doc tweaks

doc/src/Howto_grid.rst

@@ -4,40 +4,39 @@ Distributed grids
 LAMMPS has internal capabilities to create uniformly spaced grids
 which overlay the simulation domain.  For 2d and 3d simulations these
 are 2d and 3d grids respectively.  Conceptually a grid can be thought
-of as a collection of grid cells, each of which has an associated grid
+of as a collection of grid cells.  Each grid cell can store one or
-point.  Internally, the grid point is typically the center point of
+more values (data).
-the grid cell, though that is a coding option when using grids.  Each
-grid cell stores one or more values (data).
 
-The grid points and data they store are distributed across processors.
+The grid cells and data they store are distributed across processors.
-Each processor owns the grid cells (and their data) whose grid points
+Each processor owns the grid cells (and data) whose center points lie
-lie within the spatial sub-domain of the processor.  If needed for its
+within the spatial sub-domain of the processor.  If needed for its
-computations, it may also store ghost grid cells with their data.
+computations, a processor may also store ghost grid cells with their
+data.
 
-These grids can overlay orthogonal or triclinic simulation boxes; see
+Distributed grids can overlay orthogonal or triclinic simulation
-the :doc:`Howto triclinic <Howto_triclinic>` doc page for an
+boxes; see the :doc:`Howto triclinic <Howto_triclinic>` doc page for
-explanation of the latter.  For a triclinic box, the grid cells
+an explanation of the latter.  For a triclinic box, the grid cell
-conform to the shape of the simulation domain, e.g. parallelograms
+shape conforms to the shape of the simulation domain,
-instead of rectangles in 2d.
+e.g. parallelograms instead of rectangles in 2d.
 
 If the box size or shape changes during a simulation, the grid changes
 with it, so that it always overlays the entire simulation domain.  For
 non-periodic dimensions, the grid size in that dimension matches the
-box size, i.e. as set by the :doc:`boundary <boundary>` command for
+box size, as set by the :doc:`boundary <boundary>` command for fixed
-fixed or shrink-wrapped boundaries.
+or shrink-wrapped boundaries.
 
 If load-balancing is invoked by the :doc:`balance <balance>` or
 :doc:`fix balance <fix_balance>` commands, then the sub-domain owned
-by a processor will change which may also change which grid points
+by a processor can change which may also change which grid cells they
-they own.
+own.
 
-Post-processing and visualization of per-grid data can be enabled by
+Post-processing and visualization of grid cell data can be enabled by
 the :doc:`dump grid <dump>`, :doc:`dump grid/vtk <dump>`, and
-:doc:`dump image <dump_image>` commands, the latter by using its
+:doc:`dump image <dump_image>` commands.  The latter has an optional
-optional *grid* keyword.  The `OVITO visualization tool
+*grid* keyword.  The `OVITO visualization tool
 <https://www.ovito.org>`_ also plans (as of Nov 2022) to add support
-for visualizing per-grid data (along with atoms) using the :doc:`dump
+for visualizing grid cell data (along with atoms) using :doc:`dump
-grid <dump>` output format.
+grid <dump>` output files as input.
 
 .. note::
 
@@ -63,6 +62,7 @@ grids:
 * :doc:`dump grid <dump>` - output per-grid values in LAMMPS format
 * :doc:`dump grid/vtk <dump>` - output per-grid values in VTK format
 * :doc:`dump image grid <dump_image>` - include colored grid in output images
+* :doc:`pair_style amoeba <pair_amoeba>` - FFT grids
 * :doc:`kspace_style pppm <kspace_style>` (and variants) - FFT grids
 * :doc:`kspace_style msm <kspace_style>` (and variants) - MSM grids
 
@@ -75,7 +75,7 @@ sizes).  Each grid can store one or more data fields.  A data field
 can be a single value per grid point (per-grid vector) or multiple
 values per grid point (per-grid array).  See the :doc:`Howto output
 <Howto_output>` doc page for an explanation of how per-grid data can
-be generated by some commands and used by others.
+be generated by some commands and used by other commands.
 
 A command accesses grid data from a compute or fix with the following
 syntax:

src/grid2d.cpp

@@ -230,8 +230,8 @@ void Grid2d::set_yfactor(double factor)
 
 /* ----------------------------------------------------------------------
    set IDs of proc neighbors used in uniform local owned/ghost comm
-   called AFTER setup_grid() but BEFORE setup_comm() to override
+   must be called BEFORE setup_comm() to override
-     the processor neighbors stored by extract_comm()
+     the processor neighbors stored by extract_comm_info()
 ------------------------------------------------------------------------- */
 
 void Grid2d::set_proc_neighs(int pxlo, int pxhi, int pylo, int pyhi)
@@ -244,8 +244,8 @@ void Grid2d::set_proc_neighs(int pxlo, int pxhi, int pylo, int pyhi)
 
 /* ----------------------------------------------------------------------
    set allocation dimensions of caller grid used by indices() to setup pack/unpack
-   called AFTER setup_grid() but BEFORE setup_comm() to override
+   must be called BEFORE setup_comm() to override
-     the caller grid size set by setup_grid() and used in indices()
+     the caller grid size used in indices()
 ------------------------------------------------------------------------- */
 
 void Grid2d::set_caller_grid(int fxlo, int fxhi, int fylo, int fyhi)

src/grid3d.cpp

@@ -244,8 +244,8 @@ void Grid3d::set_zfactor(double factor)
 
 /* ----------------------------------------------------------------------
    set IDs of proc neighbors used in uniform local owned/ghost comm
-   called AFTER setup_grid() but BEFORE setup_comm() to override
+   must be called BEFORE setup_comm() to override
-     the processor neighbors stored by extract_comm()
+     the processor neighbors stored by extract_comm_info()
    used by MSM to exclude non-participating procs for coarse grid comm
 ------------------------------------------------------------------------- */
 
@@ -262,8 +262,8 @@ void Grid3d::set_proc_neighs(int pxlo, int pxhi, int pylo, int pyhi,
 
 /* ----------------------------------------------------------------------
    set allocation dimensions of caller grid used by indices() to setup pack/unpack
-   called AFTER setup_grid() but BEFORE setup_comm() to override
+   must be called BEFORE setup_comm() to override
-     the caller grid size set by setup_grid() and used in indices()
+     the caller grid size used in indices()
    used by MSM to allow a larger level 0 grid to be allocated
      with more ghost cells for other operations
 ------------------------------------------------------------------------- */