diff --git a/doc/html/Section_howto.html b/doc/html/Section_howto.html
index c168a5bd84..35b5419bc5 100644
--- a/doc/html/Section_howto.html
+++ b/doc/html/Section_howto.html
@@ -1086,7 +1086,7 @@ the sheared fluid and integrate the SLLOD equations of motion for the
system. Fix nvt/sllod uses compute temp/deform to compute a thermal temperature
by subtracting out the streaming velocity of the shearing atoms. The
velocity profile or other properties of the fluid can be monitored via
-the fix ave/spatial command.
+the fix ave/chunk command.
As discussed in the previous section on non-orthogonal simulation
boxes, the amount of tilt or skew that can be applied is limited by
LAMMPS for computational efficiency to be 1/2 of the parallel box
@@ -2011,13 +2011,13 @@ on each of two regions to add/subtract specified amounts of energy to
both regions. In both cases, the resulting temperatures of the two
regions can be monitored with the “compute temp/region” command and
the temperature profile of the intermediate region can be monitored
-with the fix ave/spatial and compute ke/atom commands.
The third method is to perform a reverse non-equilibrium MD simulation
using the fix thermal/conductivity
command which implements the rNEMD algorithm of Muller-Plathe.
Kinetic energy is swapped between atoms in two different layers of the
simulation box. This induces a temperature gradient between the two
-layers which can be monitored with the fix ave/spatial and compute ke/atom commands. The fix tallies the
+layers which can be monitored with the fix ave/chunk and compute ke/atom commands. The fix tallies the
cumulative energy transfer that it performs. See the fix thermal/conductivity command for
details.
The fourth method is based on the Green-Kubo (GK) formula which
@@ -2060,7 +2060,7 @@ used to shear the fluid in between them, again with some kind of
thermostat that modifies only the thermal (non-shearing) components of
velocity to prevent the fluid from heating up.
In both cases, the velocity profile setup in the fluid by this
-procedure can be monitored by the fix ave/spatial command, which determines
+procedure can be monitored by the fix ave/chunk command, which determines
grad(Vstream) in the equation above. E.g. the derivative in the
y-direction of the Vx component of fluid motion or grad(Vstream) =
dVx/dy. The Pxy off-diagonal component of the pressure or stress
@@ -2073,7 +2073,7 @@ using the fix ave/spatial command.
+monitored with the fix ave/chunk command.
The fix tallies the cummulative momentum transfer that it performs.
See the fix viscosity command for details.
The fourth method is based on the Green-Kubo (GK) formula which
diff --git a/doc/html/Section_intro.html b/doc/html/Section_intro.html
index 7c6a5c2f0a..3f41a6b156 100644
--- a/doc/html/Section_intro.html
+++ b/doc/html/Section_intro.html
@@ -391,7 +391,7 @@ molecular dynamics options:
coupled rigid body integration via the POEMS library
@@ -1272,9 +1272,8 @@ one step. Type “python src/Make.py -h -poems” to see the details.
4.1.22. PYTHON package
Contents: A python command which allow you to execute
Python code from a LAMMPS input script. The code can be in a separate
-file or embedded in the input script itself. See Section python 11.2 for an overview of using Python from
-LAMMPS and Section python for other ways to use
-LAMMPS and Python together.
+file or embedded in the input script itself. See Section python 11.2 for an overview of using Python from
+LAMMPS and for other ways to use LAMMPS and Python together.
Building with the PYTHON package assumes you have a Python shared
library available on your system, which needs to be a Python 2
version, 2.6 or later. Python 3 is not supported. The build uses the
@@ -1427,7 +1426,7 @@ few large bodies or many small bodies.
@@ -2004,7 +2003,7 @@ Dynamics. This package implements an atom, pair, and fix style which
allows electrons to be treated as explicit particles in an MD
calculation. See src/USER-AWPMD/README for more details.
Author: Ilya Valuev at the JIHT in Russia (valuev at
physik.hu-berlin.de). Contact him directly if you have questions.
@@ -2047,7 +2046,7 @@ have questions.
calculating x-ray and electron diffraction intensities based on
kinematic diffraction theory. See src/USER-DIFFRACTION/README for
more details.
-
Author: Shawn P. Coleman (shawn.p.coleman8.ctr at mail.mil) while at
the University of Arkansas. Contact him directly if you have
@@ -2065,11 +2064,13 @@ equations of motion are integrated efficiently through the Shardlow
splitting algorithm. See src/USER-DPD/README for more details.
Authors: James Larentzos (ARL) (james.p.larentzos.civ at mail.mil),
Timothy Mattox (Engility Corp) (Timothy.Mattox at engilitycorp.com)
and John Brennan (ARL) (john.k.brennan.civ at mail.mil). Contact them
@@ -2144,7 +2145,7 @@ this package. Also see src/USER-INTEL/README for more details. See
the KOKKOS, OPT, and USER-OMP packages, which also have CPU and
Phi-enabled styles.
Author: Mike Brown at Intel (michael.w.brown at intel.com). Contact
him directly if you have questions.
For the USER-INTEL package, you have 2 choices when building. You can
@@ -2261,7 +2262,7 @@ to VMD, support for new file formats can be added to LAMMPS (or VMD or
other programs that use them) without having to recompile the
application itself.
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
For the USER-OMP package, your Makefile.machine needs additional
diff --git a/doc/html/Section_start.html b/doc/html/Section_start.html
index b31c4631b5..4d422cdc2a 100644
--- a/doc/html/Section_start.html
+++ b/doc/html/Section_start.html
@@ -1365,7 +1365,7 @@ supercomputer there may be dozens or 1000s of physical nodes.
Note that the keywords do not use a leading minus sign. I.e. the
keyword is “t”, not “-t”. Also note that each of the keywords has a
default setting. Example of when to use these options and what
-settings to use on different platforms is given in Section 5.8.
+settings to use on different platforms is given in Section 5.8.
d or device
g or gpus
diff --git a/doc/html/accelerate_kokkos.html b/doc/html/accelerate_kokkos.html
index d48007a2ca..e517e0e2c5 100644
--- a/doc/html/accelerate_kokkos.html
+++ b/doc/html/accelerate_kokkos.html
@@ -351,7 +351,7 @@ used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not
necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP
provides alternative methods via environment variables for binding
threads to hardware cores. More info on binding threads to cores is
-given in this section.
+given in this section.
KOKKOS_ARCH=KNC enables compiler switches needed when compling for an
Intel Phi processor.
KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism
diff --git a/doc/html/compute_damage_atom.html b/doc/html/compute_damage_atom.html
index bc378e49e8..97a0eba0d0 100644
--- a/doc/html/compute_damage_atom.html
+++ b/doc/html/compute_damage_atom.html
@@ -170,7 +170,8 @@ LAMMPS was built with that package. See the
diff --git a/doc/html/compute_dilatation_atom.html b/doc/html/compute_dilatation_atom.html
index cf1947f3b2..798663b6a8 100644
--- a/doc/html/compute_dilatation_atom.html
+++ b/doc/html/compute_dilatation_atom.html
@@ -172,7 +172,8 @@ LAMMPS was built with that package. See the
diff --git a/doc/html/compute_erotate_rigid.html b/doc/html/compute_erotate_rigid.html
index 0e46c9e7fe..501319d8c8 100644
--- a/doc/html/compute_erotate_rigid.html
+++ b/doc/html/compute_erotate_rigid.html
@@ -172,7 +172,7 @@ LAMMPS was built with that package. See the
diff --git a/doc/html/compute_plasticity_atom.html b/doc/html/compute_plasticity_atom.html
index 11518b0c64..54bffecbd2 100644
--- a/doc/html/compute_plasticity_atom.html
+++ b/doc/html/compute_plasticity_atom.html
@@ -168,7 +168,8 @@ LAMMPS was built with that package. See the
(Mitchell) Mitchell, “A non-local, ordinary-state-based
diff --git a/doc/html/compute_reduce.html b/doc/html/compute_reduce.html
index 292fa820cb..519bc9ff3c 100644
--- a/doc/html/compute_reduce.html
+++ b/doc/html/compute_reduce.html
@@ -220,7 +220,7 @@ asterisk means all indices from n to N (inclusive). A middle asterisk
means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. these 2 compute reduce commands are
-equivalent, since the compute stress/atom
+equivalent, since the compute stress/atom
command creates a per-atom array with 6 columns:
The calculation performed by this compute is exactly like that
described by the compute temp/deform
@@ -180,7 +180,8 @@ LAMMPS was built with that package. See the
Define a computation that calculates the temperature of a group of
nuclei and electrons in the electron force field
model. A compute of this style can be used by commands that compute a
-temperature, e.g. thermo_modify, fix npt/eff, etc.
The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2 for
nuclei and sum of 1/2 (m v^2 + 3/4 m s^2) for electrons, where s
diff --git a/doc/html/dihedral_table.html b/doc/html/dihedral_table.html
index 91abb1817f..d967731158 100644
--- a/doc/html/dihedral_table.html
+++ b/doc/html/dihedral_table.html
@@ -301,7 +301,7 @@ more instructions on how to use the accelerated styles effectively.
Restrictions
This dihedral style can only be used if LAMMPS was built with the
-USER-MISC package. See the Making LAMMPS
+USER-MISC package. See the Making LAMMPS
section for more info on packages.
diff --git a/doc/html/dump.html b/doc/html/dump.html
index 40449d1202..b47465bc33 100644
--- a/doc/html/dump.html
+++ b/doc/html/dump.html
@@ -550,7 +550,7 @@ indices from n to N (inclusive). A middle asterisk means all indices
from m to n (inclusive).
Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. these 2 dump commands are
-equivalent, since the compute stress/atom
+equivalent, since the compute stress/atom
command creates a per-atom array with 6 columns:
computemyPressallstress/atomNULLdump2allcustom100tmp.dumpidmyPress[*]
diff --git a/doc/html/dump_custom_vtk.html b/doc/html/dump_custom_vtk.html
index d23a7c09f7..8bd838f671 100644
--- a/doc/html/dump_custom_vtk.html
+++ b/doc/html/dump_custom_vtk.html
@@ -157,7 +157,7 @@ mol = molecule ID
proc = ID of processor that owns atom
procp1 = ID+1 of processor that owns atom
type = atom type
-element = name of atom element, as defined by dump_modify command
+element = name of atom element, as defined by dump_modify command
mass = atom mass
x,y,z = unscaled atom coordinates
xs,ys,zs = scaled atom coordinates
@@ -194,7 +194,7 @@ depending on the filename extension specified. This can be either
for the XML format; see the VTK homepage for a detailed
description of these formats. Since this naming convention conflicts
with the way binary output is usually specified (see below),
-dump_modify binary allows to set the binary
+dump_modify binary allows to set the binary
flag for this dump style explicitly.
@@ -203,9 +203,9 @@ flag for this dump style explicitly.
timesteps in a format readable by the VTK visualization toolkit or other visualization tools that use it,
e.g. ParaView. The timesteps on which dump
output is written can also be controlled by a variable; see the
-dump_modify every command for details.
+dump_modify every command for details.
Only information for atoms in the specified group is dumped. The
-dump_modify thresh and region commands can also
+dump_modify thresh and region commands can also
alter what atoms are included; see details below.
As described below, special characters (“*”, “%”) in the filename
determine the kind of output.
@@ -218,7 +218,7 @@ box.
Warning
-
Unless the dump_modify sort
+
Unless the dump_modify sort
option is invoked, the lines of atom information written to dump files
will be in an indeterminate order for each snapshot. This is even
true when running on a single processor, if the atom_modify sort option is on, which it is by default. In this
@@ -228,7 +228,7 @@ data for a single snapshot is collected from multiple processors, each
of which owns a subset of the atoms.
For the custom/vtk style, sorting is off by default. See the
-dump_modify doc page for details.
The dimensions of the simulation box are written to a separate file
for each snapshot (either in legacy VTK or XML format depending on
@@ -261,20 +261,20 @@ timestep 0) and on the last timestep of a minimization if the
minimization converges. Note that this means a dump will not be
performed on the initial timestep after the dump command is invoked,
if the current timestep is not a multiple of N. This behavior can be
-changed via the dump_modify first command, which
+changed via the dump_modify first command, which
can also be useful if the dump command is invoked after a minimization
ended on an arbitrary timestep. N can be changed between runs by
-using the dump_modify every command.
-The dump_modify every command
+using the dump_modify every command.
+The dump_modify every command
also allows a variable to be used to determine the sequence of
timesteps on which dump files are written. In this mode a dump on the
first timestep of a run will also not be written unless the
-dump_modify first command is used.
Dump filenames can contain two wildcard characters. If a “*”
character appears in the filename, then one file per snapshot is
written and the “*” character is replaced with the timestep value.
For example, tmp.dump*.vtk becomes tmp.dump0.vtk, tmp.dump10000.vtk,
-tmp.dump20000.vtk, etc. Note that the dump_modify pad
+tmp.dump20000.vtk, etc. Note that the dump_modify pad
command can be used to insure all timestep numbers are the same length
(e.g. 00010), which can make it easier to read a series of dump files
in order with some post-processing tools.
@@ -286,7 +286,7 @@ tmp.dump_P-1.vtp, etc. This creates smaller files and can be a fast
mode of output on parallel machines that support parallel I/O for output.
By default, P = the number of processors meaning one file per
processor, but P can be set to a smaller value via the nfile or
-fileper keywords of the dump_modify command.
+fileper keywords of the dump_modify command.
These options can be the most efficient way of writing out dump files
when running on large numbers of processors.
For the legacy VTK format “%” is ignored and P = 1, i.e., only
@@ -305,7 +305,7 @@ part of the custom/vtk style.
id is the atom ID. mol is the molecule ID, included in the data
file for molecular systems. type is the atom type. element is
typically the chemical name of an element, which you must assign to
-each type via the dump_modify element command.
+each type via the dump_modify element command.
More generally, it can be any string you wish to associate with an
atom type. mass is the atom mass. vx, vy, vz, fx, fy,
fz, and q are components of atom velocity and force and atomic
diff --git a/doc/html/fix_ave_chunk.html b/doc/html/fix_ave_chunk.html
index e7bfd31839..564b91e3ef 100644
--- a/doc/html/fix_ave_chunk.html
+++ b/doc/html/fix_ave_chunk.html
@@ -251,7 +251,7 @@ asterisk means all indices from n to N (inclusive). A middle asterisk
means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. these 2 fix ave/chunk commands are
-equivalent, since the compute property/atom command creates, in this
+equivalent, since the compute property/atom command creates, in this
case, a per-atom array with 3 columns:
computemyAngallproperty/atomangmomxangmomyangmomzfix1allave/chunk1001100cc1c_myAng[*]filetmp.angmom
@@ -262,7 +262,7 @@ case, a per-atom array with 3 columns:
Note
This fix works by creating an array of size Nchunk by Nvalues
on each processor. Nchunk is the number of chunks which is defined
-by the compute chunk/atom command.
+by the compute chunk/atom command.
Nvalues is the number of input values specified. Each processor loops
over its atoms, tallying its values to the appropriate chunk. Then
the entire array is summed across all processors. This means that
diff --git a/doc/html/fix_bond_create.html b/doc/html/fix_bond_create.html
index a403dbfc40..8ab79a00a5 100644
--- a/doc/html/fix_bond_create.html
+++ b/doc/html/fix_bond_create.html
@@ -237,7 +237,7 @@ become one moleclue due to the created bond, all atoms in the new
moleclue retain their original molecule IDs.
If the atype keyword is used and if an angle potential is defined
-via the angle_style command, then any new 3-body
+via the angle_style command, then any new 3-body
interactions inferred by the creation of a bond will create new angles
of type angletype, with parameters assigned by the corresponding
angle_coeff command. Likewise, the dtype and
diff --git a/doc/html/fix_deform.html b/doc/html/fix_deform.html
index 5177899d75..e8ad31ffb0 100644
--- a/doc/html/fix_deform.html
+++ b/doc/html/fix_deform.html
@@ -570,7 +570,7 @@ is not consistent with fix nvt/sllod.
For non-equilibrium MD (NEMD) simulations using “remap v” it is
usually desirable that the fluid (or flowing material, e.g. granular
particles) stream with a velocity profile consistent with the
-deforming box. As mentioned above, using a thermostat such as fix nvt/sllod or fix lavgevin
+deforming box. As mentioned above, using a thermostat such as fix nvt/sllod or fix lavgevin
(with a bias provided by compute temp/deform), will typically accomplish
that. If you do not use a thermostat, then there is no driving force
pushing the atoms to flow in a manner consistent with the deforming
diff --git a/doc/html/fix_deposit.html b/doc/html/fix_deposit.html
index 1e1e637b35..6e7e0be54f 100644
--- a/doc/html/fix_deposit.html
+++ b/doc/html/fix_deposit.html
@@ -264,7 +264,7 @@ time a molecule is deposited, a random number is used to sample from
the list of relative probabilities. The N values must sum to 1.0.
If you wish to insert molecules via the mol keyword, that will be
treated as rigid bodies, use the rigid keyword, specifying as its
-value the ID of a separate fix rigid/small
+value the ID of a separate fix rigid/small
command which also appears in your input script.
If you wish to insert molecules via the mol keyword, that will have
their bonds or angles constrained via SHAKE, use the shake keyword,
diff --git a/doc/html/fix_ehex.html b/doc/html/fix_ehex.html
index 7e7a529acc..f1cc66f404 100644
--- a/doc/html/fix_ehex.html
+++ b/doc/html/fix_ehex.html
@@ -231,7 +231,7 @@ resulting temperature profile will therefore be the same.
the keyword hex is specified.
Compatibility with SHAKE and RATTLE (rigid molecules):
-
This fix is compatible with fix shake and fix rattle. If either of these constraining algorithms is
+
This fix is compatible with fix shake and fix rattle. If either of these constraining algorithms is
specified in the input script and the keyword constrain is set, the
bond distances will be corrected a second time at the end of the
integration step. It is recommended to specify the keyword com in
@@ -244,7 +244,7 @@ rescaling takes place if the centre of mass lies outside the region.
Note
You can only use the keyword com along with constrain.
-
To achieve the highest accuracy it is recommended to use fix rattle with the keywords constrain and com as
+
To achieve the highest accuracy it is recommended to use fix rattle with the keywords constrain and com as
shown in the second example. Only if RATTLE is employed, the velocity
constraints will be satisfied.
diff --git a/doc/html/fix_eos_table.html b/doc/html/fix_eos_table.html
index 040335fdb5..91f10fe854 100644
--- a/doc/html/fix_eos_table.html
+++ b/doc/html/fix_eos_table.html
@@ -187,7 +187,7 @@ identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the fix command.
The next line lists the number of table entries. The parameter “N” is
required and its value is the number of table entries that follow.
-Note that this may be different than the N specified in the fix eos/table command. Let Ntable = N in the fix
+Note that this may be different than the N specified in the fix eos/table command. Let Ntable = N in the fix
command, and Nfile = “N” in the tabulated file. What LAMMPS does is a
preliminary interpolation by creating splines using the Nfile
tabulated values as nodal points. It uses these to interpolate as
@@ -220,7 +220,7 @@ are not within the table cutoffs.
diff --git a/doc/html/fix_eos_table_rx.html b/doc/html/fix_eos_table_rx.html
index 95ecfb9ca7..49f1a58f76 100644
--- a/doc/html/fix_eos_table_rx.html
+++ b/doc/html/fix_eos_table_rx.html
@@ -242,7 +242,7 @@ are not within the table cutoffs.
Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various output commands. No parameter of this fix can be
+by this fix for access by various output commands. No parameter of this fix can be
used with the start/stop keywords of the run command.
This fix is not invoked during energy minimization.
diff --git a/doc/html/fix_lb_pc.html b/doc/html/fix_lb_pc.html
index 5dbd07536f..8a5281c6c3 100644
--- a/doc/html/fix_lb_pc.html
+++ b/doc/html/fix_lb_pc.html
@@ -154,7 +154,7 @@ algorithm if the force coupling constant has been set by default.
Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various output commands. No parameter of this fix can be
+by this fix for access by various output commands. No parameter of this fix can be
used with the start/stop keywords of the run command.
This fix is not invoked during energy minimization.
diff --git a/doc/html/fix_nh_eff.html b/doc/html/fix_nh_eff.html
index 72d8ef25d4..5e8d66853c 100644
--- a/doc/html/fix_nh_eff.html
+++ b/doc/html/fix_nh_eff.html
@@ -203,7 +203,7 @@ to the temperature or kinetic energy from the electron radial velocity.
Note
there are two different pressures that can be reported for eFF
-when defining the pair_style (see pair eff/cut to
+when defining the pair_style (see pair eff/cut to
understand these settings), one (default) that considers electrons do
not contribute radial virial components (i.e. electrons treated as
incompressible ‘rigid’ spheres) and one that does. The radial
diff --git a/doc/html/fix_nve_manifold_rattle.html b/doc/html/fix_nve_manifold_rattle.html
index 8d0d30a273..06d68cd6ae 100644
--- a/doc/html/fix_nve_manifold_rattle.html
+++ b/doc/html/fix_nve_manifold_rattle.html
@@ -159,7 +159,7 @@ keyword = every
atoms constrained to a curved surface (manifold) in the group each
timestep. The constraint is handled by RATTLE (Andersen)
written out for the special case of single-particle constraints as
-explained in (Paquay). V is volume; E is energy. This way,
+explained in (Paquay). V is volume; E is energy. This way,
the dynamics of particles constrained to curved surfaces can be
studied. If combined with fix langevin, this
generates Brownian motion of particles constrained to a curved
diff --git a/doc/html/fix_nvt_manifold_rattle.html b/doc/html/fix_nvt_manifold_rattle.html
index 35e6ea6135..bcb049ebeb 100644
--- a/doc/html/fix_nvt_manifold_rattle.html
+++ b/doc/html/fix_nvt_manifold_rattle.html
@@ -157,7 +157,7 @@ keyword = temp or tchain or every
This fix combines the RATTLE-based (Andersen) time integrator of fix nve/manifold/rattle(Paquay) with a Nose-Hoover-chain thermostat to sample the
canonical ensemble of particles constrained to a curved surface (manifold). This sampling does suffer from discretization bias of O(dt).
For a list of currently supported manifolds and their parameters, see manifolds
diff --git a/doc/html/fix_phonon.html b/doc/html/fix_phonon.html
index 0eed3acb9e..40d369afee 100644
--- a/doc/html/fix_phonon.html
+++ b/doc/html/fix_phonon.html
@@ -247,7 +247,7 @@ corresponding reciprocal lattice.
fix. You can use it to change the temperature compute from thermo_temp
to the one that reflects the true temperature of atoms in the group.
No global scalar or vector or per-atom quantities are stored by this
-fix for access by various output commands.
Instead, this fix outputs its initialization information (including
mapping information) and the calculated dynamical matrices to the file
prefix.log, with the specified prefix. The dynamical matrices are
diff --git a/doc/html/fix_pour.html b/doc/html/fix_pour.html
index ffe5fd5362..ca471ec2c3 100644
--- a/doc/html/fix_pour.html
+++ b/doc/html/fix_pour.html
@@ -232,7 +232,7 @@ time a molecule is inserted, a random number is used to sample from
the list of relative probabilities. The N values must sum to 1.0.
If you wish to insert molecules via the mol keyword, that will be
treated as rigid bodies, use the rigid keyword, specifying as its
-value the ID of a separate fix rigid/small
+value the ID of a separate fix rigid/small
command which also appears in your input script.
If you wish to insert molecules via the mol keyword, that will have
their bonds or angles constrained via SHAKE, use the shake keyword,
diff --git a/doc/html/fix_reax_bonds.html b/doc/html/fix_reax_bonds.html
index 5e30cb4c61..0275b0ad0e 100644
--- a/doc/html/fix_reax_bonds.html
+++ b/doc/html/fix_reax_bonds.html
@@ -155,7 +155,7 @@ specified by fix species command.
diff --git a/doc/html/fix_shardlow.html b/doc/html/fix_shardlow.html
index e54353f7eb..204f18df58 100644
--- a/doc/html/fix_shardlow.html
+++ b/doc/html/fix_shardlow.html
@@ -148,7 +148,7 @@
integrate the DPD equations of motion. The SSA splits the integration
into a stochastic and deterministic integration step. The fix
shardlow performs the stochastic integration step and must be used
-in conjunction with a deterministic integrator (e.g. fix nve or fix nph). The stochastic
+in conjunction with a deterministic integrator (e.g. fix nve or fix nph). The stochastic
integration of the dissipative and random forces is performed prior to
the deterministic integration of the conservative force. Further
details regarding the method are provided in (Lisal) and
diff --git a/doc/html/fix_smd.html b/doc/html/fix_smd.html
index 77238ccae4..5be23f5d7b 100644
--- a/doc/html/fix_smd.html
+++ b/doc/html/fix_smd.html
@@ -168,10 +168,10 @@
Description
This fix implements several options of steered MD (SMD) as reviewed in
-(Izrailev), which allows to induce conformational changes
+(Izrailev), which allows to induce conformational changes
in systems and to compute the potential of mean force (PMF) along the
-assumed reaction coordinate (Park) based on Jarzynski’s
-equality (Jarzynski). This fix borrows a lot from fix spring and fix setforce.
You can apply a moving spring force to a group of atoms (tether
style) or between two groups of atoms (couple style). The spring
can then be used in either constant velocity (cvel) mode or in
@@ -249,14 +249,12 @@ LAMMPS was built with that package. See the fix spring/rg
(Izrailev) Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar,
Wriggers, Schulten. Computational Molecular Dynamics: Challenges,
Methods, Ideas, volume 4 of Lecture Notes in Computational Science and
Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998.
-
(Park)
-Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)
-
(Jarzynski)
-Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)
+
(Park) Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)
+
(Jarzynski) Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)
diff --git a/doc/html/fix_wall_piston.html b/doc/html/fix_wall_piston.html
index 8ebde444af..ade80b4497 100644
--- a/doc/html/fix_wall_piston.html
+++ b/doc/html/fix_wall_piston.html
@@ -205,7 +205,7 @@ define the lattice spacings.
Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to binary restart files. None of the fix_modify options
are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various output commands. No parameter of this fix can
+by this fix for access by various output commands. No parameter of this fix can
be used with the start/stop keywords of the run command.
This fix is not invoked during energy minimization.
diff --git a/doc/html/kspace_style.html b/doc/html/kspace_style.html
index 21938697de..1d279e5f3e 100644
--- a/doc/html/kspace_style.html
+++ b/doc/html/kspace_style.html
@@ -195,7 +195,7 @@ style, the cutoff for Coulombic or 1/r^N interactions is effectively
infinite. If the Coulombic case, this means each charge in the system
interacts with charges in an infinite array of periodic images of the
simulation domain.
-
Note that using a long-range solver requires use of a matching pair style to perform consistent short-range pairwise
+
Note that using a long-range solver requires use of a matching pair style to perform consistent short-range pairwise
calculations. This means that the name of the pair style contains a
matching keyword to the name of the KSpace style, as in this table:
Whether a section is required depends on how the molecule
template is used by other LAMMPS commands. For example, to add a
molecule via the fix deposit command, the Coords
-and Types sections are required. To add a rigid body via the fix pour command, the Bonds (Angles, etc) sections are not
+and Types sections are required. To add a rigid body via the fix pour command, the Bonds (Angles, etc) sections are not
required, since the molecule will be treated as a rigid body. Some
sections are optional. For example, the fix pour
command can be used to add “molecules” which are clusters of
diff --git a/doc/html/neighbor.html b/doc/html/neighbor.html
index d1c2630e8b..65a47dfcc1 100644
--- a/doc/html/neighbor.html
+++ b/doc/html/neighbor.html
@@ -192,7 +192,7 @@ are printed to the screen and log file. See
diff --git a/doc/html/pair_brownian.html b/doc/html/pair_brownian.html
index 0f4bca68e6..eaf0a723c3 100644
--- a/doc/html/pair_brownian.html
+++ b/doc/html/pair_brownian.html
@@ -227,7 +227,7 @@ to be specified in an input script that reads a restart file.
Restrictions
These styles are part of the COLLOID package. They are only enabled
-if LAMMPS was built with that package. See the Making LAMMPS section for more info.
+if LAMMPS was built with that package. See the Making LAMMPS section for more info.
Only spherical monodisperse particles are allowed for pair_style
brownian.
Only spherical particles are allowed for pair_style brownian/poly.
diff --git a/doc/html/pair_dipole.html b/doc/html/pair_dipole.html
index 2325cfa256..a8b5437180 100644
--- a/doc/html/pair_dipole.html
+++ b/doc/html/pair_dipole.html
@@ -268,17 +268,15 @@ dipole interactions. The long-range portion is calculated by using
ewald_disp of the kspace_style command. If
flag_coul is set to off, Coulombic and dipole interactions are not
computed at all.
-
Atoms with dipole moments should be integrated using the fix nve/sphere update dipole or the fix nvt/sphere update dipole command to rotate the
dipole moments. The omega option on the fix langevin command can be used to thermostat the
rotational motion. The compute temp/sphere
command can be used to monitor the temperature, since it includes
-rotational degrees of freedom. The atom_style dipole command should be used since it defines the
-point dipoles and their rotational state. The magnitude of the dipole
-moment for each type of particle can be defined by the
-dipole command or in the “Dipoles” section of the data
-file read in by the read_data command. Their initial
-orientation can be defined by the set dipole command or in
-the “Atoms” section of the data file.
+rotational degrees of freedom. The atom_style hybrid dipole sphere command should be used since
+it defines the point dipoles and their rotational state.
+The magnitude and orientation of the dipole moment for each particle
+can be defined by the set command or in the “Atoms” section
+of the data file read in by the read_data command.
The following coefficients must be defined for each pair of atoms
types via the pair_coeff command as in the examples
above, or in the data file or restart files read by the
@@ -348,7 +346,8 @@ currently supported.
(Allen) Allen and Tildesley, Computer Simulation of Liquids,
diff --git a/doc/html/pair_dpd_fdt.html b/doc/html/pair_dpd_fdt.html
index a06112c8fc..cd8033694c 100644
--- a/doc/html/pair_dpd_fdt.html
+++ b/doc/html/pair_dpd_fdt.html
@@ -230,7 +230,7 @@ specified.
These commands are part of the USER-DPD package. They are only
enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.
Pair styles dpd/fdt and dpd/fdt/energy require use of the
-communicate vel yes option so that velocites are
+comm_modify vel yes option so that velocites are
stored by ghost atoms.
Pair style dpd/fdt/energy requires atom_style dpd
to be used in order to properly account for the particle internal
diff --git a/doc/html/pair_gayberne.html b/doc/html/pair_gayberne.html
index 297c77802a..0b02a49a51 100644
--- a/doc/html/pair_gayberne.html
+++ b/doc/html/pair_gayberne.html
@@ -288,7 +288,7 @@ enabled if LAMMPS was built with that package. See the atom_style. It also require they store a per-type
-shape. The particles cannot store a per-particle
+shape. The particles cannot store a per-particle
diameter.
This pair style requires that atoms be ellipsoids as defined by the
atom_style ellipsoid command.
diff --git a/doc/html/pair_line_lj.html b/doc/html/pair_line_lj.html
index f1fb92c17f..f36f573822 100644
--- a/doc/html/pair_line_lj.html
+++ b/doc/html/pair_line_lj.html
@@ -238,7 +238,7 @@ shift, table, and tail options.
Restrictions
This style is part of the ASPHERE package. It is only enabled if
-LAMMPS was built with that package. See the Making LAMMPS section for more info.
+LAMMPS was built with that package. See the Making LAMMPS section for more info.
Defining particles to be line segments so they participate in
line/line or line/particle interactions requires the use the
atom_style line command.
diff --git a/doc/html/pair_thole.html b/doc/html/pair_thole.html
index a6baecd4b6..b2742247f9 100644
--- a/doc/html/pair_thole.html
+++ b/doc/html/pair_thole.html
@@ -180,7 +180,7 @@ it also allows for mixing pair coefficients instead of listing them all.
The lj/cut/thole/long pair style is also a bit faster because it avoids an
overlay and can benefit from OMP acceleration. Moreover, it uses a more
precise approximation of the direct Coulomb interaction at short range similar
-to coul/long/cs, which stabilizes the temperature of
+to coul/long/cs, which stabilizes the temperature of
Drude particles.
The thole pair styles compute the Coulomb interaction damped at
short distances by a function
diff --git a/doc/html/pair_tri_lj.html b/doc/html/pair_tri_lj.html
index 00e10b9632..e6c6b24ddd 100644
--- a/doc/html/pair_tri_lj.html
+++ b/doc/html/pair_tri_lj.html
@@ -210,7 +210,7 @@ shift, table, and tail options.
Restrictions
This style is part of the ASPHERE package. It is only enabled if
-LAMMPS was built with that package. See the Making LAMMPS section for more info.
+LAMMPS was built with that package. See the Making LAMMPS section for more info.
Defining particles to be triangles so they participate in tri/tri or
tri/particle interactions requires the use the atom_style tri command.
diff --git a/doc/html/python.html b/doc/html/python.html
index 2962d7dcd9..f78a9df834 100644
--- a/doc/html/python.html
+++ b/doc/html/python.html
@@ -554,7 +554,7 @@ building LAMMPS. LAMMPS must also be built as a shared library and
your Python function must be able to to load the Python module in
python/lammps.py that wraps the LAMMPS library interface. These are
the same steps required to use Python by itself to wrap LAMMPS.
-Details on these steps are explained in Section python. Note that it is important that the
+Details on these steps are explained in Section python. Note that it is important that the
stand-alone LAMMPS executable and the LAMMPS shared library be
consistent (built from the same source code files) in order for this
to work. If the two have been built at different times using
diff --git a/doc/html/rerun.html b/doc/html/rerun.html
index 520ea38241..dc973298a6 100644
--- a/doc/html/rerun.html
+++ b/doc/html/rerun.html
@@ -174,7 +174,7 @@ initial simulation produced the dump file:
Calculate one or more diagnostic quantities on the snapshots that
weren’t computed in the initial run. These can also be computed with
settings not used in the initial run, e.g. computing an RDF via the
-compute rdf command with a longer cutoff than was
+compute rdf command with a longer cutoff than was
used initially.
Calculate the portion of per-atom forces resulting from a subset of
the potential. E.g. compute only Coulombic forces. This can be done
diff --git a/doc/html/search.html b/doc/html/search.html
index b1adac2009..bc305b9b18 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -120,18 +120,19 @@
diff --git a/doc/html/variable.html b/doc/html/variable.html
index 7eb3382f6c..f5eb258506 100644
--- a/doc/html/variable.html
+++ b/doc/html/variable.html
@@ -1192,7 +1192,7 @@ with a leading $ sign (e.g. $x or ${abc}) versus with a leading “