From 4dc2f9c6c4019586a02175e9b05ccbddb9b87ec1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 19 Nov 2018 11:24:17 -0500 Subject: [PATCH] fix some spelling errors in the manual --- doc/src/Build_basics.txt | 2 +- doc/src/Build_extras.txt | 2 +- doc/src/Howto_client_server.txt | 2 +- doc/src/Install_git.txt | 2 +- doc/src/Speed_kokkos.txt | 30 +++++++++++++++--------------- doc/src/Speed_omp.txt | 4 ++-- doc/src/compute_property_atom.txt | 6 +++--- doc/src/compute_ptm_atom.txt | 2 +- doc/src/fix_plumed.txt | 11 ++++++----- doc/src/fix_rigid.txt | 2 +- doc/src/fix_rigid_meso.txt | 2 +- doc/src/hyper.txt | 2 +- doc/src/kspace_modify.txt | 2 +- doc/src/message.txt | 2 +- doc/src/neb.txt | 2 +- doc/src/rerun.txt | 4 ++-- 16 files changed, 39 insertions(+), 38 deletions(-) diff --git a/doc/src/Build_basics.txt b/doc/src/Build_basics.txt index b3ff0a55c5..47801890c4 100644 --- a/doc/src/Build_basics.txt +++ b/doc/src/Build_basics.txt @@ -292,7 +292,7 @@ This will create a lammps/doc/html dir with the HTML doc pages so that you can browse them locally on your system. Type "make" from the lammps/doc dir to see other options. -NOTE: You can also download a tarball of the documention for the +NOTE: You can also download a tarball of the documentation for the current LAMMPS version (HTML and PDF files), from the website "download page"_http://lammps.sandia.gov/download.html. diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index 8881ee44c1..98937c096e 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -732,7 +732,7 @@ can be shared across multiple MD packages and can be updated, for as long as the shared PLUMED library is ABI-compatible. The third linkage mode is "runtime" which allows to switch the PLUMED kernel at runtime between different variants through setting the PLUMED_KERNEL environment -varible, which has to point to the location of the libplumedKernel.so +variable, which has to point to the location of the libplumedKernel.so dynamical shared object, which is then loaded at runtime. This is particularly convenient for doing PLUMED development and comparing multiple PLUMED versions without having to recompile the hosting MD diff --git a/doc/src/Howto_client_server.txt b/doc/src/Howto_client_server.txt index aa6b8eab76..897b0aa6ff 100644 --- a/doc/src/Howto_client_server.txt +++ b/doc/src/Howto_client_server.txt @@ -64,7 +64,7 @@ client or server. "server mc"_server_mc.html = LAMMPS is a server for computing a Monte Carlo energy :ul The server doc files give details of the message protocols -for data that is exchanged bewteen the client and server. +for data that is exchanged between the client and server. These example directories illustrate how to use LAMMPS as either a client or server code: diff --git a/doc/src/Install_git.txt b/doc/src/Install_git.txt index 538fa8aff8..80ec3e3478 100644 --- a/doc/src/Install_git.txt +++ b/doc/src/Install_git.txt @@ -45,7 +45,7 @@ git clone -b unstable https://github.com/lammps/lammps.git mylammps :pre where "mylammps" is the name of the directory you wish to create on your machine and "unstable" is one of the 3 branches listed above. (Note that you actually download all 3 branches; you can switch -between them at any time using "git checkout ".) +between them at any time using "git checkout ".) Once the command completes, your directory will contain the same files as if you unpacked a current LAMMPS tarball, with two exceptions: diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt index f74c9c9ed7..d1fb52a9f8 100644 --- a/doc/src/Speed_kokkos.txt +++ b/doc/src/Speed_kokkos.txt @@ -127,21 +127,21 @@ mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half c If the "newton"_newton.html command is used in the input script, it can also override the Newton flag defaults. -For half neighbor lists and OpenMP, the KOKKOS package uses data -duplication (i.e. thread-private arrays) by default to avoid -thread-level write conflicts in the force arrays (and other data -structures as necessary). Data duplication is typically fastest for -small numbers of threads (i.e. 8 or less) but does increase memory -footprint and is not scalable to large numbers of threads. An -alternative to data duplication is to use thread-level atomics, which -don't require duplication. The use of atomics can be forced by compiling -with the "-DLMP_KOKKOS_USE_ATOMICS" compile switch. Most but not all -Kokkos-enabled pair_styles support data duplication. Alternatively, full -neighbor lists avoid the need for duplication or atomics but require -more compute operations per atom. When using the Kokkos Serial backend -or the OpenMP backend with a single thread, no duplication or atomics are -used. For CUDA and half neighbor lists, the KOKKOS package always uses -atomics. +For half neighbor lists and OpenMP, the KOKKOS package uses data +duplication (i.e. thread-private arrays) by default to avoid +thread-level write conflicts in the force arrays (and other data +structures as necessary). Data duplication is typically fastest for +small numbers of threads (i.e. 8 or less) but does increase memory +footprint and is not scalable to large numbers of threads. An +alternative to data duplication is to use thread-level atomic operations +which do not require data duplication. The use of atomic operations can +be enforced by compiling LAMMPS with the "-DLMP_KOKKOS_USE_ATOMICS" +pre-processor flag. Most but not all Kokkos-enabled pair_styles support +data duplication. Alternatively, full neighbor lists avoid the need for +duplication or atomic operations but require more compute operations per +atom. When using the Kokkos Serial backend or the OpenMP backend with +a single thread, no duplication or atomic operations are used. For CUDA +and half neighbor lists, the KOKKOS package always uses atomic operations. [Core and Thread Affinity:] diff --git a/doc/src/Speed_omp.txt b/doc/src/Speed_omp.txt index 238909d1b4..97aa251e9e 100644 --- a/doc/src/Speed_omp.txt +++ b/doc/src/Speed_omp.txt @@ -131,7 +131,7 @@ effect worsens when using an increasing number of nodes. :l The system has a spatially inhomogeneous particle density which does not map well to the "domain decomposition scheme"_processors.html or "load-balancing"_balance.html options that LAMMPS provides. This is -because multi-threading achives parallelism over the number of +because multi-threading achieves parallelism over the number of particles, not via their distribution in space. :l A machine is being used in "capability mode", i.e. near the point @@ -143,7 +143,7 @@ the performance-limiting factor. Using multi-threading allows less MPI tasks to be invoked and can speed-up the long-range solver, while increasing overall performance by parallelizing the pairwise and bonded calculations via OpenMP. Likewise additional speedup can be -sometimes be achived by increasing the length of the Coulombic cutoff +sometimes be achieved by increasing the length of the Coulombic cutoff and thus reducing the work done by the long-range solver. Using the "run_style verlet/split"_run_style.html command, which is compatible with the USER-OMP package, is an alternative way to reduce the number diff --git a/doc/src/compute_property_atom.txt b/doc/src/compute_property_atom.txt index bc1e3049fa..3c55c88d10 100644 --- a/doc/src/compute_property_atom.txt +++ b/doc/src/compute_property_atom.txt @@ -19,7 +19,7 @@ input = one or more atom attributes :l x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz, vx, vy, vz, fx, fy, fz, q, mux, muy, muz, mu, - sp, spx, spy, spz, fmx, fmy, fmz, + sp, spx, spy, spz, fmx, fmy, fmz, radius, diameter, omegax, omegay, omegaz, angmomx, angmomy, angmomz, shapex,shapey, shapez, @@ -158,8 +158,8 @@ corresponding attribute is in, e.g. velocity units for vx, charge units for q, etc. For the spin quantities, sp is in the units of the Bohr magneton, spx, -spy, and spz are adimensional quantities, and fmx, fmy and fmz are -given in rad.THz. +spy, and spz are unitless quantities, and fmx, fmy and fmz are given +in rad/THz. [Restrictions:] none diff --git a/doc/src/compute_ptm_atom.txt b/doc/src/compute_ptm_atom.txt index 8f79fe502b..57e143404e 100644 --- a/doc/src/compute_ptm_atom.txt +++ b/doc/src/compute_ptm_atom.txt @@ -80,7 +80,7 @@ too frequently or to have multiple compute/dump commands, each with a [Output info:] -This compute calculates a per-atom arry, which can be accessed by +This compute calculates a per-atom array, which can be accessed by any command that uses per-atom values from a compute as input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. diff --git a/doc/src/fix_plumed.txt b/doc/src/fix_plumed.txt index 9c7f45af1e..a9795850f5 100644 --- a/doc/src/fix_plumed.txt +++ b/doc/src/fix_plumed.txt @@ -65,11 +65,12 @@ PLUMED input file. Instructions as to what should be included in a plumed input file can be found in the "documentation for PLUMED"_plumeddocs -The {outfile} keyword allows the user to specify the name of a file on -which to output the PLUMED log. This log file normally just parrots the -information that is contained in the input file. The names of the files -on which the results from the various analyses that have been performed -using PLUMED will be specified by the user in the PLUMED input file. +The {outfile} keyword allows the user to specify the name of a file in +which to output the PLUMED log. This log file normally just repeats the +information that is contained in the input file to confirm it was +correctly read and parsed. The names of the files in which the results +are stored from the various analysis options performed by PLUMED will +be specified by the user in the PLUMED input file. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt index 5d65856735..d45705b2b2 100644 --- a/doc/src/fix_rigid.txt +++ b/doc/src/fix_rigid.txt @@ -247,7 +247,7 @@ of atoms that form rigid bodies. An integer vector defined by the "fix property/atom"_fix_property_atom.html command can be used. Or an "atom-style or atomfile-style variable"_variable.html can be used; the floating-point value produced by the variable is rounded to an -integer. As with bondstyle {molecule}, each set of atoms in the fix +integer. As with bodystyle {molecule}, each set of atoms in the fix groups with the same integer value is treated as a different rigid body. Since fix property/atom vectors and atom-style variables produce values for all atoms, you should be careful to use a fix group diff --git a/doc/src/fix_rigid_meso.txt b/doc/src/fix_rigid_meso.txt index 79b014e671..b0a7e3cf9e 100644 --- a/doc/src/fix_rigid_meso.txt +++ b/doc/src/fix_rigid_meso.txt @@ -128,7 +128,7 @@ of particles that form rigid bodies. An integer vector defined by the "fix property/atom"_fix_property_atom.html command can be used. Or an "atom-style or atomfile-style variable"_variable.html can be used; the floating-point value produced by the variable is rounded to an -integer. As with bondstyle {molecule}, each set of particles in the fix +integer. As with bodystyle {molecule}, each set of particles in the fix groups with the same integer value is treated as a different rigid body. Since fix property/atom vectors and atom-style variables produce values for all particles, you should be careful to use a fix group diff --git a/doc/src/hyper.txt b/doc/src/hyper.txt index 0ea4ac781b..570f27ca64 100644 --- a/doc/src/hyper.txt +++ b/doc/src/hyper.txt @@ -131,7 +131,7 @@ system (coordinates and velocities) is restored, and dynamics continue. At the end of the hyper run, a variety of statistics are output to the screen and logfile. These include info relevant to both global and local hyperdynamics, such as the number of events and the elapsed -hyper time (acclerated time), And it includes info specific to one or +hyper time (accelerated time), And it includes info specific to one or the other, depending on which style of fix was specified by {fix-ID}. :line diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt index 41973601d7..218f85bd74 100644 --- a/doc/src/kspace_modify.txt +++ b/doc/src/kspace_modify.txt @@ -326,7 +326,7 @@ field_rel = relative accuracy in electric field :ul The values with suffix _rel indicate the tolerance is a relative tolerance; the other values impose an absolute tolerance on the given -quantity. Absoulte tolerance in this case means, that for a given +quantity. Absolute tolerance in this case means, that for a given quantity q and a given absolute tolerance of t_a the result should be between q-t_a and q+t_a. For a relative tolerance t_r the relative error should not be greater than t_r, i.e. abs(1 - (result/q)) < t_r. diff --git a/doc/src/message.txt b/doc/src/message.txt index 6ceb62a3e6..2b6a894e70 100644 --- a/doc/src/message.txt +++ b/doc/src/message.txt @@ -22,7 +22,7 @@ mode = {file} or {zmq} or {mpi/one} or {mpi/two} :l socket-ID for server = *:5555, see description below {mpi/one} arg = none {mpi/two} arg = filename - filename = file used to establish communication bewteen 2 MPI jobs :pre + filename = file used to establish communication between 2 MPI jobs :pre :ule [Examples:] diff --git a/doc/src/neb.txt b/doc/src/neb.txt index 75d199e0b4..e136aa2f2c 100644 --- a/doc/src/neb.txt +++ b/doc/src/neb.txt @@ -340,7 +340,7 @@ MaxAtomForce is the maximum force component of any atom in replica i. When a NEB calculation does not converge properly, the supplementary information can help understanding what is going wrong. For instance -when the path angle becomes accute, the definition of tangent used in +when the path angle becomes acute, the definition of tangent used in the NEB calculation is questionable and the NEB cannot may diverge "(Maras)"_#Maras2. diff --git a/doc/src/rerun.txt b/doc/src/rerun.txt index 71ad464bb0..9a92a7374f 100644 --- a/doc/src/rerun.txt +++ b/doc/src/rerun.txt @@ -150,8 +150,8 @@ indent"_fix_indent.html and "fix langevin"_fix_langevin.html. So you should think carefully as to whether that makes sense for the manner in which you are reprocessing the dump snapshots. -If you only want the rerun script to perform analyses that do not -involve pair interactions, such as use compute msd to calculated +If you only want the rerun script to perform an analysis that does +not involve pair interactions, such as use compute msd to calculated displacements over time, you do not need to define a "pair style"_pair_style.html, which may also mean neighbor lists will not need to be calculated which saves time. The "comm_modify