From 007f3c66a033805cbc6755fce6920da6e3e1385c Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 7 Mar 2017 00:51:31 -0500 Subject: [PATCH] Third batch of spelling fixes in manual --- doc/src/2001/input_commands.html | 4 ++-- doc/src/99/basics.html | 2 +- doc/src/99/crib.html | 2 +- doc/src/99/input_commands.html | 2 +- doc/src/Section_errors.txt | 8 +++---- doc/src/Section_history.txt | 2 +- doc/src/Section_howto.txt | 24 +++++++++---------- doc/src/Section_modify.txt | 6 ++--- doc/src/Section_packages.txt | 10 ++++---- doc/src/Section_perf.txt | 2 +- doc/src/Section_python.txt | 12 +++++----- doc/src/Section_start.txt | 14 +++++------ .../atc/man_consistent_fe_initialization.html | 2 +- doc/src/accelerate_intel.txt | 4 ++-- doc/src/accelerate_kokkos.txt | 2 +- doc/src/angle_hybrid.txt | 2 +- doc/src/atom_modify.txt | 8 +++---- doc/src/atom_style.txt | 4 ++-- doc/src/balance.txt | 16 ++++++------- doc/src/body.txt | 4 ++-- doc/src/bond_hybrid.txt | 2 +- doc/src/change_box.txt | 4 ++-- doc/src/comm_style.txt | 2 +- doc/src/compute_angmom_chunk.txt | 2 +- doc/src/compute_chunk_atom.txt | 2 +- doc/src/compute_cna_atom.txt | 2 +- doc/src/compute_com.txt | 2 +- doc/src/compute_damage_atom.txt | 2 +- doc/src/compute_dilatation_atom.txt | 2 +- doc/src/compute_displace_atom.txt | 2 +- doc/src/compute_event_displace.txt | 2 +- doc/src/compute_msd.txt | 2 +- doc/src/compute_msd_chunk.txt | 2 +- doc/src/compute_msd_nongauss.txt | 4 ++-- doc/src/compute_pair.txt | 2 +- doc/src/compute_plasticity_atom.txt | 2 +- doc/src/compute_rdf.txt | 2 +- doc/src/compute_saed.txt | 2 +- doc/src/compute_temp_chunk.txt | 2 +- doc/src/compute_temp_profile.txt | 2 +- doc/src/compute_vacf.txt | 2 +- doc/src/create_atoms.txt | 2 +- doc/src/dihedral_hybrid.txt | 2 +- doc/src/dump.txt | 2 +- doc/src/dump_image.txt | 8 +++---- doc/src/dump_modify.txt | 2 +- doc/src/fix_ave_chunk.txt | 2 +- doc/src/fix_ave_correlate.txt | 2 +- doc/src/fix_ave_time.txt | 2 +- doc/src/fix_balance.txt | 12 +++++----- doc/src/fix_bond_break.txt | 4 ++-- doc/src/fix_bond_create.txt | 4 ++-- doc/src/fix_bond_swap.txt | 2 +- doc/src/fix_box_relax.txt | 4 ++-- doc/src/fix_cmap.txt | 2 +- doc/src/fix_controller.txt | 2 +- doc/src/fix_deposit.txt | 6 ++--- doc/src/fix_evaporate.txt | 4 ++-- doc/src/fix_indent.txt | 4 ++-- doc/src/fix_lb_fluid.txt | 2 +- doc/src/fix_modify.txt | 2 +- doc/src/fix_move.txt | 2 +- doc/src/fix_mscg.txt | 2 +- doc/src/fix_phonon.txt | 2 +- doc/src/fix_pour.txt | 4 ++-- doc/src/fix_property_atom.txt | 2 +- doc/src/fix_qeq.txt | 2 +- doc/src/fix_qeq_comb.txt | 6 ++--- doc/src/fix_restrain.txt | 2 +- doc/src/fix_rigid.txt | 2 +- doc/src/fix_rx.txt | 2 +- doc/src/fix_saed_vtk.txt | 4 ++-- doc/src/fix_smd_wall_surface.txt | 2 +- doc/src/fix_spring_self.txt | 2 +- doc/src/fix_srd.txt | 8 +++---- doc/src/fix_temp_csvr.txt | 2 +- doc/src/fix_temp_rescale.txt | 2 +- doc/src/fix_tfmc.txt | 2 +- doc/src/fix_ttm.txt | 4 ++-- doc/src/fix_vector.txt | 2 +- doc/src/fix_viscosity.txt | 2 +- doc/src/fix_wall.txt | 2 +- doc/src/fix_wall_gran.txt | 2 +- doc/src/fix_wall_gran_region.txt | 4 ++-- doc/src/fix_wall_piston.txt | 2 +- doc/src/if.txt | 2 +- doc/src/improper_hybrid.txt | 2 +- doc/src/jump.txt | 2 +- doc/src/kspace_style.txt | 2 +- doc/src/minimize.txt | 2 +- doc/src/neb.txt | 8 +++---- doc/src/package.txt | 12 +++++----- doc/src/pair_airebo.txt | 2 +- doc/src/pair_bop.txt | 8 +++---- doc/src/pair_comb.txt | 2 +- doc/src/pair_coul.txt | 6 ++--- doc/src/pair_coul_diel.txt | 6 ++--- doc/src/pair_edip.txt | 2 +- doc/src/pair_eff.txt | 6 ++--- doc/src/pair_eim.txt | 2 +- doc/src/pair_exp6_rx.txt | 4 ++-- doc/src/pair_gran.txt | 2 +- doc/src/pair_hbond_dreiding.txt | 2 +- doc/src/pair_hybrid.txt | 2 +- doc/src/pair_lj.txt | 2 +- doc/src/pair_lj_long.txt | 2 +- doc/src/pair_lj_smooth.txt | 2 +- doc/src/pair_lj_soft.txt | 8 +++---- doc/src/pair_lubricate.txt | 2 +- doc/src/pair_mgpt.txt | 2 +- doc/src/pair_peri.txt | 2 +- doc/src/pair_quip.txt | 4 ++-- doc/src/pair_resquared.txt | 6 ++--- doc/src/pair_smd_ulsph.txt | 2 +- doc/src/pair_soft.txt | 2 +- doc/src/pair_sph_idealgas.txt | 2 +- doc/src/pair_sph_lj.txt | 2 +- doc/src/pair_sph_taitwater.txt | 2 +- doc/src/pair_table.txt | 2 +- doc/src/pair_tri_lj.txt | 2 +- doc/src/processors.txt | 6 ++--- doc/src/python.txt | 4 ++-- doc/src/read_data.txt | 2 +- doc/src/read_dump.txt | 4 ++-- doc/src/read_restart.txt | 2 +- doc/src/region.txt | 4 ++-- doc/src/rerun.txt | 6 ++--- doc/src/restart.txt | 2 +- doc/src/run_style.txt | 6 ++--- doc/src/set.txt | 2 +- doc/src/thermo.txt | 2 +- doc/src/thermo_style.txt | 2 +- doc/src/timer.txt | 4 ++-- doc/src/tutorial_drude.txt | 4 ++-- doc/src/units.txt | 2 +- doc/src/variable.txt | 14 +++++------ doc/src/write_dump.txt | 2 +- doc/utils/sphinx-config/false_positives.txt | 6 ++++- 138 files changed, 254 insertions(+), 250 deletions(-) diff --git a/doc/src/2001/input_commands.html b/doc/src/2001/input_commands.html index f80185a9f3..797d6bec4e 100644 --- a/doc/src/2001/input_commands.html +++ b/doc/src/2001/input_commands.html @@ -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

diff --git a/doc/src/99/basics.html b/doc/src/99/basics.html index 0276460723..b6236f4bf9 100644 --- a/doc/src/99/basics.html +++ b/doc/src/99/basics.html @@ -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.

diff --git a/doc/src/99/crib.html b/doc/src/99/crib.html index 0944980b17..80d64d3703 100755 --- a/doc/src/99/crib.html +++ b/doc/src/99/crib.html @@ -40,7 +40,7 @@ Note: this file is somewhat out-of-date for LAMMPS 99.

  • maxtype = max # of atom types
  • - maxbond = max # of bonds to compute on one procesor + maxbond = max # of bonds to compute on one processor
  • maxangle = max # of angles to compute on one processor
  • diff --git a/doc/src/99/input_commands.html b/doc/src/99/input_commands.html index 41b9cb4f7a..baea02b5c2 100644 --- a/doc/src/99/input_commands.html +++ b/doc/src/99/input_commands.html @@ -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 diff --git a/doc/src/Section_errors.txt b/doc/src/Section_errors.txt index c66a276bfa..832c5718ab 100644 --- a/doc/src/Section_errors.txt +++ b/doc/src/Section_errors.txt @@ -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 diff --git a/doc/src/Section_history.txt b/doc/src/Section_history.txt index 438284c9da..93e9947506 100644 --- a/doc/src/Section_history.txt +++ b/doc/src/Section_history.txt @@ -37,7 +37,7 @@ pitfalls or alternatives. Please see some of the closed issues for examples of how to suggest code enhancements, submit proposed changes, or report -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 diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt index 010462ce7e..8cfbe1c46c 100644 --- a/doc/src/Section_howto.txt +++ b/doc/src/Section_howto.txt @@ -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): diff --git a/doc/src/Section_modify.txt b/doc/src/Section_modify.txt index 2e2d5d77f3..7d1fe03d01 100644 --- a/doc/src/Section_modify.txt +++ b/doc/src/Section_modify.txt @@ -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 diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt index 00b1fb1067..3df66a6a5f 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -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 diff --git a/doc/src/Section_perf.txt b/doc/src/Section_perf.txt index 39fe734cce..0cc79b0943 100644 --- a/doc/src/Section_perf.txt +++ b/doc/src/Section_perf.txt @@ -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. diff --git a/doc/src/Section_python.txt b/doc/src/Section_python.txt index e1d5f0f867..50807e2d95 100644 --- a/doc/src/Section_python.txt +++ b/doc/src/Section_python.txt @@ -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) diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt index 9f6c113449..47643569e6 100644 --- a/doc/src/Section_start.txt +++ b/doc/src/Section_start.txt @@ -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. diff --git a/doc/src/USER/atc/man_consistent_fe_initialization.html b/doc/src/USER/atc/man_consistent_fe_initialization.html index 2f3bf4a6cf..f4c33f5076 100644 --- a/doc/src/USER/atc/man_consistent_fe_initialization.html +++ b/doc/src/USER/atc/man_consistent_fe_initialization.html @@ -27,7 +27,7 @@ syntax

    • fix_modify AtC consistent_fe_initialization <on | off>

    examples

    diff --git a/doc/src/accelerate_intel.txt b/doc/src/accelerate_intel.txt index cbb5e2e435..f7f655a639 100644 --- a/doc/src/accelerate_intel.txt +++ b/doc/src/accelerate_intel.txt @@ -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 diff --git a/doc/src/accelerate_kokkos.txt b/doc/src/accelerate_kokkos.txt index 26e35e23d1..3bfd4bf379 100644 --- a/doc/src/accelerate_kokkos.txt +++ b/doc/src/accelerate_kokkos.txt @@ -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 diff --git a/doc/src/angle_hybrid.txt b/doc/src/angle_hybrid.txt index 8c90e1fd3a..bdd3707ccb 100644 --- a/doc/src/angle_hybrid.txt +++ b/doc/src/angle_hybrid.txt @@ -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:] diff --git a/doc/src/atom_modify.txt b/doc/src/atom_modify.txt index 89572c0c72..d5c82f16ac 100644 --- a/doc/src/atom_modify.txt +++ b/doc/src/atom_modify.txt @@ -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) diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt index 6a8588e08a..3d5c0a4f3d 100644 --- a/doc/src/atom_style.txt +++ b/doc/src/atom_style.txt @@ -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 diff --git a/doc/src/balance.txt b/doc/src/balance.txt index 9951e44a91..9aeb03392f 100644 --- a/doc/src/balance.txt +++ b/doc/src/balance.txt @@ -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. diff --git a/doc/src/body.txt b/doc/src/body.txt index 44bd815205..d44f82d4cc 100644 --- a/doc/src/body.txt +++ b/doc/src/body.txt @@ -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. diff --git a/doc/src/bond_hybrid.txt b/doc/src/bond_hybrid.txt index 0b5731dcb4..400c3e0be4 100644 --- a/doc/src/bond_hybrid.txt +++ b/doc/src/bond_hybrid.txt @@ -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:] diff --git a/doc/src/change_box.txt b/doc/src/change_box.txt index c9c4d7a3b6..a41463baaf 100644 --- a/doc/src/change_box.txt +++ b/doc/src/change_box.txt @@ -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 diff --git a/doc/src/comm_style.txt b/doc/src/comm_style.txt index 667938768b..8248d654d3 100644 --- a/doc/src/comm_style.txt +++ b/doc/src/comm_style.txt @@ -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 diff --git a/doc/src/compute_angmom_chunk.txt b/doc/src/compute_angmom_chunk.txt index 439ff5192c..813da15eea 100644 --- a/doc/src/compute_angmom_chunk.txt +++ b/doc/src/compute_angmom_chunk.txt @@ -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 diff --git a/doc/src/compute_chunk_atom.txt b/doc/src/compute_chunk_atom.txt index b1550875a4..b3b09ffa71 100644 --- a/doc/src/compute_chunk_atom.txt +++ b/doc/src/compute_chunk_atom.txt @@ -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. diff --git a/doc/src/compute_cna_atom.txt b/doc/src/compute_cna_atom.txt index 9867d86efb..74240b515d 100644 --- a/doc/src/compute_cna_atom.txt +++ b/doc/src/compute_cna_atom.txt @@ -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: diff --git a/doc/src/compute_com.txt b/doc/src/compute_com.txt index a5fdb224bc..b0e0c14e42 100644 --- a/doc/src/compute_com.txt +++ b/doc/src/compute_com.txt @@ -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 diff --git a/doc/src/compute_damage_atom.txt b/doc/src/compute_damage_atom.txt index 94f49492d1..918fbf65ef 100644 --- a/doc/src/compute_damage_atom.txt +++ b/doc/src/compute_damage_atom.txt @@ -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:] diff --git a/doc/src/compute_dilatation_atom.txt b/doc/src/compute_dilatation_atom.txt index 04409f7e45..ce00f7f12a 100644 --- a/doc/src/compute_dilatation_atom.txt +++ b/doc/src/compute_dilatation_atom.txt @@ -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:] diff --git a/doc/src/compute_displace_atom.txt b/doc/src/compute_displace_atom.txt index 566dcfc0a0..decf0bc8b9 100644 --- a/doc/src/compute_displace_atom.txt +++ b/doc/src/compute_displace_atom.txt @@ -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). diff --git a/doc/src/compute_event_displace.txt b/doc/src/compute_event_displace.txt index 69532f1154..5e3a0c8599 100644 --- a/doc/src/compute_event_displace.txt +++ b/doc/src/compute_event_displace.txt @@ -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:] diff --git a/doc/src/compute_msd.txt b/doc/src/compute_msd.txt index 42dbca255d..f806c5e292 100644 --- a/doc/src/compute_msd.txt +++ b/doc/src/compute_msd.txt @@ -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 diff --git a/doc/src/compute_msd_chunk.txt b/doc/src/compute_msd_chunk.txt index 7382ca87de..7f31b61ed0 100644 --- a/doc/src/compute_msd_chunk.txt +++ b/doc/src/compute_msd_chunk.txt @@ -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 diff --git a/doc/src/compute_msd_nongauss.txt b/doc/src/compute_msd_nongauss.txt index 11a51229c7..198da999e0 100644 --- a/doc/src/compute_msd_nongauss.txt +++ b/doc/src/compute_msd_nongauss.txt @@ -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) diff --git a/doc/src/compute_pair.txt b/doc/src/compute_pair.txt index 7a98709f89..0602dab81b 100644 --- a/doc/src/compute_pair.txt +++ b/doc/src/compute_pair.txt @@ -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 diff --git a/doc/src/compute_plasticity_atom.txt b/doc/src/compute_plasticity_atom.txt index 75491cfb14..788213fc65 100644 --- a/doc/src/compute_plasticity_atom.txt +++ b/doc/src/compute_plasticity_atom.txt @@ -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:] diff --git a/doc/src/compute_rdf.txt b/doc/src/compute_rdf.txt index 1c9de277bc..acbc0e4f0c 100644 --- a/doc/src/compute_rdf.txt +++ b/doc/src/compute_rdf.txt @@ -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 diff --git a/doc/src/compute_saed.txt b/doc/src/compute_saed.txt index 658f41cdca..aadda49533 100644 --- a/doc/src/compute_saed.txt +++ b/doc/src/compute_saed.txt @@ -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) diff --git a/doc/src/compute_temp_chunk.txt b/doc/src/compute_temp_chunk.txt index 2e205a370b..f877f6ece8 100644 --- a/doc/src/compute_temp_chunk.txt +++ b/doc/src/compute_temp_chunk.txt @@ -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 diff --git a/doc/src/compute_temp_profile.txt b/doc/src/compute_temp_profile.txt index 54eebd6d8f..3b6f774d33 100644 --- a/doc/src/compute_temp_profile.txt +++ b/doc/src/compute_temp_profile.txt @@ -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. diff --git a/doc/src/compute_vacf.txt b/doc/src/compute_vacf.txt index 29ada25c9c..a0d9a3c5f7 100644 --- a/doc/src/compute_vacf.txt +++ b/doc/src/compute_vacf.txt @@ -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 diff --git a/doc/src/create_atoms.txt b/doc/src/create_atoms.txt index ec7a6f4d8a..da9c8809d0 100644 --- a/doc/src/create_atoms.txt +++ b/doc/src/create_atoms.txt @@ -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 diff --git a/doc/src/dihedral_hybrid.txt b/doc/src/dihedral_hybrid.txt index bddc0c0ec8..8cb40eff44 100644 --- a/doc/src/dihedral_hybrid.txt +++ b/doc/src/dihedral_hybrid.txt @@ -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:] diff --git a/doc/src/dump.txt b/doc/src/dump.txt index 5898f4ed03..1c65b1cdbf 100644 --- a/doc/src/dump.txt +++ b/doc/src/dump.txt @@ -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 diff --git a/doc/src/dump_image.txt b/doc/src/dump_image.txt index a1fc527ec4..3fa267d2b0 100644 --- a/doc/src/dump_image.txt +++ b/doc/src/dump_image.txt @@ -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. diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt index 7eafffa24c..b5daa6416e 100644 --- a/doc/src/dump_modify.txt +++ b/doc/src/dump_modify.txt @@ -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). diff --git a/doc/src/fix_ave_chunk.txt b/doc/src/fix_ave_chunk.txt index a1fe6ae6d0..8943192176 100644 --- a/doc/src/fix_ave_chunk.txt +++ b/doc/src/fix_ave_chunk.txt @@ -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 diff --git a/doc/src/fix_ave_correlate.txt b/doc/src/fix_ave_correlate.txt index 6ae9fe53b6..371f2f66a8 100644 --- a/doc/src/fix_ave_correlate.txt +++ b/doc/src/fix_ave_correlate.txt @@ -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 diff --git a/doc/src/fix_ave_time.txt b/doc/src/fix_ave_time.txt index b04f17e460..266e3f0e38 100644 --- a/doc/src/fix_ave_time.txt +++ b/doc/src/fix_ave_time.txt @@ -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, diff --git a/doc/src/fix_balance.txt b/doc/src/fix_balance.txt index 16ea1d39f9..f148e6f996 100644 --- a/doc/src/fix_balance.txt +++ b/doc/src/fix_balance.txt @@ -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. diff --git a/doc/src/fix_bond_break.txt b/doc/src/fix_bond_break.txt index d27246872c..83364b9efb 100644 --- a/doc/src/fix_bond_break.txt +++ b/doc/src/fix_bond_break.txt @@ -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 diff --git a/doc/src/fix_bond_create.txt b/doc/src/fix_bond_create.txt index 949eb7e7e3..a44c3103dd 100644 --- a/doc/src/fix_bond_create.txt +++ b/doc/src/fix_bond_create.txt @@ -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 diff --git a/doc/src/fix_bond_swap.txt b/doc/src/fix_bond_swap.txt index 5290abe185..ca7069e247 100644 --- a/doc/src/fix_bond_swap.txt +++ b/doc/src/fix_bond_swap.txt @@ -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 diff --git a/doc/src/fix_box_relax.txt b/doc/src/fix_box_relax.txt index e775074bcc..83e5a82652 100644 --- a/doc/src/fix_box_relax.txt +++ b/doc/src/fix_box_relax.txt @@ -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. diff --git a/doc/src/fix_cmap.txt b/doc/src/fix_cmap.txt index 9edd660b04..c943cde489 100644 --- a/doc/src/fix_cmap.txt +++ b/doc/src/fix_cmap.txt @@ -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 diff --git a/doc/src/fix_controller.txt b/doc/src/fix_controller.txt index 3d590cd3e1..cd4d6adfdf 100644 --- a/doc/src/fix_controller.txt +++ b/doc/src/fix_controller.txt @@ -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 diff --git a/doc/src/fix_deposit.txt b/doc/src/fix_deposit.txt index ea9c5643dd..a1dd5f6434 100644 --- a/doc/src/fix_deposit.txt +++ b/doc/src/fix_deposit.txt @@ -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. diff --git a/doc/src/fix_evaporate.txt b/doc/src/fix_evaporate.txt index ace1fae63a..ed6c6d0377 100644 --- a/doc/src/fix_evaporate.txt +++ b/doc/src/fix_evaporate.txt @@ -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. diff --git a/doc/src/fix_indent.txt b/doc/src/fix_indent.txt index be13925897..c9a791ae4e 100644 --- a/doc/src/fix_indent.txt +++ b/doc/src/fix_indent.txt @@ -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 diff --git a/doc/src/fix_lb_fluid.txt b/doc/src/fix_lb_fluid.txt index 62265a3bc1..fc6203b0f2 100644 --- a/doc/src/fix_lb_fluid.txt +++ b/doc/src/fix_lb_fluid.txt @@ -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:] diff --git a/doc/src/fix_modify.txt b/doc/src/fix_modify.txt index afdfa9e892..9c95cdc452 100644 --- a/doc/src/fix_modify.txt +++ b/doc/src/fix_modify.txt @@ -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 diff --git a/doc/src/fix_move.txt b/doc/src/fix_move.txt index 83af5b273a..7cb40ad132 100644 --- a/doc/src/fix_move.txt +++ b/doc/src/fix_move.txt @@ -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. diff --git a/doc/src/fix_mscg.txt b/doc/src/fix_mscg.txt index 6bd0876537..0e09f8a9c5 100644 --- a/doc/src/fix_mscg.txt +++ b/doc/src/fix_mscg.txt @@ -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. diff --git a/doc/src/fix_phonon.txt b/doc/src/fix_phonon.txt index 0f399f187b..aad6c2bfaa 100644 --- a/doc/src/fix_phonon.txt +++ b/doc/src/fix_phonon.txt @@ -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, diff --git a/doc/src/fix_pour.txt b/doc/src/fix_pour.txt index f1487c3aa7..f2c10184dd 100644 --- a/doc/src/fix_pour.txt +++ b/doc/src/fix_pour.txt @@ -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 diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt index 8c9164c25d..aef534ad25 100644 --- a/doc/src/fix_property_atom.txt +++ b/doc/src/fix_property_atom.txt @@ -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. diff --git a/doc/src/fix_qeq.txt b/doc/src/fix_qeq.txt index 049c3d8e2a..b1a1dd5c42 100644 --- a/doc/src/fix_qeq.txt +++ b/doc/src/fix_qeq.txt @@ -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:] diff --git a/doc/src/fix_qeq_comb.txt b/doc/src/fix_qeq_comb.txt index 58a541cc9d..30c5003e72 100644 --- a/doc/src/fix_qeq_comb.txt +++ b/doc/src/fix_qeq_comb.txt @@ -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 diff --git a/doc/src/fix_restrain.txt b/doc/src/fix_restrain.txt index 596ca54b67..c8ec20daaa 100644 --- a/doc/src/fix_restrain.txt +++ b/doc/src/fix_restrain.txt @@ -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: diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt index 54e9b16e6a..e086656f5d 100644 --- a/doc/src/fix_rigid.txt +++ b/doc/src/fix_rigid.txt @@ -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 diff --git a/doc/src/fix_rx.txt b/doc/src/fix_rx.txt index 5f29e34abe..6a800f3865 100644 --- a/doc/src/fix_rx.txt +++ b/doc/src/fix_rx.txt @@ -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:] diff --git a/doc/src/fix_saed_vtk.txt b/doc/src/fix_saed_vtk.txt index e21736b365..3523233cee 100644 --- a/doc/src/fix_saed_vtk.txt +++ b/doc/src/fix_saed_vtk.txt @@ -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. diff --git a/doc/src/fix_smd_wall_surface.txt b/doc/src/fix_smd_wall_surface.txt index 4ea592be1b..feb65b2312 100644 --- a/doc/src/fix_smd_wall_surface.txt +++ b/doc/src/fix_smd_wall_surface.txt @@ -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. diff --git a/doc/src/fix_spring_self.txt b/doc/src/fix_spring_self.txt index 3f3940cd11..68961a1512 100644 --- a/doc/src/fix_spring_self.txt +++ b/doc/src/fix_spring_self.txt @@ -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 diff --git a/doc/src/fix_srd.txt b/doc/src/fix_srd.txt index a432b511d1..31660fe77a 100644 --- a/doc/src/fix_srd.txt +++ b/doc/src/fix_srd.txt @@ -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 diff --git a/doc/src/fix_temp_csvr.txt b/doc/src/fix_temp_csvr.txt index c356070038..4129ad73c8 100644 --- a/doc/src/fix_temp_csvr.txt +++ b/doc/src/fix_temp_csvr.txt @@ -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 diff --git a/doc/src/fix_temp_rescale.txt b/doc/src/fix_temp_rescale.txt index 7369fca184..eff25297c1 100644 --- a/doc/src/fix_temp_rescale.txt +++ b/doc/src/fix_temp_rescale.txt @@ -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. diff --git a/doc/src/fix_tfmc.txt b/doc/src/fix_tfmc.txt index beb9f68933..3c81d62ee0 100644 --- a/doc/src/fix_tfmc.txt +++ b/doc/src/fix_tfmc.txt @@ -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 diff --git a/doc/src/fix_ttm.txt b/doc/src/fix_ttm.txt index 2ba84d4fa7..48dfd254a0 100644 --- a/doc/src/fix_ttm.txt +++ b/doc/src/fix_ttm.txt @@ -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 diff --git a/doc/src/fix_vector.txt b/doc/src/fix_vector.txt index 5bae961ada..47b3cfc67a 100644 --- a/doc/src/fix_vector.txt +++ b/doc/src/fix_vector.txt @@ -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 diff --git a/doc/src/fix_viscosity.txt b/doc/src/fix_viscosity.txt index 520d8b593a..5fbbc67ca5 100644 --- a/doc/src/fix_viscosity.txt +++ b/doc/src/fix_viscosity.txt @@ -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; diff --git a/doc/src/fix_wall.txt b/doc/src/fix_wall.txt index 024719f057..6d76956620 100644 --- a/doc/src/fix_wall.txt +++ b/doc/src/fix_wall.txt @@ -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. diff --git a/doc/src/fix_wall_gran.txt b/doc/src/fix_wall_gran.txt index 40cd5c8c74..5f1679604e 100644 --- a/doc/src/fix_wall_gran.txt +++ b/doc/src/fix_wall_gran.txt @@ -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. diff --git a/doc/src/fix_wall_gran_region.txt b/doc/src/fix_wall_gran_region.txt index cfee0d9977..92fb042194 100644 --- a/doc/src/fix_wall_gran_region.txt +++ b/doc/src/fix_wall_gran_region.txt @@ -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 diff --git a/doc/src/fix_wall_piston.txt b/doc/src/fix_wall_piston.txt index 594e3db06d..4d7756c237 100644 --- a/doc/src/fix_wall_piston.txt +++ b/doc/src/fix_wall_piston.txt @@ -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} diff --git a/doc/src/if.txt b/doc/src/if.txt index c678f4aa77..52fad5aea7 100644 --- a/doc/src/if.txt +++ b/doc/src/if.txt @@ -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 diff --git a/doc/src/improper_hybrid.txt b/doc/src/improper_hybrid.txt index a3bd9a973a..0c2beaef18 100644 --- a/doc/src/improper_hybrid.txt +++ b/doc/src/improper_hybrid.txt @@ -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:] diff --git a/doc/src/jump.txt b/doc/src/jump.txt index e746ea782a..1b1a209511 100644 --- a/doc/src/jump.txt +++ b/doc/src/jump.txt @@ -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 diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index e523c91d41..e5c47e8230 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -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). diff --git a/doc/src/minimize.txt b/doc/src/minimize.txt index 52701b3f54..a3f2c5d0bf 100644 --- a/doc/src/minimize.txt +++ b/doc/src/minimize.txt @@ -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 diff --git a/doc/src/neb.txt b/doc/src/neb.txt index 649e521eee..a5fa03552c 100644 --- a/doc/src/neb.txt +++ b/doc/src/neb.txt @@ -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 diff --git a/doc/src/package.txt b/doc/src/package.txt index cfb663d4b1..02afb8d620 100644 --- a/doc/src/package.txt +++ b/doc/src/package.txt @@ -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. diff --git a/doc/src/pair_airebo.txt b/doc/src/pair_airebo.txt index 6d0b1b0088..2e3083c34b 100644 --- a/doc/src/pair_airebo.txt +++ b/doc/src/pair_airebo.txt @@ -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: diff --git a/doc/src/pair_bop.txt b/doc/src/pair_bop.txt index 795d847fa6..9251fc4e70 100644 --- a/doc/src/pair_bop.txt +++ b/doc/src/pair_bop.txt @@ -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 diff --git a/doc/src/pair_comb.txt b/doc/src/pair_comb.txt index c060856d60..92e74bbba3 100644 --- a/doc/src/pair_comb.txt +++ b/doc/src/pair_comb.txt @@ -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 Cu2O, TiN and hydrocarbons, are given in the following table: diff --git a/doc/src/pair_coul.txt b/doc/src/pair_coul.txt index c598225e35..43bd13127a 100644 --- a/doc/src/pair_coul.txt +++ b/doc/src/pair_coul.txt @@ -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 diff --git a/doc/src/pair_coul_diel.txt b/doc/src/pair_coul_diel.txt index 9bd3b51c80..fc2042a901 100644 --- a/doc/src/pair_coul_diel.txt +++ b/doc/src/pair_coul_diel.txt @@ -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 diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt index 6881b53434..cdfc265752 100644 --- a/doc/src/pair_edip.txt +++ b/doc/src/pair_edip.txt @@ -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. diff --git a/doc/src/pair_eff.txt b/doc/src/pair_eff.txt index 6be8cdc785..ee7dc99932 100644 --- a/doc/src/pair_eff.txt +++ b/doc/src/pair_eff.txt @@ -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. diff --git a/doc/src/pair_eim.txt b/doc/src/pair_eim.txt index 8744d6d93e..e74bb364d4 100644 --- a/doc/src/pair_eim.txt +++ b/doc/src/pair_eim.txt @@ -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. diff --git a/doc/src/pair_exp6_rx.txt b/doc/src/pair_exp6_rx.txt index dafba2c44c..47045a5933 100644 --- a/doc/src/pair_exp6_rx.txt +++ b/doc/src/pair_exp6_rx.txt @@ -63,7 +63,7 @@ reaction kinetics solver is applied, where the difference is defined to be the internal chemical energy (uChem). The fourth argument specifies the type of scaling that will be used -to scale the EXP-6 paramters as reactions occur. Currently, there +to scale the EXP-6 parameters as reactions occur. Currently, there are three scaling options: {exponent}, {polynomial} and {none}. Exponent scaling requires two additional arguments for scaling @@ -72,7 +72,7 @@ is computed by phi^exponent, where phi is the number of molecules represented by the coarse-grain particle and exponent is specified as a pair coefficient argument for {Rm} and {epsilon}, respectively. The {Rm} and {epsilon} parameters are multiplied by the scaling -factor to give the scaled interaction paramters for the CG particle. +factor to give the scaled interaction parameters for the CG particle. Polynomial scaling requires a filename to be specified as a pair coeff argument. The file contains the coefficients to a fifth order diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt index d4530d37dd..373a82fa80 100644 --- a/doc/src/pair_gran.txt +++ b/doc/src/pair_gran.txt @@ -224,7 +224,7 @@ normal direction (along the line joining the 2 sphere centers). The last 3 (8-10) the components of the relative velocity in the tangential direction. -These extra quantites can be accessed by the "compute +These extra quantities can be accessed by the "compute pair/local"_compute_pair_local.html command, as {p1}, {p2}, ..., {p10}. diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/src/pair_hbond_dreiding.txt index f83f37657f..9641e294fa 100644 --- a/doc/src/pair_hbond_dreiding.txt +++ b/doc/src/pair_hbond_dreiding.txt @@ -101,7 +101,7 @@ pair_coeff settings for all possible I,J type pairs. Only I,J type pairs for atoms which act as joint donors/acceptors need to be specified; all other type pairs are assumed to be inactive. -NOTE: A "pair_coeff"_pair_coeff.html command can be speficied multiple +NOTE: A "pair_coeff"_pair_coeff.html command can be specified multiple times for the same donor/acceptor type pair. This enables multiple hydrogen types to be assigned to the same donor/acceptor type pair. For other pair_styles, if the pair_coeff command is re-used for the diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt index b7e46b9566..7ef54e7f07 100644 --- a/doc/src/pair_hybrid.txt +++ b/doc/src/pair_hybrid.txt @@ -63,7 +63,7 @@ Note that an individual pair style can be used multiple times as a sub-style. For efficiency this should only be done if your model requires it. E.g. if you have different regions of Si and C atoms and wish to use a Tersoff potential for pure Si for one set of atoms, and -a Tersoff potetnial for pure C for the other set (presumably with some +a Tersoff potential for pure C for the other set (presumably with some 3rd potential for Si-C interactions), then the sub-style {tersoff} could be listed twice. But if you just want to use a Lennard-Jones or other pairwise potential for several different atom type pairs in your diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt index e2af7eaeeb..fdc0b133dd 100644 --- a/doc/src/pair_lj.txt +++ b/doc/src/pair_lj.txt @@ -197,7 +197,7 @@ 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 diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt index a4fb3f0274..517bb3d20b 100644 --- a/doc/src/pair_lj_long.txt +++ b/doc/src/pair_lj_long.txt @@ -91,7 +91,7 @@ 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 style. Note that the -neighobr list cutoff for Coulomb interactions is effectively extended +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 typically best in an efficiency sense to use a diff --git a/doc/src/pair_lj_smooth.txt b/doc/src/pair_lj_smooth.txt index 0cb0a998fe..133773abd0 100644 --- a/doc/src/pair_lj_smooth.txt +++ b/doc/src/pair_lj_smooth.txt @@ -51,7 +51,7 @@ commands, or by mixing as described below: epsilon (energy units) sigma (distance units) -innner (distance units) +inner (distance units) outer (distance units) :ul The last 2 coefficients are optional inner and outer cutoffs. If not diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_lj_soft.txt index 95aa58ed37..e372092cf0 100644 --- a/doc/src/pair_lj_soft.txt +++ b/doc/src/pair_lj_soft.txt @@ -120,14 +120,14 @@ are the charges on the 2 atoms, and epsilon is the dielectric constant which can be set by the "dielectric"_dielectric.html command. The coefficient lambda is an activation parameter. When lambda = 1 the -pair potentiel is identical to a Lennard-Jones term or a Coulomb term +pair potential is identical to a Lennard-Jones term or a Coulomb term or a combination of both. When lambda = 0 the interactions are deactivated. The transition between these two extrema is smoothed by a soft repulsive core in order to avoid singularities in potential energy and forces when sites are created or annihilated and can overlap "(Beutler)"_#Beutler. -The paratemers n, alpha_LJ and alpha_C are set in the +The parameters n, alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html command, before the cutoffs. Usual choices for the exponent are n = 2 or n = 1. For the remaining coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are @@ -164,7 +164,7 @@ Style {lj/cut/tip4p/long/soft} implements a soft-core version of the TIP4P water model. The usage of this pair style is documented in the "pair_lj"_pair_lj.html styles. The soft-core version introduces the lambda parameter to the list of arguments, after epsilon and sigma in -the "pair_coeff"_pair_coeff.html command. The paratemers n, alpha_LJ +the "pair_coeff"_pair_coeff.html command. The parameters n, alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html command, before the cutoffs. @@ -175,7 +175,7 @@ an inner and outer cutoff. The usage of this pair style is documented in the "pair_charmm"_pair_charmm.html styles. The soft-core version introduces the lambda parameter to the list of arguments, after epsilon and sigma in the "pair_coeff"_pair_coeff.html command (and -before the optional eps14 and sigma14). The paratemers n, +before the optional eps14 and sigma14). The parameters n, alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html command, before the cutoffs. diff --git a/doc/src/pair_lubricate.txt b/doc/src/pair_lubricate.txt index 5dbd7f4b80..daa2e37b68 100644 --- a/doc/src/pair_lubricate.txt +++ b/doc/src/pair_lubricate.txt @@ -94,7 +94,7 @@ Style {lubricate} requires monodisperse spherical particles; style {lubricate/poly} allows for polydisperse spherical particles. The viscosity {mu} can be varied in a time-dependent manner over the -course of a simluation, in which case in which case the pair_style +course of a simulation, in which case in which case the pair_style setting for {mu} will be overridden. See the "fix adapt"_fix_adapt.html command for details. diff --git a/doc/src/pair_mgpt.txt b/doc/src/pair_mgpt.txt index 53ae53df23..f8b0c9f071 100644 --- a/doc/src/pair_mgpt.txt +++ b/doc/src/pair_mgpt.txt @@ -75,7 +75,7 @@ proceeds. After each time step, the atomic volume should be updated by the code as Omega = V/N. In addition, the volume term E_vol and the potentials v_2, v_3 and v_4 have to be removed at the end of the time step, and then respecified at the new value of Omega. In all -smulations, Omega must remain within the defined volume range for +simulations, Omega must remain within the defined volume range for E_vol and the potentials for the given material. The default option volpress yes in the "pair_coeff"_pair_coeff.html diff --git a/doc/src/pair_peri.txt b/doc/src/pair_peri.txt index 240d9f3bda..6ffd8122aa 100644 --- a/doc/src/pair_peri.txt +++ b/doc/src/pair_peri.txt @@ -116,7 +116,7 @@ cutoff distance for truncating interactions, and s00 and alpha are used as a bond breaking criteria. m_lambdai and m_taubi are the viscoelastic relaxation parameter and time constant, respectively. m_lambdai varies within zero to one. For very small -values of m_lambdai the viscoelsatic model responds very similar to a +values of m_lambdai the viscoelastic model responds very similar to a linear elastic model. For details please see the description in "(Mtchell2011)". diff --git a/doc/src/pair_quip.txt b/doc/src/pair_quip.txt index a90f65931b..12dcd244e2 100644 --- a/doc/src/pair_quip.txt +++ b/doc/src/pair_quip.txt @@ -45,12 +45,12 @@ See the "pair_coeff"_pair_coeff.html doc page for alternate ways to specify the path for the potential file. A QUIP potential is fully specified by the filename which contains the -parameters of the potential in XML format, the initialisation string, +parameters of the potential in XML format, the initialization string, and the map of atomic numbers. GAP potentials can be obtained from the Data repository section of "http://www.libatoms.org"_http://www.libatoms.org, where the -appropriate initialisation strings are also advised. The list of +appropriate initialization strings are also advised. The list of atomic numbers must be matched to the LAMMPS atom types specified in the LAMMPS data file or elsewhere. diff --git a/doc/src/pair_resquared.txt b/doc/src/pair_resquared.txt index 53737d2274..0242bab185 100644 --- a/doc/src/pair_resquared.txt +++ b/doc/src/pair_resquared.txt @@ -58,10 +58,10 @@ cutoff (distance units) :ul The parameters used depend on the type of the interacting particles, i.e. ellipsoids or LJ spheres. The type of a particle is determined -by the diameters specified for its 3 shape paramters. If all 3 shape +by the diameters specified for its 3 shape parameters. If all 3 shape parameters = 0.0, then the particle is treated as an LJ sphere. The epsilon_i_* or epsilon_j_* parameters are ignored for LJ spheres. If -the 3 shape paraemters are > 0.0, then the particle is treated as an +the 3 shape parameters are > 0.0, then the particle is treated as an ellipsoid (even if the 3 parameters are equal to each other). A12 specifies the energy prefactor which depends on the types of the @@ -80,7 +80,7 @@ strength of the spherical particles. For ellipsoid/LJ sphere interactions, the interaction is also computed by the formulas in the supplementary document referenced above. A12 -has a modifed form (see "here"_PDF/pair_resquared_extra.pdf for +has a modified form (see "here"_PDF/pair_resquared_extra.pdf for details): :c,image(Eqs/pair_resquared2.jpg) diff --git a/doc/src/pair_smd_ulsph.txt b/doc/src/pair_smd_ulsph.txt index b9efeb8fc3..393bbc0665 100644 --- a/doc/src/pair_smd_ulsph.txt +++ b/doc/src/pair_smd_ulsph.txt @@ -31,7 +31,7 @@ pair_coeff i j *COMMON rho0 c0 Q1 Cp hg & Here, {i} and {j} denote the {LAMMPS} particle types for which this pair style is defined. Note that {i} and {j} can be different, i.e., {ulsph} cross interactions -between different particle types are allowed. However, {i}--{i} respectively {j}--{j} pair_coeff lines have to preceed a cross interaction. +between different particle types are allowed. However, {i}--{i} respectively {j}--{j} pair_coeff lines have to precede a cross interaction. In contrast to the usual {LAMMPS} {pair coeff} definitions, which are given solely a number of floats and integers, the {ulsph} {pair coeff} definition is organised using keywords. These keywords mark the beginning of different sets of parameters for particle properties, diff --git a/doc/src/pair_soft.txt b/doc/src/pair_soft.txt index f240779050..ec1c06729a 100644 --- a/doc/src/pair_soft.txt +++ b/doc/src/pair_soft.txt @@ -60,7 +60,7 @@ them. This functionality is now available in a more general form through the "fix adapt"_fix_adapt.html command, as explained below. Note that if you use an old input script and specify Astart and Astop without a cutoff, then LAMMPS will interpret that as A and a cutoff, -which is probabably not what you want. +which is probably not what you want. The "fix adapt"_fix_adapt.html command can be used to vary A for one or more pair types over the course of a simulation, in which case diff --git a/doc/src/pair_sph_idealgas.txt b/doc/src/pair_sph_idealgas.txt index 21ca049272..957f901425 100644 --- a/doc/src/pair_sph_idealgas.txt +++ b/doc/src/pair_sph_idealgas.txt @@ -27,7 +27,7 @@ according to the ideal gas equation of state: where gamma = 1.4 is the heat capacity ratio, rho is the local density, and e is the internal energy per unit mass. This pair style also computes Monaghan's artificial viscosity to prevent particles -from interpentrating "(Monaghan)"_#ideal-Monoghan. +from interpenetrating "(Monaghan)"_#ideal-Monoghan. See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. diff --git a/doc/src/pair_sph_lj.txt b/doc/src/pair_sph_lj.txt index 8498841131..ef89c4ad3e 100644 --- a/doc/src/pair_sph_lj.txt +++ b/doc/src/pair_sph_lj.txt @@ -24,7 +24,7 @@ to the Lennard-Jones equation of state, which is computed according to Ree's 1980 polynomial fit "(Ree)"_#Ree. The Lennard-Jones parameters epsilon and sigma are set to unity. This pair style also computes Monaghan's artificial viscosity to prevent particles from -interpentrating "(Monaghan)"_#Monoghan. +interpenetrating "(Monaghan)"_#Monoghan. See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. diff --git a/doc/src/pair_sph_taitwater.txt b/doc/src/pair_sph_taitwater.txt index 2b0b6d119c..9177ca80b8 100644 --- a/doc/src/pair_sph_taitwater.txt +++ b/doc/src/pair_sph_taitwater.txt @@ -28,7 +28,7 @@ where gamma = 7 and B = c_0^2 rho_0 / gamma, with rho_0 being the reference density and c_0 the reference speed of sound. This pair style also computes Monaghan's artificial viscosity to -prevent particles from interpentrating "(Monaghan)"_#Monaghan. +prevent particles from interpenetrating "(Monaghan)"_#Monaghan. See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. diff --git a/doc/src/pair_table.txt b/doc/src/pair_table.txt index fa694f2177..ba79aee40d 100644 --- a/doc/src/pair_table.txt +++ b/doc/src/pair_table.txt @@ -33,7 +33,7 @@ pair_coeff * 3 morse.table ENTRY1 7.0 :pre Style {table} creates interpolation tables from potential energy and force values listed in a file(s) as a function of distance. When -performing dynamics or minimation, the interpolation tables are used +performing dynamics or minimization, the interpolation tables are used to evaluate energy and forces for pairwise interactions between particles, similar to how analytic formulas are used for other pair styles. diff --git a/doc/src/pair_tri_lj.txt b/doc/src/pair_tri_lj.txt index e4eed927f5..42a5bbdfe2 100644 --- a/doc/src/pair_tri_lj.txt +++ b/doc/src/pair_tri_lj.txt @@ -42,7 +42,7 @@ triangle, for purposes of this pair style, are generated in the following manner. Assume the triangle is of type I, and sigma_II has been specified. We want a set of spheres with centers in the plane of the triangle, none of them larger in diameter than sigma_II, which -completely cover the triangle's area, but with minimial overlap and a +completely cover the triangle's area, but with minimal overlap and a minimal total number of spheres. This is done in a recursive manner. Place a sphere at the centroid of the original triangle. Calculate what diameter it must have to just cover all 3 corner points of the diff --git a/doc/src/processors.txt b/doc/src/processors.txt index 854d41ba49..781049af9c 100644 --- a/doc/src/processors.txt +++ b/doc/src/processors.txt @@ -27,7 +27,7 @@ keyword = {grid} or {map} or {part} or {file} :l {map} arg = {cart} or {cart/reorder} or {xyz} or {xzy} or {yxz} or {yzx} or {zxy} or {zyx} cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0 cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1 - xyz,xzy,yxz,yzx,zxy,zyx = map procesors to 3d grid in IJK ordering + xyz,xzy,yxz,yzx,zxy,zyx = map processors to 3d grid in IJK ordering {numa} arg = none {part} args = Psend Precv cstyle Psend = partition # (1 to Np) which will send its processor layout @@ -104,7 +104,7 @@ regular grid is initially created, regardless of which If load-balancing is never invoked via the "balance"_balance.html or "fix balance"_fix_balance.html commands, then the initial regular grid will persist for all simulations. If balancing is performed, some of -the methods invoked by those commands retain the logical toplogy of +the methods invoked by those commands retain the logical topology of the initial 3d grid, and the mapping of processors to the grid specified by the processors command. However the grid spacings in different dimensions may change, so that processors own sub-domains of @@ -271,7 +271,7 @@ processors, it could create a 4x2x10 grid, but it will not create a 4. NOTE: If you use the "partition"_partition.html command to invoke -different "processsors" commands on different partitions, and you also +different "processors" commands on different partitions, and you also use the {part} keyword, then you must insure that both the sending and receiving partitions invoke the "processors" command that connects the 2 partitions via the {part} keyword. LAMMPS cannot easily check for diff --git a/doc/src/python.txt b/doc/src/python.txt index db379d425f..be6d1b215f 100644 --- a/doc/src/python.txt +++ b/doc/src/python.txt @@ -174,7 +174,7 @@ a longer string, the {length} keyword can be specified with its {Nlen} value set to a larger number (the code allocates space for Nlen+1 to include the string terminator). If the Python function generates a string longer than the default 63 or the specified {Nlen}, it will be -trunctated. +truncated. :line @@ -372,7 +372,7 @@ LAMMPS, more than the single value that can be passed back via a return statement. This cutoff value in the "cut" variable is then substituted (by LAMMPS) in the pair_style command that is executed next. Alternatively, the "LAMMPS command option" line could be used -in place of the 2 preceeding lines, to have Python insert the value +in place of the 2 preceding lines, to have Python insert the value into the LAMMPS command string. NOTE: When using the callback mechanism just described, recognize that diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt index b860fef848..86c123527b 100644 --- a/doc/src/read_data.txt +++ b/doc/src/read_data.txt @@ -574,7 +574,7 @@ spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. template-atom = which atom within a template molecule the atom is template-index = which molecule within the molecule template the atom is part of theta = internal temperature of a DPD particle -triangleflag = 1 for triangular particles, 0 for point or sperhical particles +triangleflag = 1 for triangular particles, 0 for point or spherical particles volume = volume of Peridynamic particle (distance^3 units) x,y,z = coordinates of atom (distance units) :ul diff --git a/doc/src/read_dump.txt b/doc/src/read_dump.txt index e454c180ab..381e29f6e0 100644 --- a/doc/src/read_dump.txt +++ b/doc/src/read_dump.txt @@ -58,7 +58,7 @@ read_dump dump.file 1000 x y z vx vy vz format molfile lammpstrj /usr/local/lib/ Read atom information from a dump file to overwrite the current atom coordinates, and optionally the atom velocities and image flags and -the simluation box dimensions. This is useful for restarting a run +the simulation box dimensions. This is useful for restarting a run from a particular snapshot in a dump file. See the "read_restart"_read_restart.html and "read_data"_read_data.html commands for alternative methods to do this. Also see the @@ -214,7 +214,7 @@ you wish to change this after the dump snapshot is read. If the {box} keyword is specified with a {yes} value, then the current simulation box dimensions are replaced by the dump snapshot box dimensions. If the {box} keyword is specified with a {no} value, the -current simulatoin box is unchanged. +current simulation box is unchanged. If the {purge} keyword is specified with a {yes} value, then all current atoms in the system are deleted before any of the operations diff --git a/doc/src/read_restart.txt b/doc/src/read_restart.txt index d59b5313fd..d0f4b16175 100644 --- a/doc/src/read_restart.txt +++ b/doc/src/read_restart.txt @@ -31,7 +31,7 @@ information is stored (and not stored) in a restart file is given below. Basically this operation will re-create the simulation box with all its atoms and their attributes as well as some related global settings, at the point in time it was written to the restart file by a -previous simluation. The simulation box will be partitioned into a +previous simulation. The simulation box will be partitioned into a regular 3d grid of rectangular bricks, one per processor, based on the number of processors in the current simulation and the settings of the "processors"_processors.html command. The partitioning can later be diff --git a/doc/src/region.txt b/doc/src/region.txt index 7b5c9e36d4..885e5e45f8 100644 --- a/doc/src/region.txt +++ b/doc/src/region.txt @@ -212,7 +212,7 @@ both of the spheres. The {units} keyword determines the meaning of the distance units used to define the region for any argument above listed as having distance -units. It also affects the scaling of the velocity vector specfied +units. It also affects the scaling of the velocity vector specified with the {vel} keyword, the amplitude vector specified with the {wiggle} keyword, and the rotation point specified with the {rotate} keyword, since they each involve a distance metric. @@ -352,7 +352,7 @@ high-coordinate flat end cap, and index 3 is the curved cone surface. In the last example above, a {cone} region is defined along the z-axis that is open at the zlo value (e.g. for use as a funnel). -For all other styles, the {open} keyword is ignored. As inidcated +For all other styles, the {open} keyword is ignored. As indicated above, this includes the {intersect} and {union} regions, though their sub-regions can be defined with the {open} keyword. diff --git a/doc/src/rerun.txt b/doc/src/rerun.txt index da8c8d6895..860ee68033 100644 --- a/doc/src/rerun.txt +++ b/doc/src/rerun.txt @@ -40,7 +40,7 @@ rerun ../run7/dump.file.gz skip 2 dump x y z box yes :pre [Description:] -Perform a psuedo simulation run where atom information is read one +Perform a pseudo simulation run where atom information is read one snapshot at a time from a dump file(s), and energies and forces are computed on the shapshot to produce thermodynamic or other output. @@ -121,7 +121,7 @@ with the {start/stop} keywords. Note that if you define neither of the {start}/{stop} or {first}/{last} keywords, then LAMMPS treats the pseudo run as going from 0 to a huge value (effectively infinity). This means that any quantity that a fix scales as a fraction of -elapsed time in the run, will essentially remain at its intiial value. +elapsed time in the run, will essentially remain at its initial value. Also note that an error will occur if you read a snapshot from the dump file with a timestep value larger than the {stop} setting you have specified. @@ -178,7 +178,7 @@ a timestep it expects to be, LAMMPS will flag an error. The various forms of LAMMPS output, as defined by the "thermo_style"_thermo_style.html, "thermo"_thermo.html, "dump"_dump.html, and "restart"_restart.html commands occur on -specific timesteps. If successvive dump snapshots skip those +specific timesteps. If successive dump snapshots skip those timesteps, then no output will be produced. E.g. if you request thermodynamic output every 100 steps, but the dump file snapshots are every 1000 steps, then you will only see thermodynamic output every diff --git a/doc/src/restart.txt b/doc/src/restart.txt index 3154465f68..5e0c2a9ea5 100644 --- a/doc/src/restart.txt +++ b/doc/src/restart.txt @@ -97,7 +97,7 @@ timestep of a run unless it is a multiple of N. A restart file is written on the last timestep of a minimization if N > 0 and the minimization converges. -Instead of a numeric value, N can be specifed as an "equal-style +Instead of a numeric value, N can be specified as an "equal-style variable"_variable.html, which should be specified as v_name, where name is the variable name. In this case, the variable is evaluated at the beginning of a run to determine the next timestep at which a diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt index f487de2831..b30a17686d 100644 --- a/doc/src/run_style.txt +++ b/doc/src/run_style.txt @@ -76,7 +76,7 @@ Specifically, this style performs all computation except the "kspace_style"_kspace_style.html portion of the force field on the 1st partition. This include the "pair style"_pair_style.html, "bond style"_bond_style.html, "neighbor list building"_neighbor.html, -"fixes"_fix.html including time intergration, and output. The +"fixes"_fix.html including time integration, and output. The "kspace_style"_kspace_style.html portion of the calculation is performed on the 2nd partition. @@ -105,7 +105,7 @@ to control this, e.g. procssors * * * part 1 2 multiple :pre You can also use the "partition"_partition.html command to explicitly -specity the processor layout on each partition. E.g. for 2 partitions +specify the processor layout on each partition. E.g. for 2 partitions of 60 and 15 processors each: partition yes 1 processors 3 4 5 @@ -182,7 +182,7 @@ for hybrid coarse-grained/all-atom models. The {hybrid} keyword requires as many level assignments as there are hybrid substyles, which assigns each sub-style to a rRESPA level, following their order of definition in the pair_style command. Since the {hybrid} keyword -operates on pair style computations, it is mututally exclusive with +operates on pair style computations, it is mutually exclusive with either the {pair} or the {inner}/{middle}/{outer} keywords. When using rRESPA (or for any MD simulation) care must be taken to diff --git a/doc/src/set.txt b/doc/src/set.txt index 42ede23b85..659eecd30d 100644 --- a/doc/src/set.txt +++ b/doc/src/set.txt @@ -374,7 +374,7 @@ header of the data file read by the "read_data"_read_data.html command. These keywords do not allow use of an atom-style variable. Keywords {meso/e}, {meso/cv}, and {meso/rho} set the energy, heat -capacity, and density of smmothed particle hydrodynamics (SPH) +capacity, and density of smoothed particle hydrodynamics (SPH) particles. See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. diff --git a/doc/src/thermo.txt b/doc/src/thermo.txt index 6faea206f4..1d5d34995c 100644 --- a/doc/src/thermo.txt +++ b/doc/src/thermo.txt @@ -30,7 +30,7 @@ The content and format of what is printed is controlled by the "thermo_style"_thermo_style.html and "thermo_modify"_thermo_modify.html commands. -Instead of a numeric value, N can be specifed as an "equal-style +Instead of a numeric value, N can be specified as an "equal-style variable"_variable.html, which should be specified as v_name, where name is the variable name. In this case, the variable is evaluated at the beginning of a run to determine the next timestep at which diff --git a/doc/src/thermo_style.txt b/doc/src/thermo_style.txt index 37b58618a6..e30e7023e4 100644 --- a/doc/src/thermo_style.txt +++ b/doc/src/thermo_style.txt @@ -236,7 +236,7 @@ time per CPU second, where simulation time is in time picoseconds per CPU second. The {spcpu} keyword is the number of timesteps per CPU second. Both quantities are on-the-fly metrics, measured relative to the last time they were invoked. Thus if you are -printing out thermodyamic output every 100 timesteps, the two keywords +printing out thermodynamic output every 100 timesteps, the two keywords will continually output the time and timestep rate for the last 100 steps. The {tpcpu} keyword does not attempt to track any changes in timestep size, e.g. due to using the "fix dt/reset"_fix_dt_reset.html diff --git a/doc/src/timer.txt b/doc/src/timer.txt index c148a9dce1..39a6c542b7 100644 --- a/doc/src/timer.txt +++ b/doc/src/timer.txt @@ -16,7 +16,7 @@ timer args :pre {off} = do not collect or print any timing information {loop} = collect only the total time for the simulation loop {normal} = collect timer information broken down by sections (default) - {full} = like {normal} but also include CPU and thread utilzation + {full} = like {normal} but also include CPU and thread utilization {sync} = explicitly synchronize MPI tasks between sections {nosync} = do not synchronize MPI tasks between sections (default) {timeout} elapse = set walltime limit to {elapse} @@ -48,7 +48,7 @@ detailed per section information. With the {normal} setting, timing information for portions of the timestep (pairwise calculations, neighbor list construction, output, etc) are collected as well as information about load imbalances for those sections across -procsessors. The {full} setting adds information about CPU +processors. The {full} setting adds information about CPU utilization and thread utilization, when multi-threading is enabled. With the {sync} setting, all MPI tasks are synchronized at each timer diff --git a/doc/src/tutorial_drude.txt b/doc/src/tutorial_drude.txt index a350521f6c..518b90854b 100644 --- a/doc/src/tutorial_drude.txt +++ b/doc/src/tutorial_drude.txt @@ -72,7 +72,7 @@ In both these force fields hydrogen atoms are treated as non-polarizable. :l The motion of of the Drude particles can be calculated by minimizing -the energy of the induced dipoles at each timestep, by an interative, +the energy of the induced dipoles at each timestep, by an iterative, self-consistent procedure. The Drude particles can be massless and therefore do not contribute to the kinetic energy. However, the relaxed method is computational slow. An extended-lagrangian method @@ -82,7 +82,7 @@ decouple the degrees of freedom associated with the Drude oscillators from those of the normal atoms. Thermalizing the Drude dipoles at temperatures comparable to the rest of the simulation leads to several problems (kinetic energy transfer, very short timestep, etc.), which -can be remediated by the "cold Drude" technique ("Lamoureux and +can be remediate by the "cold Drude" technique ("Lamoureux and Roux"_#Lamoureux). Two closely related models are used to represent polarization through diff --git a/doc/src/units.txt b/doc/src/units.txt index 87436b6307..0b856dcc68 100644 --- a/doc/src/units.txt +++ b/doc/src/units.txt @@ -73,7 +73,7 @@ dipole = reduced LJ dipole, moment where *mu = mu / (4 pi perm0 sigma^3 epsilon) electric field = force/charge, where E* = E (4 pi perm0 sigma epsilon)^1/2 sigma / epsilon density = mass/volume, where rho* = rho sigma^dim :ul -Note that for LJ units, the default mode of thermodyamic output via +Note that for LJ units, the default mode of thermodynamic output via the "thermo_style"_thermo_style.html command is to normalize all extensive quantities by the number of atoms. E.g. potential energy is extensive because it is summed over atoms, so it is output as diff --git a/doc/src/variable.txt b/doc/src/variable.txt index a46030b162..e32e82ef4d 100644 --- a/doc/src/variable.txt +++ b/doc/src/variable.txt @@ -501,7 +501,7 @@ the group. :line -Numers, constants, and thermo keywords :h4 +Numbers, constants, and thermo keywords :h4 Numbers can contain digits, scientific notation (3.0e20,3.0e-20,3.0E20,3.0E-20), and leading minus signs. @@ -576,7 +576,7 @@ returns 0.0. These relational and logical operators can be used as a masking or selection operation in a formula. For example, the number of atoms -whose properties satifsy one or more criteria could be calculated by +whose properties satisfy one or more criteria could be calculated by taking the returned per-atom vector of ones and zeroes and passing it to the "compute reduce"_compute_reduce.html command. @@ -623,7 +623,7 @@ Floor() if the largest integer not greater than its argument. Round() is the nearest integer to its argument. The ramp(x,y) function uses the current timestep to generate a value -linearly intepolated between the specified x,y values over the course +linearly interpolated between the specified x,y values over the course of a run, according to this formula: value = x + (y-x) * (timestep-startstep) / (stopstep-startstep) :pre @@ -669,7 +669,7 @@ sequence of output timesteps: The stride(x,y,z) function uses the current timestep to generate a new timestep. X,y >= 0 and z > 0 and x <= y are required. The generated timesteps increase in increments of z, from x to y, i.e. it generates -the sequece x,x+z,x+2z,...,y. If y-x is not a multiple of z, then +the sequence x,x+z,x+2z,...,y. If y-x is not a multiple of z, then similar to the way a for loop operates, the last value will be one that does not exceed y. For any current timestep, the next timestep in the sequence is returned. Thus if stride(1000,2000,100) is used @@ -1068,7 +1068,7 @@ in the reference should be replaced by the name of a variable defined elsewhere in the input script. As discussed on this doc page, equal-style variables generate a single -global numeric value, vector-style variables gerarate a vector of +global numeric value, vector-style variables generate a vector of global numeric values, and atom-style and atomfile-style variables generate a per-atom vector of numeric values. All other variables store one or more strings. @@ -1169,7 +1169,7 @@ would print out both the current and initial volume periodically during the run. Note that it is a mistake to enclose a variable formula in double -quotes if it contains variables preceeded by $ signs. For example, +quotes if it contains variables preceded by $ signs. For example, variable vratio equal "$\{vfinal\}/$\{v0\}" :pre @@ -1214,7 +1214,7 @@ three kinds of behavior: (1) The variable may be evaluated accurately. If it contains references to a compute or fix, and these values were calculated on -the last timestep of a preceeding run, then they will be accessed and +the last timestep of a preceding run, then they will be accessed and used by the variable and the result will be accurate. (2) LAMMPS may not be able to evaluate the variable and will generate diff --git a/doc/src/write_dump.txt b/doc/src/write_dump.txt index 6e99d75460..840716085f 100644 --- a/doc/src/write_dump.txt +++ b/doc/src/write_dump.txt @@ -78,7 +78,7 @@ else LAMMPS will generate an error message. For example, it is not possible to dump per-atom energy with this command before a run has been performed, since no energies and forces have yet been calculated. See the "variable"_variable.html doc page -sectinn on Variable Accuracy for more information on this topic. +section on Variable Accuracy for more information on this topic. [Related commands:] diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 63c6542237..fb08e4e97e 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -1683,6 +1683,7 @@ ohenrich ok OKeefe OKeefe +O'Keefe oldlace Oleinik Olfason @@ -1747,6 +1748,8 @@ parallelization parallelized parallelizing param +parameterization +parameterizations parameterize parameterized parametrization @@ -1785,6 +1788,7 @@ peridynamic Peridynamic peridynamics Peridynamics +permittivity Perram persp Persp @@ -2129,7 +2133,7 @@ Silbert Silling Simul simulataneous -simulatoins +simulations Sinnott sinusoid sinusoidally