loads of spelling fixes

doc/src/Howto_2d.rst

@@ -10,7 +10,7 @@ A 2d simulation box must be periodic in z as set by the :doc:`boundary
 
 If using the :doc:`create_box <create_box>` command, you must define a
 simulation box which straddles z = 0.0 in the z dimension since all
-the atoms will have a z coordinate of zero.  Typicaily the width of
+the atoms will have a z coordinate of zero.  Typically the width of
 box in the z dimension should be narrow, e.g. -0.5 to 0.5, but that is
 not required.  Example are:
 

doc/src/Howto_triclinic.rst

@@ -122,7 +122,7 @@ General triclinic simulation boxes in LAMMPS
 
 LAMMPS allows specification of general triclinic simulation boxes with
 their atoms as a convenience for users who may be converting data from
-solid-state crystallograhic representations or from DFT codes for
+solid-state crystallographic representations or from DFT codes for
 input to LAMMPS.  Likewise it allows output of dump files, data files,
 and thermodynamic data (e.g. pressure tensor) in a general triclinic
 format.
@@ -160,7 +160,7 @@ This means 4 things which are important to understand:
 * If commands such as :doc:`write_data <write_data>` or :doc:`dump
   custom <dump>` are used to output general triclinic information, it
   is effectively the inverse of the operation described in the
-  preceeding bullet.
+  preceding bullet.
 * Other LAMMPS commands such as :doc:`region <region>` or
   :doc:`velocity <velocity>` or :doc:`set <set>`, operate on a
   restricted triclinic system even if a general triclinic system was
@@ -174,13 +174,13 @@ This is the list of commands which have general triclinic options:
 * :doc:`read_data <read_data>` - read a data file for a general triclinic system
 * :doc:`write_data <write_data>` - write a data file for a general triclinic system
 * :doc:`dump atom, dump custom <dump>` - output dump snapshots in general triclinic format
-* :doc:`dump_modify <dump_modify>` - toggle a dump file between restrictied and general triclinic format
+* :doc:`dump_modify <dump_modify>` - toggle a dump file between restricted and general triclinic format
 * :doc:`thermo_style <thermo_style>` - output the pressure tensor in
   general triclinic format
 * :doc:`thermo_modify <thermo_modify>` - toggle thermo-style output
   between restricted and general triclinic format
-* :doc:`read_restart <read_restart>` - read a restart file for a general tricliinc system
+* :doc:`read_restart <read_restart>` - read a restart file for a general triclinic system
-* :doc:`write_restart <read_restart>` - write a restart file for a general tricliinc system
+* :doc:`write_restart <read_restart>` - write a restart file for a general triclinic system
 
 ----------
 
@@ -216,9 +216,8 @@ For consistency, the same rotation applied to the triclinic box edge
 vectors can also be applied to atom positions, velocities, and other
 vector quantities.  This can be conveniently achieved by first
 converting to fractional coordinates in the general triclinic
-coordinates and then converting to coordinates in the resetricted
+coordinates and then converting to coordinates in the restricted
-triclinic basis.  The transformation is given by the following
+triclinic basis.  The transformation is given by the following equation:
-equation:
 
 .. math::
 
@@ -279,10 +278,10 @@ Output of restricted and general triclinic boxes in a dump file
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 As discussed on the :doc:`dump <dump>` command doc page, when the BOX
-BOUNDS for a snapshot is written to a dump file for a resticted
+BOUNDS for a snapshot is written to a dump file for a restricted
 triclinic box, an orthogonal bounding box which encloses the triclinic
-simulation box is output, along with the 3 tilt factors (xy, xz, yz)
+simulation box is output, along with the 3 tilt factors (xy, xz, yz) of
-of the restricted triclinic box, formatted as follows:
+the restricted triclinic box, formatted as follows:
 
 .. parsed-literal::
 

doc/src/boundary.rst

@@ -88,7 +88,7 @@ box.
 
 The boundary <boundary> command settings explained above for the 6
 faces of an orthogonal box also apply in similar manner to the 6 faces
-of a restricted triclinix box (and thus to the corresponding 6 faces
+of a restricted triclinic box (and thus to the corresponding 6 faces
 of a general triclinic box), with the following context.
 
 if the second dimension of a tilt factor (e.g. y for xy) is periodic,

doc/src/create_atoms.rst

@@ -98,7 +98,7 @@ Before using this command, a lattice must typically also be defined
 using the :doc:`lattice <lattice>` command, unless you specify the
 *single* or *mesh* style with units = box or the *random* style.  To
 create atoms on a lattice for general triclinic boxes, see the
-disucssion below.
+discussion below.
 
 For the remainder of this doc page, a created atom or molecule is
 referred to as a "particle".
@@ -150,7 +150,7 @@ you want.
 ----------
 
 If the simulation box is formulated as a general triclinic box defined
-by arbitary edge vectors **A**, **B**, **C**, then the *box* and
+by arbitrary edge vectors **A**, **B**, **C**, then the *box* and
 *region* styles will create atoms on a lattice commensurate with those
 edge vectors.  See the :doc:`Howto_triclinic <Howto_triclinic>` doc
 page for a detailed explanation of orthogonal, restricted triclinic,
@@ -167,7 +167,7 @@ a simulation box which replicates that unit cell along each of the
 
    LAMMPS allows specification of general triclinic simulation boxes
    as a convenience for users who may be converting data from
-   solid-state crystallograhic representations or from DFT codes for
+   solid-state crystallographic representations or from DFT codes for
    input to LAMMPS.  However, as explained on the
    :doc:`Howto_triclinic <Howto_triclinic>` doc page, internally,
    LAMMPS only uses restricted triclinic simulation boxes.  This means
@@ -528,7 +528,7 @@ the distance units are in lattice spacings.  These are affected settings:
 
 * for *single* style: coordinates of the particle created
 * for *random* style: overlap distance *Doverlap* by the *overlap* keyword
-* for *mesh* style: *bisect* threshold valeu for *meshmode* = *bisect*
+* for *mesh* style: *bisect* threshold value for *meshmode* = *bisect*
 * for *mesh* style: *radthresh* value for *meshmode* = *bisect*
 * for *mesh* style: *density* value for *meshmode* = *qrand*
 

doc/src/create_box.rst

@@ -55,7 +55,7 @@ Description
 """""""""""
 
 This command creates a simulation box. It also partitions the box into
-a regular 3d grid of smaller sub-boxes, one per procssor (MPI task).
+a regular 3d grid of smaller sub-boxes, one per processor (MPI task).
 The geometry of the partitioning is based on the size and shape of the
 simulation box, the number of processors being used and the settings
 of the :doc:`processors <processors>` command.  The partitioning can
@@ -175,7 +175,7 @@ pair of the **A**, **B**, **C** vectors.
 To create a general triclinic boxes, the region is specified as NULL
 and the next 6 parameters (alo,ahi,blo,bhi,clo,chi) define the three
 edge vectors **A**, **B**, **C** using additional information
-previously defind by the :doc:`lattice <lattice>` command.
+previously defined by the :doc:`lattice <lattice>` command.
 
 The lattice must be of style *custom* and use its *triclinic/general*
 option.  This insures the lattice satisfies the restrictions listed
@@ -198,7 +198,7 @@ to do this is to specify clo = -0.5 and chi = 0.5 and use the
 
    LAMMPS allows specification of general triclinic simulation boxes
    as a convenience for users who may be converting data from
-   solid-state crystallograhic representations or from DFT codes for
+   solid-state crystallographic representations or from DFT codes for
    input to LAMMPS.  However, as explained on the
    :doc:`Howto_triclinic <Howto_triclinic>` doc page, internally,
    LAMMPS only uses restricted triclinic simulation boxes.  This means

doc/src/dump.rst

@@ -672,7 +672,7 @@ triclinic box, which means that 3 arbitrary box edge vectors **A**,
 triclinic boxes.
 
 This option is provided as a convenience for users who may be
-converting data from solid-state crystallograhic representations or
+converting data from solid-state crystallographic representations or
 from DFT codes for input to LAMMPS.  However, as explained on the
 :doc:`Howto_triclinic <Howto_triclinic>` doc page, internally, LAMMPS
 only uses restricted triclinic simulation boxes.  This means the box
@@ -712,12 +712,12 @@ output for unscaled atom coords, via the :doc:`dump_modify scaled no
 <dump_modify>` setting. For style *custom*, this alters output for
 either unscaled or unwrapped output of atom coords, via the *x,y,z* or
 *xu,yu,zu* attributes.  For output of scaled atom coords by both
-styles, there is no difference bewteen restricted and general
+styles, there is no difference between restricted and general
 triclinic values.
 
 Third, the output for any attribute of the *custom* style which
 represents a per-atom vector quantity will be converted (rotated) to
-be oriented consistent with the general tricinic box and its
+be oriented consistent with the general triclinic box and its
 orientation relative to the standard xyz coordinate axes.
 
 This applies to the following *custom* style attributes:

doc/src/dump_modify.rst

@@ -818,7 +818,7 @@ threshold criterion is met.  Otherwise it is not met.
    For style *custom*, the *triclinic/general* keyword alters dump
    output for general triclinic simulation boxes and their atoms.  See
    the :doc:`dump <dump>` command for details of how this changes the
-   format of dump file snapstots.  The thresh keyword may access
+   format of dump file snapshots.  The thresh keyword may access
    per-atom attributes either directly or indirectly through a compute
    or variable.  If the attribute is an atom coordinate or a per-atom
    vector (such as velocity, force, or dipole moment), its value will

doc/src/lattice.rst

@@ -200,7 +200,7 @@ the Z direction.
 The *triclinic/general* option specifies that the defined lattice is
 for use with a general triclinic simulation box, as opposed to an
 orthogonal or restricted triclinic box.  The :doc:`Howto triclinic
-<Howto_triclinic>` doc page explains all 3 kinds of simluation boxes
+<Howto_triclinic>` doc page explains all 3 kinds of simulation boxes
 LAMMPS supports.
 
 If this option is specified, a *custom* lattice style must be used.
@@ -232,7 +232,7 @@ atoms.  To do this, it also requires a lattice with the
 
    LAMMPS allows specification of general triclinic lattices and
    simulation boxes as a convenience for users who may be converting
-   data from solid-state crystallograhic representations or from DFT
+   data from solid-state crystallographic representations or from DFT
    codes for input to LAMMPS.  However, as explained on the
    :doc:`Howto_triclinic <Howto_triclinic>` doc page, internally,
    LAMMPS only uses restricted triclinic simulation boxes.  This means
@@ -277,7 +277,7 @@ difference in the min/max of the y and z coordinates.
    defined by *a1*, *a2*, *a3* edge vectors is first converted to a
    restricted triclinic orientation, which is a rotation operation.
    The min/max extent of the 8 corner points is then determined, as
-   described in the preceeding paragraph, to set the lattice
+   described in the preceding paragraph, to set the lattice
    spacings. As explained for the *triclinic/general* option above,
    this is because any use of the lattice spacings by other commands
    will be for a restricted triclinic simulation box, not a general

doc/src/read_data.rst

@@ -471,7 +471,7 @@ For 2d simulations, *cvec* = (0,0,1) is required, and the 3rd value of
 
    LAMMPS allows specification of general triclinic simulation boxes
    as a convenience for users who may be converting data from
-   solid-state crystallograhic representations or from DFT codes for
+   solid-state crystallographic representations or from DFT codes for
    input to LAMMPS.  However, as explained on the
    :doc:`Howto_triclinic <Howto_triclinic>` doc page, internally,
    LAMMPS only uses restricted triclinic simulation boxes.  This means
@@ -491,8 +491,8 @@ orthogonal, restricted triclinic, and general triclinic.
 If the system is periodic (in a dimension), then atom coordinates can
 be outside the bounds (in that dimension); they will be remapped (in a
 periodic sense) back inside the box.  For triclinic boxes, periodicity
-in x,y,z refers to the faces of the parallelepided defined by the
+in x,y,z refers to the faces of the parallelepiped defined by the
-**A**,**B**,**C** edge vectors of the simuation box.  See the
+**A**,**B**,**C** edge vectors of the simulation box.  See the
 :doc:`boundary <boundary>` command doc page for a fuller discussion.
 
 Note that if the *add* option is being used to add atoms to a

doc/src/thermo_style.rst

@@ -328,7 +328,7 @@ pressure <compute_pressure>` command doc page for details of how it is
 calculated.
 
 If the :doc:`thermo_modify triclinic/general <thermo_modify>` option
-is set and the simulation box was created as a geenral triclinic box,
+is set and the simulation box was created as a general triclinic box,
 then the components will be output as values consistent with the
 orientation of the general triclinic box relative to the standard xyz
 coordinate axes.  If this keyword is not used, the values will be

doc/src/write_data.rst

@@ -127,16 +127,16 @@ given type-kind) to be written to the data file.
 
 Use of the *triclinic/general* keyword will output a data file which
 specifies a general triclinic simulation box as well as per-atom
-quantities consistent with the general triclinic box.  The latter
+quantities consistent with the general triclinic box.  The latter means
-means that per-atom vectors, such as velocities and dipole moments
+that per-atom vectors, such as velocities and dipole moments will be
-will be oriented conistent with the 3d rotation implied by the general
+oriented consistent with the 3d rotation implied by the general
 triclinic box (relative to the associated restricted triclinic box).
 
 This option can only be requested if the simulation box was initially
 defined to be general triclinic.  If if was and the
 *triclinic/general* keyword is not used, then the data file will
 specify a restricted triclinic box, since that is the internal format
-LAMMPS uses for both general and restricited triclinic simulations.
+LAMMPS uses for both general and restricted triclinic simulations.
 See the :doc:`Howto triclinic <Howto_triclinic>` doc page for more
 explanation of how general triclinic simulation boxes are supported by
 LAMMPS.  And see the :doc:`read_data <read_data>` doc page for details

doc/utils/sphinx-config/false_positives.txt

@@ -50,6 +50,7 @@ agilio
 Agilio
 agni
 Agnolin
+ahi
 Ahrens
 Ai
 Aidan
@@ -85,6 +86,7 @@ allocator
 allocators
 allosws
 AlO
+alo
 Alonso
 Alperen
 alphak
@@ -184,6 +186,7 @@ automagically
 Auvergne
 Avalos
 avalue
+avec
 aveforce
 Avendano
 Averett
@@ -191,11 +194,14 @@ avi
 AVX
 awpmd
 AWPMD
+ax
 Axel
 Axilrod
 Ay
+ay
 Ayton
 Az
+az
 Azevedo
 azimuthal
 Azuri
@@ -268,6 +274,7 @@ Bext
 Bfrac
 bgq
 Bh
+bhi
 Bialke
 biaxial
 bicrystal
@@ -304,6 +311,7 @@ Bkappa
 blabel
 Blaise
 blanchedalmond
+blo
 blocksize
 blueviolet
 bn
@@ -383,6 +391,7 @@ burlywood
 Bussi
 Buturigakkwaishi
 Buyl
+bvec
 Bybee
 bz
 Cadarache
@@ -645,14 +654,18 @@ cv
 Cv
 Cval
 cvar
+cvec
 cvff
 cwiggle
+cx
+cy
 cygwin
 Cygwin
 cylindrically
 Cyrot
 cyrstals
 cython
+cz
 Daivis
 Dammak
 dampflag
@@ -2655,6 +2668,9 @@ organometallic
 orientational
 orientationsFile
 orientorder
+originx
+originy
+originz
 Orlikowski
 ornl
 Ornstein
@@ -2698,6 +2714,7 @@ papayawhip
 paquay
 Paquay
 parallelepiped
+parallelepipeds
 Parallelizable
 parallelization
 parallelized