Merge pull request #202 from akohlmey/doc-formatting-fixes

collected documentation updates and corrections from LAMMPS-ICMS
Merge pull request #199 from akohlmey/small-changes
2016-10-06 15:49:44 -06:00 · 2016-10-06 15:49:24 -06:00 · 2016-10-06 15:47:41 -06:00 · 2016-10-06 17:23:10 -04:00 · 2016-10-06 17:21:38 -04:00 · 2016-10-06 15:48:18 -04:00
594 changed files with 58882 additions and 24358 deletions
--- a/doc/src/JPG/gran_funnel.png
+++ b/doc/src/JPG/gran_funnel.png
--- a/doc/src/JPG/gran_funnel_small.jpg
+++ b/doc/src/JPG/gran_funnel_small.jpg
--- a/doc/src/JPG/gran_mixer.png
+++ b/doc/src/JPG/gran_mixer.png
--- a/doc/src/JPG/gran_mixer_small.jpg
+++ b/doc/src/JPG/gran_mixer_small.jpg
--- 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="5 Oct 2016 version">
+<META NAME="docnumber" CONTENT="6 Oct 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
-5 Oct 2016 version :c,h4
+6 Oct 2016 version :c,h4
 Version info: :h4
@ -109,7 +109,7 @@ it gives quick access to documentation for all LAMMPS commands.
   :caption: User Documentation
   :name: userdoc
   :includehidden:
-   
+
   Section_intro
   Section_start
   Section_commands
@ -144,7 +144,7 @@ Indices and tables
 * :ref:`genindex`
 * :ref:`search`
-   
+
 END_RST -->
 <!-- HTML_ONLY -->
--- a/doc/src/Section_accelerate.txt
+++ b/doc/src/Section_accelerate.txt
@ -117,7 +117,7 @@ PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to
 achieve the same accuracy as 4-FFT PPPM. For problems where the FFT
 cost is the performance bottleneck (typically large problems running
 on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM.
-  
+
 Staggered PPPM performs calculations using two different meshes, one
 shifted slightly with respect to the other.  This can reduce force
 aliasing errors and increase the accuracy of the method, but also
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@ -37,14 +37,14 @@ simulation with all the settings.  Rather, the input script is read
 one line at a time and each command takes effect when it is read.
 Thus this sequence of commands:
-timestep 0.5 
+timestep 0.5
-run      100 
+run      100
 run      100 :pre
 does something different than this sequence:
-run      100 
+run      100
-timestep 0.5 
+timestep 0.5
 run      100 :pre
 In the first case, the specified timestep (0.5 fmsec) is used for two
@ -97,7 +97,7 @@ single leading "#" will comment out the entire command.
 (3) The line is searched repeatedly for $ characters, which indicate
 variables that are replaced with a text string.  See an exception in
-(6).  
+(6).
 If the $ is followed by curly brackets, then the variable name is the
 text inside the curly brackets.  If no curly brackets follow the $,
@ -123,7 +123,7 @@ variable X equal (xlo+xhi)/2+sqrt(v_area)
 region 1 block $X 2 INF INF EDGE EDGE
 variable X delete :pre
-can be replaced by 
+can be replaced by
 region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
@ -599,6 +599,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "viscous"_fix_viscous.html,
 "wall/colloid"_fix_wall.html,
 "wall/gran"_fix_wall_gran.html,
 "wall/gran/region"_fix_wall_gran_region.html,
 "wall/harmonic"_fix_wall.html,
 "wall/lj1043"_fix_wall.html,
 "wall/lj126"_fix_wall.html,
--- a/doc/src/Section_errors.txt
+++ b/doc/src/Section_errors.txt
@ -159,7 +159,7 @@ As a last resort, you can send an email directly to the
 These are two alphabetic lists of the "ERROR"_#error and
 "WARNING"_#warn messages LAMMPS prints out and the reason why.  If the
 explanation here is not sufficient, the documentation for the
-offending command may help.  
+offending command may help.
 Error and warning messages also list the source file and line number
 where the error was generated.  For example, this message
--- a/doc/src/Section_example.txt
+++ b/doc/src/Section_example.txt
@ -54,30 +54,30 @@ accelerate: run with various acceleration options (OpenMP, GPU, Phi)
 balance:  dynamic load balancing, 2d system
 body:     body particles, 2d system
 colloid:  big colloid particles in a small particle solvent, 2d system
-comb:	  models using the COMB potential
+comb:     models using the COMB potential
 coreshell: core/shell model using CORESHELL package
-crack:	  crack propagation in a 2d solid
+crack:    crack propagation in a 2d solid
 deposit:  deposit atoms and molecules on a surface
 dipole:   point dipolar particles, 2d system
 dreiding: methanol via Dreiding FF
 eim:      NaCl using the EIM potential
 ellipse:  ellipsoidal particles in spherical solvent, 2d system
-flow:	  Couette and Poiseuille flow in a 2d channel
+flow:     Couette and Poiseuille flow in a 2d channel
 friction: frictional contact of spherical asperities between 2d surfaces
 hugoniostat: Hugoniostat shock dynamics
-indent:	  spherical indenter into a 2d solid
+indent:   spherical indenter into a 2d solid
 kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
-meam:	  MEAM test for SiC and shear (same as shear examples)
+meam:     MEAM test for SiC and shear (same as shear examples)
-melt:	  rapid melt of 3d LJ system
+melt:     rapid melt of 3d LJ system
 micelle:  self-assembly of small lipid-like molecules into 2d bilayers
-min:	  energy minimization of 2d LJ melt
+min:      energy minimization of 2d LJ melt
-msst:	  MSST shock dynamics
+msst:     MSST shock dynamics
 nb3b:     use of nonbonded 3-body harmonic pair style
-neb:	  nudged elastic band (NEB) calculation for barrier finding
+neb:      nudged elastic band (NEB) calculation for barrier finding
-nemd:	  non-equilibrium MD of 2d sheared system
+nemd:     non-equilibrium MD of 2d sheared system
 obstacle: flow around two voids in a 2d channel
 peptide:  dynamics of a small solvated peptide chain (5-mer)
-peri:	  Peridynamic model of cylinder impacted by indenter
+peri:     Peridynamic model of cylinder impacted by indenter
 pour:     pouring of granular particles into a 3d box, then chute flow
 prd:      parallel replica dynamics of vacancy diffusion in bulk Si
 python:   using embedded Python in a LAMMPS input script
@ -120,7 +120,7 @@ browser.
 Uppercase directories :h4
 ASPHERE: various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc
-COUPLE: examples of how to use LAMMPS as a library 
+COUPLE: examples of how to use LAMMPS as a library
 DIFFUSE: compute diffusion coefficients via several methods
 ELASTIC: compute elastic constants at zero temperature
 ELASTIC_T: compute elastic constants at finite temperature
--- a/doc/src/Section_history.txt
+++ b/doc/src/Section_history.txt
@ -37,7 +37,7 @@ pitfalls or alternatives.
 Please see some of the closed issues for examples of how to
 suggest code enhancements, submit proposed changes, or report
-elated issues and how they are resoved. 
+possible bugs and how they are resoved.
 As an alternative to using GitHub, you may e-mail the
 "core developers"_http://lammps.sandia.gov/authors.html or send
@ -71,7 +71,7 @@ a parallel framework similar to LAMMPS. Most notably, these have
 included many-body potentials - Stillinger-Weber, Tersoff, ReaxFF -
 and the associated charge-equilibration routines needed for ReaxFF.
-The "History link"_http://lammps.sandia.gov/history.html on the 
+The "History link"_http://lammps.sandia.gov/history.html on the
 LAMMPS WWW page gives a timeline of features added to the
 C++ open-source version of LAMMPS over the last several years.
@ -80,7 +80,7 @@ site"_lws, except for Warp & GranFlow which were primarily used
 internally.  A brief listing of their features is given here.
 LAMMPS 2001
-    
+
    F90 + MPI
    dynamic memory
    spatial-decomposition parallelism
@ -96,7 +96,7 @@ LAMMPS 2001
    user-defined diagnostics :ul
 LAMMPS 99
-    
+
    F77 + MPI
    static memory allocation
    spatial-decomposition parallelism
--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@ -4,7 +4,7 @@
 :link(ld,Manual.html)
 :link(lc,Section_commands.html#comm)
-:line 
+:line
 6. How-to discussions :h3
@ -68,7 +68,7 @@ Look at the {in.chain} input script provided in the {bench} directory
 of the LAMMPS distribution to see the original script that these 2
 scripts are based on.  If that script had the line
-restart	        50 tmp.restart :pre
+restart         50 tmp.restart :pre
 added to it, it would produce 2 binary restart files (tmp.restart.50
 and tmp.restart.100) as it ran.
@ -76,17 +76,17 @@ and tmp.restart.100) as it ran.
 This script could be used to read the 1st restart file and re-run the
 last 50 timesteps:
-read_restart	tmp.restart.50 :pre
+read_restart    tmp.restart.50 :pre
-neighbor	0.4 bin
+neighbor        0.4 bin
-neigh_modify	every 1 delay 1 :pre
+neigh_modify    every 1 delay 1 :pre
-fix		1 all nve
+fix             1 all nve
-fix		2 all langevin 1.0 1.0 10.0 904297 :pre
+fix             2 all langevin 1.0 1.0 10.0 904297 :pre
-timestep	0.012 :pre
+timestep        0.012 :pre
-run		50 :pre
+run             50 :pre
 Note that the following commands do not need to be repeated because
 their settings are included in the restart file: {units, atom_style,
@ -107,25 +107,25 @@ lmp_g++ -r tmp.restart.50 tmp.restart.data :pre
 Then, this script could be used to re-run the last 50 steps:
-units		lj
+units           lj
-atom_style	bond
+atom_style      bond
-pair_style	lj/cut 1.12
+pair_style      lj/cut 1.12
-pair_modify	shift yes
+pair_modify     shift yes
-bond_style	fene
+bond_style      fene
 special_bonds   0.0 1.0 1.0 :pre
-read_data	tmp.restart.data :pre
+read_data       tmp.restart.data :pre
-neighbor	0.4 bin
+neighbor        0.4 bin
-neigh_modify	every 1 delay 1 :pre
+neigh_modify    every 1 delay 1 :pre
-fix		1 all nve
+fix             1 all nve
-fix		2 all langevin 1.0 1.0 10.0 904297 :pre
+fix             2 all langevin 1.0 1.0 10.0 904297 :pre
-timestep	0.012 :pre
+timestep        0.012 :pre
-reset_timestep	50
+reset_timestep  50
-run		50 :pre
+run             50 :pre
 Note that nearly all the settings specified in the original {in.chain}
 script must be repeated, except the {pair_coeff} and {bond_coeff}
@ -522,7 +522,7 @@ H mass = 1.008
 O charge = -1.040
 H charge = 0.520
 r0 of OH bond = 0.9572
-theta of HOH angle = 104.52 
+theta of HOH angle = 104.52
 OM distance = 0.15
 LJ epsilon of O-O = 0.1550
 LJ sigma of O-O = 3.1536
@ -629,7 +629,7 @@ the SPC and SPC/E models.
 Wikipedia also has a nice article on "water
 models"_http://en.wikipedia.org/wiki/Water_model.
-:line 
+:line
 6.10 Coupling LAMMPS to other codes :link(howto_10),h4
@ -729,7 +729,7 @@ LAMMPS and half to the other code and run both codes simultaneously
 before syncing them up periodically.  Or it might instantiate multiple
 instances of LAMMPS to perform different calculations.
-:line 
+:line
 6.11 Visualizing LAMMPS snapshots :link(howto_11),h4
@ -832,7 +832,7 @@ rotation of [A], [B], and [C] and can be computed as follows:
 where A = | [A] | indicates the scalar length of [A]. The hat symbol (^)
 indicates the corresponding unit vector. {beta} and {gamma} are angles
-between the vectors described below. Note that by construction, 
+between the vectors described below. Note that by construction,
 [a], [b], and [c] have strictly positive x, y, and z components, respectively.
 If it should happen that
 [A], [B], and [C] form a left-handed basis, then the above equations
@ -841,17 +841,17 @@ to first apply an inversion. This can be achieved
 by interchanging two basis vectors or by changing the sign of one of them.
 For consistency, the same rotation/inversion applied to the basis vectors
-must also be applied to atom positions, velocities, 
+must also be applied to atom positions, velocities,
 and any other vector quantities.
-This can be conveniently achieved by first converting to 
+This can be conveniently achieved by first converting to
 fractional coordinates in the
 old basis and then converting to distance coordinates in the new basis.
 The transformation is given by the following equation:
 :c,image(Eqs/rotate.jpg)
-where {V} is the volume of the box, [X] is the original vector quantity and 
+where {V} is the volume of the box, [X] is the original vector quantity and
-[x] is the vector in the LAMMPS basis. 
+[x] is the vector in the LAMMPS basis.
 There is no requirement that a triclinic box be periodic in any
 dimension, though it typically should be in at least the 2nd dimension
@ -938,17 +938,17 @@ defined above.  The relationship between these 6 quantities
 (a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) =
 (xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows:
-:c,image(Eqs/box.jpg) 
+:c,image(Eqs/box.jpg)
 The inverse relationship can be written as follows:
-:c,image(Eqs/box_inverse.jpg) 
+:c,image(Eqs/box_inverse.jpg)
-The values of {a}, {b}, {c} , {alpha}, {beta} , and {gamma} can be printed 
+The values of {a}, {b}, {c} , {alpha}, {beta} , and {gamma} can be printed
-out or accessed by computes using the 
+out or accessed by computes using the
-"thermo_style custom"_thermo_style.html keywords 
+"thermo_style custom"_thermo_style.html keywords
 {cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, {cellgamma},
-respectively. 
+respectively.
 As discussed on the "dump"_dump.html command doc page, when the BOX
 BOUNDS for a snapshot is written to a dump file for a triclinic box,
@ -2092,11 +2092,11 @@ lattice      fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
 region       box block 0 4 0 4 0 4
 create_box   1 box
 create_atoms 1 box
-mass	     1 39.948
+mass         1 39.948
 pair_style   lj/cut 13.0
 pair_coeff   * * 0.2381 3.405
 timestep     $\{dt\}
-thermo	     $d :pre
+thermo       $d :pre
 # equilibration and thermalization :pre
@ -2130,7 +2130,7 @@ but uses the Einstein formulation, analogous to the Einstein
 mean-square-displacement formulation for self-diffusivity. The
 time-integrated momentum fluxes play the role of Cartesian
 coordinates, whose mean-square displacement increases linearly
-with time at sufficiently long times. 
+with time at sufficiently long times.
 :line
@ -2510,8 +2510,8 @@ the electrostatic environment inducing polarizability.
 Technically, shells are attached to the cores by a spring force f =
 k*r where k is a parametrized spring constant and r is the distance
 between the core and the shell. The charges of the core and the shell
-add up to the ion charge, thus q(ion) = q(core) + q(shell). This 
+add up to the ion charge, thus q(ion) = q(core) + q(shell). This
-setup introduces the ion polarizability (alpha) given by 
+setup introduces the ion polarizability (alpha) given by
 alpha = q(shell)^2 / k. In a
 similar fashion the mass of the ion is distributed on the core and the
 shell with the core having the larger mass.
@ -2526,7 +2526,7 @@ for NaCl, as found in examples/coreshell, has this format:
 432   atoms  # core and shell atoms
 216   bonds  # number of core/shell springs :pre
-4     atom types  # 2 cores and 2 shells for Na and Cl 
+4     atom types  # 2 cores and 2 shells for Na and Cl
 2     bond types :pre
 0.0 24.09597 xlo xhi
@ -2545,19 +2545,19 @@ Atoms :pre
 1    1    2   1.5005    0.00000000   0.00000000   0.00000000 # core of core/shell pair 1
 2    1    4  -2.5005    0.00000000   0.00000000   0.00000000 # shell of core/shell pair 1
 3    2    1   1.5056    4.01599500   4.01599500   4.01599500 # core of core/shell pair 2
-4    2    3  -0.5056    4.01599500   4.01599500   4.01599500 # shell of core/shell pair 2 
+4    2    3  -0.5056    4.01599500   4.01599500   4.01599500 # shell of core/shell pair 2
 (...) :pre
 Bonds   # Bond topology for spring forces :pre
 1     2     1     2   # spring for core/shell pair 1
-2     2     3     4   # spring for core/shell pair 2 
+2     2     3     4   # spring for core/shell pair 2
 (...) :pre
 Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only
 defined between the shells.  Coulombic interactions are defined
 between all cores and shells.  If desired, additional bonds can be
-specified between cores.  
+specified between cores.
 The "special_bonds"_special_bonds.html command should be used to
 turn-off the Coulombic interaction within core/shell pairs, since that
@ -2620,7 +2620,7 @@ Note that to perform thermostatting using this definition of
 temperature, the "fix modify temp"_fix_modify.html command should be
 used to assign the compute to the thermostat fix.  Likewise the
 "thermo_modify temp"_thermo_modify.html command can be used to make
-this temperature be output for the overall system. 
+this temperature be output for the overall system.
 For the NaCl example, this can be done as follows:
@ -2632,13 +2632,13 @@ fix thermostatequ all nve                               # integrator as needed f
 fix_modify thermoberendsen temp CSequ
 thermo_modify temp CSequ                                # output of center-of-mass derived temperature :pre
-If "compute temp/cs"_compute_temp_cs.html is used, the decoupled 
+If "compute temp/cs"_compute_temp_cs.html is used, the decoupled
-relative motion of the core and the shell should in theory be 
+relative motion of the core and the shell should in theory be
 stable.  However numerical fluctuation can introduce a small
 momentum to the system, which is noticable over long trajectories.
-Therefore it is recomendable to use the "fix 
+Therefore it is recomendable to use the "fix
-momentum"_fix_momentum.html command in combination with "compute 
+momentum"_fix_momentum.html command in combination with "compute
-temp/cs"_compute_temp_cs.html when equilibrating the system to 
+temp/cs"_compute_temp_cs.html when equilibrating the system to
 prevent any drift.
 When intializing the velocities of a system with core/shell pairs, it
@ -2661,17 +2661,17 @@ to the electrostatic environment.  This fast movement also limits the
 timestep size that can be used.
 The primary literature of the adiabatic core/shell model suggests that
-the fast relative motion of the core/shell pairs only allows negligible 
+the fast relative motion of the core/shell pairs only allows negligible
 energy transfer to the environment. Therefore it is not intended to
 decouple the core/shell degree of freedom from the physical system
 during production runs. In other words, the "compute
 temp/cs"_compute_temp_cs.html command should not be used during
-production runs and is only required during equilibration. This way one 
+production runs and is only required during equilibration. This way one
-is consistent with literature (based on the code packages DL_POLY or 
+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 a small drift
-in total energy over time.  This internal energy can be monitored 
+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
 energies of each core/shell pair can then be summed using the sum()
@ -2702,14 +2702,14 @@ The additional section in the date file would be formatted like this:
 CS-Info         # header of additional section :pre
-1   1           # column 1 = atom ID, column 2 = core/shell ID 
+1   1           # column 1 = atom ID, column 2 = core/shell ID
-2   1   
+2   1
-3   2   
+3   2
-4   2   
+4   2
-5   3   
+5   3
-6   3   
+6   3
-7   4   
+7   4
-8   4   
+8   4
 (...) :pre
 :line
--- a/doc/src/Section_intro.txt
+++ b/doc/src/Section_intro.txt
@ -181,7 +181,7 @@ Atom creation :h5
  displace atoms :ul
 Ensembles, constraints, and boundary conditions :h5
-("fix"_fix.html command) 
+("fix"_fix.html command)
  2d or 3d systems
  orthogonal or non-orthogonal (triclinic symmetry) simulation domains
@ -199,7 +199,7 @@ Ensembles, constraints, and boundary conditions :h5
  variety of additional boundary conditions and constraints :ul
 Integrators :h5
-("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands) 
+("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands)
  velocity-Verlet integrator
  Brownian dynamics
@ -213,7 +213,7 @@ Diagnostics :h5
  see the various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul
 Output :h5
-("dump"_dump.html, "restart"_restart.html commands) 
+("dump"_dump.html, "restart"_restart.html commands)
  log file of thermodynamic info
  text dump files of atom coords, velocities, other per-atom quantities
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@ -182,7 +182,7 @@ Supporting info: "atom_style body"_atom_style.html, "body"_body.html,
 "pair_style body"_pair_body.html, examples/body
 :line
- 
+
 CLASS2 package :link(CLASS2),h5
 Contents: Bond, angle, dihedral, improper, and pair styles for the
@ -206,9 +206,9 @@ Supporting info: "bond_style class2"_bond_class2.html, "angle_style
 class2"_angle_class2.html, "dihedral_style
 class2"_dihedral_class2.html, "improper_style
 class2"_improper_class2.html, "pair_style lj/class2"_pair_class2.html
- 
+
 :line
- 
+
 COLLOID package :link(COLLOID),h5
 Contents: Support for coarse-grained colloidal particles.  Wall fix
@ -239,9 +239,9 @@ lubricate"_pair_lubricate.html, "pair_style
 lubricateU"_pair_lubricateU.html, examples/colloid, examples/srd
 :line
- 
+
 COMPRESS package :link(COMPRESS),h5
- 
+
 Contents: Support for compressed output of dump files via the zlib
 compression library, using dump styles with a "gz" in their style
 name.
@ -271,7 +271,7 @@ atom/gz"_dump.html, "dump cfg/gz"_dump.html, "dump
 custom/gz"_dump.html, "dump xyz/gz"_dump.html
 :line
- 
+
 CORESHELL package :link(CORESHELL),h5
 Contents: Compute and pair styles that implement the adiabatic
@ -302,7 +302,7 @@ buck/coul/long/cs"_pair_cs.html, pair_style
 lj/cut/coul/long/cs"_pair_lj.html, examples/coreshell
 :line
- 
+
 DIPOLE package :link(DIPOLE),h5
 Contents: An atom style and several pair styles to support point
@ -326,9 +326,9 @@ Supporting info: "atom_style dipole"_atom_style.html, "pair_style
 lj/cut/dipole/cut"_pair_dipole.html, "pair_style
 lj/cut/dipole/long"_pair_dipole.html, "pair_style
 lj/long/dipole/long"_pair_dipole.html, examples/dipole
- 
+
 :line
- 
+
 GPU package :link(GPU),h5
 Contents: Dozens of pair styles and a version of the PPPM long-range
@ -385,9 +385,9 @@ Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5
 for any pair style listed with a (g),
 "kspace_style"_kspace_style.html, "package gpu"_package.html,
 examples/accelerate, bench/FERMI, bench/KEPLER
- 
+
 :line
- 
+
 GRANULAR package :link(GRANULAR),h5
 Contents: Fixes and pair styles that support models of finite-size
@ -412,9 +412,9 @@ Supporting info: "Section 6.6"_Section_howto.html#howto_6, "fix
 pour"_fix_pour.html, "fix wall/gran"_fix_wall_gran.html, "pair_style
 gran/hooke"_pair_gran.html, "pair_style
 gran/hertz/history"_pair_gran.html, examples/pour, bench/in.chute
- 
+
 :line
- 
+
 KIM package :link(KIM),h5
 Contents: A pair style that interfaces to the Knowledge Base for
@ -443,9 +443,9 @@ Make.py -p ^kim -a machine :pre
 Supporting info: src/KIM/README, lib/kim/README, "pair_style
 kim"_pair_kim.html, examples/kim
- 
+
 :line
- 
+
 KOKKOS package :link(KOKKOS),h5
 Contents: Dozens of atom, pair, bond, angle, dihedral, improper styles
@ -501,7 +501,7 @@ for any pair style listed with a (k), "package kokkos"_package.html,
 examples/accelerate, bench/FERMI, bench/KEPLER
 :line
- 
+
 KSPACE package :link(KSPACE),h5
 Contents: A variety of long-range Coulombic solvers, and pair styles
@ -543,7 +543,7 @@ which have "long" or "msm" in their style name,
 examples/peptide, bench/in.rhodo
 :line
- 
+
 MANYBODY package :link(MANYBODY),h5
 Contents: A variety of many-body and bond-order potentials.  These
@ -565,14 +565,14 @@ make machine :pre
 Make.py -p ^manybody -a machine :pre
-Supporting info: 
+Supporting info:
- 
+
 Examples: Pair Styles section of "Section
 3.5"_Section_commands.html#cmd_5, examples/comb, examples/eim,
 examples/nb3d, examples/vashishta
 :line
- 
+
 MC package :link(MC),h5
 Contents: Several fixes and a pair style that have Monte Carlo (MC) or
@ -598,9 +598,9 @@ Supporting info: "fix atom/swap"_fix_atom_swap.html, "fix
 bond/break"_fix_bond_break.html, "fix
 bond/create"_fix_bond_create.html, "fix bond/swap"_fix_bond_swap.html,
 "fix gcmc"_fix_gcmc.html, "pair_style dsmc"_pair_dsmc.html
- 
+
 :line
- 
+
 MEAM package :link(MEAM),h5
 Contents: A pair style for the modified embedded atom (MEAM)
@ -644,9 +644,9 @@ Make.py -p ^meam -a machine :pre
 Supporting info: lib/meam/README, "pair_style meam"_pair_meam.html,
 examples/meam
- 
+
 :line
- 
+
 MISC package :link(MISC),h5
 Contents: A variety of computes, fixes, and pair styles that are not
@ -670,9 +670,9 @@ Make.py -p ^misc -a machine :pre
 Supporting info: "compute ti"_compute_ti.html, "fix
 evaporate"_fix_evaporate.html, "fix tmm"_fix_ttm.html, "fix
 viscosity"_fix_viscosity.html, examples/misc
- 
+
 :line
- 
+
 MOLECULE package :link(MOLECULE),h5
 Contents: A large number of atom, pair, bond, angle, dihedral,
@ -704,7 +704,7 @@ lj/charmm/coul/charmm"_pair_charmm.html,
 examples/micelle, examples/peptide, bench/in.chain, bench/in.rhodo
 :line
- 
+
 MPIIO package :link(MPIIO),h5
 Contents: Support for parallel output/input of dump and restart files
@ -729,9 +729,9 @@ Make.py -p ^mpiio -a machine :pre
 Supporting info: "dump"_dump.html, "restart"_restart.html,
 "write_restart"_write_restart.html, "read_restart"_read_restart.html
- 
+
 :line
- 
+
 OPT package :link(OPT),h5
 Contents: A handful of pair styles with an "opt" in their style name
@ -768,7 +768,7 @@ Supporting info: "Section 5.3"_Section_accelerate.html#acc_3,
 listed with an (t), examples/accelerate, bench/KEPLER
 :line
- 
+
 PERI package :link(PERI),h5
 Contents: Support for the Peridynamics method, a particle-based
@ -796,9 +796,9 @@ Supporting info:
 "doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf, "atom_style
 peri"_atom_style.html, "compute damage/atom"_compute_damage_atom.html,
 "pair_style peri/pmb"_pair_peri.html, examples/peri
- 
+
 :line
- 
+
 POEMS package :link(POEMS),h5
 Contents: A fix that wraps the Parallelizable Open source Efficient
@ -839,7 +839,7 @@ Supporting info: src/POEMS/README, lib/poems/README,
 "fix poems"_fix_poems.html, examples/rigid
 :line
- 
+
 PYTHON package :link(PYTHON),h5
 Contents: A "python"_python.html command which allow you to execute
@ -873,9 +873,9 @@ make machine :pre
 Make.py -p ^python -a machine :pre
 Supporting info: examples/python
- 
+
 :line
- 
+
 QEQ package :link(QEQ),h5
 Contents: Several fixes for performing charge equilibration (QEq) via
@ -897,9 +897,9 @@ make machine :pre
 Make.py -p ^qeq -a machine :pre
 Supporting info: "fix qeq/*"_fix_qeq.html, examples/qeq
- 
+
 :line
- 
+
 REAX package :link(REAX),h5
 Contents: A pair style for the ReaxFF potential, a universal reactive
@ -941,9 +941,9 @@ Make.py -p ^reax -a machine :pre
 Supporting info: lib/reax/README, "pair_style reax"_pair_reax.html,
 "fix reax/bonds"_fix_reax_bonds.html, examples/reax
- 
+
 :line
- 
+
 REPLICA package :link(REPLICA),h5
 Contents: A collection of multi-replica methods that are used by
@ -978,7 +978,7 @@ Supporting info: "Section 6.5"_Section_howto.html#howto_5,
 examples/tad
 :line
- 
+
 RIGID package :link(RIGID),h5
 Contents: A collection of computes and fixes which enforce rigid
@ -1005,7 +1005,7 @@ Supporting info: "compute erotate/rigid"_compute_erotate_rigid.html,
 rigid/*"_fix_rigid.html, examples/ASPHERE, examples/rigid
 :line
- 
+
 SHOCK package :link(SHOCK),h5
 Contents: A small number of fixes useful for running impact
@ -1028,15 +1028,15 @@ Make.py -p ^shock -a machine :pre
 Supporting info: "fix append/atoms"_fix_append_atoms.html, "fix
 msst"_fix_msst.html, "fix nphug"_fix_nphug.html, "fix
 wall/piston"_fix_wall_piston.html, examples/hugoniostat, examples/msst
- 
+
 :line
- 
+
 SNAP package :link(SNAP),h5
 Contents: A pair style for the spectral neighbor analysis potential
 (SNAP), which is an empirical potential which can be quantum accurate
-when fit to an archive of DFT data.  Computes useful for analyzing 
+when fit to an archive of DFT data.  Computes useful for analyzing
-properties of the potential are also included. 
+properties of the potential are also included.
 To install via make or Make.py:
@ -1055,9 +1055,9 @@ Make.py -p ^snap -a machine :pre
 Supporting info: "pair snap"_pair_snap.html, "compute
 sna/atom"_compute_sna_atom.html, "compute snad/atom"_compute_sna_atom.html,
 "compute snav/atom"_compute_sna_atom.html, examples/snap
- 
+
 :line
- 
+
 SRD package :link(SRD),h5
 Contents: Two fixes which implement the Stochastic Rotation Dynamics
@ -1080,9 +1080,9 @@ Make.py -p ^srd -a machine :pre
 Supporting info: "fix srd"_fix_srd.html, "fix
 wall/srd"_fix_wall_srd.html, examples/srd, examples/ASPHERE
- 
+
 :line
- 
+
 VORONOI package :link(VORONOI),h5
 Contents: A "compute voronoi/atom"_compute_voronoi_atom.html command
@ -1129,9 +1129,9 @@ Make.py -p ^voronoi -a machine :pre
 Supporting info: src/VORONOI/README, lib/voronoi/README, "compute
 voronoi/atom"_compute_voronoi_atom.html, examples/voronoi
- 
+
 :line
- 
+
 4.2 User packages :h4,link(pkg_2)
 The current list of user-contributed packages is as follows:
@ -1302,7 +1302,7 @@ fix.  The COLVARS library itself is written and maintained by Giacomo
 Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and Jerome
 Henin (LISM, CNRS, Marseille, France).  Contact them directly if you
 have questions.
- 
+
 :line
 USER-DIFFRACTION package :link(USER-DIFFRACTION),h5
@ -1380,7 +1380,7 @@ in 2007.  See src/USER-EFF/README for more details.  There are
 auxiliary tools for using this package in tools/eff; see its README
 file.
-Supporting info: 
+Supporting info:
 Author: Andres Jaramillo-Botero at CalTech (ajaramil at
 wag.caltech.edu).  Contact him directly if you have questions.
@ -1456,21 +1456,21 @@ LINKFLAGS: add -fopenmp :ul
 For Phi mode add the following in addition to the CPU mode flags:
-CCFLAGS: add -DLMP_INTEL_OFFLOAD and 
+CCFLAGS: add -DLMP_INTEL_OFFLOAD and
 LINKFLAGS: add -offload :ul
 And also add this to CCFLAGS:
 -offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\"" :pre
-Examples: 
+Examples:
 :line
 USER-LB package :link(USER-LB),h5
-Supporting info: 
+Supporting info:
- 
+
 This package contains a LAMMPS implementation of a background
 Lattice-Boltzmann fluid, which can be used to model MD particles
 influenced by hydrodynamic forces.
@ -1489,8 +1489,8 @@ Examples: examples/USER/lb
 USER-MGPT package :link(USER-MGPT),h5
-Supporting info: 
+Supporting info:
- 
+
 This package contains a fast implementation for LAMMPS of
 quantum-based MGPT multi-ion potentials.  The MGPT or model GPT method
 derives from first-principles DFT-based generalized pseudopotential
@ -1521,8 +1521,8 @@ Examples: examples/USER/mgpt
 USER-MISC package :link(USER-MISC),h5
-Supporting info: 
+Supporting info:
- 
+
 The files in this package are a potpourri of (mostly) unrelated
 features contributed to LAMMPS by users.  Each feature is a single
 pair of files (*.cpp and *.h).
@ -1548,8 +1548,8 @@ Examples: examples/USER/misc
 USER-MANIFOLD package :link(USER-MANIFOLD),h5
-Supporting info: 
+Supporting info:
- 
+
 This package contains a dump molfile command which uses molfile
 plugins that are bundled with the
 "VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and
@ -1574,8 +1574,8 @@ Contact him directly if you have questions.
 USER-MOLFILE package :link(USER-MOLFILE),h5
-Supporting info: 
+Supporting info:
- 
+
 This package contains a dump molfile command which uses molfile
 plugins that are bundled with the
 "VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and
@ -1600,12 +1600,12 @@ The person who created this package is Axel Kohlmeyer at Temple U
 USER-OMP package :link(USER-OMP),h5
-Supporting info: 
+Supporting info:
- 
+
 This package provides OpenMP multi-threading support and
 other optimizations of various LAMMPS pair styles, dihedral
 styles, and fix styles.
- 
+
 See this section of the manual to get started:
 "Section 5.3"_Section_accelerate.html#acc_3
@ -1643,8 +1643,8 @@ Examples: examples/USER/phonon
 USER-QMMM package :link(USER-QMMM),h5
-Supporting info: 
+Supporting info:
- 
+
 This package provides a fix qmmm command which allows LAMMPS to be
 used in a QM/MM simulation, currently only in combination with pw.x
 code from the "Quantum ESPRESSO"_espresso package.
@ -1667,11 +1667,11 @@ The person who created this package is Axel Kohlmeyer at Temple U
 (akohlmey at gmail.com).  Contact him directly if you have questions.
 :line
- 
+
 USER-QTB package :link(USER-QTB),h5
-Supporting info: 
+Supporting info:
- 
+
 This package provides a self-consistent quantum treatment of the
 vibrational modes in a classical molecular dynamics simulation.  By
 coupling the MD simulation to a colored thermostat, it introduces zero
@ -1701,16 +1701,16 @@ Examples: examples/USER/qtb
 USER-QUIP package :link(USER-QUIP),h5
-Supporting info: 
+Supporting info:
- 
+
 Examples: examples/USER/quip
 :line
 USER-REAXC package :link(USER-REAXC),h5
-Supporting info: 
+Supporting info:
- 
+
 This package contains a implementation for LAMMPS of the ReaxFF force
 field.  ReaxFF uses distance-dependent bond-order functions to
 represent the contributions of chemical bonding to the potential
@ -1748,24 +1748,24 @@ Examples: examples/reax
 USER-SMD package :link(USER-SMD),h5
-Supporting info: 
+Supporting info:
- 
+
 This package implements smoothed Mach dynamics (SMD) in
 LAMMPS.  Currently, the package has the following features:
 * Does liquids via traditional Smooth Particle Hydrodynamics (SPH)
-* Also solves solids mechanics problems via a state of the art 
+* Also solves solids mechanics problems via a state of the art
  stabilized meshless method with hourglass control.
-* Can specify hydrostatic interactions independently from material 
+* Can specify hydrostatic interactions independently from material
  strength models, i.e. pressure and deviatoric stresses are separated.
-* Many material models available (Johnson-Cook, plasticity with 
+* Many material models available (Johnson-Cook, plasticity with
-  hardening, Mie-Grueneisen, Polynomial EOS).  Easy to add new 
+  hardening, Mie-Grueneisen, Polynomial EOS).  Easy to add new
  material models.
-* Rigid boundary conditions (walls) can be loaded as surface geometries 
+* Rigid boundary conditions (walls) can be loaded as surface geometries
  from *.STL files.
 See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started.
@ -1783,8 +1783,8 @@ Examples: examples/USER/smd
 USER-SMTBQ package :link(USER-SMTBQ),h5
-Supporting info: 
+Supporting info:
- 
+
 This package implements the Second Moment Tight Binding - QEq (SMTB-Q)
 potential for the description of ionocovalent bonds in oxides.
@ -1806,22 +1806,22 @@ Examples: examples/USER/smtbq
 USER-SPH package :link(USER-SPH),h5
-Supporting info: 
+Supporting info:
 This package implements smoothed particle hydrodynamics (SPH) in
 LAMMPS.  Currently, the package has the following features:
-* Tait, ideal gas, Lennard-Jones equation of states, full support for 
+* Tait, ideal gas, Lennard-Jones equation of states, full support for
  complete (i.e. internal-energy dependent) equations of state
 * Plain or Monaghans XSPH integration of the equations of motion
 * Density continuity or density summation to propagate the density field
-* Commands to set internal energy and density of particles from the 
+* Commands to set internal energy and density of particles from the
  input script
-* Output commands to access internal energy and density for dumping and 
+* Output commands to access internal energy and density for dumping and
  thermo output
 See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started.
@ -1839,7 +1839,7 @@ Examples: examples/USER/sph
 USER-TALLY package :link(USER-TALLY),h5
-Supporting info: 
+Supporting info:
 Examples: examples/USER/tally
--- a/doc/src/Section_python.txt
+++ b/doc/src/Section_python.txt
@ -23,7 +23,7 @@ In Python lingo, this is "embedding" Python in LAMMPS.
 This section describes how to do both.
 11.1 "Overview of running LAMMPS from Python"_#py_1
-11.2 "Overview of using Python from a LAMMPS script"_#py_2 
+11.2 "Overview of using Python from a LAMMPS script"_#py_2
 11.3 "Building LAMMPS as a shared library"_#py_3
 11.4 "Installing the Python wrapper into Python"_#py_4
 11.5 "Extending Python with MPI to run in parallel"_#py_5
@ -503,7 +503,7 @@ one of several ways:
 The last command requires that the first line of the script be
 something like this:
-#!/usr/local/bin/python 
+#!/usr/local/bin/python
 #!/usr/local/bin/python -i :pre
 where the path points to where you have Python installed, and that you
@ -552,32 +552,32 @@ lmp.command(cmd)         # invoke a single LAMMPS command, cmd = "run 100" :pre
 xlo = lmp.extract_global(name,type)  # extract a global quantity
                                     # name = "boxxlo", "nlocal", etc
-				     # type = 0 = int
+                                     # type = 0 = int
-				     #        1 = double :pre
+                                     #        1 = double :pre
 coords = lmp.extract_atom(name,type)      # extract a per-atom quantity
                                          # name = "x", "type", etc
-				          # type = 0 = vector of ints
+                                          # type = 0 = vector of ints
-				          #        1 = array of ints
+                                          #        1 = array of ints
-				          #        2 = vector of doubles
+                                          #        2 = vector of doubles
-				          #        3 = array of doubles :pre
+                                          #        3 = array of doubles :pre
 eng = lmp.extract_compute(id,style,type)  # extract value(s) from a compute
 v3 = lmp.extract_fix(id,style,type,i,j)   # extract value(s) from a fix
                                          # id = ID of compute or fix
-					  # style = 0 = global data
+                                          # style = 0 = global data
-					  #	    1 = per-atom data
+                                          #         1 = per-atom data
-					  #         2 = local data
+                                          #         2 = local data
-					  # type = 0 = scalar
+                                          # type = 0 = scalar
-					  #	   1 = vector
+                                          #        1 = vector
-					  #        2 = array
+                                          #        2 = array
-					  # i,j = indices of value in global vector or array :pre
+                                          # i,j = indices of value in global vector or array :pre
 var = lmp.extract_variable(name,group,flag)  # extract value(s) from a variable
-	                                     # name = name of variable
+                                             # name = name of variable
-					     # group = group ID (ignored for equal-style variables)
+                                             # group = group ID (ignored for equal-style variables)
-					     # flag = 0 = equal-style variable
+                                             # flag = 0 = equal-style variable
-					     #        1 = atom-style variable :pre
+                                             #        1 = atom-style variable :pre
 flag = lmp.set_variable(name,value)       # set existing named string-style variable to value, flag = 0 if successful
 natoms = lmp.get_natoms()                 # total # of atoms as int
@ -724,7 +724,7 @@ lmp.scatter_coords("x",1,3,x) :pre
 Alternatively, you can just change values in the vector returned by
 gather_atoms("x",1,3), since it is a ctypes vector of doubles.
-:line 
+:line
 As noted above, these Python class methods correspond one-to-one with
 the functions in the LAMMPS library interface in src/library.cpp and
@ -767,7 +767,7 @@ vizplotgui_tool.py, combination of viz_tool.py and plot.py and gui.py :tb(c=2)
 For the viz_tool.py and vizplotgui_tool.py commands, replace "tool"
 with "gl" or "atomeye" or "pymol" or "vmd", depending on what
-visualization package you have installed. 
+visualization package you have installed.
 Note that for GL, you need to be able to run the Pizza.py GL tool,
 which is included in the pizza sub-directory.  See the "Pizza.py doc
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@ -33,7 +33,7 @@ tar -xzvf lammps*.tar.gz :pre
 This will create a LAMMPS directory containing two files and several
 sub-directories:
-    
+
 README: text file
 LICENSE: the GNU General Public License (GPL)
 bench: benchmark problems
@ -600,10 +600,10 @@ LAMMPS will generate a run-time error.  As far as we know, the
 settings defined in src/lmptype.h are portable and work on every
 current system.
-In all cases, the size of problem that can be run on a per-processor  
+In all cases, the size of problem that can be run on a per-processor
-basis is limited by 4-byte integer storage to 2^31 atoms per processor  
+basis is limited by 4-byte integer storage to 2^31 atoms per processor
-(about 2 billion). This should not normally be a limitation since such  
+(about 2 billion). This should not normally be a limitation since such
-a problem would have a huge per-processor memory footprint due to  
+a problem would have a huge per-processor memory footprint due to
 neighbor lists and would run very slowly in terms of CPU secs/timestep.
 :line
@ -841,7 +841,7 @@ libpackage.a
 Makefile.lammps :pre
 The Makefile.lammps file will typically be a copy of one of the
-Makefile.lammps.* files in the library directory.  
+Makefile.lammps.* files in the library directory.
 Note that you must insure that the settings in Makefile.lammps are
 appropriate for your system.  If they are not, the LAMMPS build may
@ -883,7 +883,7 @@ A few packages require specific settings in Makefile.machine, to
 either build or use the package effectively.  These are the
 USER-INTEL, KOKKOS, USER-OMP, and OPT packages, used for accelerating
 code performance on CPUs or other hardware, as discussed in "Section
-5.3"_Section_accelerate.html#acc_3. 
+5.3"_Section_accelerate.html#acc_3.
 A summary of what Makefile.machine changes are needed for each of
 these packages is given in "Section 4"_Section_packages.html.
@ -1199,7 +1199,7 @@ installer package from "here"_http://rpm.lammps.org/windows.html
 For running the non-MPI executable, follow these steps:
-Get a command prompt by going to Start->Run... , 
+Get a command prompt by going to Start->Run... ,
 then typing "cmd". :ulb,l
 Move to the directory where you have your input, e.g. a copy of
@ -1209,7 +1209,7 @@ At the command prompt, type "lmp_serial -in in.lj", replacing [in.lj]
 with the name of your LAMMPS input script. :l
 :ule
-For the MPI version, which allows you to run LAMMPS under Windows on 
+For the MPI version, which allows you to run LAMMPS under Windows on
 multiple processors, follow these steps:
 Download and install
@ -1224,7 +1224,7 @@ For this you need to start a Command Prompt in {Administrator Mode}
 installation directory, then into the subdirectory [bin] and execute
 [smpd.exe -install]. Exit the command window.
-Get a new, regular command prompt by going to Start->Run... , 
+Get a new, regular command prompt by going to Start->Run... ,
 then typing "cmd". :l
 Move to the directory where you have your input file
@ -1488,7 +1488,7 @@ of the manual.  World- and universe-style "variables"_variable.html
 are useful in this context.
 -plog file :pre
- 
+
 Specify the base name for the partition log files, so partition N
 writes log information to file.N. If file is none, then no partition
 log files are created.  This overrides the filename specified in the
@ -1499,7 +1499,7 @@ replica_files/log.lammps) If this option is not used the log file for
 partition N is log.lammps.N or whatever is specified by the -log
 command-line option.
-pscreen file :pre 
+-pscreen file :pre
 Specify the base name for the partition screen file, so partition N
 writes screen information to file.N. If file is none, then no
@ -1511,7 +1511,7 @@ sub-directory (-pscreen replica_files/screen).  If this option is not
 used the screen file for partition N is screen.N or whatever is
 specified by the -screen command-line option.
-restart restartfile {remap} datafile keyword value ... :pre 
+-restart restartfile {remap} datafile keyword value ... :pre
 Convert the restart file into a data file and immediately exit.  This
 is the same operation as if the following 2-line input script were
@ -1572,7 +1572,7 @@ to
 so that the processors in each partition will be
-0 1 2 4 5 6 8 9 10 
+0 1 2 4 5 6 8 9 10
 3 7 11 :pre
 See the "processors" command for how to insure processors from each
@ -1663,12 +1663,12 @@ invokes the default USER-INTEL settings, as if the command "package
 intel 1" were used at the top of your input script.  These settings
 can be changed by using the "-package intel" command-line switch or
 the "package intel"_package.html command in your script. If the
-USER-OMP package is also installed, the hybrid style with "intel omp" 
+USER-OMP package is also installed, the hybrid style with "intel omp"
-arguments can be used to make the omp suffix a second choice, if a 
+arguments can be used to make the omp suffix a second choice, if a
-requested style is not available in the USER-INTEL package.  It will 
+requested style is not available in the USER-INTEL package.  It will
-also invoke the default USER-OMP settings, as if the command "package 
+also invoke the default USER-OMP settings, as if the command "package
-omp 0" were used at the top of your input script.  These settings can 
+omp 0" were used at the top of your input script.  These settings can
-be changed by using the "-package omp" command-line switch or the 
+be changed by using the "-package omp" command-line switch or the
 "package omp"_package.html command in your script.
 For the KOKKOS package, using this command-line switch also invokes
@ -1833,7 +1833,7 @@ e.g.
 Minimization stats:
  Stopping criterion = linesearch alpha is zero
-  Energy initial, next-to-last, final = 
+  Energy initial, next-to-last, final =
         -6372.3765206     -8328.46998942     -8328.46998942
  Force two-norm initial, final = 1059.36 5.36874
  Force max component initial, final = 58.6026 1.46872
--- a/doc/src/Section_tools.txt
+++ b/doc/src/Section_tools.txt
@ -104,7 +104,7 @@ since binary files are not compatible across all platforms.
 ch2lmp tool :h4,link(charmm)
 The ch2lmp sub-directory contains tools for converting files
-back-and-forth between the CHARMM MD code and LAMMPS. 
+back-and-forth between the CHARMM MD code and LAMMPS.
 They are intended to make it easy to use CHARMM as a builder and as a
 post-processor for LAMMPS. Using charmm2lammps.pl, you can convert a
--- a/doc/src/accelerate_intel.txt
+++ b/doc/src/accelerate_intel.txt
@ -29,80 +29,80 @@ Bond Styles: fene, harmonic :l
 Dihedral Styles: charmm, harmonic, opls :l
 Fixes: nve, npt, nvt, nvt/sllod :l
 Improper Styles: cvff, harmonic :l
-Pair Styles: buck/coul/cut, buck/coul/long, buck, gayberne, 
+Pair Styles: buck/coul/cut, buck/coul/long, buck, gayberne,
 charmm/coul/long, lj/cut, lj/cut/coul/long, sw, tersoff :l
 K-Space Styles: pppm :l
 :ule
 [Speed-ups to expect:]
-The speedups will depend on your simulation, the hardware, which 
+The speedups will depend on your simulation, the hardware, which
-styles are used, the number of atoms, and the floating-point 
+styles are used, the number of atoms, and the floating-point
-precision mode. Performance improvements are shown compared to 
+precision mode. Performance improvements are shown compared to
-LAMMPS {without using other acceleration packages} as these are 
+LAMMPS {without using other acceleration packages} as these are
-under active development (and subject to performance changes). The 
+under active development (and subject to performance changes). The
 measurements were performed using the input files available in
-the src/USER-INTEL/TEST directory. These are scalable in size; the 
+the src/USER-INTEL/TEST directory. These are scalable in size; the
-results given are with 512K particles (524K for Liquid Crystal). 
+results given are with 512K particles (524K for Liquid Crystal).
 Most of the simulations are standard LAMMPS benchmarks (indicated
-by the filename extension in parenthesis) with modifications to the 
+by the filename extension in parenthesis) with modifications to the
-run length and to add a warmup run (for use with offload 
+run length and to add a warmup run (for use with offload
-benchmarks). 
+benchmarks).
 :c,image(JPG/user_intel.png)
-Results are speedups obtained on Intel Xeon E5-2697v4 processors 
+Results are speedups obtained on Intel Xeon E5-2697v4 processors
-(code-named Broadwell) and Intel Xeon Phi 7250 processors 
+(code-named Broadwell) and Intel Xeon Phi 7250 processors
 (code-named Knights Landing) with "18 Jun 2016" LAMMPS built with
-Intel Parallel Studio 2016 update 3. Results are with 1 MPI task 
+Intel Parallel Studio 2016 update 3. Results are with 1 MPI task
-per physical core. See {src/USER-INTEL/TEST/README} for the raw 
+per physical core. See {src/USER-INTEL/TEST/README} for the raw
 simulation rates and instructions to reproduce.
 :line
 [Quick Start for Experienced Users:]
-LAMMPS should be built with the USER-INTEL package installed. 
+LAMMPS should be built with the USER-INTEL package installed.
 Simulations should be run with 1 MPI task per physical {core},
 not {hardware thread}.
 For Intel Xeon CPUs:
 Edit src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi as necessary. :ulb,l
-If using {kspace_style pppm} in the input script, add "neigh_modify binsize 3" and "kspace_modify diff ad" to the input script for better 
+If using {kspace_style pppm} in the input script, add "neigh_modify binsize 3" and "kspace_modify diff ad" to the input script for better
 performance. :l
 "-pk intel 0 omp 2 -sf intel" added to LAMMPS command-line :l
 :ule
-For Intel Xeon Phi CPUs for simulations without {kspace_style 
+For Intel Xeon Phi CPUs for simulations without {kspace_style
 pppm} in the input script :
 Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l
 Runs should be performed using MCDRAM. :l
-"-pk intel 0 omp 2 -sf intel" {or} "-pk intel 0 omp 4 -sf intel" 
+"-pk intel 0 omp 2 -sf intel" {or} "-pk intel 0 omp 4 -sf intel"
-should be added to the LAMMPS command-line. Choice for best 
+should be added to the LAMMPS command-line. Choice for best
 performance will depend on the simulation. :l
 :ule
-For Intel Xeon Phi CPUs for simulations with {kspace_style 
+For Intel Xeon Phi CPUs for simulations with {kspace_style
 pppm} in the input script:
 Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l
 Runs should be performed using MCDRAM. :l
-Add "neigh_modify binsize 3" to the input script for better 
+Add "neigh_modify binsize 3" to the input script for better
 performance. :l
-Add "kspace_modify diff ad" to the input script for better 
+Add "kspace_modify diff ad" to the input script for better
 performance. :l
 export KMP_AFFINITY=none :l
 "-pk intel 0 omp 3 lrt yes -sf intel" or "-pk intel 0 omp 1 lrt yes
-sf intel" added to LAMMPS command-line. Choice for best performance 
+-sf intel" added to LAMMPS command-line. Choice for best performance
 will depend on the simulation. :l
 :ule
-For Intel Xeon Phi coprocessors (Offload): 
+For Intel Xeon Phi coprocessors (Offload):
 Edit src/MAKE/OPTIONS/Makefile.intel_coprocessor as necessary :ulb,l
-"-pk intel N omp 1" added to command-line where N is the number of 
+"-pk intel N omp 1" added to command-line where N is the number of
 coprocessors per node. :l
 :ule
@ -111,7 +111,7 @@ coprocessors per node. :l
 [Required hardware/software:]
 In order to use offload to coprocessors, an Intel Xeon Phi
-coprocessor and an Intel compiler are required. For this, the 
+coprocessor and an Intel compiler are required. For this, the
 recommended version of the Intel compiler is 14.0.1.106 or
 versions 15.0.2.044 and higher.
@ -133,7 +133,7 @@ slightly lower.
 [Notes about Simultaneous Multithreading:]
-Modern CPUs often support Simultaneous Multithreading (SMT). On 
+Modern CPUs often support Simultaneous Multithreading (SMT). On
 Intel processors, this is called Hyper-Threading (HT) technology.
 SMT is hardware support for running multiple threads efficiently on
 a single core. {Hardware threads} or {logical cores} are often used
@ -141,8 +141,8 @@ to refer to the number of threads that are supported in hardware.
 For example, the Intel Xeon E5-2697v4 processor is described
 as having 36 cores and 72 threads. This means that 36 MPI processes
 or OpenMP threads can run simultaneously on separate cores, but that
-up to 72 MPI processes or OpenMP threads can be running on the CPU 
+up to 72 MPI processes or OpenMP threads can be running on the CPU
-without costly operating system context switches. 
+without costly operating system context switches.
 Molecular dynamics simulations will often run faster when making use
 of SMT. If a thread becomes stalled, for example because it is
@ -150,7 +150,7 @@ waiting on data that has not yet arrived from memory, another thread
 can start running so that the CPU pipeline is still being used
 efficiently. Although benefits can be seen by launching a MPI task
 for every hardware thread, for multinode simulations, we recommend
-that OpenMP threads are used for SMT instead, either with the 
+that OpenMP threads are used for SMT instead, either with the
 USER-INTEL package, "USER-OMP package"_accelerate_omp.html", or
 "KOKKOS package"_accelerate_kokkos.html. In the example above, up
 to 36X speedups can be observed by using all 36 physical cores with
@ -158,10 +158,10 @@ LAMMPS. By using all 72 hardware threads, an additional 10-30%
 performance gain can be achieved.
 The BIOS on many platforms allows SMT to be disabled, however, we do
-not recommend this on modern processors as there is little to no 
+not recommend this on modern processors as there is little to no
 benefit for any software package in most cases. The operating system
-will report every hardware thread as a separate core allowing one to 
+will report every hardware thread as a separate core allowing one to
-determine the number of hardware threads available. On Linux systems, 
+determine the number of hardware threads available. On Linux systems,
 this information can normally be obtained with:
 cat /proc/cpuinfo :pre
@ -182,21 +182,21 @@ Makefile.intel_cpu_openpmi  # Intel Compiler, OpenMPI, No Offload
 Makefile.intel_coprocessor  # Intel Compiler, Intel MPI, Offload :pre
 Makefile.knl is identical to Makefile.intel_cpu_intelmpi except that
-it explicitly specifies that vectorization should be for Intel 
+it explicitly specifies that vectorization should be for Intel
-Xeon Phi x200 processors making it easier to cross-compile. For 
+Xeon Phi x200 processors making it easier to cross-compile. For
-users with recent installations of Intel Parallel Studio, the 
+users with recent installations of Intel Parallel Studio, the
 process can be as simple as:
 make yes-user-intel
-source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh 
+source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
 # or psxevars.csh for C-shell
 make intel_cpu_intelmpi :pre
-Alternatively, the build can be accomplished with the src/Make.py 
+Alternatively, the build can be accomplished with the src/Make.py
-script, described in "Section 2.4"_Section_start.html#start_4 of the 
+script, described in "Section 2.4"_Section_start.html#start_4 of the
 manual. Type "Make.py -h" for help. For an example:
-Make.py -v -p intel omp -intel cpu -a file intel_cpu_intelmpi :pre 
+Make.py -v -p intel omp -intel cpu -a file intel_cpu_intelmpi :pre
 Note that if you build with support for a Phi coprocessor, the same
 binary can be used on nodes with or without coprocessors installed.
@ -205,26 +205,26 @@ without offload support will produce a smaller binary.
 The general requirements for Makefiles with the USER-INTEL package
 are as follows. "-DLAMMPS_MEMALIGN=64" is required for CCFLAGS. When
-using Intel compilers, "-restrict" is required and "-qopenmp" is 
+using Intel compilers, "-restrict" is required and "-qopenmp" is
-highly recommended for CCFLAGS and LINKFLAGS. LIB should include 
+highly recommended for CCFLAGS and LINKFLAGS. LIB should include
 "-ltbbmalloc". For builds supporting offload, "-DLMP_INTEL_OFFLOAD"
 is required for CCFLAGS and "-qoffload" is required for LINKFLAGS.
-Other recommended CCFLAG options for best performance are 
+Other recommended CCFLAG options for best performance are
-"-O2 -fno-alias -ansi-alias -qoverride-limits fp-model fast=2 
+"-O2 -fno-alias -ansi-alias -qoverride-limits fp-model fast=2
-no-prec-div". The Make.py command will add all of these 
+-no-prec-div". The Make.py command will add all of these
 automatically.
 NOTE: The vectorization and math capabilities can differ depending on
 the CPU. For Intel compilers, the "-x" flag specifies the type of
 processor for which to optimize. "-xHost" specifies that the compiler
-should build for the processor used for compiling. For Intel Xeon Phi 
+should build for the processor used for compiling. For Intel Xeon Phi
 x200 series processors, this option is "-xMIC-AVX512". For fourth
-generation Intel Xeon (v4/Broadwell) processors, "-xCORE-AVX2" should 
+generation Intel Xeon (v4/Broadwell) processors, "-xCORE-AVX2" should
 be used. For older Intel Xeon processors, "-xAVX" will perform best
 in general for the different simulations in LAMMPS. The default
 in most of the example Makefiles is to use "-xHost", however this
 should not be used when cross-compiling.
- 
+
 [Running LAMMPS with the USER-INTEL package:]
 Running LAMMPS with the USER-INTEL package is similar to normal use
@ -232,7 +232,7 @@ with the exceptions that one should 1) specify that LAMMPS should use
 the USER-INTEL package, 2) specify the number of OpenMP threads, and
 3) optionally specify the specific LAMMPS styles that should use the
 USER-INTEL package. 1) and 2) can be performed from the command-line
-or by editing the input script. 3) requires editing the input script. 
+or by editing the input script. 3) requires editing the input script.
 Advanced performance tuning options are also described below to get
 the best performance.
@ -241,14 +241,14 @@ coprocessor), best performance is normally obtained by using 1 MPI
 task per physical core and additional OpenMP threads with SMT. For
 Intel Xeon processors, 2 OpenMP threads should be used for SMT.
 For Intel Xeon Phi CPUs, 2 or 4 OpenMP threads should be used
-(best choice depends on the simulation). In cases where the user 
+(best choice depends on the simulation). In cases where the user
-specifies that LRT mode is used (described below), 1 or 3 OpenMP 
+specifies that LRT mode is used (described below), 1 or 3 OpenMP
 threads should be used. For multi-node runs, using 1 MPI task per
 physical core will often perform best, however, depending on the
 machine and scale, users might get better performance by decreasing
-the number of MPI tasks and using more OpenMP threads. For 
+the number of MPI tasks and using more OpenMP threads. For
-performance, the product of the number of MPI tasks and OpenMP 
+performance, the product of the number of MPI tasks and OpenMP
-threads should not exceed the number of available hardware threads in 
+threads should not exceed the number of available hardware threads in
 almost all cases.
 NOTE: Setting core affinity is often used to pin MPI tasks and OpenMP
@ -257,21 +257,21 @@ uniform. Unless disabled at build time, affinity for MPI tasks and
 OpenMP threads on the host (CPU) will be set by default on the host
 {when using offload to a coprocessor}. In this case, it is unnecessary
 to use other methods to control affinity (e.g. taskset, numactl,
-I_MPI_PIN_DOMAIN, etc.). This can be disabled with the {no_affinity} 
+I_MPI_PIN_DOMAIN, etc.). This can be disabled with the {no_affinity}
-option to the "package intel"_package.html command or by disabling the 
+option to the "package intel"_package.html command or by disabling the
-option at build time (by adding -DINTEL_OFFLOAD_NOAFFINITY to the 
+option at build time (by adding -DINTEL_OFFLOAD_NOAFFINITY to the
-CCFLAGS line of your Makefile). Disabling this option is not 
+CCFLAGS line of your Makefile). Disabling this option is not
-recommended, especially when running on a machine with Intel 
+recommended, especially when running on a machine with Intel
 Hyper-Threading technology disabled.
 [Run with the USER-INTEL package from the command line:]
-To enable USER-INTEL optimizations for all available styles used in 
+To enable USER-INTEL optimizations for all available styles used in
-the input script, the "-sf intel" 
+the input script, the "-sf intel"
 "command-line switch"_Section_start.html#start_7 can be used without
 any requirement for editing the input script. This switch will
-automatically append "intel" to styles that support it. It also 
+automatically append "intel" to styles that support it. It also
-invokes a default command: "package intel 1"_package.html. This 
+invokes a default command: "package intel 1"_package.html. This
 package command is used to set options for the USER-INTEL package.
 The default package command will specify that USER-INTEL calculations
 are performed in mixed precision, that the number of OpenMP threads
@ -281,16 +281,16 @@ support, that 1 coprocessor per node will be used with automatic
 balancing of work between the CPU and the coprocessor.
 You can specify different options for the USER-INTEL package by using
-the "-pk intel Nphi" "command-line switch"_Section_start.html#start_7 
+the "-pk intel Nphi" "command-line switch"_Section_start.html#start_7
 with keyword/value pairs as specified in the documentation. Here,
 Nphi = # of Xeon Phi coprocessors/node (ignored without offload
 support). Common options to the USER-INTEL package include {omp} to
 override any OMP_NUM_THREADS setting and specify the number of OpenMP
 threads, {mode} to set the floating-point precision mode, and
-{lrt} to enable Long-Range Thread mode as described below. See the 
+{lrt} to enable Long-Range Thread mode as described below. See the
-"package intel"_package.html command for details, including the 
+"package intel"_package.html command for details, including the
-default values used for all its options if not specified, and how to 
+default values used for all its options if not specified, and how to
-set the number of OpenMP threads via the OMP_NUM_THREADS environment 
+set the number of OpenMP threads via the OMP_NUM_THREADS environment
 variable if desired.
 Examples (see documentation for your MPI/Machine for differences in
@ -303,7 +303,7 @@ mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode
 As an alternative to adding command-line arguments, the input script
 can be edited to enable the USER-INTEL package. This requires adding
-the "package intel"_package.html command to the top of the input 
+the "package intel"_package.html command to the top of the input
 script. For the second example above, this would be:
 package intel 0 omp 2 mode double :pre
@ -314,46 +314,46 @@ add an "intel" suffix to the individual style, e.g.:
 pair_style lj/cut/intel 2.5 :pre
 Alternatively, the "suffix intel"_suffix.html command can be added to
-the input script to enable USER-INTEL styles for the commands that 
+the input script to enable USER-INTEL styles for the commands that
 follow in the input script.
 [Tuning for Performance:]
-NOTE: The USER-INTEL package will perform better with modifications 
+NOTE: The USER-INTEL package will perform better with modifications
-to the input script when "PPPM"_kspace_style.html is used: 
+to the input script when "PPPM"_kspace_style.html is used:
-"kspace_modify diff ad"_kspace_modify.html and "neigh_modify binsize 
+"kspace_modify diff ad"_kspace_modify.html and "neigh_modify binsize
 3"_neigh_modify.html should be added to the input script.
-Long-Range Thread (LRT) mode is an option to the "package 
+Long-Range Thread (LRT) mode is an option to the "package
 intel"_package.html command that can improve performance when using
 "PPPM"_kspace_style.html for long-range electrostatics on processors
-with SMT. It generates an extra pthread for each MPI task. The thread 
+with SMT. It generates an extra pthread for each MPI task. The thread
-is dedicated to performing some of the PPPM calculations and MPI 
+is dedicated to performing some of the PPPM calculations and MPI
 communications. On Intel Xeon Phi x200 series CPUs, this will likely
 always improve performance, even on a single node. On Intel Xeon
 processors, using this mode might result in better performance when
 using multiple nodes, depending on the machine. To use this mode,
-specify that the number of OpenMP threads is one less than would 
+specify that the number of OpenMP threads is one less than would
 normally be used for the run and add the "lrt yes" option to the "-pk"
 command-line suffix or "package intel" command. For example, if a run
 would normally perform best with "-pk intel 0 omp 4", instead use
-"-pk intel 0 omp 3 lrt yes". When using LRT, you should set the 
+"-pk intel 0 omp 3 lrt yes". When using LRT, you should set the
-environment variable "KMP_AFFINITY=none". LRT mode is not supported 
+environment variable "KMP_AFFINITY=none". LRT mode is not supported
 when using offload.
 Not all styles are supported in the USER-INTEL package. You can mix
-the USER-INTEL package with styles from the "OPT"_accelerate_opt.html 
+the USER-INTEL package with styles from the "OPT"_accelerate_opt.html
-package or the "USER-OMP package"_accelerate_omp.html". Of course, 
+package or the "USER-OMP package"_accelerate_omp.html". Of course,
 this requires that these packages were installed at build time. This
 can performed automatically by using "-sf hybrid intel opt" or
 "-sf hybrid intel omp" command-line options. Alternatively, the "opt"
 and "omp" suffixes can be appended manually in the input script. For
 the latter, the "package omp"_package.html command must be in the
-input script or the "-pk omp Nt" "command-line 
+input script or the "-pk omp Nt" "command-line
-switch"_Section_start.html#start_7 must be used where Nt is the 
+switch"_Section_start.html#start_7 must be used where Nt is the
 number of OpenMP threads. The number of OpenMP threads should not be
-set differently for the different packages. Note that the "suffix 
+set differently for the different packages. Note that the "suffix
-hybrid intel omp"_suffix.html command can also be used within the 
+hybrid intel omp"_suffix.html command can also be used within the
 input script to automatically append the "omp" suffix to styles when
 USER-INTEL styles are not available.
@ -374,33 +374,33 @@ that MPI runs are performed in MCDRAM.
 [Tuning for Offload Performance:]
-The default settings for offload should give good performance. 
+The default settings for offload should give good performance.
 When using LAMMPS with offload to Intel coprocessors, best performance
 will typically be achieved with concurrent calculations performed on
 both the CPU and the coprocessor. This is achieved by offloading only
 a fraction of the neighbor and pair computations to the coprocessor or
 using "hybrid"_pair_hybrid.html pair styles where only one style uses
-the "intel" suffix. For simulations with long-range electrostatics or 
+the "intel" suffix. For simulations with long-range electrostatics or
-bond, angle, dihedral, improper calculations, computation and data 
+bond, angle, dihedral, improper calculations, computation and data
-transfer to the coprocessor will run concurrently with computations 
+transfer to the coprocessor will run concurrently with computations
 and MPI communications for these calculations on the host CPU. This
 is illustrated in the figure below for the rhodopsin protein benchmark
-running on E5-2697v2 processors with a Intel Xeon Phi 7120p 
+running on E5-2697v2 processors with a Intel Xeon Phi 7120p
 coprocessor. In this plot, the vertical access is time and routines
 running at the same time are running concurrently on both the host and
 the coprocessor.
 :c,image(JPG/offload_knc.png)
-The fraction of the offloaded work is controlled by the {balance} 
+The fraction of the offloaded work is controlled by the {balance}
-keyword in the "package intel"_package.html command. A balance of 0 
+keyword in the "package intel"_package.html command. A balance of 0
-runs all calculations on the CPU.  A balance of 1 runs all 
+runs all calculations on the CPU.  A balance of 1 runs all
-supported calculations on the coprocessor.  A balance of 0.5 runs half 
+supported calculations on the coprocessor.  A balance of 0.5 runs half
-of the calculations on the coprocessor.  Setting the balance to -1 
+of the calculations on the coprocessor.  Setting the balance to -1
-(the default) will enable dynamic load balancing that continously 
+(the default) will enable dynamic load balancing that continously
-adjusts the fraction of offloaded work throughout the simulation. 
+adjusts the fraction of offloaded work throughout the simulation.
-Because data transfer cannot be timed, this option typically produces 
+Because data transfer cannot be timed, this option typically produces
 results within 5 to 10 percent of the optimal fixed balance.
 If running short benchmark runs with dynamic load balancing, adding a
@ -418,15 +418,15 @@ with 60 cores available for offload and 4 hardware threads per core
 each MPI task to use a subset of 10 threads on the coprocessor.  Fine
 tuning of the number of threads to use per MPI task or the number of
 threads to use per core can be accomplished with keyword settings of
-the "package intel"_package.html command. 
+the "package intel"_package.html command.
-The USER-INTEL package has two modes for deciding which atoms will be 
+The USER-INTEL package has two modes for deciding which atoms will be
-handled by the coprocessor.  This choice is controlled with the {ghost} 
+handled by the coprocessor.  This choice is controlled with the {ghost}
-keyword of the "package intel"_package.html command.  When set to 0, 
+keyword of the "package intel"_package.html command.  When set to 0,
-ghost atoms (atoms at the borders between MPI tasks) are not offloaded 
+ghost atoms (atoms at the borders between MPI tasks) are not offloaded
-to the card.  This allows for overlap of MPI communication of forces 
+to the card.  This allows for overlap of MPI communication of forces
-with computation on the coprocessor when the "newton"_newton.html 
+with computation on the coprocessor when the "newton"_newton.html
-setting is "on".  The default is dependent on the style being used, 
+setting is "on".  The default is dependent on the style being used,
 however, better performance may be achieved by setting this option
 explictly.
@ -442,10 +442,10 @@ mode is being used and indicating the number of coprocessor threads
 per MPI task.  Additionally, an offload timing summary is printed at
 the end of each run.  When offloading, the frequency for "atom
 sorting"_atom_modify.html is changed to 1 so that the per-atom data is
-effectively sorted at every rebuild of the neighbor lists. All the 
+effectively sorted at every rebuild of the neighbor lists. All the
-available coprocessor threads on each Phi will be divided among MPI 
+available coprocessor threads on each Phi will be divided among MPI
-tasks, unless the {tptask} option of the "-pk intel" "command-line 
+tasks, unless the {tptask} option of the "-pk intel" "command-line
-switch"_Section_start.html#start_7 is used to limit the coprocessor 
+switch"_Section_start.html#start_7 is used to limit the coprocessor
 threads per MPI task.
 [Restrictions:]
--- a/doc/src/accelerate_kokkos.txt
+++ b/doc/src/accelerate_kokkos.txt
@ -65,7 +65,7 @@ Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi   # or one-line build via Ma
 mpirun -np 16 lmp_mpi -k on -sf kk -in in.lj              # 1 node, 16 MPI tasks/node, no threads
 mpirun -np 2 -ppn 1 lmp_mpi -k on t 16 -sf kk -in in.lj   # 2 nodes, 1 MPI task/node, 16 threads/task
-mpirun -np 2 lmp_mpi -k on t 8 -sf kk -in in.lj           # 1 node, 2 MPI tasks/node, 8 threads/task 
+mpirun -np 2 lmp_mpi -k on t 8 -sf kk -in in.lj           # 1 node, 2 MPI tasks/node, 8 threads/task
 mpirun -np 32 -ppn 4 lmp_mpi -k on t 4 -sf kk -in in.lj   # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre
 specify variables and settings in your Makefile.machine that enable OpenMP, GPU, or Phi support
@ -178,7 +178,7 @@ make kokkos_cuda_mpich :pre
 These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
 make command line which requires a GNU-compatible make command.  Try
-"gmake" if your system's standard make complains.  
+"gmake" if your system's standard make complains.
 NOTE: If you build using make line variables and re-build LAMMPS twice
 with different KOKKOS options and the *same* target, e.g. g++ in the
@ -394,7 +394,7 @@ additional parallelism (beyond MPI) will be invoked on the host
 CPU(s).
 You can compare the performance running in different modes:
-  
+
 run with 1 MPI task/node and N threads/task
 run with N MPI tasks/node and 1 thread/task
 run with settings in between these extremes :ul
@ -427,7 +427,7 @@ e.g. src/MAKE/Makefile.cuda, is correct for your GPU hardware/software
 details).
 The -np setting of the mpirun command should set the number of MPI
-tasks/node to be equal to the # of physical GPUs on the node. 
+tasks/node to be equal to the # of physical GPUs on the node.
 Use the "-k" "command-line switch"_Section_commands.html#start_7 to
 specify the number of GPUs per node, and the number of threads per MPI
--- a/doc/src/accelerate_omp.txt
+++ b/doc/src/accelerate_omp.txt
@ -96,7 +96,7 @@ variable.
 Depending on which styles are accelerated, you should look for a
 reduction in the "Pair time", "Bond time", "KSpace time", and "Loop
-time" values printed at the end of a run.  
+time" values printed at the end of a run.
 You may see a small performance advantage (5 to 20%) when running a
 USER-OMP style (in serial or parallel) with a single thread per MPI
--- a/doc/src/angle_dipole.txt
+++ b/doc/src/angle_dipole.txt
@ -21,11 +21,11 @@ angle_coeff 6 2.1 180.0 :pre
 [Description:]
 The {dipole} angle style is used to control the orientation of a dipolar
-atom within a molecule "(Orsi)"_#Orsi. Specifically, the {dipole} angle 
+atom within a molecule "(Orsi)"_#Orsi. Specifically, the {dipole} angle
-style restrains the orientation of a point dipole mu_j (embedded in atom 
+style restrains the orientation of a point dipole mu_j (embedded in atom
-'j') with respect to a reference (bond) vector r_ij = r_i - r_j, where 'i' 
+'j') with respect to a reference (bond) vector r_ij = r_i - r_j, where 'i'
-is another atom of the same molecule (typically, 'i' and 'j' are also 
+is another atom of the same molecule (typically, 'i' and 'j' are also
-covalently bonded). 
+covalently bonded).
 It is convenient to define an angle gamma between the 'free' vector mu_j
 and the reference (bond) vector r_ij:
@ -37,21 +37,21 @@ The {dipole} angle style uses the potential:
 :c,image(Eqs/angle_dipole_potential.jpg)
 where K is a rigidity constant and gamma0 is an equilibrium (reference)
-angle. 
+angle.
-The torque on the dipole can be obtained by differentiating the 
+The torque on the dipole can be obtained by differentiating the
-potential using the 'chain rule' as in appendix C.3 of 
+potential using the 'chain rule' as in appendix C.3 of
 "(Allen)"_#Allen:
 :c,image(Eqs/angle_dipole_torque.jpg)
 Example: if gamma0 is set to 0 degrees, the torque generated by
-the potential will tend to align the dipole along the reference 
+the potential will tend to align the dipole along the reference
 direction defined by the (bond) vector r_ij (in other words, mu_j is
 restrained to point towards atom 'i').
-The dipolar torque T_j must be counterbalanced in order to conserve 
+The dipolar torque T_j must be counterbalanced in order to conserve
-the local angular momentum. This is achieved via an additional force 
+the local angular momentum. This is achieved via an additional force
 couple generating a torque equivalent to the opposite of T_j:
 :c,image(Eqs/angle_dipole_couple.jpg)
@ -118,7 +118,7 @@ This angle style should not be used with SHAKE.
 :line
 :link(Orsi)
-[(Orsi)] Orsi & Essex, The ELBA force field for coarse-grain modeling of 
+[(Orsi)] Orsi & Essex, The ELBA force field for coarse-grain modeling of
 lipid membranes, PloS ONE 6(12): e28637, 2011.
 :link(Allen)
--- a/doc/src/angle_fourier.txt
+++ b/doc/src/angle_fourier.txt
@ -62,7 +62,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 This angle style can only be used if LAMMPS was built with the
-USER_MISC package.  See the "Making LAMMPS"_Section_start.html#start_3 
+USER_MISC package.  See the "Making LAMMPS"_Section_start.html#start_3
 section for more info on packages.
 [Related commands:]
--- a/doc/src/angle_fourier_simple.txt
+++ b/doc/src/angle_fourier_simple.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
-USER_MISC package.  See the "Making LAMMPS"_Section_start.html#start_3 
+USER_MISC package.  See the "Making LAMMPS"_Section_start.html#start_3
 section for more info on packages.
 [Related commands:]
--- a/doc/src/angle_quartic.txt
+++ b/doc/src/angle_quartic.txt
@ -68,7 +68,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 This angle style can only be used if LAMMPS was built with the
-USER_MISC package.  See the "Making LAMMPS"_Section_start.html#start_3 
+USER_MISC package.  See the "Making LAMMPS"_Section_start.html#start_3
 section for more info on packages.
 [Related commands:]
--- a/doc/src/angle_sdk.txt
+++ b/doc/src/angle_sdk.txt
@ -43,7 +43,7 @@ internally; hence the units of K are in energy/radian^2.
 The also required {lj/sdk} parameters will be extracted automatically
 from the pair_style.
-[Restrictions:] 
+[Restrictions:]
 This angle style can only be used if LAMMPS was built with the
 USER-CG-CMM package.  See the "Making
--- a/doc/src/atom_modify.txt
+++ b/doc/src/atom_modify.txt
@ -1,4 +1,4 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS  
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS
 Commands"_lc :c
 :link(lws,http://lammps.sandia.gov)
@ -156,12 +156,12 @@ used with a group-ID that is not "all".
 [Default:]
-By default, {id} is yes.  By default, atomic systems (no bond topology  
+By default, {id} is yes.  By default, atomic systems (no bond topology
-info) do not use a map.  For molecular systems (with bond topology  
+info) do not use a map.  For molecular systems (with bond topology
-info), a map is used.  The default map style is array if no atom ID is  
+info), a map is used.  The default map style is array if no atom ID is
-larger than 1 million, otherwise the default is hash.  By default, a  
+larger than 1 million, otherwise the default is hash.  By default, a
-"first" group is not defined.  By default, sorting is enabled with a  
+"first" group is not defined.  By default, sorting is enabled with a
-frequency of 1000 and a binsize of 0.0, which means the neighbor  
+frequency of 1000 and a binsize of 0.0, which means the neighbor
 cutoff will be used to set the bin size.
 :line
--- a/doc/src/atom_style.txt
+++ b/doc/src/atom_style.txt
@ -14,7 +14,7 @@ atom_style style args :pre
 style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
        {dpd} or {electron} or {ellipsoid} or {full} or {line} or {meso} or \
-	{molecular} or {peri} or {smd} or {sphere} or {tri} or \
+        {molecular} or {peri} or {smd} or {sphere} or {tri} or \
        {template} or {hybrid} :ulb,l
  args = none for any style except the following
  {body} args = bstyle bstyle-args
@ -193,7 +193,7 @@ For the {body} style, the particles are arbitrary bodies with internal
 attributes defined by the "style" of the bodies, which is specified by
 the {bstyle} argument.  Body particles can represent complex entities,
 such as surface meshes of discrete points, collections of
-sub-particles, deformable objects, etc.  
+sub-particles, deformable objects, etc.
 The "body"_body.html doc page descibes the body styles LAMMPS
 currently supports, and provides more details as to the kind of body
@ -269,7 +269,7 @@ The {line} and {tri} styles are part of the ASPHERE package.
 The {body} style is part of the BODY package.
-The {dipole} style is part of the DIPOLE package.  
+The {dipole} style is part of the DIPOLE package.
 The {peri} style is part of the PERI package for Peridynamics.
--- a/doc/src/balance.txt
+++ b/doc/src/balance.txt
@ -490,7 +490,7 @@ per processor.  Note that the 4 sub-domains share vertices, so there
 will be duplicate nodes in the list.
 The "SQUARES" section lists the node IDs of the 4 vertices in a
-rectangle for each processor (1 to 4).  
+rectangle for each processor (1 to 4).
 For a 3d problem, the syntax is similar with 8 vertices listed for
 each processor, instead of 4, and "SQUARES" replaced by "CUBES".
--- a/doc/src/body.txt
+++ b/doc/src/body.txt
@ -125,7 +125,7 @@ in the {Bodies} section of the data file:
 atom-ID 1 M
 N
-ixx iyy izz ixy ixz iyz 
+ixx iyy izz ixy ixz iyz
 x1 y1 z1
 ...
 xN yN zN :pre
@ -198,11 +198,11 @@ in the {Bodies} section of the data file:
 atom-ID 1 M
 N
-ixx iyy izz ixy ixz iyz 
+ixx iyy izz ixy ixz iyz
 x1 y1 z1
 ...
 xN yN zN
-i j j k k ... 
+i j j k k ...
 radius :pre
 N is the number of vertices in the body particle.  M = 6 + 3*N + 2*N +
@ -230,11 +230,11 @@ particles whose edge length is sqrt(2):
 3 1 27
 4
-1 1 4 0 0 0 
+1 1 4 0 0 0
-0.7071 -0.7071 0 
+-0.7071 -0.7071 0
-0.7071 0.7071 0 
+-0.7071 0.7071 0
-0.7071 0.7071 0 
+0.7071 0.7071 0
-0.7071 -0.7071 0 
+0.7071 -0.7071 0
 0 1 1 2 2 3 3 0
 1.0 :pre
--- a/doc/src/change_box.txt
+++ b/doc/src/change_box.txt
@ -173,7 +173,7 @@ change_box all x scale 1.1 y volume z volume :pre
 The {volume} style changes the associated dimension so that the
 overall box volume is unchanged relative to its value before the
-preceding keyword was invoked. 
+preceding keyword was invoked.
 If the following command is used, then the z box length will shrink by
 the same 1.1 factor the x box length was increased by:
--- a/doc/src/comm_modify.txt
+++ b/doc/src/comm_modify.txt
@ -135,7 +135,7 @@ and angular momentum of a particle.  If the {vel} option is set to
 {yes}, then ghost atoms store these quantities; if {no} then they do
 not.  The {yes} setting is needed by some pair styles which require
 the velocity state of both the I and J particles to compute a pairwise
-I,J interaction.
+I,J interaction, as well as by some compute and fix commands.
 Note that if the "fix deform"_fix_deform.html command is being used
 with its "remap v" option enabled, then the velocities for ghost atoms
--- a/doc/src/compute_cna_atom.txt
+++ b/doc/src/compute_cna_atom.txt
@ -13,7 +13,7 @@ compute cna/atom command :h3
 compute ID group-ID cna/atom cutoff :pre
 ID, group-ID are documented in "compute"_compute.html command
-cna/atom = style name of this compute command 
+cna/atom = style name of this compute command
 cutoff = cutoff distance for nearest neighbors (distance units) :ul
 [Examples:]
--- a/doc/src/compute_dilatation_atom.txt
+++ b/doc/src/compute_dilatation_atom.txt
@ -63,4 +63,4 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 "compute damage/atom"_compute_damage_atom.html,
 "compute plasticity/atom"_compute_plasticity_atom.html
-[Default:] none 
+[Default:] none
--- a/doc/src/compute_dipole_chunk.txt
+++ b/doc/src/compute_dipole_chunk.txt
@ -19,7 +19,7 @@ charge-correction = {mass} or {geometry}, use COM or geometric center for charge
 [Examples:]
-compute 1 fluid dipole/chunk molchunk 
+compute 1 fluid dipole/chunk molchunk
 compute dw water dipole/chunk 1 geometry :pre
 [Description:]
--- a/doc/src/compute_dpd.txt
+++ b/doc/src/compute_dpd.txt
@ -46,7 +46,7 @@ output options.
 The vector values will be in energy and temperature "units"_units.html.
-[Restrictions:] 
+[Restrictions:]
 This command is part of the USER-DPD package.  It is only enabled if
 LAMMPS was built with that package.  See the "Making
@ -64,7 +64,7 @@ command.
 :line
-:link(Larentzos) 
+:link(Larentzos)
 [(Larentzos)] J.P. Larentzos, J.K. Brennan, J.D. Moore, and
 W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
 Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
--- a/doc/src/compute_dpd_atom.txt
+++ b/doc/src/compute_dpd_atom.txt
@ -22,7 +22,7 @@ compute 1 all dpd/atom
 [Description:]
 Define a computation that accesses the per-particle internal
-conductive energy (u_cond), internal mechanical energy (u_mech), 
+conductive energy (u_cond), internal mechanical energy (u_mech),
 internal chemical energy (u_chem) and
 internal temperatures (dpdTheta) for each particle in a group.  See
 the "compute dpd"_compute_dpd.html command if you want the total
@ -39,10 +39,10 @@ that uses per-particle values from a compute as input.  See
 "Section 6.15"_Section_howto.html#howto_15 for an overview of
 LAMMPS output options.
-The per-particle array values will be in energy (u_cond, u_mech, u_chem) 
+The per-particle array values will be in energy (u_cond, u_mech, u_chem)
 and temperature (dpdTheta) "units"_units.html.
-[Restrictions:] 
+[Restrictions:]
 This command is part of the USER-DPD package.  It is only enabled if
 LAMMPS was built with that package.  See the "Making
--- a/doc/src/compute_event_displace.txt
+++ b/doc/src/compute_event_displace.txt
@ -26,7 +26,7 @@ Define a computation that flags an "event" if any particle in the
 group has moved a distance greater than the specified threshold
 distance when compared to a previously stored reference state
 (i.e. the previous event).  This compute is typically used in
-conjunction with the "prd"_prd.html and "tad"_tad.html commands, 
+conjunction with the "prd"_prd.html and "tad"_tad.html commands,
 to detect if a transition
 to a new minimum energy basin has occurred.
@ -34,8 +34,8 @@ This value calculated by the compute is equal to 0 if no particle has
 moved far enough, and equal to 1 if one or more particles have moved
 further than the threshold distance.
-NOTE: If the system is undergoing significant center-of-mass motion, 
+NOTE: If the system is undergoing significant center-of-mass motion,
-due to thermal motion, an external force, or an initial net momentum, 
+due to thermal motion, an external force, or an initial net momentum,
 then this compute will not be able to distinguish that motion from
 local atom displacements and may generate "false postives."
--- a/doc/src/compute_fep.txt
+++ b/doc/src/compute_fep.txt
@ -64,7 +64,7 @@ these atoms:
 A coupling parameter \(\lambda\) varying from 0 to 1 connects the
 reference and perturbed systems:
-:c,image(Eqs/compute_fep_lambda.jpg) 
+:c,image(Eqs/compute_fep_lambda.jpg)
 It is possible but not necessary that the coupling parameter (or a
 function thereof) appears as a multiplication factor of the potential
--- a/doc/src/compute_gyration_chunk.txt
+++ b/doc/src/compute_gyration_chunk.txt
@ -28,7 +28,7 @@ compute 2 molecule gyration/chunk molchunk tensor :pre
 [Description:]
 Define a computation that calculates the radius of gyration Rg for
-multiple chunks of atoms. 
+multiple chunks of atoms.
 In LAMMPS, chunks are collections of atoms defined by a "compute
 chunk/atom"_compute_chunk_atom.html command, which assigns each atom
--- a/doc/src/compute_heat_flux.txt
+++ b/doc/src/compute_heat_flux.txt
@ -20,7 +20,7 @@ stress-ID = ID of a compute that calculates per-atom stress :ul
 [Examples:]
-compute myFlux all heat/flux myKE myPE myStress :pre 
+compute myFlux all heat/flux myKE myPE myStress :pre
 [Description:]
@ -38,7 +38,7 @@ subtracted to a group of atoms.
 The compute takes three arguments which are IDs of other
 "computes"_compute.html.  One calculates per-atom kinetic energy
 ({ke-ID}), one calculates per-atom potential energy ({pe-ID)}, and the
-third calcualtes per-atom stress ({stress-ID}).  
+third calcualtes per-atom stress ({stress-ID}).
 NOTE: These other computes should provide values for all the atoms in
 the group this compute specifies.  That means the other computes could
@ -152,11 +152,11 @@ lattice      fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
 region       box block 0 4 0 4 0 4
 create_box   1 box
 create_atoms 1 box
-mass	     1 39.948
+mass         1 39.948
 pair_style   lj/cut 13.0
 pair_coeff   * * 0.2381 3.405
 timestep     $\{dt\}
-thermo	     $d :pre
+thermo       $d :pre
 # equilibration and thermalization :pre
--- a/doc/src/compute_hexorder_atom.txt
+++ b/doc/src/compute_hexorder_atom.txt
@ -15,7 +15,7 @@ compute ID group-ID hexorder/atom keyword values ... :pre
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 hexorder/atom = style name of this compute command :l
 one or more keyword/value pairs may be appended :l
-keyword = {degree} or {nnn} or {cutoff} 
+keyword = {degree} or {nnn} or {cutoff}
  {cutoff} value = distance cutoff
  {nnn} value = number of nearest neighbors
  {degree} value = degree {n} of order parameter :pre
@ -24,27 +24,27 @@ keyword = {degree} or {nnn} or {cutoff}
 [Examples:]
-compute 1 all hexorder/atom 
+compute 1 all hexorder/atom
 compute 1 all hexorder/atom degree 4 nnn 4 cutoff 1.2 :pre
 [Description:]
-Define a computation that calculates {qn} the bond-orientational 
+Define a computation that calculates {qn} the bond-orientational
-order parameter for each atom in a group. The hexatic ({n} = 6) order 
+order parameter for each atom in a group. The hexatic ({n} = 6) order
 parameter was introduced by "Nelson and Halperin"_#Nelson as a way to detect
-hexagonal symmetry in two-dimensional systems. For each atom, {qn} 
+hexagonal symmetry in two-dimensional systems. For each atom, {qn}
 is a complex number (stored as two real numbers) defined as follows:
 :c,image(Eqs/hexorder.jpg)
-where the sum is over the {nnn} nearest neighbors 
+where the sum is over the {nnn} nearest neighbors
 of the central atom. The angle theta
 is formed by the bond vector rij and the {x} axis. theta is calculated
 only using the {x} and {y} components, whereas the distance from the
-central atom is calculated using all three  
+central atom is calculated using all three
 {x}, {y}, and {z} components of the bond vector.
-Neighbor atoms not in the group 
+Neighbor atoms not in the group
-are included in the order parameter of atoms in the group. 
+are included in the order parameter of atoms in the group.
 The optional keyword {cutoff} defines the distance cutoff
 used when searching for neighbors. The default value, also
@ -53,22 +53,22 @@ by the pair style.
 The optional keyword {nnn} defines the number of nearest
 neighbors used to calculate {qn}. The default value is 6.
-If the value is NULL, then all neighbors up to the 
+If the value is NULL, then all neighbors up to the
 distance cutoff are used.
-The optional keyword {degree} sets the degree {n} of the order parameter. 
+The optional keyword {degree} sets the degree {n} of the order parameter.
-The default value is 6. For a perfect hexagonal lattice with 
+The default value is 6. For a perfect hexagonal lattice with
 {nnn} = 6,
-{q}6 = exp(6 i phi) for all atoms, where the constant 0 < phi < pi/3 
+{q}6 = exp(6 i phi) for all atoms, where the constant 0 < phi < pi/3
-depends only on the orientation of the lattice relative to the {x} axis.  
+depends only on the orientation of the lattice relative to the {x} axis.
-In an isotropic liquid, local neighborhoods may still exhibit 
+In an isotropic liquid, local neighborhoods may still exhibit
 weak hexagonal symmetry, but because the orientational correlation
 decays quickly with distance, the value of phi will be different for
-different atoms, and so when {q}6 is averaged over all the atoms 
+different atoms, and so when {q}6 is averaged over all the atoms
 in the system, \|<{q}6>\| << 1.
 The value of {qn} is set to zero for atoms not in the
-specified compute group, as well as for atoms that have less than 
+specified compute group, as well as for atoms that have less than
 {nnn} neighbors within the distance cutoff.
 The neighbor list needed to compute this quantity is constructed each
@ -92,7 +92,7 @@ the neighbor list.
 [Output info:]
 This compute calculates a per-atom array with 2 columns, giving the
-real and imaginary parts {qn}, a complex number restricted to the 
+real and imaginary parts {qn}, a complex number restricted to the
 unit disk of the complex plane i.e. Re({qn})^2 + Im({qn})^2 <= 1 .
 These values can be accessed by any command that uses
@ -106,7 +106,7 @@ options.
 "compute orientorder/atom"_compute_orientorder_atom.html, "compute coord/atom"_compute_coord_atom.html, "compute centro/atom"_compute_centro_atom.html
-[Default:] 
+[Default:]
 The option defaults are {cutoff} = pair style cutoff, {nnn} = 6, {degree} = 6
--- a/doc/src/compute_inertia_chunk.txt
+++ b/doc/src/compute_inertia_chunk.txt
@ -23,7 +23,7 @@ compute 1 fluid inertia/chunk molchunk :pre
 [Description:]
 Define a computation that calculates the inertia tensor for multiple
-chunks of atoms. 
+chunks of atoms.
 In LAMMPS, chunks are collections of atoms defined by a "compute
 chunk/atom"_compute_chunk_atom.html command, which assigns each atom
--- a/doc/src/compute_ke_atom_eff.txt
+++ b/doc/src/compute_ke_atom_eff.txt
@ -48,9 +48,9 @@ thermodynamic output by using the "thermo_modify"_thermo_modify.html
 command, as shown in the following example:
 compute         effTemp all temp/eff
-thermo_style    custom step etotal pe ke temp press 
+thermo_style    custom step etotal pe ke temp press
 thermo_modify   temp effTemp :pre
- 
+
 The value of the kinetic energy will be 0.0 for atoms (nuclei or
 electrons) not in the specified compute group.
--- a/doc/src/compute_ke_eff.txt
+++ b/doc/src/compute_ke_eff.txt
@ -52,9 +52,9 @@ printed with thermodynamic output by using the
 example:
 compute         effTemp all temp/eff
-thermo_style    custom step etotal pe ke temp press 
+thermo_style    custom step etotal pe ke temp press
 thermo_modify   temp effTemp :pre
- 
+
 See "compute temp/eff"_compute_temp_eff.html.
 [Output info:]
--- a/doc/src/compute_modify.txt
+++ b/doc/src/compute_modify.txt
@ -61,4 +61,4 @@ the temperature is correctly normalized.
 [Default:]
 The option defaults are extra = 2 or 3 for 2d or 3d systems and
-dynamic = no. 
+dynamic = no.
--- a/doc/src/compute_msd.txt
+++ b/doc/src/compute_msd.txt
@ -44,7 +44,7 @@ proportional to the diffusion coefficient of the diffusing atoms.
 The displacement of an atom is from its reference position. This is
 normally the original position at the time
-the compute command was issued, unless the {average} keyword is set to {yes}.  
+the compute command was issued, unless the {average} keyword is set to {yes}.
 The value of the displacement will be
 0.0 for atoms not in the specified compute group.
--- a/doc/src/compute_orientorder_atom.txt
+++ b/doc/src/compute_orientorder_atom.txt
@ -15,7 +15,7 @@ compute ID group-ID orientorder/atom keyword values ... :pre
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 orientorder/atom = style name of this compute command :l
 one or more keyword/value pairs may be appended :l
-keyword = {cutoff} or {nnn} or {ql} 
+keyword = {cutoff} or {nnn} or {ql}
  {cutoff} value = distance cutoff
  {nnn} value = number of nearest neighbors
  {degrees} values = nlvalues, l1, l2,...  :pre
@ -24,30 +24,30 @@ keyword = {cutoff} or {nnn} or {ql}
 [Examples:]
-compute 1 all orientorder/atom 
+compute 1 all orientorder/atom
 compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5 :pre
 [Description:]
-Define a computation that calculates a set of bond-orientational 
+Define a computation that calculates a set of bond-orientational
 order parameters {Ql} for each atom in a group. These order parameters
 were introduced by "Steinhardt et al."_#Steinhardt as a way to
-characterize the local orientational order in atomic structures. 
+characterize the local orientational order in atomic structures.
 For each atom, {Ql} is a real number defined as follows:
 :c,image(Eqs/orientorder.jpg)
-The first equation defines the spherical harmonic order parameters. 
+The first equation defines the spherical harmonic order parameters.
-These are complex number components of the 3D analog of the 2D order 
+These are complex number components of the 3D analog of the 2D order
-parameter {qn}, which is implemented as LAMMPS compute 
+parameter {qn}, which is implemented as LAMMPS compute
-"hexorder/atom"_compute_hexorder_atom.html. 
+"hexorder/atom"_compute_hexorder_atom.html.
-The summation is over the {nnn} nearest 
+The summation is over the {nnn} nearest
-neighbors of the central atom. 
+neighbors of the central atom.
-The angles theta and phi are the standard spherical polar angles 
+The angles theta and phi are the standard spherical polar angles
 defining the direction of the bond vector {rij}.
 The second equation defines {Ql}, which is a
-rotationally invariant scalar quantity obtained by summing 
+rotationally invariant scalar quantity obtained by summing
-over all the components of degree {l}. 
+over all the components of degree {l}.
 The optional keyword {cutoff} defines the distance cutoff
 used when searching for neighbors. The default value, also
@ -56,23 +56,23 @@ by the pair style.
 The optional keyword {nnn} defines the number of nearest
 neighbors used to calculate {Ql}. The default value is 12.
-If the value is NULL, then all neighbors up to the 
+If the value is NULL, then all neighbors up to the
 specified distance cutoff are used.
 The optional keyword {degrees} defines the list of order parameters to
-be computed.  The first argument {nlvalues} is the number of order 
+be computed.  The first argument {nlvalues} is the number of order
 parameters. This is followed by that number of integers giving the
-degree of each order parameter. Because {Q}2 and all odd-degree 
+degree of each order parameter. Because {Q}2 and all odd-degree
-order parameters are zero for atoms in cubic crystals 
+order parameters are zero for atoms in cubic crystals
 (see "Steinhardt"_#Steinhardt), the default order parameters
 are {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12. For the
 FCC crystal with {nnn}=12, {Q}4 = sqrt(7/3)/8 = 0.19094....
 The numerical values of all order parameters up to {Q}12
-for a range of commonly encountered high-symmetry structures are given 
+for a range of commonly encountered high-symmetry structures are given
 in Table I of "Mickel et al."_#Mickel.
 The value of {Ql} is set to zero for atoms not in the
-specified compute group, as well as for atoms that have less than 
+specified compute group, as well as for atoms that have less than
 {nnn} neighbors within the distance cutoff.
 The neighbor list needed to compute this quantity is constructed each
@ -109,9 +109,9 @@ options.
 "compute coord/atom"_compute_coord_atom.html, "compute centro/atom"_compute_centro_atom.html, "compute hexorder/atom"_compute_hexorder_atom.html
-[Default:] 
+[Default:]
-The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, {degrees} = 5 4 6 8 9 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12. 
+The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, {degrees} = 5 4 6 8 9 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.
 :line
--- a/doc/src/compute_pe_atom.txt
+++ b/doc/src/compute_pe_atom.txt
@ -52,7 +52,7 @@ The KSpace contribution is calculated using the method in
 "(Heyes)"_#Heyes for the Ewald method and a related method for PPPM,
 as specified by the "kspace_style pppm"_kspace_style.html command.
 For PPPM, the calcluation requires 1 extra FFT each timestep that
-per-atom energy is calculated.  Thie "document"_PDF/kspace.pdf
+per-atom energy is calculated.  This "document"_PDF/kspace.pdf
 describes how the long-range per-atom energy calculation is performed.
 Various fixes can contribute to the per-atom potential energy of the
@ -68,9 +68,9 @@ As an example of per-atom potential energy compared to total potential
 energy, these lines in an input script should yield the same result
 in the last 2 columns of thermo output:
-compute		peratom all pe/atom
+compute        peratom all pe/atom
-compute		pe all reduce sum c_peratom
+compute        pe all reduce sum c_peratom
-thermo_style	custom step temp etotal press pe c_pe :pre
+thermo_style   custom step temp etotal press pe c_pe :pre
 NOTE: The per-atom energy does not any Lennard-Jones tail corrections
 invoked by the "pair_modify tail yes"_pair_modify.html command, since
--- a/doc/src/compute_plasticity_atom.txt
+++ b/doc/src/compute_plasticity_atom.txt
@ -30,7 +30,7 @@ The plasticity for a Peridynamic particle is the so-called consistency
 parameter (lambda).  For elastic deformation lambda = 0, otherwise
 lambda > 0 for plastic deformation.  For details, see
 "(Mitchell)"_#Mitchell and the PDF doc included in the LAMMPS
-distro in "doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf. 
+distro in "doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf.
 This command can be invoked for one of the Peridynamic "pair
 styles"_pair_peri.html: peri/eps.
@ -57,7 +57,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 "compute damage/atom"_compute_damage_atom.html,
 "compute dilatation/atom"_compute_dilatation_atom.html
-[Default:] none 
+[Default:] none
 :line
--- a/doc/src/compute_pressure.txt
+++ b/doc/src/compute_pressure.txt
@ -50,7 +50,7 @@ ordered xx, yy, zz, xy, xz, yz.  The equation for the I,J components
 (where I and J = x,y,z) is similar to the above formula, except that
 the first term uses components of the kinetic energy tensor and the
 second term uses components of the virial tensor:
-  
+
 :c,image(Eqs/pressure_tensor.jpg)
 If no extra keywords are listed, the entire equations above are
--- a/doc/src/compute_property_atom.txt
+++ b/doc/src/compute_property_atom.txt
@ -16,20 +16,20 @@ ID, group-ID are documented in "compute"_compute.html command :ulb,l
 property/atom = style name of this compute command :l
 input = one or more atom attributes :l
  possible attributes = id, mol, proc, type, mass,
- 	                x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
+                        x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
-		        vx, vy, vz, fx, fy, fz,
+                        vx, vy, vz, fx, fy, fz,
                        q, mux, muy, muz, mu,
                        radius, diameter, omegax, omegay, omegaz,
-			angmomx, angmomy, angmomz,
+                        angmomx, angmomy, angmomz,
-			shapex,shapey, shapez,
+                        shapex,shapey, shapez,
-		        quatw, quati, quatj, quatk, tqx, tqy, tqz,
+                        quatw, quati, quatj, quatk, tqx, tqy, tqz,
-			end1x, end1y, end1z, end2x, end2y, end2z,
+                        end1x, end1y, end1z, end2x, end2y, end2z,
-			corner1x, corner1y, corner1z,
+                        corner1x, corner1y, corner1z,
-			corner2x, corner2y, corner2z,
+                        corner2x, corner2y, corner2z,
-			corner3x, corner3y, corner3z,
+                        corner3x, corner3y, corner3z,
-			nbonds,
+                        nbonds,
                        vfrac, s0,
-			spin, eradius, ervel, erforce,
+                        spin, eradius, ervel, erforce,
                        rho, drho, e, de, cv,
                        i_name, d_name :pre
      id = atom ID
@ -80,7 +80,7 @@ input = one or more atom attributes :l
 [Examples:]
-compute 1 all property/atom xs vx fx mux 
+compute 1 all property/atom xs vx fx mux
 compute 2 all property/atom type
 compute 1 all property/atom ix iy iz :pre
--- a/doc/src/compute_property_chunk.txt
+++ b/doc/src/compute_property_chunk.txt
@ -16,7 +16,7 @@ ID, group-ID are documented in "compute"_compute.html command :ulb,l
 property/chunk = style name of this compute command :l
 input = one or more attributes :l
  attributes = count, id, coord1, coord2, coord3
-    count = # of atoms in chunk 
+    count = # of atoms in chunk
    id = original chunk IDs before compression by "compute chunk/atom"_compute_chunk_atom.html
    coord123 = coordinates for spatial bins calculated by "compute chunk/atom"_compute_chunk_atom.html :pre
 :ule
--- a/doc/src/compute_property_local.txt
+++ b/doc/src/compute_property_local.txt
@ -15,12 +15,12 @@ compute ID group-ID property/local attribute1 attribute2 ... keyword args ... :p
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 property/local = style name of this compute command :l
 one or more attributes may be appended :l
-  possible attributes =  natom1 natom2 ntype1 ntype2
+  possible attributes = natom1 natom2 ntype1 ntype2
-		         patom1 patom2 ptype1 ptype2
+                        patom1 patom2 ptype1 ptype2
-                         batom1 batom2 btype
+                        batom1 batom2 btype
-                         aatom1 aatom2 aatom3 atype
+                        aatom1 aatom2 aatom3 atype
-                         datom1 datom2 datom3 dtype
+                        datom1 datom2 datom3 dtype
-                         iatom1 iatom2 iatom3 itype :pre
+                        iatom1 iatom2 iatom3 itype :pre
     natom1, natom2 = IDs of 2 atoms in each pair (within neighbor cutoff)
     ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff)
@ -129,8 +129,6 @@ The attributes that start with "a", "d", "i", refer to similar values
 for "angles"_angle_style.html, "dihedrals"_dihedral_style.html, and
 "impropers"_improper_style.html.
 The optional {cutoff} keyword
 [Output info:]
 This compute calculates a local vector or local array depending on the
--- a/doc/src/compute_reduce.txt
+++ b/doc/src/compute_reduce.txt
@ -155,8 +155,8 @@ Thus, for example, if you wish to use this compute to find the bond
 with maximum stretch, you can do it as follows:
 compute 1 all property/local batom1 batom2
-compute	2 all bond/local dist
+compute 2 all bond/local dist
-compute	3 all reduce max c_1\[1\] c_1\[2\] c_2 replace 1 3 replace 2 3
+compute 3 all reduce max c_1\[1\] c_1\[2\] c_2 replace 1 3 replace 2 3
 thermo_style custom step temp c_3\[1\] c_3\[2\] c_3\[3\] :pre
 The first two input values in the compute reduce command are vectors
--- a/doc/src/compute_rigid_local.txt
+++ b/doc/src/compute_rigid_local.txt
@ -17,11 +17,11 @@ rigid/local = style name of this compute command :l
 rigidID = ID of fix rigid/small command or one of its variants :l
 input = one or more rigid body attributes :l
  possible attributes = id, mol, mass,
- 	                x, y, z, xu, yu, zu, ix, iy, iz
+                        x, y, z, xu, yu, zu, ix, iy, iz
-		        vx, vy, vz, fx, fy, fz, 
+                        vx, vy, vz, fx, fy, fz,
                        omegax, omegay, omegaz,
-			angmomx, angmomy, angmomz,
+                        angmomx, angmomy, angmomz,
-		        quatw, quati, quatj, quatk, 
+                        quatw, quati, quatj, quatk,
                        tqx, tqy, tqz,
                        inertiax, inertiay, inertiaz
      id = atom ID of atom within body which owns body properties
@ -29,7 +29,7 @@ input = one or more rigid body attributes :l
      mass = total mass of body
      x,y,z = center of mass coords of body
      xu,yu,zu = unwrapped center of mass coords of body
-      ix,iy,iz = box image that the center of mass is in 
+      ix,iy,iz = box image that the center of mass is in
      vx,vy,vz = center of mass velocities
      fx,fy,fz = force of center of mass
      omegax,omegay,omegaz = angular velocity of body
@ -71,7 +71,7 @@ it is skipped (only one atom per body is so assigned).  If it is the
 assigned atom, then the info for that body is output.  This means that
 information for N bodies is generated.  N may be less than the # of
 bodies defined by the fix rigid command, if the atoms in some bodies
-are not in the {group-ID}.  
+are not in the {group-ID}.
 NOTE: Which atom in a body owns the body info is determined internal
 to LAMMPS; it's the one nearest the geometric center of the body.
@ -109,7 +109,7 @@ sigma, etc).  Use {xu}, {yu}, {zu} if you want the COM "unwrapped" by
 the image flags for each atobody.  Unwrapped means that if the body
 COM has passed thru a periodic boundary one or more times, the value
 is generated what the COM coordinate would be if it had not been
-wrapped back into the periodic box. 
+wrapped back into the periodic box.
 The image flags for the body can be generated directly using the {ix},
 {iy}, {iz} attributes.  For periodic dimensions, they specify which
--- a/doc/src/compute_saed.txt
+++ b/doc/src/compute_saed.txt
@ -19,18 +19,18 @@ type1 type2 ... typeN = chemical symbol of each atom type (see valid options bel
 zero or more keyword/value pairs may be appended :l
 keyword = {Kmax} or {Zone} or {dR_Ewald} or {c} or {manual} or {echo} :l
-  {Kmax} value = Maximum distance explored from reciprocal space origin 
+  {Kmax} value = Maximum distance explored from reciprocal space origin
                 (inverse length units)
  {Zone} values = z1 z2 z3
-    z1,z2,z3 = Zone axis of incident radiation. If z1=z2=z3=0 all 
+    z1,z2,z3 = Zone axis of incident radiation. If z1=z2=z3=0 all
               reciprocal space will be meshed up to {Kmax}
-  {dR_Ewald} value = Thickness of Ewald sphere slice intercepting 
+  {dR_Ewald} value = Thickness of Ewald sphere slice intercepting
                     reciprocal space (inverse length units)
  {c} values = c1 c2 c3
-    c1,c2,c3 = parameters to adjust the spacing of the reciprocal 
+    c1,c2,c3 = parameters to adjust the spacing of the reciprocal
               lattice nodes in the h, k, and l directions respectively
-  {manual} = flag to use manual spacing of reciprocal lattice points   
+  {manual} = flag to use manual spacing of reciprocal lattice points
-             based on the values of the {c} parameters 
+             based on the values of the {c} parameters
  {echo} = flag to provide extra output for debugging purposes :pre
 :ule
@ -44,22 +44,22 @@ fix saed/vtk 1 1 1 c_2 file Ni_000.saed :pre
 [Description:]
-Define a computation that calculates electron diffraction intensity as 
+Define a computation that calculates electron diffraction intensity as
-described in "(Coleman)"_#saed-Coleman on a mesh of reciprocal lattice nodes 
+described in "(Coleman)"_#saed-Coleman on a mesh of reciprocal lattice nodes
-defined by the entire simulation domain (or manually) using simulated 
+defined by the entire simulation domain (or manually) using simulated
-radiation of wavelength lambda. 
+radiation of wavelength lambda.
-The electron diffraction intensity I at each reciprocal lattice point 
+The electron diffraction intensity I at each reciprocal lattice point
 is computed from the structure factor F using the equations:
-:c,image(Eqs/compute_saed1.jpg) 
+:c,image(Eqs/compute_saed1.jpg)
 :c,image(Eqs/compute_saed2.jpg)
-Here, K is the location of the reciprocal lattice node, rj is the 
+Here, K is the location of the reciprocal lattice node, rj is the
 position of each atom, fj are atomic scattering factors.
-Diffraction intensities are calculated on a three-dimensional mesh of 
+Diffraction intensities are calculated on a three-dimensional mesh of
-reciprocal lattice nodes. The mesh spacing is defined either (a)  by 
+reciprocal lattice nodes. The mesh spacing is defined either (a)  by
 the entire simulation domain or (b) manually using selected values as
 shown in the 2D diagram below.
@ -74,12 +74,12 @@ average of the (inversed) box lengths with periodic boundary conditions.
 Meshes defined by the simulation domain must contain at least one periodic
 boundary.
-If the {manual} flag is included, the mesh of reciprocal lattice nodes 
+If the {manual} flag is included, the mesh of reciprocal lattice nodes
-will defined using the {c} values for the spacing along each reciprocal 
+will defined using the {c} values for the spacing along each reciprocal
-lattice axis. Note that manual mapping of the reciprocal space mesh is 
+lattice axis. Note that manual mapping of the reciprocal space mesh is
-good for comparing diffraction results from  multiple simulations; however 
+good for comparing diffraction results from  multiple simulations; however
-it can reduce the likelihood that Bragg reflections will be satisfied 
+it can reduce the likelihood that Bragg reflections will be satisfied
-unless small spacing parameters <0.05 Angstrom^(-1) are implemented. 
+unless small spacing parameters <0.05 Angstrom^(-1) are implemented.
 Meshes with manual spacing do not require a periodic boundary.
 The limits of the reciprocal lattice mesh are determined by the use of
@ -98,17 +98,17 @@ in the below image.
 :c,image(JPG/saed_ewald_intersect_small.jpg,JPG/saed_ewald_intersect.jpg)
-The atomic scattering factors, fj, accounts for the reduction in 
+The atomic scattering factors, fj, accounts for the reduction in
-diffraction intensity due to Compton scattering.  Compute saed uses 
+diffraction intensity due to Compton scattering.  Compute saed uses
-analytical approximations of the atomic scattering factors that vary 
+analytical approximations of the atomic scattering factors that vary
-for each atom type (type1 type2 ... typeN) and angle of diffraction.  
+for each atom type (type1 type2 ... typeN) and angle of diffraction.
 The analytic approximation is computed using the formula
 "(Brown)"_#Brown:
 :c,image(Eqs/compute_saed3.jpg)
-Coefficients parameterized by "(Fox)"_#Fox are assigned for each 
+Coefficients parameterized by "(Fox)"_#Fox are assigned for each
-atom type designating the chemical symbol and charge of each atom 
+atom type designating the chemical symbol and charge of each atom
 type. Valid chemical symbols for compute saed are:
         H:      He:      Li:      Be:       B:
@ -133,14 +133,14 @@ type. Valid chemical symbols for compute saed are:
        Cm:      Bk:      Cf:tb(c=5,s=:)
-If the {echo} keyword is specified, compute saed will provide extra 
+If the {echo} keyword is specified, compute saed will provide extra
-reporting information to the screen.  
+reporting information to the screen.
 [Output info:]
-This compute calculates a global vector.  The length of the vector is 
+This compute calculates a global vector.  The length of the vector is
-the number of reciprocal lattice nodes that are explored by the mesh.  
+the number of reciprocal lattice nodes that are explored by the mesh.
-The entries of the global vector are the computed diffraction 
+The entries of the global vector are the computed diffraction
 intensities as described above.
 The vector can be accessed by any command that uses global values
@ -148,21 +148,21 @@ from a compute as input.  See "this
 section"_Section_howto.html#howto_15 for an overview of LAMMPS output
 options.
-All array values calculated by this compute are "intensive".  
+All array values calculated by this compute are "intensive".
-[Restrictions:] 
+[Restrictions:]
 This compute is part of the USER-DIFFRACTION 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 compute_saed command does not work for triclinic cells. 
+The compute_saed command does not work for triclinic cells.
-[Related commands:] 
+[Related commands:]
 "fix saed_vtk"_fix_saed_vtk.html, "compute xrd"_compute_xrd.html
-[Default:] 
+[Default:]
 The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald =
 0.01.
@ -174,7 +174,7 @@ The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald =
 (2013).
 :link(Brown)
-[(Brown)] Brown et al. International Tables for Crystallography 
+[(Brown)] Brown et al. International Tables for Crystallography
 Volume C: Mathematical and Chemical Tables, 554-95 (2004).
 :link(Fox)
--- a/doc/src/compute_smd_damage.txt
+++ b/doc/src/compute_smd_damage.txt
@ -22,7 +22,7 @@ compute 1 all smd/damage :pre
 [Description:]
 Define a computation that calculates the damage status of SPH particles
-according to the damage model which is defined via the SMD SPH pair styles, e.g., the maximum plastic strain failure criterion. 
+according to the damage model which is defined via the SMD SPH pair styles, e.g., the maximum plastic strain failure criterion.
 See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
--- a/doc/src/compute_sna_atom.txt
+++ b/doc/src/compute_sna_atom.txt
@ -31,7 +31,7 @@ keyword = {diagonal} or {rmin0} or {switchflag} :l
     {2} = subset satisfying j1 == j2 == j3
     {3} = subset satisfying j2 <= j1 <= j
  {rmin0} value = parameter in distance to angle conversion (distance units)
-  {switchflag} value = {0} or {1} 
+  {switchflag} value = {0} or {1}
     {0} = do not use switching function
     {1} = use switching function :pre
 :ule
@ -60,12 +60,12 @@ onto the 3-sphere, the surface of the unit ball in a four-dimensional
 space.  The radial distance {r} within {R_ii'} is mapped on to a third
 polar angle {theta0} defined by,
-:c,image(Eqs/compute_sna_atom1.jpg) 
+:c,image(Eqs/compute_sna_atom1.jpg)
 In this way, all possible neighbor positions are mapped on to a subset
 of the 3-sphere.  Points south of the latitude {theta0max=rfac0*Pi}
 are excluded.
- 
+
 The natural basis for functions on the 3-sphere is formed by the 4D
 hyperspherical harmonics {U^j_m,m'(theta, phi, theta0).}  These
 functions are better known as {D^j_m,m',} the elements of the Wigner
@ -78,7 +78,7 @@ radial distance. Expanding this density function as a generalized
 Fourier series in the basis functions, we can write each Fourier
 coefficient as
-:c,image(Eqs/compute_sna_atom2.jpg) 
+:c,image(Eqs/compute_sna_atom2.jpg)
 The {w_i'} neighbor weights are dimensionless numbers that are chosen
 to distinguish atoms of different types, while the central atom is
@ -86,7 +86,7 @@ arbitrarily assigned a unit weight.  The function {fc(r)} ensures that
 the contribution of each neighbor atom goes smoothly to zero at
 {R_ii'}:
-:c,image(Eqs/compute_sna_atom4.jpg) 
+:c,image(Eqs/compute_sna_atom4.jpg)
 The expansion coefficients {u^j_m,m'} are complex-valued and they are
 not directly useful as descriptors, because they are not invariant
@ -94,7 +94,7 @@ under rotation of the polar coordinate frame. However, the following
 scalar triple products of expansion coefficients can be shown to be
 real-valued and invariant under rotation "(Bartok)"_#Bartok2010.
-:c,image(Eqs/compute_sna_atom3.jpg) 
+:c,image(Eqs/compute_sna_atom3.jpg)
 The constants {H^jmm'_j1m1m1'_j2m2m2'} are coupling coefficients,
 analogous to Clebsch-Gordan coefficients for rotations on the
@ -112,17 +112,17 @@ atom.
 Compute {snad/atom} calculates the derivative of the bispectrum components
 summed separately for each atom type:
-:c,image(Eqs/compute_sna_atom5.jpg) 
+:c,image(Eqs/compute_sna_atom5.jpg)
 The sum is over all atoms {i'} of atom type {I}.  For each atom {i},
 this compute evaluates the above expression for each direction, each
 atom type, and each bispectrum component.  See section below on output
 for a detailed explanation.
- 
+
 Compute {snav/atom} calculates the virial contribution due to the
 derivatives:
-:c,image(Eqs/compute_sna_atom6.jpg) 
+:c,image(Eqs/compute_sna_atom6.jpg)
 Again, the sum is over all atoms {i'} of atom type {I}.  For each atom
 {i}, this compute evaluates the above expression for each of the six
@ -140,7 +140,7 @@ too frequently.
 The argument {rcutfac} is a scale factor that controls the ratio of
 atomic radius to radial cutoff distance.
- 
+
 The argument {rfac0} and the optional keyword {rmin0} define the
 linear mapping from radial distance to polar angle {theta0} on the
 3-sphere.
@ -176,18 +176,18 @@ each column depend on the values of {twojmax} and {diagonal}, as
 described by the following piece of python code:
 for j1 in range(0,twojmax+1):
-    if(diagonal==2): 
+    if(diagonal==2):
        print j1/2.,j1/2.,j1/2.
    elif(diagonal==1):
-        for j in range(0,min(twojmax,2*j1)+1,2): 
+        for j in range(0,min(twojmax,2*j1)+1,2):
            print j1/2.,j1/2.,j/2.
    elif(diagonal==0):
        for j2 in range(0,j1+1):
-            for j in range(j1-j2,min(twojmax,j1+j2)+1,2): 
+            for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
                print j1/2.,j2/2.,j/2.
    elif(diagonal==3):
        for j2 in range(0,j1+1):
-            for j in range(j1-j2,min(twojmax,j1+j2)+1,2): 
+            for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
                if (j>=j1): print j1/2.,j2/2.,j/2. :pre
 Compute {snad/atom} evaluates a per-atom array. The columns are
@ -227,7 +227,7 @@ The optional keyword defaults are {diagonal} = 0, {rmin0} = 0,
 :line
 :link(Thompson2014)
-[(Thompson)] Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint 
+[(Thompson)] Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint
 available at "arXiv:1409.3880"_http://arxiv.org/abs/1409.3880
 :link(Bartok2010)
@ -235,7 +235,7 @@ available at "arXiv:1409.3880"_http://arxiv.org/abs/1409.3880
 :link(Meremianin2006)
 [(Meremianin)] Meremianin, J. Phys. A,  39, 3099 (2006).
- 
+
 :link(Varshalovich1987)
 [(Varshalovich)] Varshalovich, Moskalev, Khersonskii, Quantum Theory
 of Angular Momentum, World Scientific, Singapore (1987).
--- a/doc/src/compute_stress_atom.txt
+++ b/doc/src/compute_stress_atom.txt
@ -128,10 +128,10 @@ d = dimension and V is the volume of the system, the result should be
 These lines in an input script for a 3d system should yield that
 result.  I.e. the last 2 columns of thermo output will be the same:
-compute		peratom all stress/atom NULL
+compute        peratom all stress/atom NULL
-compute		p all reduce sum c_peratom\[1\] c_peratom\[2\] c_peratom\[3\]
+compute        p all reduce sum c_peratom\[1\] c_peratom\[2\] c_peratom\[3\]
-variable	press equal -(c_p\[1\]+c_p\[2\]+c_p\[3\])/(3*vol)
+variable       press equal -(c_p\[1\]+c_p\[2\]+c_p\[3\])/(3*vol)
-thermo_style	custom step temp etotal press v_press :pre
+thermo_style   custom step temp etotal press v_press :pre
 [Output info:]
--- a/doc/src/compute_tally.txt
+++ b/doc/src/compute_tally.txt
@ -88,7 +88,7 @@ potentials only include the pair potential portion of the EAM
 interaction when used by this compute, not the embedding term.  Also
 bonded or Kspace interactions do not contribute to this compute.
-[Related commands:] 
+[Related commands:]
 {compute group/group}_compute_group_group.html, {compute
 heat/flux}_compute_heat_flux.html
--- a/doc/src/compute_temp_asphere.txt
+++ b/doc/src/compute_temp_asphere.txt
--- a/doc/src/compute_temp_body.txt
+++ b/doc/src/compute_temp_body.txt
--- a/doc/src/compute_temp_cs.txt
+++ b/doc/src/compute_temp_cs.txt
@ -16,7 +16,7 @@ ID, group-ID are documented in "compute"_compute.html command
 temp/cs = style name of this compute command
 group1 = group-ID of either cores or shells
 group2 = group-ID of either shells or cores :ul
-                        
+
 [Examples:]
 compute oxygen_c-s all temp/cs O_core O_shell
@ -64,7 +64,7 @@ calculated by this compute for use in the computation of a pressure
 tensor.  The formula for the components of the tensor is the same as
 the above formula, except that v^2 is replaced by vx*vy for the xy
 component, etc.  The 6 components of the vector are ordered xx, yy,
-zz, xy, xz, yz.  In contrast to the temperature, the velocity of 
+zz, xy, xz, yz.  In contrast to the temperature, the velocity of
 each core or shell atom is taken individually.
 The change this fix makes to core/shell atom velocities is essentially
--- a/doc/src/compute_temp_drude.txt
+++ b/doc/src/compute_temp_drude.txt
@ -14,7 +14,7 @@ compute ID group-ID temp/drude :pre
 ID, group-ID are documented in "compute"_compute.html command
 temp/drude = style name of this compute command :ul
-                        
+
 [Examples:]
 compute TDRUDE all temp/drude :pre
@ -68,7 +68,7 @@ are "extensive".
 [Restrictions:]
 The number of degrees of freedom contributing to the temperature is
-assumed to be constant for the duration of the run unless the 
+assumed to be constant for the duration of the run unless the
 {fix_modify} command sets the option {dynamic yes}.
 [Related commands:]
--- a/doc/src/compute_temp_eff.txt
+++ b/doc/src/compute_temp_eff.txt
@ -49,9 +49,9 @@ reported by LAMMPS in the thermodynamic quantities reported via the
 example:
 compute         effTemp all temp/eff
-thermo_style    custom step etotal pe ke temp press 
+thermo_style    custom step etotal pe ke temp press
 thermo_modify   temp effTemp :pre
- 
+
 A 6-component kinetic energy tensor is also calculated by this compute
 for use in the computation of a pressure tensor.  The formula for the
 components of the tensor is the same as the above formula, except that
@ -80,7 +80,7 @@ is independent of the number of atoms in the simulation.  The vector
 values are "extensive", meaning they scale with the number of atoms in
 the simulation.
-[Restrictions:] 
+[Restrictions:]
 This compute is part of the USER-EFF package.  It is only enabled if
 LAMMPS was built with that package.  See the "Making
--- a/doc/src/compute_temp_region.txt
+++ b/doc/src/compute_temp_region.txt
@ -68,7 +68,7 @@ temp/berendsen"_fix_temp_berendsen.html, and "fix
 langevin"_fix_langevin.html.  This means that when this compute
 is used to calculate the temperature for any of the thermostatting
 fixes via the "fix modify temp"_fix_modify.html command, the thermostat
-will operate only on atoms that are currently in the geometric 
+will operate only on atoms that are currently in the geometric
 region.
 Unlike other compute styles that calculate temperature, this compute
--- a/doc/src/compute_temp_sphere.txt
+++ b/doc/src/compute_temp_sphere.txt
@ -122,7 +122,7 @@ vector values will be in energy "units"_units.html.
 This fix requires that atoms store torque and angular velocity (omega)
 and a radius as defined by the "atom_style sphere"_atom_style.html
-command.  
+command.
 All particles in the group must be finite-size spheres, or point
 particles with radius = 0.0.
--- a/doc/src/compute_ti.txt
+++ b/doc/src/compute_ti.txt
@ -6,7 +6,7 @@
 :line
-compute ti command :h3 
+compute ti command :h3
 [Syntax:]
@ -35,7 +35,7 @@ keyword = pair style (lj/cut, gauss, born, etc) or {tail} or {kspace} :l
 compute 1 all ti lj/cut 1 v_lj v_dlj coul/long 2 v_c v_dc kspace 1 v_ks v_dks
 compute 1 all ti lj/cut 1*3 v_lj v_dlj coul/long * v_c v_dc kspace * v_ks v_dks :pre
-[Description:] 
+[Description:]
 Define a computation that calculates the derivative of the interaction
 potential with respect to {lambda}, the coupling parameter used in a
@ -107,7 +107,7 @@ du/dl can be found in the paper by "Eike"_#Eike.
 :line
-[Output info:] 
+[Output info:]
 This compute calculates a global scalar, namely dUs/dlambda.  This
 value can be used by any command that uses a global scalar value from
--- a/doc/src/compute_voronoi_atom.txt
+++ b/doc/src/compute_voronoi_atom.txt
@ -15,7 +15,7 @@ compute ID group-ID voronoi/atom keyword arg ... :pre
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 voronoi/atom = style name of this compute command :l
 zero or more keyword/value pairs may be appended :l
-keyword = {only_group} or {surface} or {radius} or {edge_histo} or {edge_threshold} 
+keyword = {only_group} or {surface} or {radius} or {edge_histo} or {edge_threshold}
 or {face_threshold} or {neighbors} or {peratom} :l
  {only_group} = no arg
  {occupation} = no arg
@ -25,7 +25,7 @@ or {face_threshold} or {neighbors} or {peratom} :l
  {radius} arg = v_r
    v_r = radius atom style variable for a poly-disperse Voronoi tessellation
  {edge_histo} arg = maxedge
-    maxedge = maximum number of Voronoi cell edges to be accounted in the histogram 
+    maxedge = maximum number of Voronoi cell edges to be accounted in the histogram
  {edge_threshold} arg = minlength
    minlength = minimum length for an edge to be counted
  {face_threshold} arg = minarea
@ -38,7 +38,7 @@ or {face_threshold} or {neighbors} or {peratom} :l
 compute 1 all voronoi/atom
 compute 2 precipitate voronoi/atom surface matrix
-compute 3b precipitate voronoi/atom radius v_r 
+compute 3b precipitate voronoi/atom radius v_r
 compute 4 solute voronoi/atom only_group
 compute 5 defects voronoi/atom occupation
 compute 6 all voronoi/atom neighbors yes :pre
@ -53,11 +53,11 @@ in the group.
 By default two per-atom quantities are calculated by this compute.
 The first is the volume of the Voronoi cell around each atom.  Any
 point in an atom's Voronoi cell is closer to that atom than any other.
-The second is the number of faces of the Voronoi cell. This is 
+The second is the number of faces of the Voronoi cell. This is
 equal to the number of nearest neighbors of the central atom,
-plus any exterior faces (see note below). If the {peratom} keyword 
+plus any exterior faces (see note below). If the {peratom} keyword
-is set to "no", the per-atom quantities are still calculated, 
+is set to "no", the per-atom quantities are still calculated,
-but they are not accessible. 
+but they are not accessible.
 :line
@ -122,23 +122,23 @@ to locate vacancies (the coordinates are given by the atom coordinates
 at the time step when the compute was first invoked), while column two
 data can be used to identify interstitial atoms.
-If the {neighbors} value is set to yes, then 
+If the {neighbors} value is set to yes, then
 this compute creates a local array with 3 columns. There
-is one row for each face of each Voronoi cell. The 
+is one row for each face of each Voronoi cell. The
-3 columns are the atom ID of the atom that owns the cell, 
+3 columns are the atom ID of the atom that owns the cell,
-the atom ID of the atom in the neighboring cell 
+the atom ID of the atom in the neighboring cell
-(or zero if the face is external), and the area of the face. 
+(or zero if the face is external), and the area of the face.
 The array can be accessed by any command that
 uses local values from a compute as input.  See "this
 section"_Section_howto.html#howto_15 for an overview of LAMMPS output
-options. More specifically, the array can be accessed by a 
+options. More specifically, the array can be accessed by a
 "dump local"_dump.html command to write a file containing
 all the Voronoi neighbors in a system:
 compute 6 all voronoi/atom neighbors yes
 dump d2 all local 1 dump.neighbors index c_6\[1\] c_6\[2\] c_6\[3\] :pre
-If the {face_threshold} keyword is used, then only faces 
+If the {face_threshold} keyword is used, then only faces
 with areas greater than the threshold are stored.
 :line
@ -190,7 +190,7 @@ per-atom values from a compute as input.  See "Section
 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
 options. If the {peratom} keyword is set to "no", the per-atom array
 is still created, but it is not accessible.
- 
+
 If the {edge_histo} keyword is used, then this compute generates a
 global vector of length {maxedge}+1, containing a histogram of the
 number of edges per face.
--- a/doc/src/compute_xrd.txt
+++ b/doc/src/compute_xrd.txt
@ -20,21 +20,21 @@ type1 type2 ... typeN = chemical symbol of each atom type (see valid options bel
 zero or more keyword/value pairs may be appended :l
 keyword = {2Theta} or {c} or {LP} or {manual} or {echo} :l
  {2Theta} values = Min2Theta Max2Theta
-    Min2Theta,Max2Theta = minimum and maximum 2 theta range to explore 
+    Min2Theta,Max2Theta = minimum and maximum 2 theta range to explore
    (radians or degrees)
  {c} values = c1 c2 c3
-    c1,c2,c3 = parameters to adjust the spacing of the reciprocal 
+    c1,c2,c3 = parameters to adjust the spacing of the reciprocal
               lattice nodes in the h, k, and l directions respectively
  {LP} value = switch to apply Lorentz-polarization factor
    0/1 = off/on
-  {manual} = flag to use manual spacing of reciprocal lattice points 
+  {manual} = flag to use manual spacing of reciprocal lattice points
-             based on the values of the {c} parameters 
+             based on the values of the {c} parameters
  {echo} = flag to provide extra output for debugging purposes :pre
 :ule
 [Examples:]
-compute 1 all xrd 1.541838 Al O 2Theta 0.087 0.87 c 1 1 1 LP 1 echo 
+compute 1 all xrd 1.541838 Al O 2Theta 0.087 0.87 c 1 1 1 LP 1 echo
 compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual :pre
 fix 1 all ave/histo/weight 1 1 1 0.087 0.87 250 c_1\[1\] c_1\[2\] mode vector file Rad2Theta.xrd
@ -43,11 +43,11 @@ fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2\[1\] c_2\[2\] mode vector file D
 [Description:]
 Define a computation that calculates x-ray diffraction intensity as described
-in "(Coleman)"_#xrd-Coleman on a mesh of reciprocal lattice nodes defined 
+in "(Coleman)"_#xrd-Coleman on a mesh of reciprocal lattice nodes defined
 by the entire simulation domain (or manually) using a simulated radiation
-of wavelength lambda. 
+of wavelength lambda.
-The x-ray diffraction intensity, I, at each reciprocal lattice point, k, 
+The x-ray diffraction intensity, I, at each reciprocal lattice point, k,
 is computed from the structure factor, F, using the equations:
 :c,image(Eqs/compute_xrd1.jpg)
@ -55,14 +55,14 @@ is computed from the structure factor, F, using the equations:
 :c,image(Eqs/compute_xrd3.jpg)
 :c,image(Eqs/compute_xrd4.jpg)
-Here, K is the location of the reciprocal lattice node, rj is the 
+Here, K is the location of the reciprocal lattice node, rj is the
-position of each atom, fj are atomic scattering factors, LP is the 
+position of each atom, fj are atomic scattering factors, LP is the
-Lorentz-polarization factor, and theta is the scattering angle of 
+Lorentz-polarization factor, and theta is the scattering angle of
-diffraction.  The Lorentz-polarization factor can be turned off using 
+diffraction.  The Lorentz-polarization factor can be turned off using
 the optional {LP} keyword.
-Diffraction intensities are calculated on a three-dimensional mesh of 
+Diffraction intensities are calculated on a three-dimensional mesh of
-reciprocal lattice nodes. The mesh spacing is defined either (a) 
+reciprocal lattice nodes. The mesh spacing is defined either (a)
 by the entire simulation domain or (b) manually using selected values as
 shown in the 2D diagram below.
@ -101,8 +101,8 @@ The analytic approximation is computed using the formula
 :c,image(Eqs/compute_xrd5.jpg)
-Coefficients parameterized by "(Peng)"_#Peng are assigned for each 
+Coefficients parameterized by "(Peng)"_#Peng are assigned for each
-atom type designating the chemical symbol and charge of each atom 
+atom type designating the chemical symbol and charge of each atom
 type. Valid chemical symbols for compute xrd are:
         H|    He1-|      He|      Li|    Li1+|
@ -148,39 +148,39 @@ type. Valid chemical symbols for compute xrd are:
      Np4+|    Np6+|      Pu|    Pu3+|    Pu4+|
      Pu6+|      Am|      Cm|      Bk|      Cf :tb(c=5,s=|)
-If the {echo} keyword is specified, compute xrd will provide extra 
+If the {echo} keyword is specified, compute xrd will provide extra
-reporting information to the screen.  
+reporting information to the screen.
 [Output info:]
-This compute calculates a global array.  The number of rows in the 
+This compute calculates a global array.  The number of rows in the
-array is the number of reciprocal lattice nodes that are explored 
+array is the number of reciprocal lattice nodes that are explored
-which by the mesh.  The global array has 2 columns.  
+which by the mesh.  The global array has 2 columns.
 The first column contains the diffraction angle in the units (radians
-or degrees) provided with the {2Theta} values. The second column contains 
+or degrees) provided with the {2Theta} values. The second column contains
 the computed diffraction intensities as described above.
 The array can be accessed by any command that uses global values from
 a compute as input.  See "this section"_Section_howto.html#howto_15
 for an overview of LAMMPS output options.
-All array values calculated by this compute are "intensive".  
+All array values calculated by this compute are "intensive".
-[Restrictions:] 
+[Restrictions:]
 This compute is part of the USER-DIFFRACTION 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 compute_xrd command does not work for triclinic cells. 
+The compute_xrd command does not work for triclinic cells.
-[Related commands:] 
+[Related commands:]
 "fix ave/histo"_fix_ave_histo.html,
 "compute saed"_compute_saed.html
-[Default:] 
+[Default:]
 The option defaults are 2Theta = 1 179 (degrees), c = 1 1 1, LP = 1,
 no manual flag, no echo flag.
@ -192,7 +192,7 @@ no manual flag, no echo flag.
 (2013).
 :link(Colliex)
-[(Colliex)] Colliex et al. International Tables for Crystallography 
+[(Colliex)] Colliex et al. International Tables for Crystallography
 Volume C: Mathematical and Chemical Tables, 249-429 (2004).
 :link(Peng)
--- a/doc/src/create_atoms.txt
+++ b/doc/src/create_atoms.txt
@ -48,7 +48,7 @@ keyword = {mol} or {basis} or {remap} or {var} or {set} or {units} :l
 create_atoms 1 box
 create_atoms 3 region regsphere basis 2 3
-create_atoms 3 single 0 0 5 
+create_atoms 3 single 0 0 5
 create_atoms 1 box var v set x xpos set y ypos :pre
 [Description:]
@ -218,14 +218,14 @@ larger version.
 variable        x equal 100
 variable        y equal 25
-lattice		hex 0.8442
+lattice         hex 0.8442
-region		box block 0 $x 0 $y -0.5 0.5
+region          box block 0 $x 0 $y -0.5 0.5
-create_box	1 box :pre
+create_box      1 box :pre
 variable        xx equal 0.0
 variable        yy equal 0.0
 variable        v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
-create_atoms	1 box var v set x xx set y yy :pre
+create_atoms    1 box var v set x xx set y yy :pre
 :c,image(JPG/sinusoid_small.jpg,JPG/sinusoid.jpg)
@ -245,7 +245,7 @@ style.  A {box} value selects standard distance units as defined by
 the "units"_units.html command, e.g. Angstroms for units = real or
 metal.  A {lattice} value means the distance units are in lattice
 spacings.
- 
+
 :line
 Atom IDs are assigned to created atoms in the following way.  The
--- a/doc/src/delete_bonds.txt
+++ b/doc/src/delete_bonds.txt
@ -121,7 +121,7 @@ The {special} keyword is invoked at the end of the delete_bonds
 operation, after (optional) removal.  It re-computes the pairwise 1-2,
 1-3, 1-4 weighting list.  The weighting list computation treats
 turned-off bonds the same as turned-on.  Thus, turned-off bonds must
-be removed if you wish to change the weighting list. 
+be removed if you wish to change the weighting list.
 Note that the choice of {remove} and {special} options affects how
 1-2, 1-3, 1-4 pairwise interactions will be computed across bonds that
--- a/doc/src/dielectric.txt
+++ b/doc/src/dielectric.txt
@ -6,7 +6,7 @@
 :line
-dielectric command :h3 
+dielectric command :h3
 [Syntax:]
--- a/doc/src/dihedral_class2.txt
+++ b/doc/src/dihedral_class2.txt
@ -17,10 +17,10 @@ dihedral_style class2 :pre
 dihedral_style class2
 dihedral_coeff 1 100 75 100 70 80 60
-dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228 
+dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228
 dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010
-dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270 
+dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270
-dihedral_coeff * aat -13.5271 110.2453 105.1270 
+dihedral_coeff * aat -13.5271 110.2453 105.1270
 dihedral_coeff * bb13 0.0 1.0119 1.1010 :pre
 [Description:]
--- a/doc/src/dihedral_fourier.txt
+++ b/doc/src/dihedral_fourier.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
-USER_MISC package.  See the "Making LAMMPS"_Section_start.html#start_3 
+USER_MISC package.  See the "Making LAMMPS"_Section_start.html#start_3
 section for more info on packages.
 [Related commands:]
--- a/doc/src/dihedral_nharmonic.txt
+++ b/doc/src/dihedral_nharmonic.txt
@ -63,7 +63,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 This angle style can only be used if LAMMPS was built with the
-USER_MISC package.  See the "Making LAMMPS"_Section_start.html#start_3 
+USER_MISC package.  See the "Making LAMMPS"_Section_start.html#start_3
 section for more info on packages.
 [Related commands:]
--- a/doc/src/dihedral_quadratic.txt
+++ b/doc/src/dihedral_quadratic.txt
@ -33,7 +33,7 @@ above, or in the data file or restart files read by the
 "read_data"_read_data.html or "read_restart"_read_restart.html
 commands:
-K (energy/radian^2) 
+K (energy/radian^2)
 phi0 (degrees) :ul
 :line
@ -64,7 +64,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 This angle style can only be used if LAMMPS was built with the
-USER_MISC package.  See the "Making LAMMPS"_Section_start.html#start_3 
+USER_MISC package.  See the "Making LAMMPS"_Section_start.html#start_3
 section for more info on packages.
 [Related commands:]
--- a/doc/src/dihedral_spherical.txt
+++ b/doc/src/dihedral_spherical.txt
@ -14,7 +14,7 @@ dihedral_style spherical :pre
 [Examples:]
-dihedral_coeff 1 1  286.1  1 124 1   1 90.0 0   1 90.0 0   
+dihedral_coeff 1 1  286.1  1 124 1   1 90.0 0   1 90.0 0
 dihedral_coeff 1 3  286.1  1 114 1   1 90  0    1 90.0  0  &
                    17.3   0 0.0 0   1 158 1    0 0.0   0  &
                    15.1   0 0.0 0   0 0.0 0    1 167.3 1   :pre
@ -76,7 +76,7 @@ wn (typically 0.0 or 1.0) :ul
 [Restrictions:]
 This dihedral style can only be used if LAMMPS was built with the
-USER_MISC package.  See the "Making LAMMPS"_Section_start.html#start_3 
+USER_MISC package.  See the "Making LAMMPS"_Section_start.html#start_3
 section for more info on packages.
 [Related commands:]
--- a/doc/src/dump.txt
+++ b/doc/src/dump.txt
@ -5,7 +5,7 @@
 :link(lc,Section_commands.html#comm)
 :line
-   
+
 dump command :h3
 "dump custom/vtk"_dump_custom_vtk.html command :h3
 "dump h5md"_dump_h5md.html command :h3
@ -55,13 +55,13 @@ args = list of arguments for a particular style :l
  {custom} or {custom/gz} or {custom/mpiio} args = list of atom attributes
    possible attributes = id, mol, proc, procp1, type, element, mass,
-			  x, y, z, xs, ys, zs, xu, yu, zu, 
+                          x, y, z, xs, ys, zs, xu, yu, zu,
-			  xsu, ysu, zsu, ix, iy, iz,
+                          xsu, ysu, zsu, ix, iy, iz,
-			  vx, vy, vz, fx, fy, fz,
+                          vx, vy, vz, fx, fy, fz,
                          q, mux, muy, muz, mu,
                          radius, diameter, omegax, omegay, omegaz,
-			  angmomx, angmomy, angmomz, tqx, tqy, tqz,
+                          angmomx, angmomy, angmomz, tqx, tqy, tqz,
-			  c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
+                          c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
      id = atom ID
      mol = molecule ID
@ -211,7 +211,7 @@ bounding box which encloses the triclinic simulation box is output,
 along with the 3 tilt factors (xy, xz, yz) of the triclinic box,
 formatted as follows:
-ITEM: BOX BOUNDS xy xz yz xx yy zz 
+ITEM: BOX BOUNDS xy xz yz xx yy zz
 xlo_bound xhi_bound xy
 ylo_bound yhi_bound xz
 zlo_bound zhi_bound yz :pre
@ -305,8 +305,8 @@ by the GROMACS molecular dynamics package, and described
 The precision used in XTC files can be adjusted via the
 "dump_modify"_dump_modify.html command.  The default value of 1000
 means that coordinates are stored to 1/1000 nanometer accuracy.  XTC
-files are portable binary files written in the NFS XDR data format, 
+files are portable binary files written in the NFS XDR data format,
-so that any machine which supports XDR should be able to read them. 
+so that any machine which supports XDR should be able to read them.
 The number of atoms per snapshot cannot change with the {xtc} style.
 The {unwrap} option of the "dump_modify"_dump_modify.html command allows
 XTC coordinates to be written "unwrapped" by the image flags for each
@ -499,7 +499,7 @@ values.
 Here is an example of how to dump bond info for a system, including
 the distance and energy of each bond:
-compute 1 all property/local batom1 batom2 btype 
+compute 1 all property/local batom1 batom2 btype
 compute 2 all bond/local dist eng
 dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_2\[1\] c_2\[2\] :pre
--- a/doc/src/dump_custom_vtk.txt
+++ b/doc/src/dump_custom_vtk.txt
@ -5,7 +5,7 @@
 :link(lc,Section_commands.html#comm)
 :line
-   
+
 dump custom/vtk command :h3
 [Syntax:]
@ -20,14 +20,14 @@ file = name of file to write dump info to :l
 args = list of arguments for a particular style :l
  {custom/vtk} args = list of atom attributes
    possible attributes = id, mol, proc, procp1, type, element, mass,
-			  x, y, z, xs, ys, zs, xu, yu, zu, 
+                          x, y, z, xs, ys, zs, xu, yu, zu,
-			  xsu, ysu, zsu, ix, iy, iz,
+                          xsu, ysu, zsu, ix, iy, iz,
-			  vx, vy, vz, fx, fy, fz,
+                          vx, vy, vz, fx, fy, fz,
                          q, mux, muy, muz, mu,
                          radius, diameter, omegax, omegay, omegaz,
-			  angmomx, angmomy, angmomz, tqx, tqy, tqz,
+                          angmomx, angmomy, angmomz, tqx, tqy, tqz,
-			  spin, eradius, ervel, erforce,
+                          spin, eradius, ervel, erforce,
-			  c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
+                          c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
      id = atom ID
      mol = molecule ID
--- a/doc/src/dump_image.txt
+++ b/doc/src/dump_image.txt
@ -587,7 +587,7 @@ b) Use the freely available mplayer or ffplay tool to view a
 movie. Both are available for multiple OSes and support a large
 variety of file formats and decoders. :l
-% mplayer foo.mpg 
+% mplayer foo.mpg
 % ffplay bar.avi :pre
 c) Use the "Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html
@ -631,9 +631,9 @@ Note that since FFmpeg is run as an external program via a pipe,
 LAMMPS has limited control over its execution and no knowledge about
 errors and warnings printed by it. Those warnings and error messages
 will be printed to the screen only. Due to the way image data is
-communicated to FFmpeg, it will often print the message 
+communicated to FFmpeg, it will often print the message
-pipe:: Input/output error :pre 
+pipe:: Input/output error :pre
 which can be safely ignored. Other warnings
 and errors have to be addressed according to the FFmpeg documentation.
--- a/doc/src/dump_modify.txt
+++ b/doc/src/dump_modify.txt
@ -54,7 +54,7 @@ keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} o
    these 3 args can be replaced by the word "none" to turn off thresholding
  {unwrap} arg = {yes} or {no} :pre
 these keywords apply only to the {image} and {movie} "styles"_dump_image.html :l
-keyword = {acolor} or {adiam} or {amap} or {backcolor} or {bcolor} or {bdiam} or {boxcolor} or {color} or {bitrate} or {framerate} :l 
+keyword = {acolor} or {adiam} or {amap} or {backcolor} or {bcolor} or {bdiam} or {boxcolor} or {color} or {bitrate} or {framerate} :l
  {acolor} args = type color
    type = atom type or range of types (see below)
    color = name of color or color1/color2/...
@ -215,17 +215,17 @@ to the dump file.  The {every} keyword cannot be used with the dump
 For example, the following commands will
 write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:
-variable	s equal logfreq(10,3,10)
+variable        s equal logfreq(10,3,10)
-dump		1 all atom 100 tmp.dump
+dump            1 all atom 100 tmp.dump
-dump_modify	1 every v_s first yes :pre
+dump_modify     1 every v_s first yes :pre
 The following commands would write snapshots at the timesteps listed
 in file tmp.times:
 variable        f file tmp.times
-variable	s equal next(f)
+variable        s equal next(f)
-dump		1 all atom 100 tmp.dump
+dump            1 all atom 100 tmp.dump
-dump_modify	1 every v_s :pre
+dump_modify     1 every v_s :pre
 NOTE: When using a file-style variable with the {every} keyword, the
 file of timesteps must list a first timestep that is beyond the
@ -491,7 +491,7 @@ simulation box since the last dump.  (Note that atoms that crossed
 once and then crossed back between the two dump timesteps would not be
 included.)
-region foo sphere 10 20 10 15 
+region foo sphere 10 20 10 15
 variable inregion atom rmask(foo)
 dump_modify ... thresh v_inregion |^ LAST
@ -686,10 +686,10 @@ this is used.
 variable        colors string &
                "red green blue yellow white &
                purple pink orange lime gray"
-variable	mol atom mol%10
+variable        mol atom mol%10
-dump		1 all image 250 image.*.jpg v_mol type &
+dump            1 all image 250 image.*.jpg v_mol type &
-		zoom 1.6 adiam 1.5
+                zoom 1.6 adiam 1.5
-dump_modify	1 pad 5 amap 0 10 sa 1 10 $\{colors\} :pre
+dump_modify     1 pad 5 amap 0 10 sa 1 10 $\{colors\} :pre
 In this case, 10 colors are defined, and molecule IDs are
 mapped to one of the colors, even if there are 1000s of molecules.
--- a/doc/src/fix_atc.txt
+++ b/doc/src/fix_atc.txt
@ -17,17 +17,17 @@ group = name of group fix is to be applied :l
 type = {thermal} or {two_temperature} or {hardy} or {field} :l
 {thermal} = thermal coupling with fields: temperature
 {two_temperature} = electron-phonon coupling with field: temperature and electron_temperature
- {hardy} = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields) 
+ {hardy} = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields)
- {field} = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) :pre 
+ {field} = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields) :pre
 parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file :l
-:ule 
+:ule
 [Examples:]
-fix AtC internal atc thermal Ar_thermal.dat 
+fix AtC internal atc thermal Ar_thermal.dat
 fix AtC internal atc two_temperature Ar_ttm.mat
 fix AtC internal atc hardy
-fix AtC internal atc field :pre 
+fix AtC internal atc field :pre
 [Description:]
@ -38,67 +38,67 @@ This fix is the beginning to creating a coupled FE/MD simulation and/or an on-th
 The following coupling example is typical, but non-exhaustive:
 # ... commands to create and initialize the MD system :pre
- # initial fix to designate coupling type and group to apply it to 
+ # initial fix to designate coupling type and group to apply it to
- # tag group physics material_file 
+ # tag group physics material_file
 fix AtC internal atc thermal Ar_thermal.mat :pre
- 
+
- # create a uniform 12 x 2 x 2 mesh that covers region contain the group 
+ # create a uniform 12 x 2 x 2 mesh that covers region contain the group
- # nx ny nz region periodicity 
+ # nx ny nz region periodicity
 fix_modify AtC mesh create 12 2 2 mdRegion f p p :pre
- 
+
- # specify the control method for the type of coupling 
+ # specify the control method for the type of coupling
- # physics control_type 
+ # physics control_type
 fix_modify AtC thermal control flux :pre
- 
+
- # specify the initial values for the empirical field "temperature" 
+ # specify the initial values for the empirical field "temperature"
- # field node_group value 
+ # field node_group value
 fix_modify AtC initial temperature all 30 :pre
- 
+
- # create an output stream for nodal fields 
+ # create an output stream for nodal fields
- # filename output_frequency 
+ # filename output_frequency
 fix_modify AtC output atc_fe_output 100 :pre
- 
+
- run 1000 :pre 
+ run 1000 :pre
- 
+
-likewise for this post-processing example: 
+likewise for this post-processing example:
 # ... commands to create and initialize the MD system :pre
- # initial fix to designate post-processing and the group to apply it to 
+ # initial fix to designate post-processing and the group to apply it to
- # no material file is allowed nor required 
+ # no material file is allowed nor required
 fix AtC internal atc hardy :pre
 # for hardy fix, specific kernel function (function type and range) to # be used as a localization function 
 fix AtC kernel quartic_sphere 10.0 :pre
 # create a uniform 1 x 1 x 1 mesh that covers region contain the group 
 # with periodicity this effectively creats a system average 
 fix_modify AtC mesh create 1 1 1 box p p p :pre 
- # change from default lagrangian map to eulerian 
+ # for hardy fix, specific kernel function (function type and range) to # be used as a localization function
- # refreshed every 100 steps 
+ fix AtC kernel quartic_sphere 10.0 :pre
 # create a uniform 1 x 1 x 1 mesh that covers region contain the group
 # with periodicity this effectively creats a system average
 fix_modify AtC mesh create 1 1 1 box p p p :pre
 # change from default lagrangian map to eulerian
 # refreshed every 100 steps
 fix_modify AtC atom_element_map eulerian 100 :pre
- 
+
- # start with no field defined 
+ # start with no field defined
- # add mass density, potential energy density, stress and temperature 
+ # add mass density, potential energy density, stress and temperature
 fix_modify AtC fields add density energy stress temperature :pre
- # create an output stream for nodal fields 
+ # create an output stream for nodal fields
- # filename output_frequency 
+ # filename output_frequency
 fix_modify AtC output nvtFE 100 text :pre
 run 1000 :pre
 the mesh's linear interpolation functions can be used as the localization function 
 by using the field option: 
- fix AtC internal atc field 
+the mesh's linear interpolation functions can be used as the localization function
- 
+ by using the field option:
 fix_modify AtC mesh create 1 1 1 box p p p 
- ... 
+ fix AtC internal atc field
-Note coupling and post-processing can be combined in the same simulations using separate fixes. 
+ fix_modify AtC mesh create 1 1 1 box p p p
 ...
 Note coupling and post-processing can be combined in the same simulations using separate fixes.
 :line
@ -108,17 +108,17 @@ No information about this fix is written to "binary restart files"_restart.html.
 [Restrictions:]
-Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc. 
+Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc.
-Currently, 
+Currently,
- the coupling is restricted to thermal physics 
+- the coupling is restricted to thermal physics
 - the FE computations are done in serial on each processor. :ul
 [Related commands:]
 After specifying this fix in your input script, several other "fix_modify"_fix_modify.html commands are used to setup the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.
-fix_modify commands for setup: 
+fix_modify commands for setup:
 "fix_modify AtC mesh create"_USER/atc/man_mesh_create.html
 "fix_modify AtC mesh quadrature"_USER/atc/man_mesh_quadrature.html
@ -149,7 +149,7 @@ fix_modify commands for boundary and initial conditions:
 "fix_modify AtC source"_USER/atc/man_source.html
 "fix_modify AtC remove_source"_USER/atc/man_remove_source.html :ul
-fix_modify commands for control and filtering: 
+fix_modify commands for control and filtering:
 "fix_modify AtC control"_USER/atc/man_control.html
 "fix_modify AtC control thermal"_USER/atc/man_control_thermal.html
@ -165,7 +165,7 @@ fix_modify commands for control and filtering:
 "fix_modify AtC extrinsic exchange"_USER/atc/man_extrinsic_exchange.html
 "fix_modify AtC poisson_solver"_USER/atc/man_poisson_solver.html :ul
-fix_modify commands for output: 
+fix_modify commands for output:
 "fix_modify AtC output"_USER/atc/man_output.html
 "fix_modify AtC output nodeset"_USER/atc/man_output_nodeset.html
@ -176,7 +176,7 @@ fix_modify commands for output:
 "fix_modify AtC write_restart"_USER/atc/man_write_restart.html
 "fix_modify AtC read_restart"_USER/atc/man_read_restart.html :ul
-fix_modify commands for post-processing: 
+fix_modify commands for post-processing:
 "fix_modify AtC kernel"_USER/atc/man_hardy_kernel.html
 "fix_modify AtC fields"_USER/atc/man_hardy_fields.html
@ -188,7 +188,7 @@ fix_modify commands for post-processing:
 "fix_modify AtC sample_frequency"_USER/atc/man_sample_frequency.html
 "fix_modify AtC set"_USER/atc/man_set.html :ul
-miscellaneous fix_modify commands: 
+miscellaneous fix_modify commands:
 "fix_modify AtC atom_element_map"_USER/atc/man_atom_element_map.html
 "fix_modify AtC atom_weight"_USER/atc/man_atom_weight.html
@ -210,35 +210,35 @@ miscellaneous fix_modify commands:
 "fix_modify AtC remove_species"_USER/atc/man_remove_species.html
 "fix_modify AtC remove_molecule"_USER/atc/man_remove_molecule.html :ul
-Note: a set of example input files with the attendant material files are included with this package 
+Note: a set of example input files with the attendant material files are included with this package
 [Default:]
-None 
+None
 :line
 For detailed exposition of the theory and algorithms please see:
 :link(Wagner)
-[(Wagner)] Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, "An atomistic-to-continuum coupling method for heat transfer in solids." Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351. 
+[(Wagner)] Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, "An atomistic-to-continuum coupling method for heat transfer in solids." Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.
 :link(Zimmeman2004)
-[(Zimmerman2004)] Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319. 
+[(Zimmerman2004)] Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319.
 :link(Zimmerman2010)
-[(Zimmerman2010)] Zimmerman, JA; Jones, RE; Templeton, JA, "A material frame approach for evaluating continuum variables in atomistic simulations." Journal of Computational Physics (2010), 229:2364. 
+[(Zimmerman2010)] Zimmerman, JA; Jones, RE; Templeton, JA, "A material frame approach for evaluating continuum variables in atomistic simulations." Journal of Computational Physics (2010), 229:2364.
 :link(Templeton2010)
-[(Templeton2010)] Templeton, JA; Jones, RE; Wagner, GJ, "Application of a field-based method to spatially varying thermal transport problems in molecular dynamics." Modelling and Simulation in Materials Science and Engineering (2010), 18:085007. 
+[(Templeton2010)] Templeton, JA; Jones, RE; Wagner, GJ, "Application of a field-based method to spatially varying thermal transport problems in molecular dynamics." Modelling and Simulation in Materials Science and Engineering (2010), 18:085007.
 :link(Jones)
-[(Jones)] Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, "Electron transport enhanced molecular dynamics for metals and semi-metals." International Journal for Numerical Methods in Engineering (2010), 83:940. 
+[(Jones)] Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, "Electron transport enhanced molecular dynamics for metals and semi-metals." International Journal for Numerical Methods in Engineering (2010), 83:940.
 :link(Templeton2011)
-[(Templeton2011)] Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, "A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling." Journal of Chemical Theory and Computation (2011), 7:1736. 
+[(Templeton2011)] Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, "A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling." Journal of Chemical Theory and Computation (2011), 7:1736.
 :link(Mandadapu)
-[(Mandadapu)] Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115. 
+[(Mandadapu)] Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115.
 Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes " The finite element method ", Dover 2003, for the basics of FE simulation.
--- a/doc/src/fix_atom_swap.txt
+++ b/doc/src/fix_atom_swap.txt
@ -35,7 +35,7 @@ keyword = {types} or {mu} or {ke} or {semi-grand} or {region} :l
 [Examples:]
 fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
-fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6 
+fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
 fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 0.0 4.3 -5.0 :pre
 [Description:]
@ -78,15 +78,15 @@ atoms remains constant. Whereas in the semi-grand canonical ensemble,
 the composition of the system can change. Note that when using
 {semi-grand}, atoms in the fix group whose type is not listed
 in the {types} keyword are ineligible for attempted
-conversion. An attempt is made to switch 
+conversion. An attempt is made to switch
-the selected atom (if eligible) to one of the other listed types 
+the selected atom (if eligible) to one of the other listed types
 with equal probability. Acceptance of each attempt depends upon the Metropolis criterion.
 The {mu} keyword allows users to specify chemical
-potentials. This is required and allowed only when using {semi-grand}. 
+potentials. This is required and allowed only when using {semi-grand}.
-All chemical potentials are absolute, so there is one for 
+All chemical potentials are absolute, so there is one for
-each swap type listed following the {types} keyword. 
+each swap type listed following the {types} keyword.
-In semi-grand canonical ensemble simulations the chemical composition 
+In semi-grand canonical ensemble simulations the chemical composition
 of the system is controlled by the difference in these values. So
 shifting all values by a constant amount will have no effect
 on the simulation.
@ -103,17 +103,17 @@ LAMMPS will warn you if any of the atoms eligible for swapping have a
 non-zero molecule ID, but does not check for this at the time of
 swapping.
-If not using {semi-grand} this fix checks to ensure all atoms of the 
+If not using {semi-grand} this fix checks to ensure all atoms of the
-given types have the same atomic charge. LAMMPS doesn't enforce this 
+given types have the same atomic charge. LAMMPS doesn't enforce this
-in general, but it is needed for this fix to simplify the 
+in general, but it is needed for this fix to simplify the
-swapping procedure. Successful swaps will swap the atom type and charge 
+swapping procedure. Successful swaps will swap the atom type and charge
 of the swapped atoms. Conversely, when using {semi-grand}, it is assumed that all the atom
 types involved in switches have the same charge. Otherwise, charge
 would not be conserved. As a consequence, no checks on atomic charges are
 performed, and successful switches update the atom type but not the
-atom charge. While it is possible to use {semi-grand} with groups of 
+atom charge. While it is possible to use {semi-grand} with groups of
 atoms that have different charges, these charges will not be changed when the
-atom types change. 
+atom types change.
 Since this fix computes total potential energies before and after
 proposed swaps, so even complicated potential energy calculations are
@ -123,15 +123,15 @@ OK, including the following:
  many body pair styles
  hybrid pair styles
  eam pair styles
-  triclinic systems 
+  triclinic systems
  need to include potential energy contributions from other fixes :ul
 Some fixes have an associated potential energy. Examples of such fixes
-include: "efield"_fix_efield.html, "gravity"_fix_gravity.html, 
+include: "efield"_fix_efield.html, "gravity"_fix_gravity.html,
-"addforce"_fix_addforce.html, "langevin"_fix_langevin.html, 
+"addforce"_fix_addforce.html, "langevin"_fix_langevin.html,
-"restrain"_fix_restrain.html, "temp/berendsen"_fix_temp_berendsen.html, 
+"restrain"_fix_restrain.html, "temp/berendsen"_fix_temp_berendsen.html,
-"temp/rescale"_fix_temp_rescale.html, and "wall fixes"_fix_wall.html. 
+"temp/rescale"_fix_temp_rescale.html, and "wall fixes"_fix_wall.html.
-For that energy to be included in the total potential energy of the 
+For that energy to be included in the total potential energy of the
 system (the quantity used when performing GCMC moves),
 you MUST enable the "fix_modify"_fix_modify.html {energy} option for
 that fix.  The doc pages for individual "fix"_fix.html commands
@ -170,18 +170,18 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 [Related commands:]
-"fix nvt"_fix_nh.html, "neighbor"_neighbor.html, 
+"fix nvt"_fix_nh.html, "neighbor"_neighbor.html,
 "fix deposit"_fix_deposit.html, "fix evaporate"_fix_evaporate.html,
 "delete_atoms"_delete_atoms.html, "fix gcmc"_fix_gcmc.html
 [Default:]
-The option defaults are ke = yes, semi-grand = no, mu = 0.0 for 
+The option defaults are ke = yes, semi-grand = no, mu = 0.0 for
 all atom types.
 :line
 :link(Sadigh)
-[(Sadigh)] B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and 
+[(Sadigh)] B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and
 L Zepeda-Ruiz, Phys. Rev. B, 85, 184203 (2012).
--- a/doc/src/fix_ave_atom.txt
+++ b/doc/src/fix_ave_atom.txt
@ -79,7 +79,7 @@ equivalent, since the "compute stress/atom"_compute_stress_atom.html
 command creates a per-atom array with 6 columns:
 compute my_stress all stress/atom NULL
-fix 1 all ave/atom 10 20 1000 c_my_stress\[*\] 
+fix 1 all ave/atom 10 20 1000 c_my_stress\[*\]
 fix 1 all ave/atom 10 20 1000 c_my_stress\[1\] c_my_stress\[1\] &
                              c_my_stress\[3\] c_my_stress\[4\] &
                              c_my_stress\[5\] c_my_stress\[6\] :pre
@ -93,8 +93,8 @@ that are a multiple of {Nfreq}.  The average is over {Nrepeat}
 quantities, computed in the preceding portion of the simulation every
 {Nevery} timesteps.  {Nfreq} must be a multiple of {Nevery} and
 {Nevery} must be non-zero even if {Nrepeat} is 1.  Also, the timesteps
-contributing to the average value cannot overlap, 
+contributing to the average value cannot overlap,
-i.e. Nrepeat*Nevery can not exceed Nfreq. 
+i.e. Nrepeat*Nevery can not exceed Nfreq.
 For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
 timesteps 90,92,94,96,98,100 will be used to compute the final average
--- a/doc/src/fix_ave_chunk.txt
+++ b/doc/src/fix_ave_chunk.txt
@ -77,7 +77,7 @@ fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile
 could be replaced by:
-compute cc1 flow chunk/atom bin/1d y 0.0 1.0 
+compute cc1 flow chunk/atom bin/1d y 0.0 1.0
 fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile :pre
 [Description:]
--- a/doc/src/fix_ave_correlate.txt
+++ b/doc/src/fix_ave_correlate.txt
@ -58,7 +58,7 @@ keyword = {type} or {ave} or {start} or {prefactor} or {file} or {overwrite} or
 fix 1 all ave/correlate 5 100 1000 c_myTemp file temp.correlate
 fix 1 all ave/correlate 1 50 10000 &
          c_thermo_press\[1\] c_thermo_press\[2\] c_thermo_press\[3\] &
-	  type upper ave running title1 "My correlation data" :pre
+          type upper ave running title1 "My correlation data" :pre
 fix 1 all ave/correlate 1 50 10000 c_thermo_press\[*\]
 [Description:]
@ -176,7 +176,7 @@ output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html
 or "fix temp/rescale"_fix_temp_rescale.html.  See the doc pages for
 these commands which give the IDs of these computes.  Users can also
 write code for their own compute styles and "add them to
-LAMMPS"_Section_modify.html.  
+LAMMPS"_Section_modify.html.
 If a value begins with "f_", a fix ID must follow which has been
 previously defined in the input script.  If no bracketed term is
@ -184,7 +184,7 @@ appended, the global scalar calculated by the fix is used.  If a
 bracketed term is appended, the Ith element of the global vector
 calculated by the fix is used.  See the discussion above for how I can
 be specified with a wildcard asterisk to effectively specify multiple
-values.  
+values.
 Note that some fixes only produce their values on certain timesteps,
 which must be compatible with {Nevery}, else an error will result.
--- a/doc/src/fix_ave_correlate_long.txt
+++ b/doc/src/fix_ave_correlate_long.txt
@ -55,7 +55,7 @@ keyword = {type} or {start} or {file} or {overwrite} or {title1} or {title2} or
 fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate
 fix 1 all ave/correlate/long 1 10000 &
          c_thermo_press\[1\] c_thermo_press\[2\] c_thermo_press\[3\] &
-	  type upper title1 "My correlation data" nlen 15 ncount 3 :pre
+          type upper title1 "My correlation data" nlen 15 ncount 3 :pre
 [Description:]
--- a/doc/src/fix_ave_histo.txt
+++ b/doc/src/fix_ave_histo.txt
@ -61,7 +61,7 @@ keyword = {mode} or {file} or {ave} or {start} or {beyond} or {overwrite} or {ti
 fix 1 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running
 fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press\[2\] c_thermo_press\[3\] title1 "My output values"
 fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press\[*\]
-fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra 
+fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra
 fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD\[1\] c_XRD\[2\] :pre
 [Description:]
@ -149,8 +149,8 @@ multiple of {Nfreq}.  It is averaged over {Nrepeat} histograms,
 computed in the preceding portion of the simulation every {Nevery}
 timesteps.  {Nfreq} must be a multiple of {Nevery} and {Nevery} must
 be non-zero even if {Nrepeat} is 1.  Also, the timesteps
-contributing to the histogram value cannot overlap, 
+contributing to the histogram value cannot overlap,
-i.e. Nrepeat*Nevery can not exceed Nfreq. 
+i.e. Nrepeat*Nevery can not exceed Nfreq.
 For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then input values
 on timesteps 90,92,94,96,98,100 will be used to compute the final
--- a/doc/src/fix_ave_time.txt
+++ b/doc/src/fix_ave_time.txt
@ -137,8 +137,8 @@ that are a mlutiple of {Nfreq}.  The average is over {Nrepeat}
 quantities, computed in the preceding portion of the simulation every
 {Nevery} timesteps.  {Nfreq} must be a multiple of {Nevery} and
 {Nevery} must be non-zero even if {Nrepeat} is 1.  Also, the timesteps
-contributing to the average value cannot overlap, 
+contributing to the average value cannot overlap,
-i.e. Nrepeat*Nevery can not exceed Nfreq. 
+i.e. Nrepeat*Nevery can not exceed Nfreq.
 For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
 timesteps 90,92,94,96,98,100 will be used to compute the final average
--- a/doc/src/fix_balance.txt
+++ b/doc/src/fix_balance.txt
@ -330,7 +330,7 @@ per processor.  Note that the 4 sub-domains share vertices, so there
 will be duplicate nodes in the list.
 The "SQUARES" section lists the node IDs of the 4 vertices in a
-rectangle for each processor (1 to 4).  
+rectangle for each processor (1 to 4).
 For a 3d problem, the syntax is similar with 8 vertices listed for
 each processor, instead of 4, and "SQUARES" replaced by "CUBES".
--- a/doc/src/fix_bond_break.txt
+++ b/doc/src/fix_bond_break.txt
@ -56,7 +56,7 @@ possible bonds to break.  Every atom checks its list of possible bonds
 to break and labels the longest such bond as its "sole" bond to break.
 After this is done, if atom I is bonded to atom J in its sole bond,
 and atom J is bonded to atom I in its sole bond, then the I,J bond is
-"eligible" to be broken. 
+"eligible" to be broken.
 Note that these rules mean an atom will only be part of at most one
 broken bond on a given timestep.  It also means that if atom I chooses
@ -112,7 +112,7 @@ resulting from broken bonds (and angles, dihedrals, impropers).
 No information about this fix is written to "binary restart
 files"_restart.html.  None of the "fix_modify"_fix_modify.html options
-are relevant to this fix. 
+are relevant to this fix.
 This fix computes two statistics which it stores in a global vector of
 length 2, which can be accessed by various "output
--- a/doc/src/fix_bond_create.txt
+++ b/doc/src/fix_bond_create.txt
@ -208,7 +208,7 @@ created bonds (and angles, dihedrals, impropers).
 No information about this fix is written to "binary restart
 files"_restart.html.  None of the "fix_modify"_fix_modify.html options
-are relevant to this fix. 
+are relevant to this fix.
 This fix computes two statistics which it stores in a global vector of
 length 2, which can be accessed by various "output
--- a/doc/src/fix_bond_swap.txt
+++ b/doc/src/fix_bond_swap.txt
--- a/doc/src/fix_box_relax.txt
+++ b/doc/src/fix_box_relax.txt
@ -15,13 +15,13 @@ fix ID group-ID box/relax keyword value ... :pre
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 box/relax = style name of this fix command :l
 one or more keyword value pairs may be appended
-keyword = {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {nreset} or {vmax} or {dilate} or {scaleyz} or {scalexz} or {scalexy} or {fixedpoint} 
+keyword = {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {yz} or {xz} or {couple} or {nreset} or {vmax} or {dilate} or {scaleyz} or {scalexz} or {scalexy} or {fixedpoint}
  {iso} or {aniso} or {tri} value = Ptarget = desired pressure (pressure units)
  {x} or {y} or {z} or {xy} or {yz} or {xz} value = Ptarget = desired pressure (pressure units)
  {couple} = {none} or {xyz} or {xy} or {yz} or {xz}
  {nreset} value = reset reference cell every this many minimizer iterations
  {vmax} value = fraction = max allowed volume change in one iteration
-  {dilate} value = {all} or {partial} 
+  {dilate} value = {all} or {partial}
  {scaleyz} value = {yes} or {no} = scale yz with lz
  {scalexz} value = {yes} or {no} = scale xz with lz
  {scalexy} value = {yes} or {no} = scale xy with ly
@ -99,8 +99,8 @@ chosen will not move during the simulation.  For example, if the lower
 periodic boundaries pass through (0,0,0), and this point is provided
 to {fixedpoint}, then the lower periodic boundaries will remain at
 (0,0,0), while the upper periodic boundaries will move twice as
-far. In all cases, the particle positions at each iteration are 
+far. In all cases, the particle positions at each iteration are
-unaffected by the chosen value, except that all particles are 
+unaffected by the chosen value, except that all particles are
 displaced by the same amount, different on each iteration.
 NOTE: Appling an external pressure to tilt dimensions {xy}, {xz}, {yz}
@ -178,9 +178,9 @@ these 7 keywords:
 x Ptarget
 y Ptarget
 z Ptarget
-xy 0.0 
+xy 0.0
-yz 0.0 
+yz 0.0
-xz 0.0 
+xz 0.0
 couple none :pre
 :line
@ -201,7 +201,7 @@ With this fix, the potential energy used by the minimizer is augmented
 by an additional energy provided by the fix. The overall objective
 function then is:
-:c,image(Eqs/fix_box_relax1.jpg) 
+:c,image(Eqs/fix_box_relax1.jpg)
 where {U} is the system potential energy, {P}_t is the desired
 hydrostatic pressure, {V} and {V}_0 are the system and reference
@ -211,14 +211,14 @@ Taking derivatives of {E} w.r.t. the box dimensions, and setting these
 to zero, we find that at the minimum of the objective function, the
 global system stress tensor [P] will satisfy the relation:
-:c,image(Eqs/fix_box_relax2.jpg) 
+:c,image(Eqs/fix_box_relax2.jpg)
 where [I] is the identity matrix, [h]_0 is the box dimension tensor of
 the reference cell, and [h]_0{d} is the diagonal part of
 [h]_0. [S]_{t} is a symmetric stress tensor that is chosen by LAMMPS
 so that the upper-triangular components of [P] equal the stress tensor
 specified by the user.
- 
+
 This equation only applies when the box dimensions are equal to those
 of the reference dimensions. If this is not the case, then the
 converged stress tensor will not equal that specified by the user.  We
--- a/doc/src/fix_controller.txt
+++ b/doc/src/fix_controller.txt
@ -33,7 +33,7 @@ cvar = name of control variable :l
 fix 1 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol
-fix 1 all controller 100 0.2 0.5 0 100.0 v_pxxwall 1.01325 xwall 
+fix 1 all controller 100 0.2 0.5 0 100.0 v_pxxwall 1.01325 xwall
 fix 1 all controller 10000 0.2 0.5 0 2000 v_avpe -3.785 tcontrol :pre
 [Description:]
--- a/doc/src/fix_deform.txt
+++ b/doc/src/fix_deform.txt
@ -28,7 +28,7 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
        factor = multiplicative factor for change in box length at end of run
      {vel} value = V
        V = change box length at this velocity (distance/time units),
-	    effectively an engineering strain rate
+            effectively an engineering strain rate
      {erate} value = R
        R = engineering strain rate (1/time units)
      {trate} value = R
@ -36,10 +36,10 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
      {volume} value = none = adjust this dim to preserve volume of system
      {wiggle} values = A Tp
        A = amplitude of oscillation (distance units)
-	Tp = period of oscillation (time units)
+        Tp = period of oscillation (time units)
      {variable} values = v_name1 v_name2
        v_name1 = variable with name1 for box length change as function of time
-	v_name2 = variable with name2 for change rate as function of time
+        v_name2 = variable with name2 for change rate as function of time
  {xy}, {xz}, {yz} args = style value
    style = {final} or {delta} or {vel} or {erate} or {trate} or {wiggle}
      {final} value = tilt
@ -48,17 +48,17 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
        dtilt = change in tilt factor at end of run (distance units)
      {vel} value = V
        V = change tilt factor at this velocity (distance/time units),
-	    effectively an engineering shear strain rate
+            effectively an engineering shear strain rate
      {erate} value = R
        R = engineering shear strain rate (1/time units)
      {trate} value = R
        R = true shear strain rate (1/time units)
      {wiggle} values = A Tp
        A = amplitude of oscillation (distance units)
-	Tp = period of oscillation (time units)
+        Tp = period of oscillation (time units)
      {variable} values = v_name1 v_name2
        v_name1 = variable with name1 for tilt change as function of time
-	v_name2 = variable with name2 for change rate as function of time :pre
+        v_name2 = variable with name2 for change rate as function of time :pre
 zero or more keyword/value pairs may be appended :l
 keyword = {remap} or {flip} or {units} :l
--- a/doc/src/fix_drag.txt
+++ b/doc/src/fix_drag.txt
@ -57,9 +57,9 @@ minimization"_minimize.html.
 [Restrictions:] none
-[Related commands:] 
+[Related commands:]
-"fix spring"_fix_spring.html, "fix spring/self"_fix_spring_self.html, 
+"fix spring"_fix_spring.html, "fix spring/self"_fix_spring_self.html,
 "fix spring/rg"_fix_spring_rg.html, "fix smd"_fix_smd.html
 [Default:] none
--- a/doc/src/fix_drude_transform.txt
+++ b/doc/src/fix_drude_transform.txt
@ -61,12 +61,12 @@ Velocities: \begin\{equation\} V' = \frac \{M\, V + m\, v\} \{M'\}
 Forces: \begin\{equation\} F' = F + f \end\{equation\}
 \begin\{equation\} f' = \frac \{ M\, f - m\, F\} \{M'\}
 \end\{equation\}
- 
+
 This transform conserves the total kinetic energy
-\begin\{equation\} \frac 1 2 \, (M\, V^2\ + m\, v^2) 
+\begin\{equation\} \frac 1 2 \, (M\, V^2\ + m\, v^2)
 = \frac 1 2 \, (M'\, V'^2\ + m'\, v'^2) \end\{equation\}
 and the virial defined with absolute positions
-\begin\{equation\} X\, F + x\, f = X'\, F' + x'\, f' \end\{equation\} 
+\begin\{equation\} X\, F + x\, f = X'\, F' + x'\, f' \end\{equation\}
 :line
--- a/doc/src/fix_efield.txt
+++ b/doc/src/fix_efield.txt
@ -63,7 +63,7 @@ If the {region} keyword is used, the atom must also be in the
 specified geometric "region"_region.html in order to have force added
 to it.
-:line 
+:line
 Adding a force or torque to atoms implies a change in their potential
 energy as they move or rotate due to the applied E-field.
@ -108,12 +108,12 @@ due to the electric field were a spring-like F = kx, then the energy
 formula should be E = -0.5kx^2.  If you don't do this correctly, the
 minimization will not converge properly.
-:line 
+:line
 [Restart, fix_modify, output, run start/stop, minimize info:]
 No information about this fix is written to "binary restart
-files"_restart.html.  
+files"_restart.html.
 The "fix_modify"_fix_modify.html {energy} option is supported by this
 fix to add the potential "energy" inferred by the added force due to
--- a/doc/src/fix_ehex.txt
+++ b/doc/src/fix_ehex.txt
@ -34,15 +34,15 @@ keyword = {region} or {constrain} or {com} or {hex} :l
 fix fnve all nve
 # specify regions rhot and rcold
 ...
-fix fhot all ehex 1 0.15 region rhot 
+fix fhot all ehex 1 0.15 region rhot
 fix fcold all ehex 1 -0.15 region rcold :pre
 # SPC/E water, from examples/in.ehex.spce
-fix fnve all nve    
+fix fnve all nve
 # specify regions rhot and rcold
 ...
 fix fhot all ehex 1 0.075 region rhot constrain com
-fix fcold all ehex 1 -0.075 region rcold constrain com 
+fix fcold all ehex 1 -0.075 region rcold constrain com
 fix frattle all rattle 1e-10 400 0 b 1 a 1 :pre
 [Description:]
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
sjplimp	e9fed80928	Merge pull request #202 from akohlmey/doc-formatting-fixes collected documentation updates and corrections from LAMMPS-ICMS	2016-10-06 15:49:44 -06:00
sjplimp	54fc194e5b	Merge pull request #199 from akohlmey/small-changes Collected small changes and bugfixes	2016-10-06 15:49:24 -06:00
Steve Plimpton	b3d2fb91bb	new fix wall/gran/region command, REBO bug fix, new example log files	2016-10-06 15:47:41 -06:00
Axel Kohlmeyer	19984c9bd1	Revert "bugfix for AngleAngle term in CLASS2 impropers by Ivan A. Strelnikov, ICP RAS" This reverts commit `83bcdb6a50`.	2016-10-06 17:23:10 -04:00
Axel Kohlmeyer	f92618a33b	Revert "bugfix for virial tally for improper style umbrella from Steven Vandenbrande (U Gent)" This reverts commit `4921dc18a0`.	2016-10-06 17:21:38 -04:00
Axel Kohlmeyer	0b5d71537a	collected documentation updates and corrections from LAMMPS-ICMS fixes formatting issues due to tabs, permission issues and a few typos and badly worded text.	2016-10-06 15:48:18 -04:00
sjplimp	c213457550	Merge pull request #197 from giacomofiorin/colvars_2016-10-05 Colvars 2016-10-05	2016-10-06 13:02:52 -06:00
sjplimp	0f45cd61a5	Merge pull request #196 from akohlmey/charmm-cmap-updates Some more cmap-related updates for ch2lmp	2016-10-06 13:02:27 -06:00
Steve Plimpton	493873fb93	clean up doc src	2016-10-06 13:00:46 -06:00
Axel Kohlmeyer	60a031ebac	Merge branch 'USER-DPD_pair_exp6_rx_mathfix' of https://github.com/timattox/lammps_USER-DPD into small-changes This closes #201	2016-10-06 14:28:08 -04:00
Axel Kohlmeyer	27e76a70b9	Merge branch 'USER-DPD_hybrid_atom_bugfix' of https://github.com/timattox/lammps_USER-DPD into small-changes This closes #200	2016-10-06 14:27:27 -04:00
Tim Mattox	e1e9a5c126	USER-DPD: math corrections in pair_exp6_rx.cpp (by Jim Larentzos)	2016-10-06 13:49:47 -04:00
Tim Mattox	d31121b18c	USER-DPD: bugfix in unpack_comm_hybrid(); now works with hybrid atom style	2016-10-06 13:21:27 -04:00
Axel Kohlmeyer	0853cdbe6f	update reference data files for updated/corrected clayff parameters	2016-10-06 11:47:08 -04:00
Axel Kohlmeyer	83bcdb6a50	bugfix for AngleAngle term in CLASS2 impropers by Ivan A. Strelnikov, ICP RAS this closes #56	2016-10-06 11:27:18 -04:00
Axel Kohlmeyer	22ce671804	improved whitespace handling in msi2lmp for force fields and topologies	2016-10-06 11:16:59 -04:00
Axel Kohlmeyer	4921dc18a0	bugfix for virial tally for improper style umbrella from Steven Vandenbrande (U Gent) this closes #182	2016-10-06 10:47:08 -04:00
Axel Kohlmeyer	d133167bf6	Merge branch 'master' of https://github.com/albapa/lammps into small-changes USER-QUIP related improvements from github user albapa. This closes #198	2016-10-06 09:32:50 -04:00
A Bartok-Partay	8ea063378e	add NETCDF libs (as defined in QUIP) to the linking line if QUIP was built with NETCDF support	2016-10-06 12:16:25 +01:00
A Bartok-Partay	fd16118cbb	removed dump_modify command	2016-10-06 12:02:41 +01:00
Axel Kohlmeyer	f9f955d5b5	update include statement format	2016-10-05 22:34:44 -04:00
Axel Kohlmeyer	d7d321a512	some more updates to the README file to reflect the inclusion of the CMAP example and renamed file names	2016-10-05 18:41:45 -04:00
Giacomo Fiorin	8809a603fb	Colvars update: issue a warning that cannot be ignored regarding total forces	2016-10-05 18:26:21 -04:00
Giacomo Fiorin	969d3cf4b0	Colvars update: make ABF check that the colvar isn't using already subtractAppliedForce	2016-10-05 18:25:40 -04:00
Axel Kohlmeyer	326fdf2cf1	added 1GB1 example from Robert Latour and update 1AC7 example files	2016-10-05 18:20:09 -04:00
Axel Kohlmeyer	f32819dd10	added tweak to write out the command line used for the conversion to the beginning of the LAMMPS input	2016-10-05 18:13:46 -04:00
Axel Kohlmeyer	c07a01c661	import updated README file for charmm2lammps.pl with CMAP support	2016-10-05 18:11:52 -04:00