From acdb0481f0d3ce075968cf072f07c285f3af9a2f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 1 Dec 2023 15:54:54 -0500 Subject: [PATCH] loads of spelling fixes --- doc/src/Howto_2d.rst | 2 +- doc/src/Howto_triclinic.rst | 21 ++++++++++----------- doc/src/boundary.rst | 2 +- doc/src/create_atoms.rst | 8 ++++---- doc/src/create_box.rst | 6 +++--- doc/src/dump.rst | 6 +++--- doc/src/dump_modify.rst | 2 +- doc/src/lattice.rst | 6 +++--- doc/src/read_data.rst | 6 +++--- doc/src/thermo_style.rst | 2 +- doc/src/write_data.rst | 8 ++++---- doc/utils/sphinx-config/false_positives.txt | 17 +++++++++++++++++ 12 files changed, 51 insertions(+), 35 deletions(-) diff --git a/doc/src/Howto_2d.rst b/doc/src/Howto_2d.rst index b80a424690..8bce7000bd 100644 --- a/doc/src/Howto_2d.rst +++ b/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 ` 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: diff --git a/doc/src/Howto_triclinic.rst b/doc/src/Howto_triclinic.rst index d98a4eca42..2f2ffe85cf 100644 --- a/doc/src/Howto_triclinic.rst +++ b/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 ` or :doc:`dump custom ` 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 ` or :doc:`velocity ` or :doc:`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 a data file for a general triclinic system * :doc:`write_data ` - write a data file for a general triclinic system * :doc:`dump atom, dump custom ` - output dump snapshots in general triclinic format -* :doc:`dump_modify ` - toggle a dump file between restrictied and general triclinic format +* :doc:`dump_modify ` - toggle a dump file between restricted and general triclinic format * :doc:`thermo_style ` - output the pressure tensor in general triclinic format * :doc:`thermo_modify ` - toggle thermo-style output between restricted and general triclinic format -* :doc:`read_restart ` - read a restart file for a general tricliinc system -* :doc:`write_restart ` - write a restart file for a general tricliinc system +* :doc:`read_restart ` - read a restart file for a general triclinic system +* :doc:`write_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 -triclinic basis. The transformation is given by the following -equation: +coordinates and then converting to coordinates in the restricted +triclinic basis. The transformation is given by the following equation: .. math:: @@ -279,10 +278,10 @@ Output of restricted and general triclinic boxes in a dump file """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" As discussed on the :doc:`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) -of the restricted triclinic box, formatted as follows: +simulation box is output, along with the 3 tilt factors (xy, xz, yz) of +the restricted triclinic box, formatted as follows: .. parsed-literal:: diff --git a/doc/src/boundary.rst b/doc/src/boundary.rst index c1adeb1009..06f125ed4f 100644 --- a/doc/src/boundary.rst +++ b/doc/src/boundary.rst @@ -88,7 +88,7 @@ box. The 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, diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index 71303a7d4f..2282cd6e0c 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -98,7 +98,7 @@ Before using this command, a lattice must typically also be defined using the :doc:`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 ` 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 ` 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* diff --git a/doc/src/create_box.rst b/doc/src/create_box.rst index f2b5875539..e7f76f075a 100644 --- a/doc/src/create_box.rst +++ b/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 ` 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 ` command. +previously defined by the :doc:`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 ` doc page, internally, LAMMPS only uses restricted triclinic simulation boxes. This means diff --git a/doc/src/dump.rst b/doc/src/dump.rst index bfb1cb1556..2df4f984cf 100644 --- a/doc/src/dump.rst +++ b/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 ` 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 ` 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: diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 31f1cd214e..6bc1bb8b3e 100644 --- a/doc/src/dump_modify.rst +++ b/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 ` 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 diff --git a/doc/src/lattice.rst b/doc/src/lattice.rst index ae4b9267a6..ad5ab364bd 100644 --- a/doc/src/lattice.rst +++ b/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 -` doc page explains all 3 kinds of simluation boxes +` 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 ` 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 diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index 9bea4e9df7..3bf3e8643a 100644 --- a/doc/src/read_data.rst +++ b/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 ` 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 -**A**,**B**,**C** edge vectors of the simuation box. See the +in x,y,z refers to the faces of the parallelepiped defined by the +**A**,**B**,**C** edge vectors of the simulation box. See the :doc:`boundary ` command doc page for a fuller discussion. Note that if the *add* option is being used to add atoms to a diff --git a/doc/src/thermo_style.rst b/doc/src/thermo_style.rst index 45a1eaa2a8..f73c4baa3d 100644 --- a/doc/src/thermo_style.rst +++ b/doc/src/thermo_style.rst @@ -328,7 +328,7 @@ pressure ` command doc page for details of how it is calculated. If the :doc:`thermo_modify triclinic/general ` 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 diff --git a/doc/src/write_data.rst b/doc/src/write_data.rst index e083f834b8..516685f4fe 100644 --- a/doc/src/write_data.rst +++ b/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 -means that per-atom vectors, such as velocities and dipole moments -will be oriented conistent with the 3d rotation implied by the general +quantities consistent with the general triclinic box. The latter means +that per-atom vectors, such as velocities and dipole moments will be +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 ` doc page for more explanation of how general triclinic simulation boxes are supported by LAMMPS. And see the :doc:`read_data ` doc page for details diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 75589e3115..1a19840c17 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/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