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doc/src/Developer_grid.rst

@@ -26,9 +26,9 @@ grid.
 
 More specifically, a grid point is defined for each cell (by default
 the center point), and a processor owns a grid cell if its point is
-within the processor's spatial subdomain.  The union of processor
-subdomains is the global simulation box.  If a grid point is on the
-boundary of two subdomains, the lower processor owns the grid cell.  A
+within the processor's spatial sub-domain.  The union of processor
+sub-domains is the global simulation box.  If a grid point is on the
+boundary of two sub-domains, the lower processor owns the grid cell.  A
 processor may also store copies of ghost cells which surround its
 owned cells.
 
@@ -60,7 +60,7 @@ y-dimension.  It is even possible to define a 1x1x1 3d grid, though it
 may be inefficient to use it in a computational sense.
 
 Note that the choice of grid size is independent of the number of
-processors or their layout in a grid of processor subdomains which
+processors or their layout in a grid of processor sub-domains which
 overlays the simulations domain.  Depending on the distributed grid
 size, a single processor may own many 1000s or no grid cells.
 
@@ -233,7 +233,7 @@ invoked, because they influence its operation.
    void set_zfactor(double factor);
 
 Processors own a grid cell if a point within the grid cell is inside
-the processor's subdomain.  By default this is the center point of the
+the processor's sub-domain.  By default this is the center point of the
 grid cell.  The *set_shift_grid()* method can change this.  The *shift*
 argument is a value from 0.0 to 1.0 (inclusive) which is the offset of
 the point within the grid cell in each dimension.  The default is 0.5
@@ -243,9 +243,9 @@ typically no need to change the default as it is optimal for
 minimizing the number of ghost cells needed.
 
 If a processor maps its particles to grid cells, it needs to allow for
-its particles being outside its subdomain between reneighboring.  The
+its particles being outside its sub-domain between reneighboring.  The
 *distance* argument of the *set_distance()* method sets the furthest
-distance outside a processor's subdomain which a particle can move.
+distance outside a processor's sub-domain which a particle can move.
 Typically this is half the neighbor skin distance, assuming
 reneighboring is done appropriately.  This distance is used in
 determining how many ghost cells a processor needs to store to enable
@@ -293,7 +293,7 @@ to the Grid class via the *set_zfactor()* method (*set_yfactor()* for
 2d grids).  The Grid class will then assign ownership of the 1/3 of
 grid cells that overlay the simulation box to the processors which
 also overlay the simulation box.  The remaining 2/3 of the grid cells
-are assigned to processors whose subdomains are adjacent to the upper
+are assigned to processors whose sub-domains are adjacent to the upper
 z boundary of the simulation box.
 
 ----------
@@ -547,13 +547,13 @@ Grid class remap methods for load balancing
 The following methods are used when a load-balancing operation,
 triggered by the :doc:`balance <balance>` or :doc:`fix balance
 <fix_balance>` commands, changes the partitioning of the simulation
-domain into processor subdomains.
+domain into processor sub-domains.
 
 In order to work with load-balancing, any style command (compute, fix,
 pair, or kspace style) which allocates a grid and stores per-grid data
 should define a *reset_grid()* method; it takes no arguments.  It will
 be called by the two balance commands after they have reset processor
-subdomains and migrated atoms (particles) to new owning processors.
+sub-domains and migrated atoms (particles) to new owning processors.
 The *reset_grid()* method will typically perform some or all of the
 following operations.  See the src/fix_ave_grid.cpp and
 src/EXTRA_FIX/fix_ttm_grid.cpp files for examples of *reset_grid()*
@@ -562,7 +562,7 @@ functions.
 
 First, the *reset_grid()* method can instantiate new grid(s) of the
 same global size, then call *setup_grid()* to partition them via the
-new processor subdomains.  At this point, it can invoke the
+new processor sub-domains.  At this point, it can invoke the
 *identical()* method which compares the owned and ghost grid cell
 index bounds between two grids, the old grid passed as a pointer
 argument, and the new grid whose *identical()* method is being called.
@@ -577,7 +577,7 @@ the command can simply delete the old data array(s) and grid
 instance(s).  It can then return.
 
 If the grid data does need to persist, then the data for each grid
-needs to be "remapped" from the old grld partitioning to the new grid
+needs to be "remapped" from the old grid partitioning to the new grid
 partitioning.  The *setup_remap()* and *remap()* methods are used for
 that purpose.
 

doc/src/dump.rst

@@ -66,7 +66,7 @@ Syntax
 * style = *atom* or *atom/adios* or *atom/gz* or *atom/zstd* or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *custom/adios* or *dcd* or *grid* or *grid/vtk* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml*
 * N = dump on timesteps which are multiples of N
 * file = name of file to write dump info to
-* attribute1,filel2,... = list of attributes for a particular style
+* attribute1,attribute2,... = list of attributes for a particular style
 
   .. parsed-literal::
 

doc/utils/sphinx-config/false_positives.txt

@@ -412,6 +412,7 @@ cdennist
 cdof
 ceil
 Ceil
+cekk
 centerline
 centro
 centroid
@@ -470,6 +471,7 @@ Cij
 cis
 civ
 CKD
+ckk
 Clang
 clearstore
 Cleary
@@ -559,6 +561,8 @@ Coulombic
 Coulombics
 counterion
 counterions
+CountI
+CountN
 Courant
 covalent
 covalently
@@ -1240,6 +1244,7 @@ Glosli
 Glotzer
 gmail
 gmake
+gmap
 gmask
 Gmask
 GMock
@@ -1439,6 +1444,7 @@ ieni
 ifdefs
 iff
 ifort
+ihi
 Ihle
 ij
 ijk
@@ -1449,6 +1455,7 @@ ilabel
 Ilie
 ilmenau
 Ilmenau
+ilo
 ilp
 Ilya
 im
@@ -1550,6 +1557,8 @@ Iw
 Iwers
 iwyu
 ixcm
+ixhi
+ixlo
 ixx
 Ixx
 ixy
@@ -2388,6 +2397,7 @@ nlayers
 nlen
 nlines
 Nlines
+nlist
 nlo
 nlocal
 Nlocal
@@ -2517,11 +2527,15 @@ Nwait
 nwchem
 nx
 Nx
+nxlo
 nxnodes
+Nxyz
 ny
 Ny
+nylo
 nz
 Nz
+nzlo
 ocl
 octahedral
 octants
@@ -2590,6 +2604,8 @@ overlayed
 Ovito
 oxdna
 oxDNA
+oxhi
+oxlo
 oxrna
 oxRNA
 packings
@@ -2657,6 +2673,7 @@ Peng
 peptide
 peratom
 Pergamon
+pergrid
 peri
 peridynamic
 Peridynamic
@@ -3370,6 +3387,8 @@ Sugaku
 Suhai
 Sukumaran
 Sulc
+SumI
+SumN
 sumsq
 Sunderland
 supercell