fix some spelling errors in the manual

doc/src/Build_basics.txt

@@ -292,7 +292,7 @@ This will create a lammps/doc/html dir with the HTML doc pages so that
 you can browse them locally on your system.  Type "make" from the
 lammps/doc dir to see other options.
 
-NOTE: You can also download a tarball of the documention for the
+NOTE: You can also download a tarball of the documentation for the
 current LAMMPS version (HTML and PDF files), from the website
 "download page"_http://lammps.sandia.gov/download.html.
 

doc/src/Build_extras.txt

@@ -732,7 +732,7 @@ can be shared across multiple MD packages and can be updated, for as
 long as the shared PLUMED library is ABI-compatible. The third linkage
 mode is "runtime" which allows to switch the PLUMED kernel at runtime
 between different variants through setting the PLUMED_KERNEL environment
-varible, which has to point to the location of the libplumedKernel.so
+variable, which has to point to the location of the libplumedKernel.so
 dynamical shared object, which is then loaded at runtime. This is
 particularly convenient for doing PLUMED development and comparing
 multiple PLUMED versions without having to recompile the hosting MD

doc/src/Howto_client_server.txt

@@ -64,7 +64,7 @@ client or server.
 "server mc"_server_mc.html = LAMMPS is a server for computing a Monte Carlo energy :ul
 
 The server doc files give details of the message protocols
-for data that is exchanged bewteen the client and server.
+for data that is exchanged between the client and server.
 
 These example directories illustrate how to use LAMMPS as either a
 client or server code:

doc/src/Install_git.txt

@@ -45,7 +45,7 @@ git clone -b unstable https://github.com/lammps/lammps.git mylammps :pre
 where "mylammps" is the name of the directory you wish to create on
 your machine and "unstable" is one of the 3 branches listed above.
 (Note that you actually download all 3 branches; you can switch
-between them at any time using "git checkout <branchname>".)
+between them at any time using "git checkout <branch name>".)
 
 Once the command completes, your directory will contain the same files
 as if you unpacked a current LAMMPS tarball, with two exceptions:

doc/src/Speed_kokkos.txt

@@ -127,21 +127,21 @@ mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half c
 If the "newton"_newton.html command is used in the input
 script, it can also override the Newton flag defaults.
 
-For half neighbor lists and OpenMP, the KOKKOS package uses data 
-duplication (i.e. thread-private arrays) by default to avoid 
-thread-level write conflicts in the force arrays (and other data 
-structures as necessary). Data duplication is typically fastest for 
-small numbers of threads (i.e. 8 or less) but does increase memory 
-footprint and is not scalable to large numbers of threads. An 
-alternative to data duplication is to use thread-level atomics, which 
-don't require duplication. The use of atomics can be forced by compiling 
-with the "-DLMP_KOKKOS_USE_ATOMICS" compile switch. Most but not all 
-Kokkos-enabled pair_styles support data duplication. Alternatively, full 
-neighbor lists avoid the need for duplication or atomics but require 
-more compute operations per atom. When using the Kokkos Serial backend 
-or the OpenMP backend with a single thread, no duplication or atomics are 
-used. For CUDA and half neighbor lists, the KOKKOS package always uses 
-atomics.
+For half neighbor lists and OpenMP, the KOKKOS package uses data
+duplication (i.e. thread-private arrays) by default to avoid
+thread-level write conflicts in the force arrays (and other data
+structures as necessary). Data duplication is typically fastest for
+small numbers of threads (i.e. 8 or less) but does increase memory
+footprint and is not scalable to large numbers of threads. An
+alternative to data duplication is to use thread-level atomic operations
+which do not require data duplication. The use of atomic operations can
+be enforced by compiling LAMMPS with the "-DLMP_KOKKOS_USE_ATOMICS"
+pre-processor flag. Most but not all Kokkos-enabled pair_styles support
+data duplication. Alternatively, full neighbor lists avoid the need for
+duplication or atomic operations but require more compute operations per
+atom.  When using the Kokkos Serial backend or the OpenMP backend with
+a single thread, no duplication or atomic operations are used. For CUDA
+and half neighbor lists, the KOKKOS package always uses atomic operations.
 
 [Core and Thread Affinity:]
 

doc/src/Speed_omp.txt

@@ -131,7 +131,7 @@ effect worsens when using an increasing number of nodes. :l
 The system has a spatially inhomogeneous particle density which does
 not map well to the "domain decomposition scheme"_processors.html or
 "load-balancing"_balance.html options that LAMMPS provides.  This is
-because multi-threading achives parallelism over the number of
+because multi-threading achieves parallelism over the number of
 particles, not via their distribution in space. :l
 
 A machine is being used in "capability mode", i.e. near the point
@@ -143,7 +143,7 @@ the performance-limiting factor.  Using multi-threading allows less
 MPI tasks to be invoked and can speed-up the long-range solver, while
 increasing overall performance by parallelizing the pairwise and
 bonded calculations via OpenMP.  Likewise additional speedup can be
-sometimes be achived by increasing the length of the Coulombic cutoff
+sometimes be achieved by increasing the length of the Coulombic cutoff
 and thus reducing the work done by the long-range solver.  Using the
 "run_style verlet/split"_run_style.html command, which is compatible
 with the USER-OMP package, is an alternative way to reduce the number

doc/src/compute_property_atom.txt

@@ -19,7 +19,7 @@ input = one or more atom attributes :l
                         x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
                         vx, vy, vz, fx, fy, fz,
                         q, mux, muy, muz, mu,
-			sp, spx, spy, spz, fmx, fmy, fmz,
+                        sp, spx, spy, spz, fmx, fmy, fmz,
                         radius, diameter, omegax, omegay, omegaz,
                         angmomx, angmomy, angmomz,
                         shapex,shapey, shapez,
@@ -158,8 +158,8 @@ corresponding attribute is in, e.g. velocity units for vx, charge
 units for q, etc.
 
 For the spin quantities, sp is in the units of the Bohr magneton, spx,
-spy, and spz are adimensional quantities, and fmx, fmy and fmz are 
-given in rad.THz. 
+spy, and spz are unitless quantities, and fmx, fmy and fmz are given
+in rad/THz.
 
 [Restrictions:] none
 

doc/src/compute_ptm_atom.txt

@@ -80,7 +80,7 @@ too frequently or to have multiple compute/dump commands, each with a
 
 [Output info:]
 
-This compute calculates a per-atom arry, which can be accessed by
+This compute calculates a per-atom array, which can be accessed by
 any command that uses per-atom values from a compute as input.  See
 the "Howto output"_Howto_output.html doc page for an overview of
 LAMMPS output options.

doc/src/fix_plumed.txt

@@ -65,11 +65,12 @@ PLUMED input file.  Instructions as to what should be included in a
 plumed input file can be found in the "documentation for
 PLUMED"_plumeddocs
 
-The {outfile} keyword allows the user to specify the name of a file on
-which to output the PLUMED log.  This log file normally just parrots the
-information that is contained in the input file.  The names of the files
-on which the results from the various analyses that have been performed
-using PLUMED will be specified by the user in the PLUMED input file.
+The {outfile} keyword allows the user to specify the name of a file in
+which to output the PLUMED log.  This log file normally just repeats the
+information that is contained in the input file to confirm it was
+correctly read and parsed.  The names of the files in which the results
+are stored from the various analysis options performed by PLUMED will
+be specified by the user in the PLUMED input file.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 

doc/src/fix_rigid.txt

@@ -247,7 +247,7 @@ of atoms that form rigid bodies.  An integer vector defined by the
 "fix property/atom"_fix_property_atom.html command can be used.  Or an
 "atom-style or atomfile-style variable"_variable.html can be used; the
 floating-point value produced by the variable is rounded to an
-integer.  As with bondstyle {molecule}, each set of atoms in the fix
+integer.  As with bodystyle {molecule}, each set of atoms in the fix
 groups with the same integer value is treated as a different rigid
 body.  Since fix property/atom vectors and atom-style variables
 produce values for all atoms, you should be careful to use a fix group

doc/src/fix_rigid_meso.txt

@@ -128,7 +128,7 @@ of particles that form rigid bodies.  An integer vector defined by the
 "fix property/atom"_fix_property_atom.html command can be used.  Or an
 "atom-style or atomfile-style variable"_variable.html can be used; the
 floating-point value produced by the variable is rounded to an
-integer.  As with bondstyle {molecule}, each set of particles in the fix
+integer.  As with bodystyle {molecule}, each set of particles in the fix
 groups with the same integer value is treated as a different rigid
 body.  Since fix property/atom vectors and atom-style variables
 produce values for all particles, you should be careful to use a fix group

doc/src/hyper.txt

@@ -131,7 +131,7 @@ system (coordinates and velocities) is restored, and dynamics continue.
 At the end of the hyper run, a variety of statistics are output to the
 screen and logfile.  These include info relevant to both global and
 local hyperdynamics, such as the number of events and the elapsed
-hyper time (acclerated time), And it includes info specific to one or
+hyper time (accelerated time), And it includes info specific to one or
 the other, depending on which style of fix was specified by {fix-ID}.
 
 :line

doc/src/kspace_modify.txt

@@ -326,7 +326,7 @@ field_rel = relative accuracy in electric field :ul
 
 The values with suffix _rel indicate the tolerance is a relative
 tolerance; the other values impose an absolute tolerance on the given
-quantity. Absoulte tolerance in this case means, that for a given
+quantity. Absolute tolerance in this case means, that for a given
 quantity q and a given absolute tolerance of t_a the result should
 be between q-t_a and q+t_a. For a relative tolerance t_r the relative 
 error should not be greater than t_r, i.e. abs(1 - (result/q)) < t_r. 

doc/src/message.txt

@@ -22,7 +22,7 @@ mode = {file} or {zmq} or {mpi/one} or {mpi/two} :l
     socket-ID for server = *:5555, see description below
   {mpi/one} arg = none
   {mpi/two} arg = filename
-    filename = file used to establish communication bewteen 2 MPI jobs :pre
+    filename = file used to establish communication between 2 MPI jobs :pre
 :ule
 
 [Examples:]

doc/src/neb.txt

@@ -340,7 +340,7 @@ MaxAtomForce is the maximum force component of any atom in replica i.
 
 When a NEB calculation does not converge properly, the supplementary
 information can help understanding what is going wrong. For instance
-when the path angle becomes accute, the definition of tangent used in
+when the path angle becomes acute, the definition of tangent used in
 the NEB calculation is questionable and the NEB cannot may diverge
 "(Maras)"_#Maras2.
 

doc/src/rerun.txt

@@ -150,8 +150,8 @@ indent"_fix_indent.html and "fix langevin"_fix_langevin.html.  So you
 should think carefully as to whether that makes sense for the manner
 in which you are reprocessing the dump snapshots.
 
-If you only want the rerun script to perform analyses that do not
-involve pair interactions, such as use compute msd to calculated
+If you only want the rerun script to perform an analysis that does
+not involve pair interactions, such as use compute msd to calculated
 displacements over time, you do not need to define a "pair
 style"_pair_style.html, which may also mean neighbor lists will not
 need to be calculated which saves time.  The "comm_modify