patch 17Jan17

Merge pull request #339 from akohlmey/fixes-for-srp-example
Fixes for srp example
2017-01-17 10:14:53 -07:00 · 2017-01-17 09:36:28 -07:00 · 2017-01-17 09:33:25 -07:00 · 2017-01-17 09:14:03 -07:00 · 2017-01-17 09:13:47 -07:00 · 2017-01-17 09:13:27 -07:00
401 changed files with 1393 additions and 13928 deletions
--- a/.gitignore
+++ b/.gitignore
@ -0,0 +1,34 @@
+*~
+*.o
+*.so
+*.cu_o
+*.ptx
+*_ptx.h
+*.a
+*.d
+*.x
+*.exe
+*.dll
+*.pyc
+__pycache__
+
+Obj_*
+log.lammps
+log.cite
+*.bz2
+*.gz
+*.tar
+.*.swp
+*.orig
+*.rej
+.vagrant
+\#*#
+.#*
+
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
--- a/doc/.gitignore
+++ b/doc/.gitignore
@ -0,0 +1,5 @@
+/html
+/LAMMPS.epub
+/LAMMPS.mobi
+/Manual.pdf
+/Developer.pdf
--- a/doc/src/Eqs/bond_oxdna_fene.jpg
+++ b/doc/src/Eqs/bond_oxdna_fene.jpg
--- a/doc/src/Eqs/bond_oxdna_fene.tex
+++ b/doc/src/Eqs/bond_oxdna_fene.tex
@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-\pagestyle{empty}
-
-\begin{document}
-
-$$ 
-  E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r0}{\Delta}\right)^2\right]
-$$
-
-\end{document}
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="26 Jan 2017 version">
+<META NAME="docnumber" CONTENT="17 Jan 2017 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@ -21,7 +21,7 @@
 <H1></H1>

 LAMMPS Documentation :c,h3
-26 Jan 2017 version :c,h4
+17 Jan 2017 version :c,h4

 Version info: :h4

--- a/doc/src/PDF/USER-CGDNA-overview.pdf
+++ b/doc/src/PDF/USER-CGDNA-overview.pdf
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@ -702,8 +702,6 @@ package"_Section_start.html#start_3.
 "meso"_fix_meso.html,
 "manifoldforce"_fix_manifoldforce.html,
 "meso/stationary"_fix_meso_stationary.html,
-"nve/dot"_fix_nve_dot.html,
-"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
 "nve/manifold/rattle"_fix_nve_manifold_rattle.html,
 "nvk"_fix_nvk.html,
 "nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
@ -1037,11 +1035,6 @@ package"_Section_start.html#start_3.
 "morse/soft"_pair_morse.html,
 "multi/lucy"_pair_multi_lucy.html,
 "multi/lucy/rx"_pair_multi_lucy_rx.html,
-"oxdna/coaxstk"_pair_oxdna.html,
-"oxdna/excv"_pair_oxdna.html,
-"oxdna/hbond"_pair_oxdna.html,
-"oxdna/stk"_pair_oxdna.html,
-"oxdna/xstk"_pair_oxdna.html,
 "quip"_pair_quip.html,
 "reax/c (k)"_pair_reax_c.html,
 "smd/hertz"_pair_smd_hertz.html,
@ -1090,8 +1083,7 @@ if "LAMMPS is built with the appropriate
 package"_Section_start.html#start_3.

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

 :line

--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@ -84,7 +84,7 @@ Package, Description, Author(s), Doc page, Example, Library
 "PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
 "POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
 "PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python
-"REAX"_#REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax, lib/reax
+"REAX"_#REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax,  lib/reax
 "REPLICA"_#REPLICA, multi-replica methods, -, "Section 6.6.5"_Section_howto.html#howto_5, tad, -
 "RIGID"_#RIGID, rigid bodies, -, "fix rigid"_fix_rigid.html, rigid, -
 "SHOCK"_#SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
@ -1140,7 +1140,6 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
 "USER-ATC"_#USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (1), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
 "USER-AWPMD"_#USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
 "USER-CG-CMM"_#USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
-"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, Oliver Henrich (U Edinburgh), src/USER-CGDNA/README, USER/cgdna, -, -
 "USER-COLVARS"_#USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
 "USER-DIFFRACTION"_#USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -
 "USER-DPD"_#USER-DPD, reactive dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, -
@ -1285,31 +1284,6 @@ him directly if you have questions.

 :line

-USER-CGDNA package :link(USER-CGDNA),h5
-
-Contents: The CGDNA package implements coarse-grained force fields for
-single- and double-stranded DNA. This is at the moment mainly the
-oxDNA model, developed by Doye, Louis and Ouldridge at the University
-of Oxford.  The package also contains Langevin-type rigid-body
-integrators with improved stability.
-
-See these doc pages to get started:
-
-"bond_style oxdna_fene"_bond_oxdna_fene.html
-"pair_style oxdna_excv"_pair_oxdna_excv.html
-"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul
-
-Supporting info: /src/USER-CGDNA/README, "bond_style
-oxdna_fene"_bond_oxdna_fene.html, "pair_style
-oxdna_excv"_pair_oxdna_excv.html, "fix
-nve/dotc/langevin"_fix_nve_dotc_langevin.html
-
-Author: Oliver Henrich at the University of Edinburgh, UK (o.henrich
-at epcc.ed.ac.uk or ohenrich at ph.ed.ac.uk).  Contact him directly if
-you have any questions.
-
-:line
-
 USER-COLVARS package :link(USER-COLVARS),h5

 Contents: COLVARS stands for collective variables which can be used to
--- a/doc/src/bond_oxdna_fene.txt
+++ b/doc/src/bond_oxdna_fene.txt
@ -1,70 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-bond_style oxdna_fene command :h3
-
-[Syntax:]
-
-bond_style oxdna_fene :pre
-
-[Examples:]
-
-bond_style oxdna_fene
-bond_coeff * 2.0 0.25 0.7525 :pre
-
-[Description:]
-
-The {oxdna_fene} bond style uses the potential
-
-:c,image(Eqs/bond_oxdna_fene.jpg)
-
-to define a modified finite extensible nonlinear elastic (FENE) potential
-"(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone
-in the oxDNA force field for coarse-grained modelling of DNA. 
-
-The following coefficients must be defined for the bond type via the
-"bond_coeff"_bond_coeff.html command as given in the above example, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-epsilon (energy)
-Delta (distance)
-r0 (distance) :ul
-
-NOTE: This bond style has to be used together with the corresponding oxDNA pair styles
-for excluded volume interaction {oxdna_excv}, stacking {oxdna_stk}, cross-stacking {oxdna_xstk}
-and coaxial stacking interaction {oxdna_coaxstk} as well as hydrogen-bonding interaction {oxdna_hbond} (see also documentation of 
-"pair_style oxdna_excv"_pair_oxdna_excv.html). The coefficients 
-in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
-
-Example input and data files can be found in /examples/USER/cgdna/examples/duplex1/ and /duplex2/.
-A simple python setup tool which creates single straight or helical DNA strands,
-DNA duplexes or arrays of DNA duplexes can be found in /examples/USER/cgdna/util/.
-A technical report with more information on the model, the structure of the input file,
-the setup tool and the performance of the LAMMPS-implementation of oxDNA
-can be found "here"_PDF/USER-CGDNA-overview.pdf.
-
-:line
-
-[Restrictions:]
-
-This bond style can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
-
-
-[Related commands:]
-
-"pair_style oxdna_excv"_pair_oxdna_excv.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html 
-
-[Default:] none
-
-:line
-
-:link(oxdna_fene)
-[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
--- a/doc/src/bonds.txt
+++ b/doc/src/bonds.txt
@ -15,7 +15,6 @@ Bond Styles :h1
   bond_morse
   bond_none
   bond_nonlinear
-   bond_oxdna_fene
   bond_quartic
   bond_table
   bond_zero
--- a/doc/src/compute_coord_atom.txt
+++ b/doc/src/compute_coord_atom.txt
@ -12,16 +12,19 @@ compute coord/atom command :h3

 compute ID group-ID coord/atom cstyle args ... :pre

-ID, group-ID are documented in "compute"_compute.html command :ulb,l
-coord/atom = style name of this compute command :l
-cstyle = {cutoff} or {orientorder} :l
-  {cutoff} args = cutoff typeN
-    cutoff = distance within which to count coordination neighbors (distance units)
-    typeN = atom type for Nth coordination count (see asterisk form below)
-  {orientorder} args = orientorderID threshold
-    orientorderID = ID of an orientorder/atom compute
-    threshold = minimum value of the product of two "connected" atoms :pre
-:ule
+ID, group-ID are documented in "compute"_compute.html command
+coord/atom = style name of this compute command
+one cstyle must be appended :ul
+
+cstyle = {cutoff} or {orientorder}
+
+{cutoff} args = cutoff typeN
+  cutoff = distance within which to count coordination neighbors (distance units)
+  typeN = atom type for Nth coordination count (see asterisk form below) :pre
+
+{orientorder} args = orientorderID threshold
+  orientorderID = ID of a previously defined orientorder/atom compute
+  threshold = minimum value of the scalar product between two 'connected' atoms (see text for explanation) :pre

 [Examples:]

@ -32,21 +35,21 @@ compute 1 all coord/atom orientorder 2 0.5 :pre

 [Description:]

-This compute performs calculations between neighboring atoms to
-determine a coordination value.  The specific calculation and the
-meaning of the resulting value depend on the {cstyle} keyword used.
+This compute performs generic calculations between neighboring atoms. So far,
+there are two cstyles implemented: {cutoff} and {orientorder}.
+The {cutoff} cstyle calculates one or more coordination numbers
+for each atom in a group.

-The {cutoff} cstyle calculates one or more traditional coordination
-numbers for each atom.  A coordination number is defined as the number
-of neighbor atoms with specified atom type(s) that are within the
-specified cutoff distance from the central atom.  Atoms not in the
-specified group are included in the coordination number tally.
+A coordination number is defined as the number of neighbor atoms with
+specified atom type(s) that are within the specified cutoff distance
+from the central atom.  Atoms not in the group are included in a
+coordination number of atoms in the group.

-The {typeN} keywords allow specification of which atom types
-contribute to each coordination number.  One coordination number is
-computed for each of the {typeN} keywords listed.  If no {typeN}
-keywords are listed, a single coordination number is calculated, which
-includes atoms of all types (same as the "*" format, see below).
+The {typeN} keywords allow you to specify which atom types contribute
+to each coordination number.  One coordination number is computed for
+each of the {typeN} keywords listed.  If no {typeN} keywords are
+listed, a single coordination number is calculated, which includes
+atoms of all types (same as the "*" format, see below).

 The {typeN} keywords can be specified in one of two ways.  An explicit
 numeric value can be used, as in the 2nd example above.  Or a
@ -58,27 +61,16 @@ from 1 to N.  A leading asterisk means all types from 1 to n
 (inclusive).  A middle asterisk means all types from m to n
 (inclusive).

-The {orientorder} cstyle calculates the number of "connected" neighbor
-atoms J around each central atom I.  For this {cstyle}, connected is
-defined by the orientational order parameter calculated by the
-"compute orientorder/atom"_compute_orientorder_atom.html command.
-This {cstyle} thus allows one to apply the ten Wolde's criterion to
-identify crystal-like atoms in a system, as discussed in "ten
-Wolde"_#tenWolde.
+The {orientorder} cstyle calculates the number of 'connected' atoms j 
+around each atom i. The atom j is connected to i if the scalar product
+({Ybar_lm(i)},{Ybar_lm(j)}) is larger than {threshold}. Thus, this cstyle
+will work only if a "compute orientorder/atom"_compute_orientorder_atom.html
+has been previously defined. This cstyle allows one to apply the 
+ten Wolde's criterion to identify cristal-like atoms in a system 
+(see "ten Wolde et al."_#tenWolde).

-The ID of the previously specified "compute
-orientorder/atom"_compute_orientorder/atom command is specified as
-{orientorderID}.  The compute must invoke its {components} option to
-calculate components of the {Ybar_lm} vector for each atoms, as
-described in its documenation.  Note that orientorder/atom compute
-defines its own criteria for identifying neighboring atoms.  If the
-scalar product ({Ybar_lm(i)},{Ybar_lm(j)}), calculated by the
-orientorder/atom compute is larger than the specified {threshold},
-then I and J are connected, and the coordination value of I is
-incremented by one.
-
-For all {cstyle} settings, all coordination values will be 0.0 for
-atoms not in the specified compute group.
+The value of all coordination numbers will be 0.0 for atoms not in the
+specified compute group.

 The neighbor list needed to compute this quantity is constructed each
 time the calculation is performed (i.e. each time a snapshot of atoms
@ -100,23 +92,21 @@ the neighbor list.

 [Output info:]

-For {cstyle} cutoff, this compute can calculate a per-atom vector or
-array.  If single {type1} keyword is specified (or if none are
-specified), this compute calculates a per-atom vector.  If multiple
-{typeN} keywords are specified, this compute calculates a per-atom
-array, with N columns.
-
-For {cstyle} orientorder, this compute calculates a per-atom vector.
-
-These values can be accessed by any command that uses per-atom values
-from a compute as input.  See "Section
+If single {type1} keyword is specified (or if none are specified),
+this compute calculates a per-atom vector.  If multiple {typeN}
+keywords are specified, this compute calculates a per-atom array, with
+N columns.  These values can be accessed by any command that uses
+per-atom values from a compute as input.  See "Section
 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
 options.

 The per-atom vector or array values will be a number >= 0.0, as
 explained above.

-[Restrictions:] none
+[Restrictions:]
+The cstyle {orientorder} can only be used if a 
+"compute orientorder/atom"_compute_orientorder_atom.html command
+was previously defined. Otherwise, an error message will be issued.

 [Related commands:]

@ -128,5 +118,4 @@ explained above.
 :line

 :link(tenWolde)
-[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
-J. Chem. Phys. 104, 9932 (1996).
+[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
--- a/doc/src/compute_orientorder_atom.txt
+++ b/doc/src/compute_orientorder_atom.txt
@ -19,7 +19,7 @@ keyword = {cutoff} or {nnn} or {degrees} or {components}
  {cutoff} value = distance cutoff
  {nnn} value = number of nearest neighbors
  {degrees} values = nlvalues, l1, l2,...
-  {components} value = ldegree  :pre
+  {components} value = l  :pre

 :ule

@ -64,21 +64,21 @@ specified distance cutoff are used.
 The optional keyword {degrees} defines the list of order parameters to
 be computed.  The first argument {nlvalues} is the number of order
 parameters. This is followed by that number of integers giving the
-degree of each order parameter. Because {Q}2 and all odd-degree order
-parameters are zero for atoms in cubic crystals (see
-"Steinhardt"_#Steinhardt), the default order parameters are {Q}4,
-{Q}6, {Q}8, {Q}10, and {Q}12. For the FCC crystal with {nnn}=12, {Q}4
-= sqrt(7/3)/8 = 0.19094....  The numerical values of all order
-parameters up to {Q}12 for a range of commonly encountered
-high-symmetry structures are given in Table I of "Mickel et
-al."_#Mickel.
+degree of each order parameter. Because {Q}2 and all odd-degree
+order parameters are zero for atoms in cubic crystals
+(see "Steinhardt"_#Steinhardt), the default order parameters
+are {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12. For the
+FCC crystal with {nnn}=12, {Q}4 = sqrt(7/3)/8 = 0.19094....
+The numerical values of all order parameters up to {Q}12
+for a range of commonly encountered high-symmetry structures are given
+in Table I of "Mickel et al."_#Mickel.

-The optional keyword {components} will output the components of the
-normalized complex vector {Ybar_lm} of degree {ldegree}, which must be
+The optional keyword {components} will output the components of
+the normalized complex vector {Ybar_lm} of degree {l}, which must be
 explicitly included in the keyword {degrees}. This option can be used
 in conjunction with "compute coord_atom"_compute_coord_atom.html to
-calculate the ten Wolde's criterion to identify crystal-like
-particles, as discussed in "ten Wolde"_#tenWolde.
+calculate the ten Wolde's criterion to identify crystal-like particles
+(see "ten Wolde et al."_#tenWolde96).

 The value of {Ql} is set to zero for atoms not in the
 specified compute group, as well as for atoms that have less than
@ -104,16 +104,14 @@ the neighbor list.

 [Output info:]

-This compute calculates a per-atom array with {nlvalues} columns,
-giving the {Ql} values for each atom, which are real numbers on the
-range 0 <= {Ql} <= 1.
+This compute calculates a per-atom array with {nlvalues} columns, giving the
+{Ql} values for each atom, which are real numbers on the range 0 <= {Ql} <= 1.

-If the keyword {components} is set, then the real and imaginary parts
-of each component of (normalized) {Ybar_lm} will be added to the
-output array in the following order: Re({Ybar_-m}) Im({Ybar_-m})
-Re({Ybar_-m+1}) Im({Ybar_-m+1}) ... Re({Ybar_m}) Im({Ybar_m}).  This
-way, the per-atom array will have a total of {nlvalues}+2*(2{l}+1)
-columns.
+If the keyword {components} is set, then the real and imaginary parts of each
+component of (normalized) {Ybar_lm} will be added to the output array in the
+following order:
+Re({Ybar_-m}) Im({Ybar_-m}) Re({Ybar_-m+1}) Im({Ybar_-m+1}) ... Re({Ybar_m}) Im({Ybar_m}).
+This way, the per-atom array will have a total of {nlvalues}+2*(2{l}+1) columns.

 These values can be accessed by any command that uses
 per-atom values from a compute as input.  See "Section
@ -124,25 +122,19 @@ options.

 [Related commands:]

-"compute coord/atom"_compute_coord_atom.html, "compute
-centro/atom"_compute_centro_atom.html, "compute
-hexorder/atom"_compute_hexorder_atom.html
+"compute coord/atom"_compute_coord_atom.html, "compute centro/atom"_compute_centro_atom.html, "compute hexorder/atom"_compute_hexorder_atom.html

 [Default:]

-The option defaults are {cutoff} = pair style cutoff, {nnn} = 12,
-{degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.
+The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, {degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.

 :line

 :link(Steinhardt)
-[(Steinhardt)] P. Steinhardt, D. Nelson, and M. Ronchetti,
-Phys. Rev. B 28, 784 (1983).
+[(Steinhardt)] P. Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).

 :link(Mickel)
-[(Mickel)] W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke,
-J. Chem. Phys. 138, 044501 (2013).
+[(Mickel)] W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013).

-:link(tenWolde)
-[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
-J. Chem. Phys. 104, 9932 (1996).
+:link(tenWolde96)
+[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
--- a/doc/src/compute_temp_asphere.txt
+++ b/doc/src/compute_temp_asphere.txt
--- a/doc/src/compute_temp_body.txt
+++ b/doc/src/compute_temp_body.txt
--- a/doc/src/compute_temp_sphere.txt
+++ b/doc/src/compute_temp_sphere.txt
--- a/doc/src/fix_bond_break.txt
+++ b/doc/src/fix_bond_break.txt
--- a/doc/src/fix_bond_create.txt
+++ b/doc/src/fix_bond_create.txt
--- a/doc/src/fix_bond_swap.txt
+++ b/doc/src/fix_bond_swap.txt
--- a/doc/src/fix_lb_fluid.txt
+++ b/doc/src/fix_lb_fluid.txt
--- a/doc/src/fix_lb_momentum.txt
+++ b/doc/src/fix_lb_momentum.txt
--- a/doc/src/fix_lb_pc.txt
+++ b/doc/src/fix_lb_pc.txt
--- a/doc/src/fix_lb_rigid_pc_sphere.txt
+++ b/doc/src/fix_lb_rigid_pc_sphere.txt
--- a/doc/src/fix_lb_viscous.txt
+++ b/doc/src/fix_lb_viscous.txt
--- a/doc/src/fix_nph_asphere.txt
+++ b/doc/src/fix_nph_asphere.txt
--- a/doc/src/fix_nph_body.txt
+++ b/doc/src/fix_nph_body.txt
--- a/doc/src/fix_nph_sphere.txt
+++ b/doc/src/fix_nph_sphere.txt
--- a/doc/src/fix_npt_asphere.txt
+++ b/doc/src/fix_npt_asphere.txt
--- a/doc/src/fix_npt_body.txt
+++ b/doc/src/fix_npt_body.txt
--- a/doc/src/fix_npt_sphere.txt
+++ b/doc/src/fix_npt_sphere.txt
--- a/doc/src/fix_nve_asphere.txt
+++ b/doc/src/fix_nve_asphere.txt
--- a/doc/src/fix_nve_asphere_noforce.txt
+++ b/doc/src/fix_nve_asphere_noforce.txt
--- a/doc/src/fix_nve_body.txt
+++ b/doc/src/fix_nve_body.txt
--- a/doc/src/fix_nve_dot.txt
+++ b/doc/src/fix_nve_dot.txt
@ -1,61 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-fix nve/dot command :h3
-
-[Syntax:]
-
-fix ID group-ID nve/dot :pre
-
-ID, group-ID are documented in "fix"_fix.html command :ulb,l
-nve/dot = style name of this fix command :l
-:ule
-
-[Examples:]
-
-fix 1 all nve/dot :pre
-
-[Description:]
-
-Apply a rigid-body integrator as described in "(Davidchack)"_#Davidchack
-to a group of atoms, but without Langevin dynamics. 
-This command performs Molecular dynamics (MD)
-via a velocity-Verlet algorithm and an evolution operator that rotates 
-the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller. 
-
-This command is the equivalent of the "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
-without damping and noise and can be used to determine the stability range 
-in a NVE ensemble prior to using the Langevin-type DOTC-integrator
-(see also "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html).
-The command is equivalent to the "fix nve"_fix_nve.html.
-The particles are always considered to have a finite size.
-
-An example input file can be found in /examples/USER/cgdna/examples/duplex1/.
-A technical report with more information on this integrator can be found
-"here"_PDF/USER-CGDNA-overview.pdf.
-
-:line
-
-[Restrictions:]
-
-These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
-
-[Related commands:]
-
-"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "fix nve"_fix_nve.html
-
-[Default:] none
-
-:line
-
-:link(Davidchack)
-[(Davidchack)] R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
-:link(Miller)
-[(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
--- a/doc/src/fix_nve_dotc_langevin.txt
+++ b/doc/src/fix_nve_dotc_langevin.txt
@ -1,134 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-fix nve/dotc/langevin command :h3
-
-[Syntax:]
-
-fix ID group-ID nve/dotc/langevin Tstart Tstop damp seed keyword value :pre
-
-ID, group-ID are documented in "fix"_fix.html command :ulb,l
-nve/dotc/langevin = style name of this fix command :l
-Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
-damp = damping parameter (time units) :l
-seed = random number seed to use for white noise (positive integer) :l
-keyword = {angmom} :l
-  {angmom} value = factor
-    factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below :pre
-:ule
-
-[Examples:]
-
-fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 :pre
-
-[Description:]
-
-Apply a rigid-body Langevin-type integrator of the kind "Langevin C" 
-as described in "(Davidchack)"_#Davidchack
-to a group of atoms, which models an interaction with an implicit background
-solvent.  This command performs Brownian dynamics (BD)
-via a technique that splits the integration into a deterministic Hamiltonian 
-part and the Ornstein-Uhlenbeck process for noise and damping. 
-The quaternion degrees of freedom are updated though an evolution
-operator which performs a rotation in quaternion space, preserves
-the quaternion norm and is akin to "(Miller)"_#Miller.
-
-In terms of syntax this command has been closely modelled on the 
-"fix langevin"_fix_langevin.html and its {angmom} option. But it combines 
-the "fix nve"_fix_nve.html and the "fix langevin"_fix_langevin.html in 
-one single command. The main feature is improved stability 
-over the standard integrator, permitting slightly larger timestep sizes.
-
-NOTE: Unlike the "fix langevin"_fix_langevin.html this command performs
-also time integration of the translational and quaternion degrees of freedom.
-
-The total force on each atom will have the form:
-
-F = Fc + Ff + Fr
-Ff = - (m / damp) v
-Fr is proportional to sqrt(Kb T m / (dt damp)) :pre
-
-Fc is the conservative force computed via the usual inter-particle
-interactions ("pair_style"_pair_style.html,
-"bond_style"_bond_style.html, etc).
-
-The Ff and Fr terms are implicitly taken into account by this fix 
-on a per-particle basis.
-
-Ff is a frictional drag or viscous damping term proportional to the
-particle's velocity.  The proportionality constant for each atom is
-computed as m/damp, where m is the mass of the particle and damp is
-the damping factor specified by the user.
-
-Fr is a force due to solvent atoms at a temperature T randomly bumping
-into the particle.  As derived from the fluctuation/dissipation
-theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
-dt damp), where Kb is the Boltzmann constant, T is the desired
-temperature, m is the mass of the particle, dt is the timestep size,
-and damp is the damping factor.  Random numbers are used to randomize
-the direction and magnitude of this force as described in
-"(Dunweg)"_#Dunweg, where a uniform random number is used (instead of
-a Gaussian random number) for speed.
-
-:line
-
-{Tstart} and {Tstop} have to be constant values, i.e. they cannot 
-be variables.
-
-The {damp} parameter is specified in time units and determines how
-rapidly the temperature is relaxed.  For example, a value of 0.03
-means to relax the temperature in a timespan of (roughly) 0.03 time
-units tau (see the "units"_units.html command).
-The damp factor can be thought of as inversely related to the
-viscosity of the solvent, i.e. a small relaxation time implies a
-hi-viscosity solvent and vice versa.  See the discussion about gamma
-and viscosity in the documentation for the "fix
-viscous"_fix_viscous.html command for more details.
-
-The random # {seed} must be a positive integer. A Marsaglia random
-number generator is used.  Each processor uses the input seed to
-generate its own unique seed and its own stream of random numbers.
-Thus the dynamics of the system will not be identical on two runs on
-different numbers of processors.
-
-The keyword/value option has to be used in the following way:
-
-This fix has to be used together with the {angmom} keyword. The 
-particles are always considered to have a finite size. 
-The keyword {angmom} enables thermostatting of the rotational degrees of 
-freedom in addition to the usual translational degrees of freedom. 
-
-The scale factor after the {angmom} keyword gives the ratio of the rotational to 
-the translational friction coefficient.
-
-An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
-A technical report with more information on this integrator can be found 
-"here"_PDF/USER-CGDNA-overview.pdf.
-
-:line
-
-[Restrictions:]
-
-These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
-
-[Related commands:]
-
-"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html,  
-
-[Default:] none
-
-:line
-
-:link(Davidchack)
-[(Davidchack)] R.L Davidchack, T.E. Ouldridge, M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
-:link(Miller)
-[(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
-:link(Dunweg)
-[(Dunweg)] B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991).
--- a/doc/src/fix_nve_line.txt
+++ b/doc/src/fix_nve_line.txt
--- a/doc/src/fix_nve_sphere.txt
+++ b/doc/src/fix_nve_sphere.txt
--- a/doc/src/fix_nve_tri.txt
+++ b/doc/src/fix_nve_tri.txt
--- a/doc/src/fix_nvt_asphere.txt
+++ b/doc/src/fix_nvt_asphere.txt
--- a/doc/src/fix_nvt_body.txt
+++ b/doc/src/fix_nvt_body.txt
--- a/doc/src/fix_nvt_sphere.txt
+++ b/doc/src/fix_nvt_sphere.txt
--- a/doc/src/fix_ti_spring.txt
+++ b/doc/src/fix_ti_spring.txt
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@ -84,8 +84,6 @@ Fixes :h1
   fix_nve_asphere
   fix_nve_asphere_noforce
   fix_nve_body
-   fix_nve_dot
-   fix_nve_dotc_langevin
   fix_nve_eff
   fix_nve_limit
   fix_nve_line
--- a/doc/src/kspace_style.txt
+++ b/doc/src/kspace_style.txt
@ -229,16 +229,11 @@ dramatically in z.  For example, for a triclinic system with all three
 tilt factors set to the maximum limit, the PPPM grid should be
 increased roughly by a factor of 1.5 in the y direction and 2.0 in the
 z direction as compared to the same system using a cubic orthogonal
-simulation cell.  One way to handle this issue if you have a long
-simulation where the box size changes dramatically, is to break it
-into shorter simulations (multiple "run"_run.html commands).  This
-works because the grid size is re-computed at the beginning of each
-run.  Another way to ensure the descired accuracy requirement is met
-is to run a short simulation at the maximum expected tilt or length,
-note the required grid size, and then use the
+simulation cell. One way to ensure the accuracy requirement is being
+met is to run a short simulation at the maximum expected tilt or
+length, note the required grid size, and then use the
 "kspace_modify"_kspace_modify.html {mesh} command to manually set the
-PPPM grid size to this value for the long run.  The simulation then
-will be "too accurate" for some portion of the run.
+PPPM grid size to this value.

 RMS force errors in real space for {ewald} and {pppm} are estimated
 using equation 18 of "(Kolafa)"_#Kolafa, which is also referenced as
@ -290,8 +285,6 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 See "Section 5"_Section_accelerate.html of the manual for
 more instructions on how to use the accelerated styles effectively.

-:line
-
 [Restrictions:]

 Note that the long-range electrostatic solvers in LAMMPS assume conducting
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@ -194,6 +194,7 @@ fix_meso.html
 fix_meso_stationary.html
 fix_momentum.html
 fix_move.html
+fix_mscg.html
 fix_msst.html
 fix_neb.html
 fix_nh.html
@ -209,8 +210,6 @@ fix_nve.html
 fix_nve_asphere.html
 fix_nve_asphere_noforce.html
 fix_nve_body.html
-fix_nve_dot.html
-fix_nve_dotc_langevin.html
 fix_nve_eff.html
 fix_nve_limit.html
 fix_nve_line.html
@ -218,6 +217,7 @@ fix_nve_manifold_rattle.html
 fix_nve_noforce.html
 fix_nve_sphere.html
 fix_nve_tri.html
+fix_nvk.html
 fix_nvt_asphere.html
 fix_nvt_body.html
 fix_nvt_manifold_rattle.html
@ -458,7 +458,6 @@ pair_multi_lucy_rx.html
 pair_nb3b_harmonic.html
 pair_nm.html
 pair_none.html
-pair_oxdna_excv.html
 pair_peri.html
 pair_polymorphic.html
 pair_quip.html
@ -497,7 +496,6 @@ pair_zero.html
 bond_class2.html
 bond_fene.html
 bond_fene_expand.html
-bond_oxdna_fene.html
 bond_harmonic.html
 bond_harmonic_shift.html
 bond_harmonic_shift_cut.html
--- a/doc/src/min_style.txt
+++ b/doc/src/min_style.txt
--- a/doc/src/pair_dipole.txt
+++ b/doc/src/pair_dipole.txt
--- a/doc/src/pair_gayberne.txt
+++ b/doc/src/pair_gayberne.txt
--- a/doc/src/pair_oxdna_excv.txt
+++ b/doc/src/pair_oxdna_excv.txt
@ -1,80 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-pair_style oxdna_excv command :h3
-pair_style oxdna_stk command :h3
-pair_style oxdna_hbond command :h3
-pair_style oxdna_xstk command :h3
-pair_style oxdna_coaxstk command :h3
-
-[Syntax:]
-
-pair_style style :pre
-
-style = {hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk} :ul
-
-[Examples:]
-
-pair_style hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk
-pair_coeff * * oxdna_excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna_stk     1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna_hbond   0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna_hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna_hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff * * oxdna_xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
-pair_coeff * * oxdna_coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 :pre
-
-[Description:]
-
-The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field 
-for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the 
-excluded volume interaction {oxdna_excv}, the stacking {oxdna_stk}, cross-stacking {oxdna_xstk}
-and coaxial stacking interaction {oxdna_coaxstk} as well
-as the hydrogen-bonding interaction {oxdna_hbond} between complementary pairs of nucleotides on
-opposite strands.
-
-The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients 
-in the above example. The individual potentials consist of products of modulation factors, 
-which themselves are constructed from a number of more basic potentials 
-(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. 
-We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil and "(Ouldridge)"_#Ouldridge
-for a detailed description of the oxDNA force field.
-
-NOTE: These pair styles have to be used together with the related oxDNA bond style
-{oxdna_fene} for the connectivity of the phosphate backbone (see also documentation of
-"bond_style oxdna_fene"_bond_oxdna_fene.html). The coefficients
-in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
-
-Example input and data files can be found in /examples/USER/cgdna/examples/duplex1/ and /duplex2/.
-A simple python setup tool which creates single straight or helical DNA strands, 
-DNA duplexes or arrays of DNA duplexes can be found in /examples/USER/cgdna/util/.
-A technical report with more information on the model, the structure of the input file,
-the setup tool and the performance of the LAMMPS-implementation of oxDNA 
-can be found "here"_PDF/USER-CGDNA-overview.pdf.
-
-:line
-
-[Restrictions:]
-
-These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
-
-[Related commands:]
-
-"bond_style oxdna_fene"_bond_oxdna_fene.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html 
-
-[Default:] none
-
-:line
-
-:link(Ouldridge-DPhil)
-[(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
-
-:link(Ouldridge)
-[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
--- a/doc/src/pair_resquared.txt
+++ b/doc/src/pair_resquared.txt
--- a/doc/src/pair_smtbq.txt
+++ b/doc/src/pair_smtbq.txt
--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@ -65,7 +65,6 @@ Pair Styles :h1
   pair_nb3b_harmonic
   pair_nm
   pair_none
-   pair_oxdna_excv
   pair_peri
   pair_polymorphic
   pair_quip
--- a/doc/utils/converters/.gitignore
+++ b/doc/utils/converters/.gitignore
@ -1,2 +1 @@
-__pycache__
 *.egg-info
--- a/examples/COUPLE/fortran2/.gitignore
+++ b/examples/COUPLE/fortran2/.gitignore
@ -0,0 +1 @@
+*.mod
--- a/examples/USER/cgdna/README
+++ b/examples/USER/cgdna/README
@ -1,28 +0,0 @@
-This directory contains example data and input files 
-and utility scripts for the oxDNA coarse-grained model 
-for DNA.
-
-/examples/duplex1:
-Input, data and log files for a DNA duplex (double-stranded DNA) 
-consisiting of 5 base pairs. The duplex contains two strands with 
-complementary base pairs. The topology is
-
-A - A - A - A - A
-|   |   |   |   |
-T - T - T - T - T     
-
-/examples/duplex2:
-Input, data and log files for a nicked DNA duplex (double-stranded DNA) 
-consisiting of 8 base pairs. The duplex contains strands with 
-complementary base pairs, but the backbone on one side is not continuous: 
-two individual strands on one side form a duplex with a longer single 
-strand on the other side. The topology is
-
-A - A - A - A - A - A - A - A
-|   |   |   |   |   |   |   |
-T - T - T   T - T - T - T - T
-
-/util:
-This directory contains a simple python setup tool which creates 
-single straight or helical DNA strands, DNA duplexes or arrays of DNA 
-duplexes.
--- a/examples/USER/cgdna/examples/duplex1/data.duplex1
+++ b/examples/USER/cgdna/examples/duplex1/data.duplex1
@ -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/util/generate_input.py
+++ b/examples/USER/cgdna/util/generate_input.py
@ -1,388 +0,0 @@
-# Setup tool for oxDNA input in LAMMPS format.
-
-import math,numpy as np,sys,os
-
-# system size
-lxmin = -115.0
-lxmax = +115.0
-lymin = -115.0
-lymax = +115.0
-lzmin = -115.0
-lzmax = +115.0
-
-# rise in z-direction
-r0 = 0.7
-
-# definition of single untwisted strand
-def single():
-
-  strand = inp[1].split(':')
-
-  com_start=strand[0].split(',')
-
-  posx=float(com_start[0])
-  posy=float(com_start[1])
-  posz=float(com_start[2])
-  risex=0
-  risey=0
-  risez=r0
-
-  strandstart=len(nucleotide)+1
-
-  for letter in strand[2]:
-    temp=[]
-
-    temp.append(nt2num[letter])
-    temp.append([posx,posy,posz])
-    vel=[0,0,0,0,0,0]
-    temp.append(vel)
-    temp.append(shape)
-
-    quat=[1,0,0,0]
-    temp.append(quat)
-
-    posx=posx+risex
-    posy=posy+risey
-    posz=posz+risez
-
-    if (len(nucleotide)+1 > strandstart):
-      topology.append([1,len(nucleotide),len(nucleotide)+1])
-
-    nucleotide.append(temp)
-
-  return
-
-# definition of single twisted strand
-def single_helix():
-
-  strand = inp[1].split(':')
-
-  com_start=strand[0].split(',')
-  twist=float(strand[1])
-
-  posx = float(com_start[0])
-  posy = float(com_start[1])
-  posz = float(com_start[2])
-  risex=0
-  risey=0
-  risez=math.sqrt(r0**2-4.0*math.sin(0.5*twist)**2) 
-
-  dcomh=0.76
-  axisx=dcomh + posx
-  axisy=posy
-
-  strandstart=len(nucleotide)+1
-  quat=[1,0,0,0]
-
-  qrot0=math.cos(0.5*twist)
-  qrot1=0
-  qrot2=0
-  qrot3=math.sin(0.5*twist)
-
-  for letter in strand[2]:
-    temp=[]
-
-    temp.append(nt2num[letter])
-    temp.append([posx,posy,posz])
-    vel=[0,0,0,0,0,0]
-    temp.append(vel)
-    temp.append(shape)
-
-    temp.append(quat)
-
-    quat0 = quat[0]*qrot0 - quat[1]*qrot1 - quat[2]*qrot2 - quat[3]*qrot3 
-    quat1 = quat[0]*qrot1 + quat[1]*qrot0 + quat[2]*qrot3 - quat[3]*qrot2 
-    quat2 = quat[0]*qrot2 + quat[2]*qrot0 + quat[3]*qrot1 - quat[1]*qrot3 
-    quat3 = quat[0]*qrot3 + quat[3]*qrot0 + quat[1]*qrot2 + quat[2]*qrot1 
-
-    quat = [quat0,quat1,quat2,quat3]
-
-    posx=axisx - dcomh*(quat[0]**2+quat[1]**2-quat[2]**2-quat[3]**2)
-    posy=axisy - dcomh*(2*(quat[1]*quat[2]+quat[0]*quat[3]))
-    posz=posz+risez
-
-    if (len(nucleotide)+1 > strandstart):
-      topology.append([1,len(nucleotide),len(nucleotide)+1])
-
-    nucleotide.append(temp)
-
-  return
-
-# definition of twisted duplex  
-def duplex():
-
-  strand = inp[1].split(':')
-
-  com_start=strand[0].split(',')
-  twist=float(strand[1])
-
-  compstrand=[]
-  comptopo=[]
-
-  posx1 = float(com_start[0])
-  posy1 = float(com_start[1])
-  posz1 = float(com_start[2])
-
-  risex=0
-  risey=0
-  risez=math.sqrt(r0**2-4.0*math.sin(0.5*twist)**2) 
-
-  dcomh=0.76
-  axisx=dcomh + posx1
-  axisy=posy1
-
-  posx2 = axisx + dcomh  
-  posy2 = posy1
-  posz2 = posz1
-
-  strandstart=len(nucleotide)+1
-
-  quat1=[1,0,0,0]
-  quat2=[0,0,-1,0]
-
-  qrot0=math.cos(0.5*twist)
-  qrot1=0
-  qrot2=0
-  qrot3=math.sin(0.5*twist)
-
-  for letter in strand[2]:
-    temp1=[]
-    temp2=[]
-
-    temp1.append(nt2num[letter])
-    temp2.append(compnt2num[letter])
-
-    temp1.append([posx1,posy1,posz1])
-    temp2.append([posx2,posy2,posz2])
-
-    vel=[0,0,0,0,0,0]
-    temp1.append(vel)
-    temp2.append(vel)
-
-    temp1.append(shape)
-    temp2.append(shape)
-
-    temp1.append(quat1)
-    temp2.append(quat2)
-
-    quat1_0 = quat1[0]*qrot0 - quat1[1]*qrot1 - quat1[2]*qrot2 - quat1[3]*qrot3 
-    quat1_1 = quat1[0]*qrot1 + quat1[1]*qrot0 + quat1[2]*qrot3 - quat1[3]*qrot2 
-    quat1_2 = quat1[0]*qrot2 + quat1[2]*qrot0 + quat1[3]*qrot1 - quat1[1]*qrot3 
-    quat1_3 = quat1[0]*qrot3 + quat1[3]*qrot0 + quat1[1]*qrot2 + quat1[2]*qrot1 
-
-    quat1 = [quat1_0,quat1_1,quat1_2,quat1_3]
-
-    posx1=axisx - dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
-    posy1=axisy - dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
-    posz1=posz1+risez
-
-    quat2_0 = quat2[0]*qrot0 - quat2[1]*qrot1 - quat2[2]*qrot2 + quat2[3]*qrot3 
-    quat2_1 = quat2[0]*qrot1 + quat2[1]*qrot0 - quat2[2]*qrot3 - quat2[3]*qrot2 
-    quat2_2 = quat2[0]*qrot2 + quat2[2]*qrot0 + quat2[3]*qrot1 + quat2[1]*qrot3 
-    quat2_3 =-quat2[0]*qrot3 + quat2[3]*qrot0 + quat2[1]*qrot2 + quat2[2]*qrot1 
-
-    quat2 = [quat2_0,quat2_1,quat2_2,quat2_3]
-
-    posx2=axisx + dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
-    posy2=axisy + dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
-    posz2=posz1
-
-    if (len(nucleotide)+1 > strandstart):
-      topology.append([1,len(nucleotide),len(nucleotide)+1])
-      comptopo.append([1,len(nucleotide)+len(strand[2]),len(nucleotide)+len(strand[2])+1])
-
-    nucleotide.append(temp1)
-    compstrand.append(temp2)
-
-  for ib in range(len(compstrand)):
-    nucleotide.append(compstrand[len(compstrand)-1-ib])
-
-  for ib in range(len(comptopo)):
-    topology.append(comptopo[ib])
-
-  return
-
-# definition of array of duplexes  
-def duplex_array():
-
-  strand = inp[1].split(':')
-  number=strand[0].split(',')
-  posz1_0 = float(strand[1])
-  twist=float(strand[2])
-
-  nx = int(number[0])
-  ny = int(number[1])
-
-  dx = (lxmax-lxmin)/nx
-  dy = (lymax-lymin)/ny
-
-  risex=0
-  risey=0
-  risez=math.sqrt(r0**2-4.0*math.sin(0.5*twist)**2) 
-  dcomh=0.76
-
-  for ix in range(nx):
-
-    axisx=lxmin + dx/2 + ix * dx
-
-    for iy in range(ny):
-
-      axisy=lymin + dy/2 + iy * dy
-
-      compstrand=[]
-      comptopo=[]
-
-      posx1 = axisx - dcomh
-      posy1 = axisy
-      posz1 = posz1_0
-
-      posx2 = axisx + dcomh  
-      posy2 = posy1
-      posz2 = posz1
-
-      strandstart=len(nucleotide)+1
-      quat1=[1,0,0,0]
-      quat2=[0,0,-1,0]
-
-      qrot0=math.cos(0.5*twist)
-      qrot1=0
-      qrot2=0
-      qrot3=math.sin(0.5*twist)
-
-      for letter in strand[3]:
-	temp1=[]
-	temp2=[]
-
-	temp1.append(nt2num[letter])
-	temp2.append(compnt2num[letter])
-
-	temp1.append([posx1,posy1,posz1])
-	temp2.append([posx2,posy2,posz2])
-
-	vel=[0,0,0,0,0,0]
-	temp1.append(vel)
-	temp2.append(vel)
-
-	temp1.append(shape)
-	temp2.append(shape)
-
-	temp1.append(quat1)
-	temp2.append(quat2)
-
-	quat1_0 = quat1[0]*qrot0 - quat1[1]*qrot1 - quat1[2]*qrot2 - quat1[3]*qrot3 
-	quat1_1 = quat1[0]*qrot1 + quat1[1]*qrot0 + quat1[2]*qrot3 - quat1[3]*qrot2 
-	quat1_2 = quat1[0]*qrot2 + quat1[2]*qrot0 + quat1[3]*qrot1 - quat1[1]*qrot3 
-	quat1_3 = quat1[0]*qrot3 + quat1[3]*qrot0 + quat1[1]*qrot2 + quat1[2]*qrot1 
-
-	quat1 = [quat1_0,quat1_1,quat1_2,quat1_3]
-
-	posx1=axisx - dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
-	posy1=axisy - dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
-	posz1=posz1+risez
-
-	quat2_0 = quat2[0]*qrot0 - quat2[1]*qrot1 - quat2[2]*qrot2 + quat2[3]*qrot3 
-	quat2_1 = quat2[0]*qrot1 + quat2[1]*qrot0 - quat2[2]*qrot3 - quat2[3]*qrot2 
-	quat2_2 = quat2[0]*qrot2 + quat2[2]*qrot0 + quat2[3]*qrot1 + quat2[1]*qrot3 
-	quat2_3 =-quat2[0]*qrot3 + quat2[3]*qrot0 + quat2[1]*qrot2 + quat2[2]*qrot1 
-
-	quat2 = [quat2_0,quat2_1,quat2_2,quat2_3]
-
-	posx2=axisx + dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
-	posy2=axisy + dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
-	posz2=posz1
-
-	if (len(nucleotide)+1 > strandstart):
-	  topology.append([1,len(nucleotide),len(nucleotide)+1])
-	  comptopo.append([1,len(nucleotide)+len(strand[3]),len(nucleotide)+len(strand[3])+1])
-
-	nucleotide.append(temp1)
-	compstrand.append(temp2)
-
-      for ib in range(len(compstrand)):
-	nucleotide.append(compstrand[len(compstrand)-1-ib])
-
-      for ib in range(len(comptopo)):
-	topology.append(comptopo[ib])
-
-  return
-
-# main part
-nt2num = {'A':1, 'C':2, 'G':3, 'T':4}
-compnt2num = {'T':1, 'G':2, 'C':3, 'A':4}
-shape = [1.1739845031423408,1.1739845031423408,1.1739845031423408]
-
-nucleotide=[]
-topology=[]
-
-seqfile = open(sys.argv[1],'r')
-
-# process sequence file line by line
-for line in seqfile:
-
-  inp = line.split()
-  if inp[0] == 'single':
-    single()
-  if inp[0] == 'single_helix':
-    single_helix()
-  if inp[0] == 'duplex':
-    duplex()
-  if inp[0] == 'duplex_array':
-    duplex_array()
-
-# output atom data in LAMMPS format
-out = open(sys.argv[2],'w')
-
-out.write('# LAMMPS data file\n')
-out.write('%d atoms\n' % len(nucleotide))
-out.write('%d ellipsoids\n' % len(nucleotide))
-out.write('%d bonds\n' % len(topology))
-out.write('\n')
-out.write('4 atom types\n')
-out.write('1 bond types\n')
-out.write('\n')
-out.write('# System size\n')
-out.write('%f %f xlo xhi\n' % (lxmin,lxmax))
-out.write('%f %f ylo yhi\n' % (lymin,lymax))
-out.write('%f %f zlo zhi\n' % (lzmin,lzmax))
-out.write('\n')
-out.write('Masses\n')
-out.write('\n')
-out.write('1 3.1575\n')
-out.write('2 3.1575\n')
-out.write('3 3.1575\n')
-out.write('4 3.1575\n')
-
-out.write('\n')
-out.write('# Atom-ID, type, position, molecule-ID, ellipsoid flag, density\n')
-out.write('Atoms\n')
-out.write('\n')
-for ib in range(len(nucleotide)):
-  out.write("%d %d %22.16le %22.16le %22.16le 1 1 1\n" % (ib+1,nucleotide[ib][0],nucleotide[ib][1][0],nucleotide[ib][1][1],nucleotide[ib][1][2]))
-
-out.write('\n')
-out.write('# Atom-ID, translational, rotational velocity\n')
-out.write('Velocities\n')
-out.write('\n')
-for ib in range(len(nucleotide)):
-  out.write("%d %22.16le %22.16le %22.16le %22.16le %22.16le %22.16le\n" % (ib+1,nucleotide[ib][2][0],nucleotide[ib][2][1],nucleotide[ib][2][2],nucleotide[ib][2][3],nucleotide[ib][2][4],nucleotide[ib][2][5]))
-
-out.write('\n')
-out.write('# Atom-ID, shape, quaternion\n')
-out.write('Ellipsoids\n')
-out.write('\n')
-for ib in range(len(nucleotide)):
-  out.write("%d %22.16le %22.16le %22.16le %22.16le %22.16le %22.16le %22.16le\n" % (ib+1,nucleotide[ib][3][0],nucleotide[ib][3][1],nucleotide[ib][3][2],nucleotide[ib][4][0],nucleotide[ib][4][1],nucleotide[ib][4][2],nucleotide[ib][4][3]))
-
-out.write('\n')
-out.write('# Bond topology\n')
-out.write('Bonds\n')
-out.write('\n')
-for ib in range(len(topology)):
-  out.write("%d %d %d %d\n" % (ib+1,topology[ib][0],topology[ib][1],topology[ib][2]))
-
-out.close() 
-
-seqfile.close()
-sys.exit(0)
-
-
--- a/examples/USER/cgdna/util/input.ref
+++ b/examples/USER/cgdna/util/input.ref
@ -1,77 +0,0 @@
-variable number	equal 8
-variable ofreq	equal 1000
-variable efreq	equal 1000
-
-units lj
-
-dimension 3
-
-newton off
-
-processors 1 1 1
-
-boundary  p p p
-
-atom_style hybrid bond ellipsoid
-atom_modify sort 0 1.0
-
-# Pair interactions require lists of neighbours to be calculated
-neighbor 1.0 bin
-neigh_modify every 1 delay 0 check yes
-
-read_data data.duplex2
-
-set atom * mass 3.1575
-
-group all type 1 4
-
-# oxDNA bond interactions - FENE backbone
-bond_style oxdna_fene
-bond_coeff * 2.0 0.25 0.7525
-
-# oxDNA pair interactions
-pair_style hybrid/overlay oxdna_excv oxdna_stk oxdna_hbond oxdna_xstk oxdna_coaxstk
-pair_coeff * * oxdna_excv   2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna_stk    1.61048 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65   
-pair_coeff * * oxdna_hbond  0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna_hbond  1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna_hbond  1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff * * oxdna_xstk   47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 
-pair_coeff * * oxdna_coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
-
-# NVE ensemble
-#fix 1 all   nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
-fix 1 all   nve/dot
-
-timestep 1e-5 
-
-#comm_style tiled
-#fix 3 all balance 10000 1.1 rcb
-
-#compute mol all chunk/atom molecule
-#compute mychunk all vcm/chunk mol
-#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
-
-#dump pos all xyz ${ofreq} traj.${number}.xyz
-
-#compute quat all property/atom quatw quati quatj quatk
-#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
-#dump_modify quat sort id
-#dump_modify quat format line "%d  %13.6le  %13.6le  %13.6le  %13.6le"
-
-compute erot all erotate/asphere
-compute ekin all ke
-compute epot all pe
-variable erot equal c_erot
-variable ekin equal c_ekin
-variable epot equal c_epot
-variable etot equal c_erot+c_ekin+c_epot
-fix 5 all print ${efreq} "$(step)  ekin = ${ekin} |  erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
-
-dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
-dump_modify out sort id
-dump_modify out format line "%d   %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le  %13.6le %13.6le %13.6le"
-
-run 1000000
-
-#write_restart config.${number}.*
--- a/examples/USER/cgdna/util/sequence.txt
+++ b/examples/USER/cgdna/util/sequence.txt
@ -1,4 +0,0 @@
-single 0,0,0:0.6:AAAAA
-single_helix 0,0,0:0.6:AAAAA
-duplex 0,0,0:0.6:AAAAA
-duplex_array 10,10:-112.0:0.6:AAAAA
--- a/examples/USER/misc/ti/in.ti_spring
+++ b/examples/USER/misc/ti/in.ti_spring
--- a/examples/mscg/output_9Jan17/log.lammps
+++ b/examples/mscg/output_9Jan17/log.lammps
@ -1,140 +0,0 @@
-LAMMPS (4 Nov 2016)
-units real
-atom_style full
-pair_style zero 10.0
-
-read_data data.meoh
-  orthogonal box = (-20.6917 -20.6917 -20.6917) to (20.6917 20.6917 20.6917)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  1000 atoms
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-pair_coeff * *
-
-thermo 1
-thermo_style custom step
-
-# Test 1a: range finder functionality
-fix 1 all mscg 1 range on
-rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
-Neighbor list info ...
-  1 neighbor list requests
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6 -> bins = 7 7 7
-Memory usage per processor = 5.44227 Mbytes
-Step 
-       0 
-     250 
-     500 
-     750 
-    1000 
-    1250 
-    1500 
-    1750 
-    2000 
-    2250 
-    2500 
-    2750 
-    3000 
-    3250 
-    3500 
-    3750 
-    4000 
-    4250 
-    4500 
-Loop time of 0.695789 on 1 procs for 19 steps with 1000 atoms
-
-Performance: 2.359 ns/day, 10.172 hours/ns, 27.307 timesteps/s
-92.9% 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          | 0          | 0          |   0.0 |  0.00
-Bond    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0          | 0          | 0          |   0.0 |  0.00
-Output  | 0          | 0          | 0          |   0.0 |  0.00
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 0.6958     |            |       |100.00
-
-Nlocal:    1000 ave 1000 max 1000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    2934 ave 2934 max 2934 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    50654 ave 50654 max 50654 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 50654
-Ave neighs/atom = 50.654
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-print "TEST_1a mscg range finder"
-TEST_1a mscg range finder
-unfix 1
-
-# Test 1b: force matching functionality
-fix 1 all mscg 1
-rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
-Memory usage per processor = 5.44227 Mbytes
-Step 
-       0 
-     250 
-     500 
-     750 
-    1000 
-    1250 
-    1500 
-    1750 
-    2000 
-    2250 
-    2500 
-    2750 
-    3000 
-    3250 
-    3500 
-    3750 
-    4000 
-    4250 
-    4500 
-Loop time of 1.48638 on 1 procs for 19 steps with 1000 atoms
-
-Performance: 1.104 ns/day, 21.731 hours/ns, 12.783 timesteps/s
-88.9% 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          | 0          | 0          |   0.0 |  0.00
-Bond    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0          | 0          | 0          |   0.0 |  0.00
-Output  | 0          | 0          | 0          |   0.0 |  0.00
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 1.486      |            |       |100.00
-
-Nlocal:    1000 ave 1000 max 1000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    2934 ave 2934 max 2934 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    50654 ave 50654 max 50654 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 50654
-Ave neighs/atom = 50.654
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-print "TEST_1b mscg force matching"
-TEST_1b mscg force matching
-
-print TEST_DONE
-TEST_DONE
-Total wall time: 0:00:02
--- a/examples/vashishta/InP.vashishta
+++ b/examples/vashishta/InP.vashishta
--- a/examples/vashishta/SiO.1990.vashishta
+++ b/examples/vashishta/SiO.1990.vashishta
--- a/lib/.gitignore
+++ b/lib/.gitignore
@ -0,0 +1 @@
+Makefile.lammps
--- a/lib/gpu/cudpp_mini/cudpp.h
+++ b/lib/gpu/cudpp_mini/cudpp.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // CUDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt in
 // the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_globals.h
+++ b/lib/gpu/cudpp_mini/cudpp_globals.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt in
 // the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_maximal_launch.h
+++ b/lib/gpu/cudpp_mini/cudpp_maximal_launch.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_plan.h
+++ b/lib/gpu/cudpp_mini/cudpp_plan.h
@ -2,7 +2,7 @@
 // CUDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
 // $Revision: 3572$
-// $Date$
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_plan_manager.h
+++ b/lib/gpu/cudpp_mini/cudpp_plan_manager.h
@ -2,7 +2,7 @@
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
 // $Revision: 3572$
-// $Date$
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_radixsort.h
+++ b/lib/gpu/cudpp_mini/cudpp_radixsort.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_scan.h
+++ b/lib/gpu/cudpp_mini/cudpp_scan.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt 
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_util.h
+++ b/lib/gpu/cudpp_mini/cudpp_util.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt in
 // the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/sharedmem.h
+++ b/lib/gpu/cudpp_mini/sharedmem.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt 
 // in the root directory of this source distribution.
--- a/lib/kokkos/.gitignore
+++ b/lib/kokkos/.gitignore
@ -1,8 +0,0 @@
-# Standard ignores
-*~
-*.pyc
-\#*#
-.#*
-.*.swp
-.cproject
-.project
--- a/lib/kokkos/config/configure_compton_cpu.sh
+++ b/lib/kokkos/config/configure_compton_cpu.sh
--- a/lib/kokkos/config/configure_compton_mic.sh
+++ b/lib/kokkos/config/configure_compton_mic.sh
--- a/lib/kokkos/config/configure_kokkos.sh
+++ b/lib/kokkos/config/configure_kokkos.sh
--- a/lib/kokkos/config/configure_kokkos_nvidia.sh
+++ b/lib/kokkos/config/configure_kokkos_nvidia.sh
--- a/lib/kokkos/config/configure_shannon.sh
+++ b/lib/kokkos/config/configure_shannon.sh
--- a/lib/linalg/Makefile.gfortran
+++ b/lib/linalg/Makefile.gfortran
--- a/lib/linalg/Makefile.mingw32-cross
+++ b/lib/linalg/Makefile.mingw32-cross
--- a/lib/linalg/Makefile.mingw64-cross
+++ b/lib/linalg/Makefile.mingw64-cross
--- a/lib/meam/.gitignore
+++ b/lib/meam/.gitignore
@ -0,0 +1 @@
+*.mod
--- a/lib/meam/Makefile.tbird
+++ b/lib/meam/Makefile.tbird
--- a/lib/meam/meam_data.F
+++ b/lib/meam/meam_data.F
--- a/lib/meam/meam_dens_final.F
+++ b/lib/meam/meam_dens_final.F
--- a/lib/meam/meam_dens_init.F
+++ b/lib/meam/meam_dens_init.F
--- a/lib/meam/meam_force.F
+++ b/lib/meam/meam_force.F
--- a/lib/meam/meam_setup_done.F
+++ b/lib/meam/meam_setup_done.F
--- a/lib/meam/meam_setup_global.F
+++ b/lib/meam/meam_setup_global.F
--- a/lib/meam/meam_setup_param.F
+++ b/lib/meam/meam_setup_param.F
--- a/lib/reax/Makefile.g95
+++ b/lib/reax/Makefile.g95
--- a/lib/reax/Makefile.gfortran
+++ b/lib/reax/Makefile.gfortran
--- a/potentials/WL.meam
+++ b/potentials/WL.meam
@ -1,13 +0,0 @@
-# DATE: 2017-01-25 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov,  CITATION: Lee, Baskes, Kim, Cho. Phys. Rev. B, 64, 184102 (2001) 
-rc = 3.8
-delr = 0.1
-augt1 = 0
-erose_form = 2
-zbl(1,1) = 0
-nn2(1,1) = 1
-Ec(1,1) = 8.66
-re(1,1) = 2.74
-attrac(1,1) = 0
-repuls(1,1) = 0
-Cmin(1,1,1) = 0.49
-Cmax(1,1,1) = 2.8
--- a/Show More
+++ b/Show More