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Third batch of spelling fixes in manual

This commit is contained in:
Richard Berger 2017-03-07 00:51:31 -05:00
parent 32708860a9
commit 007f3c66a0
138 changed files with 254 additions and 250 deletions
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4
doc/src/2001/input_commands.html
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@ -464,7 +464,7 @@ the angletype option can only be assigned to a "fix style" of "shake",
entirely rigid (e.g. water)
the angletype option enables an additional check when SHAKE constraints
are computed: if a cluster is of size 3 and both bonds in
the cluster are of a bondtype specified by the 2nd paramter of
the cluster are of a bondtype specified by the 2nd parameter of
angletype, then the cluster is SHAKEn with an additional angle
constraint that makes it rigid, using the equilibrium angle appropriate
to the specified angletype
@ -1566,7 +1566,7 @@ mesh dimensions that are power-of-two are fastest for FFTs, but any sizes
can be used that are supported by native machine libraries
this command is optional - if not used, a default
mesh size will be chosen to satisfy accuracy criterion - if used, the
specifed mesh size will override the default
specified mesh size will override the default
</PRE>
<HR>
<H3>

2
doc/src/99/basics.html
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@ -201,7 +201,7 @@ The tools directory also has a F77 program called setup_chain.f
(compile and link with print.c) which can be used to generate random
initial polymer configurations for bead-spring models like those used
in examples/polymer. It uses an input polymer definition file (see
examples/polymer for two sample def files) that specfies how many
examples/polymer for two sample def files) that specifies how many
chains of what length, a random number seed, etc.</P>
</BODY>
</HTML>

2
doc/src/99/crib.html
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@ -40,7 +40,7 @@ Note: this file is somewhat out-of-date for LAMMPS 99.</P>
<LI>
maxtype = max # of atom types
<LI>
maxbond = max # of bonds to compute on one procesor
maxbond = max # of bonds to compute on one processor
<LI>
maxangle = max # of angles to compute on one processor
<LI>

2
doc/src/99/input_commands.html
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@ -1124,7 +1124,7 @@ mesh dimensions that are power-of-two are fastest for FFTs, but any size
can be used that are supported by native machine libraries
this command is optional - if not used, a default
mesh size will be chosen to satisfy accuracy criterion - if used, the
specifed mesh size will override the default
specified mesh size will override the default
Default = none
</PRE>

8
doc/src/Section_errors.txt
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@ -7552,7 +7552,7 @@ Self-explanatory. :dd
Self-explanatory. :dd
{Molecule toplogy/atom exceeds system topology/atom} :dt
{Molecule topology/atom exceeds system topology/atom} :dt
The number of bonds, angles, etc per-atom in the molecule exceeds the
system setting. See the create_box command for how to specify these
@ -10707,7 +10707,7 @@ Self-explanatory. :dd
{Variable has circular dependency} :dt
A circular dependency is when variable "a" in used by variable "b" and
variable "b" is also used by varaible "a". Circular dependencies with
variable "b" is also used by variable "a". Circular dependencies with
longer chains of dependence are also not allowed. :dd
{Variable name between brackets must be alphanumeric or underscore characters} :dt
@ -11452,7 +11452,7 @@ i.e. the first molecule in the template. :dd
{Molecule template for fix shake has multiple molecules} :dt
The fix shake command will only recoginze molecules of a single
The fix shake command will only recognize molecules of a single
type, i.e. the first molecule in the template. :dd
{More than one compute centro/atom} :dt
@ -11589,7 +11589,7 @@ This may not be what you intended. :dd
{One or more dynamic groups may not be updated at correct point in timestep} :dt
If there are other fixes that act immediately after the intitial stage
If there are other fixes that act immediately after the initial stage
of time integration within a timestep (i.e. after atoms move), then
the command that sets up the dynamic group should appear after those
fixes. This will insure that dynamic group assignments are made

2
doc/src/Section_history.txt
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@ -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
possible bugs and how they are resoved.
possible bugs and how they are resolved.
As an alternative to using GitHub, you may e-mail the
"core developers"_http://lammps.sandia.gov/authors.html or send

24
doc/src/Section_howto.txt
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@ -573,7 +573,7 @@ LJ epsilon of O-O = 0.16275
LJ sigma of O-O = 3.16435
LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
Note that the when using the TIP4P pair style, the neighobr list
Note that the when using the TIP4P pair style, the neighbor list
cutoff for Coulomb interactions is effectively extended by a distance
2 * (OM distance), to account for the offset distance of the
fictitious charges on O atoms in water molecules. Thus it is
@ -863,7 +863,7 @@ boundary conditions in specific dimensions. See the command doc pages
for details.
The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
time the simluation box is created. This happens in one of 3 ways.
time the simulation box is created. This happens in one of 3 ways.
If the "create_box"_create_box.html command is used with a region of
style {prism}, then a triclinic box is setup. See the
"region"_region.html command for details. If the
@ -1525,7 +1525,7 @@ Variables that generate values to output :h5,link(variable)
"Variables"_variable.html defined in an input script can store one or
more strings. But equal-style, vector-style, and atom-style or
atomfile-style variables generate a global scalar value, global vector
or values, or a per-atom vector, resepctively, when accessed. The
or values, or a per-atom vector, respectively, when accessed. The
formulas used to define these variables can contain references to the
thermodynamic keywords and to global and per-atom data generated by
computes, fixes, and other variables. The values generated by
@ -1585,7 +1585,7 @@ Temperature is computed as kinetic energy divided by some number of
degrees of freedom (and the Boltzmann constant). Since kinetic energy
is a function of particle velocity, there is often a need to
distinguish between a particle's advection velocity (due to some
aggregate motiion of particles) and its thermal velocity. The sum of
aggregate motion of particles) and its thermal velocity. The sum of
the two is the particle's total velocity, but the latter is often what
is wanted to compute a temperature.
@ -1888,7 +1888,7 @@ instances of LAMMPS to perform different calculations.
The lammps_open_no_mpi() function is similar except that no MPI
communicator is passed from the caller. Instead, MPI_COMM_WORLD is
used to instantiate LAMMPS, and MPI is initialzed if necessary.
used to instantiate LAMMPS, and MPI is initialized if necessary.
The lammps_close() function is used to shut down an instance of LAMMPS
and free all its memory.
@ -1976,7 +1976,7 @@ The lammps_get_natoms() function returns the total number of atoms in
the system and can be used by the caller to allocate space for the
lammps_gather_atoms() and lammps_scatter_atoms() functions. The
gather function collects atom info of the requested type (atom coords,
types, forces, etc) from all procsesors, orders them by atom ID, and
types, forces, etc) from all processors, orders them by atom ID, and
returns a full list to each calling processor. The scatter function
does the inverse. It distributes the same kinds of values,
passed by the caller, to each atom owned by individual processors.
@ -2268,7 +2268,7 @@ atoms with same local defect structure | chunk ID = output of "compute centro/at
Note that chunk IDs are integer values, so for atom properties or
computes that produce a floating point value, they will be truncated
to an integer. You could also use the compute in a variable that
scales the floating point value to spread it across multiple intergers.
scales the floating point value to spread it across multiple integers.
Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins =
pencils, 3d bins = boxes, spherical bins, cylindrical bins.
@ -2444,7 +2444,7 @@ performance. This approach provides a fast initialization of the
simulation. However, it is sensitive to errors: A combination of
parameters that will perform well for one system might result in
far-from-optimal conditions for other simulations. For example,
parametes that provide accurate and fast computations for
parameters that provide accurate and fast computations for
all-atomistic force fields can provide insufficient accuracy or
united-atomistic force fields (which is related to that the latter
typically have larger dispersion coefficients).
@ -2551,7 +2551,7 @@ this is done by "fix qeq/dynamic"_fix_qeq.html, and for the
charge-on-spring models by the methods outlined in the next two
sections. The assignment of masses to the additional degrees of
freedom can lead to unphysical trajectories if care is not exerted in
choosing the parameters of the poarizable models and the simulation
choosing the parameters of the polarizable models and the simulation
conditions.
In the core-shell model the vibration of the shells is kept faster
@ -2727,12 +2727,12 @@ If "compute temp/cs"_compute_temp_cs.html is used, the decoupled
relative motion of the core and the shell should in theory be
stable. However numerical fluctuation can introduce a small
momentum to the system, which is noticable over long trajectories.
Therefore it is recomendable to use the "fix
Therefore it is recommendable to use the "fix
momentum"_fix_momentum.html command in combination with "compute
temp/cs"_compute_temp_cs.html when equilibrating the system to
prevent any drift.
When intializing the velocities of a system with core/shell pairs, it
When initializing the velocities of a system with core/shell pairs, it
is also desirable to not introduce energy into the relative motion of
the core/shell particles, but only assign a center-of-mass velocity to
the pairs. This can be done by using the {bias} keyword of the
@ -2808,7 +2808,7 @@ CS-Info # header of additional section :pre
6.27 Drude induced dipoles :link(howto_27),h4
The thermalized Drude model, similarly to the "core-shell"_#howto_26
model, representes induced dipoles by a pair of charges (the core atom
model, represents induced dipoles by a pair of charges (the core atom
and the Drude particle) connected by a harmonic spring. The Drude
model has a number of features aimed at its use in molecular systems
("Lamoureux and Roux"_#howto-Lamoureux):

6
doc/src/Section_modify.txt
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@ -369,7 +369,7 @@ pre_force_respa: same as pre_force, but for rRESPA (optional)
post_force_respa: same as post_force, but for rRESPA (optional)
final_integrate_respa: same as final_integrate, but for rRESPA (optional)
min_pre_force: called after pair & molecular forces are computed in minimizer (optional)
min_post_force: called after pair & molecular forces are computed and communicated in minmizer (optional)
min_post_force: called after pair & molecular forces are computed and communicated in minimizer (optional)
min_store: store extra data for linesearch based minimization on a LIFO stack (optional)
min_pushstore: push the minimization LIFO stack one element down (optional)
min_popstore: pop the minimization LIFO stack one element up (optional)
@ -785,10 +785,10 @@ file for how to format the cite itself. The "Restrictions" section of
the doc page should indicate that your command is only available if
LAMMPS is built with the appropriate USER-MISC or USER-FOO package.
See other user package doc files for examples of how to do this. The
prerequiste for building the HTML format files are Python 3.x and
prerequisite for building the HTML format files are Python 3.x and
virtualenv, the requirement for generating the PDF format manual
is the "htmldoc"_http://www.htmldoc.org/ software. Please run at least
"make html" and carefully inspect and proofread the resuling HTML format
"make html" and carefully inspect and proofread the resulting HTML format
doc page before submitting your code. :l
For a new package (or even a single command) you should include one or

10
doc/src/Section_packages.txt
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@ -94,7 +94,7 @@ Package, Description, Author(s), Doc page, Example, Library
:tb(ea=c)
The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
responsible for creating and maintaining the package.
(1) The COLLOID package includes Fast Lubrication Dynamics pair styles
which were created by Amit Kumar and Michael Bybee from Jonathan
@ -955,8 +955,8 @@ multi-replica simulations in LAMMPS. Multi-replica methods included
in the package are nudged elastic band (NEB), parallel replica
dynamics (PRD), temperature accelerated dynamics (TAD), parallel
tempering, and a verlet/split algorithm for performing long-range
Coulombics on one set of processors, and the remainded of the force
field calcalation on another set.
Coulombics on one set of processors, and the remainder of the force
field calculation on another set.
To install via make or Make.py:
@ -1176,7 +1176,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
:link(VMD,http://www.ks.uiuc.edu/Research/vmd)
The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
responsible for creating and maintaining the package.
(1) The ATC package was created by Reese Jones, Jeremy Templeton, and
Jon Zimmerman (Sandia).
@ -1778,7 +1778,7 @@ particularly with respect to the charge equilibration calculation. It
should also be easier to build and use since there are no complicating
issues with Fortran memory allocation or linking to a Fortran library.
For technical details about this implemention of ReaxFF, see
For technical details about this implementation of ReaxFF, see
this paper:
Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods

2
doc/src/Section_perf.txt
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@ -69,7 +69,7 @@ bench/in.lj input script.
For all the benchmarks, a useful metric is the CPU cost per atom per
timestep. Since performance scales roughly linearly with problem size
and timesteps for all LAMMPS models (i.e. inteatomic or coarse-grained
and timesteps for all LAMMPS models (i.e. interatomic or coarse-grained
potentials), the run time of any problem using the same model (atom
style, force field, cutoff, etc) can then be estimated.

12
doc/src/Section_python.txt
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@ -97,7 +97,7 @@ current LAMMPS library interface and how to call them from Python.
Section 11.8 gives some examples of coupling LAMMPS to other tools via
Python. For example, LAMMPS can easily be coupled to a GUI or other
visualization tools that display graphs or animations in real time as
LAMMPS runs. Examples of such scripts are inlcluded in the python
LAMMPS runs. Examples of such scripts are included in the python
directory.
Two advantages of using Python to run LAMMPS are how concise the
@ -177,7 +177,7 @@ of Python and your machine to successfully build LAMMPS. See the
lib/python/README file for more info.
If you want to write Python code with callbacks to LAMMPS, then you
must also follow the steps overviewed in the preceeding section (11.1)
must also follow the steps overviewed in the preceding section (11.1)
for running LAMMPS from Python. I.e. you must build LAMMPS as a
shared library and insure that Python can find the python/lammps.py
file and the shared library.
@ -325,7 +325,7 @@ sudo python setup.py install :pre
Again, the "sudo" is only needed if required to copy PyPar files into
your Python distribution's site-packages directory.
If you have successully installed PyPar, you should be able to run
If you have successfully installed PyPar, you should be able to run
Python and type
import pypar :pre
@ -369,7 +369,7 @@ user privilege into the user local directory type
python setup.py install --user :pre
If you have successully installed mpi4py, you should be able to run
If you have successfully installed mpi4py, you should be able to run
Python and type
from mpi4py import MPI :pre
@ -610,7 +610,7 @@ lmp = lammps() :pre
create an instance of LAMMPS, wrapped in a Python class by the lammps
Python module, and return an instance of the Python class as lmp. It
is used to make all subequent calls to the LAMMPS library.
is used to make all subsequent calls to the LAMMPS library.
Additional arguments to lammps() can be used to tell Python the name
of the shared library to load or to pass arguments to the LAMMPS
@ -774,7 +774,7 @@ demo.py, invoke various LAMMPS library interface routines,
simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp,
split.py, same as simple.py but running in parallel on a subset of procs,
gui.py, GUI go/stop/temperature-slider to control LAMMPS,
plot.py, real-time temeperature plot with GnuPlot via Pizza.py,
plot.py, real-time temperature plot with GnuPlot via Pizza.py,
viz_tool.py, real-time viz via some viz package,
vizplotgui_tool.py, combination of viz_tool.py and plot.py and gui.py :tb(c=2)

14
doc/src/Section_start.txt
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@ -80,7 +80,7 @@ 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.
@ -251,7 +251,7 @@ 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
@ -682,7 +682,7 @@ various make commands that can be used to manipulate 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
also type
lmp_machine -h :pre
@ -1416,8 +1416,8 @@ 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
@ -1481,7 +1481,7 @@ 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.
@ -1760,7 +1760,7 @@ 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.

2
doc/src/USER/atc/man_consistent_fe_initialization.html
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@ -27,7 +27,7 @@
syntax</a></h2>
<p>fix_modify AtC consistent_fe_initialization &lt;on | off&gt;</p>
<ul>
<li>&lt;on|off&gt; = switch to activiate/deactiviate the intial setting of FE intrinsic field to match the projected MD field </li>
<li>&lt;on|off&gt; = switch to activiate/deactiviate the initial setting of FE intrinsic field to match the projected MD field </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>

4
doc/src/accelerate_intel.txt
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@ -20,7 +20,7 @@ coprocessors via offloading neighbor list and non-bonded force
calculations to the Phi. The same C++ code is used in both cases.
When offloading to a coprocessor from a CPU, the same routine is run
twice, once on the CPU and once with an offload flag. This allows
LAMMPS to run on the CPU cores and coprocessor cores simulataneously.
LAMMPS to run on the CPU cores and coprocessor cores simultaneously.
[Currently Available USER-INTEL Styles:]
@ -115,7 +115,7 @@ coprocessor and an Intel compiler are required. For this, the
recommended version of the Intel compiler is 14.0.1.106 or
versions 15.0.2.044 and higher.
Although any compiler can be used with the USER-INTEL pacakge,
Although any compiler can be used with the USER-INTEL package,
currently, vectorization directives are disabled by default when
not using Intel compilers due to lack of standard support and
observations of decreased performance. The OpenMP standard now

2
doc/src/accelerate_kokkos.txt
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@ -217,7 +217,7 @@ best performance its CCFLAGS setting should use -O3 and have a
KOKKOS_ARCH setting that matches the compute capability of your NVIDIA
hardware and software installation, e.g. KOKKOS_ARCH=Kepler30. Note
the minimal required compute capability is 2.0, but this will give
signicantly reduced performance compared to Kepler generation GPUs
significantly reduced performance compared to Kepler generation GPUs
with compute capability 3.x. For the LINK setting, "nvcc" should not
be used; instead use g++ or another compiler suitable for linking C++
applications. Often you will want to use your MPI compiler wrapper

2
doc/src/angle_hybrid.txt
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@ -81,7 +81,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
Unlike other angle styles, the hybrid angle style does not store angle
coefficient info for individual sub-styles in a "binary restart
files"_restart.html. Thus when retarting a simulation from a restart
files"_restart.html. Thus when restarting a simulation from a restart
file, you need to re-specify angle_coeff commands.
[Related commands:]

8
doc/src/atom_modify.txt
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@ -103,7 +103,7 @@ turns off the {first} option.
It is OK to use the {first} keyword with a group that has not yet been
defined, e.g. to use the atom_modify first command at the beginning of
your input script. LAMMPS does not use the group until a simullation
your input script. LAMMPS does not use the group until a simulation
is run.
The {sort} keyword turns on a spatial sorting or reordering of atoms
@ -116,7 +116,7 @@ various other factors. As a general rule, sorting is typically more
effective at speeding up simulations of liquids as opposed to solids.
In tests we have done, the speed-up can range from zero to 3-4x.
Reordering is peformed every {Nfreq} timesteps during a dynamics run
Reordering is performed every {Nfreq} timesteps during a dynamics run
or iterations during a minimization. More precisely, reordering
occurs at the first reneighboring that occurs after the target
timestep. The reordering is performed locally by each processor,
@ -130,7 +130,7 @@ the processor's 1d list of atoms.
The goal of this procedure is for atoms to put atoms close to each
other in the processor's one-dimensional list of atoms that are also
near to each other spatially. This can improve cache performance when
pairwise intereractions and neighbor lists are computed. Note that if
pairwise interactions and neighbor lists are computed. Note that if
bins are too small, there will be few atoms/bin. Likewise if bins are
too large, there will be many atoms/bin. In both cases, the goal of
cache locality will be undermined.
@ -138,7 +138,7 @@ cache locality will be undermined.
NOTE: Running a simulation with sorting on versus off should not
change the simulation results in a statistical sense. However, a
different ordering will induce round-off differences, which will lead
to diverging trajectories over time when comparing two simluations.
to diverging trajectories over time when comparing two simulations.
Various commands, particularly those which use random numbers
(e.g. "velocity create"_velocity.html, and "fix
langevin"_fix_langevin.html), may generate (statistically identical)

4
doc/src/atom_style.txt
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@ -149,7 +149,7 @@ Hydrodynamics. Both fluids and solids can be modeled. Particles
store the mass and volume of an integration point, a kernel diameter
used for calculating the field variables (e.g. stress and deformation)
and a contact radius for calculating repulsive forces which prevent
individual physical bodies from penetretating each other.
individual physical bodies from penetrating each other.
The {wavepacket} style is similar to {electron}, but the electrons may
consist of several Gaussian wave packets, summed up with coefficients
@ -165,7 +165,7 @@ For the {tri} style, the particles are planar triangles and each
stores a per-particle mass and size and orientation (i.e. the corner
points of the triangle).
The {template} style allows molecular topolgy (bonds,angles,etc) to be
The {template} style allows molecular topology (bonds,angles,etc) to be
defined via a molecule template using the "molecule"_molecule.html
command. The template stores one or more molecules with a single copy
of the topology info (bonds,angles,etc) of each. Individual atoms

16
doc/src/balance.txt
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@ -76,13 +76,13 @@ sub-domain sizes and shapes on-the-fly during a "run"_run.html.
Load-balancing is typically most useful if the particles in the
simulation box have a spatially-varying density distribution or when
the computational cost varies signficantly between different
the computational cost varies significantly between different
particles. E.g. a model of a vapor/liquid interface, or a solid with
an irregular-shaped geometry containing void regions, or "hybrid pair
style simulations"_pair_hybrid.html which combine pair styles with
different computational cost. In these cases, the LAMMPS default of
dividing the simulation box volume into a regular-spaced grid of 3d
bricks, with one equal-volume sub-domain per procesor, may assign
bricks, with one equal-volume sub-domain per processor, may assign
numbers of particles per processor in a way that the computational
effort varies significantly. This can lead to poor performance when
the simulation is run in parallel.
@ -91,7 +91,7 @@ The balancing can be performed with or without per-particle weighting.
With no weighting, the balancing attempts to assign an equal number of
particles to each processor. With weighting, the balancing attempts
to assign an equal aggregate computational weight to each processor,
which typically inducces a different number of atoms assigned to each
which typically induces a different number of atoms assigned to each
processor. Details on the various weighting options and examples for
how they can be used are "given below"_#weighted_balance.
@ -222,7 +222,7 @@ listed in ascending order. They represent the fractional position of
the cutting place. The left (or lower) edge of the box is 0.0, and
the right (or upper) edge is 1.0. Neither of these values is
specified. Only the interior Ps-1 positions are specified. Thus is
there are 2 procesors in the x dimension, you specify a single value
there are 2 processors in the x dimension, you specify a single value
such as 0.75, which would make the left processor's sub-domain 3x
larger than the right processor's sub-domain.
@ -266,7 +266,7 @@ assigned, particles are migrated to their new owning processor, and
the balance procedure ends.
NOTE: At each rebalance operation, the bisectioning for each cutting
plane (line in 2d) typcially starts with low and high bounds separated
plane (line in 2d) typically starts with low and high bounds separated
by the extent of a processor's sub-domain in one dimension. The size
of this bracketing region shrinks by 1/2 every iteration. Thus if
{Niter} is specified as 10, the cutting plane will typically be
@ -301,7 +301,7 @@ processors at each iteration.
That is the procedure for the first cut. Subsequent cuts are made
recursively, in exactly the same manner. The subset of processors
assigned to each box make a new cut in the longest dimension of that
box, splitting the box, the subset of processsors, and the particles
box, splitting the box, the subset of processors, and the particles
in the box in two. The recursion continues until every processor is
assigned a sub-box of the entire simulation domain, and owns the
particles in that sub-box.
@ -368,7 +368,7 @@ of about 0.8 often results in the best performance, since the number
of neighbors is likely to overestimate the ideal weight.
This weight style is useful for systems where there are different
cutoffs used for different pairs of interations, or the density
cutoffs used for different pairs of interactions, or the density
fluctuates, or a large number of particles are in the vicinity of a
wall, or a combination of these effects. If a simulation uses
multiple neighbor lists, this weight style will use the first suitable
@ -402,7 +402,7 @@ decrease the weights so that the ratio of max weight to min weight
decreases by {factor}. In both cases the intermediate weight values
increase/decrease proportionally as well. A value = 1.0 has no effect
on the {time} weights. As a rule of thumb, effective values to use
are typicall between 0.5 and 1.2. Note that the timer quantities
are typically between 0.5 and 1.2. Note that the timer quantities
mentioned above can be affected by communication which occurs in the
middle of the operations, e.g. pair styles with intermediate exchange
of data witin the force computation, and likewise for KSpace solves.

4
doc/src/body.txt
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@ -82,7 +82,7 @@ internal stress that induces fragmentation :ul
then the interaction between pairs of particles is likely to be more
complex than the summation of simple sub-particle interactions. An
example is contact or frictional forces between particles with planar
sufaces that inter-penetrate.
surfaces that inter-penetrate.
These are additional LAMMPS commands that can be used with body
particles of different styles
@ -105,7 +105,7 @@ in the sections below.
The {nparticle} body style represents body particles as a rigid body
with a variable number N of sub-particles. It is provided as a
vanillia, prototypical example of a body particle, although as
vanilla, prototypical example of a body particle, although as
mentioned above, the "fix rigid"_fix_rigid.html command already
duplicates its functionality.

2
doc/src/bond_hybrid.txt
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@ -64,7 +64,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
Unlike other bond styles, the hybrid bond style does not store bond
coefficient info for individual sub-styles in a "binary restart
files"_restart.html. Thus when retarting a simulation from a restart
files"_restart.html. Thus when restarting a simulation from a restart
file, you need to re-specify bond_coeff commands.
[Related commands:]

4
doc/src/change_box.txt
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@ -258,8 +258,8 @@ command.
:line
The {ortho} and {triclinic} keywords convert the simulation box to be
orthogonal or triclinic (non-orthongonal). See "this
section"_Section_howto#howto_13 for a discussion of how non-orthongal
orthogonal or triclinic (non-orthogonal). See "this
section"_Section_howto#howto_13 for a discussion of how non-orthogonal
boxes are represented in LAMMPS.
The simulation box is defined as either orthogonal or triclinic when

2
doc/src/comm_style.txt
View File

@ -39,7 +39,7 @@ sizes and shapes. Again there is one tile per processor. To acquire
information for nearby atoms, communication must now be done with a
more complex pattern of neighboring processors.
Note that this command does not actually define a partitoining of the
Note that this command does not actually define a partitioning of the
simulation box (a domain decomposition), rather it determines what
kinds of decompositions are allowed and the pattern of communication
used to enable the decomposition. A decomposition is created when the

2
doc/src/compute_angmom_chunk.txt
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@ -22,7 +22,7 @@ compute 1 fluid angmom/chunk molchunk :pre
[Description:]
Define a computation that calculates the angular momemtum of multiple
Define a computation that calculates the angular momentum of multiple
chunks of atoms.
In LAMMPS, chunks are collections of atoms defined by a "compute

2
doc/src/compute_chunk_atom.txt
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@ -386,7 +386,7 @@ If {compress yes} is set, and the {compress} keyword comes before the
{limit} keyword, the compression operation is performed first, as
described below, which resets {Nchunk}. The {limit} keyword is then
applied to the new {Nchunk} value, exactly as described in the
preceeding paragraph. Note that in this case, all atoms will end up
preceding paragraph. Note that in this case, all atoms will end up
with chunk IDs <= {Nc}, but their original values (e.g. molecule ID or
compute/fix/variable value) may have been > {Nc}, because of the
compression operation.

2
doc/src/compute_cna_atom.txt
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@ -42,7 +42,7 @@ performed on mono-component systems.
The CNA calculation can be sensitive to the specified cutoff value.
You should insure the appropriate nearest neighbors of an atom are
found within the cutoff distance for the presumed crystal strucure.
found within the cutoff distance for the presumed crystal structure.
E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest
neighbors for perfect BCC crystals. These formulas can be used to
obtain a good cutoff distance:

2
doc/src/compute_com.txt
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@ -25,7 +25,7 @@ Define a computation that calculates the center-of-mass of the group
of atoms, including all effects due to atoms passing thru periodic
boundaries.
A vector of three quantites is calculated by this compute, which
A vector of three quantities is calculated by this compute, which
are the x,y,z coordinates of the center of mass.
NOTE: The coordinates of an atom contribute to the center-of-mass in

2
doc/src/compute_damage_atom.txt
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@ -47,7 +47,7 @@ any command that uses per-atom values from a compute as input. See
"Section 6.15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
The per-atom vector values are unitlesss numbers (damage) >= 0.0.
The per-atom vector values are unitless numbers (damage) >= 0.0.
[Restrictions:]

2
doc/src/compute_dilatation_atom.txt
View File

@ -50,7 +50,7 @@ This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
Section_howto 15 for an overview of LAMMPS output options.
The per-atom vector values are unitlesss numbers (theta) >= 0.0.
The per-atom vector values are unitless numbers (theta) >= 0.0.
[Restrictions:]

2
doc/src/compute_displace_atom.txt
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@ -25,7 +25,7 @@ Define a computation that calculates the current displacement of each
atom in the group from its original coordinates, including all effects
due to atoms passing thru periodic boundaries.
A vector of four quantites per atom is calculated by this compute.
A vector of four quantities per atom is calculated by this compute.
The first 3 elements of the vector are the dx,dy,dz displacements.
The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy +
dz*dz).

2
doc/src/compute_event_displace.txt
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@ -37,7 +37,7 @@ further than the threshold distance.
NOTE: If the system is undergoing significant center-of-mass motion,
due to thermal motion, an external force, or an initial net momentum,
then this compute will not be able to distinguish that motion from
local atom displacements and may generate "false postives."
local atom displacements and may generate "false positives."
[Output info:]

2
doc/src/compute_msd.txt
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@ -33,7 +33,7 @@ passing thru periodic boundaries. For computation of the non-Gaussian
parameter of mean-squared displacement, see the "compute
msd/nongauss"_compute_msd_nongauss.html command.
A vector of four quantites is calculated by this compute. The first 3
A vector of four quantities is calculated by this compute. The first 3
elements of the vector are the squared dx,dy,dz displacements, summed
and averaged over atoms in the group. The 4th element is the total
squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and

2
doc/src/compute_msd_chunk.txt
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@ -35,7 +35,7 @@ chunk/atom"_compute_chunk_atom.html doc page and "Section
defined and examples of how they can be used to measure properties of
a system.
Four quantites are calculated by this compute for each chunk. The
Four quantities are calculated by this compute for each chunk. The
first 3 quantities are the squared dx,dy,dz displacements of the
center-of-mass. The 4th component is the total squared displacement,
i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. These

4
doc/src/compute_msd_nongauss.txt
View File

@ -30,12 +30,12 @@ Define a computation that calculates the mean-squared displacement
(MSD) and non-Gaussian parameter (NGP) of the group of atoms,
including all effects due to atoms passing thru periodic boundaries.
A vector of three quantites is calculated by this compute. The first
A vector of three quantities is calculated by this compute. The first
element of the vector is the total squared dx,dy,dz displacements
drsquared = (dx*dx + dy*dy + dz*dz) of atoms, and the second is the
fourth power of these displacements drfourth = (dx*dx + dy*dy +
dz*dz)*(dx*dx + dy*dy + dz*dz), summed and averaged over atoms in the
group. The 3rd component is the nonGaussian diffusion paramter NGP =
group. The 3rd component is the nonGaussian diffusion parameter NGP =
3*drfourth/(5*drsquared*drsquared), i.e.
:c,image(Eqs/compute_msd_nongauss.jpg)

2
doc/src/compute_pair.txt
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@ -43,7 +43,7 @@ style van der Waals interaction or not) is tallied in {evdwl}. If
as a global scalar by this compute. This is useful when using
"pair_style hybrid"_pair_hybrid.html if you want to know the portion
of the total energy contributed by one sub-style. If {evalue} is
specfied as {evdwl} or {ecoul}, then just that portion of the energy
specified as {evdwl} or {ecoul}, then just that portion of the energy
is stored as a global scalar.
NOTE: The energy returned by the {evdwl} keyword does not include tail

2
doc/src/compute_plasticity_atom.txt
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@ -44,7 +44,7 @@ This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
Section_howto 15 for an overview of LAMMPS output options.
The per-atom vector values are unitlesss numbers (lambda) >= 0.0.
The per-atom vector values are unitless numbers (lambda) >= 0.0.
[Restrictions:]

2
doc/src/compute_rdf.txt
View File

@ -73,7 +73,7 @@ post-process a dump file to calculate it. This is because using the
which may slow down your simulation. If you specify a {Rcut} <= force
cutoff, you will force an additional neighbor list to be built at
every timestep this command is invoked (or every reneighboring
timestep, whichever is less frequent), which is inefficent. LAMMPS
timestep, whichever is less frequent), which is inefficient. LAMMPS
will warn you if this is the case. If you specify a {Rcut} > force
cutoff, you must insure ghost atom information out to {Rcut} + {skin}
is communicated, via the "comm_modify cutoff"_comm_modify.html

2
doc/src/compute_saed.txt
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@ -93,7 +93,7 @@ parameters will denote the z1=h, z2=k, and z3=l (in a global since)
zone axis of an intersecting Ewald sphere. Diffraction intensities
will only be computed at the intersection of the reciprocal lattice
mesh and a {dR_Ewald} thick surface of the Ewald sphere. See the
example 3D intestiety data and the intersection of a \[010\] zone axis
example 3D intensity data and the intersection of a \[010\] zone axis
in the below image.
:c,image(JPG/saed_ewald_intersect_small.jpg,JPG/saed_ewald_intersect.jpg)

2
doc/src/compute_temp_chunk.txt
View File

@ -208,7 +208,7 @@ This compute also optionally calculates a global array, if one or more
of the optional values are specified. The number of rows in the array
= the number of chunks {Nchunk} as calculated by the specified
"compute chunk/atom"_compute_chunk_atom.html command. The number of
columns is the number of specifed values (1 or more). These values
columns is the number of specified values (1 or more). These values
can be accessed by any command that uses global array values from a
compute as input. Again, see "Section
6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output

2
doc/src/compute_temp_profile.txt
View File

@ -118,7 +118,7 @@ needed, the subtracted degrees-of-freedom can be altered using the
NOTE: When using the {out} keyword with a value of {bin}, the
calculated temperature for each bin does not include the
degrees-of-freedom adjustment described in the preceeding paragraph,
degrees-of-freedom adjustment described in the preceding paragraph,
for fixes that constrain molecular motion. It does include the
adjustment due to the {extra} option, which is applied to each bin.

2
doc/src/compute_vacf.txt
View File

@ -27,7 +27,7 @@ function (VACF), averaged over a group of atoms. Each atom's
contribution to the VACF is its current velocity vector dotted into
its initial velocity vector at the time the compute was specified.
A vector of four quantites is calculated by this compute. The first 3
A vector of four quantities is calculated by this compute. The first 3
elements of the vector are vx * vx0 (and similarly for the y and z
components), summed and averaged over atoms in the group. Vx is the
current x-component of velocity for the atom, vx0 is the initial

2
doc/src/create_atoms.txt
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@ -101,7 +101,7 @@ positions.
For the {random} style, N particles are added to the system at
randomly generated coordinates, which can be useful for generating an
amorphous system. The particles are created one by one using the
speficied random number {seed}, resulting in the same set of particles
specified random number {seed}, resulting in the same set of particles
coordinates, independent of how many processors are being used in the
simulation. If the {region-ID} argument is specified as NULL, then
the created particles will be anywhere in the simulation box. If a

2
doc/src/dihedral_hybrid.txt
View File

@ -82,7 +82,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
Unlike other dihedral styles, the hybrid dihedral style does not store
dihedral coefficient info for individual sub-styles in a "binary
restart files"_restart.html. Thus when retarting a simulation from a
restart files"_restart.html. Thus when restarting a simulation from a
restart file, you need to re-specify dihedral_coeff commands.
[Related commands:]

2
doc/src/dump.txt
View File

@ -225,7 +225,7 @@ This bounding box is convenient for many visualization programs. The
meaning of the 6 character flags for "xx yy zz" is the same as above.
Note that the first two numbers on each line are now xlo_bound instead
of xlo, etc, since they repesent a bounding box. See "this
of xlo, etc, since they represent a bounding box. See "this
section"_Section_howto.html#howto_12 of the doc pages for a geometric
description of triclinic boxes, as defined by LAMMPS, simple formulas
for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are

8
doc/src/dump_image.txt
View File

@ -237,7 +237,7 @@ diameter, which can be used as the {diameter} setting.
:line
The various kewords listed above control how the image is rendered.
The various keywords listed above control how the image is rendered.
As listed below, all of the keywords have defaults, most of which you
will likely not need to change. The "dump modify"_dump_modify.html
also has options specific to the dump image style, particularly for
@ -442,7 +442,7 @@ degrees.
The {center} keyword determines the point in simulation space that
will be at the center of the image. {Cx}, {Cy}, and {Cz} are
speficied as fractions of the box dimensions, so that (0.5,0.5,0.5) is
specified as fractions of the box dimensions, so that (0.5,0.5,0.5) is
the center of the simulation box. These values do not have to be
between 0.0 and 1.0, if you want the simulation box to be offset from
the center of the image. Note, however, that if you choose strange
@ -476,8 +476,8 @@ smaller. {Zfactor} must be a value > 0.0.
The {persp} keyword determines how much depth perspective is present
in the image. Depth perspective makes lines that are parallel in
simulation space appear non-parallel in the image. A {pfactor} value
of 0.0 means that parallel lines will meet at infininty (1.0/pfactor),
which is an orthographic rendering with no persepctive. A {pfactor}
of 0.0 means that parallel lines will meet at infinity (1.0/pfactor),
which is an orthographic rendering with no perspective. A {pfactor}
value between 0.0 and 1.0 will introduce more perspective. A {pfactor}
value > 1 will create a highly skewed image with a large amount of
perspective.

2
doc/src/dump_modify.txt
View File

@ -426,7 +426,7 @@ regions.
The {scale} keyword applies only to the dump {atom} style. A scale
value of {yes} means atom coords are written in normalized units from
0.0 to 1.0 in each box dimension. If the simluation box is triclinic
0.0 to 1.0 in each box dimension. If the simulation box is triclinic
(tilted), then all atom coords will still be between 0.0 and 1.0. A
value of {no} means they are written in absolute distance units
(e.g. Angstroms or sigma).

2
doc/src/fix_ave_chunk.txt
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@ -301,7 +301,7 @@ sample values" divided by {Nrepeat}. In other words it is an average
of an average.
If the {norm} setting is {none}, a similar computation as for the
{sample} seting is done, except the individual "average sample values"
{sample} setting is done, except the individual "average sample values"
are "summed sample values". A summed sample value is simply the chunk
value summed over atoms in the sample, without dividing by the number
of atoms in the sample. The output value for the chunk on the

2
doc/src/fix_ave_correlate.txt
View File

@ -219,7 +219,7 @@ to {upper} then each input value is correlated with every succeeding
value. I.e. Cij = Vi*Vj, for i < j, so Npair = N*(N-1)/2. :l
If {type} is set
to {lower} then each input value is correlated with every preceeding
to {lower} then each input value is correlated with every preceding
value. I.e. Cij = Vi*Vj, for i > j, so Npair = N*(N-1)/2. :l
If {type} is set to {auto/upper} then each input value is correlated

2
doc/src/fix_ave_time.txt
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@ -320,7 +320,7 @@ input values are averaged and {mode} = vector. The global array has #
of rows = length of the input vectors and # of columns = number of
inputs.
If the fix prouduces a scalar or vector, then the scalar and each
If the fix produces a scalar or vector, then the scalar and each
element of the vector can be either "intensive" or "extensive",
depending on whether the values contributing to the scalar or vector
element are "intensive" or "extensive". If the fix produces an array,

12
doc/src/fix_balance.txt
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@ -63,14 +63,14 @@ perform "static" balancing, before or between runs, see the
Load-balancing is typically most useful if the particles in the
simulation box have a spatially-varying density distribution or
where the computational cost varies signficantly between different
where the computational cost varies significantly between different
atoms. E.g. a model of a vapor/liquid interface, or a solid with
an irregular-shaped geometry containing void regions, or
"hybrid pair style simulations"_pair_hybrid.html which combine
pair styles with different computational cost. In these cases, the
LAMMPS default of dividing the simulation box volume into a
regular-spaced grid of 3d bricks, with one equal-volume sub-domain
per procesor, may assign numbers of particles per processor in a
per processor, may assign numbers of particles per processor in a
way that the computational effort varies significantly. This can
lead to poor performance when the simulation is run in parallel.
@ -78,7 +78,7 @@ The balancing can be performed with or without per-particle weighting.
With no weighting, the balancing attempts to assign an equal number of
particles to each processor. With weighting, the balancing attempts
to assign an equal aggregate computational weight to each processor,
which typically inducces a different number of atoms assigned to each
which typically induces a different number of atoms assigned to each
processor.
NOTE: The weighting options listed above are documented with the
@ -216,7 +216,7 @@ for a single value, except that the bounds used for each bisectioning
take advantage of information from neighboring cuts if possible, as
well as counts of particles at the bounds on either side of each cuts,
which themselves were cuts in previous iterations. The latter is used
to infer a density of pariticles near each of the current cuts. At
to infer a density of particles near each of the current cuts. At
each iteration, the count of particles on either side of each plane is
tallied. If the counts do not match the target value for the plane,
the position of the cut is adjusted based on the local density. The
@ -239,7 +239,7 @@ assigned, particles migrate to their new owning processor as part of
the normal reneighboring procedure.
NOTE: At each rebalance operation, the bisectioning for each cutting
plane (line in 2d) typcially starts with low and high bounds separated
plane (line in 2d) typically starts with low and high bounds separated
by the extent of a processor's sub-domain in one dimension. The size
of this bracketing region shrinks based on the local density, as
described above, which should typically be 1/2 or more every
@ -275,7 +275,7 @@ at each iteration.
That is the procedure for the first cut. Subsequent cuts are made
recursively, in exactly the same manner. The subset of processors
assigned to each box make a new cut in the longest dimension of that
box, splitting the box, the subset of processsors, and the atoms in
box, splitting the box, the subset of processors, and the atoms in
the box in two. The recursion continues until every processor is
assigned a sub-box of the entire simulation domain, and owns the atoms
in that sub-box.

4
doc/src/fix_bond_break.txt
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@ -79,8 +79,8 @@ part of bonds, angles, etc.
NOTE: One data structure that is not updated when a bond breaks are
the molecule IDs stored by each atom. Even though one molecule
becomes two moleclues due to the broken bond, all atoms in both new
moleclues retain their original molecule IDs.
becomes two molecules due to the broken bond, all atoms in both new
molecules retain their original molecule IDs.
Computationally, each timestep this fix operates, it loops over all
the bonds in the system and computes distances between pairs of bonded

4
doc/src/fix_bond_create.txt
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@ -118,8 +118,8 @@ of new bonds, angles, etc.
NOTE: One data structure that is not updated when a bond breaks are
the molecule IDs stored by each atom. Even though two molecules
become one moleclue due to the created bond, all atoms in the new
moleclue retain their original molecule IDs.
become one molecule due to the created bond, all atoms in the new
molecule retain their original molecule IDs.
If the {atype} keyword is used and if an angle potential is defined
via the "angle_style"_angle_style.html command, then any new 3-body

2
doc/src/fix_bond_swap.txt
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@ -168,7 +168,7 @@ This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
The setings of the "special_bond" command must be 0,1,1 in order to
The settings of the "special_bond" command must be 0,1,1 in order to
use this fix, which is typical of bead-spring chains with FENE or
harmonic bonds. This means that pairwise interactions between bonded
atoms are turned off, but are turned on between atoms two or three

4
doc/src/fix_box_relax.txt
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@ -54,7 +54,7 @@ The external pressure tensor is specified using one or more of the
keywords. These keywords give you the ability to specify all 6
components of an external stress tensor, and to couple various of
these components together so that the dimensions they represent are
varied together during the mimimization.
varied together during the minimization.
Orthogonal simulation boxes have 3 adjustable dimensions (x,y,z).
Triclinic (non-orthogonal) simulation boxes have 6 adjustable
@ -122,7 +122,7 @@ well-defined minimization problem. This is because the objective
function being minimized changes if the box size/shape changes. In
practice this means the minimizer can get "stuck" before you have
reached the desired tolerance. The solution to this is to restart the
minmizer from the new adjusted box size/shape, since that creates a
minimizer from the new adjusted box size/shape, since that creates a
new objective function valid for the new box size/shape. Repeat as
necessary until the box size/shape has reached its new equilibrium.

2
doc/src/fix_cmap.txt
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@ -44,7 +44,7 @@ lammps/potentials directory: charmm22.cmap and charmm36.cmap.
The data file read by the "read_data" must contain the topology of all
the CMAP interactions, similar to the topology data for bonds, angles,
dihedrals, etc. Specically it should have a line like this
dihedrals, etc. Specially it should have a line like this
in its header section:
N crossterms :pre

2
doc/src/fix_controller.txt
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@ -107,7 +107,7 @@ When choosing the values of the four constants, it is best to first
pick a value and sign for {alpha} that is consistent with the
magnitudes and signs of {pvar} and {cvar}. The magnitude of {Kp}
should then be tested over a large positive range keeping {Ki}={Kd}=0.
A good value for {Kp} will produce a fast reponse in {pvar}, without
A good value for {Kp} will produce a fast response in {pvar}, without
overshooting the {setpoint}. For many applications, proportional
feedback is sufficient, and so {Ki}={Kd}=0 can be used. In cases where
there is a substantial lag time in the response of {pvar} to a change

6
doc/src/fix_deposit.txt
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@ -15,7 +15,7 @@ fix ID group-ID deposit N type M seed keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
deposit = style name of this fix command :l
N = # of atoms or molecules to insert :l
type = atom type to assign to inserted atoms (offset for moleclue insertion) :l
type = atom type to assign to inserted atoms (offset for molecule insertion) :l
M = insert a single atom or molecule every M steps :l
seed = random # seed (positive integer) :l
one or more keyword/value pairs may be appended to args :l
@ -140,7 +140,7 @@ the molecule.
If the molecule template contains more than one molecule, the relative
probability of depositing each molecule can be specified by the
{molfrac} keyword. N relative probablities, each from 0.0 to 1.0, are
{molfrac} keyword. N relative probabilities, each from 0.0 to 1.0, are
specified, where N is the number of molecules in the template. Each
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.
@ -192,7 +192,7 @@ LAMMPS prints a warning message.
NOTE: If you are inserting finite size particles or a molecule or
rigid body consisting of finite-size particles, then you should
typically set R larger than the distance at which any inserted
particle may overlap with either a previouly inserted particle or an
particle may overlap with either a previously inserted particle or an
existing particle. LAMMPS will issue a warning if R is smaller than
this value, based on the radii of existing and inserted particles.

4
doc/src/fix_evaporate.txt
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@ -31,9 +31,9 @@ fix 1 solvent evaporate 1000 10 surface 38277 molecule yes :pre
[Description:]
Remove M atoms from the simulation every N steps. This can be used,
for example, to model evaporation of solvent particles or moleclues
for example, to model evaporation of solvent particles or molecules
(i.e. drying) of a system. Every N steps, the number of atoms in the
fix group and within the specifed region are counted. M of these are
fix group and within the specified region are counted. M of these are
chosen at random and deleted. If there are less than M eligible
particles, then all of them are deleted.

4
doc/src/fix_indent.txt
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@ -107,7 +107,7 @@ fashion. For the latter, see the {start} and {stop} keywords of the
"run"_run.html command and the {elaplong} keyword of "thermo_style
custom"_thermo_style.html for details.
For example, if a spherical indenter's x-position is specfied as v_x,
For example, if a spherical indenter's x-position is specified as v_x,
then this variable definition will keep it's center at a relative
position in the simulation box, 1/4 of the way from the left edge to
the right edge, even if the box size changes:
@ -121,7 +121,7 @@ variable x equal "2.5 + 5*elaplong*dt"
variable x equal vdisplace(2.5,5) :pre
If a spherical indenter's radius is specified as v_r, then these
variable definitions will grow the size of the indenter at a specfied
variable definitions will grow the size of the indenter at a specified
rate.
variable r0 equal 0.0

2
doc/src/fix_lb_fluid.txt
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@ -328,7 +328,7 @@ fix must be used in conjunction with the
"lb/viscous"_fix_lb_viscous.html fix if the force coupling constant is
set by default, or either the "lb/viscous"_fix_lb_viscous.html fix or
one of the "lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html or
"lb/pc"_fix_lb_pc.html integrators, if the user chooses to specifiy
"lb/pc"_fix_lb_pc.html integrators, if the user chooses to specify
their own value for the force coupling constant.
[Related commands:]

2
doc/src/fix_modify.txt
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@ -53,7 +53,7 @@ default method for computing P.
For fixes that calculate a contribution to the potential energy of the
system, the {energy} keyword will include that contribution in
thermodynamic output of potential energy. This is because the {energy
yes} setting must be specfied to include the fix's global or per-atom
yes} setting must be specified to include the fix's global or per-atom
energy in the calculation performed by the "compute
pe"_compute_pe.html or "compute pe/atom"_compute_pe_atom.html
commands. See the "thermo_style"_thermo_style.html command for info

2
doc/src/fix_move.txt
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@ -131,7 +131,7 @@ This style also sets the velocity of each atom to (omega cross Rperp)
where omega is its angular velocity around the rotation axis and Rperp
is a perpendicular vector from the rotation axis to the atom. If the
defined "atom_style"_atom_style.html assigns an angular velocity or
angular moementum or orientation to each atom ("atom
angular momentum or orientation to each atom ("atom
styles"_atom_style.html sphere, ellipsoid, line, tri, body), then
those properties are also updated appropriately to correspond to the
atom's motion and rotation over time.

2
doc/src/fix_mscg.txt
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@ -83,7 +83,7 @@ produces additional output files. The range finder functionality
(step 4) outputs files defining pair and bonded interaction ranges.
The force matching functionality (step 5) outputs tabulated force
files for every interaction in the system. Other diagnostic files can
also be output depending on the paramters in the MS-CG library input
also be output depending on the parameters in the MS-CG library input
script. Again, see the documentation provided with the MS-CG library
for more info.

2
doc/src/fix_phonon.txt
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@ -43,7 +43,7 @@ fix 1 all phonon 10 5000 500000 GAMMA EAM0D nasr 100 :pre
Calculate the dynamical matrix from molecular dynamics simulations
based on fluctuation-dissipation theory for a group of atoms.
Consider a crystal with \(N\) unit cells in three dimensions labelled
Consider a crystal with \(N\) unit cells in three dimensions labeled
\(l = (l_1, l_2, l_3)\) where \(l_i\) are integers. Each unit cell is
defined by three linearly independent vectors \(\mathbf\{a\}_1\),
\(\mathbf\{a\}_2\), \(\mathbf\{a\}_3\) forming a parallelipiped,

4
doc/src/fix_pour.txt
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@ -107,7 +107,7 @@ atoms in the molecule.
If the molecule template contains more than one molecule, the relative
probability of depositing each molecule can be specified by the
{molfrac} keyword. N relative probablities, each from 0.0 to 1.0, are
{molfrac} keyword. N relative probabilities, each from 0.0 to 1.0, are
specified, where N is the number of molecules in the template. Each
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.
@ -144,7 +144,7 @@ command for the temperature compute you are using.
All other keywords are optional with defaults as shown below.
The {diam} option is only used when inserting atoms and specifes the
The {diam} option is only used when inserting atoms and specifies the
diameters of inserted particles. There are 3 styles: {one}, {range},
or {poly}. For {one}, all particles will have diameter {D}. For
{range}, the diameter of each particle will be chosen randomly and

2
doc/src/fix_property_atom.txt
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@ -121,7 +121,7 @@ as described below.
Per-atom properties that are defined by the "atom
style"_atom_style.html are initialized when atoms are created, e.g. by
the "read_data"_read_data.html or "create_atoms"_create_atoms.html
commands. The per-atom properaties defined by this fix are not. So
commands. The per-atom properties defined by this fix are not. So
you need to initialize them explicitly. This can be done by the
"read_data"_read_data.html command, using its {fix} keyword and
passing it the fix-ID of this fix.

2
doc/src/fix_qeq.txt
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@ -167,7 +167,7 @@ zero net charge.
NOTE: Developing QEq parameters (chi, eta, gamma, zeta, and qcore) is
non-trivial. Charges on atoms are not guaranteed to equilibrate with
arbitrary choices of these parameters. We do not develop these QEq
paramters. See the examples/qeq directory for some examples.
parameters. See the examples/qeq directory for some examples.
[Restart, fix_modify, output, run start/stop, minimize info:]

6
doc/src/fix_qeq_comb.txt
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@ -42,12 +42,12 @@ Only charges on the atoms in the specified group are equilibrated.
The fix relies on the pair style (COMB in this case) to calculate the
per-atom electronegativity (effective force on the charges). An
electronegativity equalization calculation (or QEq) is performed in an
interative fashion, which in parallel requires communication at each
iterative fashion, which in parallel requires communication at each
iteration for processors to exchange charge information about nearby
atoms with each other. See "Rappe_and_Goddard"_#Rappe_and_Goddard and
"Rick_and_Stuart"_#Rick_and_Stuart for details.
During a run, charge equilibration is peformed every {Nevery} time
During a run, charge equilibration is performed every {Nevery} time
steps. Charge equilibration is also always enforced on the first step
of each run. The {precision} argument controls the tolerance for the
difference in electronegativity for all atoms during charge
@ -55,7 +55,7 @@ equilibration. {Precision} is a trade-off between the cost of
performing charge equilibration (more iterations) and accuracy.
If the {file} keyword is used, then information about each
equilibration calculation is written to the specifed file.
equilibration calculation is written to the specified file.
:line

2
doc/src/fix_restrain.txt
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@ -88,7 +88,7 @@ conformation. You may need to experiment to determine what value of K
works best for a given application.
For the case of finding a minimum energy structure for a single
molecule with particular restratins (e.g. for fitting forcefield
molecule with particular restraints (e.g. for fitting forcefield
parameters or constructing a potential energy surface), commands such
as the following may be useful:

2
doc/src/fix_rigid.txt
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@ -325,7 +325,7 @@ simulation. The effects of these keywords are similar to those
defined in "fix npt/nph"_fix_nh.html
NOTE: Currently the {rigid/npt}, {rigid/nph}, {rigid/npt/small}, and
{rigid/nph/small} styles do not support triclinic (non-orthongonal)
{rigid/nph/small} styles do not support triclinic (non-orthogonal)
boxes.
The target pressures for each of the 6 components of the stress tensor

2
doc/src/fix_rx.txt
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@ -21,7 +21,7 @@ solver = {lammps_rk4,rkf45} = rk4 is an explicit 4th order Runge-Kutta method; r
minSteps = # of steps for rk4 solver or minimum # of steps for rkf45 (rk4 or rkf45)
maxSteps = maximum number of steps for the rkf45 solver (rkf45 only)
relTol = relative tolerance for the rkf45 solver (rkf45 only)
absTol = absolute tolernace for the rkf45 solver (rkf45 only)
absTol = absolute tolerance for the rkf45 solver (rkf45 only)
diag = Diagnostics frequency for the rkf45 solver (optional, rkf45 only) :ul
[Examples:]

4
doc/src/fix_saed_vtk.txt
View File

@ -52,7 +52,7 @@ intensities at a single snapshot.
To produce output in the image data vtk format ghost data is added
outside the {Kmax} range assigned in the compute saed. The ghost data is
assigned a value of -1 and can be removed setting a minimum isovolume
of 0 within the vizualiziton software. SAED images can be created by
of 0 within the visualization software. SAED images can be created by
visualizing a spherical slice of the data that is centered at
R_Ewald*\[h k l\]/norm(\[h k l\]), where R_Ewald=1/lambda.
@ -88,7 +88,7 @@ averaging is done; values are simply generated on timesteps
:line
The output for fix ave/time/saed is a file writen with the 3rd generation
The output for fix ave/time/saed is a file written with the 3rd generation
vtk image data formatting. The filename assigned by the {file} keyword is
appended with _N.vtk where N is an index (0,1,2...) to account for multiple
diffraction intensity outputs.

2
doc/src/fix_smd_wall_surface.txt
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@ -27,7 +27,7 @@ fix stl_surf all smd/wall_surface tool.stl 2 65535 :pre
[Description:]
This fix creates reads a traingulated surface from a file in .STL format.
This fix creates reads a triangulated surface from a file in .STL format.
For each triangle, a new particle is created which stores the barycenter of the triangle and the vertex positions.
The radius of the new particle is that of the minimum circle which encompasses the triangle vertices.

2
doc/src/fix_spring_self.txt
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@ -30,7 +30,7 @@ location at the time the fix command was issued. At each timestep,
the magnitude of the force on each atom is -Kr, where r is the
displacement of the atom from its current position to its initial
position. The distance r correctly takes into account any crossings
of periodic boundary by the atom since it was in its intitial
of periodic boundary by the atom since it was in its initial
position.
With the (optional) dir flag, one can select in which direction the

8
doc/src/fix_srd.txt
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@ -54,18 +54,18 @@ fix 1 srd srd 10 big 0.5 0.25 482984 collision slip search 0.5 :pre
[Description:]
Treat a group of partilces as stochastic rotation dynamics (SRD)
Treat a group of particles as stochastic rotation dynamics (SRD)
particles that serve as a background solvent when interacting with big
(colloidal) particles in groupbig-ID. The SRD formalism is described
in "(Hecht)"_#Hecht. The key idea behind using SRD particles as a
cheap coarse-grained solvent is that SRD particles do not interact
with each other, but only with the solute particles, which in LAMMPS
can be spheroids, ellipsoids, or line segments, or triangles, or rigid
bodies containing multiple spherioids or ellipsoids or line segments
bodies containing multiple spheriods or ellipsoids or line segments
or triangles. The collision and rotation properties of the model
imbue the SRD particles with fluid-like properties, including an
effective viscosity. Thus simulations with large solute particles can
be run more quickly, to measure solute propoerties like diffusivity
be run more quickly, to measure solute properties like diffusivity
and viscosity in a background fluid. The usual LAMMPS fixes for such
simulations, such as "fix deform"_fix_deform.html, "fix
viscosity"_fix_viscosity.html, and "fix nvt/sllod"_fix_nvt_sllod.html,
@ -230,7 +230,7 @@ error or warning is generated. Similarly, if the ratio of any bin
dimension with {hgrid} exceeds (1 +/- tolerance), then an error or
warning is generated.
NOTE: The fix srd command can be used with simluations the size and/or
NOTE: The fix srd command can be used with simulations the size and/or
shape of the simulation box changes. This can be due to non-periodic
boundary conditions or the use of fixes such as the "fix
deform"_fix_deform.html or "fix wall/srd"_fix_wall_srd.html commands

2
doc/src/fix_temp_csvr.txt
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@ -39,7 +39,7 @@ scaling factor from a suitably chosen (gaussian) distribution rather
than having it determined from the time constant directly. In the case
of {temp/csld} the velocities are updated to a linear combination of
the current velocities with a gaussian distribution of velocities at
the desired temperature. Both termostats are applied every timestep.
the desired temperature. Both thermostats are applied every timestep.
The thermostat is applied to only the translational degrees of freedom
for the particles, which is an important consideration for finite-size

2
doc/src/fix_temp_rescale.txt
View File

@ -44,7 +44,7 @@ ramped value between the {Tstart} and {Tstop} temperatures at the
beginning and end of the run.
NOTE: This thermostat will generate an error if the current
temperature is zero at the end of a timestep it is inovoked on. It
temperature is zero at the end of a timestep it is invoked on. It
cannot rescale a zero temperature.
{Tstart} can be specified as an equal-style "variable"_variable.html.

2
doc/src/fix_tfmc.txt
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@ -41,7 +41,7 @@ can be used to extend the time scale of atomistic simulations, in
particular when long time scale relaxation effects must be considered;
some interesting examples are given in the review by "(Neyts)"_#Neyts.
An example of a typical use case would be the modelling of chemical
vapour deposition (CVD) processes on a surface, in which impacts by
vapor deposition (CVD) processes on a surface, in which impacts by
gas-phase species can be performed using MD, but subsequent relaxation
of the surface is too slow to be done using MD only. Using tfMC can
allow for a much faster relaxation of the surface, so that higher

4
doc/src/fix_ttm.txt
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@ -106,7 +106,7 @@ electron stopping coupling parameter. C_e, rho_e, and kappa_e are
specified as parameters to the fix. The other quantities are derived.
The form of the heat diffusion equation used here is almost the same
as that in equation 6 of "(Duffy)"_#Duffy, with the exception that the
electronic density is explicitly reprensented, rather than being part
electronic density is explicitly represented, rather than being part
of the specific heat parameter.
Currently, fix ttm assumes that none of the user-supplied parameters
@ -151,7 +151,7 @@ output timestep. The timestep itself is given in the first column.
The next Nx*Ny*Nz columns contain the temperatures for the atomic
subsystem, and the final Nx*Ny*Nz columns contain the temperatures for
the electronic subsystem. The ordering of the Nx*Ny*Nz columns is
with the z index varing fastest, y the next fastest, and x the
with the z index varying fastest, y the next fastest, and x the
slowest.
These fixes do not change the coordinates of their atoms; they only

2
doc/src/fix_vector.txt
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@ -136,7 +136,7 @@ An array is produced if multiple input values are specified.
The length of the vector or the number of rows in the array grows
by 1 every {Nevery} timesteps.
If the fix prouduces a vector, then the entire vector will be either
If the fix produces a vector, then the entire vector will be either
"intensive" or "extensive", depending on whether the values stored in
the vector are "intensive" or "extensive". If the fix produces an
array, then all elements in the array must be the same, either

2
doc/src/fix_viscosity.txt
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@ -102,7 +102,7 @@ parameter.
An alternative method for calculating a viscosity is to run a NEMD
simulation, as described in "Section
6.13"_Section_howto.html#howto_13 of the manual. NEMD simulations
deform the simmulation box via the "fix deform"_fix_deform.html
deform the simulation box via the "fix deform"_fix_deform.html
command. Thus they cannot be run on a charged system using a "PPPM
solver"_kspace_style.html since PPPM does not currently support
non-orthogonal boxes. Using fix viscosity keeps the box orthogonal;

2
doc/src/fix_wall.txt
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@ -136,7 +136,7 @@ of 1/volume.
The {wall/colloid} interaction is derived by integrating over
constituent LJ particles of size {sigma} within the colloid particle
and a 3d half-lattice of Lennard-Jones 12/6 particles of size {sigma}
in the wall. As mentioned in the preceeding paragraph, the density of
in the wall. As mentioned in the preceding paragraph, the density of
particles in the wall and colloid can be different, as specified by
the {epsilon} pre-factor.

2
doc/src/fix_wall_gran.txt
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@ -85,7 +85,7 @@ versions used Kn and Kt from the pairwise interaction and hardwired
dampflag to 1, rather than letting them be specified directly. This
means you can set the values of the wall/particle coefficients
appropriately in the current code to reproduce the results of a
prevoius Hertzian monodisperse calculation. For example, for the
previous Hertzian monodisperse calculation. For example, for the
common case of a monodisperse system with particles of diameter 1, Kn,
Kt, gamma_n, and gamma_s should be set sqrt(2.0) larger than they were
previously.

4
doc/src/fix_wall_gran_region.txt
View File

@ -153,7 +153,7 @@ material.
[Restart, fix_modify, output, run start/stop, minimize info:]
Similiar to "fix wall/gran"_fix_wall_gran.html command, this fix
Similar to "fix wall/gran"_fix_wall_gran.html command, this fix
writes the shear friction state of atoms interacting with the wall to
"binary restart files"_restart.html, so that a simulation can continue
correctly if granular potentials with shear "history" effects are
@ -169,7 +169,7 @@ So you must re-define your region and if it is a moving region, define
its motion attributes in a way that is consistent with the simulation
that wrote the restart file. In particular, if you want to change the
region motion attributes (e.g. its velocity), then you should ensure
the postition/orientation of the region at the initial restart
the position/orientation of the region at the initial restart
timestep is the same as it was on the timestep the restart file was
written. If this is not possible, you may need to ignore info in the
restart file by defining a new fix wall/gran/region command in your

2
doc/src/fix_wall_piston.txt
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@ -24,7 +24,7 @@ keyword = {pos} or {vel} or {ramp} or {units} :l
{ramp} = use a linear velocity ramp from 0 to vz
{temp} args = target damp seed extent
target = target velocity for region immediately ahead of the piston
damp = damping paramter (time units)
damp = damping parameter (time units)
seed = random number seed for langevin kicks
extent = extent of thermostated region (distance units)
{units} value = {lattice} or {box}

2
doc/src/if.txt
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@ -93,7 +93,7 @@ system temperature has reached a certain value, and if so, breaks out
of the loop to finish the run. Note that any variable could be
checked, so long as it is current on the timestep when the run
completes. As explained on the "variable"_variable.html doc page,
this can be insured by includig the variable in thermodynamic output.
this can be insured by including the variable in thermodynamic output.
variable myTemp equal temp
label loop

2
doc/src/improper_hybrid.txt
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@ -60,7 +60,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
Unlike other improper styles, the hybrid improper style does not store
improper coefficient info for individual sub-styles in a "binary
restart files"_restart.html. Thus when retarting a simulation from a
restart files"_restart.html. Thus when restarting a simulation from a
restart file, you need to re-specify improper_coeff commands.
[Related commands:]

2
doc/src/jump.txt
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@ -87,7 +87,7 @@ system temperature has reached a certain value, and if so, breaks out
of the loop to finish the run. Note that any variable could be
checked, so long as it is current on the timestep when the run
completes. As explained on the "variable"_variable.html doc page,
this can be insured by includig the variable in thermodynamic output.
this can be insured by including the variable in thermodynamic output.
variable myTemp equal temp
label loop

2
doc/src/kspace_style.txt
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@ -341,7 +341,7 @@ kspace_style none :pre
Adam Hilger, NY (1989).
:link(Kolafa)
[(Kolafa)] Kolafa and Perram, Molecular Simualtion, 9, 351 (1992).
[(Kolafa)] Kolafa and Perram, Molecular Simulation, 9, 351 (1992).
:link(Petersen)
[(Petersen)] Petersen, J Chem Phys, 103, 3668 (1995).

2
doc/src/minimize.txt
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@ -201,7 +201,7 @@ minimum to the specified energy or force tolerance.
Note that a cutoff Lennard-Jones potential (and others) can be shifted
so that its energy is 0.0 at the cutoff via the
"pair_modify"_pair_modify.html command. See the doc pages for
inidividual "pair styles"_pair_style.html for details. Note that
individual "pair styles"_pair_style.html for details. Note that
Coulombic potentials always have a cutoff, unless versions with a
long-range component are used (e.g. "pair_style
lj/cut/coul/long"_pair_lj.html). The CHARMM potentials go to 0.0 at

8
doc/src/neb.txt
View File

@ -58,7 +58,7 @@ would see with one or more physical processors per replica. See
discussion.
NOTE: As explained below, a NEB calculation perfoms a damped dynamics
minimization across all the replicas. The mimimizer uses whatever
minimization across all the replicas. The minimizer uses whatever
timestep you have defined in your input script, via the
"timestep"_timestep.html command. Often NEB will converge more
quickly if you use a timestep about 10x larger than you would normally
@ -81,7 +81,7 @@ inter-replica springs and the forces they feel and their motion is
computed in the usual way due only to other atoms within their
replica. Conceptually, the non-NEB atoms provide a background force
field for the NEB atoms. They can be allowed to move during the NEB
minimiation procedure (which will typically induce different
minimization procedure (which will typically induce different
coordinates for non-NEB atoms in different replicas), or held fixed
using other LAMMPS commands such as "fix setforce"_fix_setforce.html.
Note that the "partition"_partition.html command can be used to invoke
@ -97,7 +97,7 @@ Conceptually, the initial configuration for the first replica should
be a state with all the atoms (NEB and non-NEB) having coordinates on
one side of the energy barrier. A perfect energy minimum is not
required, since atoms in the first replica experience no spring forces
from the 2nd replica. Thus the damped dynamics minimizaiton will
from the 2nd replica. Thus the damped dynamics minimization will
drive the first replica to an energy minimum if it is not already
there. However, you will typically get better convergence if the
initial state is already at a minimum. For example, for a system with
@ -366,7 +366,7 @@ parameters.
There are 2 Python scripts provided in the tools/python directory,
neb_combine.py and neb_final.py, which are useful in analyzing output
from a NEB calculation. Assume a NEB simulation with M replicas, and
the NEB atoms labelled with a specific atom type.
the NEB atoms labeled with a specific atom type.
The neb_combine.py script extracts atom coords for the NEB atoms from
all M dump files and creates a single dump file where each snapshot

12
doc/src/package.txt
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@ -110,7 +110,7 @@ USER-OMP.
If this command is specified in an input script, it must be near the
top of the script, before the simulation box has been defined. This
is because it specifies settings that the accelerator packages use in
their intialization, before a simultion is defined.
their initialization, before a simulation is defined.
This command can also be specified from the command-line when
launching LAMMPS, using the "-pk" "command-line
@ -199,7 +199,7 @@ the default.
The {split} keyword can be used for load balancing force calculations
between CPU and GPU cores in GPU-enabled pair styles. If 0 < {split} <
1.0, a fixed fraction of particles is offloaded to the GPU while force
calculation for the other particles occurs simulataneously on the CPU.
calculation for the other particles occurs simultaneously on the CPU.
If {split} < 0.0, the optimal fraction (based on CPU and GPU timings)
is calculated every 25 timesteps, i.e. dynamic load-balancing across
the CPU and GPU is performed. If {split} = 1.0, all force
@ -295,7 +295,7 @@ For more details, including examples of how to set the OMP_NUM_THREADS
environment variable, see the discussion of the {Nthreads} setting on
this doc page for the "package omp" command. Nthreads is a required
argument for the USER-OMP package. Its meaning is exactly the same
for the USER-INTEL pacakge.
for the USER-INTEL package.
NOTE: If you build LAMMPS with both the USER-INTEL and USER-OMP
packages, be aware that both packages allow setting of the {Nthreads}
@ -347,7 +347,7 @@ automatically throughout the run. This typically give performance
within 5 to 10 percent of the optimal fixed fraction.
The {ghost} keyword determines whether or not ghost atoms, i.e. atoms
at the boundaries of proessor sub-domains, are offloaded for neighbor
at the boundaries of processor sub-domains, are offloaded for neighbor
and force calculations. When the value = "no", ghost atoms are not
offloaded. This option can reduce the amount of data transfer with
the coprocessor and can also overlap MPI communication of forces with
@ -516,7 +516,7 @@ for OpenMPI. Check your MPI documentation for additional details.
What combination of threads and MPI tasks gives the best performance
is difficult to predict and can depend on many components of your
input. Not all features of LAMMPS support OpenMP threading via the
USER-OMP packaage and the parallel efficiency can be very different,
USER-OMP package and the parallel efficiency can be very different,
too.
Optional keyword/value pairs can also be specified. Each has a
@ -527,7 +527,7 @@ multi-threaded in addition to force calculations. If {neigh} is set
to {no} then neighbor list calculation is performed only by MPI tasks
with no OpenMP threading. If {mode} is {yes} (the default), a
multi-threaded neighbor list build is used. Using {neigh} = {yes} is
almost always faster and should produce idential neighbor lists at the
almost always faster and should produce identical neighbor lists at the
expense of using more memory. Specifically, neighbor list pages are
allocated for all threads at the same time and each thread works
within its own pages.

2
doc/src/pair_airebo.txt
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@ -53,7 +53,7 @@ The {rebo} pair style computes the Reactive Empirical Bond Order (REBO)
Potential of "(Brenner)"_#Brenner. Note that this is the so-called
2nd generation REBO from 2002, not the original REBO from 1990.
As discussed below, 2nd generation REBO is closely related to the
intial AIREBO; it is just a subset of the potential energy terms.
initial AIREBO; it is just a subset of the potential energy terms.
The AIREBO potential consists of three terms:

8
doc/src/pair_bop.txt
View File

@ -36,11 +36,11 @@ developed by Pettifor ("Pettifor_1"_#Pettifor_1,
"Pettifor_2"_#Pettifor_2, "Pettifor_3"_#Pettifor_3) and later updated
by Murdick, Zhou, and Ward ("Murdick"_#Murdick, "Ward"_#Ward).
Currently, BOP potential files for these systems are provided with
LAMMPS: AlCu, CCu, CdTe, CdTeSe, CdZnTe, CuH, GaAs. A sysstem with
LAMMPS: AlCu, CCu, CdTe, CdTeSe, CdZnTe, CuH, GaAs. A system with
only a subset of these elements, including a single element (e.g. C or
Cu or Al or Ga or Zn or CdZn), can also be modeled by using the
appropriate alloy file and assigning all atom types to the
singleelement or subset of elements via the pair_coeff command, as
single element or subset of elements via the pair_coeff command, as
discussed below.
The BOP potential consists of three terms:
@ -49,7 +49,7 @@ The BOP potential consists of three terms:
where phi_ij(r_ij) is a short-range two-body function representing the
repulsion between a pair of ion cores, beta_(sigma,ij)(r_ij) and
beta_(sigma,ij)(r_ij) are respectively sigma and pi bond ingtegrals,
beta_(sigma,ij)(r_ij) are respectively sigma and pi bond integrals,
THETA_(sigma,ij) and THETA_(pi,ij) are sigma and pi bond-orders, and
U_prom is the promotion energy for sp-valent systems.
@ -299,7 +299,7 @@ of the g_(sigma,jik)(THETA_ijk) for e_1-e_1-e_1 interaction. The
function can contain up to 10 term thus 10 constants. The first line
can contain up to five constants. If the spline has more than five
terms the second line will contain the remaining constants The
following lines will then contain the constants for the remainaing g0,
following lines will then contain the constants for the remaining g0,
g1, g2... (for e_1-e_1-e_2) and the other three body
interactions :l
:ule

2
doc/src/pair_comb.txt
View File

@ -86,7 +86,7 @@ For style {comb}, the provided potential file {ffield.comb} contains
all currently-available 2nd generation COMB parameterizations: for Si,
Cu, Hf, Ti, O, their oxides and Zr, Zn and U metals. For style
{comb3}, the potential file {ffield.comb3} contains all
currently-available 3rd generation COMB paramterizations: O, Cu, N, C,
currently-available 3rd generation COMB parameterizations: O, Cu, N, C,
H, Ti, Zn and Zr. The status of the optimization of the compounds, for
example Cu<sub>2</sub>O, TiN and hydrocarbons, are given in the
following table:

6
doc/src/pair_coul.txt
View File

@ -130,7 +130,7 @@ where {alpha} is the damping parameter, and erc() and erfc() are
error-function and complementary error-function terms. This potential
is essentially a short-range, spherically-truncated,
charge-neutralized, shifted, pairwise {1/r} summation. With a
manipulation of adding and substracting a self term (for i = j) to the
manipulation of adding and subtracting a self term (for i = j) to the
first and second term on the right-hand-side, respectively, and a
small enough {alpha} damping parameter, the second term shrinks and
the potential becomes a rapidly-converging real-space summation. With
@ -188,7 +188,7 @@ but there is no conceptual problem with extending it to nitrides and
carbides (such as SiC, TiN). Pair coul/strietz used by itself or with
any other pair style such as EAM, MEAM, Tersoff, or LJ in
hybrid/overlay mode. To do this, you would need to provide a
Streitz-Mintmire parameterizaion for the material being modeled.
Streitz-Mintmire parameterization for the material being modeled.
:line
@ -222,7 +222,7 @@ molecule is 500, then its 2 H atoms must have IDs 501 and 502.
See the "howto section"_Section_howto.html#howto_8 for more
information on how to use the TIP4P pair styles and lists of
parameters to set. Note that the neighobr list cutoff for Coulomb
parameters to set. Note that the neighbor list cutoff for Coulomb
interactions is effectively extended by a distance 2*qdist when using
the TIP4P pair style, to account for the offset distance of the
fictitious charges on O atoms in water molecules. Thus it is

6
doc/src/pair_coul_diel.txt
View File

@ -23,11 +23,11 @@ pair_coeff 1 4 78. 1.375 0.112 :pre
[Description:]
Style {coul/diel} computes a Coulomb correction for implict solvent
ion interactions in which the dielectric perimittivity is distance dependent.
Style {coul/diel} computes a Coulomb correction for implicit solvent
ion interactions in which the dielectric permittivity is distance dependent.
The dielectric permittivity epsilon_D(r) connects to limiting regimes:
One limit is defined by a small dielectric permittivity (close to vacuum)
at or close to contact seperation between the ions. At larger separations
at or close to contact separation between the ions. At larger separations
the dielectric permittivity reaches a bulk value used in the regular Coulomb
interaction coul/long or coul/cut.
The transition is modeled by a hyperbolic function which is incorporated

2
doc/src/pair_edip.txt
View File

@ -95,7 +95,7 @@ entries would be required, etc.
At the moment, only a single element parametrization is
implemented. However, the author is not aware of other
multi-element EDIP parametrizations. If you know any and
multi-element EDIP parameterization. If you know any and
you are interest in that, please contact the author of
the EDIP package.

6
doc/src/pair_eff.txt
View File

@ -149,7 +149,7 @@ command.
:line
The {limit/eradius} and {pressure/evirials} keywrods are optional.
The {limit/eradius} and {pressure/evirials} keywords are optional.
Neither or both must be specified. If not specified they are unset.
The {limit/eradius} keyword is used to restrain electron size from
@ -197,7 +197,7 @@ partitioning changes, the total energy remains similar).
:line
NOTE: This implemention of eFF gives a reasonably accurate description
NOTE: This implementation of eFF gives a reasonably accurate description
for systems containing nuclei from Z = 1-6 in "all electron"
representations. For systems with increasingly non-spherical
electrons, Users should use the ECP representations. ECPs are now
@ -284,7 +284,7 @@ that package. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
These pair styles require that particles store electron attributes
such as radius, radial velocity, and radital force, as defined by the
such as radius, radial velocity, and radial force, as defined by the
"atom_style"_atom_style.html. The {electron} atom style does all of
this.

2
doc/src/pair_eim.txt
View File

@ -97,7 +97,7 @@ pair_coeff * * Na Cl ffield.eim Na Na Na Cl :pre
The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The filename is the EIM potential file. The Na and Cl arguments
(before the file name) are the two elements for which info will be
extracted from the potentail file. The first three trailing Na
extracted from the potential file. The first three trailing Na
arguments map LAMMPS atom types 1,2,3 to the EIM Na element. The
final Cl argument maps LAMMPS atom type 4 to the EIM Cl element.

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