more manual spelling fixes

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

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

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

doc/src/Intro_nonfeatures.txt

@@ -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

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.
 

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
 

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.

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.

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,

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

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

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.
 

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

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.
 

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.

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

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.