misc doc fixes to python section

doc/src/Python_error.rst

@@ -16,7 +16,7 @@ can be handled through the Python exception handling mechanism.
    try:
       # LAMMPS will normally terminate itself and the running process if an error
       # occurs. This would kill the Python interpreter.  The library wrapper will
-      # detect that an error has occured and throw a Python exception
+      # detect that an error has occurred and throw a Python exception
 
       lmp.command('unknown')
    except MPIAbortException as ae:

doc/src/Python_neighbor.rst

@@ -2,7 +2,7 @@ Neighbor list access
 ====================
 
 Access to neighbor lists is handled through a couple of wrapper classes
-that allows to treat it like either a python list or a NumPy array.  The
+that allows one to treat it like either a python list or a NumPy array.  The
 access procedure is similar to that of the C-library interface: use one
 of the "find" functions to look up the index of the neighbor list in the
 global table of neighbor lists and then get access to the neighbor list
@@ -79,11 +79,11 @@ potential is shown below.
 * :py:meth:`lammps.get_neighlist_element_neighbors()`: Get element in neighbor list and its neighbors
 
 * :py:meth:`lammps.find_pair_neighlist() <lammps.lammps.find_pair_neighlist()>`: Find neighbor list of pair style
-* :py:meth:`lammps.find_fix_neighlist() <lammps.lammps.find_pair_neighlist()>`: Find neighbor list of pair style
+* :py:meth:`lammps.find_fix_neighlist() <lammps.lammps.find_pair_neighlist()>`: Find neighbor list of fix style
-* :py:meth:`lammps.find_compute_neighlist() <lammps.lammps.find_pair_neighlist()>`: Find neighbor list of pair style
+* :py:meth:`lammps.find_compute_neighlist() <lammps.lammps.find_pair_neighlist()>`: Find neighbor list of compute style
 
 
 **NumPy Methods:**
 
 * :py:meth:`lammps.numpy.get_neighlist() <lammps.numpy_wrapper.numpy_wrapper.get_neighlist()>`: Get neighbor list for given index, which uses NumPy arrays for its element neighbor arrays
-* :py:meth:`lammps.numpy.get_neighlist_element_neighbors() <lammps.numpy_wrapper.numpy_wrapper.get_neighlist_element_neighbors()>`: Get element in neighbor list and its neighbors (as numpy array)
+* :py:meth:`lammps.numpy.get_neighlist_element_neighbors() <lammps.numpy_wrapper.numpy_wrapper.get_neighlist_element_neighbors()>`: Get element in neighbor list and its neighbors (as a numpy array)

doc/src/Python_scatter.rst

@@ -23,19 +23,19 @@ passed by all calling processors, to individual atoms, which may be
 owned by different processors.
 
 Note that the data returned by the gather methods,
-e.g. gather_atoms("x"), is different from the data structure returned
+e.g. :code:`gather_atoms("x")`, is different from the data structure returned
-by extract_atom("x") in four ways.  (1) Gather_atoms() returns a
+by :code:`extract_atom("x")` in four ways.  (1) :code:`gather_atoms()` returns a
-vector which you index as x[i]; extract_atom() returns an array
+vector which you index as x[i]; :code:`extract_atom()` returns an array
-which you index as x[i][j].  (2) Gather_atoms() orders the atoms
+which you index as x[i][j].  (2) :code:`gather_atoms()` orders the atoms
-by atom ID while extract_atom() does not.  (3) Gather_atoms() returns
+by atom ID while :code:`extract_atom()` does not.  (3) :code:`gather_atoms()` returns
-a list of all atoms in the simulation; extract_atoms() returns just
+a list of all atoms in the simulation; :code:`extract_atoms()` returns just
-the atoms local to each processor.  (4) Finally, the gather_atoms()
+the atoms local to each processor.  (4) Finally, the :code:`gather_atoms()`
 data structure is a copy of the atom coords stored internally in
-LAMMPS, whereas extract_atom() returns an array that effectively
+LAMMPS, whereas :code:`extract_atom()` returns an array that effectively
 points directly to the internal data.  This means you can change
 values inside LAMMPS from Python by assigning a new values to the
-extract_atom() array.  To do this with the gather_atoms() vector, you
+:code:`extract_atom()` array.  To do this with the :code:`gather_atoms()` vector, you
-need to change values in the vector, then invoke the scatter_atoms()
+need to change values in the vector, then invoke the :code:`scatter_atoms()`
 method.
 
 For the scatter methods, the array of coordinates passed to must be a

python/lammps/core.py

@@ -2067,7 +2067,7 @@ class lammps(object):
     """ List of the names of enabled packages in the LAMMPS shared library
 
     This is a wrapper around the functions :cpp:func:`lammps_config_package_count`
-    and :cpp:func`lammps_config_package_name` of the library interface.
+    and :cpp:func:`lammps_config_package_name` of the library interface.
 
     :return
     """

python/lammps/numpy_wrapper.py

@@ -271,11 +271,11 @@ class numpy_wrapper:
     # -------------------------------------------------------------------------
 
   def gather_bonds(self):
-    """Retrieve global list of bonds as NumPy array
+    """Retrieve global list of bonds as a NumPy array
 
     .. versionadded:: 28Jul2021
 
-    This is a wrapper around :py:meth:`lammps.gather_bonds() <lammps.lammps.gather_bonds()>`
+    This is a wrapper around :py:meth:`lammps.gather_bonds() <lammps.lammps.gather_bonds()>`.
     It behaves the same as the original method, but returns a NumPy array instead
     of a ``ctypes`` list.
 
@@ -289,11 +289,11 @@ class numpy_wrapper:
     # -------------------------------------------------------------------------
 
   def gather_angles(self):
-    """ Retrieve global list of angles as NumPy array
+    """ Retrieve global list of angles as a NumPy array
 
     .. versionadded:: 8Feb2023
 
-    This is a wrapper around :py:meth:`lammps.gather_angles() <lammps.lammps.gather_angles()>`
+    This is a wrapper around :py:meth:`lammps.gather_angles() <lammps.lammps.gather_angles()>`.
     It behaves the same as the original method, but returns a NumPy array instead
     of a ``ctypes`` list.
 
@@ -307,11 +307,11 @@ class numpy_wrapper:
     # -------------------------------------------------------------------------
 
   def gather_dihedrals(self):
-    """ Retrieve global list of dihedrals as NumPy array
+    """ Retrieve global list of dihedrals as a NumPy array
 
     .. versionadded:: 8Feb2023
 
-    This is a wrapper around :py:meth:`lammps.gather_dihedrals() <lammps.lammps.gather_dihedrals()>`
+    This is a wrapper around :py:meth:`lammps.gather_dihedrals() <lammps.lammps.gather_dihedrals()>`.
     It behaves the same as the original method, but returns a NumPy array instead
     of a ``ctypes`` list.
 
@@ -325,11 +325,11 @@ class numpy_wrapper:
     # -------------------------------------------------------------------------
 
   def gather_impropers(self):
-    """ Retrieve global list of impropers as NumPy array
+    """ Retrieve global list of impropers as a NumPy array
 
     .. versionadded:: 8Feb2023
 
-    This is a wrapper around :py:meth:`lammps.gather_impropers() <lammps.lammps.gather_impropers()>`
+    This is a wrapper around :py:meth:`lammps.gather_impropers() <lammps.lammps.gather_impropers()>`.
     It behaves the same as the original method, but returns a NumPy array instead
     of a ``ctypes`` list.
 

python/lammps/pylammps.py

@@ -358,6 +358,7 @@ class Atom2D(Atom):
   @property
   def velocity(self):
     """Access to velocity of an atom
+
     :getter: Return velocity of atom
     :setter: Set velocity of atom
     :type: numpy.array (float, float)
@@ -372,6 +373,7 @@ class Atom2D(Atom):
   @property
   def force(self):
     """Access to force of an atom
+
     :getter: Return force of atom
     :setter: Set force of atom
     :type: numpy.array (float, float)
@@ -418,7 +420,7 @@ class PyLammps(object):
   """
   This is a Python wrapper class around the lower-level
   :py:class:`lammps` class, exposing a more Python-like,
-  object-oriented interface for prototyping system inside of IPython and
+  object-oriented interface for prototyping systems inside of IPython and
   Jupyter notebooks.
 
   It either creates its own instance of :py:class:`lammps` or can be
@@ -556,7 +558,7 @@ class PyLammps(object):
     Commands will be added to the command history but not executed.
 
     Add `commands` only to the command history, but do not execute them, so that you can
-    conveniently create Lammps input files, using
+    conveniently create LAMMPS input files, using
     :py:meth:`PyLammps.write_script()`.
     """
     self._cmd_history.append(cmd)
@@ -908,7 +910,7 @@ class PyLammps(object):
 
 class IPyLammps(PyLammps):
   """
-  IPython wrapper for LAMMPS which adds embedded graphics capabilities to PyLammmps interface
+  IPython wrapper for LAMMPS which adds embedded graphics capabilities to PyLammps interface
 
   It either creates its own instance of :py:class:`lammps` or can be
   initialized with an existing instance. The arguments are the same of the