diff --git a/doc/src/Section_example.txt b/doc/src/Section_example.txt
index b84c52edb809dca21df40bdd05b628a9e9cf3a8c..60a5ed128502b71bb80784a16f420c21b522ab97 100644
--- 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)
-melt: rapid melt of 3d LJ system
+meam: MEAM test for SiC and shear (same as shear examples)
+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
-msst: MSST shock dynamics
+min: energy minimization of 2d LJ melt
+msst: MSST shock dynamics
nb3b: use of nonbonded 3-body harmonic pair style
-neb: nudged elastic band (NEB) calculation for barrier finding
-nemd: non-equilibrium MD of 2d sheared system
+neb: nudged elastic band (NEB) calculation for barrier finding
+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
diff --git a/doc/src/Section_history.txt b/doc/src/Section_history.txt
index cae765f50495cd85ac550f2797642fa76915e027..438284c9da4173b6edbb14e415d362714bd72f86 100644
--- 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
diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt
index 5ad1de31b3c97d94678d344c436763114492720b..8dbec55e77a51f3675d7fb39cdb1ea101d5f56c9 100644
--- a/doc/src/Section_howto.txt
+++ b/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
-neigh_modify every 1 delay 1 :pre
+neighbor 0.4 bin
+neigh_modify every 1 delay 1 :pre
-fix 1 all nve
-fix 2 all langevin 1.0 1.0 10.0 904297 :pre
+fix 1 all nve
+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
-atom_style bond
-pair_style lj/cut 1.12
-pair_modify shift yes
-bond_style fene
+units lj
+atom_style bond
+pair_style lj/cut 1.12
+pair_modify shift yes
+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
-neigh_modify every 1 delay 1 :pre
+neighbor 0.4 bin
+neigh_modify every 1 delay 1 :pre
-fix 1 all nve
-fix 2 all langevin 1.0 1.0 10.0 904297 :pre
+fix 1 all nve
+fix 2 all langevin 1.0 1.0 10.0 904297 :pre
-timestep 0.012 :pre
+timestep 0.012 :pre
-reset_timestep 50
-run 50 :pre
+reset_timestep 50
+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
diff --git a/doc/src/Section_python.txt b/doc/src/Section_python.txt
index 4bfb1fbdb39fb7751c1cd666427f3c5706c8835f..64fa119706972456242bfc80fa44e46538789a53 100644
--- a/doc/src/Section_python.txt
+++ b/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
- # 1 = double :pre
+ # type = 0 = int
+ # 1 = double :pre
coords = lmp.extract_atom(name,type) # extract a per-atom quantity
# name = "x", "type", etc
- # type = 0 = vector of ints
- # 1 = array of ints
- # 2 = vector of doubles
- # 3 = array of doubles :pre
+ # type = 0 = vector of ints
+ # 1 = array of ints
+ # 2 = vector of doubles
+ # 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
- # 1 = per-atom data
- # 2 = local data
- # type = 0 = scalar
- # 1 = vector
- # 2 = array
- # i,j = indices of value in global vector or array :pre
+ # style = 0 = global data
+ # 1 = per-atom data
+ # 2 = local data
+ # type = 0 = scalar
+ # 1 = vector
+ # 2 = array
+ # 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
- # group = group ID (ignored for equal-style variables)
- # flag = 0 = equal-style variable
- # 1 = atom-style variable :pre
+ # name = name of variable
+ # group = group ID (ignored for equal-style variables)
+ # flag = 0 = equal-style variable
+ # 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
diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt
index 3a8c5d045e90646c1d5e563de1cf16e454825e74..e632d0018d8843e52f1db461339e5784d421b2b9 100644
--- 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
diff --git a/doc/src/comm_modify.txt b/doc/src/comm_modify.txt
index 6fefc5aeb7e1f01021ceda2f0d8524f5178d1164..3e8d0eca4ffe2d8c55e0998dd26384619fc712d6 100644
--- 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
diff --git a/doc/src/compute_heat_flux.txt b/doc/src/compute_heat_flux.txt
index 05eaff57fd0512a5fcec7036f7c3208f1d305af2..720d26ce761db261b51c9defdc21237309f685ab 100644
--- a/doc/src/compute_heat_flux.txt
+++ b/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
diff --git a/doc/src/compute_pe_atom.txt b/doc/src/compute_pe_atom.txt
index 78c0b8e1e68ec2d0afa0cb1a4a110c230a22cd66..319983a75144c55a0ebb22f990b0ca9b59c61989 100644
--- 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 pe all reduce sum c_peratom
-thermo_style custom step temp etotal press pe c_pe :pre
+compute peratom all pe/atom
+compute pe all reduce sum c_peratom
+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
diff --git a/doc/src/compute_property_atom.txt b/doc/src/compute_property_atom.txt
index dd65729c6c745230ca613c8163b08bcf1f6d5105..bac19918ba7ccefedb982449b91db8cd086edae7 100644
--- 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,
- vx, vy, vz, fx, fy, fz,
+ x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
+ vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
- angmomx, angmomy, angmomz,
- shapex,shapey, shapez,
- quatw, quati, quatj, quatk, tqx, tqy, tqz,
- end1x, end1y, end1z, end2x, end2y, end2z,
- corner1x, corner1y, corner1z,
- corner2x, corner2y, corner2z,
- corner3x, corner3y, corner3z,
- nbonds,
+ angmomx, angmomy, angmomz,
+ shapex,shapey, shapez,
+ quatw, quati, quatj, quatk, tqx, tqy, tqz,
+ end1x, end1y, end1z, end2x, end2y, end2z,
+ corner1x, corner1y, corner1z,
+ corner2x, corner2y, corner2z,
+ corner3x, corner3y, corner3z,
+ nbonds,
vfrac, s0,
- spin, eradius, ervel, erforce,
+ spin, eradius, ervel, erforce,
rho, drho, e, de, cv,
i_name, d_name :pre
id = atom ID
diff --git a/doc/src/compute_property_local.txt b/doc/src/compute_property_local.txt
index 98428c19a28687a95eb89bcb4830a2424950b36b..bc2ecca46671b8e656bbd9a1902974b009358c4f 100644
--- 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
- patom1 patom2 ptype1 ptype2
- batom1 batom2 btype
- aatom1 aatom2 aatom3 atype
- datom1 datom2 datom3 dtype
- iatom1 iatom2 iatom3 itype :pre
+ possible attributes = natom1 natom2 ntype1 ntype2
+ patom1 patom2 ptype1 ptype2
+ batom1 batom2 btype
+ aatom1 aatom2 aatom3 atype
+ datom1 datom2 datom3 dtype
+ 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
diff --git a/doc/src/compute_reduce.txt b/doc/src/compute_reduce.txt
index a0afc8d2c33b96d5f2425105db28099aa3ba6165..07d3c3bda7b88e277f36cb2e839398763488ca40 100644
--- 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 3 all reduce max c_1\[1\] c_1\[2\] c_2 replace 1 3 replace 2 3
+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
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
diff --git a/doc/src/compute_rigid_local.txt b/doc/src/compute_rigid_local.txt
index 808ef15e6ddcbb43e4760558636085c8ff173b54..5cdd58fbc253a8bb58a9ccd9dcb987059f2d272c 100644
--- 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
- vx, vy, vz, fx, fy, fz,
+ x, y, z, xu, yu, zu, ix, iy, iz
+ vx, vy, vz, fx, fy, fz,
omegax, omegay, omegaz,
- angmomx, angmomy, angmomz,
- quatw, quati, quatj, quatk,
+ angmomx, angmomy, angmomz,
+ quatw, quati, quatj, quatk,
tqx, tqy, tqz,
inertiax, inertiay, inertiaz
id = atom ID of atom within body which owns body properties
diff --git a/doc/src/compute_stress_atom.txt b/doc/src/compute_stress_atom.txt
index 27494784391c442de69de4bfae3b6e0cc6b619ff..08e2dd0abe0ce953343cff708dddd71a3adf2fc6 100644
--- 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 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)
-thermo_style custom step temp etotal press v_press :pre
+compute peratom all stress/atom NULL
+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)
+thermo_style custom step temp etotal press v_press :pre
[Output info:]
diff --git a/doc/src/compute_temp_asphere.txt b/doc/src/compute_temp_asphere.txt
old mode 100755
new mode 100644
diff --git a/doc/src/compute_temp_body.txt b/doc/src/compute_temp_body.txt
old mode 100755
new mode 100644
diff --git a/doc/src/compute_temp_sphere.txt b/doc/src/compute_temp_sphere.txt
old mode 100755
new mode 100644
diff --git a/doc/src/create_atoms.txt b/doc/src/create_atoms.txt
index 7f9b253abb3037abfecbe8780a9ee4dd256a7db1..ec7a6f4d8a50b872ee229c0b7f50b88d27c85f70 100644
--- a/doc/src/create_atoms.txt
+++ b/doc/src/create_atoms.txt
@@ -218,14 +218,14 @@ larger version.
variable x equal 100
variable y equal 25
-lattice hex 0.8442
-region box block 0 $x 0 $y -0.5 0.5
-create_box 1 box :pre
+lattice hex 0.8442
+region box block 0 $x 0 $y -0.5 0.5
+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)
diff --git a/doc/src/dump.txt b/doc/src/dump.txt
index e384d2182aa8d4fe903668907363e14bfcf038f3..767e791d71d9aec9560178b441be762dce96287b 100644
--- a/doc/src/dump.txt
+++ b/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,
- xsu, ysu, zsu, ix, iy, iz,
- vx, vy, vz, fx, fy, fz,
+ x, y, z, xs, ys, zs, xu, yu, zu,
+ xsu, ysu, zsu, ix, iy, iz,
+ vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
- angmomx, angmomy, angmomz, tqx, tqy, tqz,
- c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
+ angmomx, angmomy, angmomz, tqx, tqy, tqz,
+ c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
id = atom ID
mol = molecule ID
diff --git a/doc/src/dump_custom_vtk.txt b/doc/src/dump_custom_vtk.txt
index 8cb90c08320464f71a03010cce55ca6900830264..b84817327b076e077b220794f7a78c9714138dd0 100644
--- a/doc/src/dump_custom_vtk.txt
+++ b/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,
- xsu, ysu, zsu, ix, iy, iz,
- vx, vy, vz, fx, fy, fz,
+ x, y, z, xs, ys, zs, xu, yu, zu,
+ xsu, ysu, zsu, ix, iy, iz,
+ vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
- angmomx, angmomy, angmomz, tqx, tqy, tqz,
- spin, eradius, ervel, erforce,
- c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
+ angmomx, angmomy, angmomz, tqx, tqy, tqz,
+ spin, eradius, ervel, erforce,
+ c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
id = atom ID
mol = molecule ID
diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt
index bcb0a4979590ffa036e0010716b81eae6c90542b..1a49917bddf26928318ebcd7058e88ec3526575a 100644
--- a/doc/src/dump_modify.txt
+++ b/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)
-dump 1 all atom 100 tmp.dump
-dump_modify 1 every v_s first yes :pre
+variable s equal logfreq(10,3,10)
+dump 1 all atom 100 tmp.dump
+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)
-dump 1 all atom 100 tmp.dump
-dump_modify 1 every v_s :pre
+variable s equal next(f)
+dump 1 all atom 100 tmp.dump
+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
-dump 1 all image 250 image.*.jpg v_mol type &
- zoom 1.6 adiam 1.5
-dump_modify 1 pad 5 amap 0 10 sa 1 10 $\{colors\} :pre
+variable mol atom mol%10
+dump 1 all image 250 image.*.jpg v_mol type &
+ zoom 1.6 adiam 1.5
+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.
diff --git a/doc/src/fix_ave_correlate.txt b/doc/src/fix_ave_correlate.txt
index 021c00b06a2953837a3302cc60d84dfab2044a9e..bd097f291acab389c4d5c44fd9e7a3c1815b3663 100644
--- 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:]
diff --git a/doc/src/fix_ave_correlate_long.txt b/doc/src/fix_ave_correlate_long.txt
index e744ad4cb17b918e9fe33eb48cea6281a8d8d056..7b4bc53701cf9232ca87cd6cec1ceee38ac67690 100644
--- 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:]
diff --git a/doc/src/fix_bond_break.txt b/doc/src/fix_bond_break.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_bond_create.txt b/doc/src/fix_bond_create.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_bond_swap.txt b/doc/src/fix_bond_swap.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt
index 01884803abbb0f4f11ba250b8b073f7dfca1aa81..ffda84bf18376a43487c46e04cab5ef30d07b067 100644
--- 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
diff --git a/doc/src/fix_lb_fluid.txt b/doc/src/fix_lb_fluid.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_lb_momentum.txt b/doc/src/fix_lb_momentum.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_lb_pc.txt b/doc/src/fix_lb_pc.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_lb_rigid_pc_sphere.txt b/doc/src/fix_lb_rigid_pc_sphere.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_lb_viscous.txt b/doc/src/fix_lb_viscous.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_msst.txt b/doc/src/fix_msst.txt
index fb47f9a0af2e53dca5d31467bc569475a5f49b42..bd1edd805a96b32f0f565156ce66041280b7624d 100644
--- a/doc/src/fix_msst.txt
+++ b/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\[2\]
diff --git a/doc/src/fix_nph_asphere.txt b/doc/src/fix_nph_asphere.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_nph_body.txt b/doc/src/fix_nph_body.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_nph_sphere.txt b/doc/src/fix_nph_sphere.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_npt_asphere.txt b/doc/src/fix_npt_asphere.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_npt_body.txt b/doc/src/fix_npt_body.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_npt_sphere.txt b/doc/src/fix_npt_sphere.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_nve_asphere.txt b/doc/src/fix_nve_asphere.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_nve_asphere_noforce.txt b/doc/src/fix_nve_asphere_noforce.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_nve_body.txt b/doc/src/fix_nve_body.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_nve_line.txt b/doc/src/fix_nve_line.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_nve_sphere.txt b/doc/src/fix_nve_sphere.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_nve_tri.txt b/doc/src/fix_nve_tri.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_nvt_asphere.txt b/doc/src/fix_nvt_asphere.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_nvt_body.txt b/doc/src/fix_nvt_body.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_nvt_sphere.txt b/doc/src/fix_nvt_sphere.txt
old mode 100755
new mode 100644
diff --git a/doc/src/fix_qbmsst.txt b/doc/src/fix_qbmsst.txt
index 7979a8faee8b4cb7e5e85e16e5971560bec55862..468206a57bba711708efb746111fb780dc89974f 100644
--- a/doc/src/fix_qbmsst.txt
+++ b/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_modify fix_id energy yes
-variable dhug equal f_fix_id\[1\]
-variable dray equal f_fix_id\[2\]
-variable lgr_vel equal f_fix_id\[3\]
-variable lgr_pos equal f_fix_id\[4\]
-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
+fix fix_id all msst z
+fix_modify fix_id energy yes
+variable dhug equal f_fix_id\[1\]
+variable dray equal f_fix_id\[2\]
+variable lgr_vel equal f_fix_id\[3\]
+variable lgr_pos equal f_fix_id\[4\]
+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
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
diff --git a/doc/src/fix_rx.txt b/doc/src/fix_rx.txt
index bc185f76864e1a621a16edd6640d6de886fa15d3..4e26274b35251320c6e7d12b4905c9273a93040a 100644
--- a/doc/src/fix_rx.txt
+++ b/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.
diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt
index 349b3a33db02d07c3c764617b6e83537cd9d13e0..4f63556c527ca26404212d589da829f1ad8ee481 100644
--- a/doc/src/fix_shake.txt
+++ b/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
diff --git a/doc/src/fix_store_state.txt b/doc/src/fix_store_state.txt
index 6521f078b502de8e9e1bac957a94eb3911715cbb..df694fb97b4e2dd037d41a21b1200b89d3c3594a 100644
--- a/doc/src/fix_store_state.txt
+++ b/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,
- vx, vy, vz, fx, fy, fz,
+ x, y, z, xs, ys, zs, xu, yu, zu, xsu, ysu, zsu, ix, iy, iz,
+ vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, tqx, tqy, tqz,
diff --git a/doc/src/fix_ti_spring.txt b/doc/src/fix_ti_spring.txt
old mode 100755
new mode 100644
diff --git a/doc/src/group.txt b/doc/src/group.txt
index a72efebb89e972775d4bc147229071214f3cda24..ab975af75632a36b39db8a9e62e0d7d672dfc1bc 100644
--- a/doc/src/group.txt
+++ b/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
diff --git a/doc/src/if.txt b/doc/src/if.txt
index c3eb98f22a3d50d06bdbdd1991aff44a862894de..aa93c73790472a78893c4dab0a9e4c0b6b4e6bc0 100644
--- a/doc/src/if.txt
+++ b/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 "$b > 2" then "jump SELF break"
- next b
- jump in.script loopb
-label break
+ if "$b > 2" then "jump SELF break"
+ next b
+ jump in.script loopb
+label break
variable b delete
-next a
-jump SELF loopa :pre
+next a
+jump SELF loopa :pre
:line
diff --git a/doc/src/jump.txt b/doc/src/jump.txt
index 1689071bc16d97e15bdc995721f3869b58573bb8..e746ea782a83968c5684a9bf426e843b50cc2a53 100644
--- a/doc/src/jump.txt
+++ b/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 "$b > 2" then "jump SELF break"
- next b
- jump in.script loopb
-label break
+ if "$b > 2" then "jump SELF break"
+ next b
+ jump in.script loopb
+label break
variable b delete
-next a
-jump SELF loopa :pre
+next a
+jump SELF loopa :pre
[Restrictions:]
diff --git a/doc/src/min_style.txt b/doc/src/min_style.txt
old mode 100755
new mode 100644
diff --git a/doc/src/next.txt b/doc/src/next.txt
index 2802350c59f6235204faf51424ee6130d72d2e41..69bffe8bbf665a1a763a23c24fa657fdf50d263d 100644
--- a/doc/src/next.txt
+++ b/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"
- next b
- jump in.script loopb
-label break
+ if $b > 2 then "jump in.script break"
+ next b
+ jump in.script loopb
+label break
variable b delete :pre
-next a
-jump in.script loopa :pre
+next a
+jump in.script loopa :pre
[Restrictions:]
diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt
old mode 100755
new mode 100644
diff --git a/doc/src/pair_gayberne.txt b/doc/src/pair_gayberne.txt
old mode 100755
new mode 100644
diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt
index dd72ab6ebe0a487b0e75d029d13c2c24cdb9dfc6..47451cf14a8a5a5709ce73a8461a5e0d20e7dbe7 100644
--- a/doc/src/pair_hybrid.txt
+++ b/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:
diff --git a/doc/src/pair_meam.txt b/doc/src/pair_meam.txt
index a6e26e7cb7691df5521254a2f40c38c846c0d5a1..318f22067f2233f937efa7bb6b35008c560e4584 100644
--- a/doc/src/pair_meam.txt
+++ b/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
- c11 = MoSi2 structure
- l12 = Cu3Au structure (lower case L, followed by 12)
+ hcp = hexagonal close-packed
+ c11 = MoSi2 structure
+ 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).
diff --git a/doc/src/pair_reax_c.txt b/doc/src/pair_reax_c.txt
index d2d2643ff58f48e474c4fc7f06128c8fe2834bfa..bd8d7e44c9611651240ed19584884386bf7b30d9 100644
--- a/doc/src/pair_reax_c.txt
+++ b/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 ea equal c_reax\[2\]
+variable eb equal c_reax\[1\]
+variable ea equal c_reax\[2\]
\[...\]
-variable eqeq equal c_reax\[14\]
-thermo_style custom step temp epair v_eb v_ea ... v_eqeq :pre
+variable eqeq equal c_reax\[14\]
+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
diff --git a/doc/src/pair_resquared.txt b/doc/src/pair_resquared.txt
old mode 100755
new mode 100644
diff --git a/doc/src/pair_smtbq.txt b/doc/src/pair_smtbq.txt
old mode 100755
new mode 100644
index e2868ae62b60a98f1c8703878a2b2a5612977df0..c70af68b306a2f5eda1bbace68a6df71cae0eda4
--- a/doc/src/pair_smtbq.txt
+++ b/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}, {ξ<sup>0</sup>} (eV) and {q} <br/> {r<sub>c1</sub>} (Å), {r<sub>c2</sub>} (Å) and {r<sub>0</sub>} (Å) <br/> If type of potential is 'buck' : {C} (eV) and {ρ} (Å) <br/> If type of potential is 'buckPlusAttr' : {C} (eV) and {ρ} (Å) <br/> {D} (eV), {B} (Å<sup>-1</sup>), {r<sub>1</sub><sup>OO</sup>} (Å) and {r<sub>2</sub><sup>OO</sup>} (Å) </pre>
+Potential parameter: <pre><br/> If type of potential is 'second_moment' : {A (eV)}, {p}, {ξ<sup>0</sup>} (eV) and {q} <br/> {r<sub>c1</sub>} (Å), {r<sub>c2</sub>} (Å) and {r<sub>0</sub>} (Å) <br/> If type of potential is 'buck' : {C} (eV) and {ρ} (Å) <br/> If type of potential is 'buckPlusAttr' : {C} (eV) and {ρ} (Å) <br/> {D} (eV), {B} (Å<sup>-1</sup>), {r<sub>1</sub><sup>OO</sup>} (Å) and {r<sub>2</sub><sup>OO</sup>} (Å) </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
diff --git a/doc/src/pair_snap.txt b/doc/src/pair_snap.txt
index f27dce6fad5be0980defe5703748588e92f6842a..734cdaa9942f957cdcc4ab975f46a860537a3646 100644
--- a/doc/src/pair_snap.txt
+++ b/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 zblcutouter equal 4.8
- variable zblz equal 73
- pair_style hybrid/overlay &
- zbl $\{zblcutinner\} $\{zblcutouter\} snap
- pair_coeff * * zbl 0.0
- pair_coeff 1 1 zbl $\{zblz\}
- pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
- ../potentials/Ta06A.snapparam Ta :pre
+ variable zblcutinner equal 4
+ variable zblcutouter equal 4.8
+ variable zblz equal 73
+ pair_style hybrid/overlay &
+ zbl $\{zblcutinner\} $\{zblcutouter\} snap
+ pair_coeff * * zbl 0.0
+ pair_coeff 1 1 zbl $\{zblz\}
+ pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta &
+ ../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
diff --git a/doc/src/replicate.txt b/doc/src/replicate.txt
index 218963b1769ca3aaf6e7af43ad87cb7fd2ab9537..2e7153e38c312438b9e6869112eaf9b7f8fedbec 100644
--- a/doc/src/replicate.txt
+++ b/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
diff --git a/doc/src/restart.txt b/doc/src/restart.txt
index 38bf79d36741088b18f101a41a6a93e1d32f53f2..3154465f68fb5805e9650d581a4b58333cfc3282 100644
--- a/doc/src/restart.txt
+++ b/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)
-restart v_s tmp.restart :pre
+variable s equal stride(1100,1200,1)
+restart v_s tmp.restart :pre
:line
diff --git a/doc/src/run.txt b/doc/src/run.txt
index d6acee4f5f0abcc27eef72689a0b08d4fe495353..7f61f7bd64b27520e971946dfd3a1c2af89a55e3 100644
--- a/doc/src/run.txt
+++ b/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
-run 1000 start 0 stop 10000
-run 1000 start 0 stop 10000
+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 :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
diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt
index 787ea6e1a722601b07d3d77deaf6359d8c62ac92..2dafabebb594ce687d10c7608d82a0918c090775 100644
--- a/doc/src/run_style.txt
+++ b/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
- pair middle or outer (distance units)
- cut2 = outer cutoff between pair inner and
- pair middle or outer (distance units)
+ cut1 = inner cutoff between pair inner and
+ pair middle or outer (distance units)
+ cut2 = outer cutoff between pair inner and
+ 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)
- cut2 = outer 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)
{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
diff --git a/doc/src/set.txt b/doc/src/set.txt
index c6fc16640b4885000523516dd8b7deb29c7f2c4f..42ede23b8545ca6b70ea2f2f1a0b3ee3e5445896 100644
--- a/doc/src/set.txt
+++ b/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 \
- {length} or {tri} or {theta} or {theta/random} or \
+ {quat/random} or {diameter} or {shape} or \
+ {length} or {tri} or {theta} or {theta/random} or \
{angmom} or {omega} or \
- {mass} or {density} or {volume} or {image} or \
- {bond} or {angle} or {dihedral} or {improper} or \
- {meso/e} or {meso/cv} or {meso/rho} or \
- {smd/contact/radius} or {smd/mass/density} or {dpd/theta} or \
+ {mass} or {density} or {volume} or {image} or \
+ {bond} or {angle} or {dihedral} or {improper} or \
+ {meso/e} or {meso/cv} or {meso/rho} 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)
diff --git a/doc/src/thermo.txt b/doc/src/thermo.txt
index 5001fb3c21c837e489b86136cb342c0621acce7a..6faea206f49e4eda6e3b8d5670717c33e0c34c20 100644
--- a/doc/src/thermo.txt
+++ b/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)
-thermo v_s :pre
+variable s equal logfreq(10,3,10)
+thermo v_s :pre
[Restrictions:] none
diff --git a/doc/src/thermo_style.txt b/doc/src/thermo_style.txt
index 4c9811db60a7e9f1889461b971845d3bb5c5a07e..5e662e85b90a6d6d9be675e361fbb8e6ef5270a6 100644
--- a/doc/src/thermo_style.txt
+++ b/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,
- fmax, fnorm, nbuild, ndanger,
- cella, cellb, cellc, cellalpha, cellbeta, cellgamma,
- c_ID, c_ID\[I\], c_ID\[I\]\[J\],
+ pxx, pyy, pzz, pxy, pxz, pyz,
+ fmax, fnorm, nbuild, ndanger,
+ cella, cellb, cellc, cellalpha, cellbeta, cellgamma,
+ 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
diff --git a/doc/src/variable.txt b/doc/src/variable.txt
index 876c6bd4aec914a191246e99f75923a32a6cc47e..29d50a2b8e6fbd962162732fc6a72d1ce4a1cfa8 100644
--- a/doc/src/variable.txt
+++ b/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),
- vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
+ stride(x,y,z), stride2(x,y,z,a,b,c),
+ 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),
- bound(group,dir), gyration(group), ke(group),
- angmom(group,dim), torque(group,dim),
+ xcm(group,dim), vcm(group,dim), fcm(group,dim),
+ bound(group,dir), gyration(group), ke(group),
+ 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),
- bound(group,dir,region), gyration(group,region), ke(group,reigon),
- angmom(group,dim,region), torque(group,dim,region),
- inertia(group,dimdim,region), omega(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),
+ angmom(group,dim,region), torque(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 = $a"
-if "$a > 2" then "jump in.script break"
-next a
-jump in.script loop
-label break
+print "A = $a"
+if "$a > 2" then "jump in.script break"
+next a
+jump in.script loop
+label break
variable a delete :pre
:line