new 17Nov16 patch and stable

compute pressure doc change
Merge pull request #278 from akohlmey/pair-agni
2016-11-17 16:51:35 -07:00 · 2016-11-17 16:11:30 -07:00 · 2016-11-17 09:04:31 -07:00 · 2016-11-17 09:02:27 -07:00 · 2016-11-17 09:01:46 -07:00 · 2016-11-17 09:01:37 -07:00
492 changed files with 9707 additions and 1359 deletions
--- a/doc/src/Eqs/pair_agni.jpg
+++ b/doc/src/Eqs/pair_agni.jpg
--- a/doc/src/Eqs/pair_tersoff_mod_c.jpg
+++ b/doc/src/Eqs/pair_tersoff_mod_c.jpg
--- a/doc/src/Eqs/pair_tersoff_mod_c.tex
+++ b/doc/src/Eqs/pair_tersoff_mod_c.tex
@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+
+\begin{document}
+
+\begin{eqnarray*}
+  V_{ij}  & =  & f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) + c_0 \right]
+\end{eqnarray*}
+
+\end{document}
--- a/doc/src/Eqs/pressure.jpg
+++ b/doc/src/Eqs/pressure.jpg
--- a/doc/src/Eqs/pressure.tex
+++ b/doc/src/Eqs/pressure.tex
@ -3,7 +3,7 @@
 \begin{document}

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

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

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

 \end{document}
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="27 Oct 2016 version">
+<META NAME="docnumber" CONTENT="17 Nov 2016 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@ -21,7 +21,7 @@
 <H1></H1>

 LAMMPS Documentation :c,h3
-27 Oct 2016 version :c,h4
+17 Nov 2016 version :c,h4

 Version info: :h4

--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@ -886,6 +886,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "body"_pair_body.html,
 "bop"_pair_bop.html,
 "born (go)"_pair_born.html,
+"born/coul/dsf"_pair_born.html,
+"born/coul/dsf/cs"_pair_born.html,
 "born/coul/long (go)"_pair_born.html,
 "born/coul/long/cs"_pair_born.html,
 "born/coul/msm (o)"_pair_born.html,
@ -979,11 +981,12 @@ KOKKOS, o = USER-OMP, t = OPT.
 "table (gko)"_pair_table.html,
 "tersoff (gkio)"_pair_tersoff.html,
 "tersoff/mod (gko)"_pair_tersoff_mod.html,
+"tersoff/mod/c (o)"_pair_tersoff_mod.html,
 "tersoff/zbl (gko)"_pair_tersoff_zbl.html,
 "tip4p/cut (o)"_pair_coul.html,
 "tip4p/long (o)"_pair_coul.html,
 "tri/lj"_pair_tri_lj.html,
-"vashishta (o)"_pair_vashishta.html,
+"vashishta (ko)"_pair_vashishta.html,
 "vashishta/table (o)"_pair_vashishta.html,
 "yukawa (go)"_pair_yukawa.html,
 "yukawa/colloid (go)"_pair_yukawa_colloid.html,
@ -993,6 +996,7 @@ These are additional pair styles in USER packages, which can be used
 if "LAMMPS is built with the appropriate
 package"_Section_start.html#start_3.

+"agni (o)"_pair_agni.html,
 "awpmd/cut"_pair_awpmd.html,
 "buck/mdf"_pair_mdf.html,
 "coul/cut/soft (o)"_pair_lj_soft.html,
--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@ -2729,7 +2729,7 @@ production runs and is only required during equilibration. This way one
 is consistent with literature (based on the code packages DL_POLY or
 GULP for instance).

-The mentioned energy transfer will typically lead to a a small drift
+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
 temp/chunk"_compute_temp_chunk.html commands.  The internal kinetic
@ -2830,7 +2830,7 @@ temp/drude"_compute_temp_drude.html. This requires also to use the
 command {comm_modify vel yes}.

 Short-range damping of the induced dipole interactions can be achieved
-using Thole functions through the the "pair style
+using Thole functions through the "pair style
 thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html
 with a Coulomb pair style. It may be useful to use {coul/long/cs} or
 similar from the CORESHELL package if the core and Drude particle come
--- a/doc/src/Section_intro.txt
+++ b/doc/src/Section_intro.txt
@ -366,11 +366,11 @@ complementary modeling tasks.
 "DL_POLY"_dlpoly
 "Tinker"_tinker :ul

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

 CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@ -706,7 +706,7 @@ future changes to LAMMPS.
 User packages, such as user-atc or user-omp, have been contributed by
 users, and always begin with the user prefix.  If they are a single
 command (single file), they are typically in the user-misc package.
-Otherwise, they are a a set of files grouped together which add a
+Otherwise, they are a set of files grouped together which add a
 specific functionality to the code.

 User packages don't necessarily meet the requirements of the standard
--- a/doc/src/angle_charmm.txt
+++ b/doc/src/angle_charmm.txt
@ -74,7 +74,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/angle_cosine.txt
+++ b/doc/src/angle_cosine.txt
@ -61,7 +61,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/angle_cosine_delta.txt
+++ b/doc/src/angle_cosine_delta.txt
@ -66,7 +66,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/angle_cosine_periodic.txt
+++ b/doc/src/angle_cosine_periodic.txt
@ -74,7 +74,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/angle_cosine_squared.txt
+++ b/doc/src/angle_cosine_squared.txt
@ -66,7 +66,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/angle_harmonic.txt
+++ b/doc/src/angle_harmonic.txt
@ -65,11 +65,11 @@ more instructions on how to use the accelerated styles effectively.

 :line

-[Restrictions:] none
+[Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
+MOLECULE package.  See the "Making LAMMPS"_Section_start.html#start_3
+section for more info on packages.

 [Related commands:]

--- a/doc/src/angle_hybrid.txt
+++ b/doc/src/angle_hybrid.txt
@ -76,7 +76,7 @@ for specific angle types.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 Unlike other angle styles, the hybrid angle style does not store angle
--- a/doc/src/angle_table.txt
+++ b/doc/src/angle_table.txt
@ -147,7 +147,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/bond_fene.txt
+++ b/doc/src/bond_fene.txt
@ -70,7 +70,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 You typically should specify "special_bonds fene"_special_bonds.html
--- a/doc/src/bond_fene_expand.txt
+++ b/doc/src/bond_fene_expand.txt
@ -73,7 +73,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 You typically should specify "special_bonds fene"_special_bonds.html
--- a/doc/src/bond_harmonic.txt
+++ b/doc/src/bond_harmonic.txt
@ -65,7 +65,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/bond_hybrid.txt
+++ b/doc/src/bond_hybrid.txt
@ -59,7 +59,7 @@ bond types.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 Unlike other bond styles, the hybrid bond style does not store bond
--- a/doc/src/bond_morse.txt
+++ b/doc/src/bond_morse.txt
@ -64,7 +64,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/bond_nonlinear.txt
+++ b/doc/src/bond_nonlinear.txt
@ -64,7 +64,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/bond_quartic.txt
+++ b/doc/src/bond_quartic.txt
@ -99,7 +99,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 The {quartic} style requires that "special_bonds"_special_bonds.html
--- a/doc/src/bond_table.txt
+++ b/doc/src/bond_table.txt
@ -144,7 +144,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/compute_centro_atom.txt
+++ b/doc/src/compute_centro_atom.txt
@ -114,7 +114,7 @@ local defects surrounding the central atom, as described above.  For
 the {axes yes} case, the vector components are also unitless, since
 they represent spatial directions.

-Here are typical centro-symmetry values, from a a nanoindentation
+Here are typical centro-symmetry values, from a nanoindentation
 simulation into gold (FCC).  These were provided by Jon Zimmerman
 (Sandia):

--- a/doc/src/compute_chunk_atom.txt
+++ b/doc/src/compute_chunk_atom.txt
@ -536,7 +536,7 @@ For the {bin/cylinder} style the details are as follows.  If {discard}
 is set to {yes}, an out-of-domain atom will have its chunk ID set to
 0.  If {discard} is set to {no}, the atom will have its chunk ID set
 to the first or last bin in both the radial and axis dimensions.  If
-{discard} is set to {mixed}, which is the default, the the radial
+{discard} is set to {mixed}, which is the default, the radial
 dimension is treated the same as for {discard} = no.  But for the axis
 dimensinon, it will only have its chunk ID set to the first or last
 bin if bins extend to the simulation box boundary in the axis
--- a/doc/src/compute_pressure.txt
+++ b/doc/src/compute_pressure.txt
@ -37,12 +37,18 @@ The pressure is computed by the formula

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

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

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

 The temperature and kinetic energy tensor is not calculated by this
 compute, but rather by the temperature compute specified with the
--- a/doc/src/compute_stress_atom.txt
+++ b/doc/src/compute_stress_atom.txt
@ -60,7 +60,7 @@ produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3
 atoms in a Tersoff 3-body interaction) is assigned in equal portions
 to each atom in the set.  E.g. 1/4 of the dihedral virial to each of
 the 4 atoms, or 1/3 of the fix virial due to SHAKE constraints applied
-to atoms in a a water molecule via the "fix shake"_fix_shake.html
+to atoms in a water molecule via the "fix shake"_fix_shake.html
 command.

 If no extra keywords are listed, all of the terms in this formula are
--- a/doc/src/compute_temp_profile.txt
+++ b/doc/src/compute_temp_profile.txt
@ -69,8 +69,8 @@ velocity for each atom.  Note that if there is only one atom in the
 bin, its thermal velocity will thus be 0.0.

 After the spatially-averaged velocity field has been subtracted from
-each atom, the temperature is calculated by the formula KE = (dim/2 N
- dim*Nx*Ny*Nz) k T, where KE = total kinetic energy of the group of
+each atom, the temperature is calculated by the formula KE = (dim*N
+- dim*Nx*Ny*Nz) k T/2, where KE = total kinetic energy of the group of
 atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the
 simulation, N = number of atoms in the group, k = Boltzmann constant,
 and T = temperature.  The dim*Nx*Ny*Nz term are degrees of freedom
--- a/doc/src/dihedral_charmm.txt
+++ b/doc/src/dihedral_charmm.txt
@ -109,7 +109,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/dihedral_harmonic.txt
+++ b/doc/src/dihedral_harmonic.txt
@ -76,7 +76,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/dihedral_helix.txt
+++ b/doc/src/dihedral_helix.txt
@ -69,7 +69,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/dihedral_hybrid.txt
+++ b/doc/src/dihedral_hybrid.txt
@ -77,7 +77,7 @@ for specific dihedral types.
 [Restrictions:]

 This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 Unlike other dihedral styles, the hybrid dihedral style does not store
--- a/doc/src/dihedral_multi_harmonic.txt
+++ b/doc/src/dihedral_multi_harmonic.txt
@ -63,7 +63,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/dihedral_opls.txt
+++ b/doc/src/dihedral_opls.txt
@ -71,7 +71,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This dihedral style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/dihedral_table.txt
+++ b/doc/src/dihedral_table.txt
@ -154,7 +154,7 @@ radians instead of degrees.  (Note: This changes the way the forces
 are scaled in the 4th column of the data file.)

 The optional "CHECKU" keyword is followed by a filename.  This allows
-the user to save all of the the {Ntable} different entries in the
+the user to save all of the {Ntable} different entries in the
 interpolated energy table to a file to make sure that the interpolated
 function agrees with the user's expectations.  (Note: You can
 temporarily increase the {Ntable} parameter to a high value for this
--- a/doc/src/dump_modify.txt
+++ b/doc/src/dump_modify.txt
@ -165,7 +165,7 @@ extra buffering.

 :line

-The {element} keyword applies only to the the dump {cfg}, {xyz}, and
+The {element} keyword applies only to the dump {cfg}, {xyz}, and
 {image} styles.  It associates element names (e.g. H, C, Fe) with
 LAMMPS atom types.  See the list of element names at the bottom of
 this page.
@ -574,7 +574,7 @@ e.g. its x-component of velocity if the atom-attribute "vx" was
 specified.

 The basic idea of a color map is that the atom-attribute will be
-within a range of values, and that range is associated with a a series
+within a range of values, and that range is associated with a series
 of colors (e.g. red, blue, green).  An atom's specific value (vx =
 -3.2) can then mapped to the series of colors (e.g. halfway between
 red and blue), and a specific color is determined via an interpolation
--- a/doc/src/fix_cmap.txt
+++ b/doc/src/fix_cmap.txt
@ -113,7 +113,7 @@ quantity being minimized), you MUST enable the
 [Restrictions:]

 This fix can only be used if LAMMPS was built with the MOLECULE
-package (which it is by default).  See the "Making
+package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/fix_deform.txt
+++ b/doc/src/fix_deform.txt
@ -150,7 +150,7 @@ initial box length is 100 Angstroms, and V is 10 Angstroms/psec, then
 after 10 psec, the box length will have doubled.  After 20 psec, it
 will have tripled.

-The {erate} style changes a dimension of the the box at a "constant
+The {erate} style changes a dimension of the box at a "constant
 engineering strain rate".  The units of the specified strain rate are
 1/time.  See the "units"_units.html command for the time units
 associated with different choices of simulation units,
--- a/doc/src/fix_langevin.txt
+++ b/doc/src/fix_langevin.txt
@ -237,7 +237,7 @@ described in the papers cited below, the purpose of this method is to
 enable longer timesteps to be used (up to the numerical stability
 limit of the integrator), while still producing the correct Boltzmann
 distribution of atom positions.  It is implemented within LAMMPS, by
-changing how the the random force is applied so that it is composed of
+changing how the random force is applied so that it is composed of
 the average of two random forces representing half-contributions from
 the previous and current time intervals.

--- a/doc/src/fix_lb_fluid.txt
+++ b/doc/src/fix_lb_fluid.txt
@ -233,7 +233,7 @@ present, the speed of sound squared is set equal to (1/3)*(dx/dt)^2.
 Setting a0 > (dx/dt)^2 is not allowed, as this may lead to
 instabilities.

-If the {noise} keyword is used, followed by a a positive temperature
+If the {noise} keyword is used, followed by a positive temperature
 value, and a positive integer random number seed, a thermal
 lattice-Boltzmann algorithm is used.  If {LBtype} is set equal to 1
 (i.e. the standard LB integrator is chosen), the thermal LB algorithm
--- a/doc/src/fix_reax_bonds.txt
+++ b/doc/src/fix_reax_bonds.txt
@ -8,6 +8,7 @@

 fix reax/bonds command :h3
 fix reax/c/bonds command :h3
+fix reax/c/bonds/kk command :h3

 [Syntax:]

@ -47,6 +48,31 @@ commands"_Section_howto.html#howto_15.  No parameter of this fix can
 be used with the {start/stop} keywords of the "run"_run.html command.
 This fix is not invoked during "energy minimization"_minimize.html.

+: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_accelerate"_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_accelerate"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:]

 The fix reax/bonds command requires that the "pair_style
--- a/doc/src/fix_reaxc_species.txt
+++ b/doc/src/fix_reaxc_species.txt
@ -7,6 +7,7 @@
 :line

 fix reax/c/species command :h3
+fix reax/c/species/kk command :h3

 [Syntax:]

@ -129,6 +130,31 @@ No parameter of this fix can be used with the {start/stop} keywords of
 the "run"_run.html command.  This fix is not invoked during "energy
 minimization"_minimize.html.

+: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_accelerate"_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_accelerate"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:]

 The fix species currently only works with
--- a/doc/src/fix_rx.txt
+++ b/doc/src/fix_rx.txt
@ -87,7 +87,7 @@ end of each run. A positive value N means that the diagnostics are reported once
 per N time-steps.

 The diagnostics report the average # of integrator steps and RHS function evaluations
-and run-time per ODE as well as the the average/RMS/min/max per process. If the
+and run-time per ODE as well as the average/RMS/min/max per process. If the
 reporting frequency is 1, the RMS/min/max per ODE are also reported. The per ODE
 statistics can be used to adjust the tolerance and min/max step parameters. The
 statistics per MPI process can be useful to examine any load imbalance caused by the
--- a/doc/src/fix_smd_adjust_dt.txt
+++ b/doc/src/fix_smd_adjust_dt.txt
@ -28,7 +28,7 @@ fix 1 all smd/adjust_dt 0.1 :pre
 The fix calculates a new stable time increment for use with the SMD time integrators.

 The stable time increment is based on multiple conditions. For the SPH pair styles, a
-CFL criterion (Courant, Friedrichs & Lewy, 1928) is evaluated, which determines the the speed of
+CFL criterion (Courant, Friedrichs & Lewy, 1928) is evaluated, which determines the speed of
 sound cannot propagate further than a typical spacing between particles within a single time step to ensure
 no information is lost. For the contact pair styles, a linear analysis of the pair potential determines a
 stable maximum time step.
--- a/doc/src/fix_srd.txt
+++ b/doc/src/fix_srd.txt
@ -101,7 +101,7 @@ particles move in the normal way via a time integration "fix"_fix.html
 with a short timestep dt.  SRD particles advect with a large timestep
 dt_SRD >= dt.

-If the {lamda} keyword is not specified, the the SRD temperature
+If the {lamda} keyword is not specified, the SRD temperature
 {Tsrd} is used in the above formula to compute lamda.  If the {lamda}
 keyword is specified, then the {Tsrd} setting is ignored and the above
 equation is used to compute the SRD temperature.
--- a/doc/src/fix_ttm.txt
+++ b/doc/src/fix_ttm.txt
@ -107,7 +107,7 @@ specified as parameters to the fix.  The other quantities are derived.
 The form of the heat diffusion equation used here is almost the same
 as that in equation 6 of "(Duffy)"_#Duffy, with the exception that the
 electronic density is explicitly reprensented, rather than being part
-of the the specific heat parameter.
+of the specific heat parameter.

 Currently, fix ttm assumes that none of the user-supplied parameters
 will vary with temperature. Note that "(Duffy)"_#Duffy used a tanh()
--- a/doc/src/improper_cvff.txt
+++ b/doc/src/improper_cvff.txt
@ -77,7 +77,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This improper style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/improper_harmonic.txt
+++ b/doc/src/improper_harmonic.txt
@ -81,7 +81,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This improper style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/improper_hybrid.txt
+++ b/doc/src/improper_hybrid.txt
@ -55,7 +55,7 @@ types.
 [Restrictions:]

 This improper style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 Unlike other improper styles, the hybrid improper style does not store
--- a/doc/src/improper_style.txt
+++ b/doc/src/improper_style.txt
@ -27,7 +27,7 @@ between quadruplets of atoms, which remain in force for the duration
 of the simulation.  The list of improper quadruplets is read in by a
 "read_data"_read_data.html or "read_restart"_read_restart.html command
 from a data or restart file.  Note that the ordering of the 4 atoms in
-an improper quadruplet determines the the definition of the improper
+an improper quadruplet determines the definition of the improper
 angle used in the formula for each style.  See the doc pages of
 individual styles for details.

--- a/doc/src/improper_umbrella.txt
+++ b/doc/src/improper_umbrella.txt
@ -74,7 +74,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This improper style can only be used if LAMMPS was built with the
-MOLECULE package (which it is by default).  See the "Making
+MOLECULE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/info.txt
+++ b/doc/src/info.txt
@ -14,7 +14,7 @@ info args :pre

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

 [Examples:]

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

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

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

 The {time} category prints the accumulated CPU and wall time for the
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@ -59,6 +59,7 @@ dump_h5md.html
 dump_image.html
 dump_modify.html
 dump_molfile.html
+dump_nc.html
 echo.html
 fix.html
 fix_modify.html
@ -152,6 +153,7 @@ fix_colvars.html
 fix_controller.html
 fix_deform.html
 fix_deposit.html
+fix_dpd_energy.html
 fix_drag.html
 fix_drude.html
 fix_drude_transform.html
@ -272,6 +274,7 @@ fix_viscosity.html
 fix_viscous.html
 fix_wall.html
 fix_wall_gran.html
+fix_wall_gran_region.html
 fix_wall_piston.html
 fix_wall_reflect.html
 fix_wall_region.html
@ -390,6 +393,7 @@ compute_voronoi_atom.html
 compute_xrd.html

 pair_adp.html
+pair_agni.html
 pair_airebo.html
 pair_awpmd.html
 pair_beck.html
@ -622,3 +626,4 @@ USER/atc/man_unfix_flux.html
 USER/atc/man_unfix_nodes.html
 USER/atc/man_write_atom_weights.html
 USER/atc/man_write_restart.html
+
--- a/doc/src/neb.txt
+++ b/doc/src/neb.txt
@ -284,7 +284,7 @@ ID2 x2 y2 z2
 ...
 IDN xN yN zN :pre

-The fields are the the atom ID, followed by the x,y,z coordinates.
+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.

--- a/doc/src/next.txt
+++ b/doc/src/next.txt
@ -44,7 +44,7 @@ one value from their respective list of values.  A {file}-style
 variable reads the next line from its associated file.  An
 {atomfile}-style variable reads the next set of lines (one per atom)
 from its associated file.  {String-} or {atom}- or {equal}- or
-{world}-style variables cannot be used with the the next command,
+{world}-style variables cannot be used with the next command,
 since they only store a single value.

 When any of the variables in the next command has no more values, a
--- a/doc/src/pair_adp.txt
+++ b/doc/src/pair_adp.txt
@ -168,7 +168,7 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]

 This pair style is part of the MANYBODY package.  It is only enabled
-if LAMMPS was built with that package (which it is by default).
+if LAMMPS was built with that package.

 [Related commands:]

--- a/doc/src/pair_agni.txt
+++ b/doc/src/pair_agni.txt
@ -0,0 +1,128 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+pair_style agni command :h3
+pair_style agni/omp command :h3
+
+[Syntax:]
+
+pair_style agni :pre
+
+[Examples:]
+pair_style      agni
+pair_coeff      * * Al.agni Al
+
+[Description:]
+
+Style {agni} style computes the manybody vectorial force components for
+an atom as
+
+:c,image(Eqs/pair_agni.jpg)
+
+{u} labels the individual components, i.e. x, y or z, and {V} is the
+corresponding atomic fingerprint. {d} is the Euclidean distance between
+any two atomic fingerprints. A total of N_t reference atomic
+environments are considered to construct the force field file. {alpha_t}
+and {l} are the weight coefficients and length scale parameter of the
+non-linear regression model.
+
+The method implements the recently proposed machine learning access to
+atomic forces as discussed extensively in the following publications -
+"(Botu1)"_#Botu2015adaptive and "(Botu2)"_#Botu2015learning. The premise
+of the method is to map the atomic enviornment numerically into a
+fingerprint, and use machine learning methods to create a mapping to the
+vectorial atomic forces.
+
+Only a single pair_coeff command is used with the {agni} style which
+specifies an AGNI potential file containing the parameters of the
+force field for the needed elements. These are mapped to LAMMPS atom 
+types by specifying N additional arguments after the filename in the 
+pair_coeff command, where N is the number of LAMMPS atom types:
+
+filename
+N element names = mapping of AGNI elements to atom types :ul
+
+See the "pair_coeff"_pair_coeff.html doc page for alternate ways
+to specify the path for the force field file.
+
+An AGNI force field is fully specified by the filename which contains the
+parameters of the force field, i.e., the reference training environments
+used to construct the machine learning force field. Example force field 
+and input files are provided in the examples/USER/misc/agni directory. 
+
+:line
+
+Styles with {omp} suffix is functionally the same as the corresponding 
+style without the suffix. They have been optimized to run faster, depending 
+on your available hardware, as discussed in "Section 5"_Section_accelerate.html
+of the manual.  The accelerated style takes the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+The accelerated style is part of the USER-OMP.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated style explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See "Section 5"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+This pair style does not support the "pair_modify"_pair_modify.html
+shift, table, and tail options.
+
+This pair style does not write its information to "binary restart
+files"_restart.html, since it is stored in potential files.  Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the {pair} keyword of the
+"run_style respa"_run_style.html command.  It does not support the
+{inner}, {middle}, {outer} keywords.
+
+:line
+
+[Restrictions:]
+
+Currently, only elemental systems are implemented. Also, the method only
+provides access to the forces and not energies or stresses. However, one
+can access the energy via thermodynamic integration of the forces as
+discussed in "(Botu3)"_#Botu2016construct.  This pair style is part
+of the USER-MISC package. It is only enabled if LAMMPS was built with
+that package. See the "Making LAMMPS"_Section_start.html#start_3 section
+for more info.
+
+The AGNI force field files provided with LAMMPS (see the
+potentials directory) are parameterized for metal "units"_units.html.
+You can use the AGNI potential with any LAMMPS units, but you would need
+to create your own AGNI potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+
+[Default:] none
+
+:line
+
+:link(Botu2015adaptive)
+[(Botu1)] V. Botu and R. Ramprasad, Int. J. Quant. Chem., 115(16), 1074 (2015).
+
+:link(Botu2015learning)
+[(Botu2)] V. Botu and R. Ramprasad, Phys. Rev. B, 92(9), 094306 (2015).
+
+:link(Botu2016construct)
+[(Botu3)] V. Botu, R. Batra, J. Chapman and R. Ramprasad, https://arxiv.org/abs/1610.02098 (2016).
--- a/doc/src/pair_airebo.txt
+++ b/doc/src/pair_airebo.txt
@ -203,9 +203,8 @@ These pair styles can only be used via the {pair} keyword of the
 [Restrictions:]

 These pair styles are part of the MANYBODY package.  They are only
-enabled if LAMMPS was built with that package (which it is by
-default).  See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
+enabled if LAMMPS was built with that package.  See the
+"Making LAMMPS"_Section_start.html#start_3 section for more info.

 These pair potentials require the "newton"_newton.html setting to be
 "on" for pair interactions.
--- a/doc/src/pair_bop.txt
+++ b/doc/src/pair_bop.txt
@ -382,7 +382,7 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]

 These pair styles are part of the MANYBODY package.  They are only
-enabled if LAMMPS was built with that package (which it is by default).
+enabled if LAMMPS was built with that package.
 See the "Making LAMMPS"_Section_start.html#start_3 section for more
 info.

--- a/doc/src/pair_born.txt
+++ b/doc/src/pair_born.txt
@ -19,6 +19,8 @@ pair_style born/coul/msm/omp command :h3
 pair_style born/coul/wolf command :h3
 pair_style born/coul/wolf/gpu command :h3
 pair_style born/coul/wolf/omp command :h3
+pair_style born/coul/dsf command :h3
+pair_style born/coul/dsf/cs command :h3

 [Syntax:]

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

 [Examples:]

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

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

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

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

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

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

 :line

@ -174,9 +189,8 @@ respa"_run_style.html command.  They do not support the {inner},
 [Restrictions:]

 The {born/coul/long} style is part of the KSPACE package.  It is only
-enabled if LAMMPS was built with that package (which it is by
-default).  See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
+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/pair_buck.txt
+++ b/doc/src/pair_buck.txt
@ -186,9 +186,8 @@ respa"_run_style.html command.  They do not support the {inner},

 The {buck/coul/long} style is part of the KSPACE package.  The
 {buck/coul/long/cs} style is part of the CORESHELL package.  They are
-only enabled if LAMMPS was built with that package (which it is by
-default).  See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
+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/pair_comb.txt
+++ b/doc/src/pair_comb.txt
@ -156,7 +156,7 @@ These pair styles can only be used via the {pair} keyword of the
 [Restrictions:]

 These pair styles are part of the MANYBODY package.  It is only enabled
-if LAMMPS was built with that package (which it is by default).  See
+if LAMMPS was built with that package.  See
 the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 These pair styles requires the "newton"_newton.html setting to be "on"
--- a/doc/src/pair_coul.txt
+++ b/doc/src/pair_coul.txt
@ -313,9 +313,8 @@ This pair style can only be used via the {pair} keyword of the

 The {coul/long}, {coul/msm} and {tip4p/long} styles are part of the
 KSPACE package.  The {coul/long/cs} style is part of the CORESHELL
-package.  They are only enabled if LAMMPS was built with that package
-(which it is by default).  See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+package.  They are 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/pair_cs.txt
+++ b/doc/src/pair_cs.txt
@ -8,19 +8,24 @@

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

 [Syntax:]

 pair_style style args :pre

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

 [Examples:]

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

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

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

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

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

 These pair styles are part of the CORESHELL package.  They are only
--- a/doc/src/pair_eam.txt
+++ b/doc/src/pair_eam.txt
@ -412,9 +412,8 @@ The eam pair styles can only be used via the {pair} keyword of the
 [Restrictions:]

 All of these styles except the {eam/cd} style are part of the MANYBODY
-package.  They are only enabled if LAMMPS was built with that package
-(which it is by default).  See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info.
+package.  They are only enabled if LAMMPS was built with that package.
+See the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 The {eam/cd} style is part of the USER-MISC package and also requires
 the MANYBODY package.  It is only enabled if LAMMPS was built with
--- a/doc/src/pair_eim.txt
+++ b/doc/src/pair_eim.txt
@ -159,7 +159,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This style is part of the MANYBODY package.  It is only enabled if
-LAMMPS was built with that package (which it is by default).
+LAMMPS was built with that package.

 [Related commands:]

--- a/doc/src/pair_lcbop.txt
+++ b/doc/src/pair_lcbop.txt
@ -72,7 +72,7 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]

 This pair styles is part of the MANYBODY package.  It is only enabled
-if LAMMPS was built with that package (which it is by default).  See
+if LAMMPS was built with that package.  See
 the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 This pair potential requires the "newton"_newton.html setting to be
--- a/doc/src/pair_nb3b_harmonic.txt
+++ b/doc/src/pair_nb3b_harmonic.txt
@ -113,7 +113,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This pair style can only be used if LAMMPS was built with the MANYBODY
-package (which it is by default).  See the "Making
+package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/pair_polymorphic.txt
+++ b/doc/src/pair_polymorphic.txt
@ -191,7 +191,7 @@ input script. If using read_data, atomic masses must be defined in the
 atomic structure data file.

 This pair style is part of the MANYBODY package. It is only enabled if
-LAMMPS was built with that package (which it is by default). See the
+LAMMPS was built with that package. See the
 "Making LAMMPS"_Section_start.html#start_3 section for more info.

 This pair potential requires the "newtion"_newton.html setting to be
--- a/doc/src/pair_snap.txt
+++ b/doc/src/pair_snap.txt
@ -15,7 +15,7 @@ pair_style snap :pre
 [Examples:]

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

 [Description:]

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

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

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

 :link(Bartok2010)
 [(Bartok2010)] Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
--- a/doc/src/pair_srp.txt
+++ b/doc/src/pair_srp.txt
@ -99,7 +99,7 @@ The optional {exclude} keyword determines if forces are computed
 between first neighbor (directly connected) bonds.  For a setting of
 {no}, first neighbor forces are computed; for {yes} they are not
 computed. A setting of {no} cannot be used with the {min} option for
-distance calculation because the the minimum distance between directly
+distance calculation because the minimum distance between directly
 connected bonds is zero.

 Pair style {srp} turns off normalization of thermodynamic properties
--- a/doc/src/pair_sw.txt
+++ b/doc/src/pair_sw.txt
@ -192,7 +192,7 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]

 This pair style is part of the MANYBODY package.  It is only enabled
-if LAMMPS was built with that package (which it is by default).  See
+if LAMMPS was built with that package.  See
 the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 This pair style requires the "newton"_newton.html setting to be "on"
--- a/doc/src/pair_tersoff.txt
+++ b/doc/src/pair_tersoff.txt
@ -222,7 +222,7 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]

 This pair style is part of the MANYBODY package.  It is only enabled
-if LAMMPS was built with that package (which it is by default).  See
+if LAMMPS was built with that package.  See
 the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 This pair style requires the "newton"_newton.html setting to be "on"
--- a/doc/src/pair_tersoff_mod.txt
+++ b/doc/src/pair_tersoff_mod.txt
@ -7,32 +7,43 @@
 :line

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

 [Syntax:]

 pair_style tersoff/mod :pre

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

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

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

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

 :c,image(Eqs/pair_tersoff_mod.jpg)

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

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

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

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

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

 The Tersoff/MOD potential file must contain entries for all the elements
 listed in the pair_coeff command.  It can also contain entries for
@ -156,7 +170,7 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]

 This pair style is part of the MANYBODY package.  It is only enabled
-if LAMMPS was built with that package (which it is by default).  See
+if LAMMPS was built with that package.  See
 the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 This pair style requires the "newton"_newton.html setting to be "on"
--- a/doc/src/pair_tersoff_zbl.txt
+++ b/doc/src/pair_tersoff_zbl.txt
@ -232,7 +232,7 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]

 This pair style is part of the MANYBODY package.  It is only enabled
-if LAMMPS was built with that package (which it is by default).  See
+if LAMMPS was built with that package.  See
 the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 This pair style requires the "newton"_newton.html setting to be "on"
--- a/doc/src/pair_vashishta.txt
+++ b/doc/src/pair_vashishta.txt
@ -8,6 +8,7 @@

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

@ -212,9 +213,8 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]

 These pair style are part of the MANYBODY package.  They is only
-enabled if LAMMPS was built with that package (which it is by
-default).  See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info.
+enabled if LAMMPS was built with that package.  See the
+"Making LAMMPS"_Section_start.html#start_3 section for more info.

 These pair styles requires the "newton"_newton.html setting to be "on"
 for pair interactions.
--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@ -6,6 +6,7 @@ Pair Styles :h1
   :maxdepth: 1

   pair_adp
+   pair_agni
   pair_airebo
   pair_awpmd
   pair_beck
--- a/doc/src/prd.txt
+++ b/doc/src/prd.txt
@ -214,7 +214,7 @@ when a correlated event occurs during the third stage of the loop
 listed above, i.e. when only one replica is running dynamics.

 When more than one replica detects an event at the end of the same
-event check (every {t_event} steps) during the the second stage, then
+event check (every {t_event} steps) during the second stage, then
 one of them is chosen at random.  The number of coincident events is
 the number of replicas that detected an event.  Normally, this value
 should be 1.  If it is often greater than 1, then either the number of
@ -241,7 +241,7 @@ time was spent in each stage (dephasing, dynamics, quenching, etc).

 Any "dump files"_dump.html defined in the input script, will be
 written to during a PRD run at timesteps corresponding to both
-uncorrelated and correlated events.  This means the the requested dump
+uncorrelated and correlated events.  This means the requested dump
 frequency in the "dump"_dump.html command is ignored.  There will be
 one dump file (per dump command) created for all partitions.

--- a/doc/src/python.txt
+++ b/doc/src/python.txt
@ -188,7 +188,7 @@ is assumed to have been previously loaded by another python command.

 Note that the Python code that is loaded and run must contain a
 function with the specified {func} name.  To operate properly when
-later invoked, the the function code must match the {input} and
+later invoked, the function code must match the {input} and
 {return} and {format} keywords specified by the python command.
 Otherwise Python will generate an error.

--- a/doc/src/read_dump.txt
+++ b/doc/src/read_dump.txt
@ -185,7 +185,7 @@ For dump files in {xyz} format, only the {x}, {y}, and {z} fields are
 supported.  The dump file does not store atom IDs, so these are
 assigned consecutively to the atoms as they appear in the dump file,
 starting from 1.  Thus you should insure that order of atoms is
-consistent from snapshot to snapshot in the the XYZ dump file.  See
+consistent from snapshot to snapshot in the XYZ dump file.  See
 the "dump_modify sort"_dump_modify.html command if the XYZ dump file
 was written by LAMMPS.

@ -195,7 +195,7 @@ velocities, or their respective plugins may not support reading of
 velocities.  The molfile dump files do not store atom IDs, so these
 are assigned consecutively to the atoms as they appear in the dump
 file, starting from 1.  Thus you should insure that order of atoms are
-consistent from snapshot to snapshot in the the molfile dump file.
+consistent from snapshot to snapshot in the molfile dump file.
 See the "dump_modify sort"_dump_modify.html command if the dump file
 was written by LAMMPS.

--- a/doc/src/suffix.txt
+++ b/doc/src/suffix.txt
@ -94,6 +94,13 @@ Of course this is also possible by not using any suffix commands, and
 explictly appending or not appending the suffix to the relevant
 commands in your input script.

+NOTE: The default "run_style"_run_style.html verlet is invoked prior to
+reading the input script and is therefore not affected by a suffix command
+in the input script. The KOKKOS package requires "run_style verlet/kk",
+so when using the KOKKOS package it is necessary to either use the command
+line "-sf kk" command or add an explicit "run_style verlet" command to the
+input script.
+
 [Restrictions:] none

 [Related commands:]
--- a/doc/src/tad.txt
+++ b/doc/src/tad.txt
@ -231,7 +231,7 @@ time was spent in each stage (NEB, dynamics, quenching, etc).

 Any "dump files"_dump.html defined in the input script will be written
 to during a TAD run at timesteps when an event is executed.  This
-means the the requested dump frequency in the "dump"_dump.html command
+means the requested dump frequency in the "dump"_dump.html command
 is ignored.  There will be one dump file (per dump command) created
 for all partitions.  The atom coordinates of the dump snapshot are
 those of the minimum energy configuration resulting from quenching
--- a/doc/src/tutorial_drude.txt
+++ b/doc/src/tutorial_drude.txt
@ -33,7 +33,7 @@ created by the surrounding particles.  Drude oscillators represent
 these dipoles by two fixed charges: the core (DC) and the Drude
 particle (DP) bound by a harmonic potential. The Drude particle can be
 thought of as the electron cloud whose center can be displaced from
-the position of the the corresponding nucleus.
+the position of the corresponding nucleus.

 The sum of the masses of a core-Drude pair should be the mass of the
 initial (unsplit) atom, \(m_C + m_D = m\).  The sum of their charges
--- a/examples/USER/misc/addtorque/in.addtorque
+++ b/examples/USER/misc/addtorque/in.addtorque
@ -0,0 +1,64 @@
+
+units           lj
+lattice         fcc 0.8442
+boundary        f f f
+
+region          ball   sphere   0.0 0.0 0.0 5.0
+region          box    block  -10 10 -10 10 -10 10
+region          half   block  -10  0 -10 10 -10 10
+
+# add molecule ids so we can use chunk/atom
+fix             0   all property/atom mol ghost yes
+
+create_box      2  box
+create_atoms    1  region ball
+
+pair_style      lj/cut 4.0
+pair_coeff      * *  1.0 1.0
+mass            *    1.0
+set             group all mol 1
+
+# label half the sphere with a different type for better visualization
+set             region half   type 2
+
+# use a dynamic group (may require a patch to fix addtorque with older versions of LAMMPS)
+group           ball   dynamic all   region ball
+
+neigh_modify    delay 2  every 1  check yes
+
+minimize        0.0  0.0    1000  10000
+reset_timestep  0
+
+velocity        all create 1.2 12351235
+
+fix             1   all  nve
+fix             2   all  wall/reflect  xlo EDGE xhi EDGE ylo EDGE yhi EDGE zlo EDGE zhi EDGE
+
+compute 1 all chunk/atom molecule
+compute 2 ball omega/chunk 1
+compute 3 ball inertia/chunk 1
+
+# compute rotational kinetic energy: 1/2 * I * omega**2
+variable r_ke_x equal c_2[1][1]*c_2[1][1]*c_3[1][1]*0.5
+variable r_ke_y equal c_2[1][2]*c_2[1][2]*c_3[1][2]*0.5
+variable r_ke_z equal c_2[1][3]*c_2[1][3]*c_3[1][3]*0.5
+
+# output moments of inertia for x,y,z and angular velocity as well as rotational kinertic energy
+
+thermo_style custom step ke pe c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
+thermo 500
+
+# dump 1 all atom 100 dump.lammpstrj
+
+# dump 2 all movie 10 ball.mp4 type mass
+
+# equilibration w/o torque added
+run 1000 post no
+
+# start spinning the ball. rotation around z should increase and Erot_z should grow
+fix 4 ball addtorque 0.0 0.0 200.0
+run 10000 upto  post no
+
+# continue without adding more torque. rotation continues at fixed speed
+unfix 4
+run 5000
--- a/examples/USER/misc/addtorque/log.9Nov16.addtorque.g++.1
+++ b/examples/USER/misc/addtorque/log.9Nov16.addtorque.g++.1
@ -0,0 +1,202 @@
+LAMMPS (9 Nov 2016)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+
+units           lj
+lattice         fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+boundary        f f f
+
+region          ball   sphere   0.0 0.0 0.0 5.0
+region          box    block  -10 10 -10 10 -10 10
+region          half   block  -10  0 -10 10 -10 10
+
+# add molecule ids so we can use chunk/atom
+fix             0   all property/atom mol ghost yes
+
+create_box      2  box
+Created orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1  region ball
+Created 2123 atoms
+
+pair_style      lj/cut 4.0
+pair_coeff      * *  1.0 1.0
+mass            *    1.0
+set             group all mol 1
+  2123 settings made for mol
+
+# label half the sphere with a different type for better visualization
+set             region half   type 2
+  1142 settings made for type
+
+# use a dynamic group (may require a patch to fix addtorque with older versions of LAMMPS)
+group           ball   dynamic all   region ball
+dynamic group ball defined
+
+neigh_modify    delay 2  every 1  check yes
+
+minimize        0.0  0.0    1000  10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.3
+  ghost atom cutoff = 4.3
+  binsize = 2.15 -> bins = 16 16 16
+Memory usage per processor = 3.68322 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -6.2285099            0   -6.2285099  -0.38871568 
+    1000            0   -7.3616908            0   -7.3616908 -9.1828951e-16 
+Loop time of 12.4181 on 1 procs for 1000 steps with 2123 atoms
+
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+  Stopping criterion = max iterations
+  Energy initial, next-to-last, final = 
+        -6.22850993032     -7.36169083402     -7.36169083402
+  Force two-norm initial, final = 197.762 3.3539e-12
+  Force max component initial, final = 7.88704 1.52475e-13
+  Final line search alpha, max atom move = 1 1.52475e-13
+  Iterations, force evaluations = 1000 1994
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 12.282     | 12.282     | 12.282     |   0.0 | 98.91
+Neigh   | 0.06315    | 0.06315    | 0.06315    |   0.0 |  0.51
+Comm    | 0.000443   | 0.000443   | 0.000443   |   0.0 |  0.00
+Output  | 2.7e-05    | 2.7e-05    | 2.7e-05    |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.07231    |            |       |  0.58
+
+Nlocal:    2123 ave 2123 max 2123 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    270799 ave 270799 max 270799 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 270799
+Ave neighs/atom = 127.555
+Neighbor list builds = 11
+Dangerous builds = 0
+reset_timestep  0
+
+velocity        all create 1.2 12351235
+
+fix             1   all  nve
+fix             2   all  wall/reflect  xlo EDGE xhi EDGE ylo EDGE yhi EDGE zlo EDGE zhi EDGE
+
+compute 1 all chunk/atom molecule
+compute 2 ball omega/chunk 1
+compute 3 ball inertia/chunk 1
+
+# compute rotational kinetic energy: 1/2 * I * omega**2
+variable r_ke_x equal c_2[1][1]*c_2[1][1]*c_3[1][1]*0.5
+variable r_ke_y equal c_2[1][2]*c_2[1][2]*c_3[1][2]*0.5
+variable r_ke_z equal c_2[1][3]*c_2[1][3]*c_3[1][3]*0.5
+
+# output moments of inertia for x,y,z and angular velocity as well as rotational kinertic energy
+
+thermo_style custom step ke pe c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
+thermo 500
+
+# dump 1 all atom 100 dump.lammpstrj
+
+# dump 2 all movie 10 ball.mp4 type mass
+
+# equilibration w/o torque added
+run 1000 post no
+WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 2 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.3
+  ghost atom cutoff = 4.3
+  binsize = 2.15 -> bins = 16 16 16
+Memory usage per processor = 2.68359 Mbytes
+Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z 
+       0    1.7991521   -7.3616908    51125.265    51125.265    51125.265 0.0034331372 -0.0045852283 0.0091015032   0.30129221   0.53743693     2.117541 
+     500    0.8882476     -6.43927    52585.112    52205.936    52112.109 0.0033058719 -0.0043753253 0.0089502237    0.2873458   0.49970143    2.0872595 
+    1000   0.79407357    -6.337372    53754.145    54093.977    53787.624 0.0033214912 -0.0042125031 0.0090171557   0.29651603   0.47995375    2.1867116 
+Loop time of 4.26119 on 1 procs for 1000 steps with 2123 atoms
+
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+# start spinning the ball. rotation around z should increase and Erot_z should grow
+fix 4 ball addtorque 0.0 0.0 200.0
+run 10000 upto  post no
+WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
+Memory usage per processor = 2.68359 Mbytes
+Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z 
+    1000   0.79407357    -6.337372    53754.145    54093.977    53787.624 0.0033214912 -0.0042125031 0.0090171557   0.29651603   0.47995375    2.1867116 
+    1500   0.68685306   -6.2226287    55026.889    54809.958    55224.858 0.0026096779 -0.0039390202   0.01797948   0.18737807   0.42521238    8.9260406 
+    2000   0.65370325   -6.1832475    54914.897    55655.542    55405.781 0.0029310978 -0.0040761978  0.025816421   0.23589612   0.46236922    18.463634 
+    2500   0.69337585   -6.2170462     54604.66    54800.001    54488.865 0.0028821313 -0.0045216915  0.035781895   0.22679174   0.56021203    34.882245 
+    3000   0.76778067   -6.2850756    53423.198    53620.349    53692.133  0.004088872 -0.004451787  0.044703139   0.44658786   0.53133496     53.64839 
+    3500   0.79707238   -6.3044974    53055.225    53071.129    52927.537 0.0036751739 -0.0037584362  0.054889715    0.3583059    0.3748372    79.732181 
+    4000   0.80746429   -6.3010044    53519.853    53643.284    54058.105  0.003813517 -0.0041637733  0.062983015   0.38916725   0.46500703    107.22047 
+    4500   0.81206394   -6.2884719    53371.354    53883.202    53854.559   0.00385001 -0.003643712  0.072544638   0.39555051   0.35769386    141.71085 
+    5000   0.81648687   -6.2737414    53776.764    54233.367    53762.425 0.0024484228 -0.0043310965  0.080673643   0.16118978   0.50866551    174.94929 
+    5500   0.81888245   -6.2572796     53908.22    53502.342    54717.506 0.0037110524  -0.00327586  0.088836946   0.37120958   0.28707375    215.91536 
+    6000   0.86533749   -6.2804248    53687.533    53571.135    53536.171 0.0025223465 -0.0047753224  0.099646475   0.17078626   0.61081016    265.79156 
+    6500   0.88029206   -6.2719195     53344.67    53291.068    53298.665  0.003937416 -0.0033910578   0.10778737   0.41350774   0.30640427    309.61504 
+    7000    0.9066019   -6.2714707    53928.646    53524.142    54003.175 0.0028500736 -0.0039730774   0.11855069   0.21902903    0.4224485     379.4875 
+    7500   0.94601421   -6.2819912    53534.525    53547.598    53851.344 0.0028610722 -0.0049440438   0.12716472   0.21910969    0.6544472    435.41142 
+    8000    0.9562253   -6.2626222    53486.577    53033.175    53858.803 0.0025501008 -0.0048075887   0.13526164   0.17391198   0.61287549    492.69254 
+    8500   0.99679401   -6.2691139    53566.766    53721.523    53831.283 0.0034137155   -0.0039265   0.14392854    0.3121189   0.41412316    557.56894 
+    9000    1.0371056   -6.2761647    53415.879    53605.078     53985.02 0.0029321914 -0.0046362889    0.1518846    0.2296281   0.57612526     622.6884 
+    9500    1.0598491     -6.26216    53493.003    53049.859    53699.774 0.0032127038 -0.0050624912   0.16002437   0.27606311   0.67980256    687.56651 
+   10000    1.1014855   -6.2654945     53418.49    53251.964     53867.56 0.0037330249 -0.0056278017   0.17103133   0.37220602   0.84330216    787.85924 
+Loop time of 43.025 on 1 procs for 9000 steps with 2123 atoms
+
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+# continue without adding more torque. rotation continues at fixed speed
+unfix 4
+run 5000
+WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
+Memory usage per processor = 2.68359 Mbytes
+Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z 
+   10000    1.1014855   -6.2654945     53418.49    53251.964     53867.56 0.0037330249 -0.0056278017   0.17103133   0.37220602   0.84330216    787.85924 
+   10500      1.07259   -6.2363698    52825.233    52896.327    55753.551 0.0035928335 -0.0050843805   0.16344484   0.34094601   0.68370948    744.70621 
+   11000    1.0644214   -6.2282099    52016.795    51950.497    54922.101 0.0047316668 -0.0050149935   0.16196531   0.58229343   0.65328165    720.37919 
+   11500    1.0887339   -6.2525622    52602.789    52903.594     54461.53 0.0044295697 -0.0046710153   0.16698036   0.51606197   0.57713546    759.26022 
+   12000    1.0707466    -6.234719    52785.654    52997.192    54943.066 0.0057389353 -0.0030340721   0.16553451   0.86925773    0.2439353    752.76594 
+   12500    1.0758302   -6.2397291    52375.734    52783.309    55011.986 0.0047029783 -0.0023526884   0.16493895   0.57922337   0.14608158    748.29657 
+   13000    1.0716957   -6.2354221    52711.183    52788.224    55234.737 0.0034033406  -0.00206283   0.16427569   0.30526962   0.11231401    745.29615 
+   13500     1.083667   -6.2475953    52698.902    52203.324    55102.881 0.0032012254 -0.0021366488   0.16381832   0.27002507   0.11916109    739.38261 
+   14000     1.085106   -6.2490655    52767.613    52353.974    55225.438 0.0025647931 -0.0022235227    0.1636534   0.17355699   0.12942041    739.53587 
+   14500    1.0838261   -6.2477856    52292.343    51995.567    54735.836  0.001794954 -0.0029396951   0.16409339  0.084239299   0.22466783    736.92607 
+   15000    1.0827419   -6.2468971    51917.584    51388.833    54481.681 0.0017979486 -0.0025793756   0.16196568  0.083914884   0.17094953    714.60575 
+Loop time of 22.7848 on 1 procs for 5000 steps with 2123 atoms
+
+Performance: 94800.138 tau/day, 219.445 timesteps/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 18.891     | 18.891     | 18.891     |   0.0 | 82.91
+Neigh   | 3.5735     | 3.5735     | 3.5735     |   0.0 | 15.68
+Comm    | 0.005778   | 0.005778   | 0.005778   |   0.0 |  0.03
+Output  | 0.001862   | 0.001862   | 0.001862   |   0.0 |  0.01
+Modify  | 0.27476    | 0.27476    | 0.27476    |   0.0 |  1.21
+Other   |            | 0.0379     |            |       |  0.17
+
+Nlocal:    2123 ave 2123 max 2123 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    242472 ave 242472 max 242472 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 242472
+Ave neighs/atom = 114.212
+Neighbor list builds = 560
+Dangerous builds = 0
+Total wall time: 0:01:22
--- a/examples/USER/misc/addtorque/log.9Nov16.addtorque.g++.4
+++ b/examples/USER/misc/addtorque/log.9Nov16.addtorque.g++.4
@ -0,0 +1,202 @@
+LAMMPS (9 Nov 2016)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+
+units           lj
+lattice         fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+boundary        f f f
+
+region          ball   sphere   0.0 0.0 0.0 5.0
+region          box    block  -10 10 -10 10 -10 10
+region          half   block  -10  0 -10 10 -10 10
+
+# add molecule ids so we can use chunk/atom
+fix             0   all property/atom mol ghost yes
+
+create_box      2  box
+Created orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
+  1 by 2 by 2 MPI processor grid
+create_atoms    1  region ball
+Created 2123 atoms
+
+pair_style      lj/cut 4.0
+pair_coeff      * *  1.0 1.0
+mass            *    1.0
+set             group all mol 1
+  2123 settings made for mol
+
+# label half the sphere with a different type for better visualization
+set             region half   type 2
+  1142 settings made for type
+
+# use a dynamic group (may require a patch to fix addtorque with older versions of LAMMPS)
+group           ball   dynamic all   region ball
+dynamic group ball defined
+
+neigh_modify    delay 2  every 1  check yes
+
+minimize        0.0  0.0    1000  10000
+WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.3
+  ghost atom cutoff = 4.3
+  binsize = 2.15 -> bins = 16 16 16
+Memory usage per processor = 3.77014 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -6.2285099            0   -6.2285099  -0.38871568 
+    1000            0   -7.3616908            0   -7.3616908 -9.7399049e-16 
+Loop time of 8.29581 on 4 procs for 1000 steps with 2123 atoms
+
+89.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+  Stopping criterion = max iterations
+  Energy initial, next-to-last, final = 
+        -6.22850993032     -7.36169083402     -7.36169083402
+  Force two-norm initial, final = 197.762 3.40861e-12
+  Force max component initial, final = 7.88704 1.60379e-13
+  Final line search alpha, max atom move = 1 1.60379e-13
+  Iterations, force evaluations = 1000 1994
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.8462     | 6.8198     | 8.0872     |  34.0 | 82.21
+Neigh   | 0.021211   | 0.028936   | 0.035891   |   3.8 |  0.35
+Comm    | 0.10672    | 1.3842     | 2.3694     |  76.2 | 16.69
+Output  | 2.8e-05    | 3.35e-05   | 5e-05      |   0.2 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.0629     |            |       |  0.76
+
+Nlocal:    530.75 ave 543 max 514 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Nghost:    1058.25 ave 1075 max 1046 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+Neighs:    67699.8 ave 82013 max 55681 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 270799
+Ave neighs/atom = 127.555
+Neighbor list builds = 11
+Dangerous builds = 0
+reset_timestep  0
+
+velocity        all create 1.2 12351235
+
+fix             1   all  nve
+fix             2   all  wall/reflect  xlo EDGE xhi EDGE ylo EDGE yhi EDGE zlo EDGE zhi EDGE
+
+compute 1 all chunk/atom molecule
+compute 2 ball omega/chunk 1
+compute 3 ball inertia/chunk 1
+
+# compute rotational kinetic energy: 1/2 * I * omega**2
+variable r_ke_x equal c_2[1][1]*c_2[1][1]*c_3[1][1]*0.5
+variable r_ke_y equal c_2[1][2]*c_2[1][2]*c_3[1][2]*0.5
+variable r_ke_z equal c_2[1][3]*c_2[1][3]*c_3[1][3]*0.5
+
+# output moments of inertia for x,y,z and angular velocity as well as rotational kinertic energy
+
+thermo_style custom step ke pe c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z
+thermo 500
+
+# dump 1 all atom 100 dump.lammpstrj
+
+# dump 2 all movie 10 ball.mp4 type mass
+
+# equilibration w/o torque added
+run 1000 post no
+WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 2 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.3
+  ghost atom cutoff = 4.3
+  binsize = 2.15 -> bins = 16 16 16
+Memory usage per processor = 2.77052 Mbytes
+Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z 
+       0    1.7991521   -7.3616908    51125.265    51125.265    51125.265 0.0040198435 -0.0024237256 0.0011306245    0.4130702   0.15016629  0.032677011 
+     500   0.90968729   -6.4603004    52559.075    52593.598    52370.876 0.0039073429 -0.0023505431 0.0011032256   0.40121833   0.14529121  0.031870471 
+    1000   0.80269935   -6.3456699    53966.859     54192.03    54298.931 0.0040875347 -0.0023098179 0.00077010445   0.45083753   0.14456425  0.016101285 
+Loop time of 2.3842 on 4 procs for 1000 steps with 2123 atoms
+
+89.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+# start spinning the ball. rotation around z should increase and Erot_z should grow
+fix 4 ball addtorque 0.0 0.0 200.0
+run 10000 upto  post no
+WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
+Memory usage per processor = 2.77052 Mbytes
+Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z 
+    1000   0.80269935   -6.3456699    53966.859     54192.03    54298.931 0.0040875347 -0.0023098179 0.00077010445   0.45083753   0.14456425  0.016101285 
+    1500   0.68922642   -6.2266953    54966.109    54681.607    54947.256 0.0038798951 -0.0016325797 0.0099837591   0.41371853  0.072871893    2.7384461 
+    2000   0.64105167   -6.1739656    54782.995    54570.486    54910.316 0.0034645832 -0.0027243304  0.017763588   0.32878936   0.20251043    8.6633395 
+    2500   0.69929409   -6.2287557     54307.47    53952.925    54538.409 0.0035199565 -0.0022538001  0.028279733   0.33643732   0.13703004    21.808363 
+    3000   0.77013056   -6.2945597    53916.743     53801.81    53955.863 0.0039732989 -0.0024543292  0.037182149   0.42559463   0.16204384    37.297319 
+    3500   0.80807105   -6.3246605    53451.163    53387.178    53474.789 0.0043137676 -0.0020556348  0.047270147   0.49732542   0.11279735    59.743821 
+    4000   0.81007199   -6.3142362    53334.317    53243.089    53685.963 0.0038548696 -0.0031009535  0.055811043    0.3962745   0.25599044    83.612467 
+    4500    0.7850954   -6.2735818    53738.002    53682.367    53639.471 0.0033046861 -0.0018472801  0.065975851   0.29343502  0.091594032    116.74129 
+    5000   0.77992741   -6.2508277    53864.644    53804.867    53877.025 0.0038258186 -0.0028703189  0.073848203   0.39420539    0.2216419    146.91071 
+    5500   0.79428302   -6.2467907    54353.329    53987.578    54234.062 0.0034715133 -0.0030161617  0.082746129   0.32751699   0.24556875    185.66819 
+    6000   0.82211943   -6.2549436    54273.545    53195.299    54061.645 0.0030929934 -0.0031282112  0.090458895   0.25960687   0.26027676    221.18813 
+    6500   0.87630771   -6.2870988    54042.229    53505.982    54492.239 0.0026486452 -0.0024783378   0.10046947   0.18956181    0.1643211    275.02546 
+    7000   0.88614639   -6.2727488    53701.993    52682.206    53948.142 0.0035384498 -0.0035905797   0.11030427   0.33619131   0.33959641    328.19439 
+    7500   0.92102182   -6.2787281    53410.068    52577.853    53132.511 0.0033084315 -0.0031776605   0.11973875    0.2923058   0.26545312     380.8902 
+    8000   0.94010525   -6.2697758    53732.562    53384.271    53795.933 0.0046460009 -0.0032755993   0.12803006    0.5799174   0.28639462    440.90328 
+    8500   0.95359399    -6.252319    53444.305    53558.444    53789.691 0.0037919474 -0.0035729209   0.13616177   0.38423423   0.34185722    498.63117 
+    9000   0.98631627     -6.25197     53115.01    54017.327    53955.578 0.0045084495 -0.0034368377   0.14488919   0.53981096   0.31902236    566.34143 
+    9500    1.0328238   -6.2632597    53287.675    53682.978    53769.692 0.0044595175 -0.0025931203   0.15416363    0.5298739    0.1804895    638.95665 
+   10000    1.0741755   -6.2667785    53103.657    53319.569    53601.523 0.0059237675 -0.0019561182   0.16445664   0.93173079   0.10201096    724.85302 
+Loop time of 21.8398 on 4 procs for 9000 steps with 2123 atoms
+
+90.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+# continue without adding more torque. rotation continues at fixed speed
+unfix 4
+run 5000
+WARNING: One or more dynamic groups may not be updated at correct point in timestep (../fix_group.cpp:153)
+Memory usage per processor = 2.77052 Mbytes
+Step KinEng PotEng c_3[1][1] c_3[1][2] c_3[1][3] c_2[1][1] c_2[1][2] c_2[1][3] v_r_ke_x v_r_ke_y v_r_ke_z 
+   10000    1.0741755   -6.2667785    53103.657    53319.569    53601.523 0.0059237675 -0.0019561182   0.16445664   0.93173079   0.10201096    724.85302 
+   10500    1.0588571   -6.2509381    52374.303    52131.544    55020.367 0.0048843769 -0.0018716797   0.15729531   0.62475047  0.091313217    680.65188 
+   11000    1.0554911   -6.2471863    52803.345    52177.891    55200.756 0.0042073234 -0.0024283269   0.15742315   0.46735107   0.15384055    683.99392 
+   11500    1.0559499   -6.2469955    54031.351    52919.728     54882.35 0.0046703444 -0.0016225764   0.15994353   0.58926908   0.06966232    701.99832 
+   12000    1.0311805   -6.2224471     52812.51     52444.13    55356.101 0.0044986993 -0.0019225732   0.15672327   0.53441759  0.096924293    679.83334 
+   12500    1.0423882   -6.2339087    52000.562    52043.013    55003.272 0.0038688875 -0.0022935053    0.1548654   0.38917977   0.13687746    659.57977 
+   13000    1.0548857   -6.2465445    52196.499    52869.024    54622.553 0.0036650563 -0.0025542156    0.1590498   0.35056832   0.17245921    690.88895 
+   13500    1.0443009   -6.2360149    51921.746    53124.078    54750.325 0.0052756473 -0.0011658069   0.15689119   0.72255483  0.036100621    673.83538 
+   14000    1.0505583    -6.241923    51861.696    52153.234    54321.531 0.0037119391 -0.00045576703   0.15738082   0.35728798 0.0054167284    672.73745 
+   14500     1.040343   -6.2316147    52035.588    51680.479    54443.305 0.0026177168 -0.0014795729   0.15428968    0.1782854  0.056567797    648.01978 
+   15000    1.0404962   -6.2322338    52376.795    51327.453    54677.693 0.0025711787 -0.0021695312   0.15403509   0.17313044   0.12079571    648.66363 
+Loop time of 11.9695 on 4 procs for 5000 steps with 2123 atoms
+
+Performance: 180458.440 tau/day, 417.728 timesteps/s
+89.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.0313     | 8.4017     | 9.6932     |  35.5 | 70.19
+Neigh   | 0.97886    | 1.3633     | 1.7406     |  26.8 | 11.39
+Comm    | 0.34002    | 2.0227     | 3.7911     |  94.9 | 16.90
+Output  | 0.001198   | 0.0015522  | 0.002578   |   1.5 |  0.01
+Modify  | 0.12841    | 0.131      | 0.13336    |   0.5 |  1.09
+Other   |            | 0.04924    |            |       |  0.41
+
+Nlocal:    530.75 ave 534 max 529 min
+Histogram: 1 0 2 0 0 0 0 0 0 1
+Nghost:    1038 ave 1048 max 1029 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Neighs:    60482.5 ave 72547 max 49124 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+
+Total # of neighbors = 241930
+Ave neighs/atom = 113.957
+Neighbor list builds = 555
+Dangerous builds = 0
+Total wall time: 0:00:44
--- a/examples/USER/misc/agni/Al_prb.agni
+++ b/examples/USER/misc/agni/Al_prb.agni
--- a/examples/USER/misc/agni/adatom.data
+++ b/examples/USER/misc/agni/adatom.data
@ -0,0 +1,197 @@
+Data File created from VASP POSCAR
+
+181 atoms
+1 atom types
+
+0 17.121440767 xlo xhi
+0 14.8276026536 ylo yhi
+0 39.3197318979 zlo zhi
+
+Masses
+
+1 26.982
+
+Atoms
+
+1 1 0.0 1.64751140595 15.0
+2 1 2.85357346116 1.64751140595 15.0
+3 1 5.70714692232 1.64751140595 15.0
+4 1 8.56072038348 1.64751140595 15.0
+5 1 11.4142938446 1.64751140595 15.0
+6 1 14.2678673058 1.64751140595 15.0
+7 1 1.42678673058 4.11877851488 15.0
+8 1 4.28036019174 4.11877851488 15.0
+9 1 7.1339336529 4.11877851488 15.0
+10 1 9.98750711406 4.11877851488 15.0
+11 1 12.8410805752 4.11877851488 15.0
+12 1 15.6946540364 4.11877851488 15.0
+13 1 0.0 6.59004562381 15.0
+14 1 2.85357346116 6.59004562381 15.0
+15 1 5.70714692232 6.59004562381 15.0
+16 1 8.56072038348 6.59004562381 15.0
+17 1 11.4142938446 6.59004562381 15.0
+18 1 14.2678673058 6.59004562381 15.0
+19 1 1.42678673058 9.06131273274 15.0
+20 1 4.28036019174 9.06131273274 15.0
+21 1 7.1339336529 9.06131273274 15.0
+22 1 9.98750711406 9.06131273274 15.0
+23 1 12.8410805752 9.06131273274 15.0
+24 1 15.6946540364 9.06131273274 15.0
+25 1 0.0 11.5325798417 15.0
+26 1 2.85357346116 11.5325798417 15.0
+27 1 5.70714692232 11.5325798417 15.0
+28 1 8.56072038348 11.5325798417 15.0
+29 1 11.4142938446 11.5325798417 15.0
+30 1 14.2678673058 11.5325798417 15.0
+31 1 1.42678673058 14.0038469506 15.0
+32 1 4.28036019174 14.0038469506 15.0
+33 1 7.1339336529 14.0038469506 15.0
+34 1 9.98750711406 14.0038469506 15.0
+35 1 12.8410805752 14.0038469506 15.0
+36 1 15.6946540364 14.0038469506 15.0
+37 1 0.0 0.0 17.3299329745
+38 1 2.85357346116 0.0 17.3299329745
+39 1 5.70714692232 0.0 17.3299329745
+40 1 8.56072038348 0.0 17.3299329745
+41 1 11.4142938446 0.0 17.3299329745
+42 1 14.2678673058 0.0 17.3299329745
+43 1 1.42678673058 2.47126710893 17.3299329745
+44 1 4.28036019174 2.47126710893 17.3299329745
+45 1 7.1339336529 2.47126710893 17.3299329745
+46 1 9.98750711406 2.47126710893 17.3299329745
+47 1 12.8410805752 2.47126710893 17.3299329745
+48 1 15.6946540364 2.47126710893 17.3299329745
+49 1 0.0 4.94253421786 17.3299329745
+50 1 2.85357346116 4.94253421786 17.3299329745
+51 1 5.70714692232 4.94253421786 17.3299329745
+52 1 8.56072038348 4.94253421786 17.3299329745
+53 1 11.4142938446 4.94253421786 17.3299329745
+54 1 14.2678673058 4.94253421786 17.3299329745
+55 1 1.42678673058 7.41380132679 17.3299329745
+56 1 4.28036019174 7.41380132679 17.3299329745
+57 1 7.1339336529 7.41380132679 17.3299329745
+58 1 9.98750711406 7.41380132679 17.3299329745
+59 1 12.8410805752 7.41380132679 17.3299329745
+60 1 15.6946540364 7.41380132679 17.3299329745
+61 1 0.0 9.88506843572 17.3299329745
+62 1 2.85357346116 9.88506843572 17.3299329745
+63 1 5.70714692232 9.88506843572 17.3299329745
+64 1 8.56072038348 9.88506843572 17.3299329745
+65 1 11.4142938446 9.88506843572 17.3299329745
+66 1 14.2678673058 9.88506843572 17.3299329745
+67 1 1.42678673058 12.3563355446 17.3299329745
+68 1 4.28036019174 12.3563355446 17.3299329745
+69 1 7.1339336529 12.3563355446 17.3299329745
+70 1 9.98750711406 12.3563355446 17.3299329745
+71 1 12.8410805752 12.3563355446 17.3299329745
+72 1 15.6946540364 12.3563355446 17.3299329745
+73 1 1.42678673058 0.823755702976 19.6598659489
+74 1 4.28036019174 0.823755702976 19.6598659489
+75 1 7.1339336529 0.823755702976 19.6598659489
+76 1 9.98750711406 0.823755702976 19.6598659489
+77 1 12.8410805752 0.823755702976 19.6598659489
+78 1 15.6946540364 0.823755702976 19.6598659489
+79 1 0.0 3.29502281191 19.6598659489
+80 1 2.85357346116 3.29502281191 19.6598659489
+81 1 5.70714692232 3.29502281191 19.6598659489
+82 1 8.56072038348 3.29502281191 19.6598659489
+83 1 11.4142938446 3.29502281191 19.6598659489
+84 1 14.2678673058 3.29502281191 19.6598659489
+85 1 1.42678673058 5.76628992084 19.6598659489
+86 1 4.28036019174 5.76628992084 19.6598659489
+87 1 7.1339336529 5.76628992084 19.6598659489
+88 1 9.98750711406 5.76628992084 19.6598659489
+89 1 12.8410805752 5.76628992084 19.6598659489
+90 1 15.6946540364 5.76628992084 19.6598659489
+91 1 0.0 8.23755702976 19.6598659489
+92 1 2.85357346116 8.23755702976 19.6598659489
+93 1 5.70714692232 8.23755702976 19.6598659489
+94 1 8.56072038348 8.23755702976 19.6598659489
+95 1 11.4142938446 8.23755702976 19.6598659489
+96 1 14.2678673058 8.23755702976 19.6598659489
+97 1 1.42678673058 10.7088241387 19.6598659489
+98 1 4.28036019174 10.7088241387 19.6598659489
+99 1 7.1339336529 10.7088241387 19.6598659489
+100 1 9.98750711406 10.7088241387 19.6598659489
+101 1 12.8410805752 10.7088241387 19.6598659489
+102 1 15.6946540364 10.7088241387 19.6598659489
+103 1 0.0 13.1800912476 19.6598659489
+104 1 2.85357346116 13.1800912476 19.6598659489
+105 1 5.70714692232 13.1800912476 19.6598659489
+106 1 8.56072038348 13.1800912476 19.6598659489
+107 1 11.4142938446 13.1800912476 19.6598659489
+108 1 14.2678673058 13.1800912476 19.6598659489
+109 1 0.0 1.64751140595 21.9897989234
+110 1 2.85357346116 1.64751140595 21.9897989234
+111 1 5.70714692232 1.64751140595 21.9897989234
+112 1 8.56072038348 1.64751140595 21.9897989234
+113 1 11.4142938446 1.64751140595 21.9897989234
+114 1 14.2678673058 1.64751140595 21.9897989234
+115 1 1.42678673058 4.11877851488 21.9897989234
+116 1 4.28036019174 4.11877851488 21.9897989234
+117 1 7.1339336529 4.11877851488 21.9897989234
+118 1 9.98750711406 4.11877851488 21.9897989234
+119 1 12.8410805752 4.11877851488 21.9897989234
+120 1 15.6946540364 4.11877851488 21.9897989234
+121 1 0.0 6.59004562381 21.9897989234
+122 1 2.85357346116 6.59004562381 21.9897989234
+123 1 5.70714692232 6.59004562381 21.9897989234
+124 1 8.56072038348 6.59004562381 21.9897989234
+125 1 11.4142938446 6.59004562381 21.9897989234
+126 1 14.2678673058 6.59004562381 21.9897989234
+127 1 1.42678673058 9.06131273274 21.9897989234
+128 1 4.28036019174 9.06131273274 21.9897989234
+129 1 7.1339336529 9.06131273274 21.9897989234
+130 1 9.98750711406 9.06131273274 21.9897989234
+131 1 12.8410805752 9.06131273274 21.9897989234
+132 1 15.6946540364 9.06131273274 21.9897989234
+133 1 0.0 11.5325798417 21.9897989234
+134 1 2.85357346116 11.5325798417 21.9897989234
+135 1 5.70714692232 11.5325798417 21.9897989234
+136 1 8.56072038348 11.5325798417 21.9897989234
+137 1 11.4142938446 11.5325798417 21.9897989234
+138 1 14.2678673058 11.5325798417 21.9897989234
+139 1 1.42678673058 14.0038469506 21.9897989234
+140 1 4.28036019174 14.0038469506 21.9897989234
+141 1 7.1339336529 14.0038469506 21.9897989234
+142 1 9.98750711406 14.0038469506 21.9897989234
+143 1 12.8410805752 14.0038469506 21.9897989234
+144 1 15.6946540364 14.0038469506 21.9897989234
+145 1 0.0 0.0 24.3197318979
+146 1 2.85357346116 0.0 24.3197318979
+147 1 5.70714692232 0.0 24.3197318979
+148 1 8.56072038348 0.0 24.3197318979
+149 1 11.4142938446 0.0 24.3197318979
+150 1 14.2678673058 0.0 24.3197318979
+151 1 1.42678673058 2.47126710893 24.3197318979
+152 1 4.28036019174 2.47126710893 24.3197318979
+153 1 7.1339336529 2.47126710893 24.3197318979
+154 1 9.98750711406 2.47126710893 24.3197318979
+155 1 12.8410805752 2.47126710893 24.3197318979
+156 1 15.6946540364 2.47126710893 24.3197318979
+157 1 0.0 4.94253421786 24.3197318979
+158 1 2.85357346116 4.94253421786 24.3197318979
+159 1 5.70714692232 4.94253421786 24.3197318979
+160 1 8.56072038348 4.94253421786 24.3197318979
+161 1 11.4142938446 4.94253421786 24.3197318979
+162 1 14.2678673058 4.94253421786 24.3197318979
+163 1 1.42678673058 7.41380132679 24.3197318979
+164 1 4.28036019174 7.41380132679 24.3197318979
+165 1 7.1339336529 7.41380132679 24.3197318979
+166 1 9.98750711406 7.41380132679 24.3197318979
+167 1 12.8410805752 7.41380132679 24.3197318979
+168 1 15.6946540364 7.41380132679 24.3197318979
+169 1 0.0 9.88506843572 24.3197318979
+170 1 2.85357346116 9.88506843572 24.3197318979
+171 1 5.70714692232 9.88506843572 24.3197318979
+172 1 8.56072038348 9.88506843572 24.3197318979
+173 1 11.4142938446 9.88506843572 24.3197318979
+174 1 14.2678673058 9.88506843572 24.3197318979
+175 1 1.42678673058 12.3563355446 24.3197318979
+176 1 4.28036019174 12.3563355446 24.3197318979
+177 1 7.1339336529 12.3563355446 24.3197318979
+178 1 9.98750711406 12.3563355446 24.3197318979
+179 1 12.8410805752 12.3563355446 24.3197318979
+180 1 15.6946540364 12.3563355446 24.3197318979
+181 1 7.1339336529 4.11877851488 26.7197318979
+
--- a/examples/USER/misc/agni/in.adatom
+++ b/examples/USER/misc/agni/in.adatom
@ -0,0 +1,23 @@
+
+processors * * 1
+units metal
+boundary p p f
+read_data adatom.data
+
+pair_style agni
+pair_coeff * * Al_prb.agni Al
+
+neighbor 0.3 bin 
+neigh_modify delay 2 check yes 
+
+timestep 0.0005
+velocity all create 500 12345
+fix 1 all nvt temp 250 250 0.2 
+fix 5 all momentum 1 linear 1 1 1
+
+thermo 100
+thermo_style custom step ke temp
+
+# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
+
+run 1000
--- a/examples/USER/misc/agni/in.vacancy
+++ b/examples/USER/misc/agni/in.vacancy
@ -0,0 +1,23 @@
+
+units metal
+boundary p p p
+read_data vacancy.data
+
+pair_style agni
+pair_coeff * * Al_prb.agni Al
+neighbor 0.3 bin 
+neigh_modify delay 2 check yes 
+
+
+timestep 0.0005
+velocity all create 1000 12345
+fix 1 all nvt temp 900 900 200
+fix 5 all momentum 1 linear 1 1 1
+
+
+thermo 100
+thermo_style custom step ke etotal temp
+
+# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
+
+run 1000
--- a/examples/USER/misc/agni/log.9Nov16.adatom.g++.1
+++ b/examples/USER/misc/agni/log.9Nov16.adatom.g++.1
@ -0,0 +1,82 @@
+LAMMPS (9 Nov 2016)
+  using 1 OpenMP thread(s) per MPI task
+
+processors * * 1
+units metal
+boundary p p f
+read_data adatom.data
+  orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  181 atoms
+
+pair_style agni
+pair_coeff * * Al_prb.agni Al
+Reading potential file Al_prb.agni with DATE: 2016-11-11
+
+neighbor 0.3 bin
+neigh_modify delay 2 check yes
+
+timestep 0.0005
+velocity all create 500 12345
+fix 1 all nvt temp 250 250 0.2
+fix 5 all momentum 1 linear 1 1 1
+
+thermo 100
+thermo_style custom step ke temp
+
+# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
+
+run 1000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 2 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.3
+  ghost atom cutoff = 8.3
+  binsize = 4.15 -> bins = 5 4 10
+Memory usage per processor = 2.37049 Mbytes
+Step KinEng Temp 
+       0    11.633413          500 
+     100     4.049974    174.06646 
+     200    5.8983472    253.50889 
+     300    5.3667309    230.66021 
+     400    4.9343935     212.0785 
+     500    5.4054496    232.32432 
+     600    6.1779127    265.52452 
+     700    6.3749266     273.9921 
+     800    6.0701481    260.89283 
+     900    6.4582394    277.57286 
+    1000    6.4047444    275.27366 
+Loop time of 20.8273 on 1 procs for 1000 steps with 181 atoms
+
+Performance: 2.074 ns/day, 11.571 hours/ns, 48.014 timesteps/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 20.79      | 20.79      | 20.79      |   0.0 | 99.82
+Neigh   | 0.022742   | 0.022742   | 0.022742   |   0.0 |  0.11
+Comm    | 0.0040836  | 0.0040836  | 0.0040836  |   0.0 |  0.02
+Output  | 0.00011086 | 0.00011086 | 0.00011086 |   0.0 |  0.00
+Modify  | 0.0089345  | 0.0089345  | 0.0089345  |   0.0 |  0.04
+Other   |            | 0.001819   |            |       |  0.01
+
+Nlocal:    181 ave 181 max 181 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    562 ave 562 max 562 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  18810 ave 18810 max 18810 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 18810
+Ave neighs/atom = 103.923
+Neighbor list builds = 33
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:20
--- a/examples/USER/misc/agni/log.9Nov16.adatom.g++.4
+++ b/examples/USER/misc/agni/log.9Nov16.adatom.g++.4
@ -0,0 +1,82 @@
+LAMMPS (9 Nov 2016)
+  using 1 OpenMP thread(s) per MPI task
+
+processors * * 1
+units metal
+boundary p p f
+read_data adatom.data
+  orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  181 atoms
+
+pair_style agni
+pair_coeff * * Al_prb.agni Al
+Reading potential file Al_prb.agni with DATE: 2016-11-11
+
+neighbor 0.3 bin
+neigh_modify delay 2 check yes
+
+timestep 0.0005
+velocity all create 500 12345
+fix 1 all nvt temp 250 250 0.2
+fix 5 all momentum 1 linear 1 1 1
+
+thermo 100
+thermo_style custom step ke temp
+
+# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
+
+run 1000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 2 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.3
+  ghost atom cutoff = 8.3
+  binsize = 4.15 -> bins = 5 4 10
+Memory usage per processor = 2.48695 Mbytes
+Step KinEng Temp 
+       0    11.633413          500 
+     100     4.049974    174.06646 
+     200    5.8983472    253.50889 
+     300    5.3667309    230.66021 
+     400    4.9343935     212.0785 
+     500    5.4054496    232.32432 
+     600    6.1779127    265.52451 
+     700    6.3749266     273.9921 
+     800    6.0701481    260.89283 
+     900    6.4582394    277.57286 
+    1000    6.4047444    275.27366 
+Loop time of 5.96868 on 4 procs for 1000 steps with 181 atoms
+
+Performance: 7.238 ns/day, 3.316 hours/ns, 167.541 timesteps/s
+99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.4176     | 5.4602     | 5.5505     |   2.3 | 91.48
+Neigh   | 0.0056074  | 0.0060464  | 0.0062635  |   0.3 |  0.10
+Comm    | 0.39544    | 0.48696    | 0.53111    |   7.9 |  8.16
+Output  | 0.0001545  | 0.00015736 | 0.0001595  |   0.0 |  0.00
+Modify  | 0.010492   | 0.011565   | 0.012588   |   0.9 |  0.19
+Other   |            | 0.003794   |            |       |  0.06
+
+Nlocal:    45.25 ave 47 max 42 min
+Histogram: 1 0 0 0 0 0 0 0 2 1
+Nghost:    374.75 ave 380 max 373 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  4702.5 ave 4868 max 4389 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+
+Total # of neighbors = 18810
+Ave neighs/atom = 103.923
+Neighbor list builds = 33
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:05
--- a/examples/USER/misc/agni/log.9Nov16.vacancy.g++.1
+++ b/examples/USER/misc/agni/log.9Nov16.vacancy.g++.1
@ -0,0 +1,82 @@
+LAMMPS (9 Nov 2016)
+  using 1 OpenMP thread(s) per MPI task
+
+units metal
+boundary p p p
+read_data vac.data
+  orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  31 atoms
+
+pair_style agni
+pair_coeff * * Al_prb.agni Al
+Reading potential file Al_prb.agni with DATE: 2016-11-11
+neighbor 0.3 bin
+neigh_modify delay 2 check yes
+
+
+timestep 0.0005
+velocity all create 1000 12345
+fix 1 all nvt temp 900 900 200
+fix 5 all momentum 1 linear 1 1 1
+
+
+thermo 100
+thermo_style custom step ke etotal temp
+
+# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
+
+run 1000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 2 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.3
+  ghost atom cutoff = 8.3
+  binsize = 4.15 -> bins = 2 2 2
+Memory usage per processor = 2.40842 Mbytes
+Step KinEng TotEng Temp 
+       0    3.8778043    3.8778043         1000 
+     100    2.8126642    2.8126642    725.32391 
+     200    3.7110413    3.7110413     956.9955 
+     300    3.2361084    3.2361084    834.52081 
+     400    3.4625769    3.4625769    892.92201 
+     500    3.4563307    3.4563307    891.31126 
+     600    2.8486344    2.8486344    734.59982 
+     700    3.1183057    3.1183057    804.14208 
+     800    2.9164818    2.9164818    752.09618 
+     900     3.464416     3.464416    893.39629 
+    1000    3.5954546    3.5954546    927.18825 
+Loop time of 3.86777 on 1 procs for 1000 steps with 31 atoms
+
+Performance: 11.169 ns/day, 2.149 hours/ns, 258.547 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.8463     | 3.8463     | 3.8463     |   0.0 | 99.44
+Neigh   | 0.011294   | 0.011294   | 0.011294   |   0.0 |  0.29
+Comm    | 0.0057271  | 0.0057271  | 0.0057271  |   0.0 |  0.15
+Output  | 0.00014257 | 0.00014257 | 0.00014257 |   0.0 |  0.00
+Modify  | 0.0029459  | 0.0029459  | 0.0029459  |   0.0 |  0.08
+Other   |            | 0.001395   |            |       |  0.04
+
+Nlocal:    31 ave 31 max 31 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    878 ave 878 max 878 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  4334 ave 4334 max 4334 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 4334
+Ave neighs/atom = 139.806
+Neighbor list builds = 51
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03
--- a/examples/USER/misc/agni/log.9Nov16.vacancy.g++.4
+++ b/examples/USER/misc/agni/log.9Nov16.vacancy.g++.4
@ -0,0 +1,82 @@
+LAMMPS (9 Nov 2016)
+  using 1 OpenMP thread(s) per MPI task
+
+units metal
+boundary p p p
+read_data vac.data
+  orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  31 atoms
+
+pair_style agni
+pair_coeff * * Al_prb.agni Al
+Reading potential file Al_prb.agni with DATE: 2016-11-11
+neighbor 0.3 bin
+neigh_modify delay 2 check yes
+
+
+timestep 0.0005
+velocity all create 1000 12345
+fix 1 all nvt temp 900 900 200
+fix 5 all momentum 1 linear 1 1 1
+
+
+thermo 100
+thermo_style custom step ke etotal temp
+
+# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
+
+run 1000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 2 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 8.3
+  ghost atom cutoff = 8.3
+  binsize = 4.15 -> bins = 2 2 2
+Memory usage per processor = 2.3974 Mbytes
+Step KinEng TotEng Temp 
+       0    3.8778044    3.8778044         1000 
+     100    2.8126642    2.8126642    725.32391 
+     200    3.7110413    3.7110413    956.99549 
+     300    3.2361084    3.2361084    834.52081 
+     400    3.4625769    3.4625769    892.92201 
+     500    3.4563307    3.4563307    891.31126 
+     600    2.8486343    2.8486343    734.59981 
+     700    3.1183057    3.1183057    804.14208 
+     800    2.9164819    2.9164819    752.09618 
+     900    3.4644161    3.4644161    893.39631 
+    1000    3.5954546    3.5954546    927.18824 
+Loop time of 1.11007 on 4 procs for 1000 steps with 31 atoms
+
+Performance: 38.916 ns/day, 0.617 hours/ns, 900.843 timesteps/s
+99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.906      | 0.99469    | 1.0291     |   5.1 | 89.61
+Neigh   | 0.0026186  | 0.0027665  | 0.0028622  |   0.2 |  0.25
+Comm    | 0.066125   | 0.10079    | 0.1896     |  16.2 |  9.08
+Output  | 0.00012875 | 0.00014615 | 0.00018787 |   0.2 |  0.01
+Modify  | 0.0080338  | 0.0083079  | 0.00861    |   0.2 |  0.75
+Other   |            | 0.003372   |            |       |  0.30
+
+Nlocal:    7.75 ave 8 max 7 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Nghost:    623.5 ave 630 max 616 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  1083.5 ave 1131 max 988 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+
+Total # of neighbors = 4334
+Ave neighs/atom = 139.806
+Neighbor list builds = 51
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:01
--- a/examples/USER/misc/agni/vacancy.data
+++ b/examples/USER/misc/agni/vacancy.data
@ -0,0 +1,46 @@
+Data File created from VASP POSCAR
+
+31 atoms
+1 atom types
+
+0 8.071125 xlo xhi
+0 8.071125 ylo yhi
+0 8.071125 zlo zhi
+
+Masses
+
+1 26.9815
+
+Atoms
+
+1 1 8.05711986217 3.20498589607 7.09652861184
+2 1 8.05262255028 3.62006786258 3.16719841667
+3 1 2.08891866821 1.38430927213 3.14852514324
+4 1 4.25446836692 3.27689661974 3.35678388118
+5 1 7.92524269451 7.20500664579 3.03232792051
+6 1 6.04056771113 7.24499020906 1.11223380379
+7 1 2.32585852889 5.29910389395 7.31500292009
+8 1 2.09613190567 1.27658214906 7.44277603054
+9 1 3.96852985867 7.2805082905 3.37568009522
+10 1 0.0773420461671 1.29964047903 5.27451616984
+11 1 7.96501442334 1.24471347504 1.17853896176
+12 1 2.13035246804 5.36148411996 3.3817805118
+13 1 2.06211525033 7.25482811482 1.52039033766
+14 1 3.99735704234 7.4099829467 7.05753768668
+15 1 3.84113228596 5.1855444403 1.41642147402
+16 1 0.231862769544 5.38528175164 5.51171817022
+17 1 0.12718452785 5.35814065671 1.11669573581
+18 1 8.05303937039 7.38861123542 7.41398359808
+19 1 1.88506066609 3.17578974033 1.20929473631
+20 1 4.33739926831 1.37976783613 5.28141762358
+21 1 2.23200994743 3.12419127088 5.36881641316
+22 1 6.22871004896 1.34968648416 7.24032447626
+23 1 6.08380394159 1.16222146146 3.30535465675
+24 1 6.16629028099 5.22806528503 3.7675179617
+25 1 4.30194966153 1.14526017671 1.45054175732
+26 1 6.24221620153 5.05377575942 7.17573714759
+27 1 3.92820642281 2.9627641757 7.71515743722
+28 1 4.33686872315 4.73096617728 5.57649231331
+29 1 6.05033104136 3.51389714904 1.34127903322
+30 1 6.27311587476 7.19257797516 5.46814369382
+31 1 1.81274009101 7.47392095028 5.35484578074
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
Steve Plimpton	4b51719e67	new 17Nov16 patch and stable	2016-11-17 16:51:35 -07:00
Steve Plimpton	25d7be5f3d	compute pressure doc change	2016-11-17 16:11:30 -07:00
sjplimp	74c0e4dd5c	Merge pull request #278 from akohlmey/pair-agni Implementation of the AGNI manybody potential	2016-11-17 09:04:31 -07:00
sjplimp	073e8a0524	Merge pull request #276 from akohlmey/doc-updates Small bugfixes and updates	2016-11-17 09:02:27 -07:00
sjplimp	5320bbf585	Merge pull request #275 from andeplane/IP_VORONOI Initializing pointers in VORONOI	2016-11-17 09:01:46 -07:00
sjplimp	4448819824	Merge pull request #274 from andeplane/IP_POEMS Initialize pointers in POEMS	2016-11-17 09:01:37 -07:00
sjplimp	300ac30332	Merge pull request #273 from akohlmey/auto-memalign turn on -DLAMMPS_MEMALIGN=64 automatically when USER-INTEL is installed	2016-11-17 09:01:27 -07:00
sjplimp	2535e44991	Merge pull request #271 from akohlmey/tersoff-modc pair style tersoff/mod/c	2016-11-17 09:00:52 -07:00
sjplimp	cdae794383	Merge pull request #242 from andeplane/vashishta_kokkos Added KOKKOS vashishta	2016-11-17 09:00:03 -07:00
Steve Plimpton	8756a1017d	Kokkos updates by Stan	2016-11-17 08:58:22 -07:00
Axel Kohlmeyer	22d93fe8fb	add restrict to CCFLAGS for makefiles intended for intel compilers	2016-11-16 14:31:10 -05:00
Axel Kohlmeyer	57124b9b25	update documentation metadata files for recent changes	2016-11-12 09:18:21 -05:00
Axel Kohlmeyer	03b3834fe3	add documentation for pair style agni	2016-11-12 09:07:42 -05:00
Axel Kohlmeyer	d0124eac95	optimized data access and using approximate exponential for USER-OMP version	2016-11-12 08:36:27 -05:00
Axel Kohlmeyer	5685131fe2	add USER-OMP version of pair style agni	2016-11-11 19:08:01 -05:00
Axel Kohlmeyer	22fc92f9d8	use special ev_tally() function suitable for this kind of force compute	2016-11-11 18:32:55 -05:00
Axel Kohlmeyer	b9770766a8	add adatom and vacancy examples for AGNI pair style	2016-11-11 18:19:29 -05:00
Axel Kohlmeyer	9cc0c8badd	error exit when requested element is not in potential file	2016-11-11 18:10:57 -05:00
Axel Kohlmeyer	6e1492a86c	add potential file for pair style AGNI	2016-11-11 18:10:26 -05:00
Axel Kohlmeyer	9b0987d8c4	first complete implementation of AGNI pair style	2016-11-11 17:32:47 -05:00
Axel Kohlmeyer	e453adaf81	implemented parser for 1 element potential files	2016-11-11 15:53:37 -05:00
Axel Kohlmeyer	8e0fd88697	add example demonstrating the use of fix addtorque	2016-11-11 10:52:50 -05:00
Axel Kohlmeyer	fdcabd7d1d	fix addtorque is compatible with dynamic groups	2016-11-11 09:01:18 -05:00
Axel Kohlmeyer	c5c8c50e97	initialize 'nper'	2016-11-11 07:47:42 -05:00
Axel Kohlmeyer	72b0841b28	Merge branch 'doc-updates' of github.com:akohlmey/lammps into doc-updates	2016-11-11 07:44:44 -05:00
Axel Kohlmeyer	801111a7ab	dummy framework implementation for AGNI pair style	2016-11-10 15:00:36 -05:00
Axel Kohlmeyer	bfc478c320	simpler variant of the segfault workaround, that does not offend Clang c++.	2016-11-10 14:12:02 -05:00
Axel Kohlmeyer	2b75ee761d	avoid segmentation fault, when creating a LAMMPS instance from the library interface. arg[] may be NULL.	2016-11-10 13:28:32 -05:00
Axel Kohlmeyer	352e177fcd	Merge branch 'master' into small-fixes-and-updates	2016-11-10 13:26:00 -05:00
Anders Hafreager	c20ee34c7b	Initializing pointers in VORONOI	2016-11-10 09:30:07 +01:00
Anders Hafreager	95a7f7160e	Initialize pointers in POEMS	2016-11-10 09:26:52 +01:00
Axel Kohlmeyer	1f38e1a771	Merge branch 'master' into doc-updates	2016-11-09 18:18:05 -05:00
Steve Plimpton	9806da69f3	Stan bug fixes for fix reaxc/bonds/kk	2016-11-09 15:47:50 -07:00
Axel Kohlmeyer	fec87c070d	simplify compiling USER-INTEL package, by defaulting to -DLAMMPS_MEMALIGN=64 in case it is not set	2016-11-09 16:53:39 -05:00
Axel Kohlmeyer	3d3a99c082	added missing potential for tersoff/mod/c	2016-11-09 16:50:34 -05:00
Axel Kohlmeyer	3e36ec3754	remove unused class member	2016-11-09 16:17:46 -05:00
Axel Kohlmeyer	9ed5c4f0fa	Merge branch 'master' into kokkos-vashishta	2016-11-09 15:15:10 -05:00
Axel Kohlmeyer	c55fd502e0	correct typo in formula	2016-11-09 15:04:24 -05:00
Axel Kohlmeyer	71ee2ecaa1	integrate pair style tersoff/mod/c contributed by Ganga P Purja Pun (GMU) This includes docs, added testing and inclusion of USER-OMP support.	2016-11-09 14:52:39 -05:00
sjplimp	bfea3dce7d	Merge pull request #268 from arielzn/born_dsf pair styles born/coul/dsf and born/coul/dsf/cs added	2016-11-09 11:57:09 -07:00
sjplimp	eef862ee1c	Merge pull request #267 from akohlmey/pager-help use pager for help message, if connected to stdout	2016-11-09 11:53:43 -07:00
sjplimp	0cc2fbf1d6	Merge pull request #266 from andeplane/IP_USER_OMP Initializing pointers in USER-OMP	2016-11-09 11:52:05 -07:00
sjplimp	ae00666994	Merge pull request #265 from andeplane/IP_DIFF_DPD Initializing pointers in USER-DIFFRACTION and USER-DPD	2016-11-09 11:51:53 -07:00
sjplimp	51b3b5fb35	Merge pull request #264 from andeplane/IP_SNAP_SRD Initialize pointers in SNAP and SRD	2016-11-09 11:51:44 -07:00
sjplimp	176f2c3aa1	Merge pull request #263 from andeplane/IP_RIGID_SHOCK Initialize pointers in RIGID and SHOCK	2016-11-09 11:51:36 -07:00
sjplimp	3f71bfb185	Merge pull request #262 from andeplane/IP_PERI_QEQ_REPLICA Initializing pointers in PERI, QEQ and REPLICA	2016-11-09 11:51:25 -07:00
sjplimp	cf3ab51679	Merge pull request #261 from andeplane/IP_MISC_MOLECULE Initialized pointers in MISC and MOLECULE	2016-11-09 11:51:09 -07:00
sjplimp	59922f894b	Merge pull request #260 from andeplane/IP_MANYBODY_MC Initialize pointers in MANYBODY and MC	2016-11-09 11:51:01 -07:00
sjplimp	5e2b9d8bf3	Merge pull request #259 from andeplane/IP_KSPACE Initialize pointers in KSPACE	2016-11-09 11:50:50 -07:00
sjplimp	2d132cad6b	Merge pull request #258 from andeplane/IP_GRANULAR Initialize pointers in GRANULAR	2016-11-09 11:50:41 -07:00
sjplimp	ef6801f8bf	Merge pull request #257 from andeplane/IP_CORESHELL Initialize pointers in CORESHELL	2016-11-09 11:50:31 -07:00
sjplimp	c81a723642	Merge pull request #256 from andeplane/IP_BODY Initialized pointers in BODY	2016-11-09 11:50:23 -07:00
sjplimp	f9eb2a99ce	Merge pull request #255 from andeplane/IP_ASPHERE Initialize pointers in ASPHERE	2016-11-09 11:50:11 -07:00
sjplimp	16a02ef27d	Merge pull request #254 from andeplane/IP_root Initialized pointers in src folder	2016-11-09 11:47:21 -07:00
Steve Plimpton	2c801320c2	fixed links in Section_intro.txt	2016-11-09 11:46:10 -07:00
Anders Hafreager	d20b32092e	Building correct shortlists and removed rsq test in force loops	2016-11-08 18:57:27 +01:00
arielzn	9de1a2a08f	added input using born/coul/dsf/cs to examples/coreshell	2016-11-08 18:27:44 +01:00
arielzn	cdb5d47e9f	add FLERR argument to force->bounds() in born/coul/dsf	2016-11-08 18:24:54 +01:00
Steve Plimpton	a23b287a7a	sync with SVN for creation of stable release	2016-11-08 09:05:50 -07:00
Steve Plimpton	31204aab6a	sync with SVN	2016-11-08 08:57:51 -07:00
arielzn	25e7d074cf	documentation added for born/coul/dsf and born/coul/dsf/cs styles	2016-11-08 16:51:54 +01:00
arielzn	667f4dfe28	pair style born/coul/dsf added with its coreshell version	2016-11-08 11:32:38 +01:00
Axel Kohlmeyer	21694ca3a8	improve help and it through a pager, when screen == stdout	2016-11-07 17:10:12 -05:00
Axel Kohlmeyer	9b910d5511	make name of the actual executable (i.e. arg[0]) accessible	2016-11-07 17:07:40 -05:00
Anders Hafreager	054ab6bff3	Initializing pointers in USER-OMP	2016-11-07 21:07:10 +01:00
Anders Hafreager	616420cda8	Initializing pointers in USER-DIFFRACTION and USER-DPD	2016-11-07 20:51:36 +01:00
Anders Hafreager	fb3ac9afba	Initialize pointers in SNAP and SRD	2016-11-07 20:30:38 +01:00
Anders Hafreager	7cd7cda2d4	Initialize pointers in RIGID and SHOCK	2016-11-07 20:22:04 +01:00
Anders Hafreager	db0524278a	Initializing pointers in PERI, QEQ and REPLICA	2016-11-07 19:58:27 +01:00
Anders Hafreager	1ff75eaba2	Initialized pointers in MISC and MOLECULE	2016-11-07 17:15:48 +01:00
Anders Hafreager	30dede867a	Initialize pointers in MANYBODY and MC	2016-11-07 17:02:32 +01:00
Anders Hafreager	a5c6104d64	Initialize pointers in KSPACE	2016-11-07 16:54:59 +01:00
Anders Hafreager	c5869bdee2	Initialize pointers in GRANULAR	2016-11-07 16:33:50 +01:00
Anders Hafreager	e7a2c6b5d1	Initialize pointers in CORESHELL	2016-11-07 16:26:16 +01:00
Anders Hafreager	06959a9c59	Initialized pointers in BODY	2016-11-07 16:21:08 +01:00
Anders Hafreager	cd65d44d95	Initialize pointers in ASPHERE	2016-11-07 16:15:39 +01:00
Anders Hafreager	45f2e86dd6	NULLed ptrs in files	2016-11-07 16:07:37 +01:00
Anders Hafreager	f8226e8ae5	NULL ptrs in dump_custom and dump_image	2016-11-07 15:56:47 +01:00
Anders Hafreager	b221b15d24	NULLing ptrs in comm_brick and dump*.cpp	2016-11-07 15:50:18 +01:00
Axel Kohlmeyer	3a3d96b877	info styles also prints out pair styles	2016-11-04 18:18:40 -04:00
sjplimp	77bbf03f0f	Merge pull request #252 from akohlmey/preinstalled-vs-scm remove the misleading "(which it is by default)" from several doc files	2016-11-04 10:59:06 -06:00
sjplimp	7cff08ca0a	Merge pull request #249 from lammps/unstable Incorporate merge commits from "unstable" into "master"	2016-11-04 10:58:55 -06:00
sjplimp	f0131393e0	Merge pull request #248 from akohlmey/collected-small-fixes collected small bugfixes and updates	2016-11-04 10:58:42 -06:00
sjplimp	32e0a58343	Merge pull request #247 from akohlmey/bounds-error-with-code-line Propagate error error locations for a few more utility functions	2016-11-04 10:58:14 -06:00
sjplimp	60908eeab4	Merge pull request #246 from akohlmey/manybody-short-neighbor-list Manybody short neighbor list	2016-11-04 10:57:43 -06:00
sjplimp	8214555b29	Merge pull request #244 from ketankhare/patch-2 Enable write_data for dihedral style fourier	2016-11-04 10:57:20 -06:00
Steve Plimpton	f48b71f46b	added examples/threebody, fix reaxc/speceies/kk	2016-11-04 10:56:04 -06:00
Axel Kohlmeyer	6cc4eb19af	remove the misleading "(which it is by default)" from several doc files	2016-11-04 12:20:17 -04:00
Axel Kohlmeyer	7d23a0737e	add thorough checking for valid arguments to -partition or -p	2016-11-04 00:42:23 -04:00
Axel Kohlmeyer	02510ec321	add temporary force accumulation to local variables for vashishta styles	2016-11-02 22:32:30 -04:00
Axel Kohlmeyer	33140e5004	accumulate forces in temporary local variables for tersoff	2016-11-02 22:16:53 -04:00
Axel Kohlmeyer	639fb6f444	use local variables for more efficient force accumulation	2016-11-02 17:20:56 -04:00
Axel Kohlmeyer	b156771721	build short neighbor list for sw on based on ij parameters only	2016-11-02 17:09:32 -04:00
Axel Kohlmeyer	5d787f7f16	avoid tiny memory leak, when the restart command is specified multiple times	2016-11-01 21:39:12 -04:00
Axel Kohlmeyer	c8f4b55588	avoid uninitialized data for using ewald/disp with lj only	2016-11-01 16:48:30 -04:00
Axel Kohlmeyer	e13e4031cf	avoid memory leak in pppm/disp/omp	2016-11-01 16:48:00 -04:00
Axel Kohlmeyer	782a328080	avoid memory leaks when using kspace solvers for lennard-jones	2016-11-01 14:55:13 -04:00
Axel Kohlmeyer	e81ae21dbd	do not access uninitialized data for ewald/disp and pppm/disp	2016-11-01 14:54:16 -04:00
Axel Kohlmeyer	7fdd6e2807	remove work repetitions for 'the'	2016-11-01 11:40:07 -04:00
Axel Kohlmeyer	2e0d304c7e	remove word repetitions for 'a'	2016-11-01 11:36:11 -04:00
Anders Hafreager	f333d659c2	Using short neighborlists in neigh full	2016-10-29 22:54:43 +02:00
Anders Hafreager	51e2313fac	Using short neighbor lists	2016-10-29 22:35:29 +02:00
Anders Hafreager	e37d2b5c94	Calculating short neighbor lists	2016-10-29 22:20:37 +02:00
Axel Kohlmeyer	c4b86a25a7	Merge branch 'master' into manybody-short-neighbor-list	2016-10-28 11:12:21 -04:00
Axel Kohlmeyer	218e121b41	Merge branch 'master' into bounds-error-with-code-line	2016-10-28 11:11:28 -04:00
Axel Kohlmeyer	93d393aa69	permission cleanup in tools folder	2016-10-28 10:48:35 -04:00
Axel Kohlmeyer	4216be49f3	Merge branch 'master' into collected-small-fixes	2016-10-28 10:46:33 -04:00
Axel Kohlmeyer	3870780894	Merge branch 'master' into kokkos-vashishta	2016-10-28 10:43:05 -04:00
Axel Kohlmeyer	c3a1e72183	Version 27 Oct 2016	2016-10-27 11:40:36 -04:00
Axel Kohlmeyer	f9a9e27f5a	add error location propagation to atom->set_mass() and atom->check_mass()	2016-10-26 16:01:40 -04:00
Axel Kohlmeyer	35753b8f08	add error location propagation to force->bounds() and force->boundsbig()	2016-10-26 15:53:02 -04:00
Axel Kohlmeyer	f028a9a967	region cylinder is compatible with open_faces[2], so do not disallow it.	2016-10-26 15:04:18 -04:00
Axel Kohlmeyer	ef9f7c818e	fix off-by-one bug in buffer re-allocator	2016-10-26 10:14:08 -04:00
Axel Kohlmeyer	8e61bed2d8	add USER-OMP variant of manybody short neighbor list	2016-10-26 09:51:52 -04:00
Axel Kohlmeyer	3267b34590	simplify short neighbor list implementation. remove unneeded class member	2016-10-26 09:29:27 -04:00
Axel Kohlmeyer	0a417b4016	add short neighbor list support to pair style tersoff	2016-10-26 07:06:38 -04:00
Axel Kohlmeyer	399c0af150	consistent short neighbor list for vashishta and vashishta/table	2016-10-25 23:46:25 -04:00
Axel Kohlmeyer	e8b3f79690	fully tested multi-element compatible short neighbor list for Stillinger-Weber	2016-10-25 23:18:14 -04:00
stamoor	21619f6a2f	Recommitting reverted change git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15794 f3b2605a-c512-4ea7-a41b-209d697bcdaa (cherry picked from commit `c0b98f5299`)	2016-10-25 15:25:39 -04:00
Anders Hafreager	039bda9b61	Added updated vashishta for KOKKOS support (cherry picked from commit 96089a42547f625e70aa2ac3933d248d2731b731)	2016-10-25 15:07:10 -04:00
Anders Hafreager	6929603eef	Added KOKKOS vashishta (cherry picked from commit 5edc474bf0be574ddba96d00bb63894edf400ddb)	2016-10-25 15:07:10 -04:00
ketankhare	7f3f5e8c38	Clean whitespace	2016-10-25 14:46:44 -04:00
ketankhare	f350500e69	Enable write_data	2016-10-25 14:43:12 -04:00
ketankhare	d7c77a419d	Enable write_data for dihedral_fourier	2016-10-25 14:36:18 -04:00
Axel Kohlmeyer	d2da0fabb4	Version 20 Oct 2016	2016-10-19 15:29:13 -04:00
Axel Kohlmeyer	13ce1037f2	Version 18 Oct 2016	2016-10-18 15:46:56 -04:00
Axel Kohlmeyer	fa984b2c3b	Version 13 Oct 2016	2016-10-13 19:56:33 -04:00
Axel Kohlmeyer	8540a9f038	Version 11 Oct 2016	2016-10-11 17:10:24 -04:00
Axel Kohlmeyer	13b6eb1bae	Version 6 Oct 2016	2016-10-06 19:12:58 -04:00
Axel Kohlmeyer	d80a9def17	Version 5 Oct 2016	2016-10-05 18:49:08 -04:00
Axel Kohlmeyer	be4734bdce	Version 30 Sep 2016	2016-09-30 11:57:15 -04:00
Axel Kohlmeyer	2551619b07	Version 29 Sep 2016	2016-09-29 10:55:26 -04:00
Axel Kohlmeyer	d8bf149edc	Version 28 Sep 2016	2016-09-29 10:55:18 -04:00
Axel Kohlmeyer	473b12ded4	Version 26 Sep 2016	2016-09-29 10:55:10 -04:00
Axel Kohlmeyer	27c3149590	Version 21 Sep 2016	2016-09-29 10:54:59 -04:00
Axel Kohlmeyer	3b408d71fe	Version 20 Sep 2016	2016-09-29 10:53:40 -04:00