patch 23Jun17

Merge pull request #548 from lammps/doc-update
doc page clarifications for CHARMM energy and dipole pre-factors
2017-06-23 17:10:59 -06:00 · 2017-06-23 16:48:37 -06:00 · 2017-06-23 15:54:14 -06:00 · 2017-06-23 09:10:04 -06:00 · 2017-06-22 19:17:41 -04:00 · 2017-06-22 19:07:57 -04:00
1043 changed files with 82542 additions and 24158 deletions
--- a/doc/Makefile
+++ b/doc/Makefile
@ -100,6 +100,7 @@ epub: $(OBJECTS)

 pdf: utils/txt2html/txt2html.exe
 	@(\
+		set -e; \
 		cd src; \
 		../utils/txt2html/txt2html.exe -b *.txt; \
 		htmldoc --batch lammps.book;          \
--- a/doc/src/Eqs/cnp_cutoff.jpg
+++ b/doc/src/Eqs/cnp_cutoff.jpg
--- a/doc/src/Eqs/cnp_cutoff.tex
+++ b/doc/src/Eqs/cnp_cutoff.tex
@ -0,0 +1,14 @@
+\documentclass[12pt,article]{article}
+
+\usepackage{indentfirst}
+\usepackage{amsmath}
+
+\begin{document}
+
+\begin{eqnarray*}
+  r_{c}^{fcc} & = & \frac{1}{2} \left(\frac{\sqrt{2}}{2} + 1\right) \mathrm{a} \simeq 0.8536 \:\mathrm{a} \\
+  r_{c}^{bcc} & = & \frac{1}{2}(\sqrt{2} + 1) \mathrm{a} \simeq 1.207 \:\mathrm{a} \\
+  r_{c}^{hcp} & = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) \mathrm{a}
+\end{eqnarray*}
+
+\end{document}
--- a/doc/src/Eqs/cnp_cutoff2.jpg
+++ b/doc/src/Eqs/cnp_cutoff2.jpg
--- a/doc/src/Eqs/cnp_cutoff2.tex
+++ b/doc/src/Eqs/cnp_cutoff2.tex
@ -0,0 +1,12 @@
+\documentclass[12pt,article]{article}
+
+\usepackage{indentfirst}
+\usepackage{amsmath}
+
+\begin{document}
+
+$$
+  Rc + Rs > 2*{\rm cutoff}
+$$
+
+\end{document}
--- a/doc/src/Eqs/cnp_eq.jpg
+++ b/doc/src/Eqs/cnp_eq.jpg
--- a/doc/src/Eqs/cnp_eq.tex
+++ b/doc/src/Eqs/cnp_eq.tex
@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+   Q_{i} = \frac{1}{n_i}\sum_{j = 1}^{n_i} | \sum_{k = 1}^{n_{ij}}  \vec{R}_{ik} + \vec{R}_{jk} |^2
+$$
+
+\end{document}
--- a/doc/src/Eqs/pair_lj_sf.jpg
+++ b/doc/src/Eqs/pair_lj_sf.jpg
--- a/doc/src/Eqs/pair_lj_sf.tex
+++ b/doc/src/Eqs/pair_lj_sf.tex
@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
- F & = & F_{\mathrm{LJ}}(r) - F_{\mathrm{LJ}}(r_{\mathrm{c}}) \qquad r < r_{\mathrm{c}} \\
- E & = & E_{\mathrm{LJ}}(r) - E_{\mathrm{LJ}}(r_{\mathrm{c}}) + (r - r_{\mathrm{c}}) F_{\mathrm{LJ}}(r_{\mathrm{c}}) \qquad r < r_{\mathrm{c}} \\
- \mathrm{with} \qquad E_{\mathrm{LJ}}(r) & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad \mathrm{and} \qquad F_{\mathrm{LJ}}(r) = - E^\prime_{\mathrm{LJ}}(r)
-\end{eqnarray*}                           
-
-\end{document}
--- a/doc/src/JPG/user_intel.png
+++ b/doc/src/JPG/user_intel.png
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="19 May 2017 version">
+<META NAME="docnumber" CONTENT="23 Jun 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
-19 May 2017 version :c,h4
+23 Jun 2017 version :c,h4

 Version info: :h4

--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@ -717,7 +717,7 @@ package"_Section_start.html#start_3.
 "phonon"_fix_phonon.html,
 "pimd"_fix_pimd.html,
 "qbmsst"_fix_qbmsst.html,
-"qeq/reax"_fix_qeq_reax.html,
+"qeq/reax (ko)"_fix_qeq_reax.html,
 "qmmm"_fix_qmmm.html,
 "qtb"_fix_qtb.html,
 "reax/c/bonds"_fix_reax_bonds.html,
@ -831,6 +831,7 @@ package"_Section_start.html#start_3.

 "ackland/atom"_compute_ackland_atom.html,
 "basal/atom"_compute_basal_atom.html,
+"cnp/atom"_compute_cnp_atom.html,
 "dpd"_compute_dpd.html,
 "dpd/atom"_compute_dpd_atom.html,
 "fep"_compute_fep.html,
@ -963,7 +964,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "lj/expand (gko)"_pair_lj_expand.html,
 "lj/gromacs (gko)"_pair_gromacs.html,
 "lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
-"lj/long/coul/long (o)"_pair_lj_long.html,
+"lj/long/coul/long (io)"_pair_lj_long.html,
 "lj/long/dipole/long"_pair_dipole.html,
 "lj/long/tip4p/long"_pair_lj_long.html,
 "lj/smooth (o)"_pair_lj_smooth.html,
@ -1038,7 +1039,6 @@ package"_Section_start.html#start_3.
 "lj/sdk (gko)"_pair_sdk.html,
 "lj/sdk/coul/long (go)"_pair_sdk.html,
 "lj/sdk/coul/msm (o)"_pair_sdk.html,
-"lj/sf (o)"_pair_lj_sf.html,
 "meam/spline (o)"_pair_meam_spline.html,
 "meam/sw/spline"_pair_meam_sw_spline.html,
 "mgpt"_pair_mgpt.html,
@ -1057,7 +1057,7 @@ package"_Section_start.html#start_3.
 "oxdna2/excv"_pair_oxdna2.html,
 "oxdna2/stk"_pair_oxdna2.html,
 "quip"_pair_quip.html,
-"reax/c (k)"_pair_reaxc.html,
+"reax/c (ko)"_pair_reaxc.html,
 "smd/hertz"_pair_smd_hertz.html,
 "smd/tlsph"_pair_smd_tlsph.html,
 "smd/triangulated/surface"_pair_smd_triangulated_surface.html,
@ -1073,7 +1073,7 @@ package"_Section_start.html#start_3.
 "table/rx"_pair_table_rx.html,
 "tersoff/table (o)"_pair_tersoff.html,
 "thole"_pair_thole.html,
-"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c) 
+"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)

 :line

@ -1225,7 +1225,7 @@ USER-OMP, t = OPT.
 "msm/cg (o)"_kspace_style.html,
 "pppm (go)"_kspace_style.html,
 "pppm/cg (o)"_kspace_style.html,
-"pppm/disp"_kspace_style.html,
+"pppm/disp (i)"_kspace_style.html,
 "pppm/disp/tip4p"_kspace_style.html,
 "pppm/stagger"_kspace_style.html,
 "pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c)
--- a/doc/src/Section_errors.txt
+++ b/doc/src/Section_errors.txt
@ -8890,6 +8890,14 @@ This is a requirement to use this potential. :dd

 See the newton command.  This is a restriction to use this potential. :dd

+{Pair style vashishta/gpu requires atom IDs} :dt
+
+This is a requirement to use this potential. :dd
+
+{Pair style vashishta/gpu requires newton pair off} :dt
+
+See the newton command.  This is a restriction to use this potential. :dd
+
 {Pair style tersoff/gpu requires atom IDs} :dt

 This is a requirement to use the tersoff/gpu potential. :dd
--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@ -1938,7 +1938,7 @@ documentation in the src/library.cpp file for details, including
 which quantities can be queried by name:

 void *lammps_extract_global(void *, char *)
-void lammps_extract_box(void *, double *, double *, 
+void lammps_extract_box(void *, double *, double *,
                        double *, double *, double *, int *, int *)
 void *lammps_extract_atom(void *, char *)
 void *lammps_extract_compute(void *, char *, int, int)
@ -2682,14 +2682,14 @@ bond_coeff      2 25.724 0.0 :pre

 When running dynamics with the adiabatic core/shell model, the
 following issues should be considered.  The relative motion of
-the core and shell particles corresponds to the polarization, 
-hereby an instantaneous relaxation of the shells is approximated 
+the core and shell particles corresponds to the polarization,
+hereby an instantaneous relaxation of the shells is approximated
 and a fast core/shell spring frequency ensures a nearly constant
-internal kinetic energy during the simulation. 
+internal kinetic energy during the simulation.
 Thermostats can alter this polarization behaviour, by scaling the
-internal kinetic energy, meaning the shell will not react freely to 
-its electrostatic environment. 
-Therefore it is typically desirable to decouple the relative motion of 
+internal kinetic energy, meaning the shell will not react freely to
+its electrostatic environment.
+Therefore it is typically desirable to decouple the relative motion of
 the core/shell pair, which is an imaginary degree of freedom, from the
 real physical system.  To do that, the "compute
 temp/cs"_compute_temp_cs.html command can be used, in conjunction with
@ -2721,13 +2721,13 @@ fix thermostatequ all nve                               # integrator as needed f
 fix_modify thermoberendsen temp CSequ
 thermo_modify temp CSequ                                # output of center-of-mass derived temperature :pre

-The pressure for the core/shell system is computed via the regular 
-LAMMPS convention by "treating the cores and shells as individual 
-particles"_#MitchellFincham2. For the thermo output of the pressure 
-as well as for the application of a barostat, it is necessary to 
-use an additional "pressure"_compute_pressure compute based on the 
-default "temperature"_compute_temp and specifying it as a second 
-argument in "fix modify"_fix_modify.html and 
+The pressure for the core/shell system is computed via the regular
+LAMMPS convention by "treating the cores and shells as individual
+particles"_#MitchellFincham2. For the thermo output of the pressure
+as well as for the application of a barostat, it is necessary to
+use an additional "pressure"_compute_pressure compute based on the
+default "temperature"_compute_temp and specifying it as a second
+argument in "fix modify"_fix_modify.html and
 "thermo_modify"_thermo_modify.html resulting in:

 (...)
@ -2757,18 +2757,18 @@ temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
 velocity all create 1427 134 bias yes temp CSequ
 velocity all scale 1427 temp CSequ :pre

-To maintain the correct polarizability of the core/shell pairs, the 
-kinetic energy of the internal motion shall remain nearly constant. 
-Therefore the choice of spring force and mass ratio need to ensure 
-much faster relative motion of the 2 atoms within the core/shell pair 
-than their center-of-mass velocity. This allows the shells to 
-effectively react instantaneously to the electrostatic environment and 
+To maintain the correct polarizability of the core/shell pairs, the
+kinetic energy of the internal motion shall remain nearly constant.
+Therefore the choice of spring force and mass ratio need to ensure
+much faster relative motion of the 2 atoms within the core/shell pair
+than their center-of-mass velocity. This allows the shells to
+effectively react instantaneously to the electrostatic environment and
 limits energy transfer to or from the core/shell oscillators.
 This fast movement also dictates the timestep that can be used.

 The primary literature of the adiabatic core/shell model suggests that
 the fast relative motion of the core/shell pairs only allows negligible
-energy transfer to the environment. 
+energy transfer to the environment.
 The mentioned energy transfer will typically lead to a small drift
 in total energy over time.  This internal energy can be monitored
 using the "compute chunk/atom"_compute_chunk_atom.html and "compute
@ -2790,7 +2790,7 @@ pairs as chunks.

 For example if core/shell pairs are the only molecules:

-read_data NaCl_CS_x0.1_prop.data 
+read_data NaCl_CS_x0.1_prop.data
 compute prop all property/atom molecule
 compute cs_chunk all chunk/atom c_prop
 compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0     # note the chosen degrees of freedom for the core/shell pairs
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@ -585,7 +585,7 @@ do not recommend building with other acceleration packages installed

 make yes-kokkos
 make machine :pre
- 
+
 make no-kokkos
 make machine :pre

@ -839,13 +839,13 @@ written and read in parallel.
 Note that MPIIO is part of the standard message-passing interface
 (MPI) library, so you should not need any additional compiler or link
 settings, beyond what LAMMPS normally uses for MPI on your system.
- 
+
 make yes-mpiio
 make machine :pre
- 
+
 make no-mpiio
 make machine :pre
- 
+
 [Supporting info:]

 src/MPIIO: filenames -> commands
@ -855,7 +855,7 @@ src/MPIIO: filenames -> commands
 "read_restart"_read_restart.html :ul

 :line
- 
+
 MSCG package :link(mscg),h4

 [Contents:]
@ -914,7 +914,7 @@ lib/mscg/README
 examples/mscg :ul

 :line
- 
+
 OPT package :link(OPT),h4

 [Contents:]
@ -1387,7 +1387,7 @@ atomic information to continuum fields.
 [Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).

 [Install or un-install:]
-  
+
 Before building LAMMPS with this package, you must first build the ATC
 library in lib/atc.  You can do this manually if you prefer; follow
 the instructions in lib/atc/README.  You can also do it in one step
@ -1420,10 +1420,10 @@ usual manner:

 make yes-user-atc
 make machine :pre
- 
+
 make no-user-atc
 make machine :pre
- 
+
 [Supporting info:]

 src/USER-ATC: filenames -> commands
@ -1446,7 +1446,7 @@ model.
 [Author:] Ilya Valuev (JIHT, Russia).

 [Install or un-install:]
-  
+
 Before building LAMMPS with this package, you must first build the
 AWPMD library in lib/awpmd.  You can do this manually if you prefer;
 follow the instructions in lib/awpmd/README.  You can also do it in
@ -1479,10 +1479,10 @@ usual manner:

 make yes-user-awpmd
 make machine :pre
- 
+
 make no-user-awpmd
 make machine :pre
- 
+
 [Supporting info:]

 src/USER-AWPMD: filenames -> commands
@ -1502,16 +1502,16 @@ oxDNA model of Doye, Louis and Ouldridge at the University of Oxford.
 This includes Langevin-type rigid-body integrators with improved
 stability.

-[Author:] Oliver Henrich (University of Edinburgh).
+[Author:] Oliver Henrich (University of Strathclyde, Glasgow).

 [Install or un-install:]
-  
+
 make yes-user-cgdna
 make machine :pre
- 
+
 make no-user-cgdna
 make machine :pre
- 
+
 [Supporting info:]

 src/USER-CGDNA: filenames -> commands
@ -1536,13 +1536,13 @@ acids.
 [Author:] Axel Kohlmeyer (Temple U).

 [Install or un-install:]
-  
+
 make yes-user-cgsdk
 make machine :pre
- 
+
 make no-user-cgsdk
 make machine :pre
- 
+
 [Supporting info:]

 src/USER-CGSDK: filenames -> commands
@ -1570,7 +1570,7 @@ by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and
 Jerome Henin (LISM, CNRS, Marseille, France).

 [Install or un-install:]
-  
+
 Before building LAMMPS with this package, you must first build the
 COLVARS library in lib/colvars.  You can do this manually if you
 prefer; follow the instructions in lib/colvars/README.  You can also
@ -1594,10 +1594,10 @@ usual manner:

 make yes-user-colvars
 make machine :pre
- 
+
 make no-user-colvars
 make machine :pre
- 
+
 [Supporting info:]

 src/USER-COLVARS: filenames -> commands
@ -1619,13 +1619,13 @@ intensities based on kinematic diffraction theory.
 [Author:] Shawn Coleman while at the U Arkansas.

 [Install or un-install:]
-  
+
 make yes-user-diffraction
 make machine :pre
- 
+
 make no-user-diffraction
 make machine :pre
- 
+
 [Supporting info:]

 src/USER-DIFFRACTION: filenames -> commands
@ -1654,13 +1654,13 @@ algorithm.
 Brennan (ARL).

 [Install or un-install:]
-  
+
 make yes-user-dpd
 make machine :pre
- 
+
 make no-user-dpd
 make machine :pre
- 
+
 [Supporting info:]

 src/USER-DPD: filenames -> commands
@ -1696,13 +1696,13 @@ tools/drude.
 Devemy (CNRS), and Agilio Padua (U Blaise Pascal).

 [Install or un-install:]
-  
+
 make yes-user-drude
 make machine :pre
- 
+
 make no-user-drude
 make machine :pre
- 
+
 [Supporting info:]

 src/USER-DRUDE: filenames -> commands
@ -1734,13 +1734,13 @@ tools/eff; see its README file.
 [Author:] Andres Jaramillo-Botero (CalTech).

 [Install or un-install:]
-  
+
 make yes-user-eff
 make machine :pre
- 
+
 make no-user-eff
 make machine :pre
- 
+
 [Supporting info:]

 src/USER-EFF: filenames -> commands
@ -1773,13 +1773,13 @@ for using this package in tools/fep; see its README file.
 [Author:] Agilio Padua (Universite Blaise Pascal Clermont-Ferrand)

 [Install or un-install:]
-  
+
 make yes-user-fep
 make machine :pre
- 
+
 make no-user-fep
 make machine :pre
- 
+
 [Supporting info:]

 src/USER-FEP: filenames -> commands
@ -1836,13 +1836,13 @@ file.

 You can then install/un-install the package and build LAMMPS in the
 usual manner:
-  
+
 make yes-user-h5md
 make machine :pre
- 
+
 make no-user-h5md
 make machine :pre
- 
+
 [Supporting info:]

 src/USER-H5MD: filenames -> commands
@ -1908,7 +1908,7 @@ explained in "Section 5.3.2"_accelerate_intel.html.

 make yes-user-intel yes-user-omp
 make machine :pre
- 
+
 make no-user-intel no-user-omp
 make machine :pre

@ -1938,13 +1938,13 @@ can be used to model MD particles influenced by hydrodynamic forces.
 Ontario).

 [Install or un-install:]
-  
+
 make yes-user-lb
 make machine :pre
- 
+
 make no-user-lb
 make machine :pre
- 
+
 [Supporting info:]

 src/USER-LB: filenames -> commands
@ -1972,13 +1972,13 @@ matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
 [Authors:] Tomas Oppelstrup and John Moriarty (LLNL).

 [Install or un-install:]
-  
+
 make yes-user-mgpt
 make machine :pre
- 
+
 make no-user-mgpt
 make machine :pre
- 
+
 [Supporting info:]

 src/USER-MGPT: filenames -> commands
@ -2000,13 +2000,13 @@ dihedral, improper, or command style.
 src/USER-MISC/README file.

 [Install or un-install:]
-  
+
 make yes-user-misc
 make machine :pre
- 
+
 make no-user-misc
 make machine :pre
- 
+
 [Supporting info:]

 src/USER-MISC: filenames -> commands
@ -2027,17 +2027,17 @@ algorithm to formulate single-particle constraint functions
 g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold)
 n = grad(g).

-[Author:] Stefan Paquay (Eindhoven University of Technology (TU/e), The
-Netherlands)
+[Author:] Stefan Paquay (until 2017: Eindhoven University of Technology (TU/e), The
+Netherlands; since 2017: Brandeis University, Waltham, MA, USA)

 [Install or un-install:]
-  
+
 make yes-user-manifold
 make machine :pre
- 
+
 make no-user-manifold
 make machine :pre
- 
+
 [Supporting info:]

 src/USER-MANIFOLD: filenames -> commands
@ -2080,7 +2080,7 @@ at
 [Author:] Axel Kohlmeyer (Temple U).

 [Install or un-install:]
-  
+
 Note that the lib/molfile/Makefile.lammps file has a setting for a
 dynamic loading library libdl.a that should is typically present on
 all systems, which is required for LAMMPS to link with this package.
@ -2090,10 +2090,10 @@ lib/molfile/Makefile.lammps for details.

 make yes-user-molfile
 make machine :pre
- 
+
 make no-user-molfile
 make machine :pre
- 
+
 [Supporting info:]

 src/USER-MOLFILE: filenames -> commands
@ -2128,7 +2128,7 @@ tools:
 [Author:] Lars Pastewka (Karlsruhe Institute of Technology).

 [Install or un-install:]
-   
+
 Note that to follow these steps, you need the standard NetCDF software
 package installed on your system.  The lib/netcdf/Makefile.lammps file
 has settings for NetCDF include and library files that LAMMPS needs to
@ -2138,7 +2138,7 @@ lib/netcdf/README for details.

 make yes-user-netcdf
 make machine :pre
-  
+
 make no-user-netcdf
 make machine :pre

@ -2178,10 +2178,10 @@ Once you have an appropriate Makefile.machine, you can
 install/un-install the package and build LAMMPS in the usual manner:

 [Install or un-install:]
-  
+
 make yes-user-omp
 make machine :pre
- 
+
 make no-user-omp
 make machine :pre

@ -2213,13 +2213,13 @@ relations, directly from molecular dynamics simulations.
 [Author:] Ling-Ti Kong (Shanghai Jiao Tong University).

 [Install or un-install:]
-   
+
 make yes-user-phonon
 make machine :pre
-  
+
 make no-user-phonon
 make machine :pre
-  
+
 [Supporting info:]

 src/USER-PHONON: filenames -> commands
@ -2235,7 +2235,7 @@ USER-QMMM package :link(USER-QMMM),h4

 A "fix qmmm"_fix_qmmm.html command which allows LAMMPS to be used in a
 QM/MM simulation, currently only in combination with the "Quantum
-ESPRESSO"_espresso package.  
+ESPRESSO"_espresso package.

 :link(espresso,http://www.quantum-espresso.org)

@ -2275,7 +2275,7 @@ usual manner:

 make yes-user-qmmm
 make machine :pre
-  
+
 make no-user-qmmm
 make machine :pre

@ -2284,7 +2284,7 @@ for a QM/MM simulation.  You must also build Quantum ESPRESSO and
 create a new executable which links LAMMPS and Quanutm ESPRESSO
 together.  These are steps 3 and 4 described in the lib/qmmm/README
 file.
-  
+
 [Supporting info:]

 src/USER-QMMM: filenames -> commands
@ -2312,13 +2312,13 @@ simulation.
 [Author:] Yuan Shen (Stanford U).

 [Install or un-install:]
-   
+
 make yes-user-qtb
 make machine :pre
-  
+
 make no-user-qtb
 make machine :pre
-  
+
 [Supporting info:]

 src/USER-QTB: filenames -> commands
@ -2362,10 +2362,10 @@ usual manner:

 make yes-user-quip
 make machine :pre
-  
+
 make no-user-quip
 make machine :pre
-  
+
 [Supporting info:]

 src/USER-QUIP: filenames -> commands
@ -2388,13 +2388,13 @@ for monitoring molecules as bonds are created and destroyed.
 [Author:] Hasan Metin Aktulga (MSU) while at Purdue University.

 [Install or un-install:]
-   
+
 make yes-user-reaxc
 make machine :pre
-  
+
 make no-user-reaxc
 make machine :pre
-  
+
 [Supporting info:]

 src/USER-REAXC: filenames -> commands
@ -2451,10 +2451,10 @@ usual manner:

 make yes-user-smd
 make machine :pre
-  
+
 make no-user-smd
 make machine :pre
-  
+
 [Supporting info:]

 src/USER-SMD: filenames -> commands
@ -2477,13 +2477,13 @@ ionocovalent bonds in oxides.
 Tetot (LAAS-CNRS, France).

 [Install or un-install:]
-   
+
 make yes-user-smtbq
 make machine :pre
-  
+
 make no-user-smtbq
 make machine :pre
-  
+
 [Supporting info:]

 src/USER-SMTBQ: filenames -> commands
@ -2516,13 +2516,13 @@ property/atom"_compute_property_atom.html command.
 Dynamics, Ernst Mach Institute, Germany).

 [Install or un-install:]
-   
+
 make yes-user-sph
 make machine :pre
-  
+
 make no-user-sph
 make machine :pre
-  
+
 [Supporting info:]

 src/USER-SPH: filenames -> commands
@ -2544,13 +2544,13 @@ stress, etc) about individual interactions.
 [Author:] Axel Kohlmeyer (Temple U).

 [Install or un-install:]
-   
+
 make yes-user-tally
 make machine :pre
-  
+
 make no-user-tally
 make machine :pre
-  
+
 [Supporting info:]

 src/USER-TALLY: filenames -> commands
@ -2577,7 +2577,7 @@ system.
 [Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).

 [Install or un-install:]
-   
+
 The lib/vtk/Makefile.lammps file has settings for accessing VTK files
 and its library, which are required for LAMMPS to build and link with
 this package.  If the settings are not valid for your system, check if
@ -2590,10 +2590,10 @@ usual manner:

 make yes-user-vtk
 make machine :pre
-  
+
 make no-user-vtk
 make machine :pre
-  
+
 [Supporting info:]

 src/USER-VTK: filenames -> commands
--- a/doc/src/Section_python.txt
+++ b/doc/src/Section_python.txt
@ -714,7 +714,7 @@ 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. 
+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.
--- a/doc/src/accelerate_intel.txt
+++ b/doc/src/accelerate_intel.txt
@ -30,8 +30,8 @@ Dihedral Styles: charmm, harmonic, opls :l
 Fixes: nve, npt, nvt, nvt/sllod :l
 Improper Styles: cvff, harmonic :l
 Pair Styles: buck/coul/cut, buck/coul/long, buck, eam, gayberne,
-charmm/coul/long, lj/cut, lj/cut/coul/long, sw, tersoff :l
-K-Space Styles: pppm :l
+charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, sw, tersoff :l
+K-Space Styles: pppm, pppm/disp :l
 :ule

 [Speed-ups to expect:]
@ -42,62 +42,88 @@ precision mode. Performance improvements are shown compared to
 LAMMPS {without using other acceleration packages} as these are
 under active development (and subject to performance changes). The
 measurements were performed using the input files available in
-the src/USER-INTEL/TEST directory. These are scalable in size; the
-results given are with 512K particles (524K for Liquid Crystal).
-Most of the simulations are standard LAMMPS benchmarks (indicated
-by the filename extension in parenthesis) with modifications to the
-run length and to add a warmup run (for use with offload
-benchmarks).
+the src/USER-INTEL/TEST directory with the provided run script.
+These are scalable in size; the results given are with 512K
+particles (524K for Liquid Crystal). Most of the simulations are
+standard LAMMPS benchmarks (indicated by the filename extension in
+parenthesis) with modifications to the run length and to add a
+warmup run (for use with offload benchmarks).

 :c,image(JPG/user_intel.png)

 Results are speedups obtained on Intel Xeon E5-2697v4 processors
 (code-named Broadwell) and Intel Xeon Phi 7250 processors
-(code-named Knights Landing) with "18 Jun 2016" LAMMPS built with
-Intel Parallel Studio 2016 update 3. Results are with 1 MPI task
+(code-named Knights Landing) with "June 2017" LAMMPS built with
+Intel Parallel Studio 2017 update 2. Results are with 1 MPI task
 per physical core. See {src/USER-INTEL/TEST/README} for the raw
 simulation rates and instructions to reproduce.

 :line

+[Accuracy and order of operations:]
+
+In most molecular dynamics software, parallelization parameters
+(# of MPI, OpenMP, and vectorization) can change the results due
+to changing the order of operations with finite-precision
+calculations. The USER-INTEL package is deterministic. This means
+that the results should be reproducible from run to run with the
+{same} parallel configurations and when using determinstic
+libraries or library settings (MPI, OpenMP, FFT). However, there
+are differences in the USER-INTEL package that can change the
+order of operations compared to LAMMPS without acceleration:
+
+Neighbor lists can be created in a different order :ulb,l
+Bins used for sorting atoms can be oriented differently :l
+The default stencil order for PPPM is 7. By default, LAMMPS will
+calculate other PPPM parameters to fit the desired acuracy with
+this order :l
+The {newton} setting applies to all atoms, not just atoms shared
+between MPI tasks :l
+Vectorization can change the order for adding pairwise forces :l
+:ule
+
+The precision mode (described below) used with the USER-INTEL
+package can change the {accuracy} of the calculations. For the
+default {mixed} precision option, calculations between pairs or
+triplets of atoms are performed in single precision, intended to
+be within the inherent error of MD simulations. All accumulation
+is performed in double precision to prevent the error from growing
+with the number of atoms in the simulation. {Single} precision
+mode should not be used without appropriate validation.
+
+:line
+
 [Quick Start for Experienced Users:]

 LAMMPS should be built with the USER-INTEL package installed.
 Simulations should be run with 1 MPI task per physical {core},
 not {hardware thread}.

-For Intel Xeon CPUs:
-
 Edit src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi as necessary. :ulb,l
-If using {kspace_style pppm} in the input script, add "neigh_modify binsize cutoff" and "kspace_modify diff ad" to the input script for better
-performance.  Cutoff should be roughly the neighbor list cutoff.  By
-default the binsize is half the neighbor list cutoff.  :l
-"-pk intel 0 omp 2 -sf intel" added to LAMMPS command-line :l
+Set the environment variable KMP_BLOCKTIME=0 :l
+"-pk intel 0 omp $t -sf intel" added to LAMMPS command-line :l
+$t should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi :l
+For some of the simple 2-body potentials without long-range
+electrostatics, performance and scalability can be better with
+the "newton off" setting added to the input script :l
+If using {kspace_style pppm} in the input script, add
+"kspace_modify diff ad" for better performance :l
 :ule

-For Intel Xeon Phi CPUs for simulations without {kspace_style
-pppm} in the input script :
+For Intel Xeon Phi CPUs:

-Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l
-Runs should be performed using MCDRAM. :l
-"-pk intel 0 omp 2 -sf intel" {or} "-pk intel 0 omp 4 -sf intel"
-should be added to the LAMMPS command-line. Choice for best
-performance will depend on the simulation. :l
+Runs should be performed using MCDRAM. :ulb,l
 :ule

-For Intel Xeon Phi CPUs for simulations with {kspace_style
-pppm} in the input script:
+For simulations using {kspace_style pppm} on Intel CPUs
+supporting AVX-512:

-Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l
-Runs should be performed using MCDRAM. :l
-Add "neigh_modify binsize 3" to the input script for better
-performance. :l
-Add "kspace_modify diff ad" to the input script for better
-performance. :l
-export KMP_AFFINITY=none :l
-"-pk intel 0 omp 3 lrt yes -sf intel" or "-pk intel 0 omp 1 lrt yes
-sf intel" added to LAMMPS command-line. Choice for best performance
-will depend on the simulation. :l
+Add "kspace_modify diff ad" to the input script :ulb,l
+The command-line option should be changed to
+"-pk intel 0 omp $r lrt yes -sf intel" where $r is the number of
+threads minus 1. :l
+Do not use thread affinity (set KMP_AFFINITY=none) :l
+The "newton off" setting may provide better scalability :l
 :ule

 For Intel Xeon Phi coprocessors (Offload):
@ -169,6 +195,10 @@ cat /proc/cpuinfo :pre

 [Building LAMMPS with the USER-INTEL package:]

+NOTE: See the src/USER-INTEL/README file for additional flags that
+might be needed for best performance on Intel server processors
+code-named "Skylake".
+
 The USER-INTEL package must be installed into the source directory:

 make yes-user-intel :pre
@ -322,8 +352,8 @@ follow in the input script.

 NOTE: The USER-INTEL package will perform better with modifications
 to the input script when "PPPM"_kspace_style.html is used:
-"kspace_modify diff ad"_kspace_modify.html and "neigh_modify binsize
-3"_neigh_modify.html should be added to the input script.
+"kspace_modify diff ad"_kspace_modify.html should be added to the
+input script.

 Long-Range Thread (LRT) mode is an option to the "package
 intel"_package.html command that can improve performance when using
@ -342,6 +372,10 @@ would normally perform best with "-pk intel 0 omp 4", instead use
 environment variable "KMP_AFFINITY=none". LRT mode is not supported
 when using offload.

+NOTE: Changing the "newton"_newton.html setting to off can improve
+performance and/or scalability for simple 2-body potentials such as
+lj/cut or when using LRT mode on processors supporting AVX-512.
+
 Not all styles are supported in the USER-INTEL package. You can mix
 the USER-INTEL package with styles from the "OPT"_accelerate_opt.html
 package or the "USER-OMP package"_accelerate_omp.html. Of course,
@ -467,7 +501,7 @@ supported.

 Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l

-Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. 2016 International Conference for High Performance Computing. In press. :l
+Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. "Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency."_http://dl.acm.org/citation.cfm?id=3014915 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95). :l

 Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101. :l
 :ule
--- a/doc/src/bond_oxdna.txt
+++ b/doc/src/bond_oxdna.txt
@ -30,7 +30,7 @@ The {oxdna/fene} and {oxdna2/fene} bond styles use the potential

 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. 
+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
@ -43,8 +43,8 @@ r0 (distance) :ul

 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). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair 
+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). 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.

@ -66,7 +66,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]

-"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 
+"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

--- a/doc/src/compute_cna_atom.txt
+++ b/doc/src/compute_cna_atom.txt
@ -26,7 +26,7 @@ Define a computation that calculates the CNA (Common Neighbor
 Analysis) pattern for each atom in the group.  In solid-state systems
 the CNA pattern is a useful measure of the local crystal structure
 around an atom.  The CNA methodology is described in "(Faken)"_#Faken
-and "(Tsuzuki)"_#Tsuzuki.
+and "(Tsuzuki)"_#Tsuzuki1.

 Currently, there are five kinds of CNA patterns LAMMPS recognizes:

@ -93,5 +93,5 @@ above.
 :link(Faken)
 [(Faken)] Faken, Jonsson, Comput Mater Sci, 2, 279 (1994).

-:link(Tsuzuki)
+:link(Tsuzuki1)
 [(Tsuzuki)] Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007).
--- a/doc/src/compute_cnp_atom.txt
+++ b/doc/src/compute_cnp_atom.txt
@ -0,0 +1,111 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute cnp/atom command :h3
+
+[Syntax:]
+
+compute ID group-ID cnp/atom cutoff :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+cnp/atom = style name of this compute command
+cutoff = cutoff distance for nearest neighbors (distance units) :ul
+
+[Examples:]
+
+compute 1 all cnp/atom 3.08 :pre
+
+[Description:]
+
+Define a computation that calculates the Common Neighborhood
+Parameter (CNP) for each atom in the group.  In solid-state systems
+the CNP is a useful measure of the local crystal structure
+around an atom and can be used to characterize whether the
+atom is part of a perfect lattice, a local defect (e.g. a dislocation
+or stacking fault), or at a surface.
+
+The value of the CNP parameter will be 0.0 for atoms not in the
+specified compute group.  Note that normally a CNP calculation should
+only be performed on single component systems.
+
+This parameter is computed using the following formula from
+"(Tsuzuki)"_#Tsuzuki2
+
+:c,image(Eqs/cnp_eq.jpg)
+
+where the index {j} goes over the {n}i nearest neighbors of atom
+{i}, and the index {k} goes over the {n}ij common nearest neighbors
+between atom {i} and atom {j}. Rik and Rjk are the vectors connecting atom
+{k} to atoms {i} and {j}.  The quantity in the double sum is computed
+for each atom.
+
+The CNP calculation is sensitive to the specified cutoff value.
+You should ensure that the appropriate nearest neighbors of an atom are
+found within the cutoff distance for the presumed crystal structure.
+E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest
+neighbors for perfect BCC crystals.  These formulas can be used to
+obtain a good cutoff distance:
+
+:c,image(Eqs/cnp_cutoff.jpg)
+
+where a is the lattice constant for the crystal structure concerned
+and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a
+for HCP crystals.
+
+Also note that since the CNP calculation in LAMMPS uses the neighbors
+of an owned atom to find the nearest neighbors of a ghost atom, the
+following relation should also be satisfied:
+
+:c,image(Eqs/cnp_cutoff2.jpg)
+
+where Rc is the cutoff distance of the potential, Rs is the skin
+distance as specified by the "neighbor"_neighbor.html command, and
+cutoff is the argument used with the compute cnp/atom command.  LAMMPS
+will issue a warning if this is not the case.
+
+The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (e.g. each time a snapshot of atoms
+is dumped).  Thus it can be inefficient to compute/dump this quantity
+too frequently or to have multiple compute/dump commands, each with a
+{cnp/atom} style.
+
+[Output info:]
+
+This compute calculates a per-atom vector, which 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 values will be real positive numbers. Some typical CNP
+values:
+
+FCC lattice = 0.0
+BCC lattice = 0.0
+HCP lattice = 4.4 :pre
+
+FCC (111) surface ~ 13.0
+FCC (100) surface ~ 26.5
+FCC dislocation core ~ 11 :pre
+
+[Restrictions:]
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"compute cna/atom"_compute_cna_atom.html
+"compute centro/atom"_compute_centro_atom.html
+
+[Default:] none
+
+:line
+
+:link(Tsuzuki2)
+[(Tsuzuki)] Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007).
--- a/doc/src/compute_pair_local.txt
+++ b/doc/src/compute_pair_local.txt
@ -76,7 +76,9 @@ command for the types of the two atoms is used.  For the {radius}
 setting, the sum of the radii of the two particles is used as a
 cutoff.  For example, this is appropriate for granular particles which
 only interact when they are overlapping, as computed by "granular pair
-styles"_pair_gran.txt.
+styles"_pair_gran.txt.  Note that if a granular model defines atom
+types such that all particles of a specific type are monodisperse
+(same diameter), then the two settings are effectively identical.

 Note that as atoms migrate from processor to processor, there will be
 no consistent ordering of the entries within the local vector or array
--- a/doc/src/compute_property_local.txt
+++ b/doc/src/compute_property_local.txt
@ -79,6 +79,9 @@ the two atoms is used.  For the {radius} setting, the sum of the radii
 of the two particles is used as a cutoff.  For example, this is
 appropriate for granular particles which only interact when they are
 overlapping, as computed by "granular pair styles"_pair_gran.html.
+Note that if a granular model defines atom types such that all
+particles of a specific type are monodisperse (same diameter), then
+the two settings are effectively identical.

 If the inputs are bond, angle, etc attributes, the local data is
 generated by looping over all the atoms owned on a processor and
--- a/doc/src/compute_saed.txt
+++ b/doc/src/compute_saed.txt
@ -111,26 +111,26 @@ Coefficients parameterized by "(Fox)"_#Fox are assigned for each
 atom type designating the chemical symbol and charge of each atom
 type. Valid chemical symbols for compute saed are:

-         H:      He:      Li:      Be:       B:
-         C:       N:       O:       F:      Ne:
-        Na:      Mg:      Al:      Si:       P:
-         S:      Cl:      Ar:       K:      Ca:
-        Sc:      Ti:       V:      Cr:      Mn:
-        Fe:      Co:      Ni:      Cu:      Zn:
-        Ga:      Ge:      As:      Se:      Br:
-        Kr:      Rb:      Sr:       Y:      Zr:
-        Nb:      Mo:      Tc:      Ru:      Rh:
-        Pd:      Ag:      Cd:      In:      Sn:
-        Sb:      Te:       I:      Xe:      Cs:
-        Ba:      La:      Ce:      Pr:      Nd:
-        Pm:      Sm:      Eu:      Gd:      Tb:
-        Dy:      Ho:      Er:      Tm:      Yb:
-        Lu:      Hf:      Ta:       W:      Re:
-        Os:      Ir:      Pt:      Au:      Hg:
-        Tl:      Pb:      Bi:      Po:      At:
-        Rn:      Fr:      Ra:      Ac:      Th:
-        Pa:       U:      Np:      Pu:      Am:
-        Cm:      Bk:      Cf:tb(c=5,s=:)
+H:       He:      Li:      Be:       B:
+C:        N:       O:       F:      Ne:
+Na:      Mg:      Al:      Si:       P:
+S:       Cl:      Ar:       K:      Ca:
+Sc:      Ti:       V:      Cr:      Mn:
+Fe:      Co:      Ni:      Cu:      Zn:
+Ga:      Ge:      As:      Se:      Br:
+Kr:      Rb:      Sr:       Y:      Zr:
+Nb:      Mo:      Tc:      Ru:      Rh:
+Pd:      Ag:      Cd:      In:      Sn:
+Sb:      Te:       I:      Xe:      Cs:
+Ba:      La:      Ce:      Pr:      Nd:
+Pm:      Sm:      Eu:      Gd:      Tb:
+Dy:      Ho:      Er:      Tm:      Yb:
+Lu:      Hf:      Ta:       W:      Re:
+Os:      Ir:      Pt:      Au:      Hg:
+Tl:      Pb:      Bi:      Po:      At:
+Rn:      Fr:      Ra:      Ac:      Th:
+Pa:       U:      Np:      Pu:      Am:
+Cm:      Bk:      Cf:tb(c=5,s=:)


 If the {echo} keyword is specified, compute saed will provide extra
--- a/doc/src/compute_sna_atom.txt
+++ b/doc/src/compute_sna_atom.txt
@ -231,11 +231,12 @@ the numbers of columns are 930, 2790, and 5580, respectively.

 If the {quadratic} keyword value is set to 1, then additional
 columns are appended to each per-atom array, corresponding to
-a matrix of quantities that are products of two bispectrum components. If the
-number of bispectrum components is {K}, then the number of matrix elements
-is {K}^2. These are output in subblocks of {K}^2 columns, using the same
-ordering of columns and sub-blocks as was used for the bispectrum
-components.
+the products of all distinct pairs of  bispectrum components. If the
+number of bispectrum components is {K}, then the number of distinct pairs
+is  {K}({K}+1)/2. These are output in subblocks of  {K}({K}+1)/2 columns, using the same
+ordering of sub-blocks as was used for the bispectrum
+components. Within each sub-block, the ordering is upper-triangular,
+(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K})

 These values can be accessed by any command that uses per-atom values
 from a compute as input.  See "Section
--- a/doc/src/computes.txt
+++ b/doc/src/computes.txt
@ -17,6 +17,7 @@ Computes :h1
   compute_chunk_atom
   compute_cluster_atom
   compute_cna_atom
+   compute_cnp_atom
   compute_com
   compute_com_chunk
   compute_contact_atom
--- a/doc/src/dihedral_charmm.txt
+++ b/doc/src/dihedral_charmm.txt
@ -138,7 +138,15 @@ more instructions on how to use the accelerated styles effectively.

 [Restrictions:]

-This dihedral style can only be used if LAMMPS was built with the
+When using run_style "respa"_run_style.html, these dihedral styles
+must be assigned to the same r-RESPA level as {pair} or {outer}.
+
+When used in combination with CHARMM pair styles, the 1-4
+"special_bonds"_special_bonds.html scaling factors must be set to 0.0.
+Otherwise non-bonded contributions for these 1-4 pairs will be
+computed multiple times.
+
+These dihedral styles can only be used if LAMMPS was built with the
 MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

--- a/doc/src/dihedral_spherical.txt
+++ b/doc/src/dihedral_spherical.txt
@ -18,6 +18,7 @@ dihedral_coeff 1 1  286.1  1 124  1    1 90.0 0    1 90.0 0
 dihedral_coeff 1 3  69.3   1 93.9 1    1 90   0    1 90   0  &
                    49.1   0 0.00 0    1 74.4 1    0 0.00 0  &
                    25.2   0 0.00 0    0 0.00 0    1 48.1 1
+:pre

 [Description:]

--- a/doc/src/dump_modify.txt
+++ b/doc/src/dump_modify.txt
@ -16,7 +16,8 @@ dump-ID = ID of dump to modify :ulb,l
 one or more keyword/value pairs may be appended :l
 these keywords apply to various dump styles :l
 keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
-  {append} arg = {yes} or {no}
+  {append} arg = {yes} or {no} or {at} N
+    N = index of frame written upon first dump
  {buffer} arg = {yes} or {no}
  {element} args = E1 E2 ... EN, where N = # of atom types
    E1,...,EN = element name, e.g. C or Fe or Ga
@ -41,6 +42,7 @@ keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} o
  {region} arg = region-ID or "none"
  {scale} arg = {yes} or {no}
  {sfactor} arg = coordinate scaling factor (> 0.0)
+  {thermo} arg = {yes} or {no}
  {tfactor} arg = time scaling factor (> 0.0)
  {sort} arg = {off} or {id} or N or -N
     off = no sorting of per-atom lines within a snapshot
@ -139,12 +141,13 @@ and {dcd}.  It also applies only to text output files, not to binary
 or gzipped or image/movie files.  If specified as {yes}, then dump
 snapshots are appended to the end of an existing dump file.  If
 specified as {no}, then a new dump file will be created which will
-overwrite an existing file with the same name.  This keyword can only
-take effect if the dump_modify command is used after the
-"dump"_dump.html command, but before the first command that causes
-dump snapshots to be output, e.g. a "run"_run.html or
-"minimize"_minimize.html command.  Once the dump file has been opened,
-this keyword has no further effect.
+overwrite an existing file with the same name.  If the {at} option is present
+({netcdf} only), then the frame to append to can be specified.  Negative values
+are counted from the end of the file.  This keyword can only take effect if the
+dump_modify command is used after the "dump"_dump.html command, but before the
+first command that causes dump snapshots to be output, e.g. a "run"_run.html or
+"minimize"_minimize.html command.  Once the dump file has been opened, this
+keyword has no further effect.

 :line

@ -413,6 +416,13 @@ most effective when the typical magnitude of position data is between

 :line

+The {thermo} keyword ({netcdf} only) triggers writing of "thermo"_thermo.html
+information to the dump file alongside per-atom data. The data included in the
+dump file is identical to the data specified by
+"thermo_style"_thermo_style.html.
+
+:line
+
 The {region} keyword only applies to the dump {custom}, {cfg},
 {image}, and {movie} styles.  If specified, only atoms in the region
 will be written to the dump file or included in the image/movie.  Only
--- a/doc/src/dump_netcdf.txt
+++ b/doc/src/dump_netcdf.txt
@ -24,7 +24,7 @@ args = list of atom attributes, same as for "dump_style custom"_dump.html :l,ule
 [Examples:]

 dump 1 all netcdf 100 traj.nc type x y z vx vy vz
-dump_modify 1 append yes at -1 global c_thermo_pe c_thermo_temp c_thermo_press
+dump_modify 1 append yes at -1 thermo yes
 dump 1 all netcdf/mpiio 1000 traj.nc id type x y z :pre

 [Description:]
@ -44,7 +44,7 @@ rank.
 NetCDF files can be directly visualized via the following tools:

 Ovito (http://www.ovito.org/). Ovito supports the AMBER convention and
-all of the above extensions. :ule,b
+all extensions of this dump style. :ule,b

 VMD (http://www.ks.uiuc.edu/Research/vmd/). :l

@ -52,15 +52,9 @@ AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye
 contains a NetCDF reader that is not present in the standard
 distribution of AtomEye. :l,ule

-In addition to per-atom data, global data can be included in the dump
-file, which are the kinds of values output by the
-"thermo_style"_thermo_style.html command .  See "Section howto
-6.15"_Section_howto.html#howto_15 for an explanation of per-atom
-versus global data.  The global output written into the dump file can
-be from computes, fixes, or variables, by prefixing the compute/fix ID
-or variable name with "c_" or "f_" or "v_" respectively, as in the
-example above.  These global values are specified via the "dump_modify
-global"_dump_modify.html command.
+In addition to per-atom data, "thermo"_thermo.html data can be included in the
+dump file. The data included in the dump file is identical to the data specified
+by "thermo_style"_thermo_style.html.

 :link(netcdf-home,http://www.unidata.ucar.edu/software/netcdf/)
 :link(pnetcdf-home,http://trac.mcs.anl.gov/projects/parallel-netcdf/)
--- a/doc/src/dump_vtk.txt
+++ b/doc/src/dump_vtk.txt
@ -16,7 +16,7 @@ ID = user-assigned name for the dump
 group-ID = ID of the group of atoms to be dumped
 vtk = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page)
 N = dump every this many timesteps
-file = name of file to write dump info to 
+file = name of file to write dump info to
 args = same as arguments for "dump_style custom"_dump.html :ul

 [Examples:]
@ -83,7 +83,7 @@ Triclinic simulation boxes (non-orthogonal) are saved as
 hexahedrons in either legacy .vtk or .vtu XML format.

 Style {vtk} allows you to specify a list of atom attributes to be
-written to the dump file for each atom.  The list of possible attributes 
+written to the dump file for each atom.  The list of possible attributes
 is the same as for the "dump_style custom"_dump.html command; see
 its doc page for a listing and an explanation of each attribute.

--- a/doc/src/fix_adapt.txt
+++ b/doc/src/fix_adapt.txt
@ -47,7 +47,7 @@ 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
+fix 1 all adapt 10 atom diameter v_size :pre

 variable ramp_up equal "ramp(0.01,0.5)"
 fix stretch all adapt 1 bond harmonic r0 1 v_ramp_up :pre
--- a/doc/src/fix_box_relax.txt
+++ b/doc/src/fix_box_relax.txt
@ -245,7 +245,7 @@ appear the system is converging to your specified pressure.  The
 solution for this is to either (a) zero the velocities of all atoms
 before performing the minimization, or (b) make sure you are
 monitoring the pressure without its kinetic component.  The latter can
-be done by outputting the pressure from the pressure compute this 
+be done by outputting the pressure from the pressure compute this
 command creates (see below) or a pressure compute you define yourself.

 NOTE: Because pressure is often a very sensitive function of volume,
--- a/doc/src/fix_deform.txt
+++ b/doc/src/fix_deform.txt
@ -565,8 +565,10 @@ more instructions on how to use the accelerated styles effectively.

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

-No information about this fix is written to "binary restart
-files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+This fix will restore the initial box settings from "binary restart
+files"_restart.html, which allows the fix to be properly continue
+deformation, when using the start/stop options of the "run"_run.html
+command.  None of the "fix_modify"_fix_modify.html options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various "output
 commands"_Section_howto.html#howto_15.
--- a/doc/src/fix_eos_table_rx.txt
+++ b/doc/src/fix_eos_table_rx.txt
@ -45,14 +45,14 @@ species {j} in particle {i}, {u_j} is the internal energy of species j,
 {DeltaH_f,j} is the heat of formation of species {j}, N is the number of
 molecules represented by the coarse-grained particle, kb is the
 Boltzmann constant, and T is the temperature of the system.  Additionally,
-it is possible to modify the concentration-dependent particle internal 
-energy relation by adding an energy correction, temperature-dependent 
+it is possible to modify the concentration-dependent particle internal
+energy relation by adding an energy correction, temperature-dependent
 correction, and/or a molecule-dependent correction.  An energy correction can
-be specified as a constant (in energy units).  A temperature correction can be 
-specified by multiplying a temperature correction coefficient by the 
-internal temperature.  A molecular correction can be specified by 
-by multiplying a molecule correction coefficient by the average number of 
-product gas particles in the coarse-grain particle. 
+be specified as a constant (in energy units).  A temperature correction can be
+specified by multiplying a temperature correction coefficient by the
+internal temperature.  A molecular correction can be specified by
+by multiplying a molecule correction coefficient by the average number of
+product gas particles in the coarse-grain particle.

 Fix {eos/table/rx} creates interpolation tables of length {N} from {m}
 internal energy values of each species {u_j} listed in a file as a
@ -72,12 +72,12 @@ The second filename specifies a file containing heat of formation
 {DeltaH_f,j} for each species.

 In cases where the coarse-grain particle represents a single molecular
-species (i.e., no reactions occur and fix {rx} is not present in the input file), 
-fix {eos/table/rx} can be applied in a similar manner to fix {eos/table} 
-within a non-reactive DPD simulation.  In this case, the heat of formation 
+species (i.e., no reactions occur and fix {rx} is not present in the input file),
+fix {eos/table/rx} can be applied in a similar manner to fix {eos/table}
+within a non-reactive DPD simulation.  In this case, the heat of formation
 filename is replaced with the heat of formation value for the single species.
-Additionally, the energy correction and temperature correction coefficients may 
-also be specified as fix arguments.  
+Additionally, the energy correction and temperature correction coefficients may
+also be specified as fix arguments.

 :line

@ -138,8 +138,8 @@ used as the species name must correspond with the tags used to define
 the reactions with the "fix rx"_fix_rx.html command.

 Alternatively, corrections to the EOS can be included by specifying
-three additional columns that correspond to the energy correction, 
-the temperature correction coefficient and molecule correction 
+three additional columns that correspond to the energy correction,
+the temperature correction coefficient and molecule correction
 coefficient.  In this case, the format of the file is as follows:

 # HEAT OF FORMATION TABLE     (one or more comment or blank lines) :pre
--- a/doc/src/fix_filter_corotate.txt
+++ b/doc/src/fix_filter_corotate.txt
@ -70,8 +70,8 @@ minimization"_minimize.html.

 [Restrictions:]

-This fix is part of the USER-MISC package. It is only enabled if 
-LAMMPS was built with that package. See the "Making 
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.

 Currently, it does not support "molecule templates"_molecule.html.
--- a/doc/src/fix_gcmc.txt
+++ b/doc/src/fix_gcmc.txt
@ -406,7 +406,7 @@ the user for each subsequent fix gcmc command.
 [Default:]

 The option defaults are mol = no, maxangle = 10, overlap_cutoff = 0.0,
-fugacity_coeff = 1, 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_gle.txt
+++ b/doc/src/fix_gle.txt
@ -68,7 +68,7 @@ matrix that gives canonical sampling for a given A is computed automatically.
 However, the GLE framework also allow for non-equilibrium sampling, that
 can be used for instance to model inexpensively zero-point energy
 effects "(Ceriotti2)"_#Ceriotti2. This is achieved specifying the {noneq}
- keyword followed by the name of the file that contains the static covariance
+keyword followed by the name of the file that contains the static covariance
 matrix for the non-equilibrium dynamics.  Please note, that the covariance
 matrix is expected to be given in [temperature units].

--- a/doc/src/fix_grem.txt
+++ b/doc/src/fix_grem.txt
@ -85,13 +85,13 @@ No information about this fix is written to "binary restart
 files"_restart.html.

 The "thermo_modify"_thermo_modify.html {press} option is supported
-by this fix to add the rescaled kinetic pressure as part of 
+by this fix to add the rescaled kinetic pressure as part of
 "thermodynamic output"_thermo_style.html.

 [Restrictions:]

-This fix is part of the USER-MISC package. It is only enabled if 
-LAMMPS was built with that package. See the "Making 
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.

 [Related commands:]
--- a/doc/src/fix_ipi.txt
+++ b/doc/src/fix_ipi.txt
@ -58,14 +58,14 @@ input are listed in the same order as in the data file of LAMMPS. The
 initial configuration is ignored, as it will be substituted with the
 coordinates received from i-PI before forces are ever evaluated.

-A note of caution when using potentials that contain long-range 
+A note of caution when using potentials that contain long-range
 electrostatics, or that contain parameters that depend on box size:
 all of these options will be initialized based on the cell size in the
-LAMMPS-side initial configuration and kept constant during the run. 
-This is required to e.g. obtain reproducible and conserved forces. 
-If the cell varies too wildly, it may be advisable to reinitialize 
-these interactions at each call. This behavior can be requested by 
-setting the {reset} switch. 
+LAMMPS-side initial configuration and kept constant during the run.
+This is required to e.g. obtain reproducible and conserved forces.
+If the cell varies too wildly, it may be advisable to reinitialize
+these interactions at each call. This behavior can be requested by
+setting the {reset} switch.

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

--- a/doc/src/fix_langevin_drude.txt
+++ b/doc/src/fix_langevin_drude.txt
@ -67,11 +67,11 @@ The Langevin forces are computed as
 \(F_r'\) is a random force proportional to
 \(\sqrt \{ \frac \{2\, k_B \mathtt\{Tcom\}\, m'\}
                 \{\mathrm dt\, \mathtt\{damp\_com\} \}
-        \} \). :b
+        \} \).
 \(f_r'\) is a random force proportional to
 \(\sqrt \{ \frac \{2\, k_B \mathtt\{Tdrude\}\, m'\}
                 \{\mathrm dt\, \mathtt\{damp\_drude\} \}
-        \} \). :b
+        \} \).
 Then the real forces acting on the particles are computed from the inverse
 transform:
 \begin\{equation\} F = \frac M \{M'\}\, F' - f' \end\{equation\}
--- a/doc/src/fix_mscg.txt
+++ b/doc/src/fix_mscg.txt
@ -57,7 +57,7 @@ simulations is as follows:
 Perform all-atom simulations on the system to be coarse grained.
 Generate a trajectory mapped to the coarse-grained model.
 Create input files for the MS-CG library.
-Run the range finder functionality of the MS-CG library.  
+Run the range finder functionality of the MS-CG library.
 Run the force matching functionality of the MS-CG library.
 Check the results of the force matching.
 Run coarse-grained simulations using the new coarse-grained potentials. :ol
@ -70,7 +70,7 @@ Step 2 can be performed using a Python script (what is the name?)
 provided with the MS-CG library which defines the coarse-grained model
 and converts a standard LAMMPS dump file for an all-atom simulation
 (step 1) into a LAMMPS dump file which has the positions of and forces
-on the coarse-grained beads.  
+on the coarse-grained beads.

 In step 3, an input file named "control.in" is needed by the MS-CG
 library which sets parameters for the range finding and force matching
--- a/doc/src/fix_neb.txt
+++ b/doc/src/fix_neb.txt
@ -10,68 +10,183 @@ fix neb command :h3

 [Syntax:]

-fix ID group-ID neb Kspring :pre
+fix ID group-ID neb Kspring keyword value :pre

-ID, group-ID are documented in "fix"_fix.html command
-neb = style name of this fix command
-Kspring = inter-replica spring constant (force/distance units) :ul
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+neb = style name of this fix command :l
+Kspring = spring constant for parallel nudging force (force/distance units or force units, see parallel keyword) :l
+zero or more keyword/value pairs may be appended :l
+keyword = {parallel} or {perp} or {end} :l
+  {parallel} value = {neigh} or {ideal}
+    {neigh} = parallel nudging force based on distance to neighbor replicas (Kspring = force/distance units)
+    {ideal} = parallel nudging force based on interpolated ideal position (Kspring = force units)
+  {perp} value = {Kspring2}
+    {Kspring2} = spring constant for perpendicular nudging force (force/distance units)
+  {end} values = estyle Kspring3
+    {estyle} = {first} or {last} or {last/efirst} or {last/efirst/middle}
+      {first} = apply force to first replica
+      {last} = apply force to last replica
+      {last/efirst} = apply force to last replica and set its target energy to that of first replica
+      {last/efirst/middle} = same as {last/efirst} plus prevent middle replicas having lower energy than first replica
+    {Kspring3} = spring constant for target energy term (1/distance units) :pre,ule

 [Examples:]

-fix 1 active neb 10.0 :pre
+fix 1 active neb 10.0
+fix 2 all neb 1.0 perp 1.0 end last
+fix 2 all neb 1.0 perp 1.0 end first 1.0 end last 1.0
+fix 1 all neb 1.0 nudge ideal end last/efirst 1 :pre

 [Description:]

-Add inter-replica forces to atoms in the group for a multi-replica
+Add nudging forces to atoms in the group for a multi-replica
 simulation run via the "neb"_neb.html command to perform a nudged
-elastic band (NEB) calculation for transition state finding.  Hi-level
-explanations of NEB are given with the "neb"_neb.html command and in
-"Section 6.5"_Section_howto.html#howto_5 of the manual.  The fix
-neb command must be used with the "neb" command to define how
-inter-replica forces are computed.
+elastic band (NEB) calculation for finding the transition state.
+Hi-level explanations of NEB are given with the "neb"_neb.html command
+and in "Section_howto 5"_Section_howto.html#howto_5 of the manual.
+The fix neb command must be used with the "neb" command and defines
+how inter-replica nudging forces are computed.  A NEB calculation is
+divided in two stages. In the first stage n replicas are relaxed
+toward a MEP until convergence.  In the second stage, the climbing
+image scheme (see "(Henkelman2)"_#Henkelman2) is enabled, so that the
+replica having the highest energy relaxes toward the saddle point
+(i.e. the point of highest energy along the MEP), and a second
+relaxation is performed.

-Only the N atoms in the fix group experience inter-replica forces.
-Atoms in the two end-point replicas do not experience these forces,
-but those in intermediate replicas do.  During the initial stage of
-NEB, the 3N-length vector of interatomic forces Fi = -Grad(V) acting
-on the atoms of each intermediate replica I is altered, as described
-in the "(Henkelman1)"_#Henkelman1 paper, to become:
+A key purpose of the nudging forces is to keep the replicas equally
+spaced.  During the NEB calculation, the 3N-length vector of
+interatomic force Fi = -Grad(V) for each replica I is altered.  For
+all intermediate replicas (i.e. for 1 < I < N, except the climbing
+replica) the force vector becomes:

-Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (| Ri+i - Ri | - | Ri - Ri-1 |) That :pre
+Fi = -Grad(V) + (Grad(V) dot T') T' + Fnudge_parallel + Fnudge_perp :pre

-Ri are the atomic coordinates of replica I; Ri-1 and Ri+1 are the
-coordinates of its neighbor replicas.  That (t with a hat over it) is
-the unit "tangent" vector for replica I which is a function of Ri,
+T' is the unit "tangent" vector for replica I and is a function of Ri,
 Ri-1, Ri+1, and the potential energy of the 3 replicas; it points
 roughly in the direction of (Ri+i - Ri-1); see the
-"(Henkelman1)"_#Henkelman1 paper for details.
+"(Henkelman1)"_#Henkelman1 paper for details.  Ri are the atomic
+coordinates of replica I; Ri-1 and Ri+1 are the coordinates of its
+neighbor replicas.  The term (Grad(V) dot T') is used to remove the
+component of the gradient parallel to the path which would tend to
+distribute the replica unevenly along the path.  Fnudge_parallel is an
+artificial nudging force which is applied only in the tangent
+direction and which maintains the equal spacing between replicas (see
+below for more information).  Fnudge_perp is an optional artificial
+spring which is applied in a direction perpendicular to the tangent
+direction and which prevent the paths from forming acute kinks (see
+below for more information).

-The first two terms in the above equation are the component of the
-interatomic forces perpendicular to the tangent vector.  The last term
-is a spring force between replica I and its neighbors, parallel to the
-tangent vector direction with the specified spring constant {Kspring}.
+In the second stage of the NEB calculation, the interatomic force Fi
+for the climbing replica (the replica of highest energy after the
+first stage) is changed to:

-The effect of the first two terms is to push the atoms of each replica
-toward the minimum energy path (MEP) of conformational states that
-transition over the energy barrier.  The MEP for an energy barrier is
-defined as a sequence of 3N-dimensional states which cross the barrier
-at its saddle point, each of which has a potential energy gradient
-parallel to the MEP itself.
+Fi = -Grad(V) + 2 (Grad(V) dot T') T' :pre

-The effect of the last term is to push each replica away from its two
-neighbors in a direction along the MEP, so that the final set of
-states are equidistant from each other.
+and the relaxation procedure is continued to a new converged MEP.

-During the second stage of NEB, the forces on the N atoms in the
-replica nearest the top of the energy barrier are altered so that it
-climbs to the top of the barrier and finds the saddle point.  The
-forces on atoms in this replica are described in the
-"(Henkelman2)"_#Henkelman2 paper, and become:
+:line

-Fi = -Grad(V) + 2 (Grad(V) dot That) That :pre
+The keyword {parallel} specifies how the parallel nudging force is
+computed.  With a value of {neigh}, the parallel nudging force is
+computed as in "(Henkelman1)"_#Henkelman1 by connecting each
+intermediate replica with the previous and the next image:

-The inter-replica forces for the other replicas are unchanged from the
-first equation.
+Fnudge_parallel = {Kspring} * (|Ri+1 - Ri| - |Ri - Ri-1|) :pre
+
+Note that in this case the specified {Kspring) is in force/distance
+units.
+
+With a value of {ideal}, the spring force is computed as suggested in
+"(WeinenE)"_#WeinenE :
+
+Fnudge_parallel = -{Kspring} * (RD-RDideal) / (2 * meanDist) :pre
+
+where RD is the "reaction coordinate" see "neb"_neb.html section, and
+RDideal is the ideal RD for which all the images are equally spaced.
+I.e. RDideal = (I-1)*meanDist when the climbing replica is off, where
+I is the replica number).  The meanDist is the average distance
+between replicas.  Note that in this case the specified {Kspring) is
+in force units.
+
+Note that the {ideal} form of nudging can often be more effective at
+keeping the replicas equally spaced.
+
+:line
+
+The keyword {perp} specifies if and how a perpendicual nudging force
+is computed.  It adds a spring force perpendicular to the path in
+order to prevent the path from becoming too kinky.  It can
+significantly improve the convergence of the NEB calculation when the
+resolution is poor.  I.e. when few replicas are used; see
+"(Maras)"_#Maras1 for details.
+
+The perpendicular spring force is given by
+
+Fnudge_perp = {Kspring2} * F(Ri-1,Ri,Ri+1) (Ri+1 + Ri-1 - 2 Ri) :pre
+
+where {Kspring2} is the specified value.  F(Ri-1 Ri R+1) is a smooth
+scalar function of the angle Ri-1 Ri Ri+1.  It is equal to 0.0 when
+the path is straight and is equal to 1 when the angle Ri-1 Ri Ri+1 is
+acute.  F(Ri-1 Ri R+1) is defined in "(Jonsson)"_#Jonsson.
+
+If {Kspring2} is set to 0.0 (the default) then no perpendicular spring
+force is added.
+
+:line
+
+By default, no additional forces act on the first and last replicas
+during the NEB relaxation, so these replicas simply relax toward their
+respective local minima.  By using the key word {end}, additional
+forces can be applied to the first and/or last replicas, to enable
+them to relax toward a MEP while constraining their energy.
+
+The interatomic force Fi for the specified replica becomes:
+
+Fi = -Grad(V) + (Grad(V) dot T' + (E-ETarget)*Kspring3) T',  {when} Grad(V) dot T' < 0
+Fi = -Grad(V) + (Grad(V) dot T' + (ETarget- E)*Kspring3) T', {when} Grad(V) dot T' > 0
+:pre
+
+where E is the current energy of the replica and ETarget is the target
+energy.  The "spring" constant on the difference in energies is the
+specified {Kspring3} value.
+
+When {estyle} is specified as {first}, the force is applied to the
+first replica.  When {estyle} is specified as {last}, the force is
+applied to the last replica.  Note that the {end} keyword can be used
+twice to add forces to both the first and last replicas.
+
+For both these {estyle} settings, the target energy {ETarget} is set
+to the initial energy of the replica (at the start of the NEB
+calculation).
+
+If the {estyle} is specified as {last/efirst} or {last/efirst/middle},
+force is applied to the last replica, but the target energy {ETarget}
+is continuously set to the energy of the first replica, as it evolves
+during the NEB relaxation.
+
+The difference between these two {estyle} options is as follows.  When
+{estyle} is specified as {last/efirst}, no change is made to the
+inter-replica force applied to the intermediate replicas (neither
+first or last).  If the initial path is too far from the MEP, an
+intermediate repilica may relax "faster" and reach a lower energy than
+the last replica.  In this case the intermediate replica will be
+relaxing toward its own local minima.  This behavior can be prevented
+by specifying {estyle} as {last/efirst/middle} which will alter the
+inter-replica force applied to intermediate replicas by removing the
+contribution of the gradient to the inter-replica force.  This will
+only be done if a particular intermediate replica has a lower energy
+than the first replica.  This should effectively prevent the
+intermediate replicas from over-relaxing.
+
+After converging a NEB calculation using an {estyle} of
+{last/efirst/middle}, you should check that all intermediate replicas
+have a larger energy than the first replica. If this is not the case,
+the path is probably not a MEP.
+
+Finally, note that if the last replica converges toward a local
+minimum which has a larger energy than the energy of the first
+replica, a NEB calculation using an {estyle} of {last/efirst} or
+{last/efirst/middle} cannot reach final convergence.

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

@ -96,7 +211,12 @@ for more info on packages.

 "neb"_neb.html

-[Default:] none
+[Default:]
+
+The option defaults are nudge = neigh, perp = 0.0, ends is not
+specified (no inter-replica force on the end replicas).
+
+:line

 :link(Henkelman1)
 [(Henkelman1)] Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
@ -104,3 +224,15 @@ for more info on packages.
 :link(Henkelman2)
 [(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
 9901-9904 (2000).
+
+:link(WeinenE)
+[(WeinenE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
+
+:link(Jonsson)
+[(Jonsson)] Jonsson, Mills and Jacobsen, in Classical and Quantum
+Dynamics in Condensed Phase Simulations, edited by Berne, Ciccotti,
+and Coker World Scientific, Singapore, 1998, p 385.
+
+:link(Maras1)
+[(Maras)] Maras, Trushin, Stukowski, Ala-Nissila, Jonsson,
+Comp Phys Comm, 205, 13-21 (2016).
--- a/doc/src/fix_nve_dot.txt
+++ b/doc/src/fix_nve_dot.txt
@ -23,13 +23,13 @@ fix 1 all nve/dot :pre
 [Description:]

 Apply a rigid-body integrator as described in "(Davidchack)"_#Davidchack1
-to a group of atoms, but without Langevin dynamics. 
+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)"_#Miller1. 
+via a velocity-Verlet algorithm and an evolution operator that rotates
+the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller1.

 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 
+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.
--- a/doc/src/fix_nve_dotc_langevin.txt
+++ b/doc/src/fix_nve_dotc_langevin.txt
@ -28,20 +28,20 @@ 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" 
+Apply a rigid-body Langevin-type integrator of the kind "Langevin C"
 as described in "(Davidchack)"_#Davidchack2
 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. 
+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)"_#Miller2.

-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 
+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
@ -57,7 +57,7 @@ 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 
+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
@ -77,7 +77,7 @@ a Gaussian random number) for speed.

 :line

-{Tstart} and {Tstop} have to be constant values, i.e. they cannot 
+{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
@ -98,16 +98,16 @@ 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. 
+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 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 
+A technical report with more information on this integrator can be found
 "here"_PDF/USER-CGDNA-overview.pdf.

 :line
@ -120,7 +120,7 @@ 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,  
+"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html,

 [Default:] none

--- a/doc/src/fix_nvk.txt
+++ b/doc/src/fix_nvk.txt
@ -27,7 +27,7 @@ timestep.  V is volume; K is kinetic energy. This creates a system
 trajectory consistent with the isokinetic ensemble.

 The equations of motion used are those of Minary et al in
-"(Minary)"_#nvk-Minary, a variant of those initially given by Zhang in 
+"(Minary)"_#nvk-Minary, a variant of those initially given by Zhang in
 "(Zhang)"_#nvk-Zhang.

 The kinetic energy will be held constant at its value given when fix
--- a/doc/src/fix_qeq_reax.txt
+++ b/doc/src/fix_qeq_reax.txt
@ -8,17 +8,19 @@

 fix qeq/reax command :h3
 fix qeq/reax/kk command :h3
+fix qeq/reax/omp command :h3

 [Syntax:]

-fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params :pre
+fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params args :pre

 ID, group-ID are documented in "fix"_fix.html command
 qeq/reax = style name of this fix command
 Nevery = perform QEq every this many steps
 cutlo,cuthi = lo and hi cutoff for Taper radius
 tolerance = precision to which charges will be equilibrated
-params = reax/c or a filename :ul
+params = reax/c or a filename
+args   = {dual} (optional) :ul

 [Examples:]

@ -59,6 +61,10 @@ potential file, except that eta is defined here as twice the eta value
 in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
 of this fix are hard-coded to be A, eV, and electronic charge.

+The optional {dual} keyword allows to perform the optimization
+of the S and T matrices in parallel. This is only supported for
+the {qeq/reax/omp} style. Otherwise they are processed separately.
+
 [Restart, fix_modify, output, run start/stop, minimize info:]

 No information about this fix is written to "binary restart
--- a/doc/src/fix_rigid.txt
+++ b/doc/src/fix_rigid.txt
@ -31,11 +31,12 @@ bodystyle = {single} or {molecule} or {group} :l
    groupID1, groupID2, ... = list of N group IDs :pre

 zero or more keyword/value pairs may be appended :l
-keyword = {langevin} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {couple} or {tparam} or {pchain} or {dilate} or {force} or {torque} or {infile} :l
+keyword = {langevin} or {reinit} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {couple} or {tparam} or {pchain} or {dilate} or {force} or {torque} or {infile} :l
  {langevin} values = Tstart Tstop Tperiod seed
    Tstart,Tstop = desired temperature at start/stop of run (temperature units)
    Tdamp = temperature damping parameter (time units)
    seed = random number seed to use for white noise (positive integer)
+  {reinit} = {yes} or {no}
  {temp} values = Tstart Tstop Tdamp
    Tstart,Tstop = desired temperature at start/stop of run (temperature units)
    Tdamp = temperature damping parameter (time units)
@ -68,10 +69,10 @@ keyword = {langevin} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {coup

 [Examples:]

-fix 1 clump rigid single
+fix 1 clump rigid single reinit yes
 fix 1 clump rigid/small molecule
 fix 1 clump rigid single force 1 off off on langevin 1.0 1.0 1.0 428984
-fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0
+fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0 reinit no
 fix 1 polychains rigid molecule force 1*5 off off off force 6*10 off off on
 fix 1 polychains rigid/small molecule langevin 1.0 1.0 1.0 428984
 fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off
@ -87,7 +88,12 @@ means that each timestep the total force and torque on each rigid body
 is computed as the sum of the forces and torques on its constituent
 particles.  The coordinates, velocities, and orientations of the atoms
 in each body are then updated so that the body moves and rotates as a
-single entity.
+single entity.  This is implemented by creating internal data structures
+for each rigid body and performing time integration on these data
+structures.  Positions, velocities, and orientations of the constituent
+particles are regenerated from the rigid body data structures in every
+time step. This restricts which operations and fixes can be applied to
+rigid bodies. See below for a detailed discussion.

 Examples of large rigid bodies are a colloidal particle, or portions
 of a biomolecule such as a protein.
@ -148,8 +154,9 @@ differences may accumulate to produce divergent trajectories.

 NOTE: You should not update the atoms in rigid bodies via other
 time-integration fixes (e.g. "fix nve"_fix_nve.html, "fix
-nvt"_fix_nh.html, "fix npt"_fix_nh.html), or you will be integrating
-their motion more than once each timestep.  When performing a hybrid
+nvt"_fix_nh.html, "fix npt"_fix_nh.html, "fix move"_fix_move.html),
+or you will have conflicting updates to positions and velocities
+resulting in unphysical behavior in most cases. When performing a hybrid
 simulation with some atoms in rigid bodies, and some not, a separate
 time integration fix like "fix nve"_fix_nve.html or "fix
 nvt"_fix_nh.html should be used for the non-rigid particles.
@ -165,23 +172,29 @@ setting the force on them to 0.0 (via the "fix
 setforce"_fix_setforce.html command), and integrating them as usual
 (e.g. via the "fix nve"_fix_nve.html command).

-NOTE: The aggregate properties of each rigid body are calculated one
-time at the start of the first simulation run after these fixes are
-specified.  The properties include the position and velocity of the
-center-of-mass of the body, its moments of inertia, and its angular
-momentum.  This is done using the properties of the constituent atoms
-of the body at that point in time (or see the {infile} keyword
-option).  Thereafter, changing properties of individual atoms in the
-body will have no effect on a rigid body's dynamics, unless they
-affect the "pair_style"_pair_style.html interactions that individual
-particles are part of.  For example, you might think you could
-displace the atoms in a body or add a large velocity to each atom in a
-body to make it move in a desired direction before a 2nd run is
+IMPORTANT NOTE: The aggregate properties of each rigid body are
+calculated at the start of a simulation run and are maintained in
+internal data structures. The properties include the position and
+velocity of the center-of-mass of the body, its moments of inertia, and
+its angular momentum.  This is done using the properties of the
+constituent atoms of the body at that point in time (or see the {infile}
+keyword option).  Thereafter, changing these properties of individual
+atoms in the body will have no effect on a rigid body's dynamics, unless
+they effect any computation of per-atom forces or torques. If the
+keyword {reinit} is set to {yes} (the default), the rigid body data
+structures will be recreated at the beginning of each {run} command;
+if the keyword {reinit} is set to {no}, the rigid body data structures
+will be built only at the very first {run} command and maintained for
+as long as the rigid fix is defined. For example, you might think you
+could displace the atoms in a body or add a large velocity to each atom
+in a body to make it move in a desired direction before a 2nd run is
 performed, using the "set"_set.html or
 "displace_atoms"_displace_atoms.html or "velocity"_velocity.html
-command.  But these commands will not affect the internal attributes
-of the body, and the position and velocity of individual atoms in the
-body will be reset when time integration starts.
+commands.  But these commands will not affect the internal attributes
+of the body unless {reinit} is set to {yes}. With {reinit} set to {no}
+(or using the {infile} option, which implies {reinit} {no}) the position
+and velocity of individual atoms in the body will be reset when time
+integration starts again.

 :line

@ -401,6 +414,14 @@ couple none :pre

 The keyword/value option pairs are used in the following ways.

+The {reinit} keyword determines, whether the rigid body properties
+are reinitialized between run commands. With the option {yes} (the
+default) this is done, with the option {no} this is not done. Turning
+off the reinitialization can be helpful to protect rigid bodies against
+unphysical manipulations between runs or when properties cannot be
+easily recomputed (e.g. when read from a file). When using the {infile}
+keyword, the {reinit} option is automatically set to {no}.
+
 The {langevin} and {temp} and {tparam} keywords perform thermostatting
 of the rigid bodies, altering both their translational and rotational
 degrees of freedom.  What is meant by "temperature" of a collection of
@ -778,7 +799,7 @@ exclude, "fix shake"_fix_shake.html

 The option defaults are force * on on on and torque * on on on,
 meaning all rigid bodies are acted on by center-of-mass force and
-torque.  Also Tchain = Pchain = 10, Titer = 1, Torder = 3.
+torque.  Also Tchain = Pchain = 10, Titer = 1, Torder = 3, reinit = yes.

 :line

--- a/doc/src/fix_spring.txt
+++ b/doc/src/fix_spring.txt
@ -89,7 +89,7 @@ NOTE: The center of mass of a group of atoms is calculated in
 group can straddle a periodic boundary.  See the "dump"_dump.html doc
 page for a discussion of unwrapped coordinates.  It also means that a
 spring connecting two groups or a group and the tether point can cross
-a periodic boundary and its length be calculated correctly.  
+a periodic boundary and its length be calculated correctly.

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

--- a/doc/src/fix_ti_spring.txt
+++ b/doc/src/fix_ti_spring.txt
@ -144,7 +144,11 @@ this fix.

 "fix spring"_fix_spring.html, "fix adapt"_fix_adapt.html

-[Restrictions:] none
+[Restrictions:]
+
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.

 [Default:]

--- a/doc/src/kspace_modify.txt
+++ b/doc/src/kspace_modify.txt
@ -219,10 +219,10 @@ instead of using the virial equation. This option cannot be used to access
 individual components of the pressure tensor, to compute per-atom virial,
 or with suffix kspace/pair styles of MSM, like OMP or GPU.

-The {fftbench} keyword applies only to PPPM. It is on by default. If
-this option is turned off, LAMMPS will not take the time at the end
-of a run to give FFT benchmark timings, and will finish a few seconds
-faster than it would if this option were on.
+The {fftbench} keyword applies only to PPPM. It is off by default. If
+this option is turned on, LAMMPS will perform a short FFT benchmark
+computation and report its timings, and will thus finish a some seconds
+later than it would if this option were off.

 The {collective} keyword applies only to PPPM.  It is set to {no} by
 default, except on IBM BlueGene machines.  If this option is set to
@ -306,9 +306,10 @@ parameters, see the "How-To"_Section_howto.html#howto_24 discussion.
 The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp =
 5 (PPPM), order = 10 (MSM), minorder = 2, overlap = yes, force = -1.0,
 gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust =
-yes (MSM), pressure/scalar = yes (MSM), fftbench = yes (PPPM), diff = ik
+yes (MSM), pressure/scalar = yes (MSM), fftbench = no (PPPM), diff = ik
 (PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace = -1.0,
-split = 0, tol = 1.0e-6, and disp/auto = no.
+split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel, order =
+order/disp = 7.

 :line

--- a/doc/src/kspace_style.txt
+++ b/doc/src/kspace_style.txt
@ -33,12 +33,16 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg}
    accuracy = desired relative error in forces
  {pppm/gpu} value = accuracy
    accuracy = desired relative error in forces
+  {pppm/intel} value = accuracy
+    accuracy = desired relative error in forces
  {pppm/kk} value = accuracy
    accuracy = desired relative error in forces
  {pppm/omp} value = accuracy
    accuracy = desired relative error in forces
  {pppm/cg/omp} value = accuracy
    accuracy = desired relative error in forces
+  {pppm/disp/intel} value = accuracy
+    accuracy = desired relative error in forces
  {pppm/tip4p/omp} value = accuracy
    accuracy = desired relative error in forces
  {pppm/stagger} value = accuracy
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@ -301,6 +301,7 @@ compute_centro_atom.html
 compute_chunk_atom.html
 compute_cluster_atom.html
 compute_cna_atom.html
+compute_cnp_atom.html
 compute_com.html
 compute_com_chunk.html
 compute_contact_atom.html
@ -446,7 +447,6 @@ pair_lj96.html
 pair_lj_cubic.html
 pair_lj_expand.html
 pair_lj_long.html
-pair_lj_sf.html
 pair_lj_smooth.html
 pair_lj_smooth_linear.html
 pair_lj_soft.html
--- a/doc/src/manifolds.txt
+++ b/doc/src/manifolds.txt
@ -24,14 +24,15 @@ to the relevant fixes.
 {manifold} @ {parameters} @ {equation} @ {description}
 cylinder @ R @ x^2 + y^2 - R^2 = 0 @ Cylinder along z-axis, axis going through (0,0,0)
 cylinder_dent @ R l a @ x^2 + y^2 - r(z)^2 = 0, r(x) = R if | z | > l, r(z) = R - a*(1 + cos(z/l))/2 otherwise @ A cylinder with a dent around z = 0
-dumbbell @ a A B c @ -( x^2 + y^2 ) * (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0 @ A dumbbell @
+dumbbell @ a A B c @ -( x^2 + y^2 ) + (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0 @ A dumbbell
 ellipsoid @ a  b c @ (x/a)^2 + (y/b)^2 + (z/c)^2 = 0 @ An ellipsoid
+gaussian_bump @ A l rc1 rc2 @ if( x < rc1) -z + A * exp( -x^2 / (2 l^2) ); else if( x < rc2 ) -z + a + b*x + c*x^2 + d*x^3; else z @ A Gaussian bump at x = y = 0, smoothly tapered to a flat plane z = 0.
 plane @ a b c x0 y0 z0 @ a*(x-x0) + b*(y-y0) + c*(z-z0) = 0 @ A plane with normal (a,b,c) going through point (x0,y0,z0)
 plane_wiggle @ a w @ z - a*sin(w*x) = 0 @ A plane with a sinusoidal modulation on z along x.
 sphere @ R @ x^2 + y^2 + z^2 - R^2 = 0 @ A sphere of radius R
 supersphere @ R q @ | x |^q + | y |^q + | z |^q - R^q = 0 @ A supersphere of hyperradius R
-spine @ a, A, B, B2, c @ -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise  @ An approximation to a dendtritic spine
-spine_two @ a, A, B, B2, c @ -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise  @ Another approximation to a dendtritic spine
+spine @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise  @ An approximation to a dendtritic spine
+spine_two @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise  @ Another approximation to a dendtritic spine
 thylakoid @ wB LB lB @ Various, see "(Paquay)"_#Paquay1 @ A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB
 torus @ R r  @  (R - sqrt( x^2 + y^2 ) )^2 + z^2 - r^2  @ A torus with large radius R and small radius r, centered on (0,0,0) :tb(s=@)

--- a/doc/src/neb.txt
+++ b/doc/src/neb.txt
@ -10,28 +10,31 @@ neb command :h3

 [Syntax:]

-neb etol ftol N1 N2 Nevery file-style arg :pre
+neb etol ftol N1 N2 Nevery file-style arg keyword :pre

 etol = stopping tolerance for energy (energy units) :ulb,l
 ftol = stopping tolerance for force (force units) :l
 N1 = max # of iterations (timesteps) to run initial NEB :l
 N2 = max # of iterations (timesteps) to run barrier-climbing NEB :l
 Nevery = print replica energies and reaction coordinates every this many timesteps :l
-file-style= {final} or {each} or {none} :l
+file-style = {final} or {each} or {none} :l
  {final} arg = filename
    filename = file with initial coords for final replica
-      coords for intermediate replicas are linearly interpolated between first and last replica
+      coords for intermediate replicas are linearly interpolated
+      between first and last replica
  {each} arg = filename
-    filename = unique filename for each replica (except first) with its initial coords
-  {none} arg = no argument
-    all replicas assumed to already have their initial coords :pre
+    filename = unique filename for each replica (except first)
+      with its initial coords
+  {none} arg = no argument all replicas assumed to already have
+      their initial coords :pre
+keyword = {verbose}
 :ule

 [Examples:]

 neb 0.1 0.0 1000 500 50 final coords.final
 neb 0.0 0.001 1000 500 50 each coords.initial.$i
-neb 0.0 0.001 1000 500 50 none :pre
+neb 0.0 0.001 1000 500 50 none verbose :pre

 [Description:]

@ -43,8 +46,8 @@ NEB is a method for finding both the atomic configurations and height
 of the energy barrier associated with a transition state, e.g. for an
 atom to perform a diffusive hop from one energy basin to another in a
 coordinated fashion with its neighbors.  The implementation in LAMMPS
-follows the discussion in these 3 papers: "(HenkelmanA)"_#HenkelmanA,
-"(HenkelmanB)"_#HenkelmanB, and "(Nakano)"_#Nakano3.
+follows the discussion in these 4 papers: "(HenkelmanA)"_#HenkelmanA,
+"(HenkelmanB)"_#HenkelmanB, "(Nakano)"_#Nakano3 and "(Maras)"_#Maras2.

 Each replica runs on a partition of one or more processors.  Processor
 partitions are defined at run-time using the -partition command-line
@ -70,18 +73,17 @@ I.e. the simulation domain, the number of atoms, the interaction
 potentials, and the starting configuration when the neb command is
 issued should be the same for every replica.

-In a NEB calculation each atom in a replica is connected to the same
-atom in adjacent replicas by springs, which induce inter-replica
-forces.  These forces are imposed by the "fix neb"_fix_neb.html
-command, which must be used in conjunction with the neb command.  The
-group used to define the fix neb command defines the NEB atoms which
-are the only ones that inter-replica springs are applied to.  If the
-group does not include all atoms, then non-NEB atoms have no
-inter-replica springs and the forces they feel and their motion is
-computed in the usual way due only to other atoms within their
-replica.  Conceptually, the non-NEB atoms provide a background force
-field for the NEB atoms.  They can be allowed to move during the NEB
-minimization procedure (which will typically induce different
+In a NEB calculation each replica is connected to other replicas by
+inter-replica nudging forces.  These forces are imposed by the "fix
+neb"_fix_neb.html command, which must be used in conjunction with the
+neb command.  The group used to define the fix neb command defines the
+NEB atoms which are the only ones that inter-replica springs are
+applied to.  If the group does not include all atoms, then non-NEB
+atoms have no inter-replica springs and the forces they feel and their
+motion is computed in the usual way due only to other atoms within
+their replica.  Conceptually, the non-NEB atoms provide a background
+force field for the NEB atoms.  They can be allowed to move during the
+NEB minimization procedure (which will typically induce different
 coordinates for non-NEB atoms in different replicas), or held fixed
 using other LAMMPS commands such as "fix setforce"_fix_setforce.html.
 Note that the "partition"_partition.html command can be used to invoke
@ -93,33 +95,18 @@ specified in different manners via the {file-style} setting, as
 discussed below.  Only atoms whose initial coordinates should differ
 from the current configuration need be specified.

-Conceptually, the initial configuration for the first replica should
-be a state with all the atoms (NEB and non-NEB) having coordinates on
-one side of the energy barrier.  A perfect energy minimum is not
-required, since atoms in the first replica experience no spring forces
-from the 2nd replica.  Thus the damped dynamics minimization will
-drive the first replica to an energy minimum if it is not already
-there.  However, you will typically get better convergence if the
-initial state is already at a minimum.  For example, for a system with
-a free surface, the surface should be fully relaxed before attempting
-a NEB calculation.
-
-Likewise, the initial configuration of the final replica should be a
-state with all the atoms (NEB and non-NEB) on the other side of the
-energy barrier.  Again, a perfect energy minimum is not required,
-since the atoms in the last replica also experience no spring forces
-from the next-to-last replica, and thus the damped dynamics
-minimization will drive it to an energy minimum.
+Conceptually, the initial and final configurations for the first
+replica should be states on either side of an energy barrier.

 As explained below, the initial configurations of intermediate
 replicas can be atomic coordinates interpolated in a linear fashion
-between the first and last replicas.  This is often adequate state for
+between the first and last replicas.  This is often adequate for
 simple transitions.  For more complex transitions, it may lead to slow
 convergence or even bad results if the minimum energy path (MEP, see
 below) of states over the barrier cannot be correctly converged to
-from such an initial configuration.  In this case, you will want to
-generate initial states for the intermediate replicas that are
-geometrically closer to the MEP and read them in.
+from such an initial path.  In this case, you will want to generate
+initial states for the intermediate replicas that are geometrically
+closer to the MEP and read them in.

 :line

@ -135,10 +122,11 @@ is assigned to be a fraction of the distance.  E.g. if there are 10
 replicas, the 2nd replica will assign a position that is 10% of the
 distance along a line between the starting and final point, and the
 9th replica will assign a position that is 90% of the distance along
-the line.  Note that this procedure to produce consistent coordinates
-across all the replicas, the current coordinates need to be the same
-in all replicas.  LAMMPS does not check for this, but invalid initial
-configurations will likely result if it is not the case.
+the line.  Note that for this procedure to produce consistent
+coordinates across all the replicas, the current coordinates need to
+be the same in all replicas.  LAMMPS does not check for this, but
+invalid initial configurations will likely result if it is not the
+case.

 NOTE: The "distance" between the starting and final point is
 calculated in a minimum-image sense for a periodic simulation box.
@ -150,8 +138,8 @@ interpolation is outside the periodic box, the atom will be wrapped
 back into the box when the NEB calculation begins.

 For a {file-style} setting of {each}, a filename is specified which is
-assumed to be unique to each replica.  This can be done by
-using a variable in the filename, e.g.
+assumed to be unique to each replica.  This can be done by using a
+variable in the filename, e.g.

 variable i equal part
 neb 0.0 0.001 1000 500 50 each coords.initial.$i :pre
@ -198,11 +186,10 @@ The minimizer tolerances for energy and force are set by {etol} and
 A non-zero {etol} means that the NEB calculation will terminate if the
 energy criterion is met by every replica.  The energies being compared
 to {etol} do not include any contribution from the inter-replica
-forces, since these are non-conservative.  A non-zero {ftol} means
-that the NEB calculation will terminate if the force criterion is met
-by every replica.  The forces being compared to {ftol} include the
-inter-replica forces between an atom and its images in adjacent
-replicas.
+nudging forces, since these are non-conservative.  A non-zero {ftol}
+means that the NEB calculation will terminate if the force criterion
+is met by every replica.  The forces being compared to {ftol} include
+the inter-replica nudging forces.

 The maximum number of iterations in each stage is set by {N1} and
 {N2}.  These are effectively timestep counts since each iteration of
@ -220,27 +207,27 @@ finding a good energy barrier.  {N1} and {N2} must both be multiples
 of {Nevery}.

 In the first stage of NEB, the set of replicas should converge toward
-the minimum energy path (MEP) of conformational states that transition
-over the barrier.  The MEP for a barrier is defined as a sequence of
-3N-dimensional states that cross the barrier at its saddle point, each
-of which has a potential energy gradient parallel to the MEP itself.
-The replica states will also be roughly equally spaced along the MEP
-due to the inter-replica spring force added by the "fix
-neb"_fix_neb.html command.
+a minimum energy path (MEP) of conformational states that transition
+over a barrier.  The MEP for a transition is defined as a sequence of
+3N-dimensional states, each of which has a potential energy gradient
+parallel to the MEP itself.  The configuration of highest energy along
+a MEP corresponds to a saddle point.  The replica states will also be
+roughly equally spaced along the MEP due to the inter-replica nugding
+force added by the "fix neb"_fix_neb.html command.

-In the second stage of NEB, the replica with the highest energy
-is selected and the inter-replica forces on it are converted to a
-force that drives its atom coordinates to the top or saddle point of
-the barrier, via the barrier-climbing calculation described in
+In the second stage of NEB, the replica with the highest energy is
+selected and the inter-replica forces on it are converted to a force
+that drives its atom coordinates to the top or saddle point of the
+barrier, via the barrier-climbing calculation described in
 "(HenkelmanB)"_#HenkelmanB.  As before, the other replicas rearrange
 themselves along the MEP so as to be roughly equally spaced.

 When both stages are complete, if the NEB calculation was successful,
-one of the replicas should be an atomic configuration at the top or
-saddle point of the barrier, the potential energies for the set of
-replicas should represent the energy profile of the barrier along the
-MEP, and the configurations of the replicas should be a sequence of
-configurations along the MEP.
+the configurations of the replicas should be along (close to) the MEP
+and the replica with the highest energy should be an atomic
+configuration at (close to) the saddle point of the transition. The
+potential energies for the set of replicas represents the energy
+profile of the transition along the MEP.

 :line

@ -284,9 +271,9 @@ ID2 x2 y2 z2
 ...
 IDN xN yN zN :pre

-The fields are the atom ID, followed by the x,y,z coordinates.
-The lines can be listed in any order.  Additional trailing information
-on the line is OK, such as a comment.
+The fields are the atom ID, followed by the x,y,z coordinates.  The
+lines can be listed in any order.  Additional trailing information on
+the line is OK, such as a comment.

 Note that for a typical NEB calculation you do not need to specify
 initial coordinates for very many atoms to produce differing starting
@ -310,38 +297,54 @@ this case), the print-out to the screen and master log.lammps file
 contains a line of output, printed once every {Nevery} timesteps.  It
 contains the timestep, the maximum force per replica, the maximum
 force per atom (in any replica), potential gradients in the initial,
-final, and climbing replicas, the forward and backward energy barriers,
-the total reaction coordinate (RDT), and the normalized reaction
-coordinate and potential energy of each replica.
+final, and climbing replicas, the forward and backward energy
+barriers, the total reaction coordinate (RDT), and the normalized
+reaction coordinate and potential energy of each replica.

-The "maximum force per replica" is
-the two-norm of the 3N-length force vector for the atoms in each
-replica, maximized across replicas, which is what the {ftol} setting
-is checking against.  In this case, N is all the atoms in each
-replica.  The "maximum force per atom" is the maximum force component
-of any atom in any replica.  The potential gradients are the two-norm
-of the 3N-length force vector solely due to the interaction potential i.e.
-without adding in inter-replica forces. Note that inter-replica forces
-are zero in the initial and final replicas, and only affect
-the direction in the climbing replica. For this reason, the "maximum
-force per replica" is often equal to the potential gradient in the
-climbing replica. In the first stage of NEB, there is no climbing
-replica, and so the potential gradient in the highest energy replica
-is reported, since this replica will become the climbing replica
-in the second stage of NEB.
+The "maximum force per replica" is the two-norm of the 3N-length force
+vector for the atoms in each replica, maximized across replicas, which
+is what the {ftol} setting is checking against.  In this case, N is
+all the atoms in each replica.  The "maximum force per atom" is the
+maximum force component of any atom in any replica.  The potential
+gradients are the two-norm of the 3N-length force vector solely due to
+the interaction potential i.e.  without adding in inter-replica
+forces.

-The "reaction coordinate" (RD) for each
-replica is the two-norm of the 3N-length vector of distances between
-its atoms and the preceding replica's atoms, added to the RD of the
-preceding replica. The RD of the first replica RD1 = 0.0;
-the RD of the final replica RDN = RDT, the total reaction coordinate.
-The normalized RDs are divided by RDT,
-so that they form a monotonically increasing sequence
-from zero to one. When computing RD, N only includes the atoms
-being operated on by the fix neb command.
+The "reaction coordinate" (RD) for each replica is the two-norm of the
+3N-length vector of distances between its atoms and the preceding
+replica's atoms, added to the RD of the preceding replica. The RD of
+the first replica RD1 = 0.0; the RD of the final replica RDN = RDT,
+the total reaction coordinate.  The normalized RDs are divided by RDT,
+so that they form a monotonically increasing sequence from zero to
+one. When computing RD, N only includes the atoms being operated on by
+the fix neb command.
+
+The forward (reverse) energy barrier is the potential energy of the
+highest replica minus the energy of the first (last) replica.
+
+Supplementary informations for all replicas can be printed out to the
+screen and master log.lammps file by adding the verbose keyword. These
+informations include the following.  The "path angle" (pathangle) for
+the replica i which is the angle between the 3N-length vectors (Ri-1 -
+Ri) and (Ri+1 - Ri) (where Ri is the atomic coordinates of replica
+i). A "path angle" of 180 indicates that replicas i-1, i and i+1 are
+aligned.  "angletangrad" is the angle between the 3N-length tangent
+vector and the 3N-length force vector at image i. The tangent vector
+is calculated as in "(HenkelmanA)"_#HenkelmanA for all intermediate
+replicas and at R2 - R1 and RM - RM-1 for the first and last replica,
+respectively.  "anglegrad" is the angle between the 3N-length energy
+gradient vector of replica i and that of replica i+1. It is not
+defined for the final replica and reads nan.  gradV is the norm of the
+energy gradient of image i.  ReplicaForce is the two-norm of the
+3N-length force vector (including nudging forces) for replica i.
+MaxAtomForce is the maximum force component of any atom in replica i.
+
+When a NEB calculation does not converge properly, these suplementary
+informations can help understanding what is going wrong. For instance
+when the path angle becomes accute the definition of tangent used in
+the NEB calculation is questionable and the NEB cannot may diverge
+"(Maras)"_#Maras2.

-The forward (reverse) energy barrier is the potential energy of the highest
-replica minus the energy of the first (last) replica.

 When running on multiple partitions, LAMMPS produces additional log
 files for each partition, e.g. log.lammps.0, log.lammps.1, etc.  For a
@ -396,12 +399,16 @@ This command can only be used if LAMMPS was built with the REPLICA
 package.  See the "Making LAMMPS"_Section_start.html#start_3 section
 for more info on packages.

+:line
+
 [Related commands:]

-"prd"_prd.html, "temper"_temper.html, "fix
-langevin"_fix_langevin.html, "fix viscous"_fix_viscous.html
+"prd"_prd.html, "temper"_temper.html, "fix langevin"_fix_langevin.html,
+"fix viscous"_fix_viscous.html

-[Default:] none
+[Default:]
+
+none

 :line

@ -414,3 +421,7 @@ langevin"_fix_langevin.html, "fix viscous"_fix_viscous.html

 :link(Nakano3)
 [(Nakano)] Nakano, Comp Phys Comm, 178, 280-289 (2008).
+
+:link(Maras2)
+[(Maras)] Maras, Trushin, Stukowski, Ala-Nissila, Jonsson,
+Comp Phys Comm, 205, 13-21 (2016)
--- a/doc/src/package.txt
+++ b/doc/src/package.txt
@ -574,9 +574,9 @@ is used.  If it is not used, you must invoke the package intel
 command in your input script or or via the "-pk intel" "command-line
 switch"_Section_start.html#start_7.

-For the KOKKOS package, the option defaults neigh = full, neigh/qeq
- = full, newton = off, binsize = 0.0, and comm = device.  These settings
- are made automatically by the required "-k on" "command-line
+For the KOKKOS package, the option defaults neigh = full,
+neigh/qeq = full, newton = off, binsize = 0.0, and comm = device.
+These settings are made automatically by the required "-k on" "command-line
 switch"_Section_start.html#start_7.  You can change them bu using the
 package kokkos command in your input script or via the "-pk kokkos"
 "command-line switch"_Section_start.html#start_7.
--- a/doc/src/pair_agni.txt
+++ b/doc/src/pair_agni.txt
@ -40,8 +40,8 @@ vectorial atomic forces.

 Only a single pair_coeff command is used with the {agni} style which
 specifies an AGNI potential file containing the parameters of the
-force field for the needed elements. These are mapped to LAMMPS atom 
-types by specifying N additional arguments after the filename in the 
+force field for the needed elements. These are mapped to LAMMPS atom
+types by specifying N additional arguments after the filename in the
 pair_coeff command, where N is the number of LAMMPS atom types:

 filename
@ -52,13 +52,13 @@ to specify the path for the force field file.

 An AGNI force field is fully specified by the filename which contains the
 parameters of the force field, i.e., the reference training environments
-used to construct the machine learning force field. Example force field 
-and input files are provided in the examples/USER/misc/agni directory. 
+used to construct the machine learning force field. Example force field
+and input files are provided in the examples/USER/misc/agni directory.

 :line

-Styles with {omp} suffix is functionally the same as the corresponding 
-style without the suffix. They have been optimized to run faster, depending 
+Styles with {omp} suffix is functionally the same as the corresponding
+style without the suffix. They have been optimized to run faster, depending
 on your available hardware, as discussed in "Section 5"_Section_accelerate.html
 of the manual.  The accelerated style takes the same arguments and
 should produce the same results, except for round-off and precision
--- 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.
--- a/doc/src/pair_charmm.txt
+++ b/doc/src/pair_charmm.txt
@ -104,7 +104,15 @@ 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
+NOTE: The newest CHARMM pair styles reset the Coulombic energy
+conversion factor used internally in the code, from the LAMMPS value
+to the CHARMM value, as if it were effectively a parameter of the
+force field.  This is because the CHARMM code uses a slightly
+different value for the this conversion factor in "real
+units"_units.html (Kcal/mole), namely CHARMM = 332.0716, LAMMPS =
+332.06371.  This is to enable more precise agreement by LAMMPS with
+the CHARMM force field energies and forces, when using one of these
+two CHARMM pair styles.

 :c,image(Eqs/pair_charmm.jpg)

--- a/doc/src/pair_dipole.txt
+++ b/doc/src/pair_dipole.txt
@ -71,6 +71,14 @@ and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the
 torques do not act symmetrically.  These formulas are discussed in
 "(Allen)"_#Allen2 and in "(Toukmaji)"_#Toukmaji2.

+Also note, that in the code, all of these terms (except Elj) have a
+C/epsilon prefactor, the same as the Coulombic term in the LJ +
+Coulombic pair styles discussed "here"_pair_lj.html.  C is an
+energy-conversion constant and epsilon is the dielectric constant
+which can be set by the "dielectric"_dielectric.html command.  The
+same is true of the equations that follow for other dipole pair
+styles.
+
 Style {lj/sf/dipole/sf} computes "shifted-force" interactions between
 pairs of particles that each have a charge and/or a point dipole
 moment. In general, a shifted-force potential is a (sligthly) modified
--- a/doc/src/pair_exp6_rx.txt
+++ b/doc/src/pair_exp6_rx.txt
@ -55,33 +55,33 @@ defined in the reaction kinetics files specified with the "fix
 rx"_fix_rx.html command or they must correspond to the tag "1fluid",
 signifying interaction with a product species mixture determined
 through a one-fluid approximation.  The interaction potential is
-weighted by the geometric average of either the mole fraction concentrations 
-or the number of molecules associated with the interacting coarse-grained 
-particles (see the {fractional} or {molecular} weighting pair style options). 
+weighted by the geometric average of either the mole fraction concentrations
+or the number of molecules associated with the interacting coarse-grained
+particles (see the {fractional} or {molecular} weighting pair style options).
 The coarse-grained potential is stored before and after the
 reaction kinetics solver is applied, where the difference is defined
 to be the internal chemical energy (uChem).

-The fourth argument specifies the type of scaling that will be used 
+The fourth argument specifies the type of scaling that will be used
 to scale the EXP-6 parameters as reactions occur.  Currently, there
 are three scaling options:  {exponent}, {polynomial} and {none}.

-Exponent scaling requires two additional arguments for scaling 
+Exponent scaling requires two additional arguments for scaling
 the {Rm} and {epsilon} parameters, respectively.  The scaling factor
-is computed by phi^exponent, where phi is the number of molecules  
-represented by the coarse-grain particle and exponent is specified 
+is computed by phi^exponent, where phi is the number of molecules
+represented by the coarse-grain particle and exponent is specified
 as a pair coefficient argument for {Rm} and {epsilon}, respectively.
-The {Rm} and {epsilon} parameters are multiplied by the scaling 
+The {Rm} and {epsilon} parameters are multiplied by the scaling
 factor to give the scaled interaction parameters for the CG particle.

-Polynomial scaling requires a filename to be specified as a pair 
+Polynomial scaling requires a filename to be specified as a pair
 coeff argument.  The file contains the coefficients to a fifth order
-polynomial for the {alpha}, {epsilon} and {Rm} parameters that depend 
-upon phi (the number of molecules represented by the CG particle). 
+polynomial for the {alpha}, {epsilon} and {Rm} parameters that depend
+upon phi (the number of molecules represented by the CG particle).
 The format of a polynomial file is provided below.

 The {none} option to the scaling does not have any additional pair coeff
-arguments.  This is equivalent to specifying the {exponent} option with 
+arguments.  This is equivalent to specifying the {exponent} option with
 {Rm} and {epsilon} exponents of 0.0 and 0.0, respectively.

 The final argument specifies the interaction cutoff (optional).
@ -102,7 +102,7 @@ parenthesized comments):

 # POLYNOMIAL FILE          (one or more comment or blank lines) :pre
 #  General Functional Form:
-#  A*phi^5 + B*phi^4 + C*phi^3 + D*phi^2 + E*phi + F 
+#  A*phi^5 + B*phi^4 + C*phi^3 + D*phi^2 + E*phi + F
 #
 #  Parameter  A        B         C        D         E        F
                           (blank)
--- a/doc/src/pair_kolmogorov_crespi_z.txt
+++ b/doc/src/pair_kolmogorov_crespi_z.txt
@ -24,25 +24,25 @@ pair_coeff 1 2 kolmogorov/crespi/z  CC.KC      C C :pre

 [Description:]

-The {kolmogorov/crespi/z} style computes the Kolmogorov-Crespi interaction 
-potential as described in "(KC05)"_#KC05. An important simplification is made, 
-which is to take all normals along the z-axis. 
+The {kolmogorov/crespi/z} style computes the Kolmogorov-Crespi interaction
+potential as described in "(KC05)"_#KC05. An important simplification is made,
+which is to take all normals along the z-axis.

 :c,image(Eqs/pair_kolmogorov_crespi_z.jpg)

-It is important to have a suffiently large cutoff to ensure smooth forces. 
-Energies are shifted so that they go continously to zero at the cutoff assuming 
+It is important to have a suffiently large cutoff to ensure smooth forces.
+Energies are shifted so that they go continously to zero at the cutoff assuming
 that the exponential part of {Vij} (first term) decays sufficiently fast.
 This shift is achieved by the last term in the equation for {Vij} above.

-This potential is intended for interactions between two layers of graphene. 
-Therefore, to avoid interaction between layers in multi-layered materials, 
-each layer should have a separate atom type and interactions should only 
+This potential is intended for interactions between two layers of graphene.
+Therefore, to avoid interaction between layers in multi-layered materials,
+each layer should have a separate atom type and interactions should only
 be computed between atom types of neighbouring layers.

-The parameter file (e.g. CC.KC), is intended for use with metal 
-"units"_units.html, with energies in meV. An additional parameter, {S}, 
-is available to facilitate scaling of energies in accordance with 
+The parameter file (e.g. CC.KC), is intended for use with metal
+"units"_units.html, with energies in meV. An additional parameter, {S},
+is available to facilitate scaling of energies in accordance with
 "(vanWijk)"_#vanWijk.

 This potential must be used in combination with hybrid/overlay.
@ -64,7 +64,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.

 :line

-:link(KC05) 
+:link(KC05)
 [(KC05)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)

 :link(vanWijk)
--- a/doc/src/pair_lj_long.txt
+++ b/doc/src/pair_lj_long.txt
@ -7,6 +7,7 @@
 :line

 pair_style lj/long/coul/long command :h3
+pair_style lj/long/coul/long/intel command :h3
 pair_style lj/long/coul/long/omp command :h3
 pair_style lj/long/coul/long/opt command :h3
 pair_style lj/long/tip4p/long command :h3
--- a/doc/src/pair_lj_sf.txt
+++ b/doc/src/pair_lj_sf.txt
@ -1,114 +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 lj/sf command :h3
-pair_style lj/sf/omp command :h3
-
-[Syntax:]
-
-pair_style lj/sf cutoff :pre
-
-cutoff = global cutoff for Lennard-Jones interactions (distance units) :ul
-
-[Examples:]
-
-pair_style lj/sf 2.5
-pair_coeff * * 1.0 1.0
-pair_coeff 1 1 1.0 1.0 3.0 :pre
-
-[Description:]
-
-Style {lj/sf} computes a truncated and force-shifted LJ interaction
-(Shifted Force Lennard-Jones), so that both the potential and the
-force go continuously to zero at the cutoff "(Toxvaerd)"_#Toxvaerd:
-
-:c,image(Eqs/pair_lj_sf.jpg)
-
-The following coefficients must be defined for each pair of atoms
-types via the "pair_coeff"_pair_coeff.html command as in the examples
-above, or in the data file or restart files read by the
-"read_data"_read_data.html or "read_restart"_read_restart.html
-commands, or by mixing as described below:
-
-epsilon (energy units)
-sigma (distance units)
-cutoff (distance units) :ul
-
-The last coefficient is optional. If not specified, the global
-LJ cutoff specified in the pair_style command is used.
-
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed in "Section 5"_Section_accelerate.html
-of the manual.  The accelerated styles take the same arguments and
-should produce the same results, except for round-off and precision
-issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
-
-See "Section 5"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Mixing, shift, table, tail correction, restart, rRESPA info]:
-
-For atom type pairs I,J and I != J, the epsilon and sigma
-coefficients and cutoff distance for this pair style can be mixed.
-Rin is a cutoff value and is mixed like the cutoff. The
-default mix value is {geometric}.  See the "pair_modify" command for
-details.
-
-The "pair_modify"_pair_modify.html shift option is not relevant for
-this pair style, since the pair interaction goes to 0.0 at the cutoff.
-
-The "pair_modify"_pair_modify.html table option is not relevant
-for this pair style.
-
-This pair style does not support the "pair_modify"_pair_modify.html
-tail option for adding long-range tail corrections to energy and
-pressure, since the energy of the pair interaction is smoothed to 0.0
-at the cutoff.
-
-This pair style writes its information to "binary restart
-files"_restart.html, so pair_style and pair_coeff commands do not need
-to be specified in an input script that reads a restart file.
-
-This pair style can only be used via the {pair} keyword of the
-"run_style respa"_run_style.html command.  It does not support the
-{inner}, {middle}, {outer} keywords.
-
-:line
-
-[Restrictions:]
-
-This pair style is part of the USER-MISC package.  It is only enabled
-if LAMMPS was built with that package.  See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
-
-[Related commands:]
-
-"pair_coeff"_pair_coeff.html
-
-[Default:] none
-
-:line
-
-:link(Toxvaerd)
-[(Toxvaerd)] Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011).
--- a/doc/src/pair_lj_smooth_linear.txt
+++ b/doc/src/pair_lj_smooth_linear.txt
@ -11,26 +11,26 @@ pair_style lj/smooth/linear/omp command :h3

 [Syntax:]

-pair_style lj/smooth/linear Rc :pre
+pair_style lj/smooth/linear cutoff :pre

-Rc = cutoff for lj/smooth/linear interactions (distance units) :ul
+cutoff = global cutoff for Lennard-Jones interactions (distance units) :ul

 [Examples:]

-pair_style lj/smooth/linear 5.456108274435118
-pair_coeff * * 0.7242785984051078 2.598146797350056
-pair_coeff 1 1 20.0 1.3 9.0 :pre
+pair_style lj/smooth/linear 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 1 1 0.3 3.0 9.0 :pre

 [Description:]

-Style {lj/smooth/linear} computes a LJ interaction that combines the
-standard 12/6 Lennard-Jones function and subtracts a linear term that
-includes the cutoff distance Rc, as in this formula:
+Style {lj/smooth/linear} computes a truncated and force-shifted LJ
+interaction (aka Shifted Force Lennard-Jones) that combines the
+standard 12/6 Lennard-Jones function and subtracts a linear term based
+on the cutoff distance, so that both, the potential and the force, go
+continuously to zero at the cutoff Rc "(Toxvaerd)"_#Toxvaerd:

 :c,image(Eqs/pair_lj_smooth_linear.jpg)

-At the cutoff Rc, the energy and force (its 1st derivative) will be 0.0.
-
 The following coefficients must be defined for each pair of atoms
 types via the "pair_coeff"_pair_coeff.html command as in the examples
 above, or in the data file or restart files read by the
@ -41,8 +41,8 @@ epsilon (energy units)
 sigma (distance units)
 cutoff (distance units) :ul

-The last coefficient is optional.  If not specified, the global value
-for Rc is used.
+The last coefficient is optional. If not specified, the global
+LJ cutoff specified in the pair_style command is used.

 :line

@ -76,10 +76,11 @@ and cutoff distance can be mixed. The default mix value is geometric.
 See the "pair_modify" command for details.

 This pair style does not support the "pair_modify"_pair_modify.html
-shift option for the energy of the pair interaction.
+shift option for the energy of the pair interaction, since it goes
+to 0.0 at the cutoff by construction.

-The "pair_modify"_pair_modify.html table option is not relevant for
-this pair style.
+The "pair_modify"_pair_modify.html table option is not relevant
+for this pair style.

 This pair style does not support the "pair_modify"_pair_modify.html
 tail option for adding long-range tail corrections to energy and
@ -103,3 +104,8 @@ This pair style can only be used via the {pair} keyword of the
 "pair_coeff"_pair_coeff.html, "pair lj/smooth"_pair_lj_smooth.html

 [Default:] none
+
+:line
+
+:link(Toxvaerd)
+[(Toxvaerd)] Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011).
--- a/doc/src/pair_morse.txt
+++ b/doc/src/pair_morse.txt
@ -26,7 +26,7 @@ args = list of arguments for a particular style :ul
 {morse/smooth/linear} args = cutoff
   cutoff = global cutoff for Morse interactions (distance units)
 {morse/soft} args = n lf cutoff
-   n = soft-core parameter
+   n       = soft-core parameter
   lf      = transformation range is lf < lambda < 1
   cutoff  = global cutoff for Morse interactions (distance units)
 :pre
@ -36,7 +36,7 @@ args = list of arguments for a particular style :ul
 pair_style morse 2.5
 pair_style morse/smooth/linear 2.5
 pair_coeff * * 100.0 2.0 1.5
-pair_coeff 1 1 100.0 2.0 1.5 3.0
+pair_coeff 1 1 100.0 2.0 1.5 3.0 :pre

 pair_style morse/soft 4 0.9 10.0
 pair_coeff * * 100.0 2.0 1.5 1.0
--- a/doc/src/pair_multi_lucy_rx.txt
+++ b/doc/src/pair_multi_lucy_rx.txt
@ -97,9 +97,9 @@ tags must either correspond to the species defined in the reaction
 kinetics files specified with the "fix rx"_fix_rx.html command or they
 must correspond to the tag "1fluid", signifying interaction with a
 product species mixture determined through a one-fluid approximation.
-The interaction potential is weighted by the geometric average of 
-either the mole fraction concentrations or the number of molecules 
-associated with the interacting coarse-grained particles (see the 
+The interaction potential is weighted by the geometric average of
+either the mole fraction concentrations or the number of molecules
+associated with the interacting coarse-grained particles (see the
 {fractional} or {molecular} weighting pair style options). The coarse-grained potential is
 stored before and after the reaction kinetics solver is applied, where
 the difference is defined to be the internal chemical energy (uChem).
--- a/doc/src/pair_oxdna.txt
+++ b/doc/src/pair_oxdna.txt
@ -39,17 +39,17 @@ pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1

 [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 
+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. 
+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-DPhil1 and "(Ouldridge)"_#Ouldridge1
 for a detailed description of the oxDNA force field.

@ -57,8 +57,8 @@ NOTE: These pair styles have to be used together with the related oxDNA bond sty
 {oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of
 "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 
+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.

@ -79,7 +79,7 @@ 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
--- a/doc/src/pair_oxdna2.txt
+++ b/doc/src/pair_oxdna2.txt
@ -45,17 +45,17 @@ 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 
+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. 
+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.

@ -63,7 +63,7 @@ NOTE: These pair styles have to be used together with the related oxDNA2 bond st
 {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 
+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.
@ -86,7 +86,7 @@ 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 
+"bond_style oxdna/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html

 [Default:] none

--- a/doc/src/pair_python.txt
+++ b/doc/src/pair_python.txt
@ -74,7 +74,7 @@ placeholders for atom types that will be used with other potentials.
 The python potential file has to start with the following code:

 from __future__ import print_function
-
+#
 class LAMMPSPairPotential(object):
    def __init__(self):
        self.pmap=dict()
@ -163,9 +163,10 @@ pair_write  1 1 2000 rsq 0.01 2.5 lj1_lj2.table lj :pre

 Note that it is strongly recommended to try to [delete] the potential
 table file before generating it. Since the {pair_write} command will
-always append to a table file, which pair style table will use the
-first match. Thus when changing the potential function in the python
-class, the table pair style will still read the old variant.
+always [append] to a table file, while pair style table will use the
+[first match]. Thus when changing the potential function in the python
+class, the table pair style will still read the old variant unless the
+table file is first deleted.

 After switching the pair style to {table}, the potential tables need
 to be assigned to the LAMMPS atom types like this:
--- a/doc/src/pair_reaxc.txt
+++ b/doc/src/pair_reaxc.txt
@ -8,6 +8,7 @@

 pair_style reax/c command :h3
 pair_style reax/c/kk command :h3
+pair_style reax/c/omp command :h3

 [Syntax:]

--- a/doc/src/pair_snap.txt
+++ b/doc/src/pair_snap.txt
@ -10,7 +10,8 @@ pair_style snap command :h3

 [Syntax:]

-pair_style snap :pre
+pair_style snap
+:pre

 [Examples:]

@ -19,11 +20,11 @@ pair_coeff * * InP.snapcoeff In P InP.snapparam In In P P :pre

 [Description:]

-Style {snap} computes interactions
+Pair style {snap} computes interactions
 using the spectral neighbor analysis potential (SNAP)
 "(Thompson)"_#Thompson20142. Like the GAP framework of Bartok et al.
 "(Bartok2010)"_#Bartok20102, "(Bartok2013)"_#Bartok2013
-it uses bispectrum components
+which uses bispectrum components
 to characterize the local neighborhood of each atom
 in a very general way. The mathematical definition of the
 bispectrum calculation used by SNAP is identical
@ -139,10 +140,15 @@ The default values for these keywords are
 {rmin0} = 0.0
 {diagonalstyle} = 3
 {switchflag} = 0
-{bzeroflag} = 1 :ul
+{bzeroflag} = 1
+{quadraticflag} = 1 :ul

-Detailed definitions of these keywords are given on the "compute
+Detailed definitions for all the keywords are given on the "compute
 sna/atom"_compute_sna_atom.html doc page.
+If {quadraticflag} is set to 1, then the SNAP energy expression includes the quadratic term,
+0.5*B^t.alpha.B, where alpha is a symmetric {K} by {K} matrix.
+The SNAP element file should contain {K}({K}+1)/2 additional coefficients
+for each element, the upper-triangular elements of alpha.

 :line

--- a/doc/src/pair_table_rx.txt
+++ b/doc/src/pair_table_rx.txt
@ -85,9 +85,9 @@ tags must either correspond to the species defined in the reaction
 kinetics files specified with the "fix rx"_fix_rx.html command or they
 must correspond to the tag "1fluid", signifying interaction with a
 product species mixture determined through a one-fluid approximation.
-The interaction potential is weighted by the geometric average of 
-either the mole fraction concentrations or the number of molecules 
-associated with the interacting coarse-grained particles (see the 
+The interaction potential is weighted by the geometric average of
+either the mole fraction concentrations or the number of molecules
+associated with the interacting coarse-grained particles (see the
 {fractional} or {molecular} weighting pair style options). The coarse-grained potential is
 stored before and after the reaction kinetics solver is applied, where
 the difference is defined to be the internal chemical energy (uChem).
--- a/doc/src/pair_vashishta.txt
+++ b/doc/src/pair_vashishta.txt
@ -7,6 +7,7 @@
 :line

 pair_style vashishta command :h3
+pair_style vashishta/gpu command :h3
 pair_style vashishta/omp command :h3
 pair_style vashishta/kk command :h3
 pair_style vashishta/table command :h3
--- a/doc/src/pair_zero.txt
+++ b/doc/src/pair_zero.txt
@ -14,7 +14,7 @@ pair_style zero cutoff {nocoeff} :pre

 zero = style name of this pair style
 cutoff = global cutoff (distance units)
-nocoeff = ignore all pair_coeff parameters (optional) :l
+nocoeff = ignore all pair_coeff parameters (optional) :ul

 [Examples:]

--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@ -49,7 +49,6 @@ Pair Styles :h1
   pair_lj_cubic
   pair_lj_expand
   pair_lj_long
-   pair_lj_sf
   pair_lj_smooth
   pair_lj_smooth_linear
   pair_lj_soft
--- a/doc/src/python.txt
+++ b/doc/src/python.txt
@ -489,7 +489,7 @@ python"_Section_python.html.  Note that it is important that the
 stand-alone LAMMPS executable and the LAMMPS shared library be
 consistent (built from the same source code files) in order for this
 to work.  If the two have been built at different times using
-different source files, problems may occur. 
+different source files, problems may occur.

 [Related commands:]

--- a/doc/src/run_style.txt
+++ b/doc/src/run_style.txt
@ -17,7 +17,7 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
  {verlet/split} args = none
  {respa} args = N n1 n2 ... keyword values ...
    N = # of levels of rRESPA
-    n1, n2, ... = loop factor between rRESPA levels (N-1 values)
+    n1, n2, ... = loop factors between rRESPA levels (N-1 values)
    zero or more keyword/value pairings may be appended to the loop factors
    keyword = {bond} or {angle} or {dihedral} or {improper} or
              {pair} or {inner} or {middle} or {outer} or {hybrid} or {kspace}
@ -55,7 +55,7 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l

 run_style verlet
 run_style respa 4 2 2 2 bond 1 dihedral 2 pair 3 kspace 4
-run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4 :pre
+run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4
 run_style respa 3 4 2 bond 1 hybrid 2 2 1 kspace 3 :pre

 [Description:]
--- a/doc/src/set.txt
+++ b/doc/src/set.txt
@ -80,6 +80,7 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
    value can be an atom-style variable (see below)
  {image} nx ny nz
    nx,ny,nz = which periodic image of the simulation box the atom is in
+    any of nx,ny,nz can be an atom-style variable (see below)
  {bond} value = bond type for all bonds between selected atoms
  {angle} value = angle type for all angles between selected atoms
  {dihedral} value = dihedral type for all dihedrals between selected atoms
@ -363,9 +364,8 @@ A value of -1 means subtract 1 box length to get the true value.
 LAMMPS updates these flags as atoms cross periodic boundaries during
 the simulation.  The flags can be output with atom snapshots via the
 "dump"_dump.html command.  If a value of NULL is specified for any of
-nx,ny,nz, then the current image value for that dimension is
-unchanged.  For non-periodic dimensions only a value of 0 can be
-specified.  This keyword does not allow use of atom-style variables.
+nx,ny,nz, then the current image value for that dimension is unchanged.
+For non-periodic dimensions only a value of 0 can be specified.
 This command can be useful after a system has been equilibrated and
 atoms have diffused one or more box lengths in various directions.
 This command can then reset the image values for atoms so that they
--- a/doc/src/special_bonds.txt
+++ b/doc/src/special_bonds.txt
@ -65,7 +65,13 @@ sense to define permanent bonds between atoms that interact via these
 potentials, though such bonds may exist elsewhere in your system,
 e.g. when using the "pair_style hybrid"_pair_hybrid.html command.
 Thus LAMMPS ignores special_bonds settings when manybody potentials
-are calculated.
+are calculated.  Please note, that the existence of explicit bonds
+for atoms that are described by a manybody potential will alter the
+neigborlist and thus can render the computation of those interactions
+invalid, since those pairs are not only used to determine direct
+pairwise interactions but also neighbors of neighbors and more.
+The recommended course of action is to remove such bonds, or - if
+that is not possible - use a special bonds setting of 1.0 1.0 1.0.

 NOTE: Unlike some commands in LAMMPS, you cannot use this command
 multiple times in an incremental fashion: e.g. to first set the LJ
--- a/doc/src/tutorial_github.txt
+++ b/doc/src/tutorial_github.txt
@ -86,7 +86,7 @@ machine via HTTPS:
 or, if you have set up your GitHub account for using SSH keys, via SSH:

  $ git clone git@github.com:<your user name>/lammps.git :pre
-  
+
 You can find the proper URL by clicking the "Clone or download"-button:

 :c,image(JPG/tutorial_https_block.png)
--- a/doc/src/tutorial_pylammps.txt
+++ b/doc/src/tutorial_pylammps.txt
@ -10,6 +10,7 @@ PyLammps Tutorial :h1

 <!-- RST
 .. contents::
+
 END_RST -->

 Overview :h2
@ -35,7 +36,7 @@ lammps.PyLammps :h4

 higher-level abstraction built on top of original C-Types interface
 manipulation of Python objects
-communication with LAMMPS is hidden from API user 
+communication with LAMMPS is hidden from API user
 shorter, more concise Python
 better IPython integration, designed for quick prototyping :ul

@ -327,7 +328,7 @@ IPyLammps Examples :h2

 Examples of IPython notebooks can be found in the python/examples/pylammps
 subdirectory. To open these notebooks launch {jupyter notebook} inside this
-directory and navigate to one of them. If you compiled and installed 
+directory and navigate to one of them. If you compiled and installed
 a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support
 you should be able to rerun all of these notebooks.

@ -398,19 +399,19 @@ natoms = L.system.natoms :pre
 for i in range(niterations):
    iatom = random.randrange(0, natoms)
    current_atom = L.atoms\[iatom\] :pre
-    
+
    x0, y0 = current_atom.position :pre
-    
+
    dx = deltamove * random.uniform(-1, 1)
    dy = deltamove * random.uniform(-1, 1) :pre
-    
+
    current_atom.position = (x0+dx, y0+dy) :pre
-    
+
    L.run(1, "pre no post no") :pre
-    
+
    e = L.eval("pe")
    energies.append(e) :pre
-    
+
    if e <= elast:
        naccept += 1
        elast = e
@ -459,4 +460,4 @@ Feedback and Contributing :h2
 If you find this Python interface useful, please feel free to provide feedback
 and ideas on how to improve it to Richard Berger (richard.berger@temple.edu). We also
 want to encourage people to write tutorial style IPython notebooks showcasing LAMMPS usage
-and maybe their latest research results. 
+and maybe their latest research results.
--- a/examples/COUPLE/simple/simple.cpp
+++ b/examples/COUPLE/simple/simple.cpp
@ -153,7 +153,7 @@ int main(int narg, char **arg)
    for (int i = 0; i < natoms; i++) type[i] = 1;

    lmp->input->one("delete_atoms group all");
-    lammps_create_atoms(lmp,natoms,NULL,type,x,v);
+    lammps_create_atoms(lmp,natoms,NULL,type,x,v,NULL,0);
    lmp->input->one("run 10");
  }

--- a/examples/USER/cgdna/util/generate.py
+++ b/examples/USER/cgdna/util/generate.py
@ -14,7 +14,7 @@
 ------------------------------------------------------------------------- */

 /* ----------------------------------------------------------------------
-   Contributing author: Oliver Henrich (EPCC, University of Edinburgh)
+   Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
 ------------------------------------------------------------------------- */
 """

--- a/examples/USER/misc/cnp/Cu_Mishin1.eam
+++ b/examples/USER/misc/cnp/Cu_Mishin1.eam
--- a/examples/USER/misc/cnp/in.cnp
+++ b/examples/USER/misc/cnp/in.cnp
@ -0,0 +1,51 @@
+# Generation and relaxation of a partial dislocation in Cu perfect FCC crystal
+
+# Initialization
+units           metal
+boundary        p p p
+atom_style      atomic
+
+# create simulation box and system
+lattice         fcc 3.615  origin 0.01 0.01 0.01 orient x -1 -1 2 orient y 1 1 1 orient z -1 1 0 
+region          mdbox  block 0 3 0.0 14.0 0 84 units lattice
+region          system block 0 3 1.1 13.1 0 84 units lattice
+create_box      2 mdbox
+create_atoms    1 region system
+
+# Define atoms mass and force field
+mass            *  63.54                     
+pair_style      eam/alloy
+pair_coeff      * * Cu_Mishin1.eam Cu Cu
+
+# Delete a plane of atoms along the z direction to generate a partial dislocation
+region          dislocation_atoms block 0 3 7 14 41.9 42.1 units lattice
+delete_atoms    region dislocation_atoms
+region          quarter_up block 0 3 7 11 0 84 units lattice
+group           middle region quarter_up
+
+# specify simulation parameters
+timestep        0.004
+
+# Relax configuration using conjugate gradient
+#min_style cg
+#minimize 1.0e-4 1.0e-6 100 1000
+
+# Setup calculations 
+compute         1 all cnp/atom 3.086
+compute         2 all cna/atom 3.086
+compute         3 all centro/atom fcc
+compute         4 all coord/atom cutoff 3.086
+dump            1 all custom 100 dump.lammpstrj id type xu yu zu c_1 c_2 c_3 c_4 
+
+### Set up thermo display
+thermo          10
+thermo_style    custom step atoms temp press pe ke etotal
+
+# Relax the system performing a langevin dynamics (freeze motion along y 111 direction)
+fix             1 all nve
+fix             2 all langevin 50 1 0.1 699483
+fix             3 all setforce NULL 0.0 NULL
+fix             4 middle setforce 0.0  0.0 0.0
+run             100
+unfix           4
+run             200
--- a/examples/USER/misc/cnp/log.31May17.cnp.g++.4
+++ b/examples/USER/misc/cnp/log.31May17.cnp.g++.4
@ -0,0 +1,185 @@
+LAMMPS (19 May 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# Generation and relaxation of a partial dislocation in Cu perfect FCC crystal
+
+# Initialization
+units           metal
+boundary        p p p
+atom_style      atomic
+
+# create simulation box and system
+lattice         fcc 3.615  origin 0.01 0.01 0.01 orient x -1 -1 2 orient y 1 1 1 orient z -1 1 0
+Lattice spacing in x,y,z = 5.90327 6.26136 5.11238
+region          mdbox  block 0 3 0.0 14.0 0 84 units lattice
+region          system block 0 3 1.1 13.1 0 84 units lattice
+create_box      2 mdbox
+Created orthogonal box = (0 0 0) to (17.7098 87.6591 429.44)
+  1 by 1 by 4 MPI processor grid
+create_atoms    1 region system
+Created 48384 atoms
+
+# Define atoms mass and force field
+mass            *  63.54
+pair_style      eam/alloy
+pair_coeff      * * Cu_Mishin1.eam Cu Cu
+
+# Delete a plane of atoms along the z direction to generate a partial dislocation
+region          dislocation_atoms block 0 3 7 14 41.9 42.1 units lattice
+delete_atoms    region dislocation_atoms
+Deleted 76 atoms, new total = 48308
+region          quarter_up block 0 3 7 11 0 84 units lattice
+group           middle region quarter_up
+16080 atoms in group middle
+
+# specify simulation parameters
+timestep        0.004
+
+# Relax configuration using conjugate gradient
+#min_style cg
+#minimize 1.0e-4 1.0e-6 100 1000
+
+# Setup calculations
+compute         1 all cnp/atom 3.086
+compute         2 all cna/atom 3.086
+compute         3 all centro/atom fcc
+compute         4 all coord/atom cutoff 3.086
+dump            1 all custom 100 dump.lammpstrj id type xu yu zu c_1 c_2 c_3 c_4
+
+### Set up thermo display
+thermo          10
+thermo_style    custom step atoms temp press pe ke etotal
+
+# Relax the system performing a langevin dynamics (freeze motion along y 111 direction)
+fix             1 all nve
+fix             2 all langevin 50 1 0.1 699483
+fix             3 all setforce NULL 0.0 NULL
+fix             4 middle setforce 0.0  0.0 0.0
+run             100
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.50679
+  ghost atom cutoff = 7.50679
+  binsize = 3.75339, bins = 5 24 115
+  5 neighbor lists, perpetual/occasional/extra = 1 4 0
+  (1) pair eam/alloy, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) compute cnp/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) compute cna/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (4) compute centro/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (5) compute coord/atom, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 45.41 | 45.41 | 45.41 Mbytes
+Step Atoms Temp Press PotEng KinEng TotEng 
+       0    48308            0   -3388.0911   -169746.07            0   -169746.07 
+      10    48308      7.35092   -3091.0864   -169715.96    45.900393   -169670.05 
+      20    48308    9.9162268   -2822.7045   -169678.51    61.918604   -169616.59 
+      30    48308    12.351316   -2726.7195   -169666.35    77.123716   -169589.23 
+      40    48308    13.302856    -2703.586    -169662.9     83.06529   -169579.83 
+      50    48308    12.782228   -2706.8662   -169662.36    79.814401   -169582.55 
+      60    48308    12.198179   -2772.4206   -169670.02    76.167503   -169593.86 
+      70    48308    10.663322   -2841.3384   -169677.48    66.583595    -169610.9 
+      80    48308    9.1169804   -2932.3896   -169687.85    56.927974   -169630.92 
+      90    48308    7.2905076   -3029.9433   -169699.09    45.523167   -169653.56 
+     100    48308    5.4063635   -3139.4496   -169711.65    33.758252   -169677.89 
+Loop time of 10.9003 on 4 procs for 100 steps with 48308 atoms
+
+Performance: 3.171 ns/day, 7.570 hours/ns, 9.174 timesteps/s
+31.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 9.8764     | 9.9587     | 10.021     |   1.6 | 91.36
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.1232     | 0.18385    | 0.26683    |  12.1 |  1.69
+Output  | 0.45385    | 0.45451    | 0.45634    |   0.2 |  4.17
+Modify  | 0.25026    | 0.2537     | 0.25744    |   0.5 |  2.33
+Other   |            | 0.04949    |            |       |  0.45
+
+Nlocal:    12077 ave 12096 max 12020 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Nghost:    14204 ave 14261 max 14109 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+Neighs:    814050 ave 818584 max 809212 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+FullNghs:  1.6281e+06 ave 1.63296e+06 max 1.61808e+06 min
+Histogram: 1 0 0 0 0 0 1 0 0 2
+
+Total # of neighbors = 6512400
+Ave neighs/atom = 134.81
+Neighbor list builds = 0
+Dangerous builds = 0
+unfix           4
+run             200
+Per MPI rank memory allocation (min/avg/max) = 45.41 | 45.41 | 45.41 Mbytes
+Step Atoms Temp Press PotEng KinEng TotEng 
+     100    48308    5.4063635   -3139.4496   -169711.65    33.758252   -169677.89 
+     110    48308    15.260795    -2793.119   -169677.24    95.290993   -169581.95 
+     120    48308    18.548656   -2433.1584   -169624.79    115.82096   -169508.97 
+     130    48308     22.15831    -2276.626   -169604.28    138.36025   -169465.92 
+     140    48308    24.393841   -2208.1771   -169596.16    152.31929   -169443.84 
+     150    48308    24.797558   -2173.3145   -169591.43    154.84016   -169436.59 
+     160    48308     24.73371    -2188.909   -169593.08    154.44148   -169438.64 
+     170    48308    24.128467   -2220.3404   -169596.96    150.66225   -169446.29 
+     180    48308    22.975708   -2275.1244   -169602.72    143.46422   -169459.26 
+     190    48308    21.936324   -2348.3762   -169610.59    136.97413   -169473.61 
+     200    48308    20.516249   -2432.8447   -169619.98    128.10694   -169491.87 
+     210    48308    19.000566   -2510.2915   -169628.58    118.64276   -169509.93 
+     220    48308    17.490407    -2597.299   -169638.24    109.21307   -169529.03 
+     230    48308    16.062482   -2684.1203   -169648.31    100.29687   -169548.01 
+     240    48308    14.360342   -2768.2313    -169657.7    89.668411   -169568.03 
+     250    48308    12.802315   -2852.6965   -169666.99    79.939831   -169587.05 
+     260    48308    11.258205   -2944.4533   -169677.52    70.298142   -169607.23 
+     270    48308    9.6159129   -3038.6304   -169688.06    60.043393   -169628.02 
+     280    48308     7.972425   -3129.0826   -169698.03    49.781176   -169648.25 
+     290    48308    6.3752377   -3219.2054   -169708.23    39.808067   -169668.42 
+     300    48308    4.7374688   -3306.1468   -169718.27     29.58156   -169688.69 
+Loop time of 23.0164 on 4 procs for 200 steps with 48308 atoms
+
+Performance: 3.003 ns/day, 7.992 hours/ns, 8.689 timesteps/s
+31.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 20.221     | 20.423     | 20.57      |   3.1 | 88.73
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.27748    | 0.42603    | 0.62832    |  21.4 |  1.85
+Output  | 1.5454     | 1.5473     | 1.5529     |   0.3 |  6.72
+Modify  | 0.48886    | 0.49773    | 0.50842    |   1.1 |  2.16
+Other   |            | 0.1221     |            |       |  0.53
+
+Nlocal:    12077 ave 12096 max 12020 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Nghost:    14204 ave 14261 max 14109 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+Neighs:    814094 ave 818584 max 809212 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+FullNghs:  1.62852e+06 ave 1.63296e+06 max 1.61892e+06 min
+Histogram: 1 0 0 0 0 0 0 1 0 2
+
+Total # of neighbors = 6514094
+Ave neighs/atom = 134.845
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:35
--- a/examples/USER/misc/filter_corotate/in.bpti
+++ b/examples/USER/misc/filter_corotate/in.bpti
@ -28,7 +28,7 @@ thermo          100
 thermo_style    multi
 timestep	8

-run_style respa 3 2 8 bond 1 pair 2 kspace 3
+run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3

 velocity        all create 200.0 12345678 dist uniform
 #dump            dump1 all atom 100 4pti.dump
--- a/examples/USER/misc/filter_corotate/in.peptide
+++ b/examples/USER/misc/filter_corotate/in.peptide
@ -20,7 +20,7 @@ thermo          50

 timestep        8

-run_style respa 3 2 8 bond 1 pair 2 kspace 3
+run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3

 fix             1 all nvt temp 250.0 250.0 100.0 tchain 1
 fix             cor all filter/corotate m 1.0
--- a/examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.1
+++ b/examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.1
@ -1,240 +0,0 @@
-LAMMPS (10 Mar 2017)
-  using 1 OpenMP thread(s) per MPI task
-
-units           real
-
-atom_style      full
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-
-pair_style      lj/charmm/coul/long 8 10
-pair_modify     mix arithmetic
-kspace_style    pppm 1e-4
-
-read_data       data.bpti
-  orthogonal box = (-10 -10 -30) to (50 50 30)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  892 atoms
-  scanning bonds ...
-  4 = max bonds/atom
-  scanning angles ...
-  6 = max angles/atom
-  scanning dihedrals ...
-  18 = max dihedrals/atom
-  scanning impropers ...
-  2 = max impropers/atom
-  reading bonds ...
-  906 bonds
-  reading angles ...
-  1626 angles
-  reading dihedrals ...
-  2501 dihedrals
-  reading impropers ...
-  137 impropers
-  4 = max # of 1-2 neighbors
-  9 = max # of 1-3 neighbors
-  19 = max # of 1-4 neighbors
-  21 = max # of special neighbors
-
-special_bonds   charmm
-neigh_modify    delay 2 every 1
-
-
-# ------------- MINIMIZE ----------
-
-minimize 	1e-4 1e-6 1000 10000
-WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
-PPPM initialization ...
-WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302)
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
-  G vector (1/distance) = 0.203272
-  grid = 16 16 16
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0316399
-  estimated relative force accuracy = 9.52826e-05
-  using double precision FFTs
-  3d grid and FFT values/proc = 9261 4096
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6, bins = 10 10 10
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/charmm/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory usage (min/avg/max) = 17.8596/1/0 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            0   -3075.6498    943.91164   -2131.7381   -380.67776 
-     241            0    -4503.313    749.58662   -3753.7264   -29.045104 
-Loop time of 3.35722 on 1 procs for 241 steps with 892 atoms
-
-99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-Minimization stats:
-  Stopping criterion = energy tolerance
-  Energy initial, next-to-last, final = 
-        -2131.73812515     -3753.43984087     -3753.72636847
-  Force two-norm initial, final = 1086.21 26.3688
-  Force max component initial, final = 310.811 3.92748
-  Final line search alpha, max atom move = 0.00596649 0.0234333
-  Iterations, force evaluations = 241 463
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
-Pair    | 2.5003     | 2.5003     | 2.5003     |   0.0 | 74.48
-Bond    | 0.24287    | 0.24287    | 0.24287    |   0.0 |  7.23
-Kspace  | 0.53428    | 0.53428    | 0.53428    |   0.0 | 15.91
-Neigh   | 0.069765   | 0.069765   | 0.069765   |   0.0 |  2.08
-Comm    | 0.00065374 | 0.00065374 | 0.00065374 |   0.0 |  0.02
-Output  | 0          | 0          | 0          |   0.0 |  0.00
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 0.009358   |            |       |  0.28
-
-Nlocal:    892 ave 892 max 892 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    31 ave 31 max 31 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    148891 ave 148891 max 148891 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 148891
-Ave neighs/atom = 166.918
-Ave special neighs/atom = 10.9395
-Neighbor list builds = 15
-Dangerous builds = 0
-reset_timestep  0
-
-# ------------- RUN ---------------
-
-thermo          100
-thermo_style    multi
-timestep	8
-
-run_style respa 3 2 8 bond 1 pair 2 kspace 3
-Respa levels:
-  1 = bond angle dihedral improper
-  2 = pair
-  3 = kspace
-
-velocity        all create 200.0 12345678 dist uniform
-#dump            dump1 all atom 100 4pti.dump
-
-fix             1 all nvt temp 200 300 25
-fix             cor all filter/corotate m 1.0
-  163 = # of size 2 clusters
-  0 = # of size 3 clusters
-  25 = # of size 4 clusters
-  0 = # of size 5 clusters
-  100 = # of frozen angles
-
-run             1000
-PPPM initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
-  G vector (1/distance) = 0.203272
-  grid = 16 16 16
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0316399
-  estimated relative force accuracy = 9.52826e-05
-  using double precision FFTs
-  3d grid and FFT values/proc = 9261 4096
-Per MPI rank memory usage (min/avg/max) = 19.5425/1/0 Mbytes
---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
-TotEng   =     -3220.3378 KinEng   =       531.1804 Temp     =       200.0000 
-PotEng   =     -3751.5181 E_bond   =        42.2810 E_angle  =       345.2592 
-E_dihed  =       337.8361 E_impro  =        24.2103 E_vdwl   =      -288.5339 
-E_coul   =      -886.3622 E_long   =     -3326.2088 Press    =        83.2283 
---------------- Step      100 ----- CPU =      3.9414 (sec) ----------------
-TotEng   =     -2718.8970 KinEng   =       538.6206 Temp     =       202.8014 
-PotEng   =     -3257.5176 E_bond   =       203.3367 E_angle  =       566.5317 
-E_dihed  =       397.6202 E_impro  =        34.6623 E_vdwl   =      -248.7451 
-E_coul   =      -874.5122 E_long   =     -3336.4111 Press    =       135.8662 
---------------- Step      200 ----- CPU =      7.9028 (sec) ----------------
-TotEng   =     -2660.1406 KinEng   =       626.3319 Temp     =       235.8265 
-PotEng   =     -3286.4725 E_bond   =       209.5147 E_angle  =       591.7773 
-E_dihed  =       388.9591 E_impro  =        29.4992 E_vdwl   =      -243.5808 
-E_coul   =      -923.5115 E_long   =     -3339.1306 Press    =        88.9000 
---------------- Step      300 ----- CPU =     11.8246 (sec) ----------------
-TotEng   =     -2673.8090 KinEng   =       616.7924 Temp     =       232.2346 
-PotEng   =     -3290.6014 E_bond   =       202.8254 E_angle  =       568.6860 
-E_dihed  =       378.4182 E_impro  =        38.2399 E_vdwl   =      -221.3236 
-E_coul   =      -915.3004 E_long   =     -3342.1468 Press    =        78.8527 
---------------- Step      400 ----- CPU =     15.7990 (sec) ----------------
-TotEng   =     -2614.9416 KinEng   =       649.3474 Temp     =       244.4922 
-PotEng   =     -3264.2890 E_bond   =       211.6116 E_angle  =       617.2026 
-E_dihed  =       399.8744 E_impro  =        40.2678 E_vdwl   =      -211.7790 
-E_coul   =      -978.1624 E_long   =     -3343.3041 Press    =        -4.1958 
---------------- Step      500 ----- CPU =     19.8146 (sec) ----------------
-TotEng   =     -2588.6772 KinEng   =       660.1424 Temp     =       248.5568 
-PotEng   =     -3248.8196 E_bond   =       218.4786 E_angle  =       620.8605 
-E_dihed  =       390.3220 E_impro  =        41.6794 E_vdwl   =      -226.3657 
-E_coul   =      -953.1676 E_long   =     -3340.6269 Press    =        99.3200 
---------------- Step      600 ----- CPU =     23.8587 (sec) ----------------
-TotEng   =     -2550.4618 KinEng   =       693.3384 Temp     =       261.0557 
-PotEng   =     -3243.8002 E_bond   =       232.3563 E_angle  =       606.2922 
-E_dihed  =       396.2469 E_impro  =        37.1980 E_vdwl   =      -235.8425 
-E_coul   =      -937.1208 E_long   =     -3342.9303 Press    =       -21.7737 
---------------- Step      700 ----- CPU =     27.8381 (sec) ----------------
-TotEng   =     -2554.4355 KinEng   =       692.8951 Temp     =       260.8888 
-PotEng   =     -3247.3306 E_bond   =       216.3395 E_angle  =       637.7785 
-E_dihed  =       391.5940 E_impro  =        43.1426 E_vdwl   =      -187.6159 
-E_coul   =     -1008.1694 E_long   =     -3340.3998 Press    =        75.1484 
---------------- Step      800 ----- CPU =     31.8039 (sec) ----------------
-TotEng   =     -2508.3551 KinEng   =       699.0766 Temp     =       263.2163 
-PotEng   =     -3207.4317 E_bond   =       241.9936 E_angle  =       641.3631 
-E_dihed  =       386.2198 E_impro  =        43.7793 E_vdwl   =      -217.7523 
-E_coul   =      -964.6070 E_long   =     -3338.4282 Press    =      -127.7337 
---------------- Step      900 ----- CPU =     35.7700 (sec) ----------------
-TotEng   =     -2452.7644 KinEng   =       762.1842 Temp     =       286.9776 
-PotEng   =     -3214.9485 E_bond   =       243.9191 E_angle  =       649.8664 
-E_dihed  =       382.4351 E_impro  =        39.0029 E_vdwl   =      -221.3389 
-E_coul   =      -970.8965 E_long   =     -3337.9366 Press    =       122.7720 
---------------- Step     1000 ----- CPU =     39.7695 (sec) ----------------
-TotEng   =     -2386.6805 KinEng   =       799.0253 Temp     =       300.8490 
-PotEng   =     -3185.7058 E_bond   =       265.3649 E_angle  =       661.7543 
-E_dihed  =       374.6843 E_impro  =        38.6877 E_vdwl   =      -229.2030 
-E_coul   =      -960.7041 E_long   =     -3336.2899 Press    =       -17.9910 
-Loop time of 39.7695 on 1 procs for 1000 steps with 892 atoms
-
-Performance: 17.380 ns/day, 1.381 hours/ns, 25.145 timesteps/s
-99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
-Pair    | 29.169     | 29.169     | 29.169     |   0.0 | 73.34
-Bond    | 7.6249     | 7.6249     | 7.6249     |   0.0 | 19.17
-Kspace  | 1.1525     | 1.1525     | 1.1525     |   0.0 |  2.90
-Neigh   | 0.87606    | 0.87606    | 0.87606    |   0.0 |  2.20
-Comm    | 0.01563    | 0.01563    | 0.01563    |   0.0 |  0.04
-Output  | 0.00048423 | 0.00048423 | 0.00048423 |   0.0 |  0.00
-Modify  | 0.80446    | 0.80446    | 0.80446    |   0.0 |  2.02
-Other   |            | 0.1266     |            |       |  0.32
-
-Nlocal:    892 ave 892 max 892 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    27 ave 27 max 27 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    146206 ave 146206 max 146206 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 146206
-Ave neighs/atom = 163.908
-Ave special neighs/atom = 10.9395
-Neighbor list builds = 186
-Dangerous builds = 0
-
-unfix           cor
-unfix           1
-
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:43
--- a/examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.4
+++ b/examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.4
@ -1,240 +0,0 @@
-LAMMPS (10 Mar 2017)
-  using 1 OpenMP thread(s) per MPI task
-
-units           real
-
-atom_style      full
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-
-pair_style      lj/charmm/coul/long 8 10
-pair_modify     mix arithmetic
-kspace_style    pppm 1e-4
-
-read_data       data.bpti
-  orthogonal box = (-10 -10 -30) to (50 50 30)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  892 atoms
-  scanning bonds ...
-  4 = max bonds/atom
-  scanning angles ...
-  6 = max angles/atom
-  scanning dihedrals ...
-  18 = max dihedrals/atom
-  scanning impropers ...
-  2 = max impropers/atom
-  reading bonds ...
-  906 bonds
-  reading angles ...
-  1626 angles
-  reading dihedrals ...
-  2501 dihedrals
-  reading impropers ...
-  137 impropers
-  4 = max # of 1-2 neighbors
-  9 = max # of 1-3 neighbors
-  19 = max # of 1-4 neighbors
-  21 = max # of special neighbors
-
-special_bonds   charmm
-neigh_modify    delay 2 every 1
-
-
-# ------------- MINIMIZE ----------
-
-minimize 	1e-4 1e-6 1000 10000
-WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
-PPPM initialization ...
-WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302)
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
-  G vector (1/distance) = 0.203272
-  grid = 16 16 16
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0316399
-  estimated relative force accuracy = 9.52826e-05
-  using double precision FFTs
-  3d grid and FFT values/proc = 3549 1024
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6, bins = 10 10 10
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/charmm/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory usage (min/avg/max) = 16.9693/0.981879/0 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            0   -3075.6498    943.91164   -2131.7381   -380.67776 
-     241            0   -4503.3131    749.58666   -3753.7264   -29.045153 
-Loop time of 1.26594 on 4 procs for 241 steps with 892 atoms
-
-99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-Minimization stats:
-  Stopping criterion = energy tolerance
-  Energy initial, next-to-last, final = 
-        -2131.73812515     -3753.43983927     -3753.72640137
-  Force two-norm initial, final = 1086.21 26.3688
-  Force max component initial, final = 310.811 3.92751
-  Final line search alpha, max atom move = 0.00596649 0.0234334
-  Iterations, force evaluations = 241 463
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
-Pair    | 0.34267    | 0.63792    | 0.90268    |  25.2 | 50.39
-Bond    | 0.025776   | 0.063318   | 0.095631   |  10.8 |  5.00
-Kspace  | 0.21904    | 0.51601    | 0.84895    |  31.3 | 40.76
-Neigh   | 0.023185   | 0.023363   | 0.023538   |   0.1 |  1.85
-Comm    | 0.012025   | 0.014189   | 0.016335   |   1.4 |  1.12
-Output  | 0          | 0          | 0          |   0.0 |  0.00
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 0.01114    |            |       |  0.88
-
-Nlocal:    223 ave 323 max 89 min
-Histogram: 1 0 0 0 1 0 0 0 1 1
-Nghost:    613 ave 675 max 557 min
-Histogram: 1 0 0 1 0 1 0 0 0 1
-Neighs:    37222.8 ave 50005 max 20830 min
-Histogram: 1 0 0 0 1 0 0 1 0 1
-
-Total # of neighbors = 148891
-Ave neighs/atom = 166.918
-Ave special neighs/atom = 10.9395
-Neighbor list builds = 15
-Dangerous builds = 0
-reset_timestep  0
-
-# ------------- RUN ---------------
-
-thermo          100
-thermo_style    multi
-timestep	8
-
-run_style respa 3 2 8 bond 1 pair 2 kspace 3
-Respa levels:
-  1 = bond angle dihedral improper
-  2 = pair
-  3 = kspace
-
-velocity        all create 200.0 12345678 dist uniform
-#dump            dump1 all atom 100 4pti.dump
-
-fix             1 all nvt temp 200 300 25
-fix             cor all filter/corotate m 1.0
-  163 = # of size 2 clusters
-  0 = # of size 3 clusters
-  25 = # of size 4 clusters
-  0 = # of size 5 clusters
-  100 = # of frozen angles
-
-run             1000
-PPPM initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
-  G vector (1/distance) = 0.203272
-  grid = 16 16 16
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0316399
-  estimated relative force accuracy = 9.52826e-05
-  using double precision FFTs
-  3d grid and FFT values/proc = 3549 1024
-Per MPI rank memory usage (min/avg/max) = 17.142/0.97212/0 Mbytes
---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
-TotEng   =     -3220.3378 KinEng   =       531.1804 Temp     =       200.0000 
-PotEng   =     -3751.5182 E_bond   =        42.2810 E_angle  =       345.2592 
-E_dihed  =       337.8361 E_impro  =        24.2103 E_vdwl   =      -288.5339 
-E_coul   =      -886.3622 E_long   =     -3326.2088 Press    =        83.2282 
---------------- Step      100 ----- CPU =      1.5457 (sec) ----------------
-TotEng   =     -2718.9184 KinEng   =       538.6205 Temp     =       202.8014 
-PotEng   =     -3257.5389 E_bond   =       203.3365 E_angle  =       566.5311 
-E_dihed  =       397.6202 E_impro  =        34.6621 E_vdwl   =      -248.7451 
-E_coul   =      -874.5326 E_long   =     -3336.4111 Press    =       135.8435 
---------------- Step      200 ----- CPU =      3.0720 (sec) ----------------
-TotEng   =     -2660.1146 KinEng   =       626.3474 Temp     =       235.8323 
-PotEng   =     -3286.4620 E_bond   =       209.5168 E_angle  =       591.7735 
-E_dihed  =       388.9615 E_impro  =        29.5000 E_vdwl   =      -243.5840 
-E_coul   =      -923.4998 E_long   =     -3339.1299 Press    =        88.8857 
---------------- Step      300 ----- CPU =      4.5597 (sec) ----------------
-TotEng   =     -2669.7442 KinEng   =       619.3625 Temp     =       233.2023 
-PotEng   =     -3289.1067 E_bond   =       203.4405 E_angle  =       569.5281 
-E_dihed  =       378.3314 E_impro  =        38.2880 E_vdwl   =      -221.1904 
-E_coul   =      -915.3396 E_long   =     -3342.1646 Press    =        79.3780 
---------------- Step      400 ----- CPU =      5.9808 (sec) ----------------
-TotEng   =     -2618.9975 KinEng   =       644.6145 Temp     =       242.7102 
-PotEng   =     -3263.6119 E_bond   =       209.5864 E_angle  =       618.8954 
-E_dihed  =       401.3798 E_impro  =        39.9064 E_vdwl   =      -212.1271 
-E_coul   =      -977.1589 E_long   =     -3344.0940 Press    =        -7.8938 
---------------- Step      500 ----- CPU =      7.4159 (sec) ----------------
-TotEng   =     -2579.7486 KinEng   =       666.4643 Temp     =       250.9371 
-PotEng   =     -3246.2129 E_bond   =       219.2549 E_angle  =       620.3474 
-E_dihed  =       388.4395 E_impro  =        41.4499 E_vdwl   =      -225.9686 
-E_coul   =      -949.3689 E_long   =     -3340.3672 Press    =       113.2543 
---------------- Step      600 ----- CPU =      8.9252 (sec) ----------------
-TotEng   =     -2535.8235 KinEng   =       708.5919 Temp     =       266.7990 
-PotEng   =     -3244.4154 E_bond   =       243.9451 E_angle  =       606.0866 
-E_dihed  =       400.0562 E_impro  =        33.9708 E_vdwl   =      -223.1319 
-E_coul   =      -964.9940 E_long   =     -3340.3482 Press    =      -102.4475 
---------------- Step      700 ----- CPU =     10.4022 (sec) ----------------
-TotEng   =     -2552.6681 KinEng   =       702.3080 Temp     =       264.4330 
-PotEng   =     -3254.9761 E_bond   =       250.8834 E_angle  =       639.0977 
-E_dihed  =       386.4014 E_impro  =        42.3004 E_vdwl   =      -224.4816 
-E_coul   =     -1011.8551 E_long   =     -3337.3222 Press    =        10.6424 
---------------- Step      800 ----- CPU =     11.8699 (sec) ----------------
-TotEng   =     -2423.5415 KinEng   =       772.1254 Temp     =       290.7206 
-PotEng   =     -3195.6670 E_bond   =       238.5831 E_angle  =       640.9180 
-E_dihed  =       377.7994 E_impro  =        40.3135 E_vdwl   =      -216.5705 
-E_coul   =      -935.1087 E_long   =     -3341.6019 Press    =       -38.2479 
---------------- Step      900 ----- CPU =     13.3548 (sec) ----------------
-TotEng   =     -2394.4779 KinEng   =       766.6895 Temp     =       288.6739 
-PotEng   =     -3161.1673 E_bond   =       284.8428 E_angle  =       671.0959 
-E_dihed  =       380.3406 E_impro  =        51.2975 E_vdwl   =      -219.5211 
-E_coul   =      -990.6305 E_long   =     -3338.5925 Press    =       -15.2279 
---------------- Step     1000 ----- CPU =     14.7908 (sec) ----------------
-TotEng   =     -2340.1471 KinEng   =       799.0198 Temp     =       300.8469 
-PotEng   =     -3139.1669 E_bond   =       271.0389 E_angle  =       683.8278 
-E_dihed  =       407.0795 E_impro  =        39.6209 E_vdwl   =      -230.5355 
-E_coul   =      -974.2981 E_long   =     -3335.9003 Press    =       -94.3420 
-Loop time of 14.7909 on 4 procs for 1000 steps with 892 atoms
-
-Performance: 46.732 ns/day, 0.514 hours/ns, 67.609 timesteps/s
-99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
-Pair    | 4.4184     | 7.5543     | 10.133     |  74.2 | 51.07
-Bond    | 0.94027    | 1.9781     | 2.7492     |  54.4 | 13.37
-Kspace  | 0.45487    | 0.45887    | 0.46343    |   0.4 |  3.10
-Neigh   | 0.28145    | 0.28339    | 0.28539    |   0.3 |  1.92
-Comm    | 0.7515     | 4.1484     | 8.3861     | 135.5 | 28.05
-Output  | 0.00049973 | 0.00055474 | 0.00066924 |   0.0 |  0.00
-Modify  | 0.26165    | 0.31142    | 0.35023    |   6.7 |  2.11
-Other   |            | 0.05572    |            |       |  0.38
-
-Nlocal:    223 ave 313 max 122 min
-Histogram: 1 0 0 1 0 0 0 1 0 1
-Nghost:    584.5 ave 605 max 553 min
-Histogram: 1 0 0 0 0 1 0 0 0 2
-Neighs:    35448 ave 42093 max 25175 min
-Histogram: 1 0 0 0 0 0 1 1 0 1
-
-Total # of neighbors = 141792
-Ave neighs/atom = 158.96
-Ave special neighs/atom = 10.9395
-Neighbor list builds = 186
-Dangerous builds = 0
-
-unfix           cor
-unfix           1
-
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:16
--- a/examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.1
+++ b/examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.1
@ -1,146 +0,0 @@
-LAMMPS (10 Mar 2017)
-  using 1 OpenMP thread(s) per MPI task
-# Solvated 5-mer peptide, run for 8ps in NVT
-
-units           real
-atom_style      full
-
-pair_style      lj/charmm/coul/long 8.0 10.0 10.0
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-kspace_style    pppm 0.0001
-
-read_data       data.peptide
-  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  2004 atoms
-  reading velocities ...
-  2004 velocities
-  scanning bonds ...
-  3 = max bonds/atom
-  scanning angles ...
-  6 = max angles/atom
-  scanning dihedrals ...
-  14 = max dihedrals/atom
-  scanning impropers ...
-  1 = max impropers/atom
-  reading bonds ...
-  1365 bonds
-  reading angles ...
-  786 angles
-  reading dihedrals ...
-  207 dihedrals
-  reading impropers ...
-  12 impropers
-  4 = max # of 1-2 neighbors
-  7 = max # of 1-3 neighbors
-  14 = max # of 1-4 neighbors
-  18 = max # of special neighbors
-
-neighbor        2.0 bin
-neigh_modify    delay 5
-
-thermo          50
-#dump            dump1 all atom 100 peptide.dump
-
-timestep        8
-
-run_style respa 3 2 8 bond 1 pair 2 kspace 3
-Respa levels:
-  1 = bond angle dihedral improper
-  2 = pair
-  3 = kspace
-
-fix             1 all nvt temp 250.0 250.0 100.0 tchain 1
-fix             cor all filter/corotate m 1.0
-  19 = # of size 2 clusters
-  0 = # of size 3 clusters
-  3 = # of size 4 clusters
-  0 = # of size 5 clusters
-  646 = # of frozen angles
-run             1000
-PPPM initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
-  G vector (1/distance) = 0.268725
-  grid = 15 15 15
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0228209
-  estimated relative force accuracy = 6.87243e-05
-  using double precision FFTs
-  3d grid and FFT values/proc = 10648 3375
-Neighbor list info ...
-  update every 1 steps, delay 5 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6, bins = 5 5 5
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/charmm/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory usage (min/avg/max) = 22.6706/1/0 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0     190.0857   -6785.6785    70.391457   -5580.3684    19434.821 
-      50    239.46028   -7546.5667    1092.8874   -5023.9668   -24643.891 
-     100    242.81799   -7125.5527     416.0788   -5259.7139    15525.465 
-     150    235.97108   -7531.9334    932.35464   -5190.6987   -14838.489 
-     200    252.06415   -7195.6011    568.02993   -5122.6064     8841.332 
-     250    249.99431   -7586.5092    881.83491   -5212.0676    -9330.345 
-     300     240.3382   -7333.0933    633.29951   -5264.8395    5137.9757 
-     350    255.34529   -7568.2413    856.46371   -5187.2226    -6206.063 
-     400    242.99276   -7419.9031    713.23943   -5255.8602    2447.0091 
-     450    251.10653    -7622.061    844.20584   -5278.6079   -4906.6559 
-     500    255.59314    -7439.253    710.84907   -5202.3691    1571.0032 
-     550     253.2025   -7660.5101    823.05373    -5325.695    -4551.399 
-     600    249.05313   -7509.6729    741.48104   -5281.2046       992.87 
-     650    251.75984   -7593.6589    847.08244   -5243.4286   -3510.1176 
-     700    249.25027   -7601.9112     794.0912   -5319.6557    305.76021 
-     750      255.415   -7602.2674    822.98524   -5254.3109    -2333.421 
-     800    241.99621   -7643.8878    796.53352   -5402.5008   -298.66565 
-     850     253.6428   -7598.3764    816.45457   -5267.5316   -1905.3478 
-     900    247.20231   -7690.2806    789.75999   -5424.5838   -1331.7228 
-     950    255.92583   -7634.7505    831.18272   -5275.5466   -2186.5117 
-    1000     253.2126   -7647.9526    823.93602    -5312.195   -1189.9659 
-Loop time of 150.664 on 1 procs for 1000 steps with 2004 atoms
-
-Performance: 4.588 ns/day, 5.231 hours/ns, 6.637 timesteps/s
-99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
-Pair    | 135.81     | 135.81     | 135.81     |   0.0 | 90.14
-Bond    | 2.5889     | 2.5889     | 2.5889     |   0.0 |  1.72
-Kspace  | 2.0379     | 2.0379     | 2.0379     |   0.0 |  1.35
-Neigh   | 5.893      | 5.893      | 5.893      |   0.0 |  3.91
-Comm    | 1.6998     | 1.6998     | 1.6998     |   0.0 |  1.13
-Output  | 0.00077915 | 0.00077915 | 0.00077915 |   0.0 |  0.00
-Modify  | 2          | 2          | 2          |   0.0 |  1.33
-Other   |            | 0.6352     |            |       |  0.42
-
-Nlocal:    2004 ave 2004 max 2004 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    11197 ave 11197 max 11197 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    707779 ave 707779 max 707779 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 707779
-Ave neighs/atom = 353.183
-Ave special neighs/atom = 2.34032
-Neighbor list builds = 200
-Dangerous builds = 200
-unfix           cor
-unfix           1
-
-
-
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:02:30
--- a/examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.4
+++ b/examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.4
@ -1,146 +0,0 @@
-LAMMPS (10 Mar 2017)
-  using 1 OpenMP thread(s) per MPI task
-# Solvated 5-mer peptide, run for 8ps in NVT
-
-units           real
-atom_style      full
-
-pair_style      lj/charmm/coul/long 8.0 10.0 10.0
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-kspace_style    pppm 0.0001
-
-read_data       data.peptide
-  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  2004 atoms
-  reading velocities ...
-  2004 velocities
-  scanning bonds ...
-  3 = max bonds/atom
-  scanning angles ...
-  6 = max angles/atom
-  scanning dihedrals ...
-  14 = max dihedrals/atom
-  scanning impropers ...
-  1 = max impropers/atom
-  reading bonds ...
-  1365 bonds
-  reading angles ...
-  786 angles
-  reading dihedrals ...
-  207 dihedrals
-  reading impropers ...
-  12 impropers
-  4 = max # of 1-2 neighbors
-  7 = max # of 1-3 neighbors
-  14 = max # of 1-4 neighbors
-  18 = max # of special neighbors
-
-neighbor        2.0 bin
-neigh_modify    delay 5
-
-thermo          50
-#dump            dump1 all atom 100 peptide.dump
-
-timestep        8
-
-run_style respa 3 2 8 bond 1 pair 2 kspace 3
-Respa levels:
-  1 = bond angle dihedral improper
-  2 = pair
-  3 = kspace
-
-fix             1 all nvt temp 250.0 250.0 100.0 tchain 1
-fix             cor all filter/corotate m 1.0
-  19 = # of size 2 clusters
-  0 = # of size 3 clusters
-  3 = # of size 4 clusters
-  0 = # of size 5 clusters
-  646 = # of frozen angles
-run             1000
-PPPM initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
-  G vector (1/distance) = 0.268725
-  grid = 15 15 15
-  stencil order = 5
-  estimated absolute RMS force accuracy = 0.0228209
-  estimated relative force accuracy = 6.87243e-05
-  using double precision FFTs
-  3d grid and FFT values/proc = 4312 960
-Neighbor list info ...
-  update every 1 steps, delay 5 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6, bins = 5 5 5
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/charmm/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory usage (min/avg/max) = 16.8394/0.98826/0 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0     190.0857   -6785.6785    70.391457   -5580.3684    19434.821 
-      50    239.46028   -7546.5668    1092.8874   -5023.9668   -24643.891 
-     100    242.81819   -7125.5629    416.08082   -5259.7209    15525.244 
-     150    235.94928   -7531.9186    932.50658   -5190.6621   -14842.431 
-     200    255.85551   -7254.4065     568.8803   -5157.9249    8936.8651 
-     250     247.8705   -7607.4583    858.06087   -5269.4711   -9926.0442 
-     300    257.64176    -7267.424     618.5573   -5110.6004    5173.3307 
-     350    251.65439   -7572.3806    821.15745   -5248.7049    -7092.327 
-     400    256.87927   -7414.2145    655.33178    -5225.169    4119.4095 
-     450    257.12393   -7576.5541    853.39773   -5187.9819   -5224.8823 
-     500    242.42371    -7524.705    705.75357   -5371.5455    2111.3878 
-     550    248.97188    -7541.076    792.86994   -5261.7038   -2278.4185 
-     600    249.81862   -7592.0499    767.17722   -5333.3149   -1149.4759 
-     650    253.31349   -7578.2665    813.75975   -5252.0827   -2915.5706 
-     700    256.61152   -7588.1475    761.03356   -5294.9988   -747.88089 
-     750     248.3606    -7660.457    837.71615   -5339.8883   -3072.8311 
-     800    253.81464   -7638.6089     782.4229   -5340.7698    -1025.909 
-     850    245.69185   -7660.9036    795.66792   -5398.3172   -2717.5851 
-     900    249.13156   -7589.4769    806.43464   -5295.5867   -761.63361 
-     950    251.11482   -7691.4981    869.34937    -5322.852   -3282.3031 
-    1000     241.9195   -7630.9899    828.59107   -5358.0033   -95.962685 
-Loop time of 45.5507 on 4 procs for 1000 steps with 2004 atoms
-
-Performance: 15.174 ns/day, 1.582 hours/ns, 21.954 timesteps/s
-99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
-Pair    | 35.545     | 36.674     | 38.004     |  15.8 | 80.51
-Bond    | 0.51302    | 0.67796    | 0.86345    |  18.6 |  1.49
-Kspace  | 0.66031    | 0.68459    | 0.70506    |   2.1 |  1.50
-Neigh   | 1.5605     | 1.5627     | 1.5649     |   0.1 |  3.43
-Comm    | 3.4611     | 4.9841     | 6.294      |  47.2 | 10.94
-Output  | 0.00079799 | 0.00086641 | 0.0010369  |   0.0 |  0.00
-Modify  | 0.67341    | 0.69059    | 0.71186    |   1.7 |  1.52
-Other   |            | 0.2762     |            |       |  0.61
-
-Nlocal:    501 ave 523 max 473 min
-Histogram: 1 0 0 0 0 0 2 0 0 1
-Nghost:    6643.25 ave 6708 max 6566 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-Neighs:    176977 ave 185765 max 164931 min
-Histogram: 1 0 0 0 1 0 0 0 1 1
-
-Total # of neighbors = 707908
-Ave neighs/atom = 353.248
-Ave special neighs/atom = 2.34032
-Neighbor list builds = 200
-Dangerous builds = 200
-unfix           cor
-unfix           1
-
-
-
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:45
--- a/examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.1
+++ b/examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.1
@ -0,0 +1,241 @@
+LAMMPS (20 Jun 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+
+units           real
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+
+pair_style      lj/charmm/coul/long 8 10
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data       data.bpti
+  orthogonal box = (-10 -10 -30) to (50 50 30)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  892 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  906 bonds
+  reading angles ...
+  1626 angles
+  reading dihedrals ...
+  2501 dihedrals
+  reading impropers ...
+  137 impropers
+  4 = max # of 1-2 neighbors
+  9 = max # of 1-3 neighbors
+  19 = max # of 1-4 neighbors
+  21 = max # of special neighbors
+
+special_bonds   charmm
+neigh_modify    delay 2 every 1
+
+
+# ------------- MINIMIZE ----------
+
+minimize 	1e-4 1e-6 1000 10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+PPPM initialization ...
+WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302)
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.203272
+  grid = 16 16 16
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0316399
+  estimated relative force accuracy = 9.52826e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 9261 4096
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 10 10 10
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, 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) = 17.86 | 17.86 | 17.86 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -3075.6498    943.91164   -2131.7381   -380.67776 
+     241            0    -4503.313    749.58662   -3753.7264   -29.045104 
+Loop time of 7.63279 on 1 procs for 241 steps with 892 atoms
+
+32.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+  Stopping criterion = energy tolerance
+  Energy initial, next-to-last, final = 
+        -2131.73812515     -3753.43984087     -3753.72636847
+  Force two-norm initial, final = 1086.21 26.3688
+  Force max component initial, final = 310.811 3.92748
+  Final line search alpha, max atom move = 0.00596649 0.0234333
+  Iterations, force evaluations = 241 463
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.8395     | 5.8395     | 5.8395     |   0.0 | 76.51
+Bond    | 0.46414    | 0.46414    | 0.46414    |   0.0 |  6.08
+Kspace  | 1.1535     | 1.1535     | 1.1535     |   0.0 | 15.11
+Neigh   | 0.14908    | 0.14908    | 0.14908    |   0.0 |  1.95
+Comm    | 0.001932   | 0.001932   | 0.001932   |   0.0 |  0.03
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.02465    |            |       |  0.32
+
+Nlocal:    892 ave 892 max 892 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    31 ave 31 max 31 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    148891 ave 148891 max 148891 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 148891
+Ave neighs/atom = 166.918
+Ave special neighs/atom = 10.9395
+Neighbor list builds = 15
+Dangerous builds = 0
+reset_timestep  0
+
+# ------------- RUN ---------------
+
+thermo          100
+thermo_style    multi
+timestep	8
+
+run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
+Respa levels:
+  1 = bond angle
+  2 = dihedral improper pair
+  3 = kspace
+
+velocity        all create 200.0 12345678 dist uniform
+#dump            dump1 all atom 100 4pti.dump
+
+fix             1 all nvt temp 200 300 25
+fix             cor all filter/corotate m 1.0
+  163 = # of size 2 clusters
+  0 = # of size 3 clusters
+  25 = # of size 4 clusters
+  0 = # of size 5 clusters
+  100 = # of frozen angles
+
+run             1000
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.203272
+  grid = 16 16 16
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0316399
+  estimated relative force accuracy = 9.52826e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 9261 4096
+Per MPI rank memory allocation (min/avg/max) = 19.55 | 19.55 | 19.55 Mbytes
+---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
+TotEng   =     -3220.3378 KinEng   =       531.1804 Temp     =       200.0000 
+PotEng   =     -3751.5181 E_bond   =        42.2810 E_angle  =       345.2592 
+E_dihed  =       337.8361 E_impro  =        24.2103 E_vdwl   =      -288.5339 
+E_coul   =      -886.3622 E_long   =     -3326.2088 Press    =        83.2283 
+---------------- Step      100 ----- CPU =      8.4380 (sec) ----------------
+TotEng   =     -2718.4258 KinEng   =       539.6265 Temp     =       203.1802 
+PotEng   =     -3258.0524 E_bond   =       203.2307 E_angle  =       566.1893 
+E_dihed  =       397.6759 E_impro  =        34.7696 E_vdwl   =      -248.6577 
+E_coul   =      -874.8466 E_long   =     -3336.4135 Press    =       135.8640 
+---------------- Step      200 ----- CPU =     16.9012 (sec) ----------------
+TotEng   =     -2661.9611 KinEng   =       625.0674 Temp     =       235.3503 
+PotEng   =     -3287.0285 E_bond   =       208.1804 E_angle  =       590.8462 
+E_dihed  =       389.1482 E_impro  =        30.5882 E_vdwl   =      -240.5448 
+E_coul   =      -926.3091 E_long   =     -3338.9378 Press    =       103.4738 
+---------------- Step      300 ----- CPU =     25.3046 (sec) ----------------
+TotEng   =     -2662.4139 KinEng   =       622.2647 Temp     =       234.2951 
+PotEng   =     -3284.6785 E_bond   =       202.4210 E_angle  =       573.6793 
+E_dihed  =       382.8919 E_impro  =        41.8973 E_vdwl   =      -218.9895 
+E_coul   =      -924.8414 E_long   =     -3341.7372 Press    =        40.6746 
+---------------- Step      400 ----- CPU =     33.8063 (sec) ----------------
+TotEng   =     -2604.9431 KinEng   =       662.9890 Temp     =       249.6286 
+PotEng   =     -3267.9321 E_bond   =       195.9116 E_angle  =       616.1383 
+E_dihed  =       407.8502 E_impro  =        43.3560 E_vdwl   =      -219.0377 
+E_coul   =      -966.3118 E_long   =     -3345.8387 Press    =       -91.8856 
+---------------- Step      500 ----- CPU =     42.3470 (sec) ----------------
+TotEng   =     -2609.3867 KinEng   =       657.0939 Temp     =       247.4090 
+PotEng   =     -3266.4806 E_bond   =       236.4955 E_angle  =       570.6256 
+E_dihed  =       390.5111 E_impro  =        41.9250 E_vdwl   =      -223.9927 
+E_coul   =      -939.5249 E_long   =     -3342.5201 Press    =       236.7471 
+---------------- Step      600 ----- CPU =     50.9590 (sec) ----------------
+TotEng   =     -2564.7161 KinEng   =       701.8494 Temp     =       264.2603 
+PotEng   =     -3266.5655 E_bond   =       223.5820 E_angle  =       582.7722 
+E_dihed  =       394.6196 E_impro  =        43.8581 E_vdwl   =      -201.7759 
+E_coul   =      -967.4136 E_long   =     -3342.2079 Press    =        26.6595 
+---------------- Step      700 ----- CPU =     59.4791 (sec) ----------------
+TotEng   =     -2510.1142 KinEng   =       689.5931 Temp     =       259.6455 
+PotEng   =     -3199.7072 E_bond   =       254.6476 E_angle  =       611.9715 
+E_dihed  =       403.0624 E_impro  =        44.1360 E_vdwl   =      -205.6377 
+E_coul   =      -964.7455 E_long   =     -3343.1416 Press    =        60.5789 
+---------------- Step      800 ----- CPU =     67.9330 (sec) ----------------
+TotEng   =     -2452.7408 KinEng   =       777.5962 Temp     =       292.7805 
+PotEng   =     -3230.3370 E_bond   =       250.4950 E_angle  =       656.6738 
+E_dihed  =       382.4702 E_impro  =        39.5378 E_vdwl   =      -225.0375 
+E_coul   =      -994.4519 E_long   =     -3340.0244 Press    =       -19.6463 
+---------------- Step      900 ----- CPU =     76.3690 (sec) ----------------
+TotEng   =     -2339.9766 KinEng   =       808.7116 Temp     =       304.4961 
+PotEng   =     -3148.6883 E_bond   =       247.7657 E_angle  =       679.0658 
+E_dihed  =       398.2984 E_impro  =        43.7890 E_vdwl   =      -230.2498 
+E_coul   =      -945.8152 E_long   =     -3341.5422 Press    =       -64.4343 
+---------------- Step     1000 ----- CPU =     84.8757 (sec) ----------------
+TotEng   =     -2329.1819 KinEng   =       822.9820 Temp     =       309.8691 
+PotEng   =     -3152.1639 E_bond   =       264.9609 E_angle  =       691.7104 
+E_dihed  =       385.9914 E_impro  =        40.5525 E_vdwl   =      -230.5182 
+E_coul   =      -954.6203 E_long   =     -3350.2405 Press    =      -146.6649 
+Loop time of 84.8758 on 1 procs for 1000 steps with 892 atoms
+
+Performance: 8.144 ns/day, 2.947 hours/ns, 11.782 timesteps/s
+32.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 68.548     | 68.548     | 68.548     |   0.0 | 80.76
+Bond    | 10.263     | 10.263     | 10.263     |   0.0 | 12.09
+Kspace  | 2.4528     | 2.4528     | 2.4528     |   0.0 |  2.89
+Neigh   | 1.9041     | 1.9041     | 1.9041     |   0.0 |  2.24
+Comm    | 0.044126   | 0.044126   | 0.044126   |   0.0 |  0.05
+Output  | 0.000983   | 0.000983   | 0.000983   |   0.0 |  0.00
+Modify  | 1.4113     | 1.4113     | 1.4113     |   0.0 |  1.66
+Other   |            | 0.2516     |            |       |  0.30
+
+Nlocal:    892 ave 892 max 892 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    38 ave 38 max 38 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    144068 ave 144068 max 144068 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 144068
+Ave neighs/atom = 161.511
+Ave special neighs/atom = 10.9395
+Neighbor list builds = 190
+Dangerous builds = 0
+
+unfix           cor
+unfix           1
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:01:32
--- a/examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.4
+++ b/examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.4
@ -0,0 +1,241 @@
+LAMMPS (20 Jun 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+
+units           real
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+
+pair_style      lj/charmm/coul/long 8 10
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data       data.bpti
+  orthogonal box = (-10 -10 -30) to (50 50 30)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  892 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  906 bonds
+  reading angles ...
+  1626 angles
+  reading dihedrals ...
+  2501 dihedrals
+  reading impropers ...
+  137 impropers
+  4 = max # of 1-2 neighbors
+  9 = max # of 1-3 neighbors
+  19 = max # of 1-4 neighbors
+  21 = max # of special neighbors
+
+special_bonds   charmm
+neigh_modify    delay 2 every 1
+
+
+# ------------- MINIMIZE ----------
+
+minimize 	1e-4 1e-6 1000 10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+PPPM initialization ...
+WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302)
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.203272
+  grid = 16 16 16
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0316399
+  estimated relative force accuracy = 9.52826e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 3549 1024
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 10 10 10
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, 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) = 16.97 | 17.2 | 17.52 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -3075.6498    943.91164   -2131.7381   -380.67776 
+     241            0   -4503.3131    749.58665   -3753.7264   -29.044989 
+Loop time of 3.06327 on 4 procs for 241 steps with 892 atoms
+
+31.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+  Stopping criterion = energy tolerance
+  Energy initial, next-to-last, final = 
+        -2131.73812515      -3753.4398752     -3753.72640446
+  Force two-norm initial, final = 1086.21 26.3687
+  Force max component initial, final = 310.811 3.92765
+  Final line search alpha, max atom move = 0.0059665 0.0234343
+  Iterations, force evaluations = 241 463
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.91458    | 1.6235     | 2.2701     |  38.2 | 53.00
+Bond    | 0.055164   | 0.13173    | 0.19487    |  15.1 |  4.30
+Kspace  | 0.48966    | 1.1993     | 1.9847     |  48.7 | 39.15
+Neigh   | 0.053297   | 0.053442   | 0.053576   |   0.0 |  1.74
+Comm    | 0.031677   | 0.035006   | 0.038061   |   1.5 |  1.14
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.02021    |            |       |  0.66
+
+Nlocal:    223 ave 323 max 89 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Nghost:    613 ave 675 max 557 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+Neighs:    37222.8 ave 50005 max 20830 min
+Histogram: 1 0 0 0 1 0 0 1 0 1
+
+Total # of neighbors = 148891
+Ave neighs/atom = 166.918
+Ave special neighs/atom = 10.9395
+Neighbor list builds = 15
+Dangerous builds = 0
+reset_timestep  0
+
+# ------------- RUN ---------------
+
+thermo          100
+thermo_style    multi
+timestep	8
+
+run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
+Respa levels:
+  1 = bond angle
+  2 = dihedral improper pair
+  3 = kspace
+
+velocity        all create 200.0 12345678 dist uniform
+#dump            dump1 all atom 100 4pti.dump
+
+fix             1 all nvt temp 200 300 25
+fix             cor all filter/corotate m 1.0
+  163 = # of size 2 clusters
+  0 = # of size 3 clusters
+  25 = # of size 4 clusters
+  0 = # of size 5 clusters
+  100 = # of frozen angles
+
+run             1000
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.203272
+  grid = 16 16 16
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0316399
+  estimated relative force accuracy = 9.52826e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 3549 1024
+Per MPI rank memory allocation (min/avg/max) = 17.14 | 17.63 | 18.14 Mbytes
+---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
+TotEng   =     -3220.3378 KinEng   =       531.1804 Temp     =       200.0000 
+PotEng   =     -3751.5182 E_bond   =        42.2810 E_angle  =       345.2593 
+E_dihed  =       337.8361 E_impro  =        24.2103 E_vdwl   =      -288.5339 
+E_coul   =      -886.3622 E_long   =     -3326.2088 Press    =        83.2284 
+---------------- Step      100 ----- CPU =      3.4639 (sec) ----------------
+TotEng   =     -2718.4266 KinEng   =       539.6246 Temp     =       203.1794 
+PotEng   =     -3258.0513 E_bond   =       203.2306 E_angle  =       566.1887 
+E_dihed  =       397.6756 E_impro  =        34.7695 E_vdwl   =      -248.6577 
+E_coul   =      -874.8446 E_long   =     -3336.4135 Press    =       135.8653 
+---------------- Step      200 ----- CPU =      6.8898 (sec) ----------------
+TotEng   =     -2662.0450 KinEng   =       625.0178 Temp     =       235.3317 
+PotEng   =     -3287.0628 E_bond   =       208.1691 E_angle  =       590.8259 
+E_dihed  =       389.1424 E_impro  =        30.5879 E_vdwl   =      -240.5397 
+E_coul   =      -926.3110 E_long   =     -3338.9375 Press    =       103.4843 
+---------------- Step      300 ----- CPU =     10.2791 (sec) ----------------
+TotEng   =     -2661.8829 KinEng   =       623.0352 Temp     =       234.5852 
+PotEng   =     -3284.9181 E_bond   =       203.0274 E_angle  =       573.6583 
+E_dihed  =       383.0124 E_impro  =        41.9015 E_vdwl   =      -218.0696 
+E_coul   =      -926.5806 E_long   =     -3341.8675 Press    =        45.6868 
+---------------- Step      400 ----- CPU =     13.5874 (sec) ----------------
+TotEng   =     -2594.5220 KinEng   =       672.8693 Temp     =       253.3487 
+PotEng   =     -3267.3914 E_bond   =       201.3378 E_angle  =       612.7099 
+E_dihed  =       410.1920 E_impro  =        44.0201 E_vdwl   =      -217.9714 
+E_coul   =      -971.6203 E_long   =     -3346.0595 Press    =      -121.1015 
+---------------- Step      500 ----- CPU =     16.9047 (sec) ----------------
+TotEng   =     -2603.9306 KinEng   =       668.2122 Temp     =       251.5952 
+PotEng   =     -3272.1428 E_bond   =       238.1081 E_angle  =       578.3310 
+E_dihed  =       399.1305 E_impro  =        41.4314 E_vdwl   =      -216.9664 
+E_coul   =      -969.4047 E_long   =     -3342.7729 Press    =       156.7851 
+---------------- Step      600 ----- CPU =     20.1970 (sec) ----------------
+TotEng   =     -2531.1096 KinEng   =       728.1698 Temp     =       274.1705 
+PotEng   =     -3259.2794 E_bond   =       232.8396 E_angle  =       621.3323 
+E_dihed  =       398.1952 E_impro  =        37.0914 E_vdwl   =      -241.6350 
+E_coul   =      -963.1540 E_long   =     -3343.9488 Press    =        58.6784 
+---------------- Step      700 ----- CPU =     23.4360 (sec) ----------------
+TotEng   =     -2499.9495 KinEng   =       742.1211 Temp     =       279.4234 
+PotEng   =     -3242.0705 E_bond   =       240.5622 E_angle  =       582.9270 
+E_dihed  =       396.6246 E_impro  =        36.6510 E_vdwl   =      -228.4925 
+E_coul   =      -926.8734 E_long   =     -3343.4695 Press    =       -60.7458 
+---------------- Step      800 ----- CPU =     26.6709 (sec) ----------------
+TotEng   =     -2426.0217 KinEng   =       760.1083 Temp     =       286.1959 
+PotEng   =     -3186.1300 E_bond   =       266.5863 E_angle  =       652.3401 
+E_dihed  =       380.7407 E_impro  =        34.6861 E_vdwl   =      -225.3729 
+E_coul   =      -953.2382 E_long   =     -3341.8721 Press    =       -57.9824 
+---------------- Step      900 ----- CPU =     29.8152 (sec) ----------------
+TotEng   =     -2419.4636 KinEng   =       780.8361 Temp     =       294.0004 
+PotEng   =     -3200.2996 E_bond   =       269.3237 E_angle  =       665.7171 
+E_dihed  =       408.3527 E_impro  =        43.7811 E_vdwl   =      -254.0696 
+E_coul   =     -1002.0694 E_long   =     -3331.3352 Press    =       -52.0169 
+---------------- Step     1000 ----- CPU =     32.8748 (sec) ----------------
+TotEng   =     -2398.7244 KinEng   =       811.9856 Temp     =       305.7288 
+PotEng   =     -3210.7099 E_bond   =       258.2207 E_angle  =       639.3671 
+E_dihed  =       379.3353 E_impro  =        41.7602 E_vdwl   =      -207.2654 
+E_coul   =      -983.9330 E_long   =     -3338.1948 Press    =        89.4870 
+Loop time of 32.8751 on 4 procs for 1000 steps with 892 atoms
+
+Performance: 21.025 ns/day, 1.141 hours/ns, 30.418 timesteps/s
+31.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 12.449     | 19.023     | 24.612     |  99.6 | 57.86
+Bond    | 1.4547     | 2.8768     | 3.9098     |  61.4 |  8.75
+Kspace  | 1.0537     | 1.0778     | 1.0992     |   2.1 |  3.28
+Neigh   | 0.67542    | 0.67994    | 0.68323    |   0.3 |  2.07
+Comm    | 1.8602     | 8.4515     | 16.516     | 182.9 | 25.71
+Output  | 0.000839   | 0.00147    | 0.003293   |   2.7 |  0.00
+Modify  | 0.56658    | 0.63186    | 0.69304    |   6.8 |  1.92
+Other   |            | 0.133      |            |       |  0.40
+
+Nlocal:    223 ave 339 max 136 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+Nghost:    590 ave 626 max 552 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+Neighs:    36488.2 ave 41965 max 29054 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+
+Total # of neighbors = 145953
+Ave neighs/atom = 163.624
+Ave special neighs/atom = 10.9395
+Neighbor list builds = 189
+Dangerous builds = 0
+
+unfix           cor
+unfix           1
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:36
--- a/examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.1
+++ b/examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.1
@ -0,0 +1,147 @@
+LAMMPS (20 Jun 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide, run for 8ps in NVT
+
+units           real
+atom_style      full
+
+pair_style      lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style    pppm 0.0001
+
+read_data       data.peptide
+  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  2004 atoms
+  reading velocities ...
+  2004 velocities
+  scanning bonds ...
+  3 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  14 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  1365 bonds
+  reading angles ...
+  786 angles
+  reading dihedrals ...
+  207 dihedrals
+  reading impropers ...
+  12 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  14 = max # of 1-4 neighbors
+  18 = max # of special neighbors
+
+neighbor        2.0 bin
+neigh_modify    delay 5
+
+thermo          50
+#dump            dump1 all atom 100 peptide.dump
+
+timestep        8
+
+run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
+Respa levels:
+  1 = bond angle
+  2 = dihedral improper pair
+  3 = kspace
+
+fix             1 all nvt temp 250.0 250.0 100.0 tchain 1
+fix             cor all filter/corotate m 1.0
+  19 = # of size 2 clusters
+  0 = # of size 3 clusters
+  3 = # of size 4 clusters
+  0 = # of size 5 clusters
+  646 = # of frozen angles
+run             1000
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.268725
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0228209
+  estimated relative force accuracy = 6.87243e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 10648 3375
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, 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) = 22.72 | 22.72 | 22.72 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0     190.0857   -6442.7438    70.391457   -5237.4338    20361.984 
+      50    239.47667   -7205.1006    1092.7664   -4682.5237   -23733.122 
+     100    244.63086   -6788.0793    422.97204   -4904.5234    16458.011 
+     150    240.79042   -7267.0791    966.31411   -4863.1107   -13554.894 
+     200    254.77122   -6868.5713    591.00071   -4756.4431    10532.563 
+     250    241.87417   -7264.9349     856.9357   -4963.8743   -9043.4359 
+     300    251.37775      -6976.8    650.55612   -4825.3773    6986.2021 
+     350    250.81494   -7286.7011    880.11184   -4909.0829   -6392.4665 
+     400    247.55673   -7104.4036    701.89555   -4924.4551    4720.7811 
+     450    258.54988   -7215.3011    832.23692   -4839.3759   -3446.3859 
+     500    246.80928   -7151.2468    715.61007   -4962.0464    2637.5769 
+     550    246.20721   -7159.0464    805.24974   -4883.8011    -2725.227 
+     600    250.62483   -7201.7688    806.10076   -4899.2968    770.22352 
+     650    247.59777   -7260.1607    802.97277   -4978.8899   -430.42309 
+     700    246.86951   -7286.2971    825.99865   -4986.3486   -427.88651 
+     750    252.79268   -7307.8572     833.4822   -4965.0605   -614.74372 
+     800    251.73191   -7315.2457    839.59859    -4972.666    952.56448 
+     850    246.75844   -7303.6221    816.67112   -5013.6642   -2055.2823 
+     900    251.00123   -7317.4219    825.12165   -4993.6817   -356.53166 
+     950    259.20822   -7252.3466    854.62611   -4850.1016   -1719.5267 
+    1000    245.72486   -7347.5547    811.48146   -5068.9576    -717.6136 
+Loop time of 357.523 on 1 procs for 1000 steps with 2004 atoms
+
+Performance: 1.933 ns/day, 12.414 hours/ns, 2.797 timesteps/s
+32.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 328.2      | 328.2      | 328.2      |   0.0 | 91.80
+Bond    | 4.4815     | 4.4815     | 4.4815     |   0.0 |  1.25
+Kspace  | 3.9448     | 3.9448     | 3.9448     |   0.0 |  1.10
+Neigh   | 12.457     | 12.457     | 12.457     |   0.0 |  3.48
+Comm    | 3.2147     | 3.2147     | 3.2147     |   0.0 |  0.90
+Output  | 0.001689   | 0.001689   | 0.001689   |   0.0 |  0.00
+Modify  | 3.937      | 3.937      | 3.937      |   0.0 |  1.10
+Other   |            | 1.289      |            |       |  0.36
+
+Nlocal:    2004 ave 2004 max 2004 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    11191 ave 11191 max 11191 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    708610 ave 708610 max 708610 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 708610
+Ave neighs/atom = 353.598
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 200
+Dangerous builds = 200
+unfix           cor
+unfix           1
+
+
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:05:57
--- a/examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.4
+++ b/examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.4
@ -0,0 +1,147 @@
+LAMMPS (20 Jun 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide, run for 8ps in NVT
+
+units           real
+atom_style      full
+
+pair_style      lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style    pppm 0.0001
+
+read_data       data.peptide
+  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  2004 atoms
+  reading velocities ...
+  2004 velocities
+  scanning bonds ...
+  3 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  14 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  1365 bonds
+  reading angles ...
+  786 angles
+  reading dihedrals ...
+  207 dihedrals
+  reading impropers ...
+  12 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  14 = max # of 1-4 neighbors
+  18 = max # of special neighbors
+
+neighbor        2.0 bin
+neigh_modify    delay 5
+
+thermo          50
+#dump            dump1 all atom 100 peptide.dump
+
+timestep        8
+
+run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
+Respa levels:
+  1 = bond angle
+  2 = dihedral improper pair
+  3 = kspace
+
+fix             1 all nvt temp 250.0 250.0 100.0 tchain 1
+fix             cor all filter/corotate m 1.0
+  19 = # of size 2 clusters
+  0 = # of size 3 clusters
+  3 = # of size 4 clusters
+  0 = # of size 5 clusters
+  646 = # of frozen angles
+run             1000
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.268725
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0228209
+  estimated relative force accuracy = 6.87243e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 4312 960
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, 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) = 16.87 | 17.05 | 17.26 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0     190.0857   -6442.7438    70.391457   -5237.4338    20361.984 
+      50    239.47667   -7205.1005    1092.7664   -4682.5237   -23733.122 
+     100    244.63889   -6788.1152    422.96733   -4904.5161    16457.756 
+     150    239.36917   -7258.7053    967.87775   -4861.6589   -13526.261 
+     200    255.14702   -6864.0525    604.58036   -4736.1009      11013.1 
+     250    252.72919   -7303.0966    898.11178   -4896.0494   -8480.8766 
+     300    250.66477   -6989.2603    652.83649   -4839.8141    6209.3375 
+     350    243.30794   -7218.8575    838.31977   -4927.8525   -5180.4928 
+     400     256.3573    -7090.677    706.24197   -4853.8377     3302.577 
+     450    246.15776    -7274.574    834.31676    -4970.557    -3427.971 
+     500    256.28473   -7082.1447    735.42828   -4816.5524     2846.086 
+     550    251.32327    -7341.739    812.64934   -5028.5484   -1786.9277 
+     600    254.57737   -7152.3448    740.52534   -4891.8494    825.91675 
+     650    244.95305   -7207.1136    790.67659   -4953.9295   -520.79769 
+     700     249.4984   -7204.2699    779.06969   -4935.5544   -940.75384 
+     750    248.46962   -7232.1037     791.6642   -4956.9361   -548.12171 
+     800     260.2974   -7293.1982    793.23282   -4945.8435     -1171.26 
+     850    249.79023   -7258.3759    823.56789   -4943.4198   -499.76275 
+     900    249.97237   -7267.0584    784.57992   -4990.0028   -271.33531 
+     950    251.29018   -7261.0642      823.467   -4937.2534    -538.7168 
+    1000    246.05777   -7285.0948    847.90892   -4968.0826   -2613.1854 
+Loop time of 94.6835 on 4 procs for 1000 steps with 2004 atoms
+
+Performance: 7.300 ns/day, 3.288 hours/ns, 10.562 timesteps/s
+37.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 33.389     | 78.508     | 94.639     | 294.1 | 82.92
+Bond    | 0.39957    | 1.104      | 1.4443     |  40.6 |  1.17
+Kspace  | 0.53324    | 1.2631     | 1.5137     |  37.5 |  1.33
+Neigh   | 1.2668     | 3.011      | 3.5942     |  58.0 |  3.18
+Comm    | 3.4563     | 8.8707     | 11.494     | 107.9 |  9.37
+Output  | 0.000435   | 0.0017425  | 0.004136   |   3.4 |  0.00
+Modify  | 0.59335    | 1.4123     | 1.6921     |  39.8 |  1.49
+Other   |            | 0.5129     |            |       |  0.54
+
+Nlocal:    501 ave 515 max 476 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+Nghost:    6681.5 ave 6740 max 6634 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Neighs:    176872 ave 182642 max 168464 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 707486
+Ave neighs/atom = 353.037
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 200
+Dangerous builds = 200
+unfix           cor
+unfix           1
+
+
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:01:53
--- a/examples/USER/misc/grem/lj-temper/0/log.lammps.0
+++ b/examples/USER/misc/grem/lj-temper/0/log.lammps.0
--- a/examples/USER/misc/grem/lj-temper/1/log.lammps.1
+++ b/examples/USER/misc/grem/lj-temper/1/log.lammps.1
--- a/examples/USER/misc/grem/lj-temper/2/log.lammps.2
+++ b/examples/USER/misc/grem/lj-temper/2/log.lammps.2
--- a/examples/USER/misc/grem/lj-temper/3/log.lammps.3
+++ b/examples/USER/misc/grem/lj-temper/3/log.lammps.3
--- a/Show More
+++ b/Show More