diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt
index 65ae2220fe7b8c2ab37ab5aa9e9daa2e522e6c25..f4396cce7de627b41d0888a4c3ad4a197b2675d3 100644
--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@@ -454,7 +454,7 @@ NOTE: By default, for 2d systems, granular particles are still modeled
as 3d spheres, not 2d discs (circles), meaning their moment of inertia
will be the same as in 3d. If you wish to model granular particles in
2d as 2d discs, see the note on this topic in "Section
-6.2"_Section_howto.html#howto_2, where 2d simulations are disussed.
+6.2"_Section_howto.html#howto_2, where 2d simulations are discussed.
:line
diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt
index 912d371cd9451966dbe034c5cca214919e3062b6..91052888ea32f9b75f69f8a155f46cee8ae734ba 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@@ -243,7 +243,7 @@ COLLOID package :link(COLLOID),h4
[Contents:]
-Coarse-grained finite-size colloidal particles. Pair stayle and fix
+Coarse-grained finite-size colloidal particles. Pair styles and fix
wall styles for colloidal interactions. Includes the Fast Lubrication
Dynamics (FLD) method for hydrodynamic interactions, which is a
simplified approximation to Stokesian dynamics.
@@ -734,7 +734,7 @@ make lib-latte args="-b -m gfortran" # download and build in lib/latte and
Note that 3 symbolic (soft) links, "includelink" and "liblink" and
"filelink", are created in lib/latte to point into the LATTE home dir.
When LAMMPS builds in src it will use these links. You should
-also check that the Makefile.lammps file you create is apporpriate
+also check that the Makefile.lammps file you create is appropriate
for the compiler you use on your system to build LATTE.
You can then install/un-install the package and build LAMMPS in the
@@ -984,7 +984,7 @@ MSCG package :link(mscg),h4
[Contents:]
A "fix mscg"_fix_mscg.html command which can parameterize a
-Mulit-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG
+Multi-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG
library"_mscg_home.
:link(mscg_home,https://github.com/uchicago-voth/MSCG-release)
@@ -1781,7 +1781,7 @@ coarse-grained DPD-based models for energetic, reactive molecular
crystalline materials. It includes many pair styles specific to these
systems, including for reactive DPD, where each particle has internal
state for multiple species and a coupled set of chemical reaction ODEs
-are integrated each timestep. Highly accurate time intergrators for
+are integrated each timestep. Highly accurate time integrators for
isothermal, isoenergetic, isobaric and isenthalpic conditions are
included. These enable long timesteps via the Shardlow splitting
algorithm.
@@ -2231,7 +2231,7 @@ Several extensions of the the dissipative particle dynamics (DPD)
method. Specifically, energy-conserving DPD (eDPD) that can model
non-isothermal processes, many-body DPD (mDPD) for simulating
vapor-liquid coexistence, and transport DPD (tDPD) for modeling
-advection-diffuion-reaction systems. The equations of motion of these
+advection-diffusion-reaction systems. The equations of motion of these
DPD extensions are integrated through a modified velocity-Verlet (MVV)
algorithm.
@@ -2495,7 +2495,7 @@ make machine :pre
NOTE: The LAMMPS executable these steps produce is not yet functional
for a QM/MM simulation. You must also build Quantum ESPRESSO and
-create a new executable which links LAMMPS and Quanutm ESPRESSO
+create a new executable which links LAMMPS and Quantum ESPRESSO
together. These are steps 3 and 4 described in the lib/qmmm/README
file.
@@ -2554,7 +2554,7 @@ developed by the Cambridge University group.
:link(quip,https://github.com/libAtoms/QUIP)
-To use this package you must have the QUIP libAatoms library available
+To use this package you must have the QUIP libAtoms library available
on your system.
[Author:] Albert Bartok (Cambridge University)
@@ -2809,7 +2809,7 @@ USER-VTK package :link(USER-VTK),h4
A "dump vtk"_dump_vtk.html command which outputs snapshot info in the
"VTK format"_vtk, enabling visualization by "Paraview"_paraview or
-other visuzlization packages.
+other visualization packages.
:link(vtk,http://www.vtk.org)
:link(paraview,http://www.paraview.org)
diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt
index 3711342f76db8e3bba95d8fc39ab0414c32531fd..7761f77233df4b8adff3d0bf570ffaeb98ebb00f 100644
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@@ -79,7 +79,7 @@ This section has the following sub-sections:
Read this first :h5,link(start_2_1)
-If you want to avoid building LAMMPS yourself, read the preceeding
+If you want to avoid building LAMMPS yourself, read the preceding
section about options available for downloading and installing
executables. Details are discussed on the "download"_download page.
@@ -252,7 +252,7 @@ re-compile, after typing "make clean" (which will describe different
clean options).
The LMP_INC variable is used to include options that turn on ifdefs
-within the LAMMPS code. The options that are currently recogized are:
+within the LAMMPS code. The options that are currently recognized are:
-DLAMMPS_GZIP
-DLAMMPS_JPEG
@@ -363,7 +363,7 @@ installed on your platform. If MPI is installed on your system in the
usual place (under /usr/local), you also may not need to specify these
3 variables, assuming /usr/local is in your path. On some large
parallel machines which use "modules" for their compile/link
-environements, you may simply need to include the correct module in
+environments, you may simply need to include the correct module in
your build environment, before building LAMMPS. Or the parallel
machine may have a vendor-provided MPI which the compiler has no
trouble finding.
@@ -431,7 +431,7 @@ use the KISS library described above.
You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables,
so the compiler and linker can find the needed FFT header and library
files. Note that on some large parallel machines which use "modules"
-for their compile/link environements, you may simply need to include
+for their compile/link environments, you may simply need to include
the correct module in your build environment. Or the parallel machine
may have a vendor-provided FFT library which the compiler has no
trouble finding. See the src/MAKE/OPTIONS/Makefile.fftw file for an
@@ -470,7 +470,7 @@ precision.
The FFT_INC variable also allows for a -DFFT_SINGLE setting that will
use single-precision FFTs with PPPM, which can speed-up long-range
-calulations, particularly in parallel or on GPUs. Fourier transform
+calculations, particularly in parallel or on GPUs. Fourier transform
and related PPPM operations are somewhat insensitive to floating point
truncation errors and thus do not always need to be performed in
double precision. Using the -DFFT_SINGLE setting trades off a little
@@ -483,7 +483,7 @@ with support for single-precision, as explained above. For FFTW3 you
also need to include -lfftw3f with the FFT_LIB setting, in addition to
-lfftw3. For FFTW2, you also need to specify -DFFT_SIZE with the
FFT_INC setting and -lsfftw with the FFT_LIB setting (in place of
--lfftw). Similarly, if FFTW2 has been preinstalled with an explicit
+-lfftw). Similarly, if FFTW2 has been pre-installed with an explicit
double-precision library (libdfftw.a and not the default libfftw.a),
then you can specify -DFFT_SIZE (and not -DFFT_SINGLE), and specify
-ldfftw to use double-precision FFTs.
@@ -714,7 +714,7 @@ list various make commands that can be used to manage packages.
If you use a command in a LAMMPS input script that is part of a
package, you must have built LAMMPS with that package, else you will
get an error that the style is invalid or the command is unknown.
-Every command's doc page specfies if it is part of a package. You can
+Every command's doc page specifies if it is part of a package. You can
type
lmp_machine -h :pre
@@ -859,7 +859,7 @@ details for each package.
[External libraries:]
Packages in the tables "Section 4"_Section_packages.html with an "ext"
-in the last column link to exernal libraries whose source code is not
+in the last column link to external libraries whose source code is not
included with LAMMPS. You must first download and install the library
before building LAMMPS with that package installed. E.g. the voronoi
package links to the freely available "Voro++ library"_voro_home2. You
@@ -963,7 +963,7 @@ src/MAKE/Makefile.foo and perform the build in the directory
Obj_shared_foo. This is so that each file can be compiled with the
-fPIC flag which is required for inclusion in a shared library. The
build will create the file liblammps_foo.so which another application
-can link to dyamically. It will also create a soft link liblammps.so,
+can link to dynamically. It will also create a soft link liblammps.so,
which will point to the most recently built shared library. This is
the file the Python wrapper loads by default.
@@ -1329,8 +1329,8 @@ LAMMPS is compiled with CUDA=yes.
numa Nm :pre
This option is only relevant when using pthreads with hwloc support.
-In this case Nm defines the number of NUMA regions (typicaly sockets)
-on a node which will be utilizied by a single MPI rank. By default Nm
+In this case Nm defines the number of NUMA regions (typically sockets)
+on a node which will be utilized by a single MPI rank. By default Nm
= 1. If this option is used the total number of worker-threads per
MPI rank is threads*numa. Currently it is always almost better to
assign at least one MPI rank per NUMA region, and leave numa set to
@@ -1394,7 +1394,7 @@ replica runs on on one or a few processors. Note that with MPI
installed on a machine (e.g. your desktop), you can run on more
(virtual) processors than you have physical processors.
-To run multiple independent simulatoins from one input script, using
+To run multiple independent simulations from one input script, using
multiple partitions, see "Section 6.4"_Section_howto.html#howto_4
of the manual. World- and universe-style "variables"_variable.html
are useful in this context.
@@ -1673,7 +1673,7 @@ The first section provides a global loop timing summary. The {loop time}
is the total wall time for the section. The {Performance} line is
provided for convenience to help predicting the number of loop
continuations required and for comparing performance with other,
-similar MD codes. The {CPU use} line provides the CPU utilzation per
+similar MD codes. The {CPU use} line provides the CPU utilization per
MPI task; it should be close to 100% times the number of OpenMP
threads (or 1 of no OpenMP). Lower numbers correspond to delays due
to file I/O or insufficient thread utilization.
diff --git a/doc/src/accelerate_intel.txt b/doc/src/accelerate_intel.txt
index aaa38d7de28a218d85952dfb5de3dcb6c2de1095..71f5185b154f9f832d0ab5b92bd3d2e49f25df2f 100644
--- a/doc/src/accelerate_intel.txt
+++ b/doc/src/accelerate_intel.txt
@@ -78,7 +78,7 @@ order of operations compared to LAMMPS without acceleration:
Neighbor lists can be created in a different order :ulb,l
Bins used for sorting atoms can be oriented differently :l
The default stencil order for PPPM is 7. By default, LAMMPS will
-calculate other PPPM parameters to fit the desired acuracy with
+calculate other PPPM parameters to fit the desired accuracy with
this order :l
The {newton} setting applies to all atoms, not just atoms shared
between MPI tasks :l
diff --git a/doc/src/compute_cluster_atom.txt b/doc/src/compute_cluster_atom.txt
index 0aa38ae5903a61a11acb0186cf868f52173e6a56..94113de5f2422a2628acc9f5bcb22a4940eefe21 100644
--- a/doc/src/compute_cluster_atom.txt
+++ b/doc/src/compute_cluster_atom.txt
@@ -28,7 +28,7 @@ compute 1 all aggregate/atom 3.5 :pre
[Description:]
-Define a computation that assigns each atom a cluster, fragement,
+Define a computation that assigns each atom a cluster, fragment,
or aggregate ID.
A cluster is defined as a set of atoms, each of which is within the
@@ -53,7 +53,7 @@ like micelles.
Only atoms in the compute group are clustered and assigned cluster
IDs. Atoms not in the compute group are assigned a cluster ID = 0.
For fragments, only bonds where [both] atoms of the bond are included
-in the compute group are assigned to fragments, so that only fragmets
+in the compute group are assigned to fragments, so that only fragments
are detected where [all] atoms are in the compute group. Thus atoms
may be included in the compute group, yes still have a fragment ID of 0.
diff --git a/doc/src/compute_pressure_uef.txt b/doc/src/compute_pressure_uef.txt
index 065fc044417601a052d0d9fd060ababbf9aa405c..5b252b369dd012691e62a3dcf267c6e00cca11c3 100644
--- a/doc/src/compute_pressure_uef.txt
+++ b/doc/src/compute_pressure_uef.txt
@@ -25,15 +25,15 @@ compute 2 all pressure/uef my_temp_uef virial :pre
[Description:]
-This command is used to compute the pressure tensor in
+This command is used to compute the pressure tensor in
the reference frame of the applied flow field when
-"fix nvt/uef"_fix_nh_uef.html" or
-"fix npt/uef"_fix_nh_uef.html" is used.
+"fix nvt/uef"_fix_nh_uef.html" or
+"fix npt/uef"_fix_nh_uef.html" is used.
It is not necessary to use this command to compute the scalar
value of the pressure. A "compute pressure"_compute_pressure.html
may be used for that purpose.
-The keywords and output information are documented in
+The keywords and output information are documented in
"compute_pressure"_compute_pressure.html.
[Restrictions:]
@@ -46,8 +46,8 @@ This command can only be used when "fix nvt/uef"_fix_nh_uef.html
or "fix npt/uef"_fix_nh_uef.html is active.
The kinetic contribution to the pressure tensor
-will be accurate only when
-the compute specificed by {temp-ID} is a
+will be accurate only when
+the compute specified by {temp-ID} is a
"compute temp/uef"_compute_temp_uef.html.
[Related commands:]
diff --git a/doc/src/fix_halt.txt b/doc/src/fix_halt.txt
index ced489a54c5d58d65cefdfae16929f03e104edc8..08043eb5fb76659bf851d59444eeec56548b11cd 100644
--- a/doc/src/fix_halt.txt
+++ b/doc/src/fix_halt.txt
@@ -64,10 +64,10 @@ not performed once every {N} steps by this command. Instead it is
performed (typically) only a small number of times and the elapsed
times are used to predict when the end-of-the-run will be. Both of
these attributes can be useful when performing benchmark calculations
-for a desired length of time with minmimal overhead. For example, if
+for a desired length of time with minimal overhead. For example, if
a run is performing 1000s of timesteps/sec, the overhead for syncing
the timer frequently across a large number of processors may be
-non-negligble.
+non-negligible.
Equal-style variables evaluate to a numeric value. See the
"variable"_variable.html command for a description. They calculate
@@ -125,7 +125,7 @@ to the screen and logfile when the halt condition is triggered. If
{message} is set to yes, a one line message with the values that
triggered the halt is printed. If {message} is set to no, no message
is printed; the run simply exits. The latter may be desirable for
-post-processing tools that extract thermodyanmic information from log
+post-processing tools that extract thermodynamic information from log
files.
[Restart, fix_modify, output, run start/stop, minimize info:]
diff --git a/doc/src/fix_mvv_dpd.txt b/doc/src/fix_mvv_dpd.txt
index 3c1c1a7cba5aeae31aa496dbd3b2d028770fefc1..fb3c6fe8885ce8a23b58897cd05a94269a20e5d7 100644
--- a/doc/src/fix_mvv_dpd.txt
+++ b/doc/src/fix_mvv_dpd.txt
@@ -44,7 +44,7 @@ the velocity for the force evaluation:
where the parameter <font size="4">λ</font> depends on the
specific choice of DPD parameters, and needs to be tuned on a
-case-by-case basis. Specification of a {lambda} value is opttional.
+case-by-case basis. Specification of a {lambda} value is optional.
If specified, the setting must be from 0.0 to 1.0. If not specified,
a default value of 0.5 is used, which effectively reproduces the
standard velocity-Verlet (VV) scheme. For more details, see
diff --git a/doc/src/fix_neb.txt b/doc/src/fix_neb.txt
index 73b3e312665785ed7420f9b8ceb557e95be61bc4..0bc43a35cbf2b0c2f2a5e5e46e49eb075f1bfde0 100644
--- a/doc/src/fix_neb.txt
+++ b/doc/src/fix_neb.txt
@@ -113,9 +113,9 @@ keeping the replicas equally spaced.
:line
-The keyword {perp} specifies if and how a perpendicual nudging force
+The keyword {perp} specifies if and how a perpendicular nudging force
is computed. It adds a spring force perpendicular to the path in
-order to prevent the path from becoming too kinky. It can
+order to prevent the path from becoming too strongly kinked. It can
significantly improve the convergence of the NEB calculation when the
resolution is poor. I.e. when few replicas are used; see
"(Maras)"_#Maras1 for details.
diff --git a/doc/src/neb.txt b/doc/src/neb.txt
index 144fe8bdefcf350ad0d8a4170b2d443f67904f0f..56f075c301046d40a0e940045225d5c3019458e9 100644
--- a/doc/src/neb.txt
+++ b/doc/src/neb.txt
@@ -322,9 +322,9 @@ the fix neb command.
The forward (reverse) energy barrier is the potential energy of the
highest replica minus the energy of the first (last) replica.
-Supplementary informations for all replicas can be printed out to the
-screen and master log.lammps file by adding the verbose keyword. These
-informations include the following. The "path angle" (pathangle) for
+Supplementary information for all replicas can be printed out to the
+screen and master log.lammps file by adding the verbose keyword. This
+information include the following. The "path angle" (pathangle) for
the replica i which is the angle between the 3N-length vectors (Ri-1 -
Ri) and (Ri+1 - Ri) (where Ri is the atomic coordinates of replica
i). A "path angle" of 180 indicates that replicas i-1, i and i+1 are
@@ -339,8 +339,8 @@ energy gradient of image i. ReplicaForce is the two-norm of the
3N-length force vector (including nudging forces) for replica i.
MaxAtomForce is the maximum force component of any atom in replica i.
-When a NEB calculation does not converge properly, these suplementary
-informations can help understanding what is going wrong. For instance
+When a NEB calculation does not converge properly, the suplementary
+information can help understanding what is going wrong. For instance
when the path angle becomes accute the definition of tangent used in
the NEB calculation is questionable and the NEB cannot may diverge
"(Maras)"_#Maras2.