First batch of spelling fixes in manual

doc/src/2001/input_commands.html

@@ -476,7 +476,7 @@ IMPORTANT NOTE: the angletype option has one additional affect, namely
   since they will not be SHAKEn but neither will the angle force by computed
 for style region, a coeff of INF means + or - infinity (all the way 
   to the boundary)
-an atom can be assigned to multiple constraints, the contraints will be
+an atom can be assigned to multiple constraints, the constraints will be
   applied in the reverse order they are assigned to that atom
   (e.g. each timestep, the last fix assigned to an atom will be applied 
   to it first, then the next-to-last applied second, etc)
@@ -1263,7 +1263,7 @@ when using constraints with the minimizer, fixes are
   applied when atoms move except for the following
 fixes associated with temperature control are not allowed
   (rescale, hoover/drag, langevin)
-the minimizer does not invoke the "fix style shake" contraints on
+the minimizer does not invoke the "fix style shake" constraints on
   bond lengths
 the minimizer does not invoke pressure control or volume control settings
 for good convergence, should specify use of smooth nonbond force fields 

doc/src/99/basics.html

@@ -167,7 +167,7 @@ tool on the small-system data file.</P>
 <P>
 (6) flow</P>
 <P>
-2-d flow of Lennard-Jones atoms in a channel using various contraint 
+2-d flow of Lennard-Jones atoms in a channel using various constraint
 options.</P>
 <P>
 (7) polymer</P>

doc/src/99/input_commands.html

@@ -294,7 +294,7 @@ assign a group of atoms to a particular constraint
 use appropriate number of coeffs for a particular style
 the constraint itself is defined by the "fix style" command
 multiple groups of atoms can be assigned to the same constraint
-an atom can be assigned to multiple constraints, the contraints will be
+an atom can be assigned to multiple constraints, the constraints will be
   applied in the reverse order they are assigned to that atom
   (e.g. each timestep, the last fix assigned to an atom will be applied 
   to it first, then the next-to-last applied second, etc)

doc/src/Section_errors.txt

@@ -574,11 +574,11 @@ group of atoms correctly. :dd
 
 {Bad quadratic solve for particle/line collision} :dt
 
-This is an internal error.  It should nornally not occur. :dd
+This is an internal error.  It should normally not occur. :dd
 
 {Bad quadratic solve for particle/tri collision} :dt
 
-This is an internal error.  It should nornally not occur. :dd
+This is an internal error.  It should normally not occur. :dd
 
 {Bad real space Coulomb cutoff in fix tune/kspace} :dt
 
@@ -912,7 +912,7 @@ Atoms can not be added afterwards to this fix option. :dd
 
 {Cannot append atoms to a triclinic box} :dt
 
-The simulation box must be defined with edges alligned with the
+The simulation box must be defined with edges aligned with the
 Cartesian axes. :dd
 
 {Cannot balance in z dimension for 2d simulation} :dt
@@ -1327,7 +1327,7 @@ Self-explanatory. :dd
 
 This file is created when you use some LAMMPS features, to indicate
 what paper you should cite on behalf of those who implemented
-the feature.  Check that you have write priveleges into the directory
+the feature.  Check that you have write privileges into the directory
 you are running in. :dd
 
 {Cannot open log.lammps for writing} :dt
@@ -2088,7 +2088,7 @@ Self-explanatory. :dd
 
 {Cannot use lines with fix srd unless overlap is set} :dt
 
-This is because line segements are connected to each other. :dd
+This is because line segments are connected to each other. :dd
 
 {Cannot use multiple fix wall commands with pair brownian} :dt
 
@@ -2790,7 +2790,7 @@ Self-explanatory. :dd
 
 {Compute erotate/asphere requires extended particles} :dt
 
-This compute cannot be used with point paritlces. :dd
+This compute cannot be used with point particles. :dd
 
 {Compute erotate/rigid with non-rigid fix-ID} :dt
 
@@ -3079,7 +3079,7 @@ Self-explanatory. :dd
 
 {Compute temp/asphere requires extended particles} :dt
 
-This compute cannot be used with point paritlces. :dd
+This compute cannot be used with point particles. :dd
 
 {Compute temp/body requires atom style body} :dt
 
@@ -3524,12 +3524,12 @@ path and name are correct. :dd
 
 {Could not process Python file} :dt
 
-The Python code in the specified file was not run sucessfully by
+The Python code in the specified file was not run successfully by
 Python, probably due to errors in the Python code. :dd
 
 {Could not process Python string} :dt
 
-The Python code in the here string was not run sucessfully by Python,
+The Python code in the here string was not run successfully by Python,
 probably due to errors in the Python code. :dd
 
 {Coulomb PPPMDisp order has been reduced below minorder} :dt
@@ -4385,7 +4385,7 @@ Self-explanatory. :dd
 
 {Fix ave/chunk does not use chunk/atom compute} :dt
 
-The specified conpute is not for a compute chunk/atom command. :dd
+The specified compute is not for a compute chunk/atom command. :dd
 
 {Fix ave/chunk fix does not calculate a per-atom array} :dt
 
@@ -4970,7 +4970,7 @@ Self-explanatory. :dd
 
 {Fix langevin angmom requires extended particles} :dt
 
-This fix option cannot be used with point paritlces. :dd
+This fix option cannot be used with point particles. :dd
 
 {Fix langevin omega is not yet implemented with kokkos} :dt
 
@@ -7361,7 +7361,7 @@ This should not occur.  Report the problem to the developers. :dd
 Lost atoms are checked for each time thermo output is done.  See the
 thermo_modify lost command for options.  Lost atoms usually indicate
 bad dynamics, e.g. atoms have been blown far out of the simulation
-box, or moved futher than one processor's sub-domain away before
+box, or moved further than one processor's sub-domain away before
 reneighboring. :dd
 
 {MEAM library error %d} :dt
@@ -9166,7 +9166,7 @@ Self-explanatory. :dd
 
 {Python function evaluation failed} :dt
 
-The Python function did not run succesfully and/or did not return a
+The Python function did not run successfully and/or did not return a
 value (if it is supposed to return a value).  This is probably due to
 some error condition in the function. :dd
 
@@ -10654,7 +10654,7 @@ Only atom-style variables can be used. :dd
 
 {Variable for region cylinder is invalid style} :dt
 
-Only equal-style varaibles are allowed. :dd
+Only equal-style variables are allowed. :dd
 
 {Variable for region is invalid style} :dt
 
@@ -10666,7 +10666,7 @@ Self-explanatory. :dd
 
 {Variable for region sphere is invalid style} :dt
 
-Only equal-style varaibles are allowed. :dd
+Only equal-style variables are allowed. :dd
 
 {Variable for restart is invalid style} :dt
 
@@ -11414,7 +11414,7 @@ The command options you have used caused atoms to be lost. :dd
 Lost atoms are checked for each time thermo output is done.  See the
 thermo_modify lost command for options.  Lost atoms usually indicate
 bad dynamics, e.g. atoms have been blown far out of the simulation
-box, or moved futher than one processor's sub-domain away before
+box, or moved further than one processor's sub-domain away before
 reneighboring. :dd
 
 {MSM mesh too small, increasing to 2 points in each direction} :dt

doc/src/body.txt

@@ -140,7 +140,7 @@ for more details.
 The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
 values consistent with the current orientation of the rigid body
 around its center of mass.  The values are with respect to the
-simulation box XYZ axes, not with respect to the prinicpal axes of the
+simulation box XYZ axes, not with respect to the principal axes of the
 rigid body itself.  LAMMPS performs the latter calculation internally.
 The coordinates of each sub-particle are specified as its x,y,z
 displacement from the center-of-mass of the body particle.  The
@@ -218,7 +218,7 @@ wish; see the "read_data"_read_data.html command for more details.
 The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
 values consistent with the current orientation of the rigid body
 around its center of mass.  The values are with respect to the
-simulation box XYZ axes, not with respect to the prinicpal axes of the
+simulation box XYZ axes, not with respect to the principal axes of the
 rigid body itself.  LAMMPS performs the latter calculation internally.
 The coordinates of each vertex are specified as its x,y,z displacement
 from the center-of-mass of the body particle.  The center-of-mass

doc/src/compute_temp_asphere.txt

@@ -138,7 +138,7 @@ This compute is part of the ASPHERE package.  It is only enabled if
 LAMMPS was built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
-This compute requires that atoms store angular momementum and a
+This compute requires that atoms store angular momentum and a
 quaternion as defined by the "atom_style ellipsoid"_atom_style.html
 command.
 

doc/src/compute_temp_body.txt

@@ -120,7 +120,7 @@ This compute is part of the BODY package.  It is only enabled if
 LAMMPS was built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
-This compute requires that atoms store angular momementum and a
+This compute requires that atoms store angular momentum and a
 quaternion as defined by the "atom_style body"_atom_style.html
 command.
 

doc/src/dump_image.txt

@@ -638,7 +638,7 @@ pipe:: Input/output error :pre
 which can be safely ignored. Other warnings
 and errors have to be addressed according to the FFmpeg documentation.
 One known issue is that certain movie file formats (e.g. MPEG level 1
-and 2 format streams) have video bandwith limits that can be crossed
+and 2 format streams) have video bandwidth limits that can be crossed
 when rendering too large of image sizes. Typical warnings look like
 this:
 

doc/src/fix_deform.txt

@@ -580,10 +580,10 @@ This fix is not invoked during "energy minimization"_minimize.html.
 [Restrictions:]
 
 You cannot apply x, y, or z deformations to a dimension that is
-shrink-wrapped via the "boundary"_boundary.html comamnd.
+shrink-wrapped via the "boundary"_boundary.html command.
 
 You cannot apply xy, yz, or xz deformations to a 2nd dimension (y in
-xy) that is shrink-wrapped via the "boundary"_boundary.html comamnd.
+xy) that is shrink-wrapped via the "boundary"_boundary.html command.
 
 [Related commands:]
 

doc/src/fix_gle.txt

@@ -62,7 +62,7 @@ as a (Ns+1 x Ns+1) matrix in inverse time units. Matrices that are
 optimal for a given application and the system of choice can be
 obtained from "(GLE4MD)"_#GLE4MD.
 
-Equilibrium sampling a temperature T is obtained by specifiying the
+Equilibrium sampling a temperature T is obtained by specifying the
 target value as the {Tstart} and {Tstop} arguments, so that the diffusion
 matrix that gives canonical sampling for a given A is computed automatically.
 However, the GLE framework also allow for non-equilibrium sampling, that

doc/src/fix_gravity.txt

@@ -76,7 +76,7 @@ specified as an equal-style "variable"_variable.html.  If the value is
 a variable, it should be specified as v_name, where name is the
 variable name.  In this case, the variable will be evaluated each
 timestep, and its value used to determine the quantity.  You should
-insure that the variable calculates a result in the approriate units,
+insure that the variable calculates a result in the appropriate units,
 e.g. force/mass or degrees.
 
 Equal-style variables can specify formulas with various mathematical

doc/src/fix_nph_asphere.txt

@@ -136,7 +136,7 @@ This fix is part of the ASPHERE package.  It is only enabled if LAMMPS
 was built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
-This fix requires that atoms store torque and angular momementum and a
+This fix requires that atoms store torque and angular momentum and a
 quaternion as defined by the "atom_style ellipsoid"_atom_style.html
 command.
 

doc/src/fix_nph_body.txt

@@ -135,7 +135,7 @@ This fix is part of the BODY package.  It is only enabled if LAMMPS
 was built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
-This fix requires that atoms store torque and angular momementum and a
+This fix requires that atoms store torque and angular momentum and a
 quaternion as defined by the "atom_style body"_atom_style.html
 command.
 

doc/src/fix_npt_asphere.txt

@@ -161,7 +161,7 @@ This fix is part of the ASPHERE package.  It is only enabled if LAMMPS
 was built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
-This fix requires that atoms store torque and angular momementum and a
+This fix requires that atoms store torque and angular momentum and a
 quaternion as defined by the "atom_style ellipsoid"_atom_style.html
 command.
 

doc/src/fix_npt_body.txt

@@ -160,7 +160,7 @@ This fix is part of the BODY package.  It is only enabled if LAMMPS
 was built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
-This fix requires that atoms store torque and angular momementum and a
+This fix requires that atoms store torque and angular momentum and a
 quaternion as defined by the "atom_style body"_atom_style.html
 command.
 

doc/src/fix_nve_asphere.txt

@@ -71,7 +71,7 @@ This fix is part of the ASPHERE package.  It is only enabled if LAMMPS
 was built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
-This fix requires that atoms store torque and angular momementum and a
+This fix requires that atoms store torque and angular momentum and a
 quaternion as defined by the "atom_style ellipsoid"_atom_style.html
 command.
 

doc/src/fix_nve_asphere_noforce.txt

@@ -49,7 +49,7 @@ This fix is part of the ASPHERE package.  It is only enabled if LAMMPS
 was built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
-This fix requires that atoms store torque and angular momementum and a
+This fix requires that atoms store torque and angular momentum and a
 quaternion as defined by the "atom_style ellipsoid"_atom_style.html
 command.
 

doc/src/fix_nve_body.txt

@@ -47,7 +47,7 @@ This fix is part of the BODY package.  It is only enabled if LAMMPS
 was built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
-This fix requires that atoms store torque and angular momementum and a
+This fix requires that atoms store torque and angular momentum and a
 quaternion as defined by the "atom_style body"_atom_style.html
 command.
 

doc/src/fix_nve_limit.txt

@@ -48,8 +48,8 @@ unaltered, pressures computed by thermodynamic output will still be
 very large for overlapped configurations.
 
 NOTE: You should not use "fix shake"_fix_shake.html in conjunction
-with this fix.  That is because fix shake applies contraint forces
+with this fix.  That is because fix shake applies constraint forces
-based on the predicted postitions of atoms after the next timestep.
+based on the predicted positions of atoms after the next timestep.
 It has no way of knowing the timestep may change due to this fix,
 which will cause the constraint forces to be invalid.  A better
 strategy is to turn off fix shake when performing initial dynamics

doc/src/fix_nvt_asphere.txt

@@ -137,7 +137,7 @@ This fix is part of the ASPHERE package.  It is only enabled if LAMMPS
 was built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
-This fix requires that atoms store torque and angular momementum and a
+This fix requires that atoms store torque and angular momentum and a
 quaternion as defined by the "atom_style ellipsoid"_atom_style.html
 command.
 

doc/src/fix_nvt_body.txt

@@ -136,7 +136,7 @@ This fix is part of the BODY package.  It is only enabled if LAMMPS
 was built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.
 
-This fix requires that atoms store torque and angular momementum and a
+This fix requires that atoms store torque and angular momentum and a
 quaternion as defined by the "atom_style body"_atom_style.html
 command.
 

doc/src/fix_orient.txt

@@ -31,7 +31,7 @@ The fix applies an orientation-dependent force to atoms near a planar
 grain boundary which can be used to induce grain boundary migration
 (in the direction perpendicular to the grain boundary plane).  The
 motivation and explanation of this force and its application are
-described in "(Janssens)"_#Janssens. The adaptiation to bcc crystals
+described in "(Janssens)"_#Janssens. The adaptation to bcc crystals
 is described in "(Wicaksono1)"_#Wicaksono1. The computed force is only
 applied to atoms in the fix group.
 

doc/src/fix_qeq.txt

@@ -81,7 +81,7 @@ are the same.  Eventually the fix qeq/reax command will be deprecated.
 The QEq method minimizes the electrostatic energy of the system (or
 equalizes the derivative of energy with respect to charge of all the
 atoms) by adjusting the partial charge on individual atoms based on
-interactions with their neighbors within {cutoff}.  It reqires a few
+interactions with their neighbors within {cutoff}.  It requires a few
 parameters, in {metal} units, for each atom type which provided in a
 file specified by {qfile}.  The file has the following format
 
@@ -91,7 +91,7 @@ file specified by {qfile}.  The file has the following format
 Ntype chi eta gamma zeta qcore :pre
 
 There is one line per atom type with the following parameters.
-Only a subset of the parameters is used by each QEq style as descibed
+Only a subset of the parameters is used by each QEq style as described
 below, thus the others can be set to 0.0 if desired.
 
 {chi} = electronegativity in energy units

doc/src/fix_qeq_reax.txt

@@ -40,7 +40,7 @@ charge equilibration performed by fix qeq/reax, see the
 
 The QEq method minimizes the electrostatic energy of the system by
 adjusting the partial charge on individual atoms based on interactions
-with their neighbors.  It reqires some parameters for each atom type.
+with their neighbors.  It requires some parameters for each atom type.
 If the {params} setting above is the word "reax/c", then these are
 extracted from the "pair_style reax/c"_pair_reax_c.html command and
 the ReaxFF force field file it reads in.  If a file name is specified

doc/src/fix_rigid.txt

@@ -129,7 +129,7 @@ number of small rigid bodies.  Each body is assigned to the atom
 closest to the geometrical center of the body.  The fix operates using
 local lists of rigid bodies owned by each processor and information is
 exchanged and summed via local communication between neighboring
-processors when ghost atom info is accumlated.
+processors when ghost atom info is accumulated.
 
 NOTE: To use the {rigid/small} styles the ghost atom cutoff must be
 large enough to span the distance between the atom that owns the body
@@ -262,7 +262,7 @@ and bond interactions within each rigid body, as they no longer
 contribute to the motion.  The "neigh_modify
 exclude"_neigh_modify.html and "delete_bonds"_delete_bonds.html
 commands are used to do this.  If the rigid bodies have strongly
-overalapping atoms, you may need to turn off these interactions to
+overlapping atoms, you may need to turn off these interactions to
 avoid numerical problems due to large equal/opposite intra-body forces
 swamping the contribution of small inter-body forces.
 
@@ -530,7 +530,7 @@ back into the box.
 The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
 values consistent with the current orientation of the rigid body
 around its center of mass.  The values are with respect to the
-simulation box XYZ axes, not with respect to the prinicpal axes of the
+simulation box XYZ axes, not with respect to the principal axes of the
 rigid body itself.  LAMMPS performs the latter calculation internally.
 
 The (vxcm,vycm,vzcm) values are the velocity of the center of mass.
@@ -580,7 +580,7 @@ also accounted for by this fix.
 
 :line
 
-If your simlulation is a hybrid model with a mixture of rigid bodies
+If your simulation is a hybrid model with a mixture of rigid bodies
 and non-rigid particles (e.g. solvent) there are several ways these
 rigid fixes can be used in tandem with "fix nve"_fix_nve.html, "fix
 nvt"_fix_nh.html, "fix npt"_fix_nh.html, and "fix nph"_fix_nh.html.

doc/src/fix_rx.txt

@@ -63,7 +63,7 @@ control on the error. For error control, use the rkf45 ODE solver.
 
 The rkf45 method adjusts the step-size so that the local truncation error is held
 within the specified absolute and relative tolerances. The initial step-size {h0}
-can be specified by the user or estimated internally. It is recommeded that the user
+can be specified by the user or estimated internally. It is recommended that the user
 specify {h0} since this will generally reduced the number of ODE integration steps
 required. {h0} is defined as {dt / min_steps} if min_steps >= 1. If min_steps == 0,
 {h0} is estimated such that an explicit Euler method would likely produce

doc/src/fix_shake.txt

@@ -47,7 +47,7 @@ enables a longer timestep.
 [SHAKE vs RATTLE:]
 
 The SHAKE algorithm was invented for schemes such as standard Verlet
-timesteppnig, where only the coordinates are integrated and the
+timestepping, where only the coordinates are integrated and the
 velocities are approximated as finite differences to the trajectories
 ("Ryckaert et al. (1977)"_#Ryckaert).  If the velocities are
 integrated explicitly, as with velocity Verlet which is what LAMMPS

doc/src/fix_ttm.txt

@@ -300,7 +300,7 @@ See the "Making LAMMPS"_Section_start.html#start_3 section for more
 info.
 
 These fixes can only be used for 3d simulations and orthogonal
-simlulation boxes.  You must also use periodic
+simulation boxes.  You must also use periodic
 "boundary"_boundary.html conditions.
 
 [Related commands:]

doc/src/molecule.txt

@@ -155,7 +155,7 @@ The mass and center-of-mass coordinates (Xc,Yc,Zc) are
 self-explanatory.  The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)
 should be the values consistent with the current orientation of the
 rigid body around its center of mass.  The values are with respect to
-the simulation box XYZ axes, not with respect to the prinicpal axes of
+the simulation box XYZ axes, not with respect to the principal axes of
 the rigid body itself.  LAMMPS performs the latter calculation
 internally.
 

doc/src/region.txt

@@ -285,7 +285,7 @@ region 2 sphere 10.0 10.0 0.0 5 move v_dx NULL NULL :pre
 
 Note that the initial displacemet is 0.0, though that is not required.
 
-Either of these varaibles would "wiggle" the region back and forth in
+Either of these variables would "wiggle" the region back and forth in
 the y direction:
 
 variable dy equal swiggle(0,5,100)