Edits to developer doc files

doc/src/Developer_atom.rst

@@ -2,7 +2,7 @@ Accessing per-atom data
 -----------------------
 
 This page discusses how per-atom data is managed in LAMMPS, how it can
-be accessed, what communication patters apply, and some of the utility
+be accessed, what communication patterns apply, and some of the utility
 functions that exist for a variety of purposes.
 
 
@@ -14,11 +14,11 @@ As described on the :doc:`parallel partitioning algorithms
 simulation domain, either in a *brick* or *tiled* manner.  Each MPI
 process *owns* exactly one subdomain and the atoms within it. To compute
 forces for tuples of atoms that are spread across sub-domain boundaries,
-also a "halo" of *ghost* atoms are maintained within a the communication
+also a "halo" of *ghost* atoms are maintained within the communication
 cutoff distance of its subdomain.
 
 The total number of atoms is stored in `Atom::natoms` (within any
-typical class this can be referred to at `atom->natoms`. The number of
+typical class this can be referred to at `atom->natoms`). The number of
 *owned* (or "local" atoms) are stored in `Atom::nlocal`; the number of
 *ghost* atoms is stored in `Atom::nghost`.  The sum of `Atom::nlocal`
 over all MPI processes should be `Atom::natoms`. This is by default
@@ -27,8 +27,8 @@ LAMMPS stops with a "lost atoms" error.  For convenience also the
 property `Atom::nmax` is available, this is the maximum of
 `Atom::nlocal + Atom::nghost` across all MPI processes.
 
-Per-atom properties are either managed by the atom style, or individual
+Per-atom properties are either managed by the atom style, individual
-classes.  or as custom arrays by the individual classes. If only access
+classes,  or as custom arrays by the individual classes. If only access
 to *owned* atoms is needed, they are usually allocated to be of size
 `Atom::nlocal`, otherwise of size `Atom::nmax`. Please note that not all
 per-atom properties are available or updated on *ghost* atoms. For
@@ -61,7 +61,7 @@ can be found via the `Atom::sametag` array. It points to the next atom
 index with the same tag or -1 if there are no more atoms with the same
 tag.  The list will be exhaustive when starting with an index of an
 *owned* atom, since the atom IDs are unique, so there can only be one
-such atom.  Example code to count atoms with same atom ID in subdomain:
+such atom.  Example code to count atoms with same atom ID in a subdomain:
 
 .. code-block:: c++
 

doc/src/Developer_code_design.rst

@@ -69,7 +69,7 @@ The basic LAMMPS class hierarchy which is created by the LAMMPS class
 constructor is shown in :ref:`class-topology`.  When input commands
 are processed, additional class instances are created, or deleted, or
 replaced.  Likewise, specific member functions of specific classes are
-called to trigger actions such creating atoms, computing forces,
+called to trigger actions such as creating atoms, computing forces,
 computing properties, time-propagating the system, or writing output.
 
 Compositing and Inheritance
@@ -110,9 +110,10 @@ As mentioned above, there can be multiple instances of classes derived
 from the ``Fix`` or ``Compute`` base classes.  They represent a
 different facet of LAMMPS' flexibility, as they provide methods which
 can be called at different points within a timestep, as explained in
-`Developer_flow`.  This allows the input script to tailor how a specific
+the :doc:`How a timestep works <Developer_flow>` doc page.  This allows
-simulation is run, what diagnostic computations are performed, and how
+the input script to tailor how a specific simulation is run, what
-the output of those computations is further processed or output.
+diagnostic computations are performed, and how the output of those
+computations is further processed or output.
 
 Additional code sharing is possible by creating derived classes from the
 derived classes (e.g., to implement an accelerated version of a pair

doc/src/Developer_flow.rst

@@ -128,7 +128,7 @@ reflect particles off box boundaries in the :doc:`FixWallReflect class
 The ``decide()`` method in the Neighbor class determines whether
 neighbor lists need to be rebuilt on the current timestep (conditions
 can be changed using the :doc:`neigh_modify every/delay/check
-<neigh_modify>` command.  If not, coordinates of ghost atoms are
+<neigh_modify>` command).  If not, coordinates of ghost atoms are
 acquired by each processor via the ``forward_comm()`` method of the Comm
 class.  If neighbor lists need to be built, several operations within
 the inner if clause of the pseudocode are first invoked.  The

doc/src/Developer_par_comm.rst

@@ -4,8 +4,7 @@ Communication
 Following the selected partitioning scheme, all per-atom data is
 distributed across the MPI processes, which allows LAMMPS to handle very
 large systems provided it uses a correspondingly large number of MPI
-processes.  Since The per-atom data (atom IDs, positions, velocities,
+processes.  To be able to compute the short-range interactions, MPI
-types, etc.)  To be able to compute the short-range interactions, MPI
 processes need not only access to the data of atoms they "own" but also
 information about atoms from neighboring subdomains, in LAMMPS referred
 to as "ghost" atoms.  These are copies of atoms storing required
@@ -37,7 +36,7 @@ be larger than half the simulation domain.
 
 Efficient communication patterns are needed to update the "ghost" atom
 data, since that needs to be done at every MD time step or minimization
-step.  The diagrams of the `ghost-atom-comm` figure illustrate how ghost
+step.  The diagrams of the :ref:`ghost-atom-comm` figure illustrate how ghost
 atom communication is performed in two stages for a 2d simulation (three
 in 3d) for both a regular and irregular partitioning of the simulation
 box.  For the regular case (left) atoms are exchanged first in the

doc/src/Developer_par_long.rst

@@ -93,7 +93,7 @@ processors, since each tile in the initial tiling overlaps with a
 handful of tiles in the final tiling.
 
 The transformations could also be done using collective communication
-across all $P$ processors with a single call to ``MPI_Alltoall()``, but
+across all :math:`P` processors with a single call to ``MPI_Alltoall()``, but
 this is typically much slower.  However, for the specialized brick and
 pencil tiling illustrated in :ref:`fft-parallel` figure, collective
 communication across the entire MPI communicator is not required.  In
@@ -138,7 +138,7 @@ grid/particle operations that LAMMPS supports:
   :math:`O(P^{\frac{1}{2}})`.
 
 - For efficiency in performing 1d FFTs, the grid transpose
-  operations illustrated in Figure \ref{fig:fft} also involve
+  operations illustrated in Figure :ref:`fft-parallel` also involve
   reordering the 3d data so that a different dimension is contiguous
   in memory.  This reordering can be done during the packing or
   unpacking of buffers for MPI communication.

doc/src/Developer_par_neigh.rst

@@ -149,7 +149,7 @@ supports:
 
 - Dependent on the "pair" setting of the :doc:`newton <newton>` command,
   the "half" neighbor lists may contain **all** pairs of atoms where
-  atom *j* is a ghost atom (i.e. when the newton pair setting is *off*)
+  atom *j* is a ghost atom (i.e. when the newton pair setting is *off*).
   For the newton pair *on* setting the atom *j* is only added to the
   list if its *z* coordinate is larger, or if equal the *y* coordinate
   is larger, and that is equal, too, the *x* coordinate is larger.  For

doc/src/Developer_par_openmp.rst

@@ -1,13 +1,13 @@
 OpenMP Parallelism
 ^^^^^^^^^^^^^^^^^^
 
-The styles in the INTEL, KOKKOS, and OPENMP package offer to use OpenMP
+The styles in the INTEL, KOKKOS, and OPENMP packages offer to use OpenMP
 thread parallelism to predominantly distribute loops over local data
 and thus follow an orthogonal parallelization strategy to the
 decomposition into spatial domains used by the :doc:`MPI partitioning
 <Developer_par_part>`.  For clarity, this section discusses only the
 implementation in the OPENMP package, as it is the simplest. The INTEL
-and KOKKOS package offer additional options and are more complex since
+and KOKKOS packages offer additional options and are more complex since
 they support more features and different hardware like co-processors
 or GPUs.
 
@@ -16,7 +16,7 @@ keep the changes to the source code small, so that it would be easier to
 maintain the code and keep it in sync with the non-threaded standard
 implementation.  This is achieved by a) making the OPENMP version a
 derived class from the regular version (e.g. ``PairLJCutOMP`` from
-``PairLJCut``) and overriding only methods that are multi-threaded or
+``PairLJCut``) and only overriding methods that are multi-threaded or
 need to be modified to support multi-threading (similar to what was done
 in the OPT package), b) keeping the structure in the modified code very
 similar so that side-by-side comparisons are still useful, and c)