correct repeated words in docs

doc/src/Examples.txt

@@ -11,7 +11,7 @@ Section"_Tools.html :c
 Example scripts :h3
 
 The LAMMPS distribution includes an examples sub-directory with many
-sample problems.  Many are 2d models that run quickly are are
+sample problems.  Many are 2d models that run quickly and are
 straightforward to visualize, requiring at most a couple of minutes to
 run on a desktop machine.  Each problem has an input script (in.*) and
 produces a log file (log.*) when it runs.  Some use a data file

doc/src/Howto_drude2.txt

@@ -274,7 +274,7 @@ crash. Even without reaching this extreme case, the correlation
 between nearby dipoles on the same molecule may be exaggerated.  Often,
 special bond relations prevent bonded neighboring atoms to see the
 charge of each other's DP, so that the problem does not always appear.
-It is possible to use screened dipole dipole interactions by using the
+It is possible to use screened dipole-dipole interactions by using the
 "{pair_style thole}"_pair_thole.html.  This is implemented as a
 correction to the Coulomb pair_styles, which dampens at short distance
 the interactions between the charges representing the induced dipoles.

doc/src/Install_git.txt

@@ -52,7 +52,7 @@ as if you unpacked a current LAMMPS tarball, with the exception, that
 the HTML documentation files are not included.  They can be fetched
 from the LAMMPS website by typing "make fetch" in the doc directory.
 Or they can be generated from the content provided in doc/src by
-typing "make html" from the the doc directory.
+typing "make html" from the doc directory.
 
 After initial cloning, as bug fixes and new features are added to
 LAMMPS, as listed on "this page"_Errors_bugs.html, you can stay

doc/src/Install_svn.txt

@@ -40,7 +40,7 @@ as if you unpacked a current LAMMPS tarball, with the exception, that
 the HTML documentation files are not included.  They can be fetched
 from the LAMMPS website by typing "make fetch" in the doc directory.
 Or they can be generated from the content provided in doc/src by
-typing "make html" from the the doc directory.
+typing "make html" from the doc directory.
 
 After initial checkout, as bug fixes and new features are added to
 LAMMPS, as listed on "this page"_Errors_bugs.html, you can stay

doc/src/Packages_details.txt

@@ -706,7 +706,7 @@ PERI package :link(PKG-PERI),h4
 
 An atom style, several pair styles which implement different
 Peridynamics materials models, and several computes which calculate
-diagnostics.  Peridynamics is a a particle-based meshless continuum
+diagnostics.  Peridynamics is a particle-based meshless continuum
 model.
 
 [Authors:] The original package was created by Mike Parks (Sandia).
@@ -1229,7 +1229,7 @@ isothermal, isoenergetic, isobaric and isenthalpic conditions are
 included.  These enable long timesteps via the Shardlow splitting
 algorithm.
 
-[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and and John
+[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and John
 Brennan (ARL).
 
 [Supporting info:]
@@ -1537,7 +1537,7 @@ USER-MESO package :link(PKG-USER-MESO),h4
 
 [Contents:]
 
-Several extensions of the the dissipative particle dynamics (DPD)
+Several extensions of the dissipative particle dynamics (DPD)
 method.  Specifically, energy-conserving DPD (eDPD) that can model
 non-isothermal processes, many-body DPD (mDPD) for simulating
 vapor-liquid coexistence, and transport DPD (tDPD) for modeling

doc/src/Python_library.txt

@@ -180,7 +180,7 @@ doubles is returned, one value per atom, which you can use via normal
 Python subscripting. The values will be zero for atoms not in the
 specified group.
 
-The get_thermo() method returns returns the current value of a thermo
+The get_thermo() method returns the current value of a thermo
 keyword as a float.
 
 The get_natoms() method returns the total number of atoms in the

doc/src/Run_options.txt

@@ -242,7 +242,7 @@ processors.
 
 Running with multiple partitions can be useful for running
 "multi-replica simulations"_Howto_replica.html, where each replica
-runs on on one or a few processors.  Note that with MPI installed on a
+runs on one or a few processors.  Note that with MPI installed on a
 machine (e.g. your desktop), you can run on more (virtual) processors
 than you have physical processors.
 

doc/src/Run_output.txt

@@ -93,7 +93,7 @@ monitor thread utilization and load balance is provided. A new {Thread
 timings} section is also added, which lists the time spent in reducing
 the per-thread data elements to the storage for non-threaded
 computation. These thread timings are measured for the first MPI rank
-only and and thus, because the breakdown for MPI tasks can change from
+only and thus, because the breakdown for MPI tasks can change from
 MPI rank to MPI rank, this breakdown can be very different for
 individual ranks. Here is an example output for this section:
 

doc/src/compute_chunk_atom.txt

@@ -468,7 +468,7 @@ property/chunk"_compute_property_chunk.html command.
 NOTE: The compression operation requires global communication across
 all processors to share their chunk ID values.  It can require large
 memory on every processor to store them, even after they are
-compressed, if there are are a large number of unique chunk IDs with
+compressed, if there are a large number of unique chunk IDs with
 atoms assigned to them.  It uses a STL map to find unique chunk IDs
 and store them in sorted order.  Each time an atom is assigned a
 compressed chunk ID, it must access the STL map.  All of this means

doc/src/compute_chunk_spread_atom.txt

@@ -49,7 +49,7 @@ For inputs that are computes, they must be a compute that calculates
 per-chunk values.  These are computes whose style names end in
 "/chunk".
 
-For inputs that are fixes, they should be a a fix that calculates
+For inputs that are fixes, they should be a fix that calculates
 per-chunk values.  For example, "fix ave/chunk"_fix_ave_chunk.html or
 "fix ave/time"_fix_ave_time.html (assuming it is time-averaging
 per-chunk data).

doc/src/compute_voronoi_atom.txt

@@ -96,7 +96,7 @@ group. The argument {maxedge} of the this keyword is the largest number
 of edges on a single Voronoi cell face expected to occur in the
 sample. This keyword adds the generation of a global vector with
 {maxedge}+1 entries. The last entry in the vector contains the number of
-faces with with more than {maxedge} edges. Since the polygon with the
+faces with more than {maxedge} edges. Since the polygon with the
 smallest amount of edges is a triangle, entries 1 and 2 of the vector
 will always be zero.
 

doc/src/dihedral_spherical.txt

@@ -47,7 +47,7 @@ division by sin(74.4)*sin(48.1) (the minima positions for theta1 and theta2).
 
 The following coefficients must be defined for each dihedral type via the
 "dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
-the Dihedral Coeffs section of a data file file read by the
+the Dihedral Coeffs section of a data file read by the
 "read_data"_read_data.html command:
 
 n (integer >= 1)

doc/src/dihedral_table_cut.txt

@@ -174,7 +174,7 @@ radians instead of degrees.  (Note: This changes the way the forces
 are scaled in the 4th column of the data file.)
 
 The optional "CHECKU" keyword is followed by a filename.  This allows
-the user to save all of the the {Ntable} different entries in the
+the user to save all of the {Ntable} different entries in the
 interpolated energy table to a file to make sure that the interpolated
 function agrees with the user's expectations.  (Note: You can
 temporarily increase the {Ntable} parameter to a high value for this

doc/src/dump.txt

@@ -21,7 +21,7 @@ dump ID group-ID style N file args :pre
 
 ID = user-assigned name for the dump :ulb,l
 group-ID = ID of the group of atoms to be dumped :l
-style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or or {local} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
+style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or {local} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
 N = dump every this many timesteps :l
 file = name of file to write dump info to :l
 args = list of arguments for a particular style :l
@@ -196,7 +196,7 @@ For post-processing purposes the {atom}, {local}, and {custom} text
 files are self-describing in the following sense.
 
 The dimensions of the simulation box are included in each snapshot.
-For an orthogonal simulation box this information is is formatted as:
+For an orthogonal simulation box this information is formatted as:
 
 ITEM: BOX BOUNDS xx yy zz
 xlo xhi
@@ -619,7 +619,7 @@ should be replaced by the actual name of the variable that has been
 defined previously in the input script.  Only an atom-style variable
 can be referenced, since it is the only style that generates per-atom
 values.  Variables of style {atom} can reference individual atom
-attributes, per-atom atom attributes, thermodynamic keywords, or
+attributes, per-atom attributes, thermodynamic keywords, or
 invoke other computes, fixes, or variables when they are evaluated, so
 this is a very general means of creating quantities to output to a
 dump file.

doc/src/dump_modify.txt

@@ -310,7 +310,7 @@ NOTE: Atom and molecule IDs are stored internally as 4-byte or 8-byte
 signed integers, depending on how LAMMPS was compiled.  When
 specifying the {format int} option you can use a "%d"-style format
 identifier in the format string and LAMMPS will convert this to the
-corresponding 8-byte form it it is needed when outputting those
+corresponding 8-byte form if it is needed when outputting those
 values.  However, when specifying the {line} option or {format M
 string} option for those values, you should specify a format string
 appropriate for an 8-byte signed integer, e.g. one with "%ld", if

doc/src/fix_ave_chunk.txt

@@ -361,7 +361,7 @@ computes that calculate a temperature to see which ones implement a
 bias.
 
 The {adof} and {cdof} keywords define the values used in the degree of
-freedom (DOF) formula described above for for temperature calculation
+freedom (DOF) formula described above for temperature calculation
 for each chunk.  They are only used when the {temp} value is
 calculated.  They can be used to calculate a more appropriate
 temperature for some kinds of chunks.  Here are 3 examples:

doc/src/fix_halt.txt

@@ -113,12 +113,11 @@ state of the system, e.g. via a "write_dump"_write_dump.html or
 "write_restart"_write_restart.html command.
 
 If its value is {continue}, the behavior is the same as for {soft},
-except subsequent subsequent "run"_run.html or
-"minimize"_minimize.html commands are executed.  This allows your
-script to remedy the condition that triggered the halt, if necessary.
-Note that you may wish use the "unfix"_unfix.html command on the fix
-halt ID, so that the same condition is not immediately triggered in a
-subsequent run.
+except subsequent "run"_run.html or "minimize"_minimize.html commands
+are executed.  This allows your script to remedy the condition that
+triggered the halt, if necessary.  Note that you may wish use the
+"unfix"_unfix.html command on the fix halt ID, so that the same
+condition is not immediately triggered in a subsequent run.
 
 The optional {message} keyword determines whether a message is printed
 to the screen and logfile when the halt condition is triggered.  If

doc/src/fix_hyper_global.txt

@@ -188,7 +188,7 @@ No information about this fix is written to "binary restart
 files"_restart.html.
 
 The "fix_modify"_fix_modify.html {energy} option is supported by this
-fix to add the energy of the bias potential to the the system's
+fix to add the energy of the bias potential to the system's
 potential energy as part of "thermodynamic output"_thermo_style.html.
 
 This fix computes a global scalar and global vector of length 12, which

doc/src/fix_hyper_local.txt

@@ -301,7 +301,7 @@ No information about this fix is written to "binary restart
 files"_restart.html.
 
 The "fix_modify"_fix_modify.html {energy} option is supported by this
-fix to add the energy of the bias potential to the the system's
+fix to add the energy of the bias potential to the system's
 potential energy as part of "thermodynamic output"_thermo_style.html.
 
 This fix computes a global scalar and global vector of length 21,

doc/src/lattice.txt

@@ -124,7 +124,7 @@ so that they describe a tilted parallelepiped.  Via the {basis}
 keyword you add atoms, one at a time, to the unit cell.  Its arguments
 are fractional coordinates (0.0 <= x,y,z < 1.0).  The position vector
 x of a basis atom within the unit cell is thus a linear combination of
-the the unit cell's 3 edge vectors, i.e. x = bx a1 + by a2 + bz a3,
+the unit cell's 3 edge vectors, i.e. x = bx a1 + by a2 + bz a3,
 where bx,by,bz are the 3 values specified for the {basis} keyword.
 
 :line

doc/src/molecule.txt

@@ -396,7 +396,7 @@ If flag = 0, no a,b,c,d values are listed on the line, just the
 If flag = 1, a,b,c are listed, where a = ID of central atom in the
 angle, and b,c the other two atoms in the angle.
 
-If flag = 2, a,b are listed, where a = ID of atom in bond with the the
+If flag = 2, a,b are listed, where a = ID of atom in bond with the
 lowest ID, and b = ID of atom in bond with the highest ID.
 
 If flag = 3, a,b,c are listed, where a = ID of central atom,

doc/src/neigh_modify.txt

@@ -187,9 +187,9 @@ used in neighbor list construction to sort and find neighboring atoms.
 By default, for "neighbor style bin"_neighbor.html, LAMMPS uses bins
 that are 1/2 the size of the maximum pair cutoff.  For "neighbor style
 multi"_neighbor.html, the bins are 1/2 the size of the minimum pair
-cutoff.  Typically these are good values values for minimizing the
-time for neighbor list construction.  This setting overrides the
-default.  If you make it too big, there is little overhead due to
+cutoff.  Typically these are good values for minimizing thetime for
+neighbor list construction.  This setting overrides the default.
+If you make it too big, there is little overhead due to
 looping over bins, but more atoms are checked.  If you make it too
 small, the optimal number of atoms is checked, but bin overhead goes
 up.  If you set the binsize to 0.0, LAMMPS will use the default

doc/src/neighbor.txt

@@ -56,7 +56,7 @@ bin size is set to 1/2 of the shortest cutoff distance and multiple
 sets of bins are defined to search over for different atom types.
 This imposes some extra setup overhead, but the searches themselves
 may be much faster for the short-cutoff cases.  See the "comm_modify
-mode multi"_comm_modify.html command for a communication option option
+mode multi"_comm_modify.html command for a communication option
 that may also be beneficial for simulations of this kind.
 
 The "neigh_modify"_neigh_modify.html command has additional options

doc/src/package.txt

@@ -622,7 +622,7 @@ except "omp" and "mode", are ignored if LAMMPS was not built with Xeon
 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
+script or via the "-pk intel" "command-line
 switch"_Run_options.html.
 
 For the KOKKOS package, the option defaults for GPUs are neigh = full, 

doc/src/pair_fep_soft.txt

@@ -201,7 +201,7 @@ model. The usage of the TIP4P pair style is documented in the
 "pair_lj"_pair_lj.html styles. In the soft version the parameters n, alpha_LJ
 and alpha_C are set in the "pair_style"_pair_style.html command, after the
 specific parameters of the TIP4P water model and before the cutoffs. The
-activation parameter lambda is supplied as an argument of the the
+activation parameter lambda is supplied as an argument of the
 "pair_coeff"_pair_coeff.html command, after epsilon and sigma and before the
 optional cutoffs.
 
@@ -210,7 +210,7 @@ Style {lj/charmm/coul/long/soft} implements a soft-core version of the modified
 "pair_lj_charmm"_pair_charmm.html style. In the soft version the parameters n,
 alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html command, before
 the global cutoffs. The activation parameter lambda is introduced as an argument
-of the the "pair_coeff"_pair_coeff.html command, after epsilon and sigma and
+of the "pair_coeff"_pair_coeff.html command, after epsilon and sigma and
 before the optional eps14 and sigma14.
 
 Style {lj/class2/soft} implements a soft-core version of the 9-6 potential in

doc/src/pair_lj_long.txt

@@ -91,7 +91,7 @@ is to enable LAMMPS to "find" the 2 H atoms associated with each O
 atom.  For example, if the atom ID of an O atom in a TIP4P water
 molecule is 500, then its 2 H atoms must have IDs 501 and 502.
 
-See the the "Howto tip4p"_Howto_tip4p.html doc page for more
+See the "Howto tip4p"_Howto_tip4p.html doc page for more
 information on how to use the TIP4P pair style.  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

doc/src/pair_vashishta.txt

@@ -63,7 +63,7 @@ equally spaced in R^2 space from cutinner^2 to cutoff^2.  For the
 two-body term in the above equation, a linear interpolation for each
 pairwise distance between adjacent points in the table.  In practice
 the tabulated version can run 3-5x faster than the analytic version
-with with moderate to little loss of accuracy for Ntable values
+with moderate to little loss of accuracy for Ntable values
 between 10000 and 1000000. It is not recommended to use less than
 5000 tabulation points.
 

doc/src/python.txt

@@ -480,7 +480,7 @@ information on those settings.
 If you use Python code which calls back to LAMMPS, via the SELF input
 argument explained above, there is an extra step required when
 building LAMMPS.  LAMMPS must also be built as a shared library and
-your Python function must be able to to load the Python module in
+your Python function must be able to load the Python module in
 python/lammps.py that wraps the LAMMPS library interface.  These are
 the same steps required to use Python by itself to wrap LAMMPS.
 Details on these steps are explained on the "Python"_Python_head.html

doc/src/read_data.txt

@@ -701,7 +701,7 @@ of 0 means the atom is still inside the box when unwrapped.  A value
 of 2 means add 2 box lengths to get the unwrapped coordinate.  A value
 of -1 means subtract 1 box length to get the unwrapped coordinate.
 LAMMPS updates these flags as atoms cross periodic boundaries during
-the simulation.  The "dump"_dump.html command can output atom atom
+the simulation.  The "dump"_dump.html command can output atom
 coordinates in wrapped or unwrapped form, as well as the 3 image
 flags.
 

doc/src/server_md.txt

@@ -65,7 +65,7 @@ in this pseudo code is a pointer to an instance of the CSlib.
 See the src/MESSAGE/server_md.cpp and src/MESSAGE/fix_client_md.cpp
 files for details on how LAMMPS uses these messages.  See the
 examples/COUPLE/lammps_vasp/vasp_wrapper.py file for an example of how
-a quantum code (VASP) can use use these messages.
+a quantum code (VASP) can use these messages.
 
 The following pseudo-code uses these values, defined as enums.
 

doc/src/tad.txt

@@ -62,7 +62,7 @@ results at a specified lower temperature.  A good overview of
 accelerated dynamics methods for such systems is given in "this review
 paper"_#Voter2002 from the same group. In general, these methods assume
 that the long-time dynamics is dominated by infrequent events i.e. the
-system is is confined to low energy basins for long periods,
+system is confined to low energy basins for long periods,
 punctuated by brief, randomly-occurring transitions to adjacent
 basins.  TAD is suitable for infrequent-event systems, where in
 addition, the transition kinetics are well-approximated by harmonic

doc/src/variable.txt

@@ -293,7 +293,7 @@ list of runs (e.g. 1000) without having to list N strings in the input
 script.
 
 For the {string} style, a single string is assigned to the variable.
-Two differences between this this and using the {index} style exist:
+Two differences between this style and using the {index} style exist:
 a variable with {string} style can be redefined, e.g. by another command later
 in the input script, or if the script is read again in a loop. The other
 difference is that {string} performs variable substitution even if the
@@ -359,7 +359,7 @@ 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
-the count N of per-atom lines to immediately follow.  N can be be the
+the count N of per-atom lines to immediately follow.  N can be the
 total number of atoms in the system, or only a subset.  The next N
 lines have the following format
 
@@ -931,7 +931,7 @@ with ID = 243.  Or they can take a variable name, specified as v_name,
 where name is the name of the variable, like x\[v_myIndex\].  The
 variable can be of any style except {vector} or {atom} or {atomfile}
 variables.  The variable is evaluated and the result is expected to be
-numeric and is cast to an integer (i.e. 3.4 becomes 3), to use an an
+numeric and is cast to an integer (i.e. 3.4 becomes 3), to use an
 index, which must be a value from 1 to N.  Note that a "formula"
 cannot be used as the argument between the brackets, e.g. x\[243+10\]
 or x\[v_myIndex+1\] are not allowed.  To do this a single variable can

doc/src/velocity.txt

@@ -157,7 +157,7 @@ is issued.
 The {bias} keyword with a {yes} setting is used by {create} and
 {scale}, but only if the {temp} keyword is also used to specify a
 "compute"_compute.html that calculates temperature in a desired way.
-If the temperature compute also calculates a velocity bias, the the
+If the temperature compute also calculates a velocity bias, the
 bias is subtracted from atom velocities before the {create} and
 {scale} operations are performed.  After the operations, the bias is
 added back to the atom velocities.  See the "Howto

doc/src/write_data.txt

@@ -106,7 +106,7 @@ written for all I,J pairs where I <= J.  These coefficients will
 include any specific settings made in the input script up to that
 point.  The presence of these I != J coefficients in the data file
 will effectively turn off the default mixing rule for the pair style.
-Again, the coefficient values in the data file can can be overridden
+Again, the coefficient values in the data file can be overridden
 in the input script after reading the data file, by specifying
 additional "pair_coeff"_pair_coeff.html commands for any desired I,J
 pairs.