From 0bcb1bd3019be1baa76e6df939145275e7fc4263 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 19 Nov 2018 21:17:54 -0500 Subject: [PATCH] more spelling fixes and occational re-edits --- doc/src/Build_extras.txt | 6 +- doc/src/Build_settings.txt | 2 +- doc/src/Build_windows.txt | 2 +- doc/src/Commands_parse.txt | 2 +- doc/src/Errors_messages.txt | 24 ++++---- doc/src/Errors_warnings.txt | 6 +- doc/src/Examples.txt | 2 +- doc/src/Howto_chunk.txt | 4 +- doc/src/Howto_client_server.txt | 2 +- doc/src/Howto_coreshell.txt | 6 +- doc/src/Howto_dispersion.txt | 2 +- doc/src/Howto_drude.txt | 2 +- doc/src/Howto_drude2.txt | 8 +-- doc/src/Howto_elastic.txt | 2 +- doc/src/Howto_github.txt | 6 +- doc/src/Howto_manifold.txt | 4 +- doc/src/Howto_nemd.txt | 2 +- doc/src/Howto_polarizable.txt | 6 +- doc/src/Howto_pylammps.txt | 6 +- doc/src/Howto_replica.txt | 2 +- doc/src/Howto_spc.txt | 2 +- doc/src/Howto_spherical.txt | 2 +- doc/src/Howto_spins.txt | 2 +- doc/src/Howto_thermostat.txt | 2 +- doc/src/Howto_triclinic.txt | 2 +- doc/src/Howto_viscosity.txt | 2 +- doc/src/Intro_authors.txt | 2 +- doc/src/Intro_features.txt | 4 +- doc/src/Intro_nonfeatures.txt | 2 +- doc/src/Modify_contribute.txt | 4 +- doc/src/Modify_pair.txt | 2 +- doc/src/Modify_region.txt | 4 +- doc/src/Packages_details.txt | 4 +- doc/src/Packages_user.txt | 4 +- doc/src/Python_call.txt | 2 +- doc/src/Python_examples.txt | 2 +- doc/src/Speed.txt | 2 +- doc/src/Speed_intel.txt | 80 ++++++++++++------------- doc/src/Speed_kokkos.txt | 6 +- doc/src/Speed_packages.txt | 4 +- doc/src/Tools.txt | 8 +-- doc/src/angle_sdk.txt | 2 +- doc/src/atom_style.txt | 2 +- doc/src/balance.txt | 8 +-- doc/src/bond_oxdna.txt | 2 +- doc/src/comm_modify.txt | 2 +- doc/src/compute_adf.txt | 62 +++++++++---------- doc/src/compute_bond_local.txt | 2 +- doc/src/compute_chunk_atom.txt | 2 +- doc/src/compute_cna_atom.txt | 2 +- doc/src/compute_damage_atom.txt | 2 +- doc/src/compute_displace_atom.txt | 2 +- doc/src/compute_msd.txt | 2 +- doc/src/compute_msd_nongauss.txt | 2 +- doc/src/compute_pair.txt | 2 +- doc/src/compute_plasticity_atom.txt | 2 +- doc/src/compute_pressure.txt | 4 +- doc/src/compute_pressure_cylinder.txt | 2 +- doc/src/compute_reduce.txt | 2 +- doc/src/compute_reduce_chunk.txt | 2 +- doc/src/compute_smd_hourglass_error.txt | 2 +- doc/src/compute_smd_tlsph_defgrad.txt | 2 +- doc/src/compute_smd_tlsph_shape.txt | 2 +- doc/src/compute_stress_atom.txt | 4 +- doc/src/compute_tally.txt | 2 +- doc/src/compute_temp_asphere.txt | 2 +- doc/src/compute_temp_chunk.txt | 2 +- doc/src/compute_temp_cs.txt | 2 +- doc/src/create_box.txt | 2 +- doc/src/dihedral_charmm.txt | 4 +- doc/src/dump_h5md.txt | 6 +- doc/src/dump_image.txt | 11 ++-- doc/src/dump_modify.txt | 4 +- doc/src/fix.txt | 2 +- doc/src/fix_append_atoms.txt | 4 +- doc/src/fix_ave_chunk.txt | 2 +- doc/src/fix_ave_time.txt | 2 +- doc/src/fix_balance.txt | 34 +++++------ doc/src/fix_bocs.txt | 2 +- doc/src/fix_bond_break.txt | 2 +- doc/src/fix_bond_create.txt | 6 +- doc/src/fix_bond_react.txt | 2 +- doc/src/fix_bond_swap.txt | 2 +- doc/src/fix_client_md.txt | 2 +- doc/src/fix_cmap.txt | 10 ++-- doc/src/fix_colvars.txt | 2 +- doc/src/fix_deposit.txt | 2 +- doc/src/fix_drude_transform.txt | 12 ++-- doc/src/fix_ehex.txt | 8 +-- doc/src/fix_eos_table.txt | 4 +- doc/src/fix_evaporate.txt | 4 +- doc/src/fix_grem.txt | 2 +- doc/src/fix_heat.txt | 2 +- doc/src/fix_hyper_global.txt | 10 ++-- doc/src/fix_hyper_local.txt | 14 ++--- doc/src/fix_imd.txt | 2 +- doc/src/fix_indent.txt | 2 +- doc/src/fix_langevin.txt | 2 +- doc/src/fix_langevin_drude.txt | 28 ++++----- doc/src/fix_meso_move.txt | 2 +- doc/src/fix_msst.txt | 2 +- doc/src/fix_nh.txt | 2 +- doc/src/fix_nh_uef.txt | 2 +- doc/src/fix_nve_awpmd.txt | 2 +- doc/src/fix_nvt_sllod.txt | 2 +- doc/src/fix_phonon.txt | 4 +- doc/src/fix_plumed.txt | 2 +- doc/src/fix_property_atom.txt | 2 +- doc/src/fix_qmmm.txt | 2 +- doc/src/fix_recenter.txt | 4 +- doc/src/fix_restrain.txt | 6 +- doc/src/fix_tfmc.txt | 2 +- doc/src/fix_ti_spring.txt | 2 +- doc/src/fix_tune_kspace.txt | 4 +- doc/src/fix_wall_piston.txt | 4 +- doc/src/hyper.txt | 2 +- doc/src/improper_none.txt | 2 +- doc/src/kspace_modify.txt | 16 ++--- doc/src/kspace_style.txt | 6 +- doc/src/minimize.txt | 2 +- doc/src/molecule.txt | 4 +- doc/src/neb.txt | 4 +- doc/src/package.txt | 46 +++++++------- doc/src/pair_agni.txt | 2 +- doc/src/pair_awpmd.txt | 6 +- doc/src/pair_bop.txt | 2 +- doc/src/pair_charmm.txt | 2 +- doc/src/pair_coeff.txt | 2 +- doc/src/pair_coul.txt | 4 +- doc/src/pair_dipole.txt | 4 +- doc/src/pair_dpd.txt | 4 +- doc/src/pair_dpd_fdt.txt | 2 +- doc/src/pair_edip.txt | 2 +- doc/src/pair_eff.txt | 16 ++--- doc/src/pair_gran.txt | 2 +- doc/src/pair_hbond_dreiding.txt | 8 +-- doc/src/pair_hybrid.txt | 4 +- doc/src/pair_ilp_graphene_hbn.txt | 2 +- doc/src/pair_kolmogorov_crespi_z.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_modify.txt | 2 +- doc/src/pair_nb3b_harmonic.txt | 4 +- doc/src/pair_oxdna.txt | 2 +- doc/src/pair_oxdna2.txt | 2 +- doc/src/pair_peri.txt | 4 +- doc/src/pair_polymorphic.txt | 2 +- doc/src/pair_quip.txt | 4 +- doc/src/pair_sdk.txt | 2 +- doc/src/pair_smd_tlsph.txt | 2 +- doc/src/pair_smd_ulsph.txt | 2 +- doc/src/pair_smtbq.txt | 6 +- doc/src/pair_spin_dmi.txt | 2 +- doc/src/pair_spin_exchange.txt | 4 +- doc/src/pair_spin_neel.txt | 4 +- doc/src/pair_style.txt | 4 +- doc/src/pair_sw.txt | 4 +- doc/src/pair_tri_lj.txt | 2 +- doc/src/read_data.txt | 12 ++-- doc/src/read_dump.txt | 2 +- doc/src/run_style.txt | 2 +- doc/src/server_mc.txt | 2 +- doc/src/server_md.txt | 2 +- doc/src/special_bonds.txt | 4 +- doc/src/suffix.txt | 2 +- doc/src/tad.txt | 2 +- doc/src/timer.txt | 6 +- doc/src/units.txt | 14 ++--- doc/src/variable.txt | 4 +- 171 files changed, 431 insertions(+), 430 deletions(-) diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index 98937c096e..4377981662 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -750,7 +750,7 @@ a global PLUMED installation or downloading it during building LAMMPS. -D PLUMED_MODE=value # Linkage mode for PLUMED, value = static (default), shared, or runtime :pre If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be -downloaded (the version of that is hardcoded to a vetted version of +downloaded (the version of that is hard-coded to a vetted version of PLUMED, usually a recent stable release version) and built inside the CMake build directory. If DOWNLOAD_PLUMED is set to "no" (the default), CMake will try to detect an installed version of PLUMED and link to @@ -788,7 +788,7 @@ Note that 2 symbolic (soft) links, "includelink" and "liblink" are created in lib/plumed to point into the location of the PLUMED build to use and also a new file lib/plumed/Makefile.lammps is created with settings suitable for LAMMPS to compile and link PLUMED in the desired -linkage mode. After this step is compleded, you can install the +linkage mode. After this step is completed, you can install the USER-PLUMED package and compile LAMMPS in the usual manner: make yes-user-plumed @@ -804,7 +804,7 @@ operating systems, using the static linkage is expected to be the most portable, and thus set to be the default. If you want to change the linkage mode, you have to re-run "make -lib-plumed" with the desired settings [and] do a reinstall if the +lib-plumed" with the desired settings [and] do a re-install if the USER-PLUMED package with "make yes-user-plumed" to update the required makefile settings with the changes in the lib/plumed folder. diff --git a/doc/src/Build_settings.txt b/doc/src/Build_settings.txt index 500130ecee..c871d4ab42 100644 --- a/doc/src/Build_settings.txt +++ b/doc/src/Build_settings.txt @@ -139,7 +139,7 @@ adequate. [Makefile.machine setting]: LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :pre - # default is LAMMMPS_SMALLBIG if not specified + # default is LAMMPS_SMALLBIG if not specified [CMake and make info]: The default "smallbig" setting allows for simulations with: diff --git a/doc/src/Build_windows.txt b/doc/src/Build_windows.txt index 0caad589fb..6ac6f52d54 100644 --- a/doc/src/Build_windows.txt +++ b/doc/src/Build_windows.txt @@ -66,7 +66,7 @@ In case of problems, you are recommended to contact somebody with experience in using cygwin. If you do come across portability problems requiring changes to the LAMMPS source code, or figure out corrections yourself, please report them on the lammps-users mailing list, or file -them as an issue or pull request on the LAMMPS github project. +them as an issue or pull request on the LAMMPS GitHub project. Using a cross-compiler :h4,link(cross) diff --git a/doc/src/Commands_parse.txt b/doc/src/Commands_parse.txt index 1d7c754fa7..13a4c2699d 100644 --- a/doc/src/Commands_parse.txt +++ b/doc/src/Commands_parse.txt @@ -91,7 +91,7 @@ See the "variable"_variable.html command for more details of how strings are assigned to variables and evaluated, and how they can be used in input script commands. -(4) The line is broken into "words" separated by whitespace (tabs, +(4) The line is broken into "words" separated by white-space (tabs, spaces). Note that words can thus contain letters, digits, underscores, or punctuation characters. diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt index 2844749c28..de6d974dde 100644 --- a/doc/src/Errors_messages.txt +++ b/doc/src/Errors_messages.txt @@ -421,9 +421,9 @@ This is an internal error. It should normally not occur. :dd This is an internal error. It should normally not occur. :dd -{Bad real space Coulomb cutoff in fix tune/kspace} :dt +{Bad real space Coulombic cutoff in fix tune/kspace} :dt -Fix tune/kspace tried to find the optimal real space Coulomb cutoff using +Fix tune/kspace tried to find the optimal real space Coulombic cutoff using the Newton-Rhaphson method, but found a non-positive or NaN cutoff :dd {Balance command before simulation box is defined} :dt @@ -3351,21 +3351,21 @@ probably due to errors in the Python code. :dd The default minimum order is 2. This can be reset by the kspace_modify minorder command. :dd -{Coulomb cut not supported in pair_style buck/long/coul/coul} :dt +{Coulombic cutoff not supported in pair_style buck/long/coul/coul} :dt Must use long-range Coulombic interactions. :dd -{Coulomb cut not supported in pair_style lj/long/coul/long} :dt +{Coulombic cutoff not supported in pair_style lj/long/coul/long} :dt Must use long-range Coulombic interactions. :dd -{Coulomb cut not supported in pair_style lj/long/tip4p/long} :dt +{Coulombic cutoff not supported in pair_style lj/long/tip4p/long} :dt Must use long-range Coulombic interactions. :dd -{Coulomb cutoffs of pair hybrid sub-styles do not match} :dt +{Coulombic cutoffs of pair hybrid sub-styles do not match} :dt -If using a Kspace solver, all Coulomb cutoffs of long pair styles must +If using a Kspace solver, all Coulombic cutoffs of long pair styles must be the same. :dd {Coulombic cut not supported in pair_style lj/long/dipole/long} :dt @@ -5938,9 +5938,9 @@ map command will force an atom map to be created. :dd Self-explanatory. :dd -{Input line quote not followed by whitespace} :dt +{Input line quote not followed by white-space} :dt -An end quote must be followed by whitespace. :dd +An end quote must be followed by white-space. :dd {Insertion region extends outside simulation box} :dt @@ -7014,7 +7014,7 @@ The kspace accuracy designated in the input must be greater than zero. :dd {KSpace accuracy too large to estimate G vector} :dt -Reduce the accuracy request or specify gwald explicitly +Reduce the accuracy request or specify gewald explicitly via the kspace_modify command. :dd {KSpace accuracy too low} :dt @@ -9198,7 +9198,7 @@ creates one large file for all processors. :dd {Restart file byte ordering is not recognized} :dt The file does not appear to be a LAMMPS restart file since it doesn't -contain a recognized byte-orderomg flag at the beginning. :dd +contain a recognized byte-ordering flag at the beginning. :dd {Restart file byte ordering is swapped} :dt @@ -9410,7 +9410,7 @@ You may also want to boost the page size. :dd {Small to big integers are not sized correctly} :dt -This error occurs whenthe sizes of smallint, imageint, tagint, bigint, +This error occurs when the sizes of smallint, imageint, tagint, bigint, as defined in src/lmptype.h are not what is expected. Contact the developers if this occurs. :dd diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt index 0980120a10..079688c639 100644 --- a/doc/src/Errors_warnings.txt +++ b/doc/src/Errors_warnings.txt @@ -757,7 +757,7 @@ Self-explanatory. :dd This may indicate the shell command did not operate as expected. :dd -{Should not allow rigid bodies to bounce off relecting walls} :dt +{Should not allow rigid bodies to bounce off reflecting walls} :dt LAMMPS allows this, but their dynamics are not computed correctly. :dd @@ -850,10 +850,10 @@ Most FENE models need this setting for the special_bonds command. :dd Most FENE models need this setting for the special_bonds command. :dd -{Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions} :dt +{Using a many-body potential with bonds/angles/dihedrals and special_bond exclusions} :dt This is likely not what you want to do. The exclusion settings will -eliminate neighbors in the neighbor list, which the manybody potential +eliminate neighbors in the neighbor list, which the many-body potential needs to calculated its terms correctly. :dd {Using compute temp/deform with inconsistent fix deform remap option} :dt diff --git a/doc/src/Examples.txt b/doc/src/Examples.txt index 4b6db8a047..e26e6abd99 100644 --- a/doc/src/Examples.txt +++ b/doc/src/Examples.txt @@ -78,7 +78,7 @@ micelle: self-assembly of small lipid-like molecules into 2d bilayers min: energy minimization of 2d LJ melt mscg: parameterize a multi-scale coarse-graining (MSCG) model msst: MSST shock dynamics -nb3b: use of nonbonded 3-body harmonic pair style +nb3b: use of non-bonded 3-body harmonic pair style neb: nudged elastic band (NEB) calculation for barrier finding nemd: non-equilibrium MD of 2d sheared system obstacle: flow around two voids in a 2d channel diff --git a/doc/src/Howto_chunk.txt b/doc/src/Howto_chunk.txt index 82a4450d17..e29cf13167 100644 --- a/doc/src/Howto_chunk.txt +++ b/doc/src/Howto_chunk.txt @@ -22,8 +22,8 @@ commands, to calculate various properties of a system: "fix ave/chunk"_fix_ave_chunk.html any of the "compute */chunk"_compute.html commands :ul -Here, each of the 4 kinds of chunk-related commands is briefly -overviewed. Then some examples are given of how to compute different +Here a brief overview for each of the 4 kinds of chunk-related commands +is provided. Then some examples are given of how to compute different properties with chunk commands. Compute chunk/atom command: :h4 diff --git a/doc/src/Howto_client_server.txt b/doc/src/Howto_client_server.txt index 897b0aa6ff..5875a48744 100644 --- a/doc/src/Howto_client_server.txt +++ b/doc/src/Howto_client_server.txt @@ -87,7 +87,7 @@ DFT forces, thru a Python wrapper script on VASP. Here is how to launch a client and server code together for any of the 4 modes of message exchange that the "message"_message.html command and the CSlib support. Here LAMMPS is used as both the client and -server code. Another code could be subsitituted for either. +server code. Another code could be substituted for either. The examples below show launching both codes from the same window (or batch script), using the "&" character to launch the first code in the diff --git a/doc/src/Howto_coreshell.txt b/doc/src/Howto_coreshell.txt index 7503fa1ebe..d3c320cb37 100644 --- a/doc/src/Howto_coreshell.txt +++ b/doc/src/Howto_coreshell.txt @@ -19,7 +19,7 @@ polarizable"_Howto_polarizable.html doc page for a discussion of all the polarizable models available in LAMMPS. Technically, shells are attached to the cores by a spring force f = -k*r where k is a parametrized spring constant and r is the distance +k*r where k is a parameterized spring constant and r is the distance between the core and the shell. The charges of the core and the shell add up to the ion charge, thus q(ion) = q(core) + q(shell). This setup introduces the ion polarizability (alpha) given by @@ -111,7 +111,7 @@ the core and shell particles corresponds to the polarization, hereby an instantaneous relaxation of the shells is approximated and a fast core/shell spring frequency ensures a nearly constant internal kinetic energy during the simulation. -Thermostats can alter this polarization behaviour, by scaling the +Thermostats can alter this polarization behavior, by scaling the internal kinetic energy, meaning the shell will not react freely to its electrostatic environment. Therefore it is typically desirable to decouple the relative motion of @@ -165,7 +165,7 @@ fix_modify press_bar temp CSequ press thermo_press_lmp # pressure modification 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. +momentum to the system, which is noticeable over long trajectories. 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 diff --git a/doc/src/Howto_dispersion.txt b/doc/src/Howto_dispersion.txt index 8a5953d84d..510e531d1f 100644 --- a/doc/src/Howto_dispersion.txt +++ b/doc/src/Howto_dispersion.txt @@ -74,7 +74,7 @@ command. A reasonable approach that combines the upsides of both methods is to make the first run using the {kspace_modify force/disp/real} and {kspace_modify force/disp/kspace} commands, write down the PPPM -parameters from the outut, and specify these parameters using the +parameters from the output, and specify these parameters using the second approach in subsequent runs (which have the same composition, force field, and approximately the same volume). diff --git a/doc/src/Howto_drude.txt b/doc/src/Howto_drude.txt index ebdf5f8658..fdbbd19771 100644 --- a/doc/src/Howto_drude.txt +++ b/doc/src/Howto_drude.txt @@ -17,7 +17,7 @@ for a discussion of all the polarizable models available in LAMMPS. The Drude model has a number of features aimed at its use in molecular systems ("Lamoureux and Roux"_#howto-Lamoureux): -Thermostating of the additional degrees of freedom associated with the +Thermostatting of the additional degrees of freedom associated with the induced dipoles at very low temperature, in terms of the reduced coordinates of the Drude particles with respect to their cores. This makes the trajectory close to that of relaxed induced dipoles. :ulb,l diff --git a/doc/src/Howto_drude2.txt b/doc/src/Howto_drude2.txt index 0e72273723..afb528eb4a 100644 --- a/doc/src/Howto_drude2.txt +++ b/doc/src/Howto_drude2.txt @@ -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 remediate by the "cold Drude" technique ("Lamoureux and +can be remedied by the "cold Drude" technique ("Lamoureux and Roux"_#Lamoureux2). Two closely related models are used to represent polarization through @@ -213,7 +213,7 @@ of mass of the DC-DP pairs, with relaxation time 100 and with random seed 12345. This fix applies also a Langevin thermostat at temperature 1. to the relative motion of the DPs around their DCs, with relaxation time 20 and random seed 13977. Only the DCs and non-polarizable -atoms need to be in this fix's group. LAMMPS will thermostate the DPs +atoms need to be in this fix's group. LAMMPS will thermostat the DPs together with their DC. For this, ghost atoms need to know their velocities. Thus you need to add the following command: @@ -360,7 +360,7 @@ fix NPH all nph iso 1. 1. 500 :pre It is also possible to use a Nose-Hoover instead of a Langevin thermostat. This requires to use "{fix drude/transform}"_fix_drude_transform.html just before and after the -time intergation fixes. The {fix drude/transform/direct} converts the +time integration fixes. The {fix drude/transform/direct} converts the atomic masses, positions, velocities and forces into a reduced representation, where the DCs transform into the centers of mass of the DC-DP pairs and the DPs transform into their relative position @@ -396,7 +396,7 @@ global pressure and thus a global temperature whatever the fix group. We do want the pressure to correspond to the whole system, but we want the temperature to correspond to the fix group only. We must then use the {fix_modify} command for this. In the end, the block of -instructions for thermostating and barostatting will look like +instructions for thermostatting and barostatting will look like compute TATOMS ATOMS temp fix DIRECT all drude/transform/direct diff --git a/doc/src/Howto_elastic.txt b/doc/src/Howto_elastic.txt index 68b30970ca..ee8e7c26a4 100644 --- a/doc/src/Howto_elastic.txt +++ b/doc/src/Howto_elastic.txt @@ -30,7 +30,7 @@ examples/elastic directory described on the "Examples"_Examples.html doc page. Calculating elastic constants at finite temperature is more -challenging, because it is necessary to run a simulation that perfoms +challenging, because it is necessary to run a simulation that performs time averages of differential properties. One way to do this is to measure the change in average stress tensor in an NVT simulations when the cell volume undergoes a finite deformation. In order to balance diff --git a/doc/src/Howto_github.txt b/doc/src/Howto_github.txt index 3c2b9ac8c5..ef55653f37 100644 --- a/doc/src/Howto_github.txt +++ b/doc/src/Howto_github.txt @@ -96,7 +96,7 @@ machine to a directory with the name you chose. If none is given, it will default to "lammps". Typical names are "mylammps" or something similar. You can use this local clone to make changes and -test them without interfering with the repository on Github. +test them without interfering with the repository on GitHub. To pull changes from upstream into this copy, you can go to the directory and use git pull: @@ -150,7 +150,7 @@ After the commit, the changes can be pushed to the same branch on GitHub: $ git push :pre Git will ask you for your user name and password on GitHub if you have -not configured anything. If your local branch is not present on Github yet, +not configured anything. If your local branch is not present on GitHub yet, it will ask you to add it by running $ git push --set-upstream origin github-tutorial-update :pre @@ -369,7 +369,7 @@ commit and push again: $ git commit -m "Merged Axel's suggestions and updated text" $ git push git@github.com:Pakketeretet2/lammps :pre -This merge also shows up on the lammps Github page: +This merge also shows up on the lammps GitHub page: :c,image(JPG/tutorial_reverse_pull_request7.png) diff --git a/doc/src/Howto_manifold.txt b/doc/src/Howto_manifold.txt index 09a936f7d3..904432a946 100644 --- a/doc/src/Howto_manifold.txt +++ b/doc/src/Howto_manifold.txt @@ -31,8 +31,8 @@ plane @ a b c x0 y0 z0 @ a*(x-x0) + b*(y-y0) + c*(z-z0) = 0 @ A plane with norma plane_wiggle @ a w @ z - a*sin(w*x) = 0 @ A plane with a sinusoidal modulation on z along x. sphere @ R @ x^2 + y^2 + z^2 - R^2 = 0 @ A sphere of radius R supersphere @ R q @ | x |^q + | y |^q + | z |^q - R^q = 0 @ A supersphere of hyperradius R -spine @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ An approximation to a dendtritic spine -spine_two @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ Another approximation to a dendtritic spine +spine @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ An approximation to a dendritic spine +spine_two @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ Another approximation to a dendritic spine thylakoid @ wB LB lB @ Various, see "(Paquay)"_#Paquay1 @ A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB torus @ R r @ (R - sqrt( x^2 + y^2 ) )^2 + z^2 - r^2 @ A torus with large radius R and small radius r, centered on (0,0,0) :tb(s=@) diff --git a/doc/src/Howto_nemd.txt b/doc/src/Howto_nemd.txt index 10139d907c..1ec9c51f4e 100644 --- a/doc/src/Howto_nemd.txt +++ b/doc/src/Howto_nemd.txt @@ -55,5 +55,5 @@ using the "fix flow/gauss"_fix_flow_gauss.html command. :line :link(Daivis-nemd) -[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book), +[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dynamics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/src/Howto_polarizable.txt b/doc/src/Howto_polarizable.txt index b2653b117e..00a73dddd3 100644 --- a/doc/src/Howto_polarizable.txt +++ b/doc/src/Howto_polarizable.txt @@ -45,8 +45,8 @@ high symmetry around each site leads to stable trajectories of the core-shell pairs. However, bonded atoms in molecules can be so close that a core would interact too strongly or even capture the Drude particle of a neighbor. The Drude dipole model is relatively more -complex in order to remediate this and other issues. Specifically, the -Drude model includes specific thermostating of the core-Drude pairs +complex in order to remedy this and other issues. Specifically, the +Drude model includes specific thermostatting of the core-Drude pairs and short-range damping of the induced dipoles. The three polarization methods can be implemented through a @@ -77,5 +77,5 @@ motion of the Drude particles with respect to their cores is kept approaching the self-consistent regime. In both models the temperature is regulated using the velocities of the center of mass of core+shell (or Drude) pairs, but in the Drude model the actual -relative core-Drude particle motion is thermostated separately as +relative core-Drude particle motion is thermostatted separately as well. diff --git a/doc/src/Howto_pylammps.txt b/doc/src/Howto_pylammps.txt index 9706e30f6e..b731a8e31a 100644 --- a/doc/src/Howto_pylammps.txt +++ b/doc/src/Howto_pylammps.txt @@ -141,16 +141,16 @@ Python code if {L} was a lammps instance: L.command("region box block 0 10 0 5 -0.5 0.5") :pre With the PyLammps interface, any command can be split up into arbitrary parts -separated by whitespace, passed as individual arguments to a region method. +separated by white-space, passed as individual arguments to a region method. L.region("box block", 0, 10, 0, 5, -0.5, 0.5) :pre Note that each parameter is set as Python literal floating-point number. In the PyLammps interface, each command takes an arbitrary parameter list and transparently -merges it to a single command string, separating individual parameters by whitespace. +merges it to a single command string, separating individual parameters by white-space. The benefit of this approach is avoiding redundant command calls and easier -parameterization. In the original interface parametrization needed to be done +parameterization. In the original interface parameterization needed to be done manually by creating formatted strings. L.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi)) :pre diff --git a/doc/src/Howto_replica.txt b/doc/src/Howto_replica.txt index 2135e52e0e..29d1aa02fd 100644 --- a/doc/src/Howto_replica.txt +++ b/doc/src/Howto_replica.txt @@ -9,7 +9,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c Multi-replica simulations :h3 -Several commands in LAMMPS run mutli-replica simulations, meaning +Several commands in LAMMPS run multi-replica simulations, meaning that multiple instances (replicas) of your simulation are run simultaneously, with small amounts of data exchanged between replicas periodically. diff --git a/doc/src/Howto_spc.txt b/doc/src/Howto_spc.txt index 2cbf16547b..c0d4d77c5f 100644 --- a/doc/src/Howto_spc.txt +++ b/doc/src/Howto_spc.txt @@ -30,7 +30,7 @@ r0 of OH bond = 1.0 theta of HOH angle = 109.47 :all(b),p Note that as originally proposed, the SPC model was run with a 9 -Angstrom cutoff for both LJ and Coulommbic terms. It can also be used +Angstrom cutoff for both LJ and Coulombic terms. It can also be used with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing any of the parameters above, though it becomes a different model in that mode of usage. diff --git a/doc/src/Howto_spherical.txt b/doc/src/Howto_spherical.txt index d4233e7b81..a0ff90c42d 100644 --- a/doc/src/Howto_spherical.txt +++ b/doc/src/Howto_spherical.txt @@ -236,7 +236,7 @@ particles are point masses. Also note that body particles cannot be modeled with the "fix rigid"_fix_rigid.html command. Body particles are treated by LAMMPS as single particles, though they can store internal state, such as a -list of sub-particles. Individual body partices are typically treated +list of sub-particles. Individual body particles are typically treated as rigid bodies, and their motion integrated with a command like "fix nve/body"_fix_nve_body.html. Interactions between pairs of body particles are computed via a command like "pair_style diff --git a/doc/src/Howto_spins.txt b/doc/src/Howto_spins.txt index b549f99be2..88a5fbd86f 100644 --- a/doc/src/Howto_spins.txt +++ b/doc/src/Howto_spins.txt @@ -36,7 +36,7 @@ A Langevin thermostat can be applied to those magnetic spins using "fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat can be coupled to another Langevin thermostat applied to the atoms using "fix langevin"_fix_langevin.html in order to simulate -thermostated spin-lattice system. +thermostatted spin-lattice system. The magnetic Gilbert damping can also be applied using "fix langevin/spin"_fix_langevin_spin.html. It allows to either dissipate diff --git a/doc/src/Howto_thermostat.txt b/doc/src/Howto_thermostat.txt index 9f7e2f3000..aebf4555a7 100644 --- a/doc/src/Howto_thermostat.txt +++ b/doc/src/Howto_thermostat.txt @@ -96,5 +96,5 @@ temperature compute is used for default thermodynamic output. :line :link(Daivis-thermostat) -[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book), +[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dynamics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/src/Howto_triclinic.txt b/doc/src/Howto_triclinic.txt index 4b299e5ae1..2c5834a396 100644 --- a/doc/src/Howto_triclinic.txt +++ b/doc/src/Howto_triclinic.txt @@ -200,7 +200,7 @@ used with non-orthogonal basis vectors to define a lattice that will tile a triclinic simulation box via the "create_atoms"_create_atoms.html command. -A second use is to run Parinello-Rahman dynamics via the "fix +A second use is to run Parrinello-Rahman dynamics via the "fix npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt factors to compensate for off-diagonal components of the pressure tensor. The analog for an "energy minimization"_minimize.html is diff --git a/doc/src/Howto_viscosity.txt b/doc/src/Howto_viscosity.txt index b4e441557d..ee070eba58 100644 --- a/doc/src/Howto_viscosity.txt +++ b/doc/src/Howto_viscosity.txt @@ -140,5 +140,5 @@ with time at sufficiently long times. :line :link(Daivis-viscosity) -[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book), +[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dynamics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/src/Intro_authors.txt b/doc/src/Intro_authors.txt index b909265a3e..dc41727c05 100644 --- a/doc/src/Intro_authors.txt +++ b/doc/src/Intro_authors.txt @@ -48,7 +48,7 @@ Trung Ngyuen (Northwestern U), GPU and RIGID and BODY packages Mike Parks (Sandia), PERI package for Peridynamics Roy Pollock (LLNL), Ewald and PPPM solvers Christian Trott (Sandia), USER-CUDA and KOKKOS packages -Ilya Valuev (JIHT), USER-AWPMD package for wave-packet MD +Ilya Valuev (JIHT), USER-AWPMD package for wave packet MD Greg Wagner (Northwestern U), MEAM package for MEAM potential :ul :line diff --git a/doc/src/Intro_features.txt b/doc/src/Intro_features.txt index 07c549c156..d5e5b7f8b5 100644 --- a/doc/src/Intro_features.txt +++ b/doc/src/Intro_features.txt @@ -68,7 +68,7 @@ commands) pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, \ Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated charged pairwise potentials: Coulombic, point-dipole - manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \ + many-body potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \ embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, \ REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic long-range interactions for charge, point-dipoles, and LJ dispersion: \ @@ -114,7 +114,7 @@ Ensembles, constraints, and boundary conditions :h4,link(ensemble) 2d or 3d systems orthogonal or non-orthogonal (triclinic symmetry) simulation domains - constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators + constant NVE, NVT, NPT, NPH, Parrinello/Rahman integrators thermostatting options for groups and geometric regions of atoms pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions simulation box deformation (tensile and shear) diff --git a/doc/src/Intro_nonfeatures.txt b/doc/src/Intro_nonfeatures.txt index 580039f91b..5d4b556e7c 100644 --- a/doc/src/Intro_nonfeatures.txt +++ b/doc/src/Intro_nonfeatures.txt @@ -51,7 +51,7 @@ the option to insert molecule templates instead of atoms.:l Force-field assignment: The conversion tools described in the previous bullet for CHARMM, AMBER, and Insight will also assign force field coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER, -or Accelerys force field files. :l +or BIOVIA (formerly Accelrys) force field files. :l Simulation analysis: If you want to perform analysis on-the-fly as your simulation runs, see the "compute"_compute.html and diff --git a/doc/src/Modify_contribute.txt b/doc/src/Modify_contribute.txt index 8cbea8bb31..61b1405106 100644 --- a/doc/src/Modify_contribute.txt +++ b/doc/src/Modify_contribute.txt @@ -33,11 +33,11 @@ how much effort it will cause to integrate and test it, how much it requires changes to the core codebase, and of how much interest it is to the larger LAMMPS community. Please see below for a checklist of typical requirements. Once you have prepared everything, see the -"Howto github"_Howto_github.html doc page for instructions on how to +"Using GitHub with LAMMPS Howto"_Howto_github.html doc page for instructions on how to submit your changes or new files through a GitHub pull request. If you prefer to submit patches or full files, you should first make certain, that your code works correctly with the latest patch-level version of -LAMMPS and contains all bugfixes from it. Then create a gzipped tar +LAMMPS and contains all bug fixes from it. Then create a gzipped tar file of all changed or added files or a corresponding patch file using 'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip compression, as this works well on all platforms. diff --git a/doc/src/Modify_pair.txt b/doc/src/Modify_pair.txt index 0ebf2daa30..40806937d6 100644 --- a/doc/src/Modify_pair.txt +++ b/doc/src/Modify_pair.txt @@ -10,7 +10,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c Pair styles :h3 Classes that compute pairwise interactions are derived from the Pair -class. In LAMMPS, pairwise calculation include manybody potentials +class. In LAMMPS, pairwise calculation include many-body potentials such as EAM or Tersoff where particles interact without a static bond topology. New styles can be created to add new pair potentials to LAMMPS. diff --git a/doc/src/Modify_region.txt b/doc/src/Modify_region.txt index cdf192323a..c7a56bd32a 100644 --- a/doc/src/Modify_region.txt +++ b/doc/src/Modify_region.txt @@ -20,6 +20,6 @@ Here is a brief description of methods you define in your new derived class. See region.h for details. inside: determine whether a point is in the region -surface_interior: determine if a point is within a cutoff distance inside of surc -surface_exterior: determine if a point is within a cutoff distance outside of surf +surface_interior: determine if a point is within a cutoff distance inside of surface +surface_exterior: determine if a point is within a cutoff distance outside of surface shape_update : change region shape if set by time-dependent variable :tb(s=:) diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 55c7dec828..d6a3e17866 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -494,7 +494,7 @@ MANYBODY package :link(PKG-MANYBODY),h4 [Contents:] -A variety of manybody and bond-order potentials. These include +A variety of many-body and bond-order potentials. These include (AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials. [Supporting info:] @@ -518,7 +518,7 @@ MC package :link(PKG-MC),h4 Several fixes and a pair style that have Monte Carlo (MC) or MC-like attributes. These include fixes for creating, breaking, and swapping bonds, for performing atomic swaps, and performing grand-canonical MC -(GCMC) in conjuction with dynamics. +(GCMC) in conjunction with dynamics. [Supporting info:] diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt index de7984f3c0..077a7ce69d 100644 --- a/doc/src/Packages_user.txt +++ b/doc/src/Packages_user.txt @@ -38,8 +38,8 @@ int = internal library: provided with LAMMPS, but you may need to build it ext = external library: you will need to download and install it on your machine :ul Package, Description, Doc page, Example, Library -"USER-ATC"_Packages_details.html#PKG-USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int -"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int +"USER-ATC"_Packages_details.html#PKG-USER-ATC, Atom-to-Continuum coupling, "fix atc"_fix_atc.html, USER/atc, int +"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int "USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, no "USER-CGDNA"_Packages_details.html#PKG-USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, no "USER-CGSDK"_Packages_details.html#PKG-USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, no diff --git a/doc/src/Python_call.txt b/doc/src/Python_call.txt index 3c382de1ba..34b04679d5 100644 --- a/doc/src/Python_call.txt +++ b/doc/src/Python_call.txt @@ -79,7 +79,7 @@ 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 "Python +must also follow the steps summarized in the "Python run"_Python_run.html doc page. 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. diff --git a/doc/src/Python_examples.txt b/doc/src/Python_examples.txt index f4b2197464..13ef99bdf2 100644 --- a/doc/src/Python_examples.txt +++ b/doc/src/Python_examples.txt @@ -46,7 +46,7 @@ http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html :pre :link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) :link(atomeye3,http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html) -The latter link is to AtomEye 3 which has the scriping +The latter link is to AtomEye 3 which has the scripting capability needed by these Python scripts. Note that for PyMol, you need to have built and installed the diff --git a/doc/src/Speed.txt b/doc/src/Speed.txt index dd2052bac1..28aef26a5d 100644 --- a/doc/src/Speed.txt +++ b/doc/src/Speed.txt @@ -19,7 +19,7 @@ using code options that implement alternate algorithms that can speed-up a simulation. The second is to use one of the several accelerator packages provided with LAMMPS that contain code optimized for certain kinds of hardware, including multi-core CPUs, GPUs, and -Intel Xeon Phi coprocessors. +Intel Xeon Phi co-processors. The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS web site gives performance results for the various accelerator diff --git a/doc/src/Speed_intel.txt b/doc/src/Speed_intel.txt index 6f9f3dfcaf..7ff8d73ae9 100644 --- a/doc/src/Speed_intel.txt +++ b/doc/src/Speed_intel.txt @@ -14,11 +14,11 @@ Corporation. It provides two methods for accelerating simulations, depending on the hardware you have. The first is acceleration on Intel CPUs by running in single, mixed, or double precision with vectorization. The second is acceleration on Intel Xeon Phi -coprocessors via offloading neighbor list and non-bonded force +co-processors 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 +When offloading to a co-processor 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 simultaneously. +LAMMPS to run on the CPU cores and co-processor cores simultaneously. [Currently Available USER-INTEL Styles:] @@ -47,7 +47,7 @@ These are scalable in size; the results given are with 512K particles (524K for Liquid Crystal). Most of the simulations are standard LAMMPS benchmarks (indicated by the filename extension in parenthesis) with modifications to the run length and to add a -warmup run (for use with offload benchmarks). +warm-up run (for use with offload benchmarks). :c,image(JPG/user_intel.png) @@ -134,19 +134,19 @@ Do not use thread affinity (set KMP_AFFINITY=none) :l The "newton off" setting may provide better scalability :l :ule -For Intel Xeon Phi coprocessors (Offload): +For Intel Xeon Phi co-processors (Offload): -Edit src/MAKE/OPTIONS/Makefile.intel_coprocessor as necessary :ulb,l +Edit src/MAKE/OPTIONS/Makefile.intel_co-processor as necessary :ulb,l "-pk intel N omp 1" added to command-line where N is the number of -coprocessors per node. :l +co-processors per node. :l :ule :line [Required hardware/software:] -In order to use offload to coprocessors, an Intel Xeon Phi -coprocessor and an Intel compiler are required. For this, the +In order to use offload to co-processors, an Intel Xeon Phi +co-processor 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. @@ -214,7 +214,7 @@ Makefile.intel_cpu_intelmpi # Intel Compiler, Intel MPI, No Offload Makefile.knl # Intel Compiler, Intel MPI, No Offload Makefile.intel_cpu_mpich # Intel Compiler, MPICH, No Offload Makefile.intel_cpu_openpmi # Intel Compiler, OpenMPI, No Offload -Makefile.intel_coprocessor # Intel Compiler, Intel MPI, Offload :pre +Makefile.intel_co-processor # Intel Compiler, Intel MPI, Offload :pre Makefile.knl is identical to Makefile.intel_cpu_intelmpi except that it explicitly specifies that vectorization should be for Intel Xeon @@ -227,9 +227,9 @@ source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh # or psxevars.csh for C-shell make intel_cpu_intelmpi :pre -Note that if you build with support for a Phi coprocessor, the same -binary can be used on nodes with or without coprocessors installed. -However, if you do not have coprocessors on your system, building +Note that if you build with support for a Phi co-processor, the same +binary can be used on nodes with or without co-processors installed. +However, if you do not have co-processors on your system, building without offload support will produce a smaller binary. The general requirements for Makefiles with the USER-INTEL package @@ -272,7 +272,7 @@ Advanced performance tuning options are also described below to get the best performance. When running on a single node (including runs using offload to a -coprocessor), best performance is normally obtained by using 1 MPI +co-processor), best performance is normally obtained by using 1 MPI task per physical core and additional OpenMP threads with SMT. For Intel Xeon processors, 2 OpenMP threads should be used for SMT. For Intel Xeon Phi CPUs, 2 or 4 OpenMP threads should be used @@ -290,7 +290,7 @@ NOTE: Setting core affinity is often used to pin MPI tasks and OpenMP threads to a core or group of cores so that memory access can be uniform. Unless disabled at build time, affinity for MPI tasks and OpenMP threads on the host (CPU) will be set by default on the host -{when using offload to a coprocessor}. In this case, it is unnecessary +{when using offload to a co-processor}. In this case, it is unnecessary to use other methods to control affinity (e.g. taskset, numactl, I_MPI_PIN_DOMAIN, etc.). This can be disabled with the {no_affinity} option to the "package intel"_package.html command or by disabling the @@ -310,15 +310,15 @@ editing the input script. This switch will automatically append options for the USER-INTEL package. The default package command will specify that USER-INTEL calculations are performed in mixed precision, that the number of OpenMP threads is specified by the OMP_NUM_THREADS -environment variable, and that if coprocessors are present and the -binary was built with offload support, that 1 coprocessor per node +environment variable, and that if co-processors are present and the +binary was built with offload support, that 1 co-processor per node will be used with automatic balancing of work between the CPU and the -coprocessor. +co-processor. You can specify different options for the USER-INTEL package by using the "-pk intel Nphi" "command-line switch"_Run_options.html with keyword/value pairs as specified in the documentation. Here, Nphi = # -of Xeon Phi coprocessors/node (ignored without offload +of Xeon Phi co-processors/node (ignored without offload support). Common options to the USER-INTEL package include {omp} to override any OMP_NUM_THREADS setting and specify the number of OpenMP threads, {mode} to set the floating-point precision mode, and {lrt} to @@ -332,7 +332,7 @@ Examples (see documentation for your MPI/Machine for differences in launching MPI applications): mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads -mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double # Don't use any coprocessors that might be available, use 2 OpenMP threads for each task, use double precision :pre +mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double # Don't use any co-processors that might be available, use 2 OpenMP threads for each task, use double precision :pre [Or run with the USER-INTEL package by editing an input script:] @@ -364,7 +364,7 @@ intel"_package.html command that can improve performance when using "PPPM"_kspace_style.html for long-range electrostatics on processors with SMT. It generates an extra pthread for each MPI task. The thread is dedicated to performing some of the PPPM calculations and MPI -communications. This feature requires setting the preprocessor flag +communications. This feature requires setting the pre-processor flag -DLMP_INTEL_USELRT in the makefile when compiling LAMMPS. It is unset in the default makefiles ({Makefile.mpi} and {Makefile.serial}) but it is set in all makefiles tuned for the USER-INTEL package. On Intel @@ -422,29 +422,29 @@ that MPI runs are performed in MCDRAM. The default settings for offload should give good performance. -When using LAMMPS with offload to Intel coprocessors, best performance +When using LAMMPS with offload to Intel co-processors, best performance will typically be achieved with concurrent calculations performed on -both the CPU and the coprocessor. This is achieved by offloading only -a fraction of the neighbor and pair computations to the coprocessor or +both the CPU and the co-processor. This is achieved by offloading only +a fraction of the neighbor and pair computations to the co-processor or using "hybrid"_pair_hybrid.html pair styles where only one style uses the "intel" suffix. For simulations with long-range electrostatics or bond, angle, dihedral, improper calculations, computation and data -transfer to the coprocessor will run concurrently with computations +transfer to the co-processor will run concurrently with computations and MPI communications for these calculations on the host CPU. This is illustrated in the figure below for the rhodopsin protein benchmark running on E5-2697v2 processors with a Intel Xeon Phi 7120p -coprocessor. In this plot, the vertical access is time and routines +co-processor. In this plot, the vertical access is time and routines running at the same time are running concurrently on both the host and -the coprocessor. +the co-processor. :c,image(JPG/offload_knc.png) The fraction of the offloaded work is controlled by the {balance} keyword in the "package intel"_package.html command. A balance of 0 runs all calculations on the CPU. A balance of 1 runs all -supported calculations on the coprocessor. A balance of 0.5 runs half -of the calculations on the coprocessor. Setting the balance to -1 -(the default) will enable dynamic load balancing that continously +supported calculations on the co-processor. A balance of 0.5 runs half +of the calculations on the co-processor. Setting the balance to -1 +(the default) will enable dynamic load balancing that continuously adjusts the fraction of offloaded work throughout the simulation. Because data transfer cannot be timed, this option typically produces results within 5 to 10 percent of the optimal fixed balance. @@ -455,23 +455,23 @@ near-optimal setting that will carry over to additional runs. The default for the "package intel"_package.html command is to have all the MPI tasks on a given compute node use a single Xeon Phi -coprocessor. In general, running with a large number of MPI tasks on +co-processor. In general, running with a large number of MPI tasks on each node will perform best with offload. Each MPI task will automatically get affinity to a subset of the hardware threads -available on the coprocessor. For example, if your card has 61 cores, +available on the co-processor. For example, if your card has 61 cores, with 60 cores available for offload and 4 hardware threads per core (240 total threads), running with 24 MPI tasks per node will cause -each MPI task to use a subset of 10 threads on the coprocessor. Fine +each MPI task to use a subset of 10 threads on the co-processor. Fine tuning of the number of threads to use per MPI task or the number of threads to use per core can be accomplished with keyword settings of the "package intel"_package.html command. The USER-INTEL package has two modes for deciding which atoms will be -handled by the coprocessor. This choice is controlled with the {ghost} +handled by the co-processor. This choice is controlled with the {ghost} keyword of the "package intel"_package.html command. When set to 0, ghost atoms (atoms at the borders between MPI tasks) are not offloaded to the card. This allows for overlap of MPI communication of forces -with computation on the coprocessor when the "newton"_newton.html +with computation on the co-processor when the "newton"_newton.html setting is "on". The default is dependent on the style being used, however, better performance may be achieved by setting this option explicitly. @@ -482,21 +482,21 @@ cores. This is due to the fact that additional threads are generated internally to handle the asynchronous offload tasks. If pair computations are being offloaded to an Intel Xeon Phi -coprocessor, a diagnostic line is printed to the screen (not to the +co-processor, a diagnostic line is printed to the screen (not to the log file), during the setup phase of a run, indicating that offload -mode is being used and indicating the number of coprocessor threads +mode is being used and indicating the number of co-processor threads per MPI task. Additionally, an offload timing summary is printed at the end of each run. When offloading, the frequency for "atom sorting"_atom_modify.html is changed to 1 so that the per-atom data is effectively sorted at every rebuild of the neighbor lists. All the -available coprocessor threads on each Phi will be divided among MPI +available co-processor threads on each Phi will be divided among MPI tasks, unless the {tptask} option of the "-pk intel" "command-line -switch"_Run_options.html is used to limit the coprocessor threads per +switch"_Run_options.html is used to limit the co-processor threads per MPI task. [Restrictions:] -When offloading to a coprocessor, "hybrid"_pair_hybrid.html styles +When offloading to a co-processor, "hybrid"_pair_hybrid.html styles that require skip lists for neighbor builds cannot be offloaded. Using "hybrid/overlay"_pair_hybrid.html is allowed. Only one intel accelerated style may be used with hybrid styles when offloading. diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt index 3373982e9f..0a24753a9f 100644 --- a/doc/src/Speed_kokkos.txt +++ b/doc/src/Speed_kokkos.txt @@ -17,7 +17,7 @@ different back end languages such as CUDA, OpenMP, or Pthreads. The Kokkos library also provides data abstractions to adjust (at compile time) the memory layout of data structures like 2d and 3d arrays to optimize performance on different hardware. For more information on -Kokkos, see "Github"_https://github.com/kokkos/kokkos. Kokkos is part +Kokkos, see "GitHub"_https://github.com/kokkos/kokkos. Kokkos is part of "Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos library was written primarily by Carter Edwards, Christian Trott, and Dan Sunderland (all Sandia). @@ -193,7 +193,7 @@ threads/task as Nt. The product of these two values should be N, i.e. NOTE: The default for the "package kokkos"_package.html command is to use "full" neighbor lists and set the Newton flag to "off" for both pairwise and bonded interactions. When running on KNL, this will -typically be best for pair-wise potentials. For manybody potentials, +typically be best for pair-wise potentials. For many-body potentials, using "half" neighbor lists and setting the Newton flag to "on" may be faster. It can also be faster to use non-threaded communication. Use the "-pk kokkos" "command-line switch"_Run_options.html to change the @@ -207,7 +207,7 @@ mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton on neigh half co NOTE: MPI tasks and threads should be bound to cores as described above for CPUs. -NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors +NOTE: To build with Kokkos support for Intel Xeon Phi co-processors such as Knight's Corner (KNC), your system must be configured to use them in "native" mode, not "offload" mode like the USER-INTEL package supports. diff --git a/doc/src/Speed_packages.txt b/doc/src/Speed_packages.txt index 4c87091e7e..2f72a46b3a 100644 --- a/doc/src/Speed_packages.txt +++ b/doc/src/Speed_packages.txt @@ -14,7 +14,7 @@ Accelerated versions of various "pair_style"_pair_style.html, been added to LAMMPS, which will typically run faster than the standard non-accelerated versions. Some require appropriate hardware to be present on your system, e.g. GPUs or Intel Xeon Phi -coprocessors. +co-processors. All of these commands are in packages provided with LAMMPS. An overview of packages is give on the "Packages"_Packages.html doc @@ -161,7 +161,7 @@ package. These styles support vectorized single and mixed precision calculations, in addition to full double precision. In extreme cases, this can provide speedups over 3.5x on CPUs. The package also supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM) -coprocessors. This can result in additional speedup over 2x depending +co-processors. This can result in additional speedup over 2x depending on the hardware configuration. :l Styles with a "kk" suffix are part of the KOKKOS package, and can be diff --git a/doc/src/Tools.txt b/doc/src/Tools.txt index a9ad5032ce..1ec4969620 100644 --- a/doc/src/Tools.txt +++ b/doc/src/Tools.txt @@ -163,7 +163,7 @@ for the "chain benchmark"_Speed_bench.html. colvars tools :h4,link(colvars) -The colvars directory contains a collection of tools for postprocessing +The colvars directory contains a collection of tools for post-processing data produced by the colvars collective variable library. To compile the tools, edit the makefile for your system and run "make". @@ -406,15 +406,15 @@ supports it. It has its own WWW page at msi2lmp tool :h4,link(msi) The msi2lmp sub-directory contains a tool for creating LAMMPS template -input and data files from BIOVIA's Materias Studio files (formerly Accelrys' -Insight MD code, formerly MSI/Biosym and its Discover MD code). +input and data files from BIOVIA's Materias Studio files (formerly +Accelrys' Insight MD code, formerly MSI/Biosym and its Discover MD code). This tool was written by John Carpenter (Cray), Michael Peachey (Cray), and Steve Lustig (Dupont). Several people contributed changes to remove bugs and adapt its output to changes in LAMMPS. This tool has several known limitations and is no longer under active -development, so there are no changes except for the occasional bugfix. +development, so there are no changes except for the occasional bug fix. See the README file in the tools/msi2lmp folder for more information. diff --git a/doc/src/angle_sdk.txt b/doc/src/angle_sdk.txt index 22238880fe..9382d560d3 100644 --- a/doc/src/angle_sdk.txt +++ b/doc/src/angle_sdk.txt @@ -28,7 +28,7 @@ The {sdk} angle style is a combination of the harmonic angle potential, where theta0 is the equilibrium value of the angle and K a prefactor, with the {repulsive} part of the non-bonded {lj/sdk} pair style between the atoms 1 and 3. This angle potential is intended for -coarse grained MD simulations with the CMM parametrization using the +coarse grained MD simulations with the CMM parameterization using the "pair_style lj/sdk"_pair_sdk.html. Relative to the pair_style {lj/sdk}, however, the energy is shifted by {epsilon}, to avoid sudden jumps. Note that the usual 1/2 factor is included in K. diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt index db2e285dc4..ff714e31d9 100644 --- a/doc/src/atom_style.txt +++ b/doc/src/atom_style.txt @@ -87,7 +87,7 @@ quantities. {line} | end points, angular velocity | rigid bodies | {meso} | rho, e, cv | SPH particles | {molecular} | bonds, angles, dihedrals, impropers | uncharged molecules | -{peri} | mass, volume | mesocopic Peridynamic models | +{peri} | mass, volume | mesoscopic Peridynamic models | {smd} | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles | {sphere} | diameter, mass, angular velocity | granular models | {spin} | magnetic moment | system with magnetic particles | diff --git a/doc/src/balance.txt b/doc/src/balance.txt index 49202b0149..3afc469a39 100644 --- a/doc/src/balance.txt +++ b/doc/src/balance.txt @@ -247,7 +247,7 @@ to {Niter} times. After each dimension finishes, the imbalance factor is re-computed, and the balancing operation halts if the {stopthresh} criterion is met. -A rebalance operation in a single dimension is performed using a +A re-balance operation in a single dimension is performed using a recursive multisectioning algorithm, where the position of each cutting plane (line in 2d) in the dimension is adjusted independently. This is similar to a recursive bisectioning for a single value, except @@ -261,11 +261,11 @@ information, so that they become closer together over time. Thus as the recursion progresses, the count of particles on either side of the plane gets closer to the target value. -Once the rebalancing is complete and final processor sub-domains +Once the re-balancing is complete and final processor sub-domains assigned, particles are migrated to their new owning processor, and the balance procedure ends. -NOTE: At each rebalance operation, the bisectioning for each cutting +NOTE: At each re-balance operation, the bisectioning for each cutting 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 @@ -348,7 +348,7 @@ specified groups, its weight is not changed. If it belongs to multiple groups, its weight is the product of the weight factors. This weight style is useful in combination with pair style -"hybrid"_pair_hybrid.html, e.g. when combining a more costly manybody +"hybrid"_pair_hybrid.html, e.g. when combining a more costly many-body potential with a fast pair-wise potential. It is also useful when using "run_style respa"_run_style.html where some portions of the system have many bonded interactions and others none. It assumes that diff --git a/doc/src/bond_oxdna.txt b/doc/src/bond_oxdna.txt index 724951f961..88afe435e6 100644 --- a/doc/src/bond_oxdna.txt +++ b/doc/src/bond_oxdna.txt @@ -52,7 +52,7 @@ hydrogen-bonding interaction {oxdna/hbond} (see also documentation of "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair style {oxdna2/dh} have to be defined. The coefficients in the above example have to be kept fixed and cannot -be changed without reparametrizing the entire model. +be changed without reparameterizing the entire model. Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python diff --git a/doc/src/comm_modify.txt b/doc/src/comm_modify.txt index 489278523b..482259142b 100644 --- a/doc/src/comm_modify.txt +++ b/doc/src/comm_modify.txt @@ -154,6 +154,6 @@ Communication mode {multi} is currently only available for [Default:] -The option defauls are mode = single, group = all, cutoff = 0.0, vel = +The option defaults are mode = single, group = all, cutoff = 0.0, vel = no. The cutoff default of 0.0 means that ghost cutoff = neighbor cutoff = pairwise force cutoff + neighbor skin. diff --git a/doc/src/compute_adf.txt b/doc/src/compute_adf.txt index 3d0646e294..20b9fad3f6 100644 --- a/doc/src/compute_adf.txt +++ b/doc/src/compute_adf.txt @@ -33,22 +33,22 @@ keyword = {ordinate} :l compute 1 fluid adf 32 1 1 1 0.0 1.2 0.0 1.2 & 1 1 2 0.0 1.2 0.0 1.5 & - 1 2 2 0.0 1.5 0.0 1.5 & + 1 2 2 0.0 1.5 0.0 1.5 & 2 1 1 0.0 1.2 0.0 1.2 & 2 1 2 0.0 1.5 2.0 3.5 & - 2 2 2 2.0 3.5 2.0 3.5 + 2 2 2 2.0 3.5 2.0 3.5 compute 1 fluid adf 32 1*2 1*2 1*2 0.5 3.5 compute 1 fluid adf 32 :pre [Description:] Define a computation that calculates one or more angular distribution functions -(ADF) for a group of particles. Each ADF is calculated in histogram form +(ADF) for a group of particles. Each ADF is calculated in histogram form by measuring the angle formed by a central atom and two neighbor atoms and binning these angles into {Nbin} bins. Only neighbors for which {Rinner} < {R} < {Router} are counted, where {Rinner} and {Router} are specified separately for the first and second -neighbor atom in each requested ADF. +neighbor atom in each requested ADF. NOTE: If you have a bonded system, then the settings of "special_bonds"_special_bonds.html command can remove pairwise @@ -66,18 +66,18 @@ the dump file. The rerun script can use a "special_bonds"_special_bonds.html command that includes all pairs in the neighbor list. -NOTE: If you request any outer cutoff {Router} > force cutoff, or if no +NOTE: If you request any outer cutoff {Router} > force cutoff, or if no pair style is defined, e.g. the "rerun"_rerun.html command is being used to -post-process a dump file of snapshots you must insure ghost atom information -out to the largest value of {Router} + {skin} is communicated, via the -"comm_modify cutoff"_comm_modify.html command, else the ADF computation -cannot be performed, and LAMMPS will give an error message. The {skin} value -is what is specified with the "neighbor"_neighbor.html command. +post-process a dump file of snapshots you must insure ghost atom information +out to the largest value of {Router} + {skin} is communicated, via the +"comm_modify cutoff"_comm_modify.html command, else the ADF computation +cannot be performed, and LAMMPS will give an error message. The {skin} value +is what is specified with the "neighbor"_neighbor.html command. The {itypeN},{jtypeN},{ktypeN} settings can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card asterisk can be used to specify a range of atom -types as in the 2nd example above. +types as in the 2nd example above. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of atom types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n @@ -88,13 +88,13 @@ all types from 1 to N. A leading asterisk means all types from 1 to n If {itypeN}, {jtypeN}, and {ktypeN} are single values, as in the 1st example above, this means that the ADF is computed where atoms of type {itypeN} are the central atom, and neighbor atoms of type {jtypeN} and {ktypeN} -are forming the angle. If any of {itypeN}, {jtypeN}, or {ktypeN} +are forming the angle. If any of {itypeN}, {jtypeN}, or {ktypeN} represent a range of values via the wild-card asterisk, as in the 2nd example above, this means that the ADF is computed where atoms of any of the range of types represented by {itypeN} are the central atom, and the angle is formed by two neighbors, -one neighbor in the range of types represented by {jtypeN} and another neighbor -in the range of types represented by {ktypeN}. +one neighbor in the range of types represented by {jtypeN} and another neighbor +in the range of types represented by {ktypeN}. If no {itypeN}, {jtypeN}, {ktypeN} settings are specified, then LAMMPS will generate a single ADF for all atoms in the group. @@ -106,13 +106,13 @@ Such an ADF is both uninformative and extremely expensive to compute. For example, with liquid water with a 10 A force cutoff, there are 80,000 angles per atom. In addition, most of the interesting angular structure occurs for -neighbors that are the closest to the central atom, involving +neighbors that are the closest to the central atom, involving just a few dozen angles. -Angles for each ADF are generated by double-looping over the list of -neighbors of each central atom I, -just as they would be in the force calculation for -a threebody potential such as "Stillinger-Weber"_pair_sw.html. +Angles for each ADF are generated by double-looping over the list of +neighbors of each central atom I, +just as they would be in the force calculation for +a three-body potential such as "Stillinger-Weber"_pair_sw.html. The angle formed by central atom I and neighbor atoms J and K is included in an ADF if the following criteria are met: @@ -121,12 +121,12 @@ the distance between atoms I,J is between Rjinner and Rjouter the distance between atoms I,K is between Rkinner and Rkouter the type of the I atom matches itypeN (one or a range of types) atoms I,J,K are distinct -the type of the J atom matches jtypeN (one or a range of types) +the type of the J atom matches jtypeN (one or a range of types) the type of the K atom matches ktypeN (one or a range of types) :ul Each unique angle satisfying the above criteria is counted only once, regardless of whether either or both of the neighbor atoms making up the -angle appear in both the J and K lists. +angle appear in both the J and K lists. It is OK if a particular angle is included in more than one individual histogram, due to the way the {itypeN}, {jtypeN}, {ktypeN} arguments are specified. @@ -146,15 +146,15 @@ number radial distribution function. The {ordinate} optional keyword determines whether the bins are of uniform angular size from zero -to 180 ({degree}), zero to Pi ({radian}), or the +to 180 ({degree}), zero to Pi ({radian}), or the cosine of the angle uniform in the range \[-1,1\] ({cosine}). {cosine} has the advantage of eliminating the {acos()} function call, which speeds up the compute by 2-3x, and it is also preferred -on physical grounds, because the for uniformly distributed particles +on physical grounds, because the for uniformly distributed particles in 3D, the angular probability density w.r.t dtheta is -sin(theta)/2, while for d(cos(theta)), it is 1/2, -Regardless of which ordinate is chosen, the first column of ADF -values is normalized w.r.t. the range of that ordinate, so that +sin(theta)/2, while for d(cos(theta)), it is 1/2, +Regardless of which ordinate is chosen, the first column of ADF +values is normalized w.r.t. the range of that ordinate, so that the integral is 1. The simplest way to output the results of the compute adf calculation @@ -170,7 +170,7 @@ This compute calculates a global array with the number of rows = {Nbins}, and the number of columns = 1 + 2*Ntriples, where Ntriples is the number of I,J,K triples specified. The first column has the bin coordinate (angle-related ordinate at midpoint of bin). Each subsequent column has -the two ADF values for a specific set of ({itypeN},{jtypeN},{ktypeN}) +the two ADF values for a specific set of ({itypeN},{jtypeN},{ktypeN}) interactions, as described above. These values can be used by any command that uses a global values from a compute as input. See the "Howto output"_Howto_output.html doc page for an overview of @@ -181,15 +181,15 @@ The array values calculated by this compute are all "intensive". The first column of array values is the angle-related ordinate, either the angle in degrees or radians, or the cosine of the angle. Each subsequent pair of columns gives the first and second kinds of ADF -for a specific set of ({itypeN},{jtypeN},{ktypeN}). The values +for a specific set of ({itypeN},{jtypeN},{ktypeN}). The values in the first ADF column are normalized numbers >= 0.0, whose integral w.r.t. the ordinate is 1, -i.e. the first ADF is a normalized probability distribution. +i.e. the first ADF is a normalized probability distribution. The values in the second ADF column are also numbers >= 0.0. They are the cumulative density distribution of angles per atom. By definition, this ADF is monotonically increasing from zero to a maximum value equal to the average total number of -angles per atom satisfying the ADF criteria. +angles per atom satisfying the ADF criteria. [Restrictions:] @@ -200,7 +200,7 @@ distances, you can use the "rerun"_rerun.html command to post-process a dump file and set the cutoff for the potential to be longer in the rerun script. Note that in the rerun context, the force cutoff is arbitrary, since you aren't running dynamics and thus are not changing -your model. +your model. [Related commands:] diff --git a/doc/src/compute_bond_local.txt b/doc/src/compute_bond_local.txt index 4afd1aec40..6055d28770 100644 --- a/doc/src/compute_bond_local.txt +++ b/doc/src/compute_bond_local.txt @@ -68,7 +68,7 @@ in the bond, which is simply 1/2 m1 v1^2 + 1/2 m2 v2^2, where v1 and v2 are the magnitude of the velocity of the 2 atoms along the bond direction, after the COM velocity has been subtracted from each. -The value {engrot} is the rotationsl kinetic energy of the two atoms +The value {engrot} is the rotational kinetic energy of the two atoms in the bond, which is simply 1/2 m1 v1^2 + 1/2 m2 v2^2, where v1 and v2 are the magnitude of the velocity of the 2 atoms perpendicular to the bond direction, after the COM velocity has been subtracted from diff --git a/doc/src/compute_chunk_atom.txt b/doc/src/compute_chunk_atom.txt index c29a5600a9..b924f90da8 100644 --- a/doc/src/compute_chunk_atom.txt +++ b/doc/src/compute_chunk_atom.txt @@ -210,7 +210,7 @@ between {crmin} and {crmax}. For example, if {crmin} = 1.0 and {crmax} = 10.0 and {ncbin} = 9, then the first bin spans 1.0 < r < 2.0, and the last bin spans 9.0 < r 10.0. The geometry of the bins in the radial dimensions is the same whether the simulation box is -orthogonal or triclinic; i.e. the concetric circles are not tilted or +orthogonal or triclinic; i.e. the concentric circles are not tilted or scaled differently in the two different dimensions to transform them into ellipses. diff --git a/doc/src/compute_cna_atom.txt b/doc/src/compute_cna_atom.txt index d69c5e9c46..56ad7dd715 100644 --- a/doc/src/compute_cna_atom.txt +++ b/doc/src/compute_cna_atom.txt @@ -33,7 +33,7 @@ Currently, there are five kinds of CNA patterns LAMMPS recognizes: fcc = 1 hcp = 2 bcc = 3 -icosohedral = 4 +icosahedral = 4 unknown = 5 :ul The value of the CNA pattern will be 0 for atoms not in the specified diff --git a/doc/src/compute_damage_atom.txt b/doc/src/compute_damage_atom.txt index 2594dfe356..c3e822d79f 100644 --- a/doc/src/compute_damage_atom.txt +++ b/doc/src/compute_damage_atom.txt @@ -26,7 +26,7 @@ in a group. This is a quantity relevant for "Peridynamics models"_pair_peri.html. See "this document"_PDF/PDLammps_overview.pdf for an overview of LAMMPS commands for Peridynamics modeling. -The "damage" of a Peridymaics particles is based on the bond breakage +The "damage" of a Peridynamics particles is based on the bond breakage between the particle and its neighbors. If all the bonds are broken the particle is considered to be fully damaged. diff --git a/doc/src/compute_displace_atom.txt b/doc/src/compute_displace_atom.txt index 7cea62c7b3..141d0cc51b 100644 --- a/doc/src/compute_displace_atom.txt +++ b/doc/src/compute_displace_atom.txt @@ -57,7 +57,7 @@ correctly with time=0 atom coordinates from the restart file. :line -The {refresh} option can be used in conjuction with the "dump_modify +The {refresh} option can be used in conjunction with the "dump_modify refresh" command to generate incremental dump files. The definition and motivation of an incremental dump file is as diff --git a/doc/src/compute_msd.txt b/doc/src/compute_msd.txt index b54e05bc64..50f8b103d3 100644 --- a/doc/src/compute_msd.txt +++ b/doc/src/compute_msd.txt @@ -50,7 +50,7 @@ The value of the displacement will be If the {com} option is set to {yes} then the effect of any drift in the center-of-mass of the group of atoms is subtracted out before the -displacment of each atom is calculated. +displacement of each atom is calculated. If the {average} option is set to {yes} then the reference position of an atom is based on the average position of that atom, corrected for diff --git a/doc/src/compute_msd_nongauss.txt b/doc/src/compute_msd_nongauss.txt index c6e89a1061..c22b458178 100644 --- a/doc/src/compute_msd_nongauss.txt +++ b/doc/src/compute_msd_nongauss.txt @@ -48,7 +48,7 @@ others. If the {com} option is set to {yes} then the effect of any drift in the center-of-mass of the group of atoms is subtracted out before the -displacment of each atom is calculated. +displacement of each atom is calculated. See the "compute msd"_compute_msd.html doc page for further important NOTEs, which also apply to this compute. diff --git a/doc/src/compute_pair.txt b/doc/src/compute_pair.txt index b36d61f71c..1ced6eecfc 100644 --- a/doc/src/compute_pair.txt +++ b/doc/src/compute_pair.txt @@ -15,7 +15,7 @@ compute ID group-ID pair pstyle \[nstyle\] \[evalue\] :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l pair = style name of this compute command :l pstyle = style name of a pair style that calculates additional values :l -nsub = {n}-instance of a substyle, if a pair style is used multiple times in a hybrid style :l +nsub = {n}-instance of a sub-style, if a pair style is used multiple times in a hybrid style :l {evalue} = {epair} or {evdwl} or {ecoul} or blank (optional) :l :ule diff --git a/doc/src/compute_plasticity_atom.txt b/doc/src/compute_plasticity_atom.txt index b82179712a..6c21cecd6c 100644 --- a/doc/src/compute_plasticity_atom.txt +++ b/doc/src/compute_plasticity_atom.txt @@ -30,7 +30,7 @@ The plasticity for a Peridynamic particle is the so-called consistency parameter (lambda). For elastic deformation lambda = 0, otherwise lambda > 0 for plastic deformation. For details, see "(Mitchell)"_#Mitchell and the PDF doc included in the LAMMPS -distro in "doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf. +distribution in "doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf. This command can be invoked for one of the Peridynamic "pair styles"_pair_peri.html: peri/eps. diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt index 6acbaf7d3d..bd6e38e392 100644 --- a/doc/src/compute_pressure.txt +++ b/doc/src/compute_pressure.txt @@ -40,7 +40,7 @@ below), Kb is the Boltzmann constant, T is the temperature, d is the dimensionality of the system (2 or 3 for 2d/3d), and V is the system volume (or area in 2d). The second term is the virial, equal to -dU/dV, computed for all pairwise as well as 2-body, 3-body, 4-body, -manybody, and long-range interactions, where r_i and f_i are the +many-body, and long-range interactions, where r_i and f_i are the position and force vector of atom i, and the black dot indicates a dot product. When periodic boundary conditions are used, N' necessarily includes periodic image (ghost) atoms outside the central box, and the @@ -68,7 +68,7 @@ compute temperature or ke and/or the virial. The {virial} keyword means include all terms except the kinetic energy {ke}. Details of how LAMMPS computes the virial efficiently for the entire -system, including for manybody potentials and accounting for the +system, including for many-body potentials and accounting for the effects of periodic boundary conditions are discussed in "(Thompson)"_#Thompson1. diff --git a/doc/src/compute_pressure_cylinder.txt b/doc/src/compute_pressure_cylinder.txt index 4865fe8a79..f4312e67bc 100644 --- a/doc/src/compute_pressure_cylinder.txt +++ b/doc/src/compute_pressure_cylinder.txt @@ -58,7 +58,7 @@ This compute currently calculates the pressure tensor contributions for pair styles only (i.e. no bond, angle, dihedral, etc. contributions and in the presence of bonded interactions, the result will be incorrect due to exclusions for special bonds) and requires pair-wise force -calculations not available for most manybody pair styles. K-space +calculations not available for most many-body pair styles. K-space calculations are also excluded. Note that this pressure compute outputs the configurational terms only; the kinetic contribution is not included and may be calculated from the number density output by P_kin=density*k*T. diff --git a/doc/src/compute_reduce.txt b/doc/src/compute_reduce.txt index 0bd2accf3c..1e9cc651e1 100644 --- a/doc/src/compute_reduce.txt +++ b/doc/src/compute_reduce.txt @@ -61,7 +61,7 @@ or {max} options find the minimum or maximum value across all vector values. The {ave} setting adds the vector values into a global total, then divides by the number of values in the vector. The {sumsq} option sums the square of the values in the vector into a global -total. The {avesq} setting does the same as {sumsq}, then divdes the +total. The {avesq} setting does the same as {sumsq}, then divides the sum of squares by the number of values. The last two options can be useful for calculating the variance of some quantity, e.g. variance = sumsq - ave^2. diff --git a/doc/src/compute_reduce_chunk.txt b/doc/src/compute_reduce_chunk.txt index 3628c0f1ad..f19ed00c6a 100644 --- a/doc/src/compute_reduce_chunk.txt +++ b/doc/src/compute_reduce_chunk.txt @@ -137,7 +137,7 @@ compute micelle all chunk/atom c_spread compress yes :pre Further analysis on a per-micelle basis can now be performed using any of the per-chunk computes listed on the "Howto chunk"_Howto_chunk.html doc page. E.g. count the number of atoms in each micelle, calculate -its center or mass, shape (moments of intertia), radius of gyration, +its center or mass, shape (moments of inertia), radius of gyration, etc. compute prop all property/chunk micelle count diff --git a/doc/src/compute_smd_hourglass_error.txt b/doc/src/compute_smd_hourglass_error.txt index 5bc3e3a2de..28f1f351a8 100644 --- a/doc/src/compute_smd_hourglass_error.txt +++ b/doc/src/compute_smd_hourglass_error.txt @@ -29,7 +29,7 @@ within the neighborhood of the central node and the deformation gradient, the approximated relative separation will coincide with the actual relative separation of the particles i and j in the deformed configuration. This compute is only really useful for debugging the -hourglass control mechanim which is part of the Total-Lagrangian SPH +hourglass control mechanism which is part of the Total-Lagrangian SPH pair style. See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth diff --git a/doc/src/compute_smd_tlsph_defgrad.txt b/doc/src/compute_smd_tlsph_defgrad.txt index a733a3d6a7..bdd3a26a8f 100644 --- a/doc/src/compute_smd_tlsph_defgrad.txt +++ b/doc/src/compute_smd_tlsph_defgrad.txt @@ -30,7 +30,7 @@ Mach Dynamics in LAMMPS. [Output info:] -This compute outputss a per-particle vector of vectors (tensors), +This compute outputs a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle 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/compute_smd_tlsph_shape.txt b/doc/src/compute_smd_tlsph_shape.txt index 9c17194ec1..0ecfec0187 100644 --- a/doc/src/compute_smd_tlsph_shape.txt +++ b/doc/src/compute_smd_tlsph_shape.txt @@ -38,7 +38,7 @@ overview of LAMMPS output options. The per-particle vector has 7 entries. The first three entries correspond to the lengths of the ellipsoid's axes and have units of -length. These axis valus are computed as the contact radius times the +length. These axis values are computed as the contact radius times the xx, yy, or zz components of the Green-Lagrange strain tensor associated with the particle. The next 4 values are quaternions (order: q, x, y, z) which describe the spatial rotation of the diff --git a/doc/src/compute_stress_atom.txt b/doc/src/compute_stress_atom.txt index 222513da61..d81d97061c 100644 --- a/doc/src/compute_stress_atom.txt +++ b/doc/src/compute_stress_atom.txt @@ -73,9 +73,9 @@ Note that the stress for each atom is due to its interaction with all other atoms in the simulation, not just with other atoms in the group. Details of how LAMMPS computes the virial for individual atoms for -either pairwise or manybody potentials, and including the effects of +either pairwise or many-body potentials, and including the effects of periodic boundary conditions is discussed in "(Thompson)"_#Thompson2. -The basic idea for manybody potentials is to treat each component of +The basic idea for many-body potentials is to treat each component of the force computation between a small cluster of atoms in the same manner as in the formula above for bond, angle, dihedral, etc interactions. Namely the quantity R dot F is summed over the atoms in diff --git a/doc/src/compute_tally.txt b/doc/src/compute_tally.txt index a4a8441f9e..6401be54e9 100644 --- a/doc/src/compute_tally.txt +++ b/doc/src/compute_tally.txt @@ -47,7 +47,7 @@ the based classes of LAMMPS. The pairwise contributions are computing via a callback that the compute registers with the non-bonded pairwise force computation. This limits the use to systems that have no bonds, no Kspace, and no -manybody interactions. On the other hand, the computation does not +many-body interactions. On the other hand, the computation does not have to compute forces or energies a second time and thus can be much more efficient. The callback mechanism allows to write more complex pairwise property computations. diff --git a/doc/src/compute_temp_asphere.txt b/doc/src/compute_temp_asphere.txt index eb73891e82..0b06ae0b48 100644 --- a/doc/src/compute_temp_asphere.txt +++ b/doc/src/compute_temp_asphere.txt @@ -60,7 +60,7 @@ same. If it does not rotate around the axis perpendicular to its circular cross section, then it should have 5 dof instead of 6 in 3d. The latter is the case for uniaxial ellipsoids in a "GayBerne model"_pair_gayberne.html since there is no induced torque around the -optical axis. It will also be the case for biaxial ellipsoids when +optical axis. It will also be the case for bi-axial ellipsoids when exactly two of the semiaxes have the same length and the corresponding relative well depths are equal. diff --git a/doc/src/compute_temp_chunk.txt b/doc/src/compute_temp_chunk.txt index de8c850a70..30dda79caf 100644 --- a/doc/src/compute_temp_chunk.txt +++ b/doc/src/compute_temp_chunk.txt @@ -118,7 +118,7 @@ or "fix rigid"_fix_rigid.html. This is because those degrees of freedom (e.g. a constrained bond) could apply to sets of atoms that are both included and excluded from a specific chunk, and hence the concept is somewhat ill-defined. In some cases, you can use the -{adof} and {cdof} keywords to adjust the calculated degress of freedom +{adof} and {cdof} keywords to adjust the calculated degrees of freedom appropriately, as explained below. Note that the per-chunk temperature calculated by this compute and the diff --git a/doc/src/compute_temp_cs.txt b/doc/src/compute_temp_cs.txt index 0236319f54..5fc939e375 100644 --- a/doc/src/compute_temp_cs.txt +++ b/doc/src/compute_temp_cs.txt @@ -74,7 +74,7 @@ relative to the COM velocity of the core/shell pair. If this compute is used with a fix command that performs thermostatting then this bias will be subtracted from each atom, thermostatting of the remaining COM velocity will be performed, and the bias will be added back in. This -means the thermostating will effectively be performed on the +means the thermostatting will effectively be performed on the core/shell pairs, instead of on the individual core and shell atoms. Thermostatting fixes that work in this way include "fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix diff --git a/doc/src/create_box.txt b/doc/src/create_box.txt index 0993b4f927..cc57c96f93 100644 --- a/doc/src/create_box.txt +++ b/doc/src/create_box.txt @@ -58,7 +58,7 @@ edge vectors starting from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C = (xz,yz,zhi-zlo). {Xy,xz,yz} can be 0.0 or positive or negative values and are called "tilt factors" because they are the amount of displacement applied to faces of an originally -orthogonal box to transform it into the parallelipiped. +orthogonal box to transform it into the parallelepiped. By default, a {prism} region used with the create_box command must have tilt factors (xy,xz,yz) that do not skew the box more than half diff --git a/doc/src/dihedral_charmm.txt b/doc/src/dihedral_charmm.txt index 637a10102d..043188466a 100644 --- a/doc/src/dihedral_charmm.txt +++ b/doc/src/dihedral_charmm.txt @@ -41,7 +41,7 @@ field. NOTE: The newer {charmmfsw} style was released in March 2017. We recommend it be used instead of the older {charmm} style when running a simulation with the CHARMM force field, either with long-range -Coulombics or a Coulomb cutoff, via the "pair_style +Coulombics or a Coulombic cutoff, via the "pair_style lj/charmmfsw/coul/long"_pair_charmm.html and "pair_style lj/charmmfsw/coul/charmmfsh"_pair_charmm.html commands respectively. Otherwise the older {charmm} style is fine to use. See the discussion @@ -87,7 +87,7 @@ special_bonds 1-4 scaling factor to 0.0 (which is the default). Otherwise 1-4 non-bonded interactions in dihedrals will be computed twice. -For simulations using the CHARMM force field with a Coulomb cutoff, +For simulations using the CHARMM force field with a Coulombic cutoff, the difference between the {charmm} and {charmmfsw} styles is in the computation of the 1-4 non-bond interactions, though only if the distance between the two atoms is within the switching region of the diff --git a/doc/src/dump_h5md.txt b/doc/src/dump_h5md.txt index a3849f103c..6e9e7284df 100644 --- a/doc/src/dump_h5md.txt +++ b/doc/src/dump_h5md.txt @@ -17,7 +17,7 @@ group-ID = ID of the group of atoms to be imaged :l h5md = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l N = dump every this many timesteps :l file.h5 = name of file to write to :l -args = list of data elements to dump, with their dump "subintervals" +args = list of data elements to dump, with their dump "sub-intervals" position options image velocity options @@ -63,7 +63,7 @@ another particle group must specify {create_group yes}. :link(h5md,http://nongnu.org/h5md/) Each data element is written every N*N_element steps. For {image}, no -subinterval is needed as it must be present at the same interval as +sub-interval is needed as it must be present at the same interval as {position}. {image} must be given after {position} in any case. The box information (edges in each dimension) is stored at the same interval than the {position} element, if present. Else it is stored @@ -76,7 +76,7 @@ written to a dump file may be slightly outside the simulation box. [Use from write_dump:] It is possible to use this dump style with the -"write_dump"_write_dump.html command. In this case, the subintervals +"write_dump"_write_dump.html command. In this case, the sub-intervals must not be set at all. The write_dump command can be used either to create a new file or to add current data to an existing dump file by using the {file_from} keyword. diff --git a/doc/src/dump_image.txt b/doc/src/dump_image.txt index df1ff324c1..2b10e9f230 100644 --- a/doc/src/dump_image.txt +++ b/doc/src/dump_image.txt @@ -541,10 +541,11 @@ a) Use the ImageMagick convert program. :ulb,l % convert *.jpg foo.gif % convert -loop 1 *.ppm foo.mpg :pre -Animated GIF files from ImageMagick are unoptimized. You can use a -program like gifsicle to optimize and massively shrink them. -MPEG files created by ImageMagick are in MPEG-1 format with rather -inefficient compression and low quality. +Animated GIF files from ImageMagick are not optimized. You can use +a program like gifsicle to optimize and thus massively shrink them. +MPEG files created by ImageMagick are in MPEG-1 format with a rather +inefficient compression and low quality compared to more modern +compression styles like MPEG-4, H.264, VP8, VP9, H.265 and so on. b) Use QuickTime. :l @@ -564,7 +565,7 @@ allows extremely flexible encoding and decoding of movies. cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi :pre -Frontends for FFmpeg exist for multiple platforms. For more +Front ends for FFmpeg exist for multiple platforms. For more information see the "FFmpeg homepage"_http://www.ffmpeg.org/ :ule diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt index 72f4935916..464caf714f 100644 --- a/doc/src/dump_modify.txt +++ b/doc/src/dump_modify.txt @@ -201,7 +201,7 @@ atom type (1 to Ntype) in the simulation. The same element name can be given to multiple atom types. In the case of {xyz} format dumps, there are no restrictions to what -label can be used as an element name. Any whitespace separated text +label can be used as an element name. Any white-space separated text will be accepted. :link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) @@ -667,7 +667,7 @@ command, when its atom diameter setting is {type}, to set the size that atoms of each type will be drawn in the image. The specified {type} should be an integer from 1 to Ntypes. As with the {acolor} keyword, a wildcard asterisk can be used as part of the {type} -argument to specify a range of atomt types. The specified {diam} is +argument to specify a range of atom types. The specified {diam} is the size in whatever distance "units"_units.html the input script is using, e.g. Angstroms. diff --git a/doc/src/fix.txt b/doc/src/fix.txt index 1a216319b0..d5ce600cb6 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -202,7 +202,7 @@ accelerated styles exist. "dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces "edpd/source"_fix_dpd_source.html - "efield"_fix_efield.html - impose electric field on system -"ehex"_fix_ehex.html - ehanced heat exchange algorithm +"ehex"_fix_ehex.html - enhanced heat exchange algorithm "enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force "eos/cv"_fix_eos_cv.html - "eos/table"_fix_eos_table.html - diff --git a/doc/src/fix_append_atoms.txt b/doc/src/fix_append_atoms.txt index d83f265982..860be9c9fa 100644 --- a/doc/src/fix_append_atoms.txt +++ b/doc/src/fix_append_atoms.txt @@ -28,7 +28,7 @@ keyword = {basis} or {size} or {freq} or {temp} or {random} or {units} :l target = target temperature for the region between zhi-extent and zhi (temperature units) damp = damping parameter (time units) seed = random number seed for langevin kicks - extent = extent of thermostated region (distance units) + extent = extent of thermostatted region (distance units) {random} args = xmax ymax zmax seed {xmax}, {ymax}, {zmax} = maximum displacement in particular direction (distance units) {seed} = random number seed for random displacement @@ -68,7 +68,7 @@ be added. The {random} keyword will give the atoms random displacements around their lattice points to simulate some initial temperature. -The {temp} keyword will cause a region to be thermostated with a +The {temp} keyword will cause a region to be thermostatted with a Langevin thermostat on the zhi boundary. The size of the region is measured from zhi and is set with the {extent} argument. diff --git a/doc/src/fix_ave_chunk.txt b/doc/src/fix_ave_chunk.txt index d331e51295..4e036367e2 100644 --- a/doc/src/fix_ave_chunk.txt +++ b/doc/src/fix_ave_chunk.txt @@ -240,7 +240,7 @@ shake"_fix_shake.html or "fix rigid"_fix_rigid.html. This is because those degrees of freedom (e.g. a constrained bond) could apply to sets of atoms that are both included and excluded from a specific chunk, and hence the concept is somewhat ill-defined. In some cases, you can -use the {adof} and {cdof} keywords to adjust the calculated degress of +use the {adof} and {cdof} keywords to adjust the calculated degrees of freedom appropriately, as explained below. Also note that a bias can be subtracted from atom velocities before diff --git a/doc/src/fix_ave_time.txt b/doc/src/fix_ave_time.txt index a53e318d3f..cca881f2f8 100644 --- a/doc/src/fix_ave_time.txt +++ b/doc/src/fix_ave_time.txt @@ -133,7 +133,7 @@ fix 2 all ave/time 100 1 100 c_myRDF\[1\] c_myRDF\[2\] c_myRDF\[3\] file tmp2.rd The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what timesteps the input values will be used in order to contribute to the average. The final averaged quantities are generated on timesteps -that are a mlutiple of {Nfreq}. The average is over {Nrepeat} +that are a multiple of {Nfreq}. The average is over {Nrepeat} quantities, computed in the preceding portion of the simulation every {Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and {Nevery} must be non-zero even if {Nrepeat} is 1. Also, the timesteps diff --git a/doc/src/fix_balance.txt b/doc/src/fix_balance.txt index 77ad13033e..516df3ff64 100644 --- a/doc/src/fix_balance.txt +++ b/doc/src/fix_balance.txt @@ -57,7 +57,7 @@ This command adjusts the size and shape of processor sub-domains within the simulation box, to attempt to balance the number of particles and thus the computational cost (load) evenly across processors. The load balancing is "dynamic" in the sense that -rebalancing is performed periodically during the simulation. To +re-balancing is performed periodically during the simulation. To perform "static" balancing, before or between runs, see the "balance"_balance.html command. @@ -178,15 +178,15 @@ The {group-ID} is ignored. However the impact of balancing on different groups of atoms can be affected by using the {group} weight style as described below. -The {Nfreq} setting determines how often a rebalance is performed. If -{Nfreq} > 0, then rebalancing will occur every {Nfreq} steps. Each -time a rebalance occurs, a reneighboring is triggered, so {Nfreq} -should not be too small. If {Nfreq} = 0, then rebalancing will be +The {Nfreq} setting determines how often a re-balance is performed. If +{Nfreq} > 0, then re-balancing will occur every {Nfreq} steps. Each +time a re-balance occurs, a reneighboring is triggered, so {Nfreq} +should not be too small. If {Nfreq} = 0, then re-balancing will be done every time reneighboring normally occurs, as determined by the the "neighbor"_neighbor.html and "neigh_modify"_neigh_modify.html command settings. -On rebalance steps, rebalancing will only be attempted if the current +On re-balance steps, re-balancing will only be attempted if the current imbalance factor, as defined above, exceeds the {thresh} setting. :line @@ -208,7 +208,7 @@ to {Niter} times. After each dimension finishes, the imbalance factor is re-computed, and the balancing operation halts if the {stopthresh} criterion is met. -A rebalance operation in a single dimension is performed using a +A re-balance operation in a single dimension is performed using a density-dependent recursive multisectioning algorithm, where the position of each cutting plane (line in 2d) in the dimension is adjusted independently. This is similar to a recursive bisectioning @@ -226,19 +226,19 @@ the recursion progresses, the count of particles on either side of the plane gets closer to the target value. The density-dependent part of this algorithm is often an advantage -when you rebalance a system that is already nearly balanced. It +when you re-balance a system that is already nearly balanced. It typically converges more quickly than the geometric bisectioning algorithm used by the "balance"_balance.html command. However, if can -be a disadvantage if you attempt to rebalance a system that is far +be a disadvantage if you attempt to re-balance a system that is far from balanced, and converge more slowly. In this case you probably want to use the "balance"_balance.html command before starting a run, so that you begin the run with a balanced system. -Once the rebalancing is complete and final processor sub-domains +Once the re-balancing is complete and final processor sub-domains 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 +NOTE: At each re-balance operation, the bisectioning for each cutting 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 @@ -248,7 +248,7 @@ typically be positioned to better than 1 part in 1000 accuracy (relative to the perfect target position). For {Niter} = 20, it will be accurate to better than 1 part in a million. Thus there is no need to set {Niter} to a large value. This is especially true if you are -rebalancing often enough that each time you expect only an incremental +re-balancing often enough that each time you expect only an incremental adjustment in the cutting planes is necessary. LAMMPS will check if the threshold accuracy is reached (in a dimension) is less iterations than {Niter} and exit early. @@ -283,7 +283,7 @@ in that sub-box. :line The {out} keyword writes text to the specified {filename} with the -results of each rebalancing operation. The file contains the bounds +results of each re-balancing operation. The file contains the bounds of the sub-domain for each processor after the balancing operation completes. The format of the file is compatible with the "Pizza.py"_pizza {mdump} tool which has support for manipulating and @@ -344,13 +344,13 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global scalar which is the imbalance factor -after the most recent rebalance and a global vector of length 3 with -additional information about the most recent rebalancing. The 3 +after the most recent re-balance and a global vector of length 3 with +additional information about the most recent re-balancing. The 3 values in the vector are as follows: 1 = max # of particles per processor -2 = total # iterations performed in last rebalance -3 = imbalance factor right before the last rebalance was performed :ul +2 = total # iterations performed in last re-balance +3 = imbalance factor right before the last re-balance was performed :ul As explained above, the imbalance factor is the ratio of the maximum number of particles (or total weight) on any processor to the average diff --git a/doc/src/fix_bocs.txt b/doc/src/fix_bocs.txt index b7d4e7badf..cbcd1138d3 100644 --- a/doc/src/fix_bocs.txt +++ b/doc/src/fix_bocs.txt @@ -91,7 +91,7 @@ package"_Build_package.html doc page for more info. [Related:] For more details about the pressure correction and the entire BOCS software -package, visit the "BOCS package on github"_bocsgithub and read the release +package, visit the "BOCS package on GitHub"_bocsgithub and read the release paper by Dunn et. al. "(Dunn2)"_#bocs-Dunn2 . diff --git a/doc/src/fix_bond_break.txt b/doc/src/fix_bond_break.txt index 5927ceb4e5..bde0beae02 100644 --- a/doc/src/fix_bond_break.txt +++ b/doc/src/fix_bond_break.txt @@ -101,7 +101,7 @@ NOTE: Breaking a bond typically alters the energy of a system. You should be careful not to choose bond breaking criteria that induce a dramatic change in energy. For example, if you define a very stiff harmonic bond and break it when 2 atoms are separated by a distance -far from the equilibribum bond length, then the 2 atoms will be +far from the equilibrium bond length, then the 2 atoms will be dramatically released when the bond is broken. More generally, you may need to thermostat your system to compensate for energy changes resulting from broken bonds (and angles, dihedrals, impropers). diff --git a/doc/src/fix_bond_create.txt b/doc/src/fix_bond_create.txt index de1a9f93f1..e78a283ece 100644 --- a/doc/src/fix_bond_create.txt +++ b/doc/src/fix_bond_create.txt @@ -139,8 +139,8 @@ for "extra angle per atom", "extra dihedral per atom", and "extra improper per atom" if angles, dihedrals, or impropers are being added when bonds are created. See the "read_data"_read_data.html or "create_box"_create_box.html command for more details. Note that a -data file with no atoms can be used if you wish to add unbonded atoms -via the "create atoms"_create_atoms.html command, e.g. for a +data file with no atoms can be used if you wish to add non-bonded +atoms via the "create atoms"_create_atoms.html command, e.g. for a percolation simulation. NOTE: LAMMPS stores and maintains a data structure with a list of the @@ -196,7 +196,7 @@ NOTE: Creating a bond typically alters the energy of a system. You should be careful not to choose bond creation criteria that induce a dramatic change in energy. For example, if you define a very stiff harmonic bond and create it when 2 atoms are separated by a distance -far from the equilibribum bond length, then the 2 atoms will oscillate +far from the equilibrium bond length, then the 2 atoms will oscillate dramatically when the bond is formed. More generally, you may need to thermostat your system to compensate for energy changes resulting from created bonds (and angles, dihedrals, impropers). diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt index 55a5785f7f..c0d47f5f89 100644 --- a/doc/src/fix_bond_react.txt +++ b/doc/src/fix_bond_react.txt @@ -79,7 +79,7 @@ probabilistic criteria to effect predetermined topology changes in simulations using standard force fields. This fix was created to facilitate the dynamic creation of polymeric, -amorphous or highly-crosslinked systems. A suggested workflow for +amorphous or highly cross-linked systems. A suggested workflow for using this fix is: 1) identify a reaction to be simulated 2) build a molecule template of the reaction site before the reaction has occurred 3) build a molecule template of the reaction site after the diff --git a/doc/src/fix_bond_swap.txt b/doc/src/fix_bond_swap.txt index 3c90bb53f6..9a4e7c2b55 100644 --- a/doc/src/fix_bond_swap.txt +++ b/doc/src/fix_bond_swap.txt @@ -84,7 +84,7 @@ the molecule IDs for your polymer chains in a certain way, typically in the data file, read by the "read_data"_read_data.html command. Consider a system of 6-mer chains. You have 2 choices. If the molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then -swaps will conserve chain length. For a particular momoner there will +swaps will conserve chain length. For a particular monomer there will be only one other monomer on another chain which is a potential swap partner. If the molecule IDs for monomers on each chain are set to 1,2,3,3,2,1 then swaps will conserve chain length but swaps will be diff --git a/doc/src/fix_client_md.txt b/doc/src/fix_client_md.txt index 77f6b82c5e..6828731021 100644 --- a/doc/src/fix_client_md.txt +++ b/doc/src/fix_client_md.txt @@ -51,7 +51,7 @@ md"_server_md.html doc page. Note that when using LAMMPS as an MD client, your LAMMPS input script should not normally contain force field commands, like a "pair_style"_pair_style.html, "bond_style"_bond_style.html, or -"kspace_style"_kspace_style.html commmand. However it is possible for +"kspace_style"_kspace_style.html command. However it is possible for a server code to only compute a portion of the full force-field, while LAMMPS computes the remaining part. Your LAMMPS script can also specify boundary conditions or force constraints in the usual way, diff --git a/doc/src/fix_cmap.txt b/doc/src/fix_cmap.txt index ef48e8b51c..aef565e89e 100644 --- a/doc/src/fix_cmap.txt +++ b/doc/src/fix_cmap.txt @@ -24,12 +24,12 @@ fix_modify myCMAP energy yes :pre [Description:] -This command enables CMAP crossterms to be added to simulations which +This command enables CMAP cross-terms to be added to simulations which use the CHARMM force field. These are relevant for any CHARMM model of a peptide or protein sequences that is 3 or more amino-acid residues long; see "(Buck)"_#Buck and "(Brooks)"_#Brooks2 for details, including the analytic energy expressions for CMAP interactions. The -CMAP crossterms add additional potential energy contributions to pairs +CMAP cross-terms add additional potential energy contributions to pairs of overlapping phi-psi dihedrals of amino-acids, which are important to properly represent their conformational behavior. @@ -49,7 +49,7 @@ in its header section: N crossterms :pre -where N is the number of CMAP crossterms. It should also have a section +where N is the number of CMAP cross-terms. It should also have a section in the body of the data file like this with N lines: CMAP :pre @@ -69,7 +69,7 @@ sections match those specified in the read_data command following the data file name; see the "read_data"_read_data.html doc page for more details. -A data file containing CMAP crossterms can be generated from a PDB +A data file containing CMAP cross-terms can be generated from a PDB file using the charmm2lammps.pl script in the tools/ch2lmp directory of the LAMMPS distribution. The script must be invoked with the optional "-cmap" flag to do this; see the tools/ch2lmp/README file for @@ -87,7 +87,7 @@ the note below about how to include the CMAP energy when performing an [Restart, fix_modify, output, run start/stop, minimize info:] -This fix writes the list of CMAP crossterms to "binary restart +This fix writes the list of CMAP cross-terms to "binary restart files"_restart.html. See the "read_restart"_read_restart.html command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an diff --git a/doc/src/fix_colvars.txt b/doc/src/fix_colvars.txt index d702fb264e..d9eb9ac5aa 100644 --- a/doc/src/fix_colvars.txt +++ b/doc/src/fix_colvars.txt @@ -81,7 +81,7 @@ the image flags to reconstruct the absolute atom positions. Setting this to {no} will use the current local coordinates that are wrapped back into the simulation cell at each re-neighboring instead. -The {tstat} keyword can be either NULL or the label of a thermostating +The {tstat} keyword can be either NULL or the label of a thermostatting fix that thermostats all atoms in the fix colvars group. This will be used to provide the colvars module with the current thermostat target temperature. diff --git a/doc/src/fix_deposit.txt b/doc/src/fix_deposit.txt index 265f43bd4b..fd12d4bb45 100644 --- a/doc/src/fix_deposit.txt +++ b/doc/src/fix_deposit.txt @@ -255,7 +255,7 @@ temperature compute you are using. This fix writes the state of the deposition to "binary restart files"_restart.html. This includes information about how many -particles have been depositied, the random number generator seed, the +particles have been deposited, the random number generator seed, the next timestep for deposition, etc. See the "read_restart"_read_restart.html command for info on how to re-specify a fix in an input script that reads a restart file, so that the diff --git a/doc/src/fix_drude_transform.txt b/doc/src/fix_drude_transform.txt index 2135c0bd4f..a102368b5c 100644 --- a/doc/src/fix_drude_transform.txt +++ b/doc/src/fix_drude_transform.txt @@ -91,8 +91,8 @@ different temperatures, two Nose-Hoover thermostats must be defined, acting on two distinct groups. NOTE: The {fix drude/transform/direct} command must appear before any -Nose-Hoover thermostating fixes. The {fix drude/transform/inverse} -command must appear after any Nose-Hoover thermostating fixes. +Nose-Hoover thermostatting fixes. The {fix drude/transform/inverse} +command must appear after any Nose-Hoover thermostatting fixes. Example: @@ -106,8 +106,8 @@ thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDR In this example, {gCORES} is the group of the atom cores and {gDRUDES} is the group of the Drude particles (electrons). The centers of mass -of the Drude oscillators will be thermostated at 300.0 and the -internal degrees of freedom will be thermostated at 1.0. The +of the Drude oscillators will be thermostatted at 300.0 and the +internal degrees of freedom will be thermostatted at 1.0. The temperatures of cores and Drude particles, in center-of-mass and relative coordinates, are calculated using "compute temp/drude"_compute_temp_drude.html @@ -130,8 +130,8 @@ fix fINVERSE all drude/transform/inverse :pre In this example, {gCORES} is the group of the atom cores and {gDRUDES} is the group of the Drude particles. The centers of mass of the Drude -oscillators will be thermostated at 298.0 and the internal degrees of -freedom will be thermostated at 5.0. The whole system will be +oscillators will be thermostatted at 298.0 and the internal degrees of +freedom will be thermostatted at 5.0. The whole system will be barostatted at 1.0. In order to avoid the flying ice cube problem (irreversible transfer diff --git a/doc/src/fix_ehex.txt b/doc/src/fix_ehex.txt index 75651e21a4..79cfce4b01 100644 --- a/doc/src/fix_ehex.txt +++ b/doc/src/fix_ehex.txt @@ -80,9 +80,9 @@ position to the respective reservoir. The quantity \(F_\{\Gamma_\{k(\mathbf r_i)\}\}\) corresponds to the input parameter {F}, which is the energy flux into the reservoir. Furthermore, \(K_\{\Gamma_\{k(\mathbf r_i)\}\}\) and \(v_\{\Gamma_\{k(\mathbf r_i)\}\}\) -denote the non-translational kinetic energy and the centre of mass +denote the non-translational kinetic energy and the center of mass velocity of that reservoir. The thermostatting force does not affect -the centre of mass velocities of the individual reservoirs and the +the center of mass velocities of the individual reservoirs and the entire simulation box. A derivation of the equations and details on the numerical implementation with velocity Verlet in LAMMPS can be found in reference "(Wirnsberger)"#_Wirnsberger. @@ -116,10 +116,10 @@ specified in the input script and the keyword {constrain} is set, the bond distances will be corrected a second time at the end of the integration step. It is recommended to specify the keyword {com} in addition to the keyword {constrain}. With this option all sites of a -constrained cluster are rescaled, if its centre of mass is located +constrained cluster are rescaled, if its center of mass is located inside the region. Rescaling all sites of a cluster by the same factor does not introduce any velocity components along fixed bonds. No -rescaling takes place if the centre of mass lies outside the region. +rescaling takes place if the center of mass lies outside the region. NOTE: You can only use the keyword {com} along with {constrain}. diff --git a/doc/src/fix_eos_table.txt b/doc/src/fix_eos_table.txt index 53b3204372..72c8523662 100644 --- a/doc/src/fix_eos_table.txt +++ b/doc/src/fix_eos_table.txt @@ -35,13 +35,13 @@ temperature. The interpolation tables are created by fitting cubic splines to the file values and interpolating energy values at each of {N} internal -temperatures, and vice-versa. During a simulation, these tables are +temperatures, and vice versa. During a simulation, these tables are used to interpolate internal energy or temperature values as needed. The interpolation is done with the {linear} style. For the {linear} style, the internal temperature is used to find 2 surrounding table values from which an internal energy is computed by -linear interpolation, and vice-versa. +linear interpolation, and vice versa. The filename specifies a file containing tabulated internal temperature and internal energy values. The keyword specifies a diff --git a/doc/src/fix_evaporate.txt b/doc/src/fix_evaporate.txt index 59dab43d9a..69572b96cf 100644 --- a/doc/src/fix_evaporate.txt +++ b/doc/src/fix_evaporate.txt @@ -54,8 +54,8 @@ just the single atom is deleted. As an example, if you wish to delete 10 water molecules every {N} steps, you should set {M} to 30. If only the water's oxygen atoms were in the fix group, then two hydrogen atoms would be deleted when -an oxygen atom is selected for deletion, whether the hydrogens are -inside the evaporation region or not. +an oxygen atom is selected for deletion, whether the hydrogen atoms +are inside the evaporation region or not. Note that neighbor lists are re-built on timesteps that atoms are removed. Thus you should not remove atoms too frequently or you will diff --git a/doc/src/fix_grem.txt b/doc/src/fix_grem.txt index e096d4bd3c..edf11b337c 100644 --- a/doc/src/fix_grem.txt +++ b/doc/src/fix_grem.txt @@ -53,7 +53,7 @@ particles as usual. Either constant volume or constant pressure algorithms can be used. The fix enforces a generalized ensemble in a single replica -only. Typically, this ideaology is combined with replica exchange with +only. Typically, this ideology is combined with replica exchange with replicas differing by {lambda} only for simplicity, but this is not required. A multi-replica simulation can be run within the LAMMPS environment using the "temper/grem"_temper_grem.html command. This diff --git a/doc/src/fix_heat.txt b/doc/src/fix_heat.txt index 6db7592609..640b211f99 100644 --- a/doc/src/fix_heat.txt +++ b/doc/src/fix_heat.txt @@ -109,7 +109,7 @@ are relevant to this fix. This fix computes a global scalar which can be accessed by various "output commands"_Howto_output.html. This scalar is the most recent -value by which velocites were scaled. The scalar value calculated by +value by which velocities were scaled. The scalar value calculated by this fix is "intensive". If {eflux} is specified as an atom-style variable, this fix computes the average value by which the velocities were scaled for all of the atoms that had their velocities scaled. diff --git a/doc/src/fix_hyper_global.txt b/doc/src/fix_hyper_global.txt index 4b9e971e14..a7a938b144 100644 --- a/doc/src/fix_hyper_global.txt +++ b/doc/src/fix_hyper_global.txt @@ -205,12 +205,12 @@ the current timestep. The vector stores the following quantities: 7 = max drift distance of any atom during this run (distance units) 8 = max bond length during this run (distance units) :ul -9 = cummulative hyper time since fix was defined (time units) -10 = cummulative count of event timesteps since fix was defined -11 = cummulative count of atoms in events since fix was defined :ul +9 = cumulative hyper time since fix was defined (time units) +10 = cumulative count of event timesteps since fix was defined +11 = cumulative count of atoms in events since fix was defined :ul The first 5 quantities are for the current timestep. Quantities 6-8 -are for the current hyper run. Quantities 9-11 are cummulative across +are for the current hyper run. Quantities 9-11 are cumulative across multiple runs (since the fix was defined in the input script). For value 7, drift is the distance an atom moves between timesteps @@ -228,7 +228,7 @@ For value 11, each time the "hyper"_hyper.html command checks for an event, it invokes a compute to flag zero or more atoms as participating in one or more events. E.g. atoms that have displaced more than some distance from the previous quench state. Value 11 is -the cummulative count of the number of atoms participating in any of +the cumulative count of the number of atoms participating in any of the events that were found. The scalar and vector values calculated by this fix are all diff --git a/doc/src/fix_hyper_local.txt b/doc/src/fix_hyper_local.txt index 4af6ab5a55..c34b9ba7da 100644 --- a/doc/src/fix_hyper_local.txt +++ b/doc/src/fix_hyper_local.txt @@ -310,14 +310,14 @@ quantities: 18 = count of bias overlaps found during this run 19 = count of non-matching bias coefficients found during this run :ul -20 = cummulative hyper time since fix created (time units) -21 = cummulative count of event timesteps since fix created -22 = cummulative count of atoms in events since fix created -23 = cummulative # of new bonds since fix created :ul +20 = cumulative hyper time since fix created (time units) +21 = cumulative count of event timesteps since fix created +22 = cumulative count of atoms in events since fix created +23 = cumulative # of new bonds since fix created :ul The first quantities (1-5) are for the current timestep. Quantities 6-19 are for the current hyper run. They are reset each time a new -hyper run is performed. Quantities 20-23 are cummulative across +hyper run is performed. Quantities 20-23 are cumulative across multiple runs (since the fix was defined in the input script). For value 6, the numerator is a count of all biased bonds on every @@ -333,7 +333,7 @@ For values 13 and 14, the maxstrain of a ghost atom is the maxstrain of any bond it is part of, and it is checked for ghost atoms within the bond neighbor cutoff. -Values 15-19 are mostly useful for debugging and diagnositc purposes. +Values 15-19 are mostly useful for debugging and diagnostic purposes. For values 15-17, it is possible that a ghost atom owned by another processor will move far enough (e.g. as part of an event-in-progress) @@ -367,7 +367,7 @@ For value 22, each time the "hyper"_hyper.html command checks for an event, it invokes a compute to flag zero or more atoms as participating in one or more events. E.g. atoms that have displaced more than some distance from the previous quench state. Value 22 is -the cummulative count of the number of atoms participating in any of +the cumulative count of the number of atoms participating in any of the events that were found. Value 23 tallies the number of new bonds created by the bond reset diff --git a/doc/src/fix_imd.txt b/doc/src/fix_imd.txt index a58cfdb3d3..3e7792d51a 100644 --- a/doc/src/fix_imd.txt +++ b/doc/src/fix_imd.txt @@ -41,7 +41,7 @@ it allows LAMMPS to connect an IMD client, for example the "VMD visualization program"_VMD, so that it can monitor the progress of the simulation and interactively apply forces to selected atoms. -If LAMMPS is compiled with the preprocessor flag -DLAMMPS_ASYNC_IMD +If LAMMPS is compiled with the pre-processor flag -DLAMMPS_ASYNC_IMD then fix imd will use POSIX threads to spawn a IMD communication thread on MPI rank 0 in order to offload data reading and writing from the main execution thread and potentially lower the inferred diff --git a/doc/src/fix_indent.txt b/doc/src/fix_indent.txt index 9931793c0b..ca93c78c79 100644 --- a/doc/src/fix_indent.txt +++ b/doc/src/fix_indent.txt @@ -129,7 +129,7 @@ variable rate equal 1.0 variable r equal "v_r0 + step*dt*v_rate" :pre If the {side} keyword is specified as {out}, which is the default, -then particles outside the indenter are pushded away from its outer +then particles outside the indenter are pushed away from its outer surface, as described above. This only applies to spherical or cylindrical indenters. If the {side} keyword is specified as {in}, the action of the indenter is reversed. Particles inside the indenter diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt index 62325fdef3..85c97a3436 100644 --- a/doc/src/fix_langevin.txt +++ b/doc/src/fix_langevin.txt @@ -179,7 +179,7 @@ options. For the {omega} keyword there is also a scale factor of 10.0/3.0 that is applied as a multiplier on the Ff (damping) term in the equation above and of sqrt(10.0/3.0) as a multiplier on the Fr term. This does -not affect the thermostatting behaviour of the Langevin formalism but +not affect the thermostatting behavior of the Langevin formalism but insures that the randomized rotational diffusivity of spherical particles is correct. diff --git a/doc/src/fix_langevin_drude.txt b/doc/src/fix_langevin_drude.txt index 19a3f87ffc..dae12fb156 100644 --- a/doc/src/fix_langevin_drude.txt +++ b/doc/src/fix_langevin_drude.txt @@ -78,22 +78,22 @@ transform: \begin\{equation\} F = \frac M \{M'\}\, F' - f' \end\{equation\} \begin\{equation\} f = \frac m \{M'\}\, F' + f' \end\{equation\} -This fix also thermostates non-polarizable atoms in the group at +This fix also thermostats non-polarizable atoms in the group at temperature {Tcom}, as if they had a massless Drude partner. The Drude particles themselves need not be in the group. The center of -mass and the dipole are thermostated iff the core atom is in the +mass and the dipole are thermostatted iff the core atom is in the group. Note that the thermostat effect of this fix is applied to only the translational degrees of freedom of the particles, which is an important consideration if finite-size particles, which have -rotational degrees of freedom, are being thermostated. The +rotational degrees of freedom, are being thermostatted. The translational degrees of freedom can also have a bias velocity removed -from them before thermostating takes place; see the description below. +from them before thermostatting takes place; see the description below. NOTE: Like the "fix langevin"_fix_langevin.html command, this fix does NOT perform time integration. It only modifies forces to effect -thermostating. Thus you must use a separate time integration fix, like +thermostatting. Thus you must use a separate time integration fix, like "fix nve"_fix_nve.html or "fix nph"_fix_nh.html to actually update the velocities and positions of atoms using the modified forces. Likewise, this fix should not normally be used on atoms that also have @@ -102,7 +102,7 @@ nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html commands. See the "Howto thermostat"_Howto_thermostat.html doc page for a discussion of different ways to compute temperature and perform -thermostating. +thermostatting. :line @@ -126,7 +126,7 @@ comm_modify vel yes :pre :line {Tcom} is the target temperature of the centers of mass, which would -be used to thermostate the non-polarizable atoms. {Tdrude} is the +be used to thermostat the non-polarizable atoms. {Tdrude} is the (normally low) target temperature of the core-Drude particle pairs (dipoles). {Tcom} and {Tdrude} can be specified as an equal-style "variable"_variable.html. If the value is a variable, it should be @@ -139,7 +139,7 @@ functions, and include "thermo_style"_thermo_style.html command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent temperature. -Like other fixes that perform thermostating, this fix can be used with +Like other fixes that perform thermostatting, this fix can be used with "compute commands"_compute.html that remove a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms. This is not done by default, but only if the @@ -147,11 +147,11 @@ atoms. This is not done by default, but only if the compute to this fix that includes such a bias term. See the doc pages for individual "compute commands"_compute.html to determine which ones include a bias. In this case, the thermostat works in the following -manner: bias is removed from each atom, thermostating is performed on +manner: bias is removed from each atom, thermostatting is performed on the remaining thermal degrees of freedom, and the bias is added back in. NOTE: this feature has not been tested. -Note: The temperature thermostating the core-Drude particle pairs +Note: The temperature thermostatting the core-Drude particle pairs should be chosen low enough, so as to mimic as closely as possible the self-consistent minimization. It must however be high enough, so that the dipoles can follow the local electric field exerted by the @@ -213,7 +213,7 @@ the system, but is a bit slower. :l Use two different random seeds to avoid unphysical correlations. :l Temperature is controlled by the fix {langevin/drude}, so the -time-integration fixes do not thermostate. Don't forget to +time-integration fixes do not thermostat. Don't forget to time-integrate both cores and Drude particles. :l Pressure is time-integrated only once by using {nve} for Drude @@ -223,11 +223,11 @@ for both. :l The temperatures of cores and Drude particles are calculated by "compute temp/drude"_compute_temp_drude.html :l -Contrary to the alternative thermostating using Nose-Hoover thermostat +Contrary to the alternative thermostatting using Nose-Hoover thermostat fix {npt} and "fix drude/transform"_fix_drude_transform.html, the {fix_modify} command is not required here, because the fix {nph} computes the global pressure even if its group is {ATOMS}. This is -what we want. If we thermostated {ATOMS} using {npt}, the pressure +what we want. If we thermostatted {ATOMS} using {npt}, the pressure should be the global one, but the temperature should be only that of the cores. That's why the command {fix_modify} should be called in that case. :l @@ -247,7 +247,7 @@ restarted simulation should produce the same behavior. The "fix_modify"_fix_modify.html {temp} option is supported by this fix. You can use it to assign a temperature "compute"_compute.html -you have defined to this fix which will be used in its thermostating +you have defined to this fix which will be used in its thermostatting procedure, as described above. For consistency, the group used by the compute should include the group of this fix and the Drude particles. diff --git a/doc/src/fix_meso_move.txt b/doc/src/fix_meso_move.txt index 0a222e79ed..1b8e7b76d7 100644 --- a/doc/src/fix_meso_move.txt +++ b/doc/src/fix_meso_move.txt @@ -63,7 +63,7 @@ meso"_fix_meso.html command). It is up to you to decide whether periodic boundaries are appropriate with the kind of particle motion you are prescribing with this fix. -NOTE: As dicsussed below, particles are moved relative to their initial +NOTE: As discussed below, particles are moved relative to their initial position at the time the fix is specified. These initial coordinates are stored by the fix in "unwrapped" form, by using the image flags associated with each particle. See the "dump custom"_dump.html command diff --git a/doc/src/fix_msst.txt b/doc/src/fix_msst.txt index 7f0e5512ae..64195abb37 100644 --- a/doc/src/fix_msst.txt +++ b/doc/src/fix_msst.txt @@ -74,7 +74,7 @@ equations, but is used in calculating the deviation from the Hugoniot. The keyword {beta} is a scaling term that can be added to the MSST ionic equations of motion to account for drift in the conserved -quantity during long timescale simulations, similar to a Berendson +quantity during long timescale simulations, similar to a Berendsen thermostat. See "(Reed)"_#Reed and "(Goldman)"_#Goldman2 for more details. The value of {beta} must be between 0.0 and 1.0 inclusive. A value of 0.0 means no contribution, a value of 1.0 means a full diff --git a/doc/src/fix_nh.txt b/doc/src/fix_nh.txt index 174547d775..1071e1f808 100644 --- a/doc/src/fix_nh.txt +++ b/doc/src/fix_nh.txt @@ -286,7 +286,7 @@ negligible. The keyword {tloop} can be used to improve the accuracy of integration scheme at little extra cost. The initial and final updates of the -thermostat variables are broken up into {tloop} substeps, each of +thermostat variables are broken up into {tloop} sub-steps, each of length {dt}/{tloop}. This corresponds to using a first-order Suzuki-Yoshida scheme "(Tuckerman)"_#nh-Tuckerman. The keyword {ploop} does the same thing for the barostat thermostat. diff --git a/doc/src/fix_nh_uef.txt b/doc/src/fix_nh_uef.txt index dc05948de3..4d58ee7c49 100644 --- a/doc/src/fix_nh_uef.txt +++ b/doc/src/fix_nh_uef.txt @@ -37,7 +37,7 @@ fix biax_npt all npt/uef temp 400 400 100 erate -0.00001 0.000005 x 1 1 3000 :pr [Description:] This fix can be used to simulate non-equilibrium molecular dynamics -(NEMD) under diagonal flow fields, including uniaxial and biaxial +(NEMD) under diagonal flow fields, including uniaxial and bi-axial flow. Simulations under continuous extensional flow may be carried out for an indefinite amount of time. It is an implementation of the boundary conditions from "(Dobson)"_#Dobson, and also uses numerical diff --git a/doc/src/fix_nve_awpmd.txt b/doc/src/fix_nve_awpmd.txt index c266d46eee..11951c2fe1 100644 --- a/doc/src/fix_nve_awpmd.txt +++ b/doc/src/fix_nve_awpmd.txt @@ -29,7 +29,7 @@ ensemble. The operation of this fix is exactly like that described by the "fix nve"_fix_nve.html command, except that the width and width-velocity of -the electron wavefunctions are also updated. +the electron wave functions are also updated. :line diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt index 7a350e48b5..7050be58b3 100644 --- a/doc/src/fix_nvt_sllod.txt +++ b/doc/src/fix_nvt_sllod.txt @@ -184,5 +184,5 @@ Same as "fix nvt"_fix_nh.html, except tchain = 1. [(Daivis and Todd)] Daivis and Todd, J Chem Phys, 124, 194103 (2006). :link(Daivis-sllod) -[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book), +[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dynamics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/src/fix_phonon.txt b/doc/src/fix_phonon.txt index 7d8f4d3379..23d4d09552 100644 --- a/doc/src/fix_phonon.txt +++ b/doc/src/fix_phonon.txt @@ -46,7 +46,7 @@ based on fluctuation-dissipation theory for a group of atoms. 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, +\(\mathbf\{a\}_2\), \(\mathbf\{a\}_3\) forming a parallelepiped, containing \(K\) basis atoms labeled \(k\). Based on fluctuation-dissipation theory, the force constant @@ -103,7 +103,7 @@ computation is then done. After every {Noutput} measurements, the matrix \(\mathbf\{G\}(\mathbf\{q\})\) is calculated and inverted to obtain the elastic stiffness coefficients. The dynamical matrices are then constructed and written to {prefix}.bin.timestep files in binary -format and to the file {prefix}.log for each wavevector +format and to the file {prefix}.log for each wave-vector \(\mathbf\{q\}\). A detailed description of this method can be found in diff --git a/doc/src/fix_plumed.txt b/doc/src/fix_plumed.txt index a9795850f5..30e8b2766c 100644 --- a/doc/src/fix_plumed.txt +++ b/doc/src/fix_plumed.txt @@ -49,7 +49,7 @@ The command to make LAMMPS call PLUMED during a run requires two keyword value pairs pointing to the PLUMED input file and an output file for the PLUMED log. The user must specify these arguments every time PLUMED is to be used. Furthermore, the fix plumed command should appear in the -LAMMPS input file [after] relevant input paramters (e.g. the timestep) +LAMMPS input file [after] relevant input parameters (e.g. the timestep) have been set. The {group-ID} entry is ignored. LAMMPS will always pass all the atoms diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt index 0751a272ac..a62f523c5d 100644 --- a/doc/src/fix_property_atom.txt +++ b/doc/src/fix_property_atom.txt @@ -100,7 +100,7 @@ then you most likely want to set {ghost} yes, since these properties are stored with ghost atoms if you use an "atom_style"_atom_style.html that defines them, and many LAMMPS operations that use molecule IDs or charge, such as neighbor lists and pair styles, will expect ghost -atoms to have these valuse. LAMMPS will issue a warning it you define +atoms to have these values. LAMMPS will issue a warning it you define those vectors but do not set {ghost} yes. NOTE: The properties for ghost atoms are not updated every timestep, diff --git a/doc/src/fix_qmmm.txt b/doc/src/fix_qmmm.txt index 4163275056..c39a58ed86 100644 --- a/doc/src/fix_qmmm.txt +++ b/doc/src/fix_qmmm.txt @@ -22,7 +22,7 @@ fix 1 qmol qmmm [Description:] This fix provides functionality to enable a quantum -mechanics/molecular mechanice (QM/MM) coupling of LAMMPS to a quantum +mechanics/molecular mechanics (QM/MM) coupling of LAMMPS to a quantum mechanical code. The current implementation only supports an ONIOM style mechanical coupling to the "Quantum ESPRESSO"_espresso plane wave DFT package. Electrostatic coupling is in preparation and the diff --git a/doc/src/fix_recenter.txt b/doc/src/fix_recenter.txt index cfac756cd1..05c93c3e2f 100644 --- a/doc/src/fix_recenter.txt +++ b/doc/src/fix_recenter.txt @@ -79,10 +79,10 @@ in solvent) without using the {shift} keyword to adjust the positions of all atoms in the system, then the results can be unpredictable. For example, if the molecule is pushed consistently in one direction by a flowing solvent, its velocity will increase. But its coordinates -will be recentered, meaning it is moved back towards the force. Thus +will be re-centered, meaning it is moved back towards the force. Thus over time, the velocity and effective temperature of the molecule could become very large, though it won't actually be moving due to the -recentering. If you are thermostatting the entire system, then the +re-centering. If you are thermostatting the entire system, then the solvent would be cooled to compensate. A better solution for this simulation scenario is to use the "fix spring"_fix_spring.html command to tether the molecule in place. diff --git a/doc/src/fix_restrain.txt b/doc/src/fix_restrain.txt index 2edc7e3296..8e962f4cc9 100644 --- a/doc/src/fix_restrain.txt +++ b/doc/src/fix_restrain.txt @@ -49,7 +49,7 @@ file, as specified by the "read_data"_read_data.html command, albeit with a time-varying pre-factor coefficient, and except for exclusion rules, as explained below. -For the purpose of forcefield parameter-fitting or mapping a molecular +For the purpose of force field parameter-fitting or mapping a molecular potential energy surface, this fix reduces the hassle and risk associated with modifying data files. In other words, use this fix to temporarily force a molecule to adopt a particular conformation. To @@ -82,7 +82,7 @@ self-consistent minimization problem (see below). In order for a restraint to be effective, the restraint force must typically be significantly larger than the forces associated with -conventional forcefield terms. If the restraint is applied during a +conventional force field terms. If the restraint is applied during a dynamics run (as opposed to during an energy minimization), a large restraint coefficient can significantly reduce the stable timestep size, especially if the atoms are initially far from the preferred @@ -90,7 +90,7 @@ 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 restraints (e.g. for fitting forcefield +molecule with particular restraints (e.g. for fitting force field parameters or constructing a potential energy surface), commands such as the following may be useful: diff --git a/doc/src/fix_tfmc.txt b/doc/src/fix_tfmc.txt index 2d4f003607..e14663bebd 100644 --- a/doc/src/fix_tfmc.txt +++ b/doc/src/fix_tfmc.txt @@ -54,7 +54,7 @@ estimation of the effective time scale of such a simulation, but it was later shown that the speed-up one can gain from a tfMC simulation is system- and process-dependent, ranging from none to several orders of magnitude. In general, solid-state processes such as -(re)crystallisation or growth can be accelerated by up to two or three +(re)crystallization or growth can be accelerated by up to two or three orders of magnitude, whereas diffusion in the liquid phase is not accelerated at all. The observed pseudodynamics when using the tfMC method is not the actual dynamics one would obtain using MD, but the diff --git a/doc/src/fix_ti_spring.txt b/doc/src/fix_ti_spring.txt index 290ee95b9a..d212579510 100644 --- a/doc/src/fix_ti_spring.txt +++ b/doc/src/fix_ti_spring.txt @@ -35,7 +35,7 @@ solid of interest and an Einstein crystal. A detailed explanation of how to use this command and choose its parameters for optimal performance and accuracy is given in the paper by "Freitas"_#Freitas1. The paper also presents a short summary of the -theory of nonequilibrium thermodynamic integrations. +theory of nonequilibrium thermodynamic integration. The thermodynamic integration procedure is performed by rescaling the force on each atom. Given an atomic configuration the force (F) on diff --git a/doc/src/fix_tune_kspace.txt b/doc/src/fix_tune_kspace.txt index 147bb1eb3d..c398bf9157 100644 --- a/doc/src/fix_tune_kspace.txt +++ b/doc/src/fix_tune_kspace.txt @@ -26,7 +26,7 @@ fix 2 all tune/kspace 100 :pre This fix tests each kspace style (Ewald, PPPM, and MSM), and automatically selects the fastest style to use for the remainder of the run. If the fastest style is Ewald or PPPM, the fix also -adjusts the coulomb cutoff towards optimal speed. Future versions +adjusts the Coulombic cutoff towards optimal speed. Future versions of this fix will automatically select other kspace parameters to use for maximum simulation speed. The kspace parameters may include the style, cutoff, grid points in each direction, order, @@ -55,7 +55,7 @@ inordinate amount of wall time to complete. An N of 100 for most problems seems reasonable. Once an optimal parameter set is found, that set is used for the remainder of the run. -This fix uses heristics to guide it's selection of parameter sets to test, +This fix uses heuristics to guide it's selection of parameter sets to test, but the actual timed results will be used to decide which set to use in the simulation. diff --git a/doc/src/fix_wall_piston.txt b/doc/src/fix_wall_piston.txt index b1968e0d49..475517ed66 100644 --- a/doc/src/fix_wall_piston.txt +++ b/doc/src/fix_wall_piston.txt @@ -26,7 +26,7 @@ keyword = {pos} or {vel} or {ramp} or {units} :l target = target velocity for region immediately ahead of the piston damp = damping parameter (time units) seed = random number seed for langevin kicks - extent = extent of thermostated region (distance units) + extent = extent of thermostatted region (distance units) {units} value = {lattice} or {box} {lattice} = the wall position is defined in lattice units {box} = the wall position is defined in simulation box units :pre @@ -69,7 +69,7 @@ the {ramp} keyword is omitted then the wall/piston moves at a constant velocity defined by {vel}. The {temp} keyword will cause the region immediately in front of the -wall/piston to be thermostated with a Langevin thermostat. This +wall/piston to be thermostatted with a Langevin thermostat. This region moves with the piston. The damping and kicking are measured in the reference frame of the piston. So, a temperature of zero would mean all particles were moving at exactly the speed of the diff --git a/doc/src/hyper.txt b/doc/src/hyper.txt index 570f27ca64..f379d09580 100644 --- a/doc/src/hyper.txt +++ b/doc/src/hyper.txt @@ -41,7 +41,7 @@ hyper 5000 100 HG event min 1.0e-6 1.0e-6 100 100 dump 1 dump 5 :pre Run a bond-boost hyperdynamics (HD) simulation where time is accelerated by application of a bias potential to one or more pairs of nearby atoms in the system. This command can be used to run both -global and local hyperdyamics. In global HD a single bond within the +global and local hyperdynamics. In global HD a single bond within the system is biased on each timestep. In local HD multiple bonds (separated by a sufficient distance) can be biased simultaneously at each timestep. In the bond-boost hyperdynamics context, a "bond" is diff --git a/doc/src/improper_none.txt b/doc/src/improper_none.txt index f97af101fc..78a7489837 100644 --- a/doc/src/improper_none.txt +++ b/doc/src/improper_none.txt @@ -18,7 +18,7 @@ improper_style none :pre [Description:] -Using an improper style of none means imroper forces and energies are +Using an improper style of none means improper forces and energies are not computed, even if quadruplets of improper atoms were listed in the data file read by the "read_data"_read_data.html command. diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt index 218f85bd74..c4bd4db3ee 100644 --- a/doc/src/kspace_modify.txt +++ b/doc/src/kspace_modify.txt @@ -317,10 +317,10 @@ The {tolerance} option affects how the {accuracy} specified with the "kspace_style"_kspace_style.html command is interpreted by ScaFaCoS. The following values may be used: -energy = absolute accuracy in total Coulomic energy -energy_rel = relative accuracy in total Coulomic energy -potential = absolute accuracy in total Coulomic potential -potential_rel = relative accuracy in total Coulomic potential +energy = absolute accuracy in total Coulombic energy +energy_rel = relative accuracy in total Coulombic energy +potential = absolute accuracy in total Coulombic potential +potential_rel = relative accuracy in total Coulombic potential field = absolute accuracy in electric field field_rel = relative accuracy in electric field :ul @@ -338,12 +338,12 @@ of 1e-3 would mean that the result has to be between 999999.999 and 1e-9. The energy and energy_rel values, set a tolerance based on the total -Coulomic energy of the system. The potential and potential_rel set a -tolerance based on the per-atom Coulomic energy. The field and +Coulombic energy of the system. The potential and potential_rel set a +tolerance based on the per-atom Coulombic energy. The field and field_rel tolerance types set a tolerance based on the electric field values computed by ScaFaCoS. Since per-atom forces are derived from the per-atom electric field, this effectively sets a tolerance on the -forces, simimlar to other LAMMPS KSpace styles, as explained on the +forces, similar to other LAMMPS KSpace styles, as explained on the "kspace_style"_kspace_style.html doc page. Note that not all ScaFaCoS solvers support all tolerance types. @@ -363,7 +363,7 @@ The {fmm_tuning} option is only relevant when using the FMM method. It activates (value=1) or deactivates (value=0) an internal tuning mechanism for the FMM solver. The tuning operation runs sequentially and can be very time-consuming. Usually it is not needed for systems -with a homogenous charge distribution. The default for this option is +with a homogeneous charge distribution. The default for this option is therefore {0}. The FMM internal tuning is performed once, when the solver is set up. diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index 6d8a289470..fdf78ce4ec 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -193,7 +193,7 @@ the -DFFT_SINGLE compiler switch. The {msm} style invokes a multi-level summation method MSM solver, "(Hardy)"_#Hardy2006 or "(Hardy2)"_#Hardy2009, which maps atom charge to a 3d mesh, and uses a multi-level hierarchy of coarser and coarser -meshes on which direct coulomb solves are done. This method does not +meshes on which direct Coulomb solvers are done. This method does not use FFTs and scales as N. It may therefore be faster than the other K-space solvers for relatively large problems when running on large core counts. MSM can also be used for non-periodic boundary conditions @@ -201,7 +201,7 @@ and for mixed periodic and non-periodic boundaries. MSM is most competitive versus Ewald and PPPM when only relatively low accuracy forces, about 1e-4 relative error or less accurate, -are needed. Note that use of a larger coulomb cutoff (i.e. 15 +are needed. Note that use of a larger Coulombic cutoff (i.e. 15 angstroms instead of 10 angstroms) provides better MSM accuracy for both the real space and grid computed forces. @@ -237,7 +237,7 @@ See details on "this page"_Section_packages.html#USER-SCAFACOS. NOTE: Unlike other KSpace solvers in LAMMPS, ScaFaCoS computes all Coulombic interactions, both short- and long-range. Thus you should -NOT use a Coulmbic pair style when using kspace_style scafacos. This +NOT use a Coulombic pair style when using kspace_style scafacos. This also means the total Coulombic energy (short- and long-range) will be tallied for "thermodynamic output"_thermo_style.html command as part of the {elong} keyword; the {ecoul} keyword will be zero. diff --git a/doc/src/minimize.txt b/doc/src/minimize.txt index 73858fc249..ffda749ec5 100644 --- a/doc/src/minimize.txt +++ b/doc/src/minimize.txt @@ -190,7 +190,7 @@ it when running dynamics). If you do not do this, the total energy of the system will have discontinuities when the relative distance between any pair of atoms changes from cutoff+epsilon to cutoff-epsilon and the minimizer may behave poorly. Some of the -manybody potentials use splines and other internal cutoffs that +many-body potentials use splines and other internal cutoffs that inherently have this problem. The "long-range Coulombic styles"_kspace_style.html (PPPM, Ewald) are approximate to within the user-specified tolerance, which means their energy and forces may not diff --git a/doc/src/molecule.txt b/doc/src/molecule.txt index 88c6292d8b..4c066b5e2e 100644 --- a/doc/src/molecule.txt +++ b/doc/src/molecule.txt @@ -96,7 +96,7 @@ the molecule (header keyword = com), and the moments of inertia of the molecule (header keyword = inertia). NOTE: The molecule command can be used to define molecules with bonds, -angles, dihedrals, imporopers, or special bond lists of neighbors +angles, dihedrals, impropers, or special bond lists of neighbors within a molecular topology, so that you can later add the molecules to your simulation, via one or more of the commands listed above. Since this topology-related information requires that suitable storage @@ -117,7 +117,7 @@ A molecule file has a header and a body. The header appears first. The first line of the header is always skipped; it typically contains a description of the file. Then lines are read one at a time. Lines can have a trailing comment starting with '#' that is ignored. If the -line is blank (only whitespace after comment is deleted), it is +line is blank (only white-space after comment is deleted), it is skipped. If the line contains a header keyword, the corresponding value(s) is read from the line. If it doesn't contain a header keyword, the line begins the body of the file. diff --git a/doc/src/neb.txt b/doc/src/neb.txt index e136aa2f2c..fbe06d3d3d 100644 --- a/doc/src/neb.txt +++ b/doc/src/neb.txt @@ -59,7 +59,7 @@ performance speed-up you would see with one or more physical processors per replica. See the "Howto replica"_Howto_replica.html doc page for further discussion. -NOTE: As explained below, a NEB calculation perfoms a damped dynamics +NOTE: As explained below, a NEB calculation performs a damped dynamics 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 @@ -211,7 +211,7 @@ over a barrier. The MEP for a transition is defined as a sequence of 3N-dimensional states, each of which has a potential energy gradient parallel to the MEP itself. The configuration of highest energy along a MEP corresponds to a saddle point. The replica states will also be -roughly equally spaced along the MEP due to the inter-replica nugding +roughly equally spaced along the MEP due to the inter-replica nudging force added by the "fix neb"_fix_neb.html command. In the second stage of NEB, the replica with the highest energy is diff --git a/doc/src/package.txt b/doc/src/package.txt index 65117ba3c3..f9ed0734c9 100644 --- a/doc/src/package.txt +++ b/doc/src/package.txt @@ -40,7 +40,7 @@ args = arguments specific to the style :l {blocksize} value = size size = thread block size for pair force computation {intel} args = NPhi keyword value ... - Nphi = # of coprocessors per node + Nphi = # of co-processors per node zero or more keyword/value pairs may be appended keywords = {mode} or {omp} or {lrt} or {balance} or {ghost} or {tpc} or {tptask} or {no_affinity} {mode} value = {single} or {mixed} or {double} @@ -53,14 +53,14 @@ args = arguments specific to the style :l yes = use additional thread dedicated for some PPPM calculations no = do not dedicate an extra thread for some PPPM calculations {balance} value = split - split = fraction of work to offload to coprocessor, -1 for dynamic + split = fraction of work to offload to co-processor, -1 for dynamic {ghost} value = {yes} or {no} yes = include ghost atoms for offload no = do not include ghost atoms for offload {tpc} value = Ntpc - Ntpc = max number of coprocessor threads per coprocessor core (default = 4) + Ntpc = max number of co-processor threads per co-processor core (default = 4) {tptask} value = Ntptask - Ntptask = max number of coprocessor threads per MPI task (default = 240) + Ntptask = max number of co-processor threads per MPI task (default = 240) {no_affinity} values = none {kokkos} args = keyword value ... zero or more keyword/value pairs may be appended @@ -289,7 +289,7 @@ MAX_BIO_SHARED_TYPES :ul The {blocksize} keyword allows you to tweak the number of threads used per thread block. This number should be a multiple of 32 (for GPUs) and its maximum depends on the specific GPU hardware. Typical choices -are 64, 128, or 256. A larger blocksize increases occupancy of +are 64, 128, or 256. A larger block size increases occupancy of individual GPU cores, but reduces the total number of thread blocks, thus may lead to load imbalance. @@ -298,13 +298,13 @@ thus may lead to load imbalance. The {intel} style invokes settings associated with the use of the USER-INTEL package. All of its settings, except the {omp} and {mode} keywords, are ignored if LAMMPS was not built with Xeon Phi -coprocessor support. All of its settings, including the {omp} and -{mode} keyword are applicable if LAMMPS was built with coprocessor +co-processor support. All of its settings, including the {omp} and +{mode} keyword are applicable if LAMMPS was built with co-processor support. -The {Nphi} argument sets the number of coprocessors per node. +The {Nphi} argument sets the number of co-processors per node. This can be set to any value, including 0, if LAMMPS was not -built with coprocessor support. +built with co-processor support. Optional keyword/value pairs can also be specified. Each has a default value as listed below. @@ -312,14 +312,14 @@ default value as listed below. The {omp} keyword determines the number of OpenMP threads allocated for each MPI task when any portion of the interactions computed by a USER-INTEL pair style are run on the CPU. This can be the case even -if LAMMPS was built with coprocessor support; see the {balance} +if LAMMPS was built with co-processor support; see the {balance} keyword discussion below. If you are running with less MPI tasks/node than there are CPUs, it can be advantageous to use OpenMP threading on the CPUs. -NOTE: The {omp} keyword has nothing to do with coprocessor threads on +NOTE: The {omp} keyword has nothing to do with co-processor threads on the Xeon Phi; see the {tpc} and {tptask} keywords below for a -discussion of coprocessor threads. +discussion of co-processor threads. The {Nthread} value for the {omp} keyword sets the number of OpenMP threads allocated for each MPI task. Setting {Nthread} = 0 (the @@ -346,7 +346,7 @@ command, followed by a "package omp" command, both with a setting of {Nthreads} = 0. The {mode} keyword determines the precision mode to use for -computing pair style forces, either on the CPU or on the coprocessor, +computing pair style forces, either on the CPU or on the co-processor, when using a USER-INTEL supported "pair style"_pair_style.html. It can take a value of {single}, {mixed} which is the default, or {double}. {Single} means single precision is used for the entire @@ -371,13 +371,13 @@ from the USER-INTEL package is not used, then the LRT setting is ignored and no extra threads are generated. Enabling LRT will replace the "run_style"_run_style.html with the {verlet/lrt/intel} style that is identical to the default {verlet} style aside from supporting the -LRT feature. This feature requires setting the preprocessor flag +LRT feature. This feature requires setting the pre-processor flag -DLMP_INTEL_USELRT in the makefile when compiling LAMMPS. The {balance} keyword sets the fraction of "pair -style"_pair_style.html work offloaded to the coprocessor for split +style"_pair_style.html work offloaded to the co-processor for split values between 0.0 and 1.0 inclusive. While this fraction of work is -running on the coprocessor, other calculations will run on the host, +running on the co-processor, other calculations will run on the host, including neighbor and pair calculations that are not offloaded, as well as angle, bond, dihedral, kspace, and some MPI communications. If {split} is set to -1, the fraction of work is dynamically adjusted @@ -388,18 +388,18 @@ The {ghost} keyword determines whether or not ghost atoms, i.e. atoms 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 -computation on the coprocessor when the "newton pair"_newton.html +the co-processor and can also overlap MPI communication of forces with +computation on the co-processor when the "newton pair"_newton.html setting is "on". When the value = "yes", ghost atoms are offloaded. In some cases this can provide better performance, especially if the {balance} fraction is high. -The {tpc} keyword sets the max # of coprocessor threads {Ntpc} that -will run on each core of the coprocessor. The default value = 4, +The {tpc} keyword sets the max # of co-processor threads {Ntpc} that +will run on each core of the co-processor. The default value = 4, which is the number of hardware threads per core supported by the current generation Xeon Phi chips. -The {tptask} keyword sets the max # of coprocessor threads (Ntptask} +The {tptask} keyword sets the max # of co-processor threads (Ntptask} assigned to each MPI task. The default value = 240, which is the total # of threads an entire current generation Xeon Phi chip can run (240 = 60 cores * 4 threads/core). This means each MPI task assigned @@ -415,7 +415,7 @@ most problems, regardless of how many MPI tasks you assign to a Phi. The {no_affinity} keyword will turn off automatic setting of core affinity for MPI tasks and OpenMP threads on the host when using -offload to a coprocessor. Affinity settings are used when possible +offload to a co-processor. Affinity settings are used when possible to prevent MPI tasks and OpenMP threads from being on separate NUMA domains and to prevent offload threads from interfering with other processes/threads used for LAMMPS. @@ -617,7 +617,7 @@ tptask = 240. The default ghost option is determined by the pair style being used. This value is output to the screen in the offload report at the end of each run. Note that all of these settings, except "omp" and "mode", are ignored if LAMMPS was not built with Xeon -Phi coprocessor support. These settings are made automatically if the +Phi co-processor support. These settings are made automatically if the "-sf intel" "command-line switch"_Run_options.html is used. If it is not used, you must invoke the package intel command in your input script or or via the "-pk intel" "command-line diff --git a/doc/src/pair_agni.txt b/doc/src/pair_agni.txt index 74aef41255..8cb1bf34e4 100644 --- a/doc/src/pair_agni.txt +++ b/doc/src/pair_agni.txt @@ -19,7 +19,7 @@ pair_coeff * * Al.agni Al [Description:] -Style {agni} style computes the manybody vectorial force components for +Style {agni} style computes the many-body vectorial force components for an atom as :c,image(Eqs/pair_agni.jpg) diff --git a/doc/src/pair_awpmd.txt b/doc/src/pair_awpmd.txt index ec87101d0d..4401f5b706 100644 --- a/doc/src/pair_awpmd.txt +++ b/doc/src/pair_awpmd.txt @@ -58,7 +58,7 @@ keyword is used, then an unrestricted Hartree-Fock trial wave function is used. The {free}, {pbc}, and {fix} keywords specify a width constraint on -the electron wavepackets. If the {free} keyword is specified, then there is no +the electron wave packets. If the {free} keyword is specified, then there is no constraint. If the {pbc} keyword is used and {Plen} is specified as -1, then the maximum width is half the shortest box length. If {Plen} is a positive value, then the value is the maximum width. If the @@ -68,7 +68,7 @@ positive value, then the constant width for all electrons is set to {Flen}. The {harm} keyword allow oscillations in the width of the -electron wavepackets. More details are needed. +electron wave packets. More details are needed. The {ermscale} keyword specifies a unitless scaling factor between the electron masses and the width variable mass. More @@ -119,5 +119,5 @@ This pair style can only be used via the {pair} keyword of the [Default:] These are the defaults for the pair_style keywords: {hartree} for the -initial wavefunction, {free} for the wavepacket width. +initial wave function, {free} for the wave packet width. diff --git a/doc/src/pair_bop.txt b/doc/src/pair_bop.txt index f9b4262f0c..ef6fff2963 100644 --- a/doc/src/pair_bop.txt +++ b/doc/src/pair_bop.txt @@ -28,7 +28,7 @@ comm_modify cutoff 14.70 :pre [Description:] The {bop} pair style computes Bond-Order Potentials (BOP) based on -quantum mechanical theory incorporating both sigma and pi bondings. +quantum mechanical theory incorporating both sigma and pi bonding. By analytically deriving the BOP from quantum mechanical theory its transferability to different phases can approach that of quantum mechanical methods. This potential is similar to the original BOP diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt index 131e289227..7f0104266c 100644 --- a/doc/src/pair_charmm.txt +++ b/doc/src/pair_charmm.txt @@ -131,7 +131,7 @@ same for both formulas or different depending on whether 2 or 4 arguments are used in the pair_style command. For the {lj/charmmfsw/coul/charmmfsh} style, the LJ term requires both an inner and outer cutoff, while the Coulombic term requires only one -cutoff. If the Coulomb cutoff is not specified (2 instead of 3 +cutoff. If the Coulombic cutoff is not specified (2 instead of 3 arguments), the LJ outer cutoff is used for the Coulombic cutoff. In all cases where an inner and outer cutoff are specified, the inner cutoff distance must be less than the outer cutoff. It is typical to diff --git a/doc/src/pair_coeff.txt b/doc/src/pair_coeff.txt index 88f95b5b2c..be2699285f 100644 --- a/doc/src/pair_coeff.txt +++ b/doc/src/pair_coeff.txt @@ -90,7 +90,7 @@ is looked for in the current working directory. If it is specified as directory, assuming it is a sister directory of the current working directory. If the file is not found, it is then looked for in the directory specified by the LAMMPS_POTENTIALS environment variable. -Thus if this is set to the potentials directory in the LAMMPS distro, +Thus if this is set to the potentials directory in the LAMMPS distribution, then you can use those files from anywhere on your system, without copying them into your working directory. Environment variables are set in different ways for different shells. Here are example settings diff --git a/doc/src/pair_coul.txt b/doc/src/pair_coul.txt index cf66c711c8..06838a97e6 100644 --- a/doc/src/pair_coul.txt +++ b/doc/src/pair_coul.txt @@ -197,7 +197,7 @@ option. The Coulombic cutoff specified for this style means that pairwise interactions within this distance are computed directly; interactions outside that distance are computed in reciprocal space. -Styles {tip4p/cut} and {tip4p/long} implement the coulomb part of +Styles {tip4p/cut} and {tip4p/long} implement the Coulomb part of the TIP4P water model of "(Jorgensen)"_#Jorgensen3, which introduces a massless site located a short distance away from the oxygen atom along the bisector of the HOH angle. The atomic types of the oxygen and @@ -219,7 +219,7 @@ 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 typically best in an -efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2*qdist, to +efficiency sense to use a LJ cutoff >= Coulombic cutoff + 2*qdist, to shrink the size of the neighbor list. This leads to slightly larger cost for the long-range calculation, so you can test the trade-off for your model. diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt index b3ce55535e..c695601061 100644 --- a/doc/src/pair_dipole.txt +++ b/doc/src/pair_dipole.txt @@ -103,8 +103,8 @@ the two particles. Note that Eqq and Fqq are simply Coulombic energy and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the torques do not act symmetrically. The shifted-force formula for the Lennard-Jones potential is reported in "(Stoddard)"_#Stoddard. The -original (unshifted) formulas for the electrostatic potentials, forces -and torques can be found in "(Price)"_#Price2. The shifted-force +original (non-shifted) formulas for the electrostatic potentials, +forces and torques can be found in "(Price)"_#Price2. The shifted-force electrostatic potentials have been obtained by applying equation 5.13 of "(Allen)"_#Allen2. The formulas for the corresponding forces and torques have been obtained by applying the 'chain rule' as in appendix diff --git a/doc/src/pair_dpd.txt b/doc/src/pair_dpd.txt index 55ae298682..db6fc174d4 100644 --- a/doc/src/pair_dpd.txt +++ b/doc/src/pair_dpd.txt @@ -97,7 +97,7 @@ The GPU-accelerated versions of these styles are implemented based on the work of "(Afshar)"_#Afshar and "(Phillips)"_#Phillips. NOTE: If you are modeling DPD polymer chains, you may want to use the -"pair_style srp"_pair_srp.html command in conjuction with these pair +"pair_style srp"_pair_srp.html command in conjunction with these pair styles. It is a soft segmental repulsive potential (SRP) that can prevent DPD polymer chains from crossing each other. @@ -178,7 +178,7 @@ simulation), you should experiment with forcing reneighboring more often and see if system energies/trajectories change. These pair styles requires you to use the "comm_modify vel -yes"_comm_modify.html command so that velocites are stored by ghost +yes"_comm_modify.html command so that velocities are stored by ghost atoms. These pair styles will not restart exactly when using the diff --git a/doc/src/pair_dpd_fdt.txt b/doc/src/pair_dpd_fdt.txt index 4f2459588a..52605aef39 100644 --- a/doc/src/pair_dpd_fdt.txt +++ b/doc/src/pair_dpd_fdt.txt @@ -155,7 +155,7 @@ enabled if LAMMPS was built with that package. See the "Build package"_Build_package.html doc page for more info. Pair styles {dpd/fdt} and {dpd/fdt/energy} require use of the -"comm_modify vel yes"_comm_modify.html option so that velocites are +"comm_modify vel yes"_comm_modify.html option so that velocities are stored by ghost atoms. Pair style {dpd/fdt/energy} requires "atom_style dpd"_atom_style.html diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt index e0e8fbb27e..09eb6ee63a 100644 --- a/doc/src/pair_edip.txt +++ b/doc/src/pair_edip.txt @@ -99,7 +99,7 @@ specify EDIP parameters for all permutations of the two elements interacting in three-body configurations. Thus for 3 elements, 27 entries would be required, etc. -At the moment, only a single element parametrization is +At the moment, only a single element parameterization is implemented. However, the author is not aware of other multi-element EDIP parameterization. If you know any and you are interest in that, please contact the author of diff --git a/doc/src/pair_eff.txt b/doc/src/pair_eff.txt index a665654af0..1df94ebecc 100644 --- a/doc/src/pair_eff.txt +++ b/doc/src/pair_eff.txt @@ -48,21 +48,21 @@ structure methods to describe atomic structure, bonding, and chemistry in materials, and of plasma methods to describe nonequilibrium dynamics of large systems with a large number of highly excited electrons. Yet, eFF relies on a simplification of the electronic -wavefunction in which electrons are described as floating Gaussian +wave function in which electrons are described as floating Gaussian wave packets whose position and size respond to the various dynamic forces between interacting classical nuclear particles and spherical -Gaussian electron wavepackets. The wavefunction is taken to be a +Gaussian electron wave packets. The wave function is taken to be a Hartree product of the wave packets. To compensate for the lack of -explicit antisymmetry in the resulting wavefunction, a spin-dependent +explicit antisymmetry in the resulting wave function, a spin-dependent Pauli potential is included in the Hamiltonian. Substituting this -wavefunction into the time-dependent Schrodinger equation produces +wave function into the time-dependent Schrodinger equation produces equations of motion that correspond - to second order - to classical Hamiltonian relations between electron position and size, and their -conjugate momenta. The N-electron wavefunction is described as a +conjugate momenta. The N-electron wave function is described as a product of one-electron Gaussian functions, whose size is a dynamical variable and whose position is not constrained to a nuclear center. This form allows for straightforward propagation of the -wavefunction, with time, using a simple formulation from which the +wave function, with time, using a simple formulation from which the equations of motion are then integrated with conventional MD algorithms. In addition to this spin-dependent Pauli repulsion potential term between Gaussians, eFF includes the electron kinetic @@ -229,7 +229,7 @@ system. The charge for a pseudo-core atom should be given by the number of outer shell electrons. In general, eFF excels at computing the properties of materials in -extreme conditions and tracing the system dynamics over multi-picosend +extreme conditions and tracing the system dynamics over multi-picosecond timescales; this is particularly relevant where electron excitations can change significantly the nature of bonding in the system. It can capture with surprising accuracy the behavior of such systems because @@ -289,7 +289,7 @@ such as radius, radial velocity, and radial force, as defined by the this. Thes pair styles require you to use the "comm_modify vel -yes"_comm_modify.html command so that velocites are stored by ghost +yes"_comm_modify.html command so that velocities are stored by ghost atoms. [Related commands:] diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt index e322f8da15..f747d15ec4 100644 --- a/doc/src/pair_gran.txt +++ b/doc/src/pair_gran.txt @@ -242,7 +242,7 @@ require a per-particle radius is stored. The {sphere} atom style does all of this. This pair style requires you to use the "comm_modify vel -yes"_comm_modify.html command so that velocites are stored by ghost +yes"_comm_modify.html command so that velocities are stored by ghost atoms. These pair styles will not restart exactly when using the diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/src/pair_hbond_dreiding.txt index d4bdcd9258..9dd0bed87f 100644 --- a/doc/src/pair_hbond_dreiding.txt +++ b/doc/src/pair_hbond_dreiding.txt @@ -66,7 +66,7 @@ that the Morse form gives improved results for Dendrimer simulations, when n = 2. See the "Howto bioFF"_Howto_bioFF.html doc page for more information -on the DREIDING forcefield. +on the DREIDING force field. NOTE: Because the Dreiding hydrogen bond potential is only one portion of an overall force field which typically includes other pairwise @@ -135,9 +135,9 @@ distance cutoff Rin (distance units) distance cutoff Rout (distance units) angle cutoff (degrees) :ul -A single hydrogen atom type K can be specified, or a wild-card -asterisk can be used in place of or in conjunction with the K -arguments to select multiple types as hydrogens. This takes the form +A single hydrogen atom type K can be specified, or a wild-card asterisk +can be used in place of or in conjunction with the K arguments to +select multiple types as hydrogen atoms. This takes the form "*" or "*n" or "n*" or "m*n". See the "pair_coeff"_pair_coeff.html command doc page for details. diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt index 97a5972bfb..59af479b9f 100644 --- a/doc/src/pair_hybrid.txt +++ b/doc/src/pair_hybrid.txt @@ -229,7 +229,7 @@ For use with the various "compute */tally"_compute_tally.html computes, the "pair_modify compute/tally"_pair_modify.html command can be used to selectively turn off processing of the compute tally styles, for example, if those pair styles -(e.g. manybody styles) do not support this feature. +(e.g. many-body styles) do not support this feature. See the "pair_modify"_pair_modify.html doc page for details on the specific syntax, requirements and restrictions. @@ -270,7 +270,7 @@ atoms when the potential computes 3-body or 4-body interactions. However, you can still use the pair_coeff none setting or the "neigh_modify exclude"_neigh_modify.html command to exclude certain -type pairs from the neighbor list that will be passed to a manybody +type pairs from the neighbor list that will be passed to a many-body sub-style. This will alter the calculations made by a many-body potential, since it builds its list of 3-body, 4-body, etc interactions from the pair list. You will need to think carefully as diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt index f048b16ccf..f9b500d066 100644 --- a/doc/src/pair_ilp_graphene_hbn.txt +++ b/doc/src/pair_ilp_graphene_hbn.txt @@ -40,7 +40,7 @@ in "(Kolmogorov)"_#Kolmogorov2. Where Tap(r_ij) is the taper function which provides a continuous cutoff (up to third derivative) for interatomic separations larger than -r_c "(Maaravi)"_#Maaravi2. The definitons of each parameter in the above +r_c "(Maaravi)"_#Maaravi2. The definitions of each parameter in the above equation can be found in "(Leven1)"_#Leven1 and "(Maaravi)"_#Maaravi2. diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt index 912fca1657..a494c927b8 100644 --- a/doc/src/pair_kolmogorov_crespi_z.txt +++ b/doc/src/pair_kolmogorov_crespi_z.txt @@ -31,7 +31,7 @@ which is to take all normals along the z-axis. :c,image(Eqs/pair_kolmogorov_crespi_z.jpg) It is important to have a sufficiently large cutoff to ensure smooth forces. -Energies are shifted so that they go continously to zero at the cutoff assuming +Energies are shifted so that they go continuously to zero at the cutoff assuming that the exponential part of {Vij} (first term) decays sufficiently fast. This shift is achieved by the last term in the equation for {Vij} above. diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt index 9c61e0bf25..40730d67a7 100644 --- a/doc/src/pair_lj.txt +++ b/doc/src/pair_lj.txt @@ -223,7 +223,7 @@ 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 typically best in an -efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2*qdist, to +efficiency sense to use a LJ cutoff >= Coulombic cutoff + 2*qdist, to shrink the size of the neighbor list. This leads to slightly larger cost for the long-range calculation, so you can test the trade-off for your model. diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt index 47a554ef4f..9f95fc0347 100644 --- a/doc/src/pair_lj_long.txt +++ b/doc/src/pair_lj_long.txt @@ -97,7 +97,7 @@ 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 -LJ cutoff >= Coulomb cutoff + 2*qdist, to shrink the size of the +LJ cutoff >= Coulombic cutoff + 2*qdist, to shrink the size of the neighbor list. This leads to slightly larger cost for the long-range calculation, so you can test the trade-off for your model. diff --git a/doc/src/pair_lj_smooth.txt b/doc/src/pair_lj_smooth.txt index 0c66dd0f66..d320cb83ff 100644 --- a/doc/src/pair_lj_smooth.txt +++ b/doc/src/pair_lj_smooth.txt @@ -34,7 +34,7 @@ cause the force to vary smoothly from the inner cutoff Rin to the outer cutoff Rc. At the inner cutoff the force and its 1st derivative -will match the unsmoothed LJ formula. At the outer cutoff the force +will match the non-smoothed LJ formula. At the outer cutoff the force and its 1st derivative will be 0.0. The inner cutoff cannot be 0.0. NOTE: this force smoothing causes the energy to be discontinuous both diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_lj_soft.txt index 967f88205f..4e400d1c0a 100644 --- a/doc/src/pair_lj_soft.txt +++ b/doc/src/pair_lj_soft.txt @@ -103,7 +103,7 @@ pair_coeff 1 1 1.0 9.5 :pre [Description:] -The {lj/cut/soft} style and substyles compute the 12/6 Lennard-Jones +The {lj/cut/soft} style and sub-styles compute the 12/6 Lennard-Jones and Coulomb potential modified by a soft core, in order to avoid singularities during free energy calculations when sites are created or annihilated "(Beutler)"_#Beutler, @@ -179,13 +179,13 @@ 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. -The {coul/cut/soft}, {coul/long/soft} and {tip4p/long/soft} substyles +The {coul/cut/soft}, {coul/long/soft} and {tip4p/long/soft} sub-styles are designed to be combined with other pair potentials via the "pair_style hybrid/overlay"_pair_hybrid.html command. This is because they have no repulsive core. Hence, if used by themselves, there will be no repulsion to keep two oppositely charged particles from overlapping each other. In this case, if lambda = 1, a singularity may -occur. These substyles are suitable to represent charges embedded in +occur. These sub-styles are suitable to represent charges embedded in the Lennard-Jones radius of another site (for example hydrogen atoms in several water models). @@ -253,7 +253,7 @@ To avoid division by zero do not set sigma = 0; use the lambda parameter instead to activate/deactivate interactions, or use epsilon = 0 and sigma = 1. Alternatively, when sites do not interact though the Lennard-Jones term the {coul/long/soft} or -similar substyle can be used via the +similar sub-style can be used via the "pair_style hybrid/overlay"_pair_hybrid.html command. :line diff --git a/doc/src/pair_modify.txt b/doc/src/pair_modify.txt index c043fde5a7..4824a3d83e 100644 --- a/doc/src/pair_modify.txt +++ b/doc/src/pair_modify.txt @@ -183,7 +183,7 @@ an approximation. :l The tail corrections are computed at the beginning of each simulation run. If the number of atoms changes during the run, e.g. due to atoms leaving the simulation domain, or use of the "fix gcmc"_fix_gcmc.html -command, then the corrections are not updates to relect the changed +command, then the corrections are not updated to reflect the changed atom count. If this is a large effect in your simulation, you should break the long run into several short runs, so that the correction factors are re-computed multiple times. diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/src/pair_nb3b_harmonic.txt index 2b2152a873..3a6d1026ed 100644 --- a/doc/src/pair_nb3b_harmonic.txt +++ b/doc/src/pair_nb3b_harmonic.txt @@ -19,7 +19,7 @@ pair_coeff * * MgOH.nb3bharmonic Mg O H :pre [Description:] -This pair style computes a nonbonded 3-body harmonic potential for the +This pair style computes a non-bonded 3-body harmonic potential for the energy E of a system of atoms as :c,image(Eqs/pair_nb3b_harmonic.jpg) @@ -60,7 +60,7 @@ other potentials. An example of a pair_coeff command for use with the pair_coeff * * nb3b/harmonic MgOH.nb3b.harmonic Mg O H -Three-body nonbonded harmonic files in the {potentials} directory of +Three-body non-bonded harmonic files in the {potentials} directory of the LAMMPS distribution have a ".nb3b.harmonic" suffix. Lines that are not blank or comments (starting with #) define parameters for a triplet of elements. diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt index b24e3c07df..153fc50189 100644 --- a/doc/src/pair_oxdna.txt +++ b/doc/src/pair_oxdna.txt @@ -61,7 +61,7 @@ for a detailed description of the oxDNA force field. NOTE: These pair styles have to be used together with the related oxDNA bond style {oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of "bond_style oxdna/fene"_bond_oxdna.html). Most of the coefficients -in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. +in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. Exceptions are the first and second coefficient after {oxdna/stk} (seq=seqdep and T=0.1 in the above example) and the first coefficient after {oxdna/hbond} (seq=seqdep in the above example). When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt index c5662abdeb..a928bdf886 100644 --- a/doc/src/pair_oxdna2.txt +++ b/doc/src/pair_oxdna2.txt @@ -67,7 +67,7 @@ and "(Ouldridge)"_#Ouldridge2 for a detailed description of the oxDNA2 force fi NOTE: These pair styles have to be used together with the related oxDNA2 bond style {oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of "bond_style oxdna2/fene"_bond_oxdna.html). Most of the coefficients -in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. +in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. Exceptions are the first and the second coefficient after {oxdna2/stk} (seq=seqdep and T=0.1 in the above example), the first coefficient after {oxdna/hbond} (seq=seqdep in the above example) and the three coefficients after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat diff --git a/doc/src/pair_peri.txt b/doc/src/pair_peri.txt index b6baa4edc5..5c5a41ca6c 100644 --- a/doc/src/pair_peri.txt +++ b/doc/src/pair_peri.txt @@ -36,7 +36,7 @@ pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 118.43 :pre [Description:] The peridynamic pair styles implement material models that can be used -at the mescscopic and macroscopic scales. See "this +at the mesoscopic and macroscopic scales. See "this document"_PDF/PDLammps_overview.pdf for an overview of LAMMPS commands for Peridynamics modeling. @@ -63,7 +63,7 @@ R. Rahman and J. T. Foster at University of Texas at San Antonio. The original VES formulation is described in "(Mitchell2011)" and the original EPS formulation is in "(Mitchell2011a)". Additional PDF docs that describe the VES and EPS implementations are include in the -LAMMPS distro in "doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf and +LAMMPS distribution in "doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf and "doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf. For questions regarding the VES and EPS models in LAMMPS you can contact R. Rahman (rezwanur.rahman at utsa.edu). diff --git a/doc/src/pair_polymorphic.txt b/doc/src/pair_polymorphic.txt index 7460044043..d9e73d8492 100644 --- a/doc/src/pair_polymorphic.txt +++ b/doc/src/pair_polymorphic.txt @@ -95,7 +95,7 @@ N element names = mapping of Tersoff elements to atom types :ul See the pair_coeff doc page for alternate ways to specify the path for the potential file. Several files for polymorphic potentials are -included in the potentials dir of the LAMMPS distro. They have a +included in the potentials dir of the LAMMPS distribution. They have a "poly" suffix. As an example, imagine the SiC_tersoff.polymorphic file has tabulated diff --git a/doc/src/pair_quip.txt b/doc/src/pair_quip.txt index 1f794d0c84..30f1d80450 100644 --- a/doc/src/pair_quip.txt +++ b/doc/src/pair_quip.txt @@ -77,7 +77,7 @@ This pair style is part of the USER-QUIP package. It is only enabled if LAMMPS was built with that package. See the "Build package"_Build_package.html doc page for more info. -QUIP potentials are parametrized in electron-volts and Angstroms and +QUIP potentials are parameterized in electron-volts and Angstroms and therefore should be used with LAMMPS metal "units"_units.html. QUIP potentials are generally not designed to work with the scaling @@ -93,7 +93,7 @@ because it may remove pairs from the neighbor list that are still required. Pair style {quip} cannot be used with pair style {hybrid}, only -with {hybrid/overlay} and only the {quip} substyle is applied to +with {hybrid/overlay} and only the {quip} sub-style is applied to all atom types. [Related commands:] diff --git a/doc/src/pair_sdk.txt b/doc/src/pair_sdk.txt index 06a0a42d5a..7c596ed1d8 100644 --- a/doc/src/pair_sdk.txt +++ b/doc/src/pair_sdk.txt @@ -48,7 +48,7 @@ given by :c,image(Eqs/pair_cmm.jpg) -as required for the SDK Coarse-grained MD parametrization discussed in +as required for the SDK Coarse-grained MD parameterization discussed in "(Shinoda)"_#Shinoda3 and "(DeVane)"_#DeVane. Rc is the cutoff. Style {lj/sdk/coul/long} computes the adds Coulombic interactions diff --git a/doc/src/pair_smd_tlsph.txt b/doc/src/pair_smd_tlsph.txt index 44b0c6cae8..13ffbbabc1 100644 --- a/doc/src/pair_smd_tlsph.txt +++ b/doc/src/pair_smd_tlsph.txt @@ -33,7 +33,7 @@ pair style is defined. Note that {i} and {j} must be equal, i.e., no {tlsph} cross interactions between different particle types are allowed. In contrast to the usual {LAMMPS} {pair coeff} definitions, which are given solely a number of floats and integers, the {tlsph} -{pair coeff} definition is organised using keywords. These keywords +{pair coeff} definition is organized using keywords. These keywords mark the beginning of different sets of parameters for particle properties, material constitutive models, and damage models. The {pair coeff} line must be terminated with the {*END} keyword. The use the diff --git a/doc/src/pair_smd_ulsph.txt b/doc/src/pair_smd_ulsph.txt index f28dd9043c..39e9c76841 100644 --- a/doc/src/pair_smd_ulsph.txt +++ b/doc/src/pair_smd_ulsph.txt @@ -37,7 +37,7 @@ pair style is defined. Note that {i} and {j} can be different, i.e., 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 +and integers, the {ulsph} {pair coeff} definition is organized using keywords. These keywords mark the beginning of different sets of parameters for particle properties, material constitutive models, and damage models. The {pair coeff} line must be terminated with the diff --git a/doc/src/pair_smtbq.txt b/doc/src/pair_smtbq.txt index f3b69f2861..41e124a94f 100644 --- a/doc/src/pair_smtbq.txt +++ b/doc/src/pair_smtbq.txt @@ -28,7 +28,7 @@ is given by three contributions: where {Etot} is the total potential energy of the system, {EES} is the electrostatic part of the total energy, -{EOO} is the interaction between oxygens and +{EOO} is the interaction between oxygen atoms and {EMO} is a short-range interaction between metal and oxygen atoms. This interactions depend on interatomic distance {rij} and/or the charge {Qi} of atoms @@ -107,7 +107,7 @@ Thus parameter μ, indicated above, is given by : μ = (√n The potential offers the possibility to consider the polarizability of the electron clouds of oxygen by changing the slater radius of the -charge density around the oxygens through the parameters {rBB, rB and +charge density around the oxygen atoms through the parameters {rBB, rB and rS} in the ffield.SMTBQ.Syst. This change in radius is performed according to the method developed by E. Maras "SMTB-Q_2"_#SMTB-Q_2. This method needs to determine the number of @@ -142,7 +142,7 @@ For the anion (oxygen) : Name of element (char) and stoichiometry in oxide Formal charge and mass of element -Principal quantic number of outer orbital ({n}), electronegativity ({χ0i}) and hardness ({J0i}) +Principal quantum number of outer orbital ({n}), electronegativity ({χ0i}) and hardness ({J0i}) Ionic radius parameters : max coordination number ({coordBB} = 6 by default), bulk coordination number {(coordB)}, surface coordination number {(coordS)} and {rBB, rB and rS} the slater radius for each coordination number. (note : If you don't want to change the slater radius, use three identical radius values) Number of orbital shared by the element in the oxide ({di}) Divided line :ul diff --git a/doc/src/pair_spin_dmi.txt b/doc/src/pair_spin_dmi.txt index bd605bd064..a040f27d68 100644 --- a/doc/src/pair_spin_dmi.txt +++ b/doc/src/pair_spin_dmi.txt @@ -37,7 +37,7 @@ and D is the DM vector defining the intensity (in eV) and the direction of the interaction. In "(Rohart)"_#Rohart, D is defined as the direction normal to the film oriented -from the high spin-orbit layer to the magnetic ultrathin film. +from the high spin-orbit layer to the magnetic ultra-thin film. The application of a spin-lattice Poisson bracket to this energy (as described in "(Tranchida)"_#Tranchida5) allows to derive a magnetic torque omega, and a diff --git a/doc/src/pair_spin_exchange.txt b/doc/src/pair_spin_exchange.txt index 2f158704a9..fdbac9df3e 100644 --- a/doc/src/pair_spin_exchange.txt +++ b/doc/src/pair_spin_exchange.txt @@ -41,7 +41,7 @@ where a, b and d are the three constant coefficients defined in the associated The coefficients a, b, and d need to be fitted so that the function above matches with the value of the exchange interaction for the N neighbor shells taken into account. -Examples and more explanations about this function and its parametrization are reported +Examples and more explanations about this function and its parameterization are reported in "(Tranchida)"_#Tranchida3. From this exchange interaction, each spin i will be submitted @@ -69,7 +69,7 @@ b (adim parameter) d (distance units) :ul Note that rc is the radius cutoff of the considered exchange interaction, -and a, b and d are the three coefficients performing the parametrization +and a, b and d are the three coefficients performing the parameterization of the function J(rij) defined above. None of those coefficients is optional. If not specified, the diff --git a/doc/src/pair_spin_neel.txt b/doc/src/pair_spin_neel.txt index 7af71021a0..4458a0767b 100644 --- a/doc/src/pair_spin_neel.txt +++ b/doc/src/pair_spin_neel.txt @@ -50,8 +50,8 @@ above matches with the values of the magneto-elastic constant of the materials at stake. Examples and more explanations about this function and its -parametrization are reported in "(Tranchida)"_#Tranchida6. More -examples of parametrization will be provided in future work. +parameterization are reported in "(Tranchida)"_#Tranchida6. More +examples of parameterization will be provided in future work. From this DM interaction, each spin i will be submitted to a magnetic torque omega and its associated atom to a force F (for spin-lattice diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt index f6098fa005..8489815c62 100644 --- a/doc/src/pair_style.txt +++ b/doc/src/pair_style.txt @@ -205,7 +205,7 @@ pair"_Commands_pair.html doc page are followed by one or more of "lj/cut/dipole/cut"_pair_dipole.html - point dipoles with cutoff "lj/cut/dipole/long"_pair_dipole.html - point dipoles with long-range Ewald "lj/cut/soft"_pair_lj_soft.html - LJ with a soft core -"lj/cut/thole/long"_pair_thole.html - LJ with Coulomibics with thole damping +"lj/cut/thole/long"_pair_thole.html - LJ with Coulombics with thole damping "lj/cut/tip4p/cut"_pair_lj.html - LJ with cutoff Coulomb for TIP4P water "lj/cut/tip4p/long"_pair_lj.html - LJ with long-range Coulomb for TIP4P water "lj/cut/tip4p/long/soft"_pair_lj_soft.html - LJ with cutoff Coulomb for TIP4P water with a soft core @@ -242,7 +242,7 @@ pair"_Commands_pair.html doc page are followed by one or more of "morse/soft"_pair_morse.html - Morse potential with a soft core "multi/lucy"_pair_multi_lucy.html - DPD potential with density-dependent force "multi/lucy/rx"_pair_multi_lucy_rx.html - reactive DPD potential with density-dependent force -"nb3b/harmonic"_pair_nb3b_harmonic.html - nonbonded 3-body harmonic potential +"nb3b/harmonic"_pair_nb3b_harmonic.html - non-bonded 3-body harmonic potential "nm/cut"_pair_nm.html - N-M potential "nm/cut/coul/cut"_pair_nm.html - N-M potential with cutoff Coulomb "nm/cut/coul/long"_pair_nm.html - N-M potential with long-range Coulombics diff --git a/doc/src/pair_sw.txt b/doc/src/pair_sw.txt index ff83316419..33c3892c62 100644 --- a/doc/src/pair_sw.txt +++ b/doc/src/pair_sw.txt @@ -124,13 +124,13 @@ configuration. In the literature, however, the three-body parameters are usually defined by simple formulas involving two sets of pair-wise parameters, corresponding to the ij and ik pairs, where i is the center atom. The user must ensure that the correct combining rule is -used to calculate the values of the threebody parameters for +used to calculate the values of the three-body parameters for alloys. Note also that the function phi3 contains two exponential screening factors with parameter values from the ij pair and ik pairs. So phi3 for a C atom bonded to a Si atom and a second C atom will depend on the three-body parameters for the CSiC entry, and also on the two-body parameters for the CCC and CSiSi entries. Since the -order of the two neighbors is arbitrary, the threebody parameters for +order of the two neighbors is arbitrary, the three-body parameters for entries CSiC and CCSi should be the same. Similarly, the two-body parameters for entries SiCC and CSiSi should also be the same. The parameters used only for two-body interactions (A, B, p, and q) in diff --git a/doc/src/pair_tri_lj.txt b/doc/src/pair_tri_lj.txt index 98bb4e284e..75108c0743 100644 --- a/doc/src/pair_tri_lj.txt +++ b/doc/src/pair_tri_lj.txt @@ -52,7 +52,7 @@ spheres. It the diameter is larger than sigma_II, then split the triangle into 2 triangles by bisecting its longest side. Repeat the process on each sub-triangle, recursing as far as needed to generate a set of covering spheres. When finished, the original criteria are -met, and the set of covering spheres shoule be near minimal in number +met, and the set of covering spheres should be near minimal in number and overlap, at least for input triangles with a reasonable aspect-ratio. diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt index 6aa30d9e63..7669b78f85 100644 --- a/doc/src/read_data.txt +++ b/doc/src/read_data.txt @@ -220,7 +220,7 @@ A data file has a header and a body. The header appears first. The first line of the header is always skipped; it typically contains a description of the file. Then lines are read one at a time. Lines can have a trailing comment starting with '#' that is ignored. If the -line is blank (only whitespace after comment is deleted), it is +line is blank (only white-space after comment is deleted), it is skipped. If the line contains a header keyword, the corresponding value(s) is read from the line. If it doesn't contain a header keyword, the line begins the body of the file. @@ -249,7 +249,7 @@ standard header settings, such as the number of atoms. The formatting of individual lines in the data file (indentation, spacing between words and numbers) is not important except that header and section keywords (e.g. atoms, xlo xhi, Masses, Bond Coeffs) must -be capitalized as shown and can't have extra white space between their +be capitalized as shown and can't have extra white-space between their words - e.g. two spaces or a tab between the 2 words in "xlo xhi" or the 2 words in "Bond Coeffs", is not valid. @@ -577,7 +577,7 @@ atom-type = type of atom (1-Ntype) bodyflag = 1 for body particles, 0 for point particles cc = chemical concentration for tDPD particles for each species (mole/volume units) contact-radius = ??? (distance units) -cs_re,cs_im = real/imaginary parts of wavepacket coefficients +cs_re,cs_im = real/imaginary parts of wave packet coefficients cv = heat capacity (need units) for SPH particles density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle) diameter = diameter of spherical atom (distance units) @@ -586,7 +586,7 @@ edpd_temp = temperature for eDPD particles (temperature units) edpd_cv = volumetric heat capacity for eDPD particles (energy/temperature/volume units) ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles eradius = electron radius (or fixed-core radius) -etag = integer ID of electron that each wavepacket belongs to +etag = integer ID of electron that each wave packet belongs to kernel-radius = ??? (distance units) lineflag = 1 for line segment particles, 0 for point or spherical particles mass = mass of particle (mass units) @@ -620,7 +620,7 @@ to 0. The molecule ID is a 2nd identifier attached to an atom. Normally, it is a number from 1 to N, identifying which molecule the atom belongs -to. It can be 0 if it is an unbonded atom or if you don't care to +to. It can be 0 if it is a non-bonded atom or if you don't care to keep track of molecule assignments. The diameter specifies the size of a finite-size spherical particle. @@ -682,7 +682,7 @@ were used in the input script, each atom line would have these fields: atom-ID atom-type x y z q diameter density :pre Note that if a non-standard value is defined by multiple sub-styles, -it must appear mutliple times in the atom line. E.g. the atom line +it must appear multiple times in the atom line. E.g. the atom line for atom_style hybrid dipole full would list "q" twice: atom-ID atom-type x y z q mux muy myz molecule-ID q :pre diff --git a/doc/src/read_dump.txt b/doc/src/read_dump.txt index db9cfca825..fbcc89a453 100644 --- a/doc/src/read_dump.txt +++ b/doc/src/read_dump.txt @@ -119,7 +119,7 @@ Support for other dump format readers may be added in the future. Global information is first read from the dump file, namely timestep and box information. -The dump file is scanned for a snapshot with a time stamp that matches +The dump file is scanned for a snapshot with a timestamp that matches the specified {Nstep}. This means the LAMMPS timestep the dump file snapshot was written on for the {native} format. Note that the {xyz} and {molfile} formats do not store the timestep. For these formats, diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt index 9defd1314e..bf13d20439 100644 --- a/doc/src/run_style.txt +++ b/doc/src/run_style.txt @@ -191,7 +191,7 @@ hybrid/overlay"_pair_hybrid.html command. In this scenario, different sub-styles of the hybrid pair style are evaluated at different rRESPA levels. This can be useful, for example, to set different timesteps for hybrid coarse-grained/all-atom models. The {hybrid} keyword -requires as many level assignments as there are hybrid substyles, +requires as many level assignments as there are hybrid sub-styles, 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 mutually exclusive with diff --git a/doc/src/server_mc.txt b/doc/src/server_mc.txt index 58ca415be3..638d3dadfb 100644 --- a/doc/src/server_mc.txt +++ b/doc/src/server_mc.txt @@ -60,7 +60,7 @@ pages for more details on the actual library syntax. The "cs" object in this pseudo code is a pointer to an instance of the CSlib. See the src/MESSAGE/server_mc.cpp file for details on how LAMMPS uses -these messages. See the examples/COUPLE/lammmps_mc/mc.cpp file for an +these messages. See the examples/COUPLE/lammps_mc/mc.cpp file for an example of how an MC driver code can use these messages. Define NATOMS=1, EINIT=2, DISPLACE=3, ACCEPT=4, RUN=5. diff --git a/doc/src/server_md.txt b/doc/src/server_md.txt index 753542dc75..fc9ae5d53a 100644 --- a/doc/src/server_md.txt +++ b/doc/src/server_md.txt @@ -119,7 +119,7 @@ The units for various quantities that are sent and received iva messages are defined for atomic-scale simulations in the table below. The client and server codes (including LAMMPS) can use internal units different than these (e.g. "real units"_units.html in LAMMPS), so long -as they convert to these units for meesaging. +as they convert to these units for messaging. COORDS, ORIGIN, BOX = Angstroms CHARGE = multiple of electron charge (1.0 is a proton) diff --git a/doc/src/special_bonds.txt b/doc/src/special_bonds.txt index e90535e65f..f932f51c47 100644 --- a/doc/src/special_bonds.txt +++ b/doc/src/special_bonds.txt @@ -61,9 +61,9 @@ Tersoff, COMB, AIREBO, and ReaxFF. In fact, it generally makes no sense to define permanent bonds between atoms that interact via these potentials, though such bonds may exist elsewhere in your system, e.g. when using the "pair_style hybrid"_pair_hybrid.html command. -Thus LAMMPS ignores special_bonds settings when manybody potentials +Thus LAMMPS ignores special_bonds settings when many-body potentials are calculated. Please note, that the existence of explicit bonds -for atoms that are described by a manybody potential will alter the +for atoms that are described by a many-body potential will alter the neighbor list and thus can render the computation of those interactions invalid, since those pairs are not only used to determine direct pairwise interactions but also neighbors of neighbors and more. diff --git a/doc/src/suffix.txt b/doc/src/suffix.txt index 62e41ed29a..e9fae44088 100644 --- a/doc/src/suffix.txt +++ b/doc/src/suffix.txt @@ -46,7 +46,7 @@ run on one or more GPUs or multicore CPU/GPU nodes :ulb,l USER-INTEL = a collection of pair styles and neighbor routines optimized to run in single, mixed, or double precision on CPUs and -Intel(R) Xeon Phi(TM) coprocessors. :l +Intel(R) Xeon Phi(TM) co-processors. :l KOKKOS = a collection of atom, pair, and fix styles optimized to run using the Kokkos library on various kinds of hardware, including GPUs diff --git a/doc/src/tad.txt b/doc/src/tad.txt index 9b34a68636..effb998f94 100644 --- a/doc/src/tad.txt +++ b/doc/src/tad.txt @@ -18,7 +18,7 @@ t_event = timestep interval between event checks :l T_lo = temperature at which event times are desired :l T_hi = temperature at which MD simulation is performed :l delta = desired confidence level for stopping criterion :l -tmax = reciprocal of lowest expected preexponential factor (time units) :l +tmax = reciprocal of lowest expected pre-exponential factor (time units) :l compute-ID = ID of the compute used for event detection :l zero or more keyword/value pairs may be appended :l keyword = {min} or {neb} or {min_style} or {neb_style} or {neb_log} :l diff --git a/doc/src/timer.txt b/doc/src/timer.txt index 4025af9ea6..6da74ca153 100644 --- a/doc/src/timer.txt +++ b/doc/src/timer.txt @@ -19,7 +19,7 @@ timer args :pre {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} + {timeout} elapse = set wall time limit to {elapse} {every} Ncheck = perform timeout check every {Ncheck} steps :pre [Examples:] @@ -57,13 +57,13 @@ though it can also slow down the simulation by prohibiting overlapping independent computations on different MPI ranks Using the {nosync} setting (which is the default) turns this synchronization off. -With the {timeout} keyword a walltime limit can be imposed, that +With the {timeout} keyword a wall time limit can be imposed, that affects the "run"_run.html and "minimize"_minimize.html commands. This can be convenient when calculations have to comply with execution time limits, e.g. when running under a batch system when you want to maximize the utilization of the batch time slot, especially for runs where the time per timestep varies much and thus it becomes difficult -to predict how many steps a simulation can perform for a given walltime +to predict how many steps a simulation can perform for a given wall time limit. This also applies for difficult to converge minimizations. The timeout {elapse} value should be somewhat smaller than the maximum wall time requested from the batch system, as there is usually diff --git a/doc/src/units.txt b/doc/src/units.txt index 8df8fe6810..844504d977 100644 --- a/doc/src/units.txt +++ b/doc/src/units.txt @@ -201,13 +201,13 @@ The units command also sets the timestep size and neighbor skin distance to default values for each style: For style {lj} these are dt = 0.005 tau and skin = 0.3 sigma. -For style {real} these are dt = 1.0 fmsec and skin = 2.0 Angstroms. -For style {metal} these are dt = 0.001 psec and skin = 2.0 Angstroms. -For style {si} these are dt = 1.0e-8 sec and skin = 0.001 meters. -For style {cgs} these are dt = 1.0e-8 sec and skin = 0.1 cm. -For style {electron} these are dt = 0.001 fmsec and skin = 2.0 Bohr. -For style {micro} these are dt = 2.0 microsec and skin = 0.1 micrometers. -For style {nano} these are dt = 0.00045 nanosec and skin = 0.1 nanometers. :ul +For style {real} these are dt = 1.0 femtoseconds and skin = 2.0 Angstroms. +For style {metal} these are dt = 0.001 picoseconds and skin = 2.0 Angstroms. +For style {si} these are dt = 1.0e-8 seconds and skin = 0.001 meters. +For style {cgs} these are dt = 1.0e-8 seconds and skin = 0.1 centimeters. +For style {electron} these are dt = 0.001 femtoseconds and skin = 2.0 Bohr. +For style {micro} these are dt = 2.0 microseconds and skin = 0.1 micrometers. +For style {nano} these are dt = 0.00045 nanoseconds and skin = 0.1 nanometers. :ul [Restrictions:] diff --git a/doc/src/variable.txt b/doc/src/variable.txt index a8d50503ac..77c1f6eeb0 100644 --- a/doc/src/variable.txt +++ b/doc/src/variable.txt @@ -339,7 +339,7 @@ below. The rules for formatting the file are as follows. A comment character "#" can be used anywhere on a line; text starting with the comment character is stripped. Blank lines are skipped. The first "word" of -a non-blank line, delimited by white space, is the "string" assigned +a non-blank line, delimited by white-space, is the "string" assigned to the variable. For the {atomfile} style, a filename is provided which contains one or @@ -358,7 +358,7 @@ The rules for formatting the file are as follows. Each time a set of per-atom values is read, a non-blank line is searched for in the file. A comment character "#" can be used anywhere on a line; text starting with the comment character is stripped. Blank lines are skipped. The -first "word" of a non-blank line, delimited by white space, is read as +first "word" of a non-blank line, delimited by white-space, is read as the count N of per-atom lines to immediately follow. N can be be the total number of atoms in the system, or only a subset. The next N lines have the following format