diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt index 695b949f7e..2844749c28 100644 --- a/doc/src/Errors_messages.txt +++ b/doc/src/Errors_messages.txt @@ -460,7 +460,7 @@ compute. :dd {Big particle in fix srd cannot be point particle} :dt -Big particles must be extended spheriods or ellipsoids. :dd +Big particles must be extended spheroids or ellipsoids. :dd {Bigint setting in lmptype.h is invalid} :dt @@ -780,7 +780,7 @@ Cannot use tilt factors unless the simulation box is non-orthogonal. :dd Self-explanatory. :dd -{Cannot change box z boundary to nonperiodic for a 2d simulation} :dt +{Cannot change box z boundary to non-periodic for a 2d simulation} :dt Self-explanatory. :dd @@ -1288,7 +1288,7 @@ are defined. :dd You cannot reset the timestep when a fix that keeps track of elapsed time is in place. :dd -{Cannot run 2d simulation with nonperiodic Z dimension} :dt +{Cannot run 2d simulation with non-periodic Z dimension} :dt Use the boundary command to make the z dimension periodic in order to run a 2d simulation. :dd @@ -2116,29 +2116,29 @@ Self-explanatory. :dd Fix setforce cannot be used in this manner. Use fix addforce instead. :dd -{Cannot use nonperiodic boundares with fix ttm} :dt +{Cannot use non-periodic boundares with fix ttm} :dt This fix requires a fully periodic simulation box. :dd -{Cannot use nonperiodic boundaries with Ewald} :dt +{Cannot use non-periodic boundaries with Ewald} :dt For kspace style ewald, all 3 dimensions must have periodic boundaries unless you use the kspace_modify command to define a 2d slab with a non-periodic z dimension. :dd -{Cannot use nonperiodic boundaries with EwaldDisp} :dt +{Cannot use non-periodic boundaries with EwaldDisp} :dt For kspace style ewald/disp, all 3 dimensions must have periodic boundaries unless you use the kspace_modify command to define a 2d slab with a non-periodic z dimension. :dd -{Cannot use nonperiodic boundaries with PPPM} :dt +{Cannot use non-periodic boundaries with PPPM} :dt For kspace style pppm, all 3 dimensions must have periodic boundaries unless you use the kspace_modify command to define a 2d slab with a non-periodic z dimension. :dd -{Cannot use nonperiodic boundaries with PPPMDisp} :dt +{Cannot use non-periodic boundaries with PPPMDisp} :dt For kspace style pppm/disp, all 3 dimensions must have periodic boundaries unless you use the kspace_modify command to define a 2d @@ -8014,7 +8014,7 @@ Self-explanatory. :dd {Package command after simulation box is defined} :dt -The package command cannot be used afer a read_data, read_restart, or +The package command cannot be used after a read_data, read_restart, or create_box command. :dd {Package gpu command without GPU package installed} :dt diff --git a/doc/src/Howto_drude2.txt b/doc/src/Howto_drude2.txt index a342d4a87d..0e72273723 100644 --- a/doc/src/Howto_drude2.txt +++ b/doc/src/Howto_drude2.txt @@ -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 barostating will look like +instructions for thermostating and barostatting will look like compute TATOMS ATOMS temp fix DIRECT all drude/transform/direct diff --git a/doc/src/Howto_spherical.txt b/doc/src/Howto_spherical.txt index 4dfe4e2f6c..d4233e7b81 100644 --- a/doc/src/Howto_spherical.txt +++ b/doc/src/Howto_spherical.txt @@ -35,7 +35,7 @@ There are several "atom styles"_atom_style.html that allow for definition of finite-size particles: sphere, dipole, ellipsoid, line, tri, peri, and body. -The sphere style defines particles that are spheriods and each +The sphere style defines particles that are spheroids and each particle can have a unique diameter and mass (or density). These particles store an angular velocity (omega) and can be acted upon by torque. The "set" command can be used to modify the diameter and mass diff --git a/doc/src/Intro_nonfeatures.txt b/doc/src/Intro_nonfeatures.txt index 316e661475..580039f91b 100644 --- a/doc/src/Intro_nonfeatures.txt +++ b/doc/src/Intro_nonfeatures.txt @@ -33,7 +33,7 @@ the library interface is provided. Thus, GUI interfaces can be written in Python (or C or C++ if desired) that run LAMMPS and visualize or plot its output. Examples of this are provided in the python directory and described on the "Python"_Python_head.html doc -page. Also, there are several external wrappers or GUI frontends.:ulb,l +page. Also, there are several external wrappers or GUI front ends.:ulb,l Builder: Several pre-processing tools are packaged with LAMMPS. Some of them convert input files in formats produced by other MD codes such @@ -64,7 +64,7 @@ post-processing codes. To some degree, that conversion can be done directly inside of LAMMPS by interfacing to the VMD molfile plugins. The "rerun"_rerun.html command also allows to do some post-processing of existing trajectories, and through being able to read a variety -of file formats, this can also be used for analysing trajectories +of file formats, this can also be used for analyzing trajectories from other MD codes. Some post-processing tools packaged with LAMMPS will do these conversions. Scripts provided in the tools/python directory can extract and massage data in dump files to diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 5f50e80271..55c7dec828 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -1207,7 +1207,7 @@ USER-PLUMED package :link(PKG-USER-PLUMED),h4 [Contents:] The fix plumed command allows you to use the PLUMED free energy plugin -for molecular dynamics to analyse and bias your LAMMPS trajectory on +for molecular dynamics to analyze and bias your LAMMPS trajectory on the fly. The PLUMED library is called from within the LAMMPS input script by using the "fix plumed _fix_plumed.html command. diff --git a/doc/src/Speed_intel.txt b/doc/src/Speed_intel.txt index d35a311f46..6f9f3dfcaf 100644 --- a/doc/src/Speed_intel.txt +++ b/doc/src/Speed_intel.txt @@ -510,7 +510,7 @@ supported. [References:] -Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l +Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. "Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency."_http://dl.acm.org/citation.cfm?id=3014915 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95). :l diff --git a/doc/src/compute_basal_atom.txt b/doc/src/compute_basal_atom.txt index 5c28b8e378..c74bd4342e 100644 --- a/doc/src/compute_basal_atom.txt +++ b/doc/src/compute_basal_atom.txt @@ -28,7 +28,7 @@ The results enable efficient identification and characterization of twins and grains in hexagonal close-packed structures. The output of the compute is thus the 3 components of a unit vector -associdate with each atom. The components are set to 0.0 for +associated with each atom. The components are set to 0.0 for atoms not in the group. Details of the calculation are given in "(Barrett)"_#Barrett. diff --git a/doc/src/compute_rigid_local.txt b/doc/src/compute_rigid_local.txt index 67c6209bdf..294c70cda2 100644 --- a/doc/src/compute_rigid_local.txt +++ b/doc/src/compute_rigid_local.txt @@ -106,7 +106,7 @@ There are two options for outputting the coordinates of the center of mass (COM) of the body. The {x}, {y}, {z} attributes write the COM "unscaled", in the appropriate distance "units"_units.html (Angstroms, sigma, etc). Use {xu}, {yu}, {zu} if you want the COM "unwrapped" by -the image flags for each atobody. Unwrapped means that if the body +the image flags for each body. Unwrapped means that if the body COM has passed thru a periodic boundary one or more times, the value is generated what the COM coordinate would be if it had not been wrapped back into the periodic box. diff --git a/doc/src/compute_ti.txt b/doc/src/compute_ti.txt index 9057cab476..0dec297183 100644 --- a/doc/src/compute_ti.txt +++ b/doc/src/compute_ti.txt @@ -45,7 +45,7 @@ described in "Eike"_#Eike. Typically this compute will be used in conjunction with the "fix adapt"_fix_adapt.html command which can perform alchemical -transformations by adusting the strength of an interaction potential +transformations by adjusting the strength of an interaction potential as a simulation runs, as defined by one or more "pair_style"_pair_style.html or "kspace_style"_kspace_style.html commands. This scaling is done via a prefactor on the energy, forces, diff --git a/doc/src/fix_drude_transform.txt b/doc/src/fix_drude_transform.txt index 8864cc4eb6..2135c0bd4f 100644 --- a/doc/src/fix_drude_transform.txt +++ b/doc/src/fix_drude_transform.txt @@ -132,7 +132,7 @@ 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 -barostated at 1.0. +barostatted at 1.0. In order to avoid the flying ice cube problem (irreversible transfer of linear momentum to the center of mass of the system), you may need diff --git a/doc/src/fix_phonon.txt b/doc/src/fix_phonon.txt index ede3bb5cfd..7d8f4d3379 100644 --- a/doc/src/fix_phonon.txt +++ b/doc/src/fix_phonon.txt @@ -127,7 +127,7 @@ which lattice point; the lattice indices start from 0. An auxiliary code, "latgen"_http://code.google.com/p/latgen, can be employed to generate the compatible map file for various crystals. -In case one simulates a nonperiodic system, where the whole simulation +In case one simulates a non-periodic system, where the whole simulation box is treated as a unit cell, one can set {map_file} as {GAMMA}, so that the mapping info will be generated internally and a file is not needed. In this case, the dynamical matrix at only the gamma-point diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt index 19e3b0ca40..0751a272ac 100644 --- a/doc/src/fix_property_atom.txt +++ b/doc/src/fix_property_atom.txt @@ -170,7 +170,7 @@ assigned a molecule ID of 4. Note that "atomfile-style variables"_variable.html can also be used in place of atom-style variables, which means in this case that the -molecule IDs could be read-in from a separate file and assinged by the +molecule IDs could be read-in from a separate file and assigned by the "set"_set.html command. This allows you to initialize new per-atom properties in a completely general fashion. diff --git a/doc/src/fix_qmmm.txt b/doc/src/fix_qmmm.txt index 2dbf935f93..4163275056 100644 --- a/doc/src/fix_qmmm.txt +++ b/doc/src/fix_qmmm.txt @@ -58,7 +58,7 @@ library provided with LAMMPS. See the "Build package"_Build_package.html doc page for more info. The fix is only functional when LAMMPS is built as a library and -linked with a compatible QM program and a QM/MM frontend into a QM/MM +linked with a compatible QM program and a QM/MM front end into a QM/MM executable. See the lib/qmmm/README file for details. [Related commands:] none diff --git a/doc/src/fix_srd.txt b/doc/src/fix_srd.txt index 557eee1cfc..1cc8dad178 100644 --- a/doc/src/fix_srd.txt +++ b/doc/src/fix_srd.txt @@ -61,7 +61,7 @@ in "(Hecht)"_#Hecht. The key idea behind using SRD particles as a cheap coarse-grained solvent is that SRD particles do not interact with each other, but only with the solute particles, which in LAMMPS can be spheroids, ellipsoids, or line segments, or triangles, or rigid -bodies containing multiple spheriods or ellipsoids or line segments +bodies containing multiple spheroids or ellipsoids or line segments or triangles. The collision and rotation properties of the model imbue the SRD particles with fluid-like properties, including an effective viscosity. Thus simulations with large solute particles can diff --git a/doc/src/message.txt b/doc/src/message.txt index 2b6a894e70..d258cfbd08 100644 --- a/doc/src/message.txt +++ b/doc/src/message.txt @@ -93,7 +93,7 @@ localhost:5555 # client and server running on same machine 192.168.1.1:5555 # server is 192.168.1.1 deptbox.uni.edu:5555 # server is deptbox.uni.edu :pre -The server specifes "*:5555" where "*" represents all available +The server specifies "*:5555" where "*" represents all available interfaces on the server's machine, and the port ID must match what the client specifies. diff --git a/doc/src/pair_atm.txt b/doc/src/pair_atm.txt index 63a450c51a..adbc6b6f3b 100644 --- a/doc/src/pair_atm.txt +++ b/doc/src/pair_atm.txt @@ -118,7 +118,7 @@ pair_coeff 3 3 3 nu10 :pre By default the nu value for all triplets is set to 0.0. Thus it is not required to provide pair_coeff commands that enumerate triplet interactions for all K types. If some I,J,K combination is not -speficied, then there will be no 3-body ATM interactions for that +specified, then there will be no 3-body ATM interactions for that combination and all its permutations. However, as with all pair styles, it is required to specify a pair_coeff command for all I,J combinations, else an error will result. diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt index bdf37983b6..b3ce55535e 100644 --- a/doc/src/pair_dipole.txt +++ b/doc/src/pair_dipole.txt @@ -82,7 +82,7 @@ styles. Style {lj/sf/dipole/sf} computes "shifted-force" interactions between pairs of particles that each have a charge and/or a point dipole -moment. In general, a shifted-force potential is a (sligthly) modified +moment. In general, a shifted-force potential is a (slightly) modified potential containing extra terms that make both the energy and its derivative go to zero at the cutoff distance; this removes (cutoff-related) problems in energy conservation and any numerical diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_lj_soft.txt index 9bcc83fa66..967f88205f 100644 --- a/doc/src/pair_lj_soft.txt +++ b/doc/src/pair_lj_soft.txt @@ -189,7 +189,7 @@ occur. These substyles are suitable to represent charges embedded in the Lennard-Jones radius of another site (for example hydrogen atoms in several water models). -NOTES: When using the core-softed Coulomb potentials with long-range +NOTES: When using the soft-core Coulomb potentials with long-range solvers ({coul/long/soft}, {lj/cut/coul/long/soft}, etc.) in a free energy calculation in which sites holding electrostatic charges are being created or annihilated (using "fix adapt/fep"_fix_adapt_fep.html @@ -197,7 +197,7 @@ and "compute fep"_compute_fep.html) it is important to adapt both the lambda activation parameter (from 0 to 1, or the reverse) and the value of the charge (from 0 to its final value, or the reverse). This ensures that long-range electrostatic terms (kspace) are correct. It -is not necessary to use core-softed Coulomb potentials if the van der +is not necessary to use soft-core Coulomb potentials if the van der Waals site is present during the free-energy route, thus avoiding overlap of the charges. Examples are provided in the LAMMPS source directory tree, under examples/USER/fep.