151    1.0200168    4.6983643    4.3681131    -2.194921   0.12831024 
+   66000    17.316444   -0.5729385   0.85254108    3.5769963    4.5526705   -2.3321328  0.040452643 
+   67000     17.19011   -0.8814312    1.1381258    3.8605789    4.4183813    -2.299607  0.091527355 
+   68000    18.223367    -1.362189   0.74472056     3.259165     4.486512   -2.2181134  0.048952796 
+   69000    17.646348  -0.91647162   0.73990335    3.9313692    5.2663097   -3.3816778   0.27769877 
+   70000    18.173493   -1.3107718   0.96484426     3.219728    4.5045124   -2.3349534  0.082327407 
+   71000      17.0627  -0.58509083   0.85964129    3.8490884     4.437895   -2.1673348   0.24151404 
+   72000    17.809764  -0.35128902   0.65479258    3.3945008    4.6160508   -2.5486166   0.10829531 
+   73000     18.27769   -1.0739758   0.80890957    3.6070901    4.6256762   -2.4576547  0.080025736 
+   74000    18.109437   -1.0691837   0.66679323    3.5923203    4.4825716   -2.5048169   0.21372319 
+   75000    17.914569   -1.3500765    1.2993494     3.362421    4.4160377   -2.1278163   0.19397641 
+   76000    16.563928  -0.16539261    1.0067302    3.5742755    4.8581915   -2.1362429  0.059822408 
+   77000    18.130477  -0.38361279   0.43406954    3.4725995    4.7005855   -2.8836242   0.11958174 
+   78000    16.746204   -1.1732959    0.7455507    3.6296638    5.6344113    -2.459208   0.16099803 
+   79000    18.243999   -1.5850155    1.0108545    3.4727867    4.3367411    -2.316686  0.070480814 
+   80000    16.960715  -0.84100929   0.91604996     3.862215     4.780949   -2.3711596  0.073916605 
+   81000    17.697722   -1.1126605     0.952804    3.7114455    4.4216316   -2.2770085  0.091372066 
+   82000    17.835901   -1.3091474   0.71867629    3.8168122    5.0150205   -2.4730634  0.062592852 
+   83000    19.168418    -1.476938   0.75592316    3.2304519    4.3946471   -2.2991395   0.13083324 
+   84000    17.945778   -1.5223622    1.0859941    3.4334011    5.0286682   -2.7550892    0.2476269 
+   85000    17.950251  -0.85843846   0.86888218    3.3101287    4.5511879   -2.3640013   0.12080834 
+   86000    17.480699  -0.97493649   0.85049761    3.4973085    4.6344922    -2.343121    0.2009677 
+   87000    17.980244    -1.114983   0.88796989    3.4113329    4.3535853   -2.2535412   0.14494917 
+   88000    18.023866    -1.226683   0.62339706    3.7649269    4.5923973   -2.3923523   0.10464375 
+   89000    16.362829    -0.311462    1.0265375    4.0101723    4.4184777   -2.0314129  0.056570704 
+   90000    17.533149  -0.41526788    1.0362029    3.4247412    4.2734431   -2.4776658   0.16960663 
+   91000    17.719099   -1.1956801    1.0069945    3.2380672    4.8982805   -2.2154906   0.12950936 
+   92000    17.762654    -1.170027   0.95814525    3.5217717    4.5405343   -2.5983677   0.15037754 
+   93000    17.393958  -0.45641026    0.6579069    3.6002204    4.5942053   -2.5559641   0.12026544 
+   94000      16.8182  -0.92962066   0.86801362    4.2914398     4.659848   -2.5251987   0.18000415 
+   95000    17.642086   -0.7994896    0.7003756    3.8036697    4.5252487   -2.4166307   0.15686517 
+   96000    18.114292   -1.5102104    1.2635908    3.2764427    5.0659496   -2.2777806  0.054309645 
+   97000    18.575765   -1.6015311   0.69500699    3.1649317    4.9945742   -2.4012125  0.067373724 
+   98000    16.578893  -0.78030229   0.91524222    4.4429655    4.4622392   -2.4052655   0.15355705 
+   99000     17.26063  -0.57832833    0.7098846    3.9000046    4.5576484   -2.5333026   0.25517222 
+  100000    18.377235  -0.89109577   0.68988617    2.8751751    4.4115591   -2.3560731   0.12185212 
+Loop time of 2.96043 on 1 procs for 100000 steps with 34 atoms
+
+Performance: 5836.990 ns/day, 0.004 hours/ns, 33778.875 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.074      | 1.074      | 1.074      |   0.0 | 36.28
+Bond    | 1.6497     | 1.6497     | 1.6497     |   0.0 | 55.72
+Neigh   | 0.007576   | 0.007576   | 0.007576   |   0.0 |  0.26
+Comm    | 0.012847   | 0.012847   | 0.012847   |   0.0 |  0.43
+Output  | 0.0010746  | 0.0010746  | 0.0010746  |   0.0 |  0.04
+Modify  | 0.16485    | 0.16485    | 0.16485    |   0.0 |  5.57
+Other   |            | 0.05037    |            |       |  1.70
+
+Nlocal:    34 ave 34 max 34 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    395 ave 395 max 395 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 395
+Ave neighs/atom = 11.6176
+Ave special neighs/atom = 9.52941
+Neighbor list builds = 253
+Dangerous builds = 0
+Total wall time: 0:00:02
--- a/examples/cmap/log.11Apr17.cmap.g++.4
+++ b/examples/cmap/log.11Apr17.cmap.g++.4
@ -0,0 +1,205 @@
+LAMMPS (31 Mar 2017)
+# Created by charmm2lammps v1.8.2.6 beta on Thu Mar  3 20:56:57 EST 2016
+
+units           real
+neigh_modify    delay 2 every 1
+#newton          off
+
+boundary        p p p
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmmfsw
+improper_style  harmonic
+
+pair_style      lj/charmmfsw/coul/charmmfsh 8 12
+pair_modify     mix arithmetic
+
+fix             cmap all cmap charmm22.cmap
+Reading potential file charmm22.cmap with DATE: 2016-09-26
+fix_modify      cmap energy yes
+
+read_data       gagg.data fix cmap crossterm CMAP
+  orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  34 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  12 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  33 bonds
+  reading angles ...
+  57 angles
+  reading dihedrals ...
+  75 dihedrals
+  reading impropers ...
+  7 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  13 = max # of 1-4 neighbors
+  16 = max # of special neighbors
+
+special_bonds   charmm
+fix             1 all nve
+
+#fix             1 all nvt temp 300 300 100.0
+#fix             2 all shake 1e-9 500 0 m 1.0
+
+velocity        all create 0.0 12345678 dist uniform
+
+thermo          1000
+thermo_style    custom step ecoul evdwl ebond eangle edihed f_cmap eimp
+timestep        2.0
+
+run             100000
+Neighbor list info ...
+  update every 1 steps, delay 2 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7, bins = 12 12 12
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmmfsw/coul/charmmfsh, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 14.94 | 15.57 | 16.2 Mbytes
+Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro 
+       0    16.287573  -0.85933785    1.2470497    4.8441789    4.5432816    -1.473352   0.10453023 
+    1000    18.816462  -0.84379243   0.78931817    2.7554247    4.4371421   -2.7762038   0.12697656 
+    2000    18.091571    -1.045888   0.72306589    3.0951524    4.6725102   -2.3580092   0.22712496 
+    3000    17.835596   -1.2171641   0.72666403    2.6696491    5.4373798   -2.0737041  0.075101693 
+    4000    16.211232  -0.42713611   0.99472642    3.8961462    5.2009895   -2.5626866   0.17356243 
+    5000     17.72183  -0.57081189   0.90733068    3.4376382    4.5457582   -2.3727543   0.12354518 
+    6000    18.753977   -1.5772499   0.81468321    2.9236782    4.6033216   -2.3380859   0.12835782 
+    7000    18.186024  -0.84205609   0.58996181    3.0329584    4.7221473   -2.5733244   0.10047631 
+    8000    18.214306   -1.1360934   0.72597583    3.7493032    4.7319959   -2.8957975   0.20060467 
+    9000    17.248415  -0.48642024   0.90266262    2.9721744    4.7651003   -2.1473349   0.13020438 
+   10000    17.760663   -1.2968458   0.92384687    3.7007432    4.7378917   -2.2147799   0.06940514 
+   11000     17.63395  -0.57366075   0.84871737    3.4276851    4.2853865   -2.2369491   0.17205075 
+   12000    18.305713   -1.0672299   0.75876262    2.8852171    4.6850229   -2.4090072  0.087568888 
+   13000    17.383367  -0.99678627   0.66712651    3.8060954     5.233865   -2.4180629  0.062014239 
+   14000    17.510901  -0.68723297   0.92448551    3.7550867    4.7321218   -2.6059088   0.11504409 
+   15000    18.080165     -1.13316   0.99982253      3.09947    4.8171402   -2.2713372   0.14580371 
+   16000    17.383245   -0.4535296   0.57826268    3.6453593    4.6541138   -2.2434512   0.13285609 
+   17000    17.111153   -0.3414839   0.73667584    3.7485311    4.6262965   -2.6166049   0.12635815 
+   18000    16.862046   -1.3592061    1.2371142    4.4878937    4.2937117   -2.2112584  0.066145125 
+   19000    18.313891    -1.654238   0.90644101    3.3934089     4.550735   -2.1862171  0.081267736 
+   20000    19.083561   -1.3081747   0.56257812    2.7633848    4.6211438   -2.5196707   0.13763071 
+   21000     18.23741    -1.051353   0.64408722    3.1735565    4.6912533   -2.2491947  0.099394904 
+   22000    17.914515  -0.89769621   0.61793801    3.1224992    4.8683543    -2.282475   0.14524537 
+   23000    16.756122  -0.98277883    1.2554905    3.7916115    4.7301443   -2.3094994   0.10226772 
+   24000    16.109857  -0.54593177   0.86934462    4.4293574     4.926985   -2.2652264   0.11414331 
+   25000    18.590559    -1.497327    1.1898361    2.9134403    4.7854107   -2.4437918  0.067416154 
+   26000    18.493391   -1.0533797    0.4889578    3.6563013    4.6171721   -2.3240835   0.11607829 
+   27000    18.646522   -1.1229601   0.67956815    2.7937638    4.8991207   -2.4068997   0.10109147 
+   28000    18.545103   -1.7237438   0.72488022    3.8041665    4.6459974   -2.4339333   0.21943258 
+   29000    17.840505   -1.0909667   0.88133248    3.3698456    5.0311644   -2.5116617   0.08102693 
+   30000    17.649527  -0.65409177   0.86781692      3.24112    4.9903073   -2.6234925   0.14799777 
+   31000    18.156812  -0.77476556   0.83192789    2.9620784    4.9160635   -2.8571635   0.22283201 
+   32000    18.251583   -1.3384075    0.8059007    3.2588176    4.4365328   -2.1875071  0.087883637 
+   33000    17.702785  -0.88311587   0.98573641    3.4645713    4.2650091   -2.0909158   0.14233004 
+   34000    17.123413   -1.4873429    1.0419563    4.2628178    4.6318762   -2.2292095     0.105354 
+   35000    18.162061   -1.0136007   0.82436129    3.6365024    4.5801677   -2.6856989   0.28648222 
+   36000     17.65618    -1.094718    0.8872444    3.5075241    4.6382423   -2.3895134   0.18116961 
+   37000    17.336475   -1.0657995   0.98869254    3.9252927    4.4383632   -2.2048244   0.22285949 
+   38000    17.369467  -0.97623132    0.6712095    4.1349304     4.597754   -2.4088341   0.14608514 
+   39000    18.170206   -1.2344285   0.77546195    3.6451049    4.7482287   -2.9895286   0.25768859 
+   40000    16.210866  -0.81407781   0.99246271    4.2676233    5.0253763   -2.2929865   0.13348624 
+   41000    17.641798   -1.0868157   0.80119513    3.4302526     5.280872   -2.4025406   0.22747391 
+   42000    18.349848    -1.613759    1.1497004    3.7800682    4.3237683   -2.8676401    0.2120425 
+   43000    19.130245    -1.196778   0.71845659    2.9325758    4.3684415    -2.433424   0.12240982 
+   44000    18.061321   -1.2410101    1.0329373    3.0751569    4.7138313   -2.2880904  0.075814461 
+   45000    18.162713   -1.4414622     1.009159    4.2298758     4.589593   -2.8502298   0.21606844 
+   46000    18.591574  -0.99730412    1.0955215    3.3965004     4.359466   -3.1049731   0.17322629 
+   47000    18.380259   -1.2717381   0.72291269    3.3958016    4.6099628   -2.4605065   0.19825185 
+   48000    18.130478   -1.5051279    1.2087492    3.2488529    4.6690881   -2.2518174   0.05633061 
+   49000    16.419912  -0.89320635   0.98926144    4.0388252    4.9919488   -2.1699511   0.15646479 
+   50000    16.453196   -1.0433497     0.778346    4.6078069    4.7320614   -2.3760788   0.17161976 
+   51000    18.245221  -0.89550444    0.9310446    3.0758194    4.3944595   -2.3082379   0.19983428 
+   52000    17.839632   -1.0221781   0.76425017    3.3331547    4.5368437   -2.0988773   0.21098435 
+   53000    18.693035   -1.4231915   0.76333082    3.1612761     4.583242   -2.4485762  0.089191206 
+   54000    16.334672  -0.36309884    1.0200365    4.6700448    4.1628702   -2.1713841   0.11431995 
+   55000     17.33842  -0.61522682   0.89847366    3.4970659     4.673495   -2.4743036  0.068004878 
+   56000    17.790294   -1.0150845   0.73697112    3.6000297    4.5988343   -2.4822509   0.11434632 
+   57000    18.913486   -1.0985507    1.0231848    2.7483267    4.4421755    -2.574424    0.1763388 
+   58000    17.586896  -0.98284126   0.96965633    3.3330357    4.5325543   -2.1936869  0.083230915 
+   59000     17.77788   -1.1649953   0.83092298    3.8004148    4.3940176   -2.3136642  0.017207608 
+   60000    17.013042  -0.21728023    1.1688832    3.5374476    4.5462244   -2.4425301   0.15028297 
+   61000    17.236242   -1.1342147    1.0301086     3.685948    4.6842331    -2.328108  0.070210812 
+   62000    17.529852   -1.2961547    1.0323133    3.4474598    5.1435839   -2.4553423  0.060842687 
+   63000    18.754704   -1.1816999   0.51806039     3.140172    4.5832701   -2.2713213   0.06327871 
+   64000     17.54594   -1.3592836    0.9694558    4.1363258    4.3547729   -2.3818433   0.12634448 
+   65000    16.962312  -0.54192775   0.90321315    4.0788618    4.2008255   -2.1376711  0.039504515 
+   66000    18.078619   -1.3552947    1.0716861    3.3285374    4.7229362   -2.3331115   0.21978698 
+   67000    17.132732   -1.4376876   0.91486534    4.4461852    4.6894176   -2.3655045  0.068150385 
+   68000     18.69286   -1.2856207    0.3895394    3.0620063    4.9922992   -2.3459189  0.079879643 
+   69000    18.329552   -1.1545957   0.88632275    3.1741058    4.4562418   -2.7094867   0.25329613 
+   70000    16.681168  -0.94434373    1.2450393    4.5737944    4.4902996   -2.4581775   0.15313095 
+   71000    17.375032   -1.0514442    1.0741595    3.4896146    4.8407713   -2.5302576   0.13640847 
+   72000    17.833013   -0.9047134   0.87067876    3.1658924    4.8825932   -2.4398117    0.2343991 
+   73000    17.421411   -1.2190741   0.73706811       4.2895    4.6464636   -2.3872727   0.19696525 
+   74000    17.383158  -0.34208984   0.71333984    3.2718891    4.2718495   -2.2484281   0.10827022 
+   75000     17.20885   -1.2710479     1.125102    3.8414467    5.3222741    -2.375505   0.12910797 
+   76000    16.811578    -0.545162   0.59076961    3.9118604    4.8031296   -2.2777895  0.063015508 
+   77000    16.679231 -0.080955983    0.7253398    3.4203454    5.0987608    -2.379614   0.12961874 
+   78000    18.164524   -1.3115525   0.92526408    3.5764487    4.3814882   -2.3712488  0.073436724 
+   79000    17.738686   -1.0697859    1.2186866    3.0593848    4.6551053   -2.2505871  0.075340661 
+   80000    16.767483  -0.84777477      1.03128    4.1982958    4.6992227   -2.4146425  0.079774219 
+   81000    16.257265   0.62803774   0.84032194    3.3873471    5.0961071   -2.7219776   0.20467848 
+   82000    18.232082   -1.2129302   0.50746051    3.9207128    4.5073437    -2.599371  0.094522372 
+   83000    16.618985  -0.60917055    0.8825847     3.805497    4.9560959   -2.2194726   0.14852687 
+   84000     17.90762  -0.82336075   0.90504161    3.0324198    4.7444271   -2.5036073   0.15860682 
+   85000    16.699883  -0.50297228   0.83405307    3.8598996    4.7971968   -2.2427788   0.10338668 
+   86000    16.353038 -0.0096880616   0.80705167    4.0865115    4.5364338   -2.4548873  0.098456203 
+   87000    17.887331  -0.75281219    1.0030148    4.0117123    4.3443074   -2.9774392   0.16190152 
+   88000    18.583708   -1.4867053   0.86324814    3.3971237    4.3526221    -2.221239   0.14459352 
+   89000    17.684828    -1.283764    1.0021118    3.5426808    4.9057005   -2.3921967   0.05844702 
+   90000      17.2597  -0.84306489   0.99797936    3.8896866    4.4315457   -2.5662899   0.18270206 
+   91000    16.705581  -0.44704047   0.75239556     3.470805     4.976868   -2.1894571   0.12312848 
+   92000    17.548071   -1.2222664   0.92898812    4.0813773    4.3432647   -2.1631158   0.14071343 
+   93000    17.163675  -0.94994776   0.96876981    3.9137692    4.4388666   -2.1260232   0.13187968 
+   94000    18.842071   -1.2822113   0.58767049    3.1393475    4.5820965   -2.7264682   0.10406266 
+   95000    18.112287   -1.1011381   0.63546648    3.4672667     4.486275   -2.2991936  0.041589685 
+   96000    17.102713   -0.6877313    0.8389032    3.6892719    4.5676004   -2.1905327   0.13507011 
+   97000    16.778253   -1.2902153    1.1588744    4.2820083    4.9537657   -2.4798159   0.35696636 
+   98000     18.34638   -1.2908146     1.185356    3.0739807    4.4575453   -2.3959144   0.22407922 
+   99000    17.995148   -1.3939639    0.7727299    3.8774144    4.4345458   -2.1142776   0.13550099 
+  100000    18.444746   -1.2456693   0.86061526     3.468696    4.5264336   -2.4239851  0.074369539 
+Loop time of 2.52011 on 4 procs for 100000 steps with 34 atoms
+
+Performance: 6856.851 ns/day, 0.004 hours/ns, 39680.850 timesteps/s
+98.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.072506   | 0.28131    | 0.69088    |  46.2 | 11.16
+Bond    | 0.050544   | 0.45307    | 0.9416     |  57.6 | 17.98
+Neigh   | 0.0060885  | 0.0061619  | 0.0062056  |   0.1 |  0.24
+Comm    | 0.44686    | 1.3679     | 2.0111     |  53.5 | 54.28
+Output  | 0.0028057  | 0.0029956  | 0.003264   |   0.3 |  0.12
+Modify  | 0.028202   | 0.095174   | 0.15782    |  19.8 |  3.78
+Other   |            | 0.3135     |            |       | 12.44
+
+Nlocal:    8.5 ave 14 max 2 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Nghost:    25.5 ave 32 max 20 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Neighs:    98.75 ave 242 max 31 min
+Histogram: 2 0 1 0 0 0 0 0 0 1
+
+Total # of neighbors = 395
+Ave neighs/atom = 11.6176
+Ave special neighs/atom = 9.52941
+Neighbor list builds = 246
+Dangerous builds = 0
+Total wall time: 0:00:02
--- a/examples/cmap/log.5Oct16.cmap.g++.1
+++ b/examples/cmap/log.5Oct16.cmap.g++.1
@ -1,201 +0,0 @@
-LAMMPS (5 Oct 2016)
-# Created by charmm2lammps v1.8.2.6 beta on Thu Mar  3 20:56:57 EST 2016
-
-units           real
-neigh_modify    delay 2 every 1
-#newton          off
-
-boundary        p p p
-
-atom_style      full
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-
-pair_style      lj/charmm/coul/charmm 8 12
-#pair_style      lj/charmmfsw/coul/charmmfsh 8 12
-pair_modify     mix arithmetic
-
-fix             cmap all cmap charmm22.cmap
-Reading potential file charmm22.cmap with DATE: 2016-09-26
-fix_modify      cmap energy yes
-
-read_data       gagg.data fix cmap crossterm CMAP
-  orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  34 atoms
-  scanning bonds ...
-  4 = max bonds/atom
-  scanning angles ...
-  6 = max angles/atom
-  scanning dihedrals ...
-  12 = max dihedrals/atom
-  scanning impropers ...
-  1 = max impropers/atom
-  reading bonds ...
-  33 bonds
-  reading angles ...
-  57 angles
-  reading dihedrals ...
-  75 dihedrals
-  reading impropers ...
-  7 impropers
-  4 = max # of 1-2 neighbors
-  7 = max # of 1-3 neighbors
-  13 = max # of 1-4 neighbors
-  16 = max # of special neighbors
-
-special_bonds   charmm
-fix             1 all nve
-
-#fix             1 all nvt temp 300 300 100.0
-#fix             2 all shake 1e-9 500 0 m 1.0
-
-velocity        all create 0.0 12345678 dist uniform
-
-thermo          1000
-thermo_style    custom step ecoul evdwl ebond eangle edihed f_cmap eimp
-timestep        2.0
-
-run             100000
-Neighbor list info ...
-  1 neighbor list requests
-  update every 1 steps, delay 2 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 14
-  ghost atom cutoff = 14
-  binsize = 7 -> bins = 12 12 12
-Memory usage per processor = 14.6355 Mbytes
-Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro 
-       0    26.542777  -0.93822087    1.2470497    4.8441789    4.5432816    -1.473352   0.10453023 
-    1000    28.673005  -0.47724367   0.80029132     3.151679    4.4684446   -2.3928648   0.18604953 
-    2000     27.67955    -1.170342   0.72018905    4.0400131    4.4713764   -2.5490207   0.21834436 
-    3000    29.256656  -0.35856055   0.73303546    3.7411606    4.4710568   -2.8939692   0.37728884 
-    4000    30.097549   -1.1353905   0.79007053    3.0688444    4.4091469   -2.3383587   0.20743631 
-    5000    28.357525   -1.0723742    0.9180297    3.6579424    4.8792664   -2.3185572  0.088366962 
-    6000    29.214175  -0.95299225   0.81926009    3.6805429    4.6742897   -2.9343577   0.26697813 
-    7000    27.018614  -0.52423475   0.72502764    3.8840137    4.7780956   -2.3916009   0.24952584 
-    8000    29.682167   -1.0939711   0.76111486    3.1090116    4.9359719   -2.5662984    0.1411154 
-    9000    27.909695  -0.80905986   0.78952533     4.203187    4.1301204    -2.000402  0.088859259 
-   10000    27.480298  -0.86273377    1.1293962    4.3857421     4.899282   -3.3895621   0.12126215 
-   11000    28.303203   -1.0221152   0.62762348     4.055414    4.5863024   -2.5842816   0.17996907 
-   12000    28.311127  -0.94227367   0.91859012    3.6673926    4.7018632    -3.902715   0.30065704 
-   13000    30.818607   -1.5220116   0.95710386    3.3364371     4.543427   -3.0423067   0.16712905 
-   14000    27.643736   -1.0144117   0.95806952    4.1046912     4.800236   -4.0534389   0.29293405 
-   15000    27.660491   -1.0390086   0.78061056    4.1139174    4.7197202   -2.3670379   0.22126985 
-   16000    27.845157  -0.63654502   0.78007478    3.9365994     4.949418   -3.1470214   0.22335355 
-   17000     28.44772   -1.0255112   0.70402007    4.0573343    4.2887527   -2.2099596  0.048050962 
-   18000    27.128323  -0.96218536    1.1327159    4.3222585     4.326607   -2.2881766   0.13491257 
-   19000    27.337633  -0.78999574   0.80152298    4.2239689    4.7073478   -2.2924164   0.12710292 
-   20000    27.780537  -0.46458072   0.79707671    3.7232618     4.943417   -2.5290628   0.26191223 
-   21000    26.435484   -0.7803224    1.0753217    4.4196051    5.9945933   -2.3340925   0.16448475 
-   22000    28.619429   -1.1623149    0.9401731    3.8508844    5.1636737   -2.5551846   0.25318434 
-   23000    28.399338  -0.79700962   0.85575503     4.488526    4.5975422   -2.5663549   0.13601693 
-   24000    29.645532    -1.158744   0.83180313    3.8193399      4.60319   -2.6847864   0.24260466 
-   25000    28.695339   -1.4802204   0.76583757    3.6786272    4.8959496   -2.3627896  0.080867326 
-   26000    28.149711    -1.029689   0.79383806    3.7885067    4.3345813   -2.1041553   0.14598209 
-   27000    29.580373   -1.0525813    1.0262723    3.7767318    4.6119758   -2.2802386  0.088556038 
-   28000     28.44308  -0.93411225    0.8794395     3.948079     4.780246   -2.1814583   0.14340149 
-   29000    29.335621   -1.6087988   0.71803091    3.7819186    4.6688385   -2.4282242   0.16061111 
-   30000    28.706138   -1.3938241   0.67713818     4.031275    4.4756505   -2.1807056   0.11461356 
-   31000    27.451944  0.010297225   0.65064883    3.6402029    4.3607811   -2.5511516   0.12637237 
-   32000    27.070878    -1.103158    1.1932199    5.1329709    4.5201653   -2.2224479   0.11215427 
-   33000    29.889976   -1.6228316   0.69407996    3.5361991    4.3502767   -1.9847454   0.09089949 
-   34000    28.223151    -0.927208     1.043253    3.4650939    5.1028142   -2.8127219   0.10648823 
-   35000    27.985986  -0.48153861   0.63878449    3.3724641    4.9551679   -2.6565919   0.12123115 
-   36000    28.580688   -1.4500694     1.055762    4.0490064     4.423782   -2.3103578  0.072747638 
-   37000    29.192947  -0.49678176    1.1146731    2.9233947    4.5738603   -2.4376144   0.22874047 
-   38000    26.954594  -0.53812359   0.79230685    4.3356989    5.0284656   -2.3791255    0.0486081 
-   39000    27.567555  -0.57870028   0.73614374     4.191991    4.9209556   -2.6122044   0.08635571 
-   40000    28.494172  -0.79057135   0.79072816    4.1893209    4.4826919   -2.4179635   0.14612898 
-   41000     28.44904   -1.1002948   0.93405654    4.3586358    4.4338415   -2.2950944   0.15705834 
-   42000     28.95725   -1.0297067    1.1632348     4.274711    4.9979487   -2.7611464   0.15944725 
-   43000    28.640394  -0.70938882   0.68100893    3.1844315    5.1817454   -2.2837487   0.14189233 
-   44000    27.997558   -1.0115099   0.59125208    4.0883422    4.6033907   -2.2775964  0.094273258 
-   45000     27.67163  -0.67992747    1.1225552    3.9020703    4.8171056   -2.1952679  0.041418433 
-   46000    28.822607   -0.6687953   0.74160059    3.3193715    4.5546965   -2.3024572  0.047569065 
-   47000     29.20147   -1.4456785   0.79223353    3.8288813    4.5811826   -2.5154936  0.061230141 
-   48000    27.843026   -1.0222301   0.87322137    4.3432743    4.4266307   -2.1414153   0.06802794 
-   49000    28.199573   -1.1887794    1.2781088    4.0779644    4.5881353    -2.319775  0.094803547 
-   50000    28.759212    -1.354416   0.68534569    3.8394841    4.2308134   -2.1281844    0.1395951 
-   51000    27.876455   -1.5705462   0.76557156    4.5335223     4.523708    -2.203702   0.14679803 
-   52000    27.930587   -1.2277489   0.96071516     3.960953    5.1152188   -2.4101451  0.060949521 
-   53000    27.031236   -1.4746477    1.2341141    5.0540975    4.3656865   -2.1288513  0.092725656 
-   54000    28.809394   -1.1162427   0.94350207    3.4013958    4.4755547   -2.3342811   0.18855912 
-   55000    28.948415   -1.1560418    0.6260139    3.5386373    4.5244978    -2.340212   0.17474657 
-   56000    28.048368  -0.95784532   0.76432571    4.1404665    4.4570033   -2.0899628  0.045693628 
-   57000    28.707642    -1.366574    0.9907873     3.729903    4.3131997   -2.2777698  0.065420213 
-   58000    26.361663   -1.0424403    1.0452563    5.0977108    4.7035231   -2.3101244   0.13671642 
-   59000    29.218218   -1.2210564   0.62435875    3.4236327    4.5481681   -2.1575943  0.037984042 
-   60000    27.655546   -1.1053224   0.86323501    3.7641375    4.8946898   -2.2422249  0.077725979 
-   61000    27.252108   -1.3744824    1.1150806    5.0444848    4.4878135   -2.2743829  0.058331257 
-   62000    27.163469   -1.1715781   0.72099321    4.5295501    4.9509918   -2.2993961  0.050401105 
-   63000    29.581575   -1.2238537   0.86303245    3.1194038    5.2218965   -2.5002427  0.055032632 
-   64000    27.897822   -1.1011516   0.74540883    4.2869228    4.3394269   -2.2552393    0.1403321 
-   65000    27.083245   -1.0633392   0.92771724    5.0805224    4.2747962   -2.2388039  0.064196692 
-   66000    29.072723   -1.5514209   0.89798805    4.2600224    4.4261812   -2.3524752   0.15067414 
-   67000    27.308181  -0.72224802   0.97109517    4.5074578    4.4559352   -2.1381121  0.089297603 
-   68000    27.505686  -0.43855431   0.80785812    4.1917251    5.0157721   -2.3382145   0.11105164 
-   69000    29.041681  -0.64735378   0.89874684    3.3891579    4.3753361   -2.2320941   0.14716747 
-   70000    29.735756   -1.7061457    0.9206878    3.5767878    4.3851664   -2.2516304  0.097196062 
-   71000    28.224352  -0.92217702   0.86093586    3.9507157    4.5596589   -2.2173397  0.089116669 
-   72000    29.282336    -1.056142   0.65185725    3.8735742    4.4839333   -2.4314756  0.071909704 
-   73000    26.257283  -0.64273826   0.98300685     5.063943     5.045958   -2.5544375    0.2180275 
-   74000    28.825119  -0.97736616   0.87201848      3.55875    4.3653309   -2.2303567  0.098963875 
-   75000    29.239507  -0.96508809   0.74517323    3.4306236    4.7651921   -2.6077732   0.17883654 
-   76000    27.349841  -0.50990238    1.1183613    4.4252451    4.4097775   -2.4125794   0.18483606 
-   77000    28.130197   -1.4081219   0.94921357    4.2572132    4.5162849   -2.4013797  0.073744606 
-   78000    28.235774   -0.9214321    0.6324981    3.8697686    4.8092154   -2.2272847  0.092108346 
-   79000    26.732846  -0.55949486    1.0989617    5.0088609    4.4930687    -2.277945   0.03855146 
-   80000    28.529208  -0.94244671   0.79407482     3.961106    4.3930011   -2.3127726  0.091124948 
-   81000    29.603852   -1.6116062     1.060847    3.7824932     4.151001   -1.9139868   0.19875986 
-   82000    28.232876   -1.1833011    1.0182713    3.4195758    5.1394333   -2.4632697   0.28501012 
-   83000    29.565482   -1.3479552   0.99056973    3.7851802    4.4781011   -2.7872481    0.2031991 
-   84000    28.780274   -1.3073882    1.0512637     4.004638     4.502282   -2.3789146  0.015656202 
-   85000    27.262312   -1.1305346     1.203524    4.7938623    4.1747105   -2.0952844  0.054240361 
-   86000    28.157348   -1.0662817   0.81163796    3.9912709    4.8320213    -2.255237   0.14698333 
-   87000    28.445543   -1.3365026   0.78156195    4.4767689    4.4457575   -2.5008786   0.13879386 
-   88000    27.656717   -1.1490599   0.87974869    4.4629952    4.7023033   -2.3258145  0.081904139 
-   89000    28.838821    -1.020709   0.85587929    3.7110705    4.4938307   -2.4914483   0.11447952 
-   90000    27.356497  -0.59107077   0.81879666    4.5209332    4.4703836   -2.3806717  0.071307775 
-   91000    27.780445  -0.80564513   0.94752313    3.8468943    4.2924253   -2.1011134    0.1118672 
-   92000    28.555276   -1.3514732   0.80826674    3.9590742    4.5775954   -2.4891232  0.054254978 
-   93000    28.747267   -1.2133243   0.75507246    4.1319789    4.9048611   -2.4913887   0.13045693 
-   94000    27.479343  -0.69973695   0.99696121    3.5966229     4.549025   -2.4155312   0.41745762 
-   95000    27.726945   -1.1905026    1.1120842    4.7433275    4.5386861   -2.7947142   0.33671682 
-   96000    28.021114   -1.0341645    0.6663033    4.2397505    4.6203984   -1.9904034   0.10972565 
-   97000    28.382022   -1.3916008     1.180588    4.0729621    4.6741792    -2.554927   0.13462346 
-   98000    27.895969   -0.7496449    1.3072185    4.2611888    4.3726077   -2.1320701   0.15376665 
-   99000    28.517889   -1.2183957     1.279778     3.957647    4.2638434   -2.2888407  0.042705003 
-  100000    28.109211   -1.2538948   0.83671785    4.3734766     4.544545   -2.3076497  0.042189096 
-Loop time of 2.84552 on 1 procs for 100000 steps with 34 atoms
-
-Performance: 6072.706 ns/day, 0.004 hours/ns, 35142.973 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
-Pair    | 0.94207    | 0.94207    | 0.94207    |   0.0 | 33.11
-Bond    | 1.6125     | 1.6125     | 1.6125     |   0.0 | 56.67
-Neigh   | 0.0073986  | 0.0073986  | 0.0073986  |   0.0 |  0.26
-Comm    | 0.012739   | 0.012739   | 0.012739   |   0.0 |  0.45
-Output  | 0.00075531 | 0.00075531 | 0.00075531 |   0.0 |  0.03
-Modify  | 0.21483    | 0.21483    | 0.21483    |   0.0 |  7.55
-Other   |            | 0.05524    |            |       |  1.94
-
-Nlocal:    34 ave 34 max 34 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    395 ave 395 max 395 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 395
-Ave neighs/atom = 11.6176
-Ave special neighs/atom = 9.52941
-Neighbor list builds = 237
-Dangerous builds = 0
-Total wall time: 0:00:02
--- a/examples/cmap/log.5Oct16.cmap.g++.4
+++ b/examples/cmap/log.5Oct16.cmap.g++.4
@ -1,201 +0,0 @@
-LAMMPS (5 Oct 2016)
-# Created by charmm2lammps v1.8.2.6 beta on Thu Mar  3 20:56:57 EST 2016
-
-units           real
-neigh_modify    delay 2 every 1
-#newton          off
-
-boundary        p p p
-
-atom_style      full
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-
-pair_style      lj/charmm/coul/charmm 8 12
-#pair_style      lj/charmmfsw/coul/charmmfsh 8 12
-pair_modify     mix arithmetic
-
-fix             cmap all cmap charmm22.cmap
-Reading potential file charmm22.cmap with DATE: 2016-09-26
-fix_modify      cmap energy yes
-
-read_data       gagg.data fix cmap crossterm CMAP
-  orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  34 atoms
-  scanning bonds ...
-  4 = max bonds/atom
-  scanning angles ...
-  6 = max angles/atom
-  scanning dihedrals ...
-  12 = max dihedrals/atom
-  scanning impropers ...
-  1 = max impropers/atom
-  reading bonds ...
-  33 bonds
-  reading angles ...
-  57 angles
-  reading dihedrals ...
-  75 dihedrals
-  reading impropers ...
-  7 impropers
-  4 = max # of 1-2 neighbors
-  7 = max # of 1-3 neighbors
-  13 = max # of 1-4 neighbors
-  16 = max # of special neighbors
-
-special_bonds   charmm
-fix             1 all nve
-
-#fix             1 all nvt temp 300 300 100.0
-#fix             2 all shake 1e-9 500 0 m 1.0
-
-velocity        all create 0.0 12345678 dist uniform
-
-thermo          1000
-thermo_style    custom step ecoul evdwl ebond eangle edihed f_cmap eimp
-timestep        2.0
-
-run             100000
-Neighbor list info ...
-  1 neighbor list requests
-  update every 1 steps, delay 2 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 14
-  ghost atom cutoff = 14
-  binsize = 7 -> bins = 12 12 12
-Memory usage per processor = 15.9307 Mbytes
-Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro 
-       0    26.542777  -0.93822087    1.2470497    4.8441789    4.5432816    -1.473352   0.10453023 
-    1000    28.673005  -0.47724367   0.80029132     3.151679    4.4684446   -2.3928648   0.18604953 
-    2000     27.67955    -1.170342   0.72018905    4.0400131    4.4713764   -2.5490207   0.21834436 
-    3000    29.256656  -0.35856055   0.73303546    3.7411606    4.4710568   -2.8939692   0.37728884 
-    4000    30.097549   -1.1353905   0.79007053    3.0688444    4.4091469   -2.3383587   0.20743631 
-    5000    28.357525   -1.0723742    0.9180297    3.6579424    4.8792663   -2.3185572  0.088366962 
-    6000    29.214175  -0.95299239   0.81926011    3.6805428    4.6742897   -2.9343578   0.26697816 
-    7000    27.018614  -0.52423469   0.72502751    3.8840141    4.7780958   -2.3916014   0.24952572 
-    8000    29.682494   -1.0940368   0.76113051    3.1089345    4.9357863   -2.5662256   0.14112613 
-    9000    27.853918   -0.7913741   0.79503268    4.2177256     4.146792     -2.00475  0.090585666 
-   10000     27.13754  -0.80551128    1.1325023    4.4718283    5.2460631   -3.4947725   0.11893125 
-   11000    28.277434   -1.4897448   0.90075953    4.1895717    4.3594269   -1.9553119  0.090222212 
-   12000    28.630973    -1.222206   0.67796385    3.3905661    4.9691334   -2.9052721   0.13897658 
-   13000    28.593007  -0.95684026   0.75585196    3.7242568    4.7417932   -2.3893117    0.2074121 
-   14000    26.147115   -0.6026921   0.93591488    5.1292829    4.9821952   -2.2571835   0.11872421 
-   15000     26.29432  -0.82424162     1.048979    4.5569495    5.1189308   -2.9750422   0.16195676 
-   16000    29.189992  -0.80998247   0.74093508    3.8299275    4.4536688   -2.5497538   0.19155639 
-   17000    25.878012   -0.3519646    1.0988924    4.7359591    5.3923098   -2.7211029   0.13405223 
-   18000    27.726135  -0.28229987   0.63072344    4.1777888    4.7237271   -2.2177157   0.15939372 
-   19000    27.153504  -0.66477422   0.77910129    4.2036117     5.113851   -2.3494315  0.094793307 
-   20000    28.044833   -1.2835827   0.88745367    3.9955526    4.5077788   -3.0116467   0.17197859 
-   21000    27.205696  -0.74090037    1.0023251    4.3421733     4.912671   -2.3473271   0.26089356 
-   22000    27.385785  -0.93740972   0.84554838     4.562743     4.883866   -2.2110955   0.11573301 
-   23000     27.05534  -0.95605442   0.96719024    3.9277618    5.0359014   -2.6135949   0.21368061 
-   24000    28.273378  -0.97543103    0.8983443    4.2067985    4.4782971   -2.4230505   0.30311692 
-   25000    27.477789  -0.20383849    0.8380706    3.8037992    4.8312504   -2.5831791  0.093843746 
-   26000    30.344199   -1.9773473   0.92882437    3.7821405    4.5176677   -2.3020968    0.2194307 
-   27000     27.32767   -0.9803839   0.92988865    3.7611603    5.0328211   -2.4647656   0.18213622 
-   28000     27.34208    -1.037938   0.74488346    4.1727342    4.7056812   -2.2718346   0.17741362 
-   29000    27.682777  -0.51006495   0.57074224    4.7332237    4.7080462   -2.0491512    0.2130517 
-   30000    24.925731   0.13670248   0.84976065    4.4143762    6.0677158   -3.5479173   0.28059419 
-   31000    28.623419  -0.90725708    1.0710501    3.6930688    4.6639301   -2.2225373   0.20988139 
-   32000    27.732286   -1.1948367   0.89230134    4.4398373    4.8923907   -3.5849327   0.49167488 
-   33000    28.800772   -1.5319589   0.93455495    4.1634728    4.6107706   -2.3503486   0.22636535 
-   34000    27.374398   -1.0957453   0.89450276    3.9829508     4.991786   -2.3548834   0.15869465 
-   35000     28.38753  -0.89261166   0.90000776     3.536864    4.4293294   -2.4218118   0.10640557 
-   36000    27.713974  0.088038031   0.85190574    3.8969601    4.6256355   -2.7935475   0.34671662 
-   37000     29.13007    -1.378597   0.74412556     3.131538    4.6458653   -2.9373734   0.38035616 
-   38000    28.556573   -1.4055344     1.139984    4.0035753    4.2938358    -2.489329   0.25338326 
-   39000    26.447036   -1.1829705   0.87032438    5.0804461    4.5772023   -2.7346466   0.32165802 
-   40000    27.991454  -0.64295679   0.61020872     4.165871    4.4623087   -2.2244194   0.13826991 
-   41000    29.483296   -1.2400745   0.66926627    3.3473666    4.5766617   -2.3051145   0.12171554 
-   42000    26.948627   -1.2162288    1.1440628    4.3993073    5.1176533   -2.4734485   0.15497709 
-   43000     28.04459  -0.26543193   0.83647367    3.5160747    4.6964397   -2.2805068   0.12618821 
-   44000    28.213608    -1.216128    0.9132792    4.0206483    4.9483599   -2.3387049   0.10132022 
-   45000    28.283506   -1.0390766   0.86113772     4.504509    4.7209088   -2.3043085   0.14588362 
-   46000    27.433853  -0.57912107   0.78448334    4.5998579    5.1181394   -2.6165094   0.18722528 
-   47000    27.552939   -1.1128925   0.80087638    4.3448001    4.8062869   -2.4296883    0.2702479 
-   48000    28.874034   -1.3242519   0.71770727    3.5648565    4.4671824   -2.2608958   0.16115978 
-   49000    29.216186   -1.2210307   0.76937497    3.9260628    4.7550577   -2.7316081  0.085505664 
-   50000    28.065856   -1.1545547   0.86953819    4.4137666     4.732157   -2.4450867   0.23320539 
-   51000    26.308975  -0.99728352   0.90408444    4.2400186    5.6340425   -2.2090554  0.079882158 
-   52000    28.517571   -1.5027398   0.83520278    3.8176552    4.3001251   -2.0731682    0.1665375 
-   53000     28.77579   -1.3564268   0.97253881    3.6866407    4.8532347   -2.5330776   0.17668411 
-   54000    29.135315   -1.0994106   0.67605671    3.6819254    4.3134408   -1.9796929  0.076951331 
-   55000    26.168938  -0.76247492   0.88784685    4.6533473    6.0484793   -2.1334561  0.036876985 
-   56000    27.471775  -0.68648837    1.0576168    4.0354311    4.4767052   -2.2368959   0.24950568 
-   57000    29.787083   -1.4914384    1.0702944    3.5388133    4.5173097   -2.6694464   0.27937092 
-   58000    28.705448   -1.3016617   0.63337853    3.9552713    4.4119825   -1.8774657   0.17540021 
-   59000    29.130155  -0.91647363   0.84384883    3.1076903    4.5346348   -2.3457338   0.16674486 
-   60000    26.874199  -0.81598034    1.3432151    5.1322624    4.9545484   -2.9566615   0.25950486 
-   61000    27.401306  -0.82895856    1.1636949     4.020154    4.5745928    -2.601466   0.18061051 
-   62000    28.930313   -1.5231967   0.85173243    4.3517328    4.4878662   -2.5859205    0.1755493 
-   63000     26.56874  0.026147233   0.60836216    4.4231618    4.4390677   -2.1721849   0.08594237 
-   64000    26.729023  -0.76953985   0.76734633    4.5104288    5.0886456   -2.2118551   0.11339216 
-   65000    28.900471   -1.3901477   0.86194657    4.2774976     4.498325   -2.3672362   0.20668335 
-   66000    26.884253  -0.21198879   0.98509625    4.0843117    4.4344172   -2.3289416   0.23631017 
-   67000    27.210888  -0.84075559    1.0396559    4.7253607    4.4314589   -2.2985702   0.19326507 
-   68000    28.042102   -1.1898715     1.053534    3.8748712    4.4358449   -2.3998723    0.2431659 
-   69000    28.939141   -1.6968936   0.98155912    4.0460838    5.0075204   -2.5547087   0.28645131 
-   70000     27.15577  -0.85202797    1.1469079    4.7645212    4.6133209   -2.3410451  0.086576572 
-   71000    25.507417  -0.27780727   0.95157881    4.8759406     4.853401   -2.9598705   0.41011008 
-   72000    29.804703   -1.4847015   0.96345767    3.6797304    4.3678377   -2.4594626   0.14480206 
-   73000    28.602798   -1.4906143   0.72497266    4.2442974    4.5360598   -2.3621638   0.14385651 
-   74000      28.4928  -0.91319873    1.0377472    3.8033127    4.3991601   -2.4051911  0.095567428 
-   75000     26.38168  -0.70733237    1.1557817     5.697939    4.5935618   -2.4285007  0.058980519 
-   76000     27.16626  -0.83631031   0.84844246    4.7460887    4.5801472   -2.1260014   0.12845946 
-   77000    29.040661   -1.3089499   0.80285084     4.664804    4.5215895   -2.6861939   0.13215598 
-   78000    27.477871   -1.0600977   0.88595045    4.6264017    5.4095605    -2.474411   0.10987174 
-   79000    26.151797  -0.55779685   0.91382436      4.99964    4.9184022   -2.2547241   0.22854038 
-   80000     28.14523  -0.54460026    0.8982411    3.5374555    4.3785673   -2.3196807  0.088567964 
-   81000    29.029941   -1.6467789   0.79042284    3.7269899    4.7407998   -2.3795824    0.1408727 
-   82000    27.920287  -0.72798032    1.0076975    3.4449461    4.5621371   -2.8239074   0.25103454 
-   83000    29.131054    -1.114367   0.76887285     3.459639    4.5163922    -2.607825   0.19991648 
-   84000    28.249768  -0.69944068    1.0510846    4.0436296    4.6430538   -2.4213355  0.077299966 
-   85000     28.06888  -0.62132922   0.91829312    4.1294147    4.3099557    -2.354063   0.15866186 
-   86000    28.664264   -1.1022906   0.87831695    4.5773522    4.6045802   -2.9206875   0.33950063 
-   87000    27.960967   -1.2852756   0.77694253    3.9011301    4.9114139   -3.2374868    0.3068138 
-   88000    27.190678   -1.2803268    1.1545301    4.5769709    5.2404761   -2.3825838   0.10356039 
-   89000    26.792931  -0.44516641    1.0236244    4.2007253    4.7098685   -2.3608551  0.034447062 
-   90000    27.173991  -0.87185611     1.065719    4.1953618    4.6856408   -2.6539232   0.16957757 
-   91000    28.626528    -1.239257   0.89524651    4.7048012    4.6344201   -2.7367901   0.43534143 
-   92000    27.661812    -1.109044   0.92817391    5.0294489    4.3890711   -2.4108669   0.12570139 
-   93000    28.156793   -1.0820907   0.92812693     4.938385    4.4901426   -2.4023366   0.30135781 
-   94000    28.842149   -1.3524969    1.1451109    4.3125908    4.6959035   -2.6747199    0.2254607 
-   95000    27.862247   -1.2119045    1.0218976    4.2614082    4.4931316   -2.6902934   0.16345201 
-   96000    27.084973  -0.93738328    1.3984324    4.5647189    4.4232205   -2.2834097   0.11217888 
-   97000    27.587078  -0.89397255   0.78218462    3.8944421    4.3981479   -2.4205318   0.16570942 
-   98000    27.981746   -1.2380545   0.84847869     4.311441    4.7340377   -2.4270441  0.023565612 
-   99000    27.476625   -0.8569146   0.82550381    4.1656963    4.4064921   -2.4169708     0.160814 
-  100000    26.121325  -0.63610855    1.0803389    4.9257118    4.7073263   -2.4010334  0.066303044 
-Loop time of 2.693 on 4 procs for 100000 steps with 34 atoms
-
-Performance: 6416.646 ns/day, 0.004 hours/ns, 37133.367 timesteps/s
-98.4% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
-Pair    | 0.065478   | 0.2501     | 0.63682    |  45.6 |  9.29
-Bond    | 0.066944   | 0.44772    | 0.88814    |  53.7 | 16.63
-Neigh   | 0.0076509  | 0.0077319  | 0.0078275  |   0.1 |  0.29
-Comm    | 0.57917    | 1.4166     | 1.9823     |  46.9 | 52.60
-Output  | 0.0033755  | 0.0035856  | 0.0037644  |   0.2 |  0.13
-Modify  | 0.03866    | 0.1366     | 0.23978    |  24.6 |  5.07
-Other   |            | 0.4306     |            |       | 15.99
-
-Nlocal:    8.5 ave 15 max 2 min
-Histogram: 1 1 0 0 0 0 0 0 1 1
-Nghost:    25.5 ave 32 max 19 min
-Histogram: 1 1 0 0 0 0 0 0 1 1
-Neighs:    98.75 ave 257 max 18 min
-Histogram: 1 1 1 0 0 0 0 0 0 1
-
-Total # of neighbors = 395
-Ave neighs/atom = 11.6176
-Ave special neighs/atom = 9.52941
-Neighbor list builds = 294
-Dangerous builds = 0
-Total wall time: 0:00:02
--- a/examples/gcmc/in.gcmc.lj
+++ b/examples/gcmc/in.gcmc.lj
@ -1,18 +1,23 @@
 # GCMC for LJ simple fluid, no dynamics
+# T = 2.0
+# rho ~ 0.5
+# p ~ 1.5
+# mu_ex ~ 0.0
+# comparable to Frenkel and Smit GCMC Case Study, Figure 5.8 

-# variables available on command line
+# variables modifiable using -var command line switch

-variable        mu index -21.0
-variable	disp index 1.0
+variable        mu index -1.25
 variable        temp index 2.0
-variable        lbox index 10.0
+variable	disp index 1.0
+variable        lbox index 5.0

 # global model settings

 units           lj
 atom_style      atomic
-pair_style      lj/cut 3.0
-pair_modify	tail yes
+pair_style      lj/cut 3.0 
+pair_modify	tail no # turn of to avoid triggering full_energy

 # box

@ -28,15 +33,27 @@ mass		* 1.0

 fix             mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}

+# averaging
+
+variable	rho equal density
+variable	p equal press
+variable	nugget equal 1.0e-8
+variable        lambda equal 1.0
+variable     	muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget})
+fix 		ave all ave/time 10 100 1000 v_rho v_p v_muex ave one file rho_vs_p.dat
+variable	rhoav equal f_ave[1]
+variable	pav equal f_ave[2]
+variable	muexav equal f_ave[3]
+
 # output

-variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
-variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
-variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
+variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget})
+variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget})
+variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
 compute_modify  thermo_temp dynamic yes
-thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc
-thermo          100
+thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
+thermo          1000

 # run

-run             1000
+run             10000
--- a/examples/gcmc/log.24Mar17.gcmc.lj.g++.1
+++ b/examples/gcmc/log.24Mar17.gcmc.lj.g++.1
@ -1,28 +1,35 @@
 LAMMPS (17 Mar 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
 # GCMC for LJ simple fluid, no dynamics
+# T = 2.0
+# rho ~ 0.5
+# p ~ 1.5
+# mu_ex ~ 0.0
+# comparable to Frenkel and Smit GCMC Case Study, Figure 5.8

-# variables available on command line
+# variables modifiable using -var command line switch

-variable        mu index -21.0
-variable	disp index 1.0
+variable        mu index -1.25
 variable        temp index 2.0
-variable        lbox index 10.0
+variable	disp index 1.0
+variable        lbox index 5.0

 # global model settings

 units           lj
 atom_style      atomic
 pair_style      lj/cut 3.0
-pair_modify	tail yes
+pair_modify	tail no # turn of to avoid triggering full_energy

 # box

 region		box block 0 ${lbox} 0 ${lbox} 0 ${lbox}
-region		box block 0 10.0 0 ${lbox} 0 ${lbox}
-region		box block 0 10.0 0 10.0 0 ${lbox}
-region		box block 0 10.0 0 10.0 0 10.0
+region		box block 0 5.0 0 ${lbox} 0 ${lbox}
+region		box block 0 5.0 0 5.0 0 ${lbox}
+region		box block 0 5.0 0 5.0 0 5.0
 create_box	1 box
-Created orthogonal box = (0 0 0) to (10 10 10)
+Created orthogonal box = (0 0 0) to (5 5 5)
  1 by 1 by 1 MPI processor grid

 # lj parameters
@ -34,70 +41,89 @@ mass		* 1.0

 fix             mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
 fix             mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
-fix             mygcmc all gcmc 1 100 100 1 29494 2.0 -21.0 ${disp}
-fix             mygcmc all gcmc 1 100 100 1 29494 2.0 -21.0 1.0
+fix             mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
+fix             mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
+
+# averaging
+
+variable	rho equal density
+variable	p equal press
+variable	nugget equal 1.0e-8
+variable        lambda equal 1.0
+variable     	muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget})
+variable     	muex equal -1.25-${temp}*ln(density*${lambda}+${nugget})
+variable     	muex equal -1.25-2.0*ln(density*${lambda}+${nugget})
+variable     	muex equal -1.25-2.0*ln(density*1+${nugget})
+variable     	muex equal -1.25-2.0*ln(density*1+1e-08)
+fix 		ave all ave/time 10 100 1000 v_rho v_p v_muex ave one file rho_vs_p.dat
+variable	rhoav equal f_ave[1]
+variable	pav equal f_ave[2]
+variable	muexav equal f_ave[3]

 # output

-variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
-variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
-variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
+variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget})
+variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+1e-08)
+variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget})
+variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08)
+variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
+variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+1e-08)
 compute_modify  thermo_temp dynamic yes
-thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc
-thermo          100
+thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
+thermo          1000

 # run

-run             1000
+run             10000
 Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 3.3
  ghost atom cutoff = 3.3
-  binsize = 1.65, bins = 7 7 7
+  binsize = 1.65, bins = 4 4 4
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d/newton
      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 0.4369 | 0.4369 | 0.4369 Mbytes
-Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc 
-       0            0            0            0           -0            0        0            0            0            0 
-     100    1.9042848   0.39026453   -1.7692765    2.8466449        0.292      292    0.3619855   0.30247792   0.40278761 
-     200    1.8651924   0.47815517   -1.8494955    2.7886155        0.305      305   0.34021109   0.30357196   0.37759189 
-     300    2.0626994   0.52068504   -1.8197295    3.0834166        0.291      291   0.32055605    0.3003043   0.36103862 
-     400    2.0394818   0.53751435   -1.7636699    3.0482184        0.278      278   0.31698808   0.29995864   0.35441275 
-     500    1.9628066   0.54594742   -1.7145336    2.9339513        0.287      287   0.31211861   0.29724228   0.35161407 
-     600    1.9845913   0.40846162   -1.8199325    2.9669308        0.299      299   0.30976643   0.29612711   0.34933559 
-     700    1.8582606   0.53445462   -1.7869306     2.777974        0.296      296   0.30642103   0.29446478   0.34633665 
-     800    2.0340641   0.66057698   -1.7075279    3.0403148        0.283      283   0.30730979   0.29746793   0.34768045 
-     900    2.0830765   0.63731971    -1.894775     3.114911        0.322      322   0.30636338   0.29737705   0.34737644 
-    1000    1.9688933   0.50024802   -1.7013944    2.9428299        0.281      281    0.3053174   0.29772245   0.34788254 
-Loop time of 3.98286 on 1 procs for 1000 steps with 281 atoms
+Per MPI rank memory allocation (min/avg/max) = 0.433 | 0.433 | 0.433 Mbytes
+Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav 
+       0            0            0            0           -0            0        0            0            0            0            0            0            0 
+    1000    2.4038954    2.1735585   -2.7041368    3.5476844        0.496       62  0.064790036   0.06313096    0.1081294      0.54304    1.4513524 -0.025479219 
+    2000    2.0461168    1.1913842   -2.9880181    3.0212194        0.512       64  0.067416408  0.066335853   0.11306166      0.52736    1.3274665  0.034690004 
+    3000    1.7930436    1.3788681   -3.2212667    2.6505861        0.552       69  0.067733191  0.066877836    0.1133516       0.5344    1.3834744 0.0070582537 
+    4000     1.981449    1.2541054   -2.8222868    2.9217977        0.472       59  0.068546991  0.067856412   0.11442807      0.52504    1.3815629  0.043309657 
+    5000    2.0946818    1.0701629   -3.5213291    3.0977688        0.568       71   0.06813743  0.067567891   0.11342906      0.53824    1.4049567 -0.0054539777 
+    6000    1.9793484   0.68224187    -3.410211    2.9247088        0.536       67  0.067797628  0.067420108   0.11295333       0.5384     1.401683 -0.0066894359 
+    7000    2.1885798    1.6745012    -3.185499    3.2345922        0.544       68  0.068630201  0.068261832   0.11403705       0.5244     1.449239  0.045987399 
+    8000    2.2175324    1.5897263    -3.078898    3.2759002        0.528       66  0.068180395  0.067899629   0.11332691      0.53928    1.5488388  -0.01075766 
+    9000    1.8610779    1.0396231    -2.923262    2.7465908        0.496       62  0.068346453  0.068028117    0.1134132      0.52912    1.4352871  0.027082544 
+   10000    2.1079271    1.1746643   -2.9112062    3.1091925         0.48       60  0.068352878  0.068054948   0.11335434       0.5316    1.4462327  0.018503094 
+Loop time of 13.05 on 1 procs for 10000 steps with 60 atoms

-Performance: 108464.750 tau/day, 251.076 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 331035.016 tau/day, 766.285 timesteps/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads

 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.10563    | 0.10563    | 0.10563    |   0.0 |  2.65
-Neigh   | 0.33428    | 0.33428    | 0.33428    |   0.0 |  8.39
-Comm    | 0.027969   | 0.027969   | 0.027969   |   0.0 |  0.70
-Output  | 0.00017285 | 0.00017285 | 0.00017285 |   0.0 |  0.00
-Modify  | 3.5096     | 3.5096     | 3.5096     |   0.0 | 88.12
-Other   |            | 0.005197   |            |       |  0.13
+Pair    | 0.37239    | 0.37239    | 0.37239    |   0.0 |  2.85
+Neigh   | 0.94764    | 0.94764    | 0.94764    |   0.0 |  7.26
+Comm    | 0.092473   | 0.092473   | 0.092473   |   0.0 |  0.71
+Output  | 0.00023365 | 0.00023365 | 0.00023365 |   0.0 |  0.00
+Modify  | 11.627     | 11.627     | 11.627     |   0.0 | 89.09
+Other   |            | 0.01054    |            |       |  0.08

-Nlocal:    281 ave 281 max 281 min
+Nlocal:    60 ave 60 max 60 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    977 ave 977 max 977 min
+Nghost:    663 ave 663 max 663 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    5902 ave 5902 max 5902 min
+Neighs:    2133 ave 2133 max 2133 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

-Total # of neighbors = 5902
-Ave neighs/atom = 21.0036
-Neighbor list builds = 1000
+Total # of neighbors = 2133
+Ave neighs/atom = 35.55
+Neighbor list builds = 10000
 Dangerous builds = 0
-Total wall time: 0:00:03
+Total wall time: 0:00:13
--- a/examples/gcmc/log.24Mar17.gcmc.lj.g++.4
+++ b/examples/gcmc/log.24Mar17.gcmc.lj.g++.4
@ -1,28 +1,35 @@
 LAMMPS (17 Mar 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
 # GCMC for LJ simple fluid, no dynamics
+# T = 2.0
+# rho ~ 0.5
+# p ~ 1.5
+# mu_ex ~ 0.0
+# comparable to Frenkel and Smit GCMC Case Study, Figure 5.8

-# variables available on command line
+# variables modifiable using -var command line switch

-variable        mu index -21.0
-variable	disp index 1.0
+variable        mu index -1.25
 variable        temp index 2.0
-variable        lbox index 10.0
+variable	disp index 1.0
+variable        lbox index 5.0

 # global model settings

 units           lj
 atom_style      atomic
 pair_style      lj/cut 3.0
-pair_modify	tail yes
+pair_modify	tail no # turn of to avoid triggering full_energy

 # box

 region		box block 0 ${lbox} 0 ${lbox} 0 ${lbox}
-region		box block 0 10.0 0 ${lbox} 0 ${lbox}
-region		box block 0 10.0 0 10.0 0 ${lbox}
-region		box block 0 10.0 0 10.0 0 10.0
+region		box block 0 5.0 0 ${lbox} 0 ${lbox}
+region		box block 0 5.0 0 5.0 0 ${lbox}
+region		box block 0 5.0 0 5.0 0 5.0
 create_box	1 box
-Created orthogonal box = (0 0 0) to (10 10 10)
+Created orthogonal box = (0 0 0) to (5 5 5)
  1 by 2 by 2 MPI processor grid

 # lj parameters
@ -34,70 +41,89 @@ mass		* 1.0

 fix             mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
 fix             mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
-fix             mygcmc all gcmc 1 100 100 1 29494 2.0 -21.0 ${disp}
-fix             mygcmc all gcmc 1 100 100 1 29494 2.0 -21.0 1.0
+fix             mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
+fix             mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
+
+# averaging
+
+variable	rho equal density
+variable	p equal press
+variable	nugget equal 1.0e-8
+variable        lambda equal 1.0
+variable     	muex equal ${mu}-${temp}*ln(density*${lambda}+${nugget})
+variable     	muex equal -1.25-${temp}*ln(density*${lambda}+${nugget})
+variable     	muex equal -1.25-2.0*ln(density*${lambda}+${nugget})
+variable     	muex equal -1.25-2.0*ln(density*1+${nugget})
+variable     	muex equal -1.25-2.0*ln(density*1+1e-08)
+fix 		ave all ave/time 10 100 1000 v_rho v_p v_muex ave one file rho_vs_p.dat
+variable	rhoav equal f_ave[1]
+variable	pav equal f_ave[2]
+variable	muexav equal f_ave[3]

 # output

-variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
-variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
-variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
+variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+${nugget})
+variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+1e-08)
+variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+${nugget})
+variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+1e-08)
+variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+${nugget})
+variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+1e-08)
 compute_modify  thermo_temp dynamic yes
-thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc
-thermo          100
+thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav
+thermo          1000

 # run

-run             1000
+run             10000
 Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 3.3
  ghost atom cutoff = 3.3
-  binsize = 1.65, bins = 7 7 7
+  binsize = 1.65, bins = 4 4 4
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d/newton
      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 0.434 | 0.434 | 0.434 Mbytes
-Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc 
-       0            0            0            0           -0            0        0            0            0            0 
-     100    2.0328045   0.58661762   -1.6812724    3.0385824        0.287      287   0.35917318   0.30067507   0.38663622 
-     200    1.9594279   0.50682399   -1.7308396    2.9287927        0.284      284   0.33788365   0.30337335   0.37300293 
-     300    2.0602937    0.7028247   -1.9278541    3.0806296        0.315      315   0.31882007   0.29697498   0.36167185 
-     400     1.995183    0.4328246   -1.8715454     2.983026        0.307      307   0.31527654   0.29681901   0.35673374 
-     500    2.1390101   0.48232215    -1.554138    3.1960306        0.257      257   0.31372975   0.30003067   0.35558858 
-     600    2.0584244    0.4929049   -1.6995569    3.0767263        0.283      283   0.31114213   0.29801665   0.35160109 
-     700    1.9155066   0.49654243   -1.5770611    2.8624174        0.265      265   0.31056419   0.29944173   0.35157337 
-     800    2.0883562   0.52731947   -1.8261112    3.1220925          0.3      300   0.30730979   0.29704354   0.34898892 
-     900    2.0470677    0.5605993   -2.0130053    3.0610656        0.322      322   0.30484441   0.29586719   0.34678883 
-    1000     2.004135   0.50642204   -1.6956257    2.9955798        0.283      283   0.30396929   0.29634309   0.34770304 
-Loop time of 3.688 on 4 procs for 1000 steps with 283 atoms
+Per MPI rank memory allocation (min/avg/max) = 0.4477 | 0.4477 | 0.4477 Mbytes
+Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav 
+       0            0            0            0           -0            0        0            0            0            0            0            0            0 
+    1000     1.956397    1.7699101   -2.7889468    2.8864874        0.488       61  0.068894746  0.067229075    0.1141726      0.53288    1.3832798  0.013392866 
+    2000     2.040943   0.56060899   -2.8001647    3.0077055        0.456       57  0.069858594  0.068831934   0.11629114       0.5232    1.3587174  0.049995794 
+    3000    2.0004866    1.5736515   -3.3098044    2.9572411        0.552       69  0.069594029  0.068727791   0.11592543      0.53096    1.4129434  0.020022578 
+    4000    2.1127942     2.642809   -2.8865084    3.1211733        0.528       66  0.070268697  0.069533235   0.11693806      0.52424    1.3444615  0.046884078 
+    5000    2.3663648     1.354269   -3.1917346    3.4957662        0.528       66  0.070519633  0.069960064   0.11710321      0.52688    1.3595814  0.036270867 
+    6000    1.9224136   0.82756699      -3.1965     2.839257         0.52       65   0.06985018  0.069474645   0.11628632        0.536      1.47062   0.00141549 
+    7000    2.0266192    1.5593811   -2.9972341    2.9931606         0.52       65  0.070244693  0.069880791   0.11666541      0.52528    1.3246332  0.040754793 
+    8000    1.7790467    1.8680568   -2.8028819    2.6275151         0.52       65  0.070454494  0.070172368   0.11736806        0.524    1.4213649  0.047985191 
+    9000    1.7968847    1.3195587    -3.261001    2.6550983        0.536       67  0.069952011  0.069618327   0.11650087      0.53904    1.4624201  -0.01069837 
+   10000    2.1566109    1.1015729   -3.4999837    3.1880335        0.552       69  0.069603309  0.069284134   0.11625548      0.53128    1.3587249   0.02075238 
+Loop time of 13.0611 on 4 procs for 10000 steps with 69 atoms

-Performance: 117136.751 tau/day, 271.150 timesteps/s
-99.2% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 330753.007 tau/day, 765.632 timesteps/s
+99.7% CPU use with 4 MPI tasks x 1 OpenMP threads

 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.024644   | 0.026027   | 0.027483   |   0.6 |  0.71
-Neigh   | 0.085449   | 0.088998   | 0.092893   |   0.9 |  2.41
-Comm    | 0.045756   | 0.051296   | 0.056578   |   1.7 |  1.39
-Output  | 0.00028491 | 0.00030857 | 0.00035262 |   0.0 |  0.01
-Modify  | 3.5189     | 3.5191     | 3.5194     |   0.0 | 95.42
-Other   |            | 0.002221   |            |       |  0.06
+Pair    | 0.08888    | 0.09443    | 0.099889   |   1.4 |  0.72
+Neigh   | 0.27721    | 0.28532    | 0.29177    |   1.1 |  2.18
+Comm    | 0.27648    | 0.28875    | 0.30268    |   1.9 |  2.21
+Output  | 0.00029635 | 0.00043058 | 0.00048113 |   0.0 |  0.00
+Modify  | 12.384     | 12.384     | 12.384     |   0.0 | 94.82
+Other   |            | 0.008055   |            |       |  0.06

-Nlocal:    70.75 ave 77 max 68 min
-Histogram: 1 2 0 0 0 0 0 0 0 1
-Nghost:    514.25 ave 520 max 507 min
-Histogram: 1 0 0 0 1 0 0 1 0 1
-Neighs:    1483.5 ave 1715 max 1359 min
-Histogram: 2 0 0 1 0 0 0 0 0 1
+Nlocal:    17.25 ave 23 max 10 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Nghost:    506.5 ave 519 max 490 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Neighs:    705.75 ave 998 max 369 min
+Histogram: 1 0 0 0 0 1 1 0 0 1

-Total # of neighbors = 5934
-Ave neighs/atom = 20.9682
-Neighbor list builds = 1000
+Total # of neighbors = 2823
+Ave neighs/atom = 40.913
+Neighbor list builds = 10000
 Dangerous builds = 0
-Total wall time: 0:00:03
+Total wall time: 0:00:13
--- a/lib/voronoi/Install.py
+++ b/lib/voronoi/Install.py
@ -0,0 +1,116 @@
+#!/usr/bin/env python
+
+# install.py tool to download, unpack, build, and link to the Voro++ library
+# used to automate the steps described in the README file in this dir
+
+import sys,os,re,urllib,commands
+
+# help message
+
+help = """
+Syntax: install.py -v version -g gdir [gname] -b bdir -l ldir
+  specify one or more options, order does not matter
+  gdir,bdir,ldir can be paths relative to lib/latte, full paths, or contain ~
+  -v = version of Voro++ to download and build
+       default = voro++-0.4.6 (current as of Jan 2015)
+  -g = grab (download) from math.lbl.gov/voro++ website
+       unpack tarfile in gdir to produce version dir (e.g. voro++-0.4.6)
+       if optional gname specified, rename version dir to gname within gdir
+  -b = build Voro++, bdir = Voro++ home directory
+       note that bdir must include the version suffix unless renamed
+  -l = create 2 softlinks (includelink,liblink)
+         in lib/voronoi to src dir of ldir = Voro++ home directory
+       note that ldir must include the version suffix unless renamed
+"""
+
+# settings
+
+version = "voro++-0.4.6"
+url = "http://math.lbl.gov/voro++/download/dir/%s.tar.gz" % version
+
+# print error message or help
+
+def error(str=None):
+  if not str: print help
+  else: print "ERROR",str
+  sys.exit()
+
+# expand to full path name
+# process leading '~' or relative path
+  
+def fullpath(path):
+  return os.path.abspath(os.path.expanduser(path))
+  
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
+
+grabflag = 0
+buildflag = 0
+linkflag = 0
+
+iarg = 0
+while iarg < nargs:
+  if args[iarg] == "-v":
+    if iarg+2 > nargs: error()
+    version = args[iarg+1]
+    iarg += 2  
+  elif args[iarg] == "-g":
+    if iarg+2 > nargs: error()
+    grabflag = 1
+    grabdir = args[iarg+1]
+    grabname = None
+    if iarg+2 < nargs and args[iarg+2][0] != '-':
+      grabname = args[iarg+2]
+      iarg += 1
+    iarg += 2
+  elif args[iarg] == "-b":
+    if iarg+2 > nargs: error()
+    buildflag = 1
+    builddir = args[iarg+1]
+    iarg += 2
+  elif args[iarg] == "-l":
+    if iarg+2 > nargs: error()
+    linkflag = 1
+    linkdir = args[iarg+1]
+    iarg += 2
+  else: error()
+
+# download and unpack Voro++ tarball
+
+if grabflag:
+  print "Downloading Voro++ ..."
+  grabdir = fullpath(grabdir)
+  if not os.path.isdir(grabdir): error("Grab directory does not exist")
+  urllib.urlretrieve(url,"%s/%s.tar.gz" % (grabdir,version))
+  
+  print "Unpacking Voro++ tarball ..."
+  tardir = "%s/%s" % (grabdir,version)
+  if os.path.exists(tardir): commands.getoutput("rm -rf %s" % tardir)
+  cmd = "cd %s; tar zxvf %s.tar.gz" % (grabdir,version)
+  txt = commands.getoutput(cmd)
+  print tardir,grabdir,grabname
+  if grabname: os.rename(tardir,"%s/%s" % (grabdir,grabname))
+
+# build Voro++
+
+if buildflag:
+  print "Building Voro++ ..."
+  cmd = "cd %s; make" % builddir
+  txt = commands.getoutput(cmd)
+  print txt
+
+# create 2 links in lib/voronoi to Voro++ src dir
+
+if linkflag:
+  print "Creating links to Voro++ include and lib files"
+  if os.path.isfile("includelink") or os.path.islink("includelink"):
+    os.remove("includelink")
+  if os.path.isfile("liblink") or os.path.islink("liblink"):
+    os.remove("liblink")
+  cmd = "ln -s %s/src includelink" % linkdir
+  commands.getoutput(cmd)
+  cmd = "ln -s %s/src liblink" % linkdir
+  commands.getoutput(cmd)
--- a/lib/voronoi/README
+++ b/lib/voronoi/README
@ -9,8 +9,8 @@ Laboratory.
 -----------------

 You must perform the following steps yourself, or you can use the
-install.py Python script to automate any or all steps of the process.
-Type "python install.py" for instructions.
+Install.py Python script to automate any or all steps of the process.
+Type "python Install.py" for instructions.

 1.  Download Voro++ at http://math.lbl.gov/voro++/download
    either as a tarball or via SVN, and unpack the
--- a/lib/voronoi/install.py
+++ b/lib/voronoi/install.py
@ -1,163 +0,0 @@
-#!usr/local/python
-
-# install.py tool to download, unpack, build, and link to the Voro++ library
-# used to automate the steps described in the README file in this dir
-
-import sys,os,re,urllib,commands
-
-help = """
-Syntax: install.py -d dir -v version -g -b -i installdir -l incdir libdir
-        specify one or more options, order does not matter
-        -d = dir to download tarball to, unpack tarball in, perform build in
-             dir will be created if it doesn't exist (only last level)
-             default = this dir
-        -v = version of Voro++ to download and work with
-             default = voro++-0.4.6 (current as of Jan 2015)
-        -g = download (grab) tarball from
-             http://math.lbl.gov/voro++/download/dir/version
-        -b = build Voro++ by invoking "make" in its home dir
-             no default
-        -i = install Voro++ by invoking "make install" in its home dir
-             installdir arg is optional:
-               if not specified, installs at PREFIX defined in config.mk file
-               if specified, will overwrite PREFIX and install there
-             if PREFIX starts with /usr, will invoke "sudo make install"
-        -l = create two links to incdir and libdir
-             incdir and libdir are optional (specify neither or both):
-               if specified, includelink and liblink are to those two dirs
-                 these are dirs where Voro++ include files and lib file are
-               if not specified and no install, links are to Voro++ src dir
-               if not specified and install performed,
-                 links are to include and lib dirs under PREFIX
-"""
-
-def error():
-  print help
-  sys.exit()
-  
-# parse args
-
-args = sys.argv
-
-if len(args) == 1: error()
-
-dir = "."
-version = "voro++-0.4.6"
-grabflag = 0
-buildflag = 0
-installflag = 0
-linkflag = 0
-
-iarg = 1
-while iarg < len(args):
-  if args[iarg] == "-d":
-    if iarg+2 > len(args): error()
-    dir = args[iarg+1]
-    iarg += 2  
-  elif args[iarg] == "-v":
-    if iarg+2 > len(args): error()
-    version = args[iarg+1]
-    iarg += 2  
-  elif args[iarg] == "-g":
-    grabflag = 1
-    iarg += 1
-  elif args[iarg] == "-b":
-    buildflag = 1
-    iarg += 1
-  elif args[iarg] == "-i":
-    installflag = 1
-    if iarg+1 == len(args) or args[iarg+1][0] == '-':
-      installdir = ""
-      iarg += 1
-    else:
-      if iarg+2 > len(args): error()
-      installdir = args[iarg+1]
-      iarg += 2  
-  elif args[iarg] == "-l":
-    linkflag = 1
-    if iarg+1 == len(args) or args[iarg+1][0] == '-' or \
-          iarg+2 == len(args) or args[iarg+2][0] == '-':
-      includedir = libdir = ""
-      iarg += 1
-    else:
-      if iarg+3 > len(args): error()
-      includedir = args[iarg+1]
-      libdir = args[iarg+2]
-      iarg += 3
-  else: error()
-
-dir = os.path.abspath(dir)
-url = "http://math.lbl.gov/voro++/download/dir/%s.tar.gz" % version
-
-# create dir if does not exist
-
-if not os.path.isdir(dir):
-  if os.path.isfile(dir):
-    print "ERROR: Dir already exists as file"
-    sys.exit()
-  os.mkdir(dir)
-  if not os.path.isdir(dir):
-    print "ERROR: Unable to create dir"
-    sys.exit()
-
-# download and unpack tarball
-
-if grabflag:
-  print "Downloading Voro++ tarball ..."
-  urllib.urlretrieve(url,"%s/%s.tar.gz" % (dir,version))
-  print "Unpacking Voro++ tarball ..."
-  cmd = "cd %s; tar zxvf %s.tar.gz" % (dir,version)
-  txt = commands.getoutput(cmd)
-
-# build Voro++ in its dir
-
-if buildflag:
-  print "Building Voro++ ..."
-  cmd = "cd %s/%s; make" % (dir,version)
-  txt = commands.getoutput(cmd)
-  print txt
-
-# install Voro++
-# if installdir set, overwrite PREFIX var in its config.mk file
-# if PREFIX var starts with /usr, invoke sudo make install, else make install
-  
-if installflag:
-  print "Installing Voro++ ..."
-  if installdir:
-    txt = open("%s/%s/config.mk" % (dir,version),'r').read()
-    txt = re.sub("PREFIX=.*?\n","PREFIX=%s\n" % installdir,txt)
-    open("%s/%s/config.mk" % (dir,version),'w').write(txt)
-    print "TXT:",txt
-  txt = open("%s/%s/config.mk" % (dir,version),'r').read()
-  var = re.findall("PREFIX=.*?\n",txt)
-  prefix = var[0].split('=')[1].strip()
-  if prefix.startswith("/usr"):
-    cmd = "cd %s/%s; sudo make install" % (dir,version)
-  else:
-    cmd = "cd %s/%s; make install" % (dir,version)
-  txt = commands.getoutput(cmd)
-  print txt
-  
-# create links in this dir to Voro++ include and lib files
-
-if linkflag:
-  print "Creating links to Voro++ include and lib files"
-  if os.path.isfile("includelink") or os.path.islink("includelink"):
-    os.remove("includelink")
-  if os.path.isfile("liblink") or os.path.islink("liblink"):
-    os.remove("liblink")
-  if includedir:
-    cmd = "ln -s %s includelink" % includedir
-    txt = commands.getoutput(cmd)
-    cmd = "ln -s %s liblink" % linkdir
-    txt = commands.getoutput(cmd)
-  elif not installflag:
-    cmd = "ln -s %s/%s/src includelink" % (dir,version)
-    txt = commands.getoutput(cmd)
-    cmd = "ln -s %s/%s/src liblink" % (dir,version)
-    txt = commands.getoutput(cmd)
-  else:
-    cmd = "ln -s %s/include includelink" % prefix
-    txt = commands.getoutput(cmd)
-    cmd = "ln -s %s/lib liblink" % prefix
-    txt = commands.getoutput(cmd)
--- a/potentials/InP.vashishta
+++ b/potentials/InP.vashishta
--- a/potentials/SiC.vashishta
+++ b/potentials/SiC.vashishta
--- a/potentials/SiO.1990.vashishta
+++ b/potentials/SiO.1990.vashishta
--- a/potentials/SiO.1994.vashishta
+++ b/potentials/SiO.1994.vashishta
--- a/potentials/SiO.1997.vashishta
+++ b/potentials/SiO.1997.vashishta
--- a/potentials/ffield.smtbq.Al
+++ b/potentials/ffield.smtbq.Al
--- a/potentials/ffield.smtbq.Al2O3
+++ b/potentials/ffield.smtbq.Al2O3
--- a/potentials/ffield.smtbq.TiO2
+++ b/potentials/ffield.smtbq.TiO2
--- a/src/.gitignore
+++ b/src/.gitignore
@ -76,6 +76,13 @@
 /pair_awpmd_cut.cpp
 /pair_awpmd_cut.h

+/dihedral_charmmfsh.cpp
+/dihedral_charmmfsh.h
+/pair_lj_charmmfsw_coul_charmmfsh.cpp
+/pair_lj_charmmfsw_coul_charmmfsh.h
+/pair_lj_charmmfsw_coul_long.cpp
+/pair_lj_charmmfsw_coul_long.h
+
 /angle_cg_cmm.cpp
 /angle_cg_cmm.h
 /angle_charmm.cpp
--- a/src/ASPHERE/compute_temp_asphere.cpp
+++ b/src/ASPHERE/compute_temp_asphere.cpp
@ -73,6 +73,11 @@ ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) :
    } else error->all(FLERR,"Illegal compute temp/asphere command");
  }

+  // when computing only the rotational temperature,
+  // do not remove DOFs for translation as set by default
+
+  if (mode == ROTATE) extra_dof = 0;
+
  vector = new double[6];

 }
--- a/src/COMPRESS/Install.sh
+++ b/src/COMPRESS/Install.sh
@ -29,7 +29,7 @@ action () {
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/GRANULAR/fix_wall_gran_region.cpp
+++ b/src/GRANULAR/fix_wall_gran_region.cpp
@ -131,9 +131,8 @@ void FixWallGranRegion::init()
 void FixWallGranRegion::post_force(int vflag)
 {
  int i,m,nc,iwall;
-  double rinv,fx,fy,fz,tooclose;
  double dx,dy,dz,rsq,meff;
-  double xc[3],vwall[3];
+  double vwall[3];

  // do not update shear history during setup

--- a/src/Install.sh
+++ b/src/Install.sh
@ -33,5 +33,5 @@ action () {
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done
--- a/src/KIM/Install.sh
+++ b/src/KIM/Install.sh
@ -29,7 +29,7 @@ action () {
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/KOKKOS/pppm_kokkos.cpp
+++ b/src/KOKKOS/pppm_kokkos.cpp
@ -3158,7 +3158,7 @@ double PPPMKokkos<DeviceType>::memory_usage()
  if (peratom_allocate_flag)
    bytes += 6 * nbrick * sizeof(FFT_SCALAR);

-  bytes += cg->memory_usage();
+  if (cg) bytes += cg->memory_usage();

  return bytes;
 }
--- a/src/KOKKOS/verlet_kokkos.cpp
+++ b/src/KOKKOS/verlet_kokkos.cpp
@ -64,14 +64,17 @@ VerletKokkos::VerletKokkos(LAMMPS *lmp, int narg, char **arg) :
   setup before run
 ------------------------------------------------------------------------- */

-void VerletKokkos::setup()
+void VerletKokkos::setup(int flag)
 {
  if (comm->me == 0 && screen) {
    fprintf(screen,"Setting up Verlet run ...\n");
-    fprintf(screen,"  Unit style    : %s\n", update->unit_style);
-    fprintf(screen,"  Current step  : " BIGINT_FORMAT "\n", update->ntimestep);
-    fprintf(screen,"  Time step     : %g\n", update->dt);
-    timer->print_timeout(screen);
+    if (flag) {
+      fprintf(screen,"  Unit style    : %s\n", update->unit_style);
+      fprintf(screen,"  Current step  : " BIGINT_FORMAT "\n",
+              update->ntimestep);
+      fprintf(screen,"  Time step     : %g\n", update->dt);
+      timer->print_timeout(screen);
+    }
  }

  update->setupflag = 1;
@ -169,7 +172,7 @@ void VerletKokkos::setup()
  if (force->newton) comm->reverse_comm();

  modify->setup(vflag);
-  output->setup();
+  output->setup(flag);
  lmp->kokkos->auto_sync = 1;
  update->setupflag = 1;
 }
--- a/src/KOKKOS/verlet_kokkos.h
+++ b/src/KOKKOS/verlet_kokkos.h
@ -29,7 +29,7 @@ class VerletKokkos : public Verlet {
 public:
  VerletKokkos(class LAMMPS *, int, char **);
  ~VerletKokkos() {}
-  void setup();
+  void setup(int flag=1);
  void setup_minimal(int);
  void run(int);

--- a/src/KSPACE/pppm.cpp
+++ b/src/KSPACE/pppm.cpp
@ -3085,7 +3085,7 @@ double PPPM::memory_usage()
    bytes += 2 * nfft_both * sizeof(FFT_SCALAR);;
  }

-  bytes += cg->memory_usage();
+  if (cg) bytes += cg->memory_usage();

  return bytes;
 }
--- a/src/KSPACE/pppm_disp.cpp
+++ b/src/KSPACE/pppm_disp.cpp
@ -8240,7 +8240,7 @@ double PPPMDisp::memory_usage()
    bytes += 6 * nfft_both * sizeof(double);      // vg
    bytes += nfft_both * sizeof(double);          // greensfn
    bytes += nfft_both * 3 * sizeof(FFT_SCALAR);    // density_FFT, work1, work2
-    bytes += cg->memory_usage();
+    if (cg) bytes += cg->memory_usage();
  }

  if (function[1] + function[2] + function[3]) {
@ -8250,7 +8250,7 @@ double PPPMDisp::memory_usage()
    bytes += 6 * nfft_both_6 * sizeof(double);      // vg
    bytes += nfft_both_6 * sizeof(double);          // greensfn
    bytes += nfft_both_6 * (mixing + 2) * sizeof(FFT_SCALAR);    // density_FFT, work1, work2
-    bytes += cg_6->memory_usage();
+    if (cg_6) bytes += cg_6->memory_usage();
  }
  return bytes;
 }
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@ -60,7 +60,7 @@ using namespace MathConst;
 // this must be lower than MAXENERGYSIGNAL
 // by a large amount, so that it is still
 // less than total energy when negative
-// energy changes are added to MAXENERGYSIGNAL
+// energy contributions are added to MAXENERGYSIGNAL

 #define MAXENERGYTEST 1.0e50

@ -72,7 +72,7 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
  Fix(lmp, narg, arg),
  idregion(NULL), full_flag(0), ngroups(0), groupstrings(NULL), ngrouptypes(0), grouptypestrings(NULL),
  grouptypebits(NULL), grouptypes(NULL), local_gas_list(NULL), atom_coord(NULL), random_equal(NULL), random_unequal(NULL), 
-  coords(NULL), imageflags(NULL), idrigid(NULL), idshake(NULL), fixrigid(NULL), fixshake(NULL)
+  coords(NULL), imageflags(NULL), fixrigid(NULL), fixshake(NULL), idrigid(NULL), idshake(NULL)
 {
  if (narg < 11) error->all(FLERR,"Illegal fix gcmc command");

@ -260,7 +260,7 @@ void FixGCMC::options(int narg, char **arg)
  grouptypebits = NULL;
  energy_intra = 0.0;
  tfac_insert = 1.0;
-  overlap_cutoff = 0.0;
+  overlap_cutoffsq = 0.0;
  overlap_flag = 0;

  int iarg = 0;
@ -366,7 +366,8 @@ void FixGCMC::options(int narg, char **arg)
      iarg += 2;
    } else if (strcmp(arg[iarg],"overlap_cutoff") == 0) {
      if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command");
-      overlap_cutoff = force->numeric(FLERR,arg[iarg+1]);
+      double rtmp = force->numeric(FLERR,arg[iarg+1]);
+      overlap_cutoffsq = rtmp*rtmp;
      overlap_flag = 1;
      iarg += 2;
    } else error->all(FLERR,"Illegal fix gcmc command");
@ -432,7 +433,8 @@ void FixGCMC::init()
        (force->pair == NULL) ||
        (force->pair->single_enable == 0) ||
        (force->pair_match("hybrid",0)) ||
-        (force->pair_match("eam",0))
+        (force->pair_match("eam",0)) ||
+        (force->pair->tail_flag)
        ) {
      full_flag = true;
      if (comm->me == 0)
@ -618,13 +620,18 @@ void FixGCMC::init()
  }

  // compute beta, lambda, sigma, and the zz factor
-
+  // For LJ units, lambda=1
  beta = 1.0/(force->boltz*reservoir_temperature);
-  double lambda = sqrt(force->hplanck*force->hplanck/
-                       (2.0*MY_PI*gas_mass*force->mvv2e*
+  if (strcmp(update->unit_style,"lj") == 0)
+    zz = exp(beta*chemical_potential);
+  else {
+    double lambda = sqrt(force->hplanck*force->hplanck/
+                         (2.0*MY_PI*gas_mass*force->mvv2e*
                        force->boltz*reservoir_temperature));
+    zz = exp(beta*chemical_potential)/(pow(lambda,3.0));
+  }
+  
  sigma = sqrt(force->boltz*reservoir_temperature*tfac_insert/gas_mass/force->mvv2e);
-  zz = exp(beta*chemical_potential)/(pow(lambda,3.0));
  if (pressure_flag) zz = pressure*fugacity_coeff*beta/force->nktv2p;

  imagezero = ((imageint) IMGMAX << IMG2BITS) |
@ -695,6 +702,9 @@ void FixGCMC::pre_exchange()

  if (full_flag) {
    energy_stored = energy_full();
+    if (overlap_flag && energy_stored > MAXENERGYTEST)
+        error->warning(FLERR,"Energy of old configuration in "
+                       "fix gcmc is > MAXENERGYTEST.");

    if (mode == MOLECULE) {
      for (int i = 0; i < ncycles; i++) {
@ -772,6 +782,9 @@ void FixGCMC::attempt_atomic_translation()
  if (i >= 0) {
    double **x = atom->x;
    double energy_before = energy(i,ngcmc_type,-1,x[i]);
+    if (overlap_flag && energy_before > MAXENERGYTEST)
+        error->warning(FLERR,"Energy of old configuration in "
+                       "fix gcmc is > MAXENERGYTEST.");
    double rsq = 1.1;
    double rx,ry,rz;
    rx = ry = rz = 0.0;
@ -992,6 +1005,9 @@ void FixGCMC::attempt_molecule_translation()
  if (translation_molecule == -1) return;

  double energy_before_sum = molecule_energy(translation_molecule);
+  if (overlap_flag && energy_before_sum > MAXENERGYTEST)
+    error->warning(FLERR,"Energy of old configuration in "
+                   "fix gcmc is > MAXENERGYTEST.");

  double **x = atom->x;
  double rx,ry,rz;
@ -1089,6 +1105,9 @@ void FixGCMC::attempt_molecule_rotation()
  if (rotation_molecule == -1) return;

  double energy_before_sum = molecule_energy(rotation_molecule);
+  if (overlap_flag && energy_before_sum > MAXENERGYTEST)
+    error->warning(FLERR,"Energy of old configuration in "
+                   "fix gcmc is > MAXENERGYTEST.");

  int nlocal = atom->nlocal;
  int *mask = atom->mask;
@ -2128,7 +2147,7 @@ double FixGCMC::energy(int i, int itype, tagint imolecule, double *coord)
    // if overlap check requested, if overlap,
    // return signal value for energy 

-    if (overlap_flag && rsq < overlap_cutoff)
+    if (overlap_flag && rsq < overlap_cutoffsq)
      return MAXENERGYSIGNAL;
    
    if (rsq < cutsq[itype][jtype])
@ -2164,6 +2183,8 @@ double FixGCMC::molecule_energy(tagint gas_molecule_id)

 double FixGCMC::energy_full()
 {
+  int imolecule;
+  
  if (triclinic) domain->x2lamda(atom->nlocal);
  domain->pbc();
  comm->exchange();
@ -2179,14 +2200,15 @@ double FixGCMC::energy_full()
  // return signal value for energy 

  if (overlap_flag) {
+    int overlaptestall;
+    int overlaptest = 0;
    double delx,dely,delz,rsq;
    double **x = atom->x;
    tagint *molecule = atom->molecule;
    int nall = atom->nlocal + atom->nghost;
    for (int i = 0; i < atom->nlocal; i++) {
-      int imolecule = molecule[i];
+      if (mode == MOLECULE) imolecule = molecule[i];
      for (int j = i+1; j < nall; j++) {
-
        if (mode == MOLECULE)
          if (imolecule == molecule[j]) continue;
      
@ -2195,11 +2217,18 @@ double FixGCMC::energy_full()
        delz = x[i][2] - x[j][2];
        rsq = delx*delx + dely*dely + delz*delz;
      
-        if (rsq < overlap_cutoff) return MAXENERGYSIGNAL;
+        if (rsq < overlap_cutoffsq) {
+          overlaptest = 1;
+          break;
+        }
      }
+      if (overlaptest) break;
    }
+    MPI_Allreduce(&overlaptest, &overlaptestall, 1,
+                  MPI_INT, MPI_MAX, world);
+    if (overlaptestall) return MAXENERGYSIGNAL;
  }
-  
+
  // clear forces so they don't accumulate over multiple
  // calls within fix gcmc timestep, e.g. for fix shake
  
--- a/src/MC/fix_gcmc.h
+++ b/src/MC/fix_gcmc.h
@ -106,13 +106,13 @@ class FixGCMC : public Fix {
  double xlo,xhi,ylo,yhi,zlo,zhi;
  double region_xlo,region_xhi,region_ylo,region_yhi,region_zlo,region_zhi;
  double region_volume;
-  double energy_stored;
+  double energy_stored;  // full energy of old/current configuration
  double *sublo,*subhi;
  int *local_gas_list;
  double **cutsq;
  double **atom_coord;
  imageint imagezero;
-  double overlap_cutoff;
+  double overlap_cutoffsq; // square distance cutoff for overlap 
  int overlap_flag;
  
  double energy_intra;
@ -214,9 +214,14 @@ W: Fix gcmc using full_energy option

 Fix gcmc has automatically turned on the full_energy option since it
 is required for systems like the one specified by the user. User input
-included one or more of the following: kspace, triclinic, a hybrid
-pair style, an eam pair style, or no "single" function for the pair
-style.
+included one or more of the following: kspace, a hybrid
+pair style, an eam pair style, tail correction, 
+or no "single" function for the pair style.
+
+W: Energy of old configuration in fix gcmc is > MAXENERGYTEST. 
+
+This probably means that a pair of atoms are closer than the 
+overlap cutoff distance for keyword overlap_cutoff.

 E: Invalid atom type in fix gcmc command

--- a/src/MEAM/Install.sh
+++ b/src/MEAM/Install.sh
@ -29,7 +29,7 @@ action () {
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/MOLECULE/bond_harmonic.cpp
+++ b/src/MOLECULE/bond_harmonic.cpp
@ -13,6 +13,7 @@

 #include <math.h>
 #include <stdlib.h>
+#include <string.h>
 #include "bond_harmonic.h"
 #include "atom.h"
 #include "neighbor.h"
@ -26,7 +27,10 @@ using namespace LAMMPS_NS;

 /* ---------------------------------------------------------------------- */

-BondHarmonic::BondHarmonic(LAMMPS *lmp) : Bond(lmp) {}
+BondHarmonic::BondHarmonic(LAMMPS *lmp) : Bond(lmp)
+{
+  reinitflag = 1;
+}

 /* ---------------------------------------------------------------------- */

@ -196,3 +200,16 @@ double BondHarmonic::single(int type, double rsq, int i, int j,
  if (r > 0.0) fforce = -2.0*rk/r;
  return rk*dr;
 }
+
+/* ----------------------------------------------------------------------
+    Return ptr to internal members upon request.
+------------------------------------------------------------------------ */
+void *BondHarmonic::extract( char *str, int &dim )
+{
+  dim = 1;
+  if( strcmp(str,"kappa")==0) return (void*) k;
+  if( strcmp(str,"r0")==0) return (void*) r0;
+  return NULL;
+}
+
+
--- a/src/MOLECULE/bond_harmonic.h
+++ b/src/MOLECULE/bond_harmonic.h
@ -36,6 +36,7 @@ class BondHarmonic : public Bond {
  void read_restart(FILE *);
  void write_data(FILE *);
  double single(int, double, int, int, double &);
+  virtual void *extract(char *, int &);

 protected:
  double *k,*r0;
--- a/src/MOLECULE/dihedral_charmmfsw.cpp
+++ b/src/MOLECULE/dihedral_charmmfsw.cpp
@ -21,7 +21,7 @@
 #include <mpi.h>
 #include <math.h>
 #include <stdlib.h>
-#include "dihedral_charmmfsh.h"
+#include "dihedral_charmmfsw.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
@ -40,7 +40,7 @@ using namespace MathConst;

 /* ---------------------------------------------------------------------- */

-DihedralCharmmfsh::DihedralCharmmfsh(LAMMPS *lmp) : Dihedral(lmp)
+DihedralCharmmfsw::DihedralCharmmfsw(LAMMPS *lmp) : Dihedral(lmp)
 {
  weightflag = 0;
  writedata = 1;
@ -48,7 +48,7 @@ DihedralCharmmfsh::DihedralCharmmfsh(LAMMPS *lmp) : Dihedral(lmp)

 /* ---------------------------------------------------------------------- */

-DihedralCharmmfsh::~DihedralCharmmfsh()
+DihedralCharmmfsw::~DihedralCharmmfsw()
 {
  if (allocated && !copymode) {
    memory->destroy(setflag);
@ -63,7 +63,7 @@ DihedralCharmmfsh::~DihedralCharmmfsh()

 /* ---------------------------------------------------------------------- */

-void DihedralCharmmfsh::compute(int eflag, int vflag)
+void DihedralCharmmfsw::compute(int eflag, int vflag)
 {
  int i1,i2,i3,i4,i,m,n,type;
  double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
@ -322,7 +322,7 @@ void DihedralCharmmfsh::compute(int eflag, int vflag)

 /* ---------------------------------------------------------------------- */

-void DihedralCharmmfsh::allocate()
+void DihedralCharmmfsw::allocate()
 {
  allocated = 1;
  int n = atom->ndihedraltypes;
@ -342,7 +342,7 @@ void DihedralCharmmfsh::allocate()
   set coeffs for one type
 ------------------------------------------------------------------------- */

-void DihedralCharmmfsh::coeff(int narg, char **arg)
+void DihedralCharmmfsw::coeff(int narg, char **arg)
 {
  if (narg != 5) error->all(FLERR,"Incorrect args for dihedral coefficients");
  if (!allocated) allocate();
@ -384,7 +384,7 @@ void DihedralCharmmfsh::coeff(int narg, char **arg)
   error check and initialize all values needed for force computation
 ------------------------------------------------------------------------- */

-void DihedralCharmmfsh::init_style()
+void DihedralCharmmfsw::init_style()
 {
  // insure use of CHARMM pair_style if any weight factors are non-zero
  // set local ptrs to LJ 14 arrays setup by Pair
@ -392,14 +392,14 @@ void DihedralCharmmfsh::init_style()
  if (weightflag) {
    int itmp;
    if (force->pair == NULL)
-      error->all(FLERR,"Dihedral charmmfsh is incompatible with Pair style");
+      error->all(FLERR,"Dihedral charmmfsw is incompatible with Pair style");
    lj14_1 = (double **) force->pair->extract("lj14_1",itmp);
    lj14_2 = (double **) force->pair->extract("lj14_2",itmp);
    lj14_3 = (double **) force->pair->extract("lj14_3",itmp);
    lj14_4 = (double **) force->pair->extract("lj14_4",itmp);
    int *ptr = (int *) force->pair->extract("implicit",itmp);
    if (!lj14_1 || !lj14_2 || !lj14_3 || !lj14_4 || !ptr)
-      error->all(FLERR,"Dihedral charmmfsh is incompatible with Pair style");
+      error->all(FLERR,"Dihedral charmmfsw is incompatible with Pair style");
    implicit = *ptr;
  }

@ -414,7 +414,7 @@ void DihedralCharmmfsh::init_style()
  
  if (p_cutcoul == NULL || p_cutljinner == NULL || 
      p_cutlj == NULL || p_dihedflag == NULL)
-    error->all(FLERR,"Dihedral charmmfsh is incompatible with Pair style");
+    error->all(FLERR,"Dihedral charmmfsw is incompatible with Pair style");
  
  dihedflag = *p_dihedflag;
  cut_coul14 = *p_cutcoul;
@ -433,7 +433,7 @@ void DihedralCharmmfsh::init_style()
   proc 0 writes out coeffs to restart file
 ------------------------------------------------------------------------- */

-void DihedralCharmmfsh::write_restart(FILE *fp)
+void DihedralCharmmfsw::write_restart(FILE *fp)
 {
  fwrite(&k[1],sizeof(double),atom->ndihedraltypes,fp);
  fwrite(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
@ -446,7 +446,7 @@ void DihedralCharmmfsh::write_restart(FILE *fp)
   proc 0 reads coeffs from restart file, bcasts them
 ------------------------------------------------------------------------- */

-void DihedralCharmmfsh::read_restart(FILE *fp)
+void DihedralCharmmfsw::read_restart(FILE *fp)
 {
  allocate();

@ -474,7 +474,7 @@ void DihedralCharmmfsh::read_restart(FILE *fp)
   proc 0 writes to data file
 ------------------------------------------------------------------------- */

-void DihedralCharmmfsh::write_data(FILE *fp)
+void DihedralCharmmfsw::write_data(FILE *fp)
 {
  for (int i = 1; i <= atom->ndihedraltypes; i++)
    fprintf(fp,"%d %g %d %d %g\n",i,k[i],multiplicity[i],shift[i],weight[i]);
--- a/src/MOLECULE/dihedral_charmmfsw.h
+++ b/src/MOLECULE/dihedral_charmmfsw.h
@ -13,22 +13,22 @@

 #ifdef DIHEDRAL_CLASS

-DihedralStyle(charmmfsh,DihedralCharmmfsh)
+DihedralStyle(charmmfsw,DihedralCharmmfsw)

 #else

-#ifndef LMP_DIHEDRAL_CHARMMFSH_H
-#define LMP_DIHEDRAL_CHARMMFSH_H
+#ifndef LMP_DIHEDRAL_CHARMMFSW_H
+#define LMP_DIHEDRAL_CHARMMFSW_H

 #include <stdio.h>
 #include "dihedral.h"

 namespace LAMMPS_NS {

-class DihedralCharmmfsh : public Dihedral {
+class DihedralCharmmfsw : public Dihedral {
 public:
-  DihedralCharmmfsh(class LAMMPS *);
-  virtual ~DihedralCharmmfsh();
+  DihedralCharmmfsw(class LAMMPS *);
+  virtual ~DihedralCharmmfsw();
  virtual void compute(int, int);
  virtual void coeff(int, char **);
  virtual void init_style();
@ -73,9 +73,9 @@ E: Incorrect weight arg for dihedral coefficients

 Self-explanatory.  Check the input script or data file.

-E: Dihedral charmmfsh is incompatible with Pair style
+E: Dihedral charmmfsw is incompatible with Pair style

-Dihedral style charmmfsh must be used with a pair style charmm
+Dihedral style charmmfsw must be used with a pair style charmm
 in order for the 1-4 epsilon/sigma parameters to be defined.

 */
--- a/src/MOLECULE/fix_cmap.cpp
+++ b/src/MOLECULE/fix_cmap.cpp
@ -964,22 +964,22 @@ void FixCMAP::bc_coeff(double *gs, double *d1gs, double *d2gs, double *d12gs)
  // calculate the bicubic interpolation coefficients c_ij

  static int wt[16][16] =
-    { 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
-      -3, 0, 0, 3, 0, 0, 0, 0,-2, 0, 0,-1, 0, 0, 0, 0,
-      2, 0, 0,-2, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0,
-      0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
-      0, 0, 0, 0,-3, 0, 0, 3, 0, 0, 0, 0,-2, 0, 0,-1,
-      0, 0, 0, 0, 2, 0, 0,-2, 0, 0, 0, 0, 1, 0, 0, 1,
-      -3, 3, 0, 0,-2,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      0, 0, 0, 0, 0, 0, 0, 0,-3, 3, 0, 0,-2,-1, 0, 0,
-      9,-9, 9,-9, 6, 3,-3,-6, 6,-6,-3, 3, 4, 2, 1, 2,
-      -6, 6,-6, 6,-4,-2, 2, 4,-3, 3, 3,-3,-2,-1,-1,-2,
-      2,-2, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-      0, 0, 0, 0, 0, 0, 0, 0, 2,-2, 0, 0, 1, 1, 0, 0,
-      -6, 6,-6, 6,-3,-3, 3, 3,-4, 4, 2,-2,-2,-2,-1,-1,
-      4,-4, 4,-4, 2, 2,-2,-2, 2,-2,-2, 2, 1, 1, 1, 1
+    { {1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+      {0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0},
+      {-3, 0, 0, 3, 0, 0, 0, 0,-2, 0, 0,-1, 0, 0, 0, 0},
+      {2, 0, 0,-2, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0},
+      {0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+      {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0},
+      {0, 0, 0, 0,-3, 0, 0, 3, 0, 0, 0, 0,-2, 0, 0,-1},
+      {0, 0, 0, 0, 2, 0, 0,-2, 0, 0, 0, 0, 1, 0, 0, 1},
+      {-3, 3, 0, 0,-2,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+      {0, 0, 0, 0, 0, 0, 0, 0,-3, 3, 0, 0,-2,-1, 0, 0},
+      {9,-9, 9,-9, 6, 3,-3,-6, 6,-6,-3, 3, 4, 2, 1, 2},
+      {-6, 6,-6, 6,-4,-2, 2, 4,-3, 3, 3,-3,-2,-1,-1,-2},
+      {2,-2, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
+      {0, 0, 0, 0, 0, 0, 0, 0, 2,-2, 0, 0, 1, 1, 0, 0},
+      {-6, 6,-6, 6,-3,-3, 3, 3,-4, 4, 2,-2,-2,-2,-1,-1},
+      {4,-4, 4,-4, 2, 2,-2,-2, 2,-2,-2, 2, 1, 1, 1, 1}
    };

  int i, j, k, in;
--- a/src/MPIIO/Install.sh
+++ b/src/MPIIO/Install.sh
@ -36,7 +36,7 @@ touch ../write_restart.cpp
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package to include/exclude LMP_MPIIO setting
--- a/src/MSCG/Install.sh
+++ b/src/MSCG/Install.sh
@ -25,7 +25,7 @@ action () {
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/Makefile
+++ b/src/Makefile
@ -43,6 +43,15 @@ endif

 # Package variables

+# PACKAGE    = standard packages
+# PACKUSER   = user packagse
+# PACKLIB    = all packages that require an additional lib
+# PACKSYS    = subset that reqiure a common system library
+# PACKINT    = subset that require an internal (provided) library
+# PACKEXT    = subset that require an external (downloaded) library
+# PACKLIB    = PACKSYS + PACKING + PACKEXT
+# PACKSCRIPT = libs under lammps/lib that have an Install.py script
+
 PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
 	  granular kim kokkos kspace manybody mc meam misc molecule \
 	  mpiio mscg opt peri poems \
@ -55,10 +64,21 @@ PACKUSER = user-atc user-awpmd user-cg-cmm user-cgdna user-colvars \
 	   user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
 	   user-vtk

-PACKLIB = compress gpu kim kokkos meam mpiio mscg poems python reax voronoi \
-	  user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \
+PACKLIB = compress gpu kim kokkos meam mpiio mscg poems \
+	  python reax voronoi \
+	  user-atc user-awpmd user-colvars user-h5md user-molfile \
 	  user-nc-dump user-qmmm user-quip user-smd user-vtk

+PACKSYS = compress mpiio python
+
+PACKINT = gpu kokkos meam poems reax user-atc user-awpmd user-colvars
+
+PACKEXT = kim mscg voronoi \
+	  user-h5md user-molfile user-nc-dump user-qmmm user-quip \
+	  user-smd user-vtk
+
+PACKSCRIPT = voronoi
+
 PACKALL = $(PACKAGE) $(PACKUSER)

 PACKAGEUC = $(shell echo $(PACKAGE) | tr a-z A-Z)
@ -66,6 +86,7 @@ PACKUSERUC = $(shell echo $(PACKUSER) | tr a-z A-Z)

 YESDIR = $(shell echo $(@:yes-%=%) | tr a-z A-Z)
 NODIR  = $(shell echo $(@:no-%=%) | tr a-z A-Z)
+LIBDIR = $(shell echo $(@:lib-%=%))

 # List of all targets

@ -75,9 +96,9 @@ help:
 	@echo 'make clean-machine       delete object files for one machine'
 	@echo 'make mpi-stubs           build dummy MPI library in STUBS'
 	@echo 'make install-python      install LAMMPS wrapper in Python'
-	@echo 'make tar                 create lmp_src.tar.gz of src dir and packages'
+	@echo 'make tar                 create lmp_src.tar.gz for src dir and packages'
 	@echo ''
-	@echo 'make package                 list available packages'
+	@echo 'make package                 list available packages and their dependencies'
 	@echo 'make package-status (ps)     status of all packages'
 	@echo 'make yes-package             install a single pgk in src dir'
 	@echo 'make no-package              remove a single pkg from src dir'
@ -87,11 +108,16 @@ help:
 	@echo 'make no-standard (no-std)    remove all standard pkgs'
 	@echo 'make yes-user                install all user pkgs'
 	@echo 'make no-user                 remove all user pkgs'
-	@echo 'make no-lib                  remove all pkgs with external libs'
+	@echo 'make yes-lib       install all pkgs with libs (incldued or ext)'
+	@echo 'make no-lib        remove all pkgs with libs (included or ext)'
+	@echo 'make yes-ext                 install all pkgs with external libs'
+	@echo 'make no-ext                  remove all pkgs with external libs'
 	@echo ''
 	@echo 'make package-update (pu) replace src files with updated package files'
 	@echo 'make package-overwrite   replace package files with src files'
 	@echo 'make package-diff (pd)   diff src files against package files'
+	@echo ''
+	@echo 'make lib-package         download/build/install a package library'
 	@echo 'make purge               purge obsolete copies of source files'
 	@echo ''
 	@echo 'make machine             build LAMMPS for machine'
@ -221,6 +247,13 @@ package:
 	@echo ''
 	@echo 'User-contributed packages:' $(PACKUSER)
 	@echo ''
+	@echo 'Packages that need system libraries:' $(PACKSYS)
+	@echo ''
+	@echo 'Packages that need provided libraries:' $(PACKINT)
+	@echo ''
+	@echo 'Packages that need external libraries:' $(PACKEXT)
+	@echo ''
+	@echo 'make package                 list available packages'
 	@echo 'make package                 list available packages'
 	@echo 'make package-status (ps)     status of all packages'
 	@echo 'make yes-package             install a single pgk in src dir'
@ -229,13 +262,18 @@ package:
 	@echo 'make no-all                  remove all pkgs from src dir'
 	@echo 'make yes-standard (yes-std)  install all standard pkgs'
 	@echo 'make no-standard (no-srd)    remove all standard pkgs'
-	@echo ''
 	@echo 'make yes-user                install all user pkgs'
 	@echo 'make no-user                 remove all user pkgs'
-	@echo 'make no-lib                  remove all pkgs with external libs'
+	@echo 'make yes-lib       install all pkgs with libs (included or ext)'
+	@echo 'make no-lib        remove all pkgs with libs (included or ext)'
+	@echo 'make yes-ext                 install all pkgs with external libs'
+	@echo 'make no-ext                  remove all pkgs with external libs'
+	@echo ''
 	@echo 'make package-update (pu)  replace src files with package files'
 	@echo 'make package-overwrite    replace package files with src files'
 	@echo 'make package-diff (pd)    diff src files against package file'
+	@echo ''
+	@echo 'make lib-package      download/build/install a package library'

 yes-all:
 	@for p in $(PACKALL); do $(MAKE) yes-$$p; done
@ -255,9 +293,18 @@ yes-user:
 no-user:
 	@for p in $(PACKUSER); do $(MAKE) no-$$p; done

+yes-lib:
+	@for p in $(PACKLIB); do $(MAKE) yes-$$p; done
+
 no-lib:
 	@for p in $(PACKLIB); do $(MAKE) no-$$p; done

+yes-ext:
+	@for p in $(PACKEXT); do $(MAKE) yes-$$p; done
+
+no-ext:
+	@for p in $(PACKEXT); do $(MAKE) no-$$p; done
+
 yes-%:
 	@if [ ! -e Makefile.package ]; \
 	  then cp Makefile.package.empty Makefile.package; fi
@ -288,6 +335,16 @@ no-%:
 		$(SHELL) Depend.sh $(NODIR) 0; \
        fi;

+# download/build/install a package library
+
+lib-%:
+	@if [ ! -e ../lib/$(LIBDIR)/Install.py ]; then \
+	  echo "Install script for lib $(@:lib-%=%) does not exist"; \
+	else \
+	  echo "Installing lib for package $(@:lib-%=%)"; \
+	  cd ../lib/$(LIBDIR); python Install.py $(args); \
+	fi;
+
 # status = list src files that differ from package files
 # update = replace src files with newer package files
 # overwrite = overwrite package files with newer src files
--- a/src/OPT/pair_eam_opt.cpp
+++ b/src/OPT/pair_eam_opt.cpp
@ -67,11 +67,6 @@ void PairEAMOpt::eval()
    double rhor0j,rhor1j,rhor2j,rhor3j;
  } fast_alpha_t;

-  typedef struct {
-    double frho0,frho1,frho2,frho3,frho4,frho5,frho6;
-    double _pad[1];
-  } fast_beta_t;
-
  typedef struct {
    double rhor4i,rhor5i,rhor6i;
    double rhor4j,rhor5j,rhor6j;
--- a/src/POEMS/Install.sh
+++ b/src/POEMS/Install.sh
@ -29,7 +29,7 @@ action () {
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
Steve Plimpton	2f32fb7f8b	patch 13Apr17	2017-04-13 11:19:48 -06:00
sjplimp	cb867ea91d	Merge pull request #450 from rbberger/python_destruction_fix Prevent segfault if Python was never initialized	2017-04-12 13:58:23 -06:00
Richard Berger	961096f9df	Prevent segfault if Python was never initialized	2017-04-12 11:17:15 -04:00
Steve Plimpton	4da8c1c4e2	patch 11Apr17	2017-04-11 09:00:37 -06:00
Steve Plimpton	49dd9449b8	fix gcmc updates from Aidan, trimming of output for replica commands	2017-04-11 08:35:09 -06:00
sjplimp	76fd936972	Merge pull request #443 from Pakketeretet2/user-manifold-fix-every-keyword User manifold fix every keyword	2017-04-11 08:27:53 -06:00
sjplimp	06cebb9fb4	Merge pull request #445 from Pakketeretet2/extract_for_bond Extract for bond	2017-04-11 08:27:31 -06:00
sjplimp	b9d844ca8d	Merge pull request #444 from ohenrich/user-cgdna Minor updates to docu of USER-CGDNA package	2017-04-11 08:25:09 -06:00
sjplimp	ccc9367de7	Merge pull request #442 from akohlmey/small-updates-and-bugfixes collected small updates and bugfixes	2017-04-11 08:24:32 -06:00
sjplimp	4c4a3fe5d1	Merge pull request #439 from rbberger/python_mixed_use_support Support mixed Python use by honoring Python GIL	2017-04-11 08:24:06 -06:00
Axel Kohlmeyer	84ea8a79e6	correct link for dispersion parameter how-to and reformat	2017-04-10 20:43:24 -04:00
Stefan Paquay	f19f558220	Removed changed bond_harmonic from wrong position.	2017-04-10 10:06:03 -04:00
Stefan Paquay	1ad7d856fe	Added forgotten #include string to bond_harmonic.cpp	2017-04-10 09:57:54 -04:00
Axel Kohlmeyer	d6357420ae	propagate global package installation bugfix to explicit package scripts	2017-04-07 15:29:56 -04:00
Axel Kohlmeyer	62b9fa22b8	when computing only rotational temperature, we must not subtract the default n-dim extra DOFs	2017-04-07 15:11:26 -04:00
Axel Kohlmeyer	1725832b6c	address issue where uninstalling an empty package will erase all code in src	2017-04-06 11:08:57 -04:00
Stefan Paquay	874944f2ec	Made fix adapt support bond harmonic.	2017-04-04 19:37:17 -04:00
Oliver Henrich	497a5d88af	Merge branch 'master' into user-cgdna	2017-04-04 20:03:57 +01:00
Oliver Henrich	8993daaa31	Minor update to docu	2017-04-04 19:54:22 +01:00
Axel Kohlmeyer	e190eb15f5	remove debug printf	2017-04-04 17:54:33 +00:00
Stefan Paquay	b6bc33bac6	Merge branch 'user_manifold_fix' into user-manifold-fix-every-keyword	2017-04-04 13:31:22 -04:00
Stefan Paquay	03a6f5237f	Made every keyword for user-manifold work as advertised.	2017-04-04 13:30:49 -04:00
Stefan Paquay	28e86917a0	Made fix adapt work with bond_harmonic.	2017-04-04 12:35:26 -04:00
Axel Kohlmeyer	6f1bbd3cec	protect fix ave/histo from segfaulting on non-existing computes, fixes or variables	2017-04-03 18:08:15 -04:00
Steve Plimpton	ae56b9ad89	patch 31Mar17 for stable release	2017-03-30 10:07:27 -06:00
sjplimp	4466d9fb4a	Merge pull request #440 from ohenrich/user-cgdna Updated lammps.book, USER-CGDNA install script	2017-03-30 09:34:35 -06:00
Oliver Henrich	ac1aa9edea	Updated README	2017-03-29 11:18:04 +01:00
Oliver Henrich	c733204a70	Updated lammps.book and install script	2017-03-29 08:28:03 +01:00
Richard Berger	1544b51dcb	Support mixed Python use by honoring Python GIL This enables support to both drive LAMMPS with a Python interpreter and evaluating Python expressions inside of LAMMPS using that same interpreter. Previously this has been avoided through an error message because the binding code did not ensure that the necessary GIL (global interpreter lock) structures exist (see issue #438). All code paths which call Python C API functions must first acquire the GIL through a call PyGILState_Ensure and release it with PyGILState_Release.	2017-03-29 01:49:15 -04:00
Steve Plimpton	4b9d0a9566	sync with SVN	2017-03-28 13:26:12 -06:00
Steve Plimpton	0637f23875	patch 28Mar17	2017-03-28 13:12:23 -06:00
sjplimp	9f6e126a2f	Merge pull request #437 from ohenrich/user-cgdna User cgdna	2017-03-28 12:52:26 -06:00
sjplimp	645f56cf70	Merge pull request #436 from Pakketeretet2/better_incorrect_input_handling_nh Changed the check on initial and final temperature to <= 0 for both.	2017-03-28 12:51:17 -06:00
sjplimp	80e5111dca	Merge pull request #434 from akohlmey/imgflags-in-library improved image flag handling in library interface	2017-03-28 12:50:13 -06:00
sjplimp	7e9f05b617	Merge pull request #433 from akohlmey/fixes-for-stable More small fixes for stable release	2017-03-28 12:49:09 -06:00
Axel Kohlmeyer	1d8f0c762d	Merge branch 'master' into fixes-for-stable	2017-03-28 14:37:30 -04:00
Axel Kohlmeyer	ef6070cbde	remove executable permissions for potential files	2017-03-28 14:35:58 -04:00
Steve Plimpton	61f3ff1d2b	Merge branch 'master' of github.com:lammps/lammps	2017-03-28 12:35:33 -06:00
Steve Plimpton	111d350a22	fix gcmc units change for chemical potential	2017-03-28 12:34:46 -06:00
sjplimp	1dfd61f532	Merge pull request #432 from Pakketeretet2/user_manifold_fix Fixed a bug with equal-style variables as manifold params.	2017-03-28 12:33:45 -06:00
Oliver Henrich	5c1f5462e7	Removed contribution line from header files	2017-03-28 19:08:24 +01:00
Oliver Henrich	66a6375405	Resolved merge conflict	2017-03-28 18:58:31 +01:00
Oliver Henrich	604afebf6f	Update to oxDNA2	2017-03-28 18:22:02 +01:00
Oliver Henrich	8afed61db1	Upgrade to oxDNA2	2017-03-28 18:16:36 +01:00
Stefan Paquay	ee55a98103	Changed the check on initial and final temperature to <= 0 for both.	2017-03-28 11:22:10 -04:00
Axel Kohlmeyer	f8da9a866a	synchronize dump custom/vtk documentation with that of dump custom	2017-03-28 11:00:22 -04:00
Axel Kohlmeyer	28bdebd3c0	avoid segfault when calling PPPM*::memory_usage() before grid communication is initialized	2017-03-28 07:50:48 -04:00
Axel Kohlmeyer	fc51c38abb	add some docs for the special treatment of image flags	2017-03-28 02:22:45 -04:00
Axel Kohlmeyer	443ea13eff	add image flag packing/unpacking to library/python interface	2017-03-28 02:05:05 -04:00
Axel Kohlmeyer	5feeb79c13	one more line of dead code removed	2017-03-27 15:16:28 -04:00
Axel Kohlmeyer	a241b2d0f7	fix problems with references	2017-03-27 15:01:32 -04:00
Axel Kohlmeyer	61e7595a94	remove references to xmovie, streamline dump and viz descriptions	2017-03-27 14:59:58 -04:00
Axel Kohlmeyer	da9096750e	update .gitignore for newly added files	2017-03-27 14:30:21 -04:00
Axel Kohlmeyer	87ea9ba661	bugfix for library interface	2017-03-27 14:29:13 -04:00
Axel Kohlmeyer	c041727e4f	remove dead code and reduce trivial compiler warnings (clang++)	2017-03-27 14:28:50 -04:00
Stefan Paquay	3feffbe1de	Removed diagnostics.	2017-03-27 13:49:53 -04:00
Stefan Paquay	04fd038d35	Fixed a bug with equal-style variables as manifold params.	2017-03-27 13:46:57 -04:00
Oliver Henrich	af0b5b0e84	Removed dead code	2017-03-22 16:23:29 +00:00
Oliver Henrich	7435084375	Verified oxDNA with modified nucleotide layout	2017-03-22 15:59:10 +00:00