correctly spell "through"

doc/src/Build_link.txt

@@ -78,7 +78,7 @@ description of the Python interface to LAMMPS, which wraps the C-style
 interface.
 
 See the sample codes in examples/COUPLE/simple for examples of C++ and
-C and Fortran codes that invoke LAMMPS thru its library interface.
+C and Fortran codes that invoke LAMMPS through its library interface.
 Other examples in the COUPLE directory use coupling ideas discussed on
 the "Howto couple"_Howto_couple.html doc page.
 

doc/src/Errors_messages.txt

@@ -6917,7 +6917,7 @@ types. :dd
 
 {Invalid use of library file() function} :dt
 
-This function is called thru the library interface.  This
+This function is called through the library interface.  This
 error should not occur.  Contact the developers if it does. :dd
 
 {Invalid value in set command} :dt

doc/src/Howto_client_server.txt

@@ -82,7 +82,7 @@ Monte Carlo client code as the driver.
 
 The lammps_vasp dir shows how to couple LAMMPS as a client code
 running MD timestepping to VASP acting as a server providing quantum
-DFT forces, thru a Python wrapper script on VASP.
+DFT forces, through 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

doc/src/Howto_couple.txt

@@ -50,7 +50,7 @@ In this scenario, the other code can be called as a library, as in
 (1), or it could be a stand-alone code, invoked by a system() call
 made by the command (assuming your parallel machine allows one or more
 processors to start up another program).  In the latter case the
-stand-alone code could communicate with LAMMPS thru files that the
+stand-alone code could communicate with LAMMPS through files that the
 command writes and reads.
 
 See the "Modify command"_Modify_command.html doc page for info on how

doc/src/Howto_library.txt

@@ -87,7 +87,7 @@ commands to LAMMPS to execute, the same as if they were coming from an
 input script.
 
 Via these functions, the calling code can read or generate a series of
-LAMMPS commands one or multiple at a time and pass it thru the library
+LAMMPS commands one or multiple at a time and pass it through the library
 interface to setup a problem and then run it in stages.  The caller
 can interleave the command function calls with operations it performs,
 calls to extract information from or set information within LAMMPS, or

doc/src/Install_windows.txt

@@ -42,7 +42,7 @@ environment manipulations.
 
 Note that to update to a newer version of LAMMPS, you should typically
 uninstall the version you currently have, download a new installer,
-and go thru the install procedure described above.  I.e. the same
+and go through the install procedure described above.  I.e. the same
 procedure for installing/updating most Windows programs.  You can
 install multiple versions of LAMMPS (in different directories), but
 only the executable for the last-installed package will be found

doc/src/Intro_features.txt

@@ -40,7 +40,7 @@ General features :h4,link(general)
   syntax for defining and using variables and formulas
   syntax for looping over runs and breaking out of loops
   run one or multiple simulations simultaneously (in parallel) from one script
-  build as library, invoke LAMMPS thru library interface or provided Python wrapper
+  build as library, invoke LAMMPS through library interface or provided Python wrapper
   couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul
 
 Particle and model types :h4,link(particle)

doc/src/Intro_nonfeatures.txt

@@ -15,7 +15,7 @@ functionality for setting up simulations and analyzing their output.
 
 Specifically, LAMMPS was not conceived and designed for:
 
-being run thru a GUI
+being run through a GUI
 building molecular systems, or building molecular topologies
 assign force-field coefficients automagically
 perform sophisticated analysis of your MD simulation

doc/src/Python_examples.txt

@@ -15,7 +15,7 @@ things that are possible when Python wraps LAMMPS.  If you create your
 own scripts, send them to us and we can include them in the LAMMPS
 distribution.
 
-trivial.py, read/run a LAMMPS input script thru Python,
+trivial.py, read/run a LAMMPS input script through Python,
 demo.py, invoke various LAMMPS library interface routines,
 simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp,
 split.py, same as simple.py but running in parallel on a subset of procs,

doc/src/Python_run.txt

@@ -31,7 +31,7 @@ language is, and that it can be run interactively, enabling rapid
 development and debugging.  If you use it to mostly invoke costly
 operations within LAMMPS, such as running a simulation for a
 reasonable number of timesteps, then the overhead cost of invoking
-LAMMPS thru Python will be negligible.
+LAMMPS through Python will be negligible.
 
 The Python wrapper for LAMMPS uses the "ctypes" package in Python,
 which auto-generates the interface code needed between Python and a

doc/src/Python_test.txt

@@ -32,7 +32,7 @@ first importing from the lammps.py file:
 >>> from ctypes import CDLL
 >>> CDLL("liblammps.so") :pre
 
-If an error occurs, carefully go thru the steps on the
+If an error occurs, carefully go through the steps on the
 "Build_basics"_Build_basics.html doc page about building a shared
 library and the "Python_install"_Python_install.html doc page about
 insuring Python can find the necessary two files it needs.

doc/src/compute_angmom_chunk.txt

@@ -37,7 +37,7 @@ they can be used to measure properties of a system.
 This compute calculates the 3 components of the angular momentum
 vector for each chunk, due to the velocity/momentum of the individual
 atoms in the chunk around the center-of-mass of the chunk.  The
-calculation includes all effects due to atoms passing thru periodic
+calculation includes all effects due to atoms passing through periodic
 boundaries.
 
 Note that only atoms in the specified group contribute to the

doc/src/compute_com.txt

@@ -22,7 +22,7 @@ compute 1 all com :pre
 [Description:]
 
 Define a computation that calculates the center-of-mass of the group
-of atoms, including all effects due to atoms passing thru periodic
+of atoms, including all effects due to atoms passing through periodic
 boundaries.
 
 A vector of three quantities is calculated by this compute, which

doc/src/compute_com_chunk.txt

@@ -35,7 +35,7 @@ doc pages for details of how chunks can be defined and examples of how
 they can be used to measure properties of a system.
 
 This compute calculates the x,y,z coordinates of the center-of-mass
-for each chunk, which includes all effects due to atoms passing thru
+for each chunk, which includes all effects due to atoms passing through
 periodic boundaries.
 
 Note that only atoms in the specified group contribute to the

doc/src/compute_dipole_chunk.txt

@@ -38,7 +38,7 @@ they can be used to measure properties of a system.
 
 This compute calculates the x,y,z coordinates of the dipole vector
 and the total dipole moment for each chunk, which includes all effects
-due to atoms passing thru periodic boundaries. For chunks with a net
+due to atoms passing through periodic boundaries. For chunks with a net
 charge the resulting dipole is made position independent by subtracting
 the position vector of the center of mass or geometric center times the
 net charge from the computed dipole vector.

doc/src/compute_displace_atom.txt

@@ -29,7 +29,7 @@ compute 1 all displace/atom refresh myVar :pre
 
 Define a computation that calculates the current displacement of each
 atom in the group from its original (reference) coordinates, including
-all effects due to atoms passing thru periodic boundaries.
+all effects due to atoms passing through periodic boundaries.
 
 A vector of four quantities per atom is calculated by this compute.
 The first 3 elements of the vector are the dx,dy,dz displacements.

doc/src/compute_gyration.txt

@@ -22,7 +22,7 @@ compute 1 molecule gyration :pre
 [Description:]
 
 Define a computation that calculates the radius of gyration Rg of the
-group of atoms, including all effects due to atoms passing thru
+group of atoms, including all effects due to atoms passing through
 periodic boundaries.
 
 Rg is a measure of the size of the group of atoms, and is computed as

doc/src/compute_gyration_chunk.txt

@@ -40,7 +40,7 @@ doc pages for details of how chunks can be defined and examples of how
 they can be used to measure properties of a system.
 
 This compute calculates the radius of gyration Rg for each chunk,
-which includes all effects due to atoms passing thru periodic
+which includes all effects due to atoms passing through periodic
 boundaries.
 
 Rg is a measure of the size of a chunk, and is computed by this

doc/src/compute_inertia_chunk.txt

@@ -36,7 +36,7 @@ they can be used to measure properties of a system.
 
 This compute calculates the 6 components of the symmetric inertia
 tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz.  The
-calculation includes all effects due to atoms passing thru periodic
+calculation includes all effects due to atoms passing through periodic
 boundaries.
 
 Note that only atoms in the specified group contribute to the

doc/src/compute_msd.txt

@@ -29,7 +29,7 @@ compute 1 upper msd com yes average yes :pre
 
 Define a computation that calculates the mean-squared displacement
 (MSD) of the group of atoms, including all effects due to atoms
-passing thru periodic boundaries.  For computation of the non-Gaussian
+passing through periodic boundaries.  For computation of the non-Gaussian
 parameter of mean-squared displacement, see the "compute
 msd/nongauss"_compute_msd_nongauss.html command.
 

doc/src/compute_msd_chunk.txt

@@ -38,7 +38,7 @@ Four quantities are calculated by this compute for each chunk.  The
 first 3 quantities are the squared dx,dy,dz displacements of the
 center-of-mass.  The 4th component is the total squared displacement,
 i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass.  These
-calculations include all effects due to atoms passing thru periodic
+calculations include all effects due to atoms passing through periodic
 boundaries.
 
 Note that only atoms in the specified group contribute to the

doc/src/compute_msd_nongauss.txt

@@ -28,7 +28,7 @@ compute 1 upper msd/nongauss com yes :pre
 
 Define a computation that calculates the mean-squared displacement
 (MSD) and non-Gaussian parameter (NGP) of the group of atoms,
-including all effects due to atoms passing thru periodic boundaries.
+including all effects due to atoms passing through periodic boundaries.
 
 A vector of three quantities is calculated by this compute.  The first
 element of the vector is the total squared dx,dy,dz displacements

doc/src/compute_omega_chunk.txt

@@ -38,7 +38,7 @@ This compute calculates the 3 components of the angular velocity
 vector for each chunk, via the formula L = Iw where L is the angular
 momentum vector of the chunk, I is its moment of inertia tensor, and w
 is omega = angular velocity of the chunk.  The calculation includes
-all effects due to atoms passing thru periodic boundaries.
+all effects due to atoms passing through periodic boundaries.
 
 Note that only atoms in the specified group contribute to the
 calculation.  The "compute chunk/atom"_compute_chunk_atom.html command

doc/src/compute_rigid_local.txt

@@ -107,7 +107,7 @@ 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 body.  Unwrapped means that if the body
-COM has passed thru a periodic boundary one or more times, the value
+COM has passed through 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_torque_chunk.txt

@@ -37,7 +37,7 @@ they can be used to measure properties of a system.
 This compute calculates the 3 components of the torque vector for eqch
 chunk, due to the forces on the individual atoms in the chunk around
 the center-of-mass of the chunk.  The calculation includes all effects
-due to atoms passing thru periodic boundaries.
+due to atoms passing through periodic boundaries.
 
 Note that only atoms in the specified group contribute to the
 calculation.  The "compute chunk/atom"_compute_chunk_atom.html command

doc/src/displace_atoms.txt

@@ -83,7 +83,7 @@ used in such a way that the displacement of a particular atom is the
 same, regardless of how many processors are being used.
 
 The {rotate} style rotates each atom in the group by the angle {theta}
-around a rotation axis {R} = (Rx,Ry,Rz) that goes thru a point {P} =
+around a rotation axis {R} = (Rx,Ry,Rz) that goes through a point {P} =
 (Px,Py,Pz).  The direction of rotation for the atoms around the
 rotation axis is consistent with the right-hand rule: if your
 right-hand thumb points along {R}, then your fingers wrap around the

doc/src/dump.txt

@@ -312,7 +312,7 @@ so that any machine which supports XDR should be able to read them.
 The number of atoms per snapshot cannot change with the {xtc} style.
 The {unwrap} option of the "dump_modify"_dump_modify.html command allows
 XTC coordinates to be written "unwrapped" by the image flags for each
-atom.  Unwrapped means that if the atom has passed thru a periodic
+atom.  Unwrapped means that if the atom has passed through a periodic
 boundary one or more times, the value is printed for what the
 coordinate would be if it had not been wrapped back into the periodic
 box.  Note that these coordinates may thus be far outside the box size
@@ -534,7 +534,7 @@ on the "Howto triclinic"_Howto_triclinic.html doc page.
 
 Use {xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the
 image flags for each atom.  Unwrapped means that if the atom has
-passed thru a periodic boundary one or more times, the value is
+passed through a periodic boundary one or more times, the value is
 printed for what the coordinate would be if it had not been wrapped
 back into the periodic box.  Note that using {xu}, {yu}, {zu} means
 that the coordinate values may be far outside the box bounds printed

doc/src/dump_modify.txt

@@ -344,7 +344,7 @@ The {image} keyword applies only to the dump {atom} style.  If the
 image value is {yes}, 3 flags are appended to each atom's coords which
 are the absolute box image of the atom in each dimension.  For
 example, an x image flag of -2 with a normalized coord of 0.5 means
-the atom is in the center of the box, but has passed thru the box
+the atom is in the center of the box, but has passed through the box
 boundary 2 times and is really 2 box lengths to the left of its
 current coordinate.  Note that for dump style {custom} these various
 values can be printed in the dump file by using the appropriate atom
@@ -622,7 +622,7 @@ threshold criterion is met.  Otherwise it is not met.
 
 The {unwrap} keyword only applies to the dump {dcd} and {xtc} styles.
 If set to {yes}, coordinates will be written "unwrapped" by the image
-flags for each atom.  Unwrapped means that if the atom has passed thru
+flags for each atom.  Unwrapped means that if the atom has passed through
 a periodic boundary one or more times, the value is printed for what
 the coordinate would be if it had not been wrapped back into the
 periodic box.  Note that these coordinates may thus be far outside the

doc/src/fix_ave_histo.txt

@@ -241,7 +241,7 @@ first bin and values > {hi} are counted in the last bin.  If {beyond}
 is set to {extend} then two extra bins are created, so that there are
 Nbins+2 total bins.  Values < {lo} are counted in the first bin and
 values > {hi} are counted in the last bin (Nbins+1).  Values between
-{lo} and {hi} (inclusive) are counted in bins 2 thru Nbins+1.  The
+{lo} and {hi} (inclusive) are counted in bins 2 through Nbins+1.  The
 "coordinate" stored and printed for these two extra bins is {lo} and
 {hi}.
 

doc/src/fix_meso_move.txt

@@ -56,7 +56,7 @@ by other fixes (e.g. "fix meso"_fix_meso.html, "fix
 meso/stationary"_fix_meso_stationary.html), since that will change their
 positions and velocities twice.
 
-NOTE: As particles move due to this fix, they will pass thru periodic
+NOTE: As particles move due to this fix, they will pass through periodic
 boundaries and be remapped to the other side of the simulation box,
 just as they would during normal time integration (e.g. via the "fix
 meso"_fix_meso.html command).  It is up to you to decide whether periodic
@@ -126,7 +126,7 @@ variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
 fix 1 boundary move variable v_x NULL NULL v_v NULL NULL :pre
 
 The {rotate} style rotates particles around a rotation axis {R} =
-(Rx,Ry,Rz) that goes thru a point {P} = (Px,Py,Pz).  The {period} of
+(Rx,Ry,Rz) that goes through a point {P} = (Px,Py,Pz).  The {period} of
 the rotation is also specified.  The direction of rotation for the
 particles around the rotation axis is consistent with the right-hand
 rule: if your right-hand thumb points along {R}, then your fingers wrap

doc/src/fix_move.txt

@@ -51,7 +51,7 @@ integrated by other fixes (e.g. "fix nve"_fix_nve.html, "fix
 nvt"_fix_nh.html), since that will change their positions and
 velocities twice.
 
-NOTE: As atoms move due to this fix, they will pass thru periodic
+NOTE: As atoms move due to this fix, they will pass through periodic
 boundaries and be remapped to the other side of the simulation box,
 just as they would during normal time integration (e.g. via the "fix
 nve"_fix_nve.html command).  It is up to you to decide whether
@@ -121,7 +121,7 @@ variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
 fix 1 boundary move variable v_x NULL NULL v_v NULL NULL :pre
 
 The {rotate} style rotates atoms around a rotation axis {R} =
-(Rx,Ry,Rz) that goes thru a point {P} = (Px,Py,Pz).  The {period} of
+(Rx,Ry,Rz) that goes through a point {P} = (Px,Py,Pz).  The {period} of
 the rotation is also specified.  The direction of rotation for the
 atoms around the rotation axis is consistent with the right-hand rule:
 if your right-hand thumb points along {R}, then your fingers wrap

doc/src/fix_srd.txt

@@ -117,7 +117,7 @@ Lamda cannot be smaller than 0.6 * hgrid, else an error is generated
 SRD particles are bounded by Vmax, which is set so that an SRD
 particle will not advect further than Dmax = 4*lamda in dt_SRD.  This
 means that roughly speaking, Dmax should not be larger than a big
-particle diameter, else SRDs may pass thru big particles without
+particle diameter, else SRDs may pass through big particles without
 colliding.  A warning is generated if this is the case.
 
 Collisions between SRD particles and big particles or walls are

doc/src/fix_wall_reflect.txt

@@ -41,7 +41,7 @@ fix top all wall/reflect zhi v_pressdown :pre
 [Description:]
 
 Bound the simulation with one or more walls which reflect particles
-in the specified group when they attempt to move thru them.
+in the specified group when they attempt to move through them.
 
 Reflection means that if an atom moves outside the wall on a timestep
 by a distance delta (e.g. due to "fix nve"_fix_nve.html), then it is

doc/src/if.txt

@@ -107,7 +107,7 @@ print "ALL DONE" :pre
 
 Here is an example of a double loop which uses the if and
 "jump"_jump.html commands to break out of the inner loop when a
-condition is met, then continues iterating thru the outer loop.
+condition is met, then continues iterating through the outer loop.
 
 label       loopa
 variable    a loop 5

doc/src/jump.txt

@@ -100,7 +100,7 @@ print "ALL DONE" :pre
 
 Here is an example of a double loop which uses the if and
 "jump"_jump.html commands to break out of the inner loop when a
-condition is met, then continues iterating thru the outer loop.
+condition is met, then continues iterating through the outer loop.
 
 label       loopa
 variable    a loop 5

doc/src/minimize.txt

@@ -82,12 +82,12 @@ coordinates:
 
 where the first term is the sum of all non-bonded "pairwise
 interactions"_pair_style.html including "long-range Coulombic
-interactions"_kspace_style.html, the 2nd thru 5th terms are
+interactions"_kspace_style.html, the 2nd through 5th terms are
 "bond"_bond_style.html, "angle"_angle_style.html,
 "dihedral"_dihedral_style.html, and "improper"_improper_style.html
 interactions respectively, and the last term is energy due to
 "fixes"_fix.html which can act as constraints or apply force to atoms,
-such as thru interaction with a wall.  See the discussion below about
+such as through interaction with a wall.  See the discussion below about
 how fix commands affect minimization.
 
 The starting point for the minimization is the current configuration

doc/src/next.txt

@@ -79,7 +79,7 @@ and after such a LAMMPS run.
 Here is an example of running a series of simulations using the next
 command with an {index}-style variable.  If this input script is named
 in.polymer, 8 simulations would be run using data files from
-directories run1 thru run8.
+directories run1 through run8.
 
 variable d index run1 run2 run3 run4 run5 run6 run7 run8
 shell cd $d
@@ -114,7 +114,7 @@ jump in.script :pre
 
 Here is an example of a double loop which uses the "if"_if.html and
 "jump"_jump.html commands to break out of the inner loop when a
-condition is met, then continues iterating thru the outer loop.
+condition is met, then continues iterating through the outer loop.
 
 label       loopa
 variable    a loop 5

doc/src/region.txt

@@ -298,7 +298,7 @@ variable dysame equal 5*sin(2*PI*elaplong*dt/100)
 region 2 sphere 10.0 10.0 0.0 5 move NULL v_dy NULL :pre
 
 The {rotate} keyword rotates the region around a rotation axis {R} =
-(Rx,Ry,Rz) that goes thru a point {P} = (Px,Py,Pz).  The rotation
+(Rx,Ry,Rz) that goes through a point {P} = (Px,Py,Pz).  The rotation
 angle is calculated, presumably as a function of time, by a variable
 specified as v_theta, where theta is the variable name.  The variable
 should generate its result in radians.  The direction of rotation for