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

collected documentation updates and corrections from LAMMPS-ICMS

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

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

doc/src/Section_howto.txt

@@ -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}
@@ -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
 

doc/src/Section_python.txt

@@ -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

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

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

doc/src/compute_heat_flux.txt

@@ -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
 

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

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

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

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

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

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:]
 

doc/src/create_atoms.txt

@@ -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)
 

doc/src/dump.txt

@@ -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

doc/src/dump_custom_vtk.txt

@@ -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

doc/src/dump_modify.txt

@@ -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
@@ -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.

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:]

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:]
 

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

doc/src/fix_msst.txt

@@ -120,7 +120,7 @@ The global vector contains four values in this order:
 To print these quantities to the log file with descriptive column
 headers, the following LAMMPS commands are suggested:
 
-fix		 msst all msst z
+fix              msst all msst z
 fix_modify       msst energy yes
 variable dhug    equal f_msst\[1\]
 variable dray    equal f_msst\[2\]

doc/src/fix_qbmsst.txt

@@ -167,14 +167,14 @@ headers, the following LAMMPS commands are suggested. Here the
 the thermo keyword {etotal} to print the quantity <i>etot</i>.  See
 also the "thermo_style"_thermo_style.html command.
 
-fix		fix_id all msst z
+fix             fix_id all msst z
-fix_modify	fix_id energy yes
+fix_modify      fix_id energy yes
-variable	dhug	equal f_fix_id\[1\]
+variable        dhug    equal f_fix_id\[1\]
-variable	dray	equal f_fix_id\[2\]
+variable        dray    equal f_fix_id\[2\]
-variable	lgr_vel	equal f_fix_id\[3\]
+variable        lgr_vel equal f_fix_id\[3\]
-variable	lgr_pos	equal f_fix_id\[4\]
+variable        lgr_pos equal f_fix_id\[4\]
-variable	T_qm	equal f_fix_id\[5\]
+variable        T_qm    equal f_fix_id\[5\]
-thermo_style	custom	step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id :pre
+thermo_style    custom  step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id :pre
 
 The global scalar under the entry f_fix_id is the quantity of thermo
 energy as an extra part of <i>etot</i>. This global scalar and the

doc/src/fix_rx.txt

@@ -75,7 +75,7 @@ but no more than max_steps will be taken. If max_steps is reached, an error warn
 is printed and the simulation is stopped.
 
 After each ODE step, the solution error {e} is tested and weighted using the absTol
-and relTol values. The error vector is weighted as {e} / (relTol * | {u} | + absTol)
+and relTol values. The error vector is weighted as {e} / (relTol * |{u}| + absTol)
 where {u} is the solution vector. If the norm of the error is <= 1, the solution is
 accepted, {h} is increased by a proportional amount, and the next ODE step is begun.
 Otherwise, {h} is shrunk and the ODE step is repeated.

doc/src/fix_shake.txt

@@ -172,7 +172,7 @@ more instructions on how to use the accelerated styles effectively.
 The velocity constraints lead to a linear system of equations which
 can be solved analytically.  The implementation of the algorithm in
 LAMMPS closely follows ("Andersen (1983)"_#Andersen).
-	
+
 NOTE: The fix rattle command modifies forces and velocities and thus
 should be defined after all other integration fixes in your input
 script.  If you define other fixes that modify velocities or forces

doc/src/fix_store_state.txt

@@ -17,8 +17,8 @@ store/state = style name of this fix command :l
 N = store atom attributes every N steps, N = 0 for initial store only :l
 input = one or more atom attributes :l
   possible attributes = id, mol, type, mass,
- 	                x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz,
+                        x, y, z, xs, ys, zs, xu, yu, zu, 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,

doc/src/group.txt

@@ -253,7 +253,7 @@ group           mobile dynamic all region ss
 fix             1 mobile nve
 run             $\{nsteps\}
 group           mobile static
-run	        $\{nsteps\} :pre
+run             $\{nsteps\} :pre
 
 NOTE: All fixes and computes take a group ID as an argument, but they
 do not all allow for use of a dynamic group.  If you get an error

doc/src/if.txt

@@ -109,19 +109,19 @@ Here is an example of a double loop which uses the if and
 "jump"_jump.html commands to break out of the inner loop when a
 condition is met, then continues iterating thru the outer loop.
 
-label	    loopa
+label       loopa
 variable    a loop 5
-  label	    loopb
+  label     loopb
   variable  b loop 5
-  print	    "A,B = $a,$b"
+  print     "A,B = $a,$b"
   run       10000
-  if	    "$b > 2" then "jump SELF break"
+  if        "$b > 2" then "jump SELF break"
-  next	    b
+  next      b
-  jump	    in.script loopb
+  jump      in.script loopb
-label	    break
+label       break
 variable    b delete
-next	    a
+next        a
-jump	    SELF loopa :pre
+jump        SELF loopa :pre
 
 :line
 

doc/src/jump.txt

@@ -103,19 +103,19 @@ Here is an example of a double loop which uses the if and
 "jump"_jump.html commands to break out of the inner loop when a
 condition is met, then continues iterating thru the outer loop.
 
-label	    loopa
+label       loopa
 variable    a loop 5
-  label	    loopb
+  label     loopb
   variable  b loop 5
-  print	    "A,B = $a,$b"
+  print     "A,B = $a,$b"
   run       10000
-  if	    "$b > 2" then "jump SELF break"
+  if        "$b > 2" then "jump SELF break"
-  next	    b
+  next      b
-  jump	    in.script loopb
+  jump      in.script loopb
-label	    break
+label       break
 variable    b delete
-next	    a
+next        a
-jump	    SELF loopa :pre
+jump        SELF loopa :pre
 
 [Restrictions:]
 

doc/src/next.txt

@@ -116,19 +116,19 @@ Here is an example of a double loop which uses the "if"_if.html and
 "jump"_jump.html commands to break out of the inner loop when a
 condition is met, then continues iterating thru the outer loop.
 
-label	    loopa
+label       loopa
 variable    a loop 5
-  label	    loopb
+  label     loopb
   variable  b loop 5
-  print	    "A,B = $a,$b"
+  print     "A,B = $a,$b"
   run       10000
-  if	    $b > 2 then "jump in.script break"
+  if        $b > 2 then "jump in.script break"
-  next	    b
+  next      b
-  jump	    in.script loopb
+  jump      in.script loopb
-label	    break
+label       break
 variable    b delete :pre
-next	    a
+next        a
-jump	    in.script loopa :pre
+jump        in.script loopa :pre
 
 [Restrictions:]
 

doc/src/pair_hybrid.txt

@@ -170,7 +170,7 @@ so that there is effectively no interaction (e.g. epsilon = 0.0 in a
 LJ potential).  Or, for {hybrid} and {hybrid/overlay} simulations, you
 can use this form of the pair_coeff command in your input script:
 
-pair_coeff	2 3 none :pre
+pair_coeff        2 3 none :pre
 
 or this form in the "Pair Coeffs" section of the data file:
 

doc/src/pair_meam.txt

@@ -188,9 +188,9 @@ lattce(I,J) = lattice structure of I-J reference structure:
                 bcc = body centered cubic
                 dim = dimer
                 b1  = rock salt (NaCl structure)
-		hcp = hexagonal close-packed
+                hcp = hexagonal close-packed
-		c11 = MoSi2 structure
+                c11 = MoSi2 structure
-		l12 = Cu3Au structure (lower case L, followed by 12)
+                l12 = Cu3Au structure (lower case L, followed by 12)
                 b2  = CsCl structure (interpenetrating simple cubic)
 nn2(I,J)    = turn on second-nearest neighbor MEAM formulation for
               I-J pair (see for example "(Lee)"_#Lee).

doc/src/pair_reax_c.txt

@@ -41,7 +41,9 @@ supplemental information of the following paper: "(Chenoweth et al.,
 2008)"_#Chenoweth_2008.  The version integrated into LAMMPS matches
 the most up-to-date version of ReaxFF as of summer 2010.  For more
 technical details about the pair reax/c implementation of ReaxFF, see
-the "(Aktulga)"_#Aktulga paper.
+the "(Aktulga)"_#Aktulga paper. The {reax/c} style was initially
+implemented as a stand-alone C code and is now integrated into LAMMPS
+as a package.
 
 The {reax/c/kk} style is a Kokkos version of the ReaxFF potential that is
 derived from the {reax/c} style. The Kokkos version can run on GPUs and
@@ -163,11 +165,11 @@ To print these quantities to the log file (with descriptive column
 headings) the following commands could be included in an input script:
 
 compute reax all pair reax/c
-variable eb  	 equal c_reax\[1\]
+variable eb      equal c_reax\[1\]
-variable ea  	 equal c_reax\[2\]
+variable ea      equal c_reax\[2\]
 \[...\]
-variable eqeq 	 equal c_reax\[14\]
+variable eqeq    equal c_reax\[14\]
-thermo_style custom step temp epair v_eb v_ea ... v_eqeq :pre
+thermo_style custom step temp epair v_eb v_ea \[...\] v_eqeq :pre
 
 Only a single pair_coeff command is used with the {reax/c} style which
 specifies a ReaxFF potential file with parameters for all needed
@@ -237,7 +239,7 @@ nbrhood_cutoff: Denotes the near neighbors cutoff (in Angstroms)
 regarding the bonded interactions. (default value = 5.0)
 
 hbond_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen
-bond interactions.(default value = 7.5. Value of 0.0 turns off
+bond interactions.(default value = 7.5. A value of 0.0 turns off
 hydrogen bonds)
 
 bond_graph_cutoff: is the threshold used in determining what is a

doc/src/pair_smtbq.txt

@@ -158,7 +158,7 @@ Divided line :ul
 3) Potential parameters:
 
 Keyword for element1, element2 and interaction potential ('second_moment' or 'buck' or 'buckPlusAttr') between element 1 and 2.  If the potential is 'second_moment', specify 'oxide' or 'metal' for metal-oxygen or metal-metal interactions respectively.
-Potential parameter: <pre><br/>	If type of potential is 'second_moment' : {A (eV)}, {p}, {&#958<sup>0</sup>} (eV) and {q} <br/>						  {r<sub>c1</sub>} (&#197), {r<sub>c2</sub>} (&#197) and {r<sub>0</sub>} (&#197) <br/> 	If type of potential is 'buck' : {C} (eV) and {&#961} (&#197) <br/>	If type of potential is 'buckPlusAttr' : {C} (eV) and {&#961} (&#197) <br/>						 {D} (eV), {B} (&#197<sup>-1</sup>), {r<sub>1</sub><sup>OO</sup>} (&#197) and {r<sub>2</sub><sup>OO</sup>} (&#197) </pre>
+Potential parameter: <pre><br/> If type of potential is 'second_moment' : {A (eV)}, {p}, {&#958<sup>0</sup>} (eV) and {q} <br/> {r<sub>c1</sub>} (&#197), {r<sub>c2</sub>} (&#197) and {r<sub>0</sub>} (&#197) <br/> If type of potential is 'buck' : {C} (eV) and {&#961} (&#197) <br/> If type of potential is 'buckPlusAttr' : {C} (eV) and {&#961} (&#197) <br/> {D} (eV), {B} (&#197<sup>-1</sup>), {r<sub>1</sub><sup>OO</sup>} (&#197) and {r<sub>2</sub><sup>OO</sup>} (&#197) </pre>
 Divided line :ul
 
 4) Tables parameters:
@@ -185,7 +185,7 @@ Divided line :ul
 
 8) Mode for the electronegativity equalization (Qeq) :
 
-Keyword mode: <pre> <br/>		QEqAll  (one QEq group)			|   no parameters <br/>		QEqAllParallel (several QEq groups)	|   no parameters <br/>		Surface			|   zlim   (QEq only for z>zlim)   </pre>
+Keyword mode: <pre> <br/> QEqAll  (one QEq group) |   no parameters <br/> QEqAllParallel (several QEq groups) |   no parameters <br/> Surface |   zlim   (QEq only for z>zlim)   </pre>
 Parameter if necessary
 Divided line :ul
 

doc/src/pair_snap.txt

@@ -96,15 +96,15 @@ tantalum potential provided in the LAMMPS potentials directory
 combines the {snap} and {zbl} pair styles. It is invoked
 by the following commands:
 
-	variable zblcutinner equal 4
+        variable zblcutinner equal 4
-	variable zblcutouter equal 4.8
+        variable zblcutouter equal 4.8
-	variable zblz equal 73
+        variable zblz equal 73
-	pair_style hybrid/overlay &
+        pair_style hybrid/overlay &
-	zbl $\{zblcutinner\} $\{zblcutouter\} snap
+        zbl $\{zblcutinner\} $\{zblcutouter\} snap
-	pair_coeff * * zbl 0.0
+        pair_coeff * * zbl 0.0
-	pair_coeff 1 1 zbl $\{zblz\}
+        pair_coeff 1 1 zbl $\{zblz\}
-	pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
+        pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
-	../potentials/Ta06A.snapparam Ta :pre
+        ../potentials/Ta06A.snapparam Ta :pre
 
 It is convenient to keep these commands in a separate file that can
 be inserted in any LAMMPS input script using the "include"_include.html

doc/src/replicate.txt

@@ -74,11 +74,14 @@ larger version of your molecule as a pre-processing step and input a
 new data file to LAMMPS.
 
 If the current simulation was read in from a restart file (before a
-run is performed), there can have been no fix information stored in
+run is performed), there must not be any fix information stored in
 the file for individual atoms.  Similarly, no fixes can be defined at
 the time the replicate command is used that require vectors of atom
 information to be stored.  This is because the replicate command does
 not know how to replicate that information for new atoms it creates.
+To work around this restriction, restart files may be converted into
+data files and fixes may be undefined via the "unfix"_unfix.html
+command before and redefined after the replicate command.
 
 [Related commands:] none
 

doc/src/restart.txt

@@ -113,8 +113,8 @@ For example, the following commands will write restart files
 every step from 1100 to 1200, and could be useful for debugging
 a simulation where something goes wrong at step 1163:
 
-variable	s equal stride(1100,1200,1)
+variable       s equal stride(1100,1200,1)
-restart		v_s tmp.restart :pre
+restart        v_s tmp.restart :pre
 
 :line
 

doc/src/run.txt

@@ -66,11 +66,11 @@ keywords.
 
 For example, consider this fix followed by 10 run commands:
 
-fix	     1 all nvt 200.0 300.0 1.0
+fix         1 all nvt 200.0 300.0 1.0
-run	     1000 start 0 stop 10000
+run         1000 start 0 stop 10000
-run	     1000 start 0 stop 10000
+run         1000 start 0 stop 10000
 ...
-run	     1000 start 0 stop 10000 :pre
+run         1000 start 0 stop 10000 :pre
 
 The NVT fix ramps the target temperature from 200.0 to 300.0 during a
 run.  If the run commands did not have the start/stop keywords (just

doc/src/run_style.txt

@@ -20,7 +20,7 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
     n1, n2, ... = loop factor between rRESPA levels (N-1 values)
     zero or more keyword/value pairings may be appended to the loop factors
     keyword = {bond} or {angle} or {dihedral} or {improper} or
-	      {pair} or {inner} or {middle} or {outer} or {hybrid} or {kspace}
+              {pair} or {inner} or {middle} or {outer} or {hybrid} or {kspace}
       {bond} value = M
         M = which level (1-N) to compute bond forces in
       {angle} value = M
@@ -33,14 +33,14 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
         M = which level (1-N) to compute pair forces in
       {inner} values = M cut1 cut2
         M = which level (1-N) to compute pair inner forces in
-	cut1 = inner cutoff between pair inner and
+        cut1 = inner cutoff between pair inner and
-	       pair middle or outer  (distance units)
+               pair middle or outer  (distance units)
-	cut2 = outer cutoff between pair inner and
+        cut2 = outer cutoff between pair inner and
-	       pair middle or outer  (distance units)
+               pair middle or outer  (distance units)
       {middle} values = M cut1 cut2
         M = which level (1-N) to compute pair middle forces in
-	cut1 = inner cutoff between pair middle and pair outer (distance units)
+        cut1 = inner cutoff between pair middle and pair outer (distance units)
-	cut2 = outer cutoff between pair middle and pair outer (distance units)
+        cut2 = outer cutoff between pair middle and pair outer (distance units)
       {outer} value = M
         M = which level (1-N) to compute pair outer forces in
       {hybrid} values = M1 M2 ... (as many values as there are hybrid sub-styles
@@ -230,7 +230,7 @@ rRESPA:
 
 fix             2 all shake 0.000001 500 0 m 1.0 a 1
 timestep        4.0
-run_style	respa 2 2 inner 1 4.0 5.0 outer 2 :pre
+run_style       respa 2 2 inner 1 4.0 5.0 outer 2 :pre
 
 With these settings, users can expect good energy conservation and
 roughly a 1.5 fold speedup over the {verlet} style with SHAKE and a

doc/src/set.txt

@@ -17,13 +17,13 @@ ID = atom ID range or type range or mol ID range or group ID or region ID :l
 one or more keyword/value pairs may be appended :l
 keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
           {charge} or {dipole} or {dipole/random} or {quat} or \
-	  {quat/random} or {diameter} or {shape} or \
+          {quat/random} or {diameter} or {shape} or \
-	  {length} or {tri} or {theta} or {theta/random} or \
+          {length} or {tri} or {theta} or {theta/random} or \
           {angmom} or {omega} or \
-	  {mass} or {density} or {volume} or {image} or \
+          {mass} or {density} or {volume} or {image} or \
-	  {bond} or {angle} or {dihedral} or {improper} or \
+          {bond} or {angle} or {dihedral} or {improper} or \
-	  {meso/e} or {meso/cv} or {meso/rho} or \
+          {meso/e} or {meso/cv} or {meso/rho} or \
-	  {smd/contact/radius} or {smd/mass/density} or {dpd/theta} or \
+          {smd/contact/radius} or {smd/mass/density} or {dpd/theta} or \
           {i_name} or {d_name} :l
   {type} value = atom type
     value can be an atom-style variable (see below)

doc/src/thermo.txt

@@ -45,8 +45,8 @@ options for "equal-style variables"_variable.html.
 For example, the following commands will output thermodynamic info 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)
-thermo	        v_s :pre
+thermo          v_s :pre
 
 [Restrictions:] none
 

doc/src/thermo_style.txt

@@ -23,12 +23,12 @@ args = list of arguments for a particular style :l
                         evdwl, ecoul, epair, ebond, eangle, edihed, eimp,
                         emol, elong, etail,
                         vol, density, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
-		        xy, xz, yz, xlat, ylat, zlat,
+                        xy, xz, yz, xlat, ylat, zlat,
                         bonds, angles, dihedrals, impropers,
-		        pxx, pyy, pzz, pxy, pxz, pyz,
+                        pxx, pyy, pzz, pxy, pxz, pyz,
-			fmax, fnorm, nbuild, ndanger,
+                        fmax, fnorm, nbuild, ndanger,
-			cella, cellb, cellc, cellalpha, cellbeta, cellgamma,
+                        cella, cellb, cellc, cellalpha, cellbeta, cellgamma,
-			c_ID, c_ID\[I\], c_ID\[I\]\[J\],
+                        c_ID, c_ID\[I\], c_ID\[I\]\[J\],
                         f_ID, f_ID\[I\], f_ID\[I\]\[J\],
                         v_name, v_name\[I\]
       step = timestep

doc/src/variable.txt

@@ -52,18 +52,18 @@ style = {delete} or {index} or {loop} or {world} or {universe} or {uloop} or {st
                      sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x),
                      random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x)
                      ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z),
-		     stride(x,y,z), stride2(x,y,z,a,b,c),
+                     stride(x,y,z), stride2(x,y,z,a,b,c),
-		     vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
+                     vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
     group functions = count(group), mass(group), charge(group),
-		      xcm(group,dim), vcm(group,dim), fcm(group,dim),
+                      xcm(group,dim), vcm(group,dim), fcm(group,dim),
-		      bound(group,dir), gyration(group), ke(group),
+                      bound(group,dir), gyration(group), ke(group),
-		      angmom(group,dim), torque(group,dim),
+                      angmom(group,dim), torque(group,dim),
                       inertia(group,dimdim), omega(group,dim)
     region functions = count(group,region), mass(group,region), charge(group,region),
-		      xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region),
+                      xcm(group,dim,region), vcm(group,dim,region), fcm(group,dim,region),
-		      bound(group,dir,region), gyration(group,region), ke(group,reigon),
+                      bound(group,dir,region), gyration(group,region), ke(group,reigon),
-		      angmom(group,dim,region), torque(group,dim,region),
+                      angmom(group,dim,region), torque(group,dim,region),
-		      inertia(group,dimdim,region), omega(group,dim,region)
+                      inertia(group,dimdim,region), omega(group,dim,region)
     special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x)
     feature functions = is_active(category,feature,exact), is_defined(category,id,exact)
     atom value = id\[i\], mass\[i\], type\[i\], mol\[i\], x\[i\], y\[i\], z\[i\], vx\[i\], vy\[i\], vz\[i\], fx\[i\], fy\[i\], fz\[i\], q\[i\]
@@ -219,13 +219,13 @@ script or when the input script is looped over.  This can be useful
 when breaking out of a loop via the "if"_if.html and "jump"_jump.html
 commands before the variable would become exhausted.  For example,
 
-label	    loop
+label       loop
 variable    a loop 5
-print	    "A = $a"
+print       "A = $a"
-if	    "$a > 2" then "jump in.script break"
+if          "$a > 2" then "jump in.script break"
-next	    a
+next        a
-jump	    in.script loop
+jump        in.script loop
-label	    break
+label       break
 variable    a delete :pre
 
 :line