Math replacements; code-block LAMMPS; clarity and parsing-friendly edits

doc/src/compute_bond_local.rst

@@ -123,7 +123,7 @@ directly.  The *set* keyword is used to identify the name of this
 other variable associated with theta.
 
 As an example, these commands can be added to the bench/in.rhodo
-script to compute the length\^2 of every bond in the system and
+script to compute the length\ :math:`^2` of every bond in the system and
 output the statistics in various ways:
 
 .. code-block:: LAMMPS
@@ -141,11 +141,11 @@ output the statistics in various ways:
    fix 10 all ave/histo 10 10 100 0 6 20 c_2[3] mode vector file tmp.histo
 
 The :doc:`dump local <dump>` command will output the energy, length,
-and length\^2 for every bond in the system.  The
+and length\ :math:`^2` for every bond in the system.  The
 :doc:`thermo_style <thermo_style>` command will print the average of
 those quantities via the :doc:`compute reduce <compute_reduce>` command
 with thermo output, and the :doc:`fix ave/histo <fix_ave_histo>`
-command will histogram the length\^2 values and write them to a file.
+command will histogram the length\ :math:`^2` values and write them to a file.
 
 ----------
 

doc/src/compute_chunk_atom.rst

@@ -602,7 +602,7 @@ be used.  For non-orthogonal (triclinic) simulation boxes, only the
 *reduced* option may be used.
 
 A *box* value selects standard distance units as defined by the
-:doc:`units <units>` command (e.g., Ångströms for units = *real* or *metal*).
+:doc:`units <units>` command (e.g., Angstroms for units = *real* or *metal*).
 A *lattice* value means the distance units are in lattice spacings.
 The :doc:`lattice <lattice>` command must have been previously used to
 define the lattice spacing.  A *reduced* value means normalized

doc/src/compute_coord_atom.rst

@@ -11,11 +11,11 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   compute ID group-ID coord/atom cstyle args ...
+   compute ID group-ID coord/atom style args ...
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * coord/atom = style name of this compute command
-* cstyle = *cutoff* or *orientorder*
+* style = *cutoff* or *orientorder*
 
   .. parsed-literal::
 

doc/src/compute_entropy_atom.rst

@@ -98,13 +98,13 @@ by the corresponding volume. This option can be useful when dealing with
 inhomogeneous systems such as those that have surfaces.
 
 Here are typical input parameters for fcc aluminum (lattice
-constant 4.05 Ångströms),
+constant 4.05 Angstroms),
 
 .. parsed-literal::
 
    compute 1 all entropy/atom 0.25 5.7 avg yes 3.7
 
-and for bcc sodium (lattice constant 4.23 Ångströms),
+and for bcc sodium (lattice constant 4.23 Angstroms),
 
 .. parsed-literal::
 

doc/src/compute_global_atom.rst

@@ -6,7 +6,7 @@ compute global/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID style index input1 input2 ...
 
@@ -55,18 +55,20 @@ reference a global vector or array from a :doc:`compute <compute>` or
 :doc:`fix <fix>` or the evaluation of an vector-style
 :doc:`variable <variable>`.  Details are given below.
 
-The *index* value for an atom is used as a index I (from 1 to N) into
+The *index* value for an atom is used as an index :math:`I` (from 1 to
-the vector associated with each of the input values.  The Ith value
+:math:`N`, where :math:`N` is the number of atoms) into the vector
+associated with each of the input values.  The :math:`I`\ th value
 from the input vector becomes one output value for that atom.  If the
-atom is not in the specified group, or the index I < 1 or I > M, where
+atom is not in the specified group, or the index :math:`I < 1` or
-M is the actual length of the input vector, then an output value of
+:math:`I > M`, where :math:`M` is the actual length of the input vector,
-0.0 is assigned to the atom.
+then an output value of 0.0 is assigned to the atom.
 
 An example of how this command is useful, is in the context of
 "chunks" which are static or dynamic subsets of atoms.  The :doc:`compute chunk/atom <compute_chunk_atom>` command assigns unique chunk IDs
-to each atom.  It's output can be used as the *index* parameter for
+to each atom.  Its output can be used as the *index* parameter for
 this command.  Various other computes with "chunk" in their style
-name, such as :doc:`compute com/chunk <compute_com_chunk>` or :doc:`compute msd/chunk <compute_msd_chunk>`, calculate properties for each
+name, such as :doc:`compute com/chunk <compute_com_chunk>` or
+:doc:`compute msd/chunk <compute_msd_chunk>`, calculate properties for each
 chunk.  The output of these commands are global vectors or arrays,
 with one or more values per chunk, and can be used as input values for
 this command.  This command will then assign the global chunk value to
@@ -102,17 +104,18 @@ they work.
 Note that for input values from a compute or fix, the bracketed index
 I can be specified using a wildcard asterisk with the index to
 effectively specify multiple values.  This takes the form "\*" or "\*n"
-or "n\*" or "m\*n".  If N = the size of the vector (for *mode* = scalar)
+or "m\*" or "m\*n".  If :math:`N` is the size of the vector
+(for *mode* = scalar)
 or the number of columns in the array (for *mode* = vector), then an
-asterisk with no numeric values means all indices from 1 to N.  A
+asterisk with no numeric values means all indices from 1 to :math:`N`.
-leading asterisk means all indices from 1 to n (inclusive).  A
+A leading asterisk means all indices from 1 to n (inclusive).  A
-trailing asterisk means all indices from n to N (inclusive).  A middle
+trailing asterisk means all indices from m to :math:`N` (inclusive).
-asterisk means all indices from m to n (inclusive).
+A middle asterisk means all indices from m to n (inclusive).
 
 Using a wildcard is the same as if the individual columns of the array
-had been listed one by one.  E.g. these 2 compute global/atom commands
+had been listed one by one. For example, the following two compute global/atom
-are equivalent, since the :doc:`compute com/chunk <compute_com_chunk>`
+commands are equivalent, since the :doc:`compute com/chunk <compute_com_chunk>`
-command creates a global array with 3 columns:
+command creates a global array with three columns:
 
 .. code-block:: LAMMPS
 
@@ -124,14 +127,14 @@ command creates a global array with 3 columns:
 ----------
 
 This section explains the *index* parameter.  Note that it must
-reference per-atom values, as contrasted with the *input* values which
+reference per-atom values, as contrasted with the *input* values, which
 must reference global values.
 
 Note that all of these options generate floating point values.  When
 they are used as an index into the specified input vectors, they
 simple rounded down to convert the value to integer indices.  The
-final values should range from 1 to N (inclusive), since they are used
+final values should range from 1 to :math:`N` (inclusive), since they are used
-to access values from N-length vectors.
+to access values from :math:`N`-length vectors.
 
 If *index* begins with "c\_", a compute ID must follow which has been
 previously defined in the input script.  The compute must generate
@@ -177,7 +180,8 @@ global vector or array.  See the individual :doc:`compute <compute>` doc
 page for details.  If no bracketed integer is appended, the vector
 calculated by the compute is used.  If a bracketed integer is
 appended, the Ith column of the array calculated by the compute is
-used.  Users can also write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.  See the discussion above for how
+used.  Users can also write code for their own compute styles and
+:doc:`add them to LAMMPS <Modify>`.  See the discussion above for how
 I can be specified with a wildcard asterisk to effectively specify
 multiple values.
 

doc/src/compute_group_group.rst

@@ -6,7 +6,7 @@ compute group/group command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID group/group group2-ID keyword value ...
 
@@ -102,19 +102,20 @@ frequently.
 
    If you have a bonded system, then the settings of
    :doc:`special_bonds <special_bonds>` command can remove pairwise
-   interactions between atoms in the same bond, angle, or dihedral.  This
+   interactions between atoms in the same bond, angle, or dihedral.  This is
-   is the default setting for the :doc:`special_bonds <special_bonds>`
+   the default setting for the :doc:`special_bonds <special_bonds>` command,
-   command, and means those pairwise interactions do not appear in the
+   and means those pairwise interactions do not appear in the neighbor list.
-   neighbor list.  Because this compute uses a neighbor list, it also
+   Because this compute uses a neighbor list, it also means those pairs will
-   means those pairs will not be included in the group/group interaction.
+   not be included in the group/group interaction.  This does not apply when
-   This does not apply when using long-range coulomb interactions
+   using long-range Coulomb interactions
-   (\ *coul/long*, *coul/msm*, *coul/wolf* or similar.  One way to get
+   (\ *coul/long*, *coul/msm*, *coul/wolf* or similar).  One way to get
-   around this would be to set special_bond scaling factors to very tiny
+   around this would be to set *special_bond* scaling factors to very tiny
-   numbers that are not exactly zero (e.g. 1.0e-50). Another workaround
+   numbers that are not exactly zero (e.g., :math:`1.0 \times 10^{-50}`).
-   is to write a dump file, and use the :doc:`rerun <rerun>` command to
+   Another workaround would be to write a dump file and use the
-   compute the group/group interactions for snapshots in the dump file.
+   :doc:`rerun <rerun>` command to compute the group/group interactions for
-   The rerun script can use a :doc:`special_bonds <special_bonds>` command
+   snapshots in the dump file. The rerun script can use a
-   that includes all pairs in the neighbor list.
+   :doc:`special_bonds <special_bonds>` command that includes all pairs in the
+   neighbor list.
 
 If you desire a breakdown of the interactions into a pairwise and
 Kspace component, simply invoke the compute twice with the appropriate
@@ -132,20 +133,21 @@ Output info
 """""""""""
 
 This compute calculates a global scalar (the energy) and a global
-vector of length 3 (force), which can be accessed by indices 1-3.
+vector of length 3 (force), which can be accessed by indices 1--3.
 These values can be used by any command that uses global scalar or
-vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
+vector values from a compute as input.  See the
+:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
 Both the scalar and vector values calculated by this compute are
-"extensive".  The scalar value will be in energy :doc:`units <units>`.
+"extensive."  The scalar value will be in energy :doc:`units <units>`.
 The vector values will be in force :doc:`units <units>`.
 
 Restrictions
 """"""""""""
 
 Not all pair styles can be evaluated in a pairwise mode as required by
-this compute.  For example, 3-body and other many-body potentials,
+this compute.  For example, three-body and other many-body potentials,
 such as :doc:`Tersoff <pair_tersoff>` and
 :doc:`Stillinger-Weber <pair_sw>` cannot be used.  :doc:`EAM <pair_eam>`
 potentials will re-use previously computed embedding term contributions,

doc/src/compute_gyration.rst

@@ -6,7 +6,7 @@ compute gyration command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID gyration
 
@@ -23,51 +23,54 @@ Examples
 Description
 """""""""""
 
-Define a computation that calculates the radius of gyration Rg of the
+Define a computation that calculates the radius of gyration :math:`R_g` of the
 group of atoms, including all effects due to atoms passing through
 periodic boundaries.
 
-Rg is a measure of the size of the group of atoms, and is computed as
+:math:`R_g` is a measure of the size of the group of atoms, and is computed as
-the square root of the Rg\^2 value in this formula
+the square root of the :math:`R_g^2` value in this formula
 
 .. math::
 
- {R_g}^2 = \frac{1}{M} \sum_i m_i (r_i - r_{cm})^2
+   R_g^2 = \frac{1}{M} \sum_i m_i (r_i - r_{\text{cm}})^2
 
-where :math:`M` is the total mass of the group, :math:`r_{cm}` is the
+where :math:`M` is the total mass of the group, :math:`r_{\text{cm}}` is the
 center-of-mass position of the group, and the sum is over all atoms in
 the group.
 
-A :math:`{R_g}^2` tensor, stored as a 6-element vector, is also calculated
+A :math:`R_g^2` tensor, stored as a 6-element vector, is also calculated
 by this compute.  The formula for the components of the tensor is the
-same as the above formula, except that :math:`(r_i - r_{cm})^2` is replaced
+same as the above formula, except that :math:`(r_i - r_{\text{cm}})^2` is
-by :math:`(r_{i,x} - r_{cm,x}) \cdot (r_{i,y} - r_{cm,y})` for the xy component,
+replaced by
-and so on.  The 6 components of the vector are ordered xx, yy, zz, xy, xz, yz.
+:math:`(r_{i,x} - r_{\text{cm},x}) \cdot (r_{i,y} - r_{\text{cm},y})` for the
-Note that unlike the scalar :math:`R_g`, each of the 6 values of the tensor
+:math:`xy` component, and so on.  The six components of the vector are ordered
+:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
+Note that unlike the scalar :math:`R_g`, each of the six values of the tensor
 is effectively a "squared" value, since the cross-terms may be negative
-and taking a sqrt() would be invalid.
+and taking a square root would be invalid.
 
 .. note::
 
    The coordinates of an atom contribute to :math:`R_g` in "unwrapped" form,
-   by using the image flags associated with each atom.  See the :doc:`dump custom <dump>` command for a discussion of "unwrapped" coordinates.
+   by using the image flags associated with each atom.  See the
+   :doc:`dump custom <dump>` command for a discussion of "unwrapped" coordinates.
    See the Atoms section of the :doc:`read_data <read_data>` command for a
    discussion of image flags and how they are set for each atom.  You can
-   reset the image flags (e.g. to 0) before invoking this compute by
+   reset the image flags (e.g., to 0) before invoking this compute by
    using the :doc:`set image <set>` command.
 
 Output info
 """""""""""
 
 This compute calculates a global scalar (:math:`R_g`) and a global vector of
-length 6 (:math:`{R_g}^2` tensor), which can be accessed by indices 1-6.  These
+length 6 (:math:`R_g^2` tensor), which can be accessed by indices 1--6.  These
 values can be used by any command that uses a global scalar value or
 vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
 The scalar and vector values calculated by this compute are
-"intensive".  The scalar and vector values will be in distance and
+"intensive."  The scalar and vector values will be in distance and
-distance\^2 :doc:`units <units>` respectively.
+distance\ :math:`^2` :doc:`units <units>`, respectively.
 
 Restrictions
 """"""""""""

doc/src/compute_gyration_chunk.rst

@@ -6,7 +6,7 @@ compute gyration/chunk command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID gyration/chunk chunkID keyword value ...
 
@@ -31,28 +31,31 @@ Examples
 Description
 """""""""""
 
-Define a computation that calculates the radius of gyration Rg for
+Define a computation that calculates the radius of gyration :math:`R_g` for
 multiple chunks of atoms.
 
-In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+In LAMMPS, chunks are collections of atoms defined by a
+:doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
 to a single chunk (or no chunk).  The ID for this command is specified
 as chunkID.  For example, a single chunk could be the atoms in a
-molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
+molecule or atoms in a spatial bin.
+See the :doc:`compute chunk/atom <compute_chunk_atom>` and
+:doc:`Howto chunk <Howto_chunk>`
 doc pages for details of how chunks can be defined and examples of how
 they can be used to measure properties of a system.
 
-This compute calculates the radius of gyration Rg for each chunk,
+This compute calculates the radius of gyration :math:`R_g` for each chunk,
 which includes all effects due to atoms passing through periodic
 boundaries.
 
-Rg is a measure of the size of a chunk, and is computed by this
+:math:`R_g` is a measure of the size of a chunk, and is computed by the
 formula
 
 .. math::
 
- {R_g}^2 = \frac{1}{M} \sum_i m_i (r_i - r_{cm})^2
+   R_g^2 = \frac{1}{M} \sum_i m_i (r_i - r_{\text{cm}})^2
 
-where :math:`M` is the total mass of the chunk, :math:`r_{cm}` is
+where :math:`M` is the total mass of the chunk, :math:`r_{\text{cm}}` is
 the center-of-mass position of the chunk, and the sum is over all atoms in the
 chunk.
 
@@ -64,13 +67,13 @@ thus also not contribute to this calculation.  You can specify the
 "all" group for this command if you simply want to include atoms with
 non-zero chunk IDs.
 
-If the *tensor* keyword is specified, then the scalar Rg value is not
+If the *tensor* keyword is specified, then the scalar :math:`R_g` value is not
-calculated, but an Rg tensor is instead calculated for each chunk.
+calculated, but an :math:`R_g` tensor is instead calculated for each chunk.
 The formula for the components of the tensor is the same as the above
-formula, except that :math:`(r_i - r_{cm})^2` is replaced by
+formula, except that :math:`(r_i - r_{\text{cm}})^2` is replaced by
-:math:`(r_{i,x} - r_{cm,x}) \cdot (r_{i,y} - r_{cm,y})` for the xy
+:math:`(r_{i,x} - r_{\text{cm},x}) \cdot (r_{i,y} - r_{\text{cm},y})` for the
-component, and so on.  The 6 components of the tensor are
+:math:`xy` component, and so on.  The six components of the tensor are
-ordered xx, yy, zz, xy, xz, yz.
+ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
 
 .. note::
 
@@ -79,7 +82,7 @@ ordered xx, yy, zz, xy, xz, yz.
    command for a discussion of "unwrapped" coordinates.
    See the Atoms section of the :doc:`read_data <read_data>` command for a
    discussion of image flags and how they are set for each atom.  You can
-   reset the image flags (e.g. to 0) before invoking this compute by
+   reset the image flags (e.g., to 0) before invoking this compute by
    using the :doc:`set image <set>` command.
 
 The simplest way to output the results of the compute gyration/chunk
@@ -98,8 +101,9 @@ Output info
 This compute calculates a global vector if the *tensor* keyword is not
 specified and a global array if it is.  The length of the vector or
 number of rows in the array = the number of chunks *Nchunk* as
-calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  If the *tensor* keyword
+calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>`
-is specified, the global array has 6 columns.  The vector or array can
+command.  If the *tensor* keyword is specified, the global array has six
+columns.  The vector or array can
 be accessed by any command that uses global values from a compute as
 input.  See the :doc:`Howto output <Howto_output>` page for an
 overview of LAMMPS output options.

doc/src/compute_gyration_shape.rst

@@ -6,7 +6,7 @@ compute gyration/shape command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID gyration/shape compute-ID
 
@@ -28,30 +28,33 @@ Define a computation that calculates the eigenvalues of the gyration tensor of a
 group of atoms and three shape parameters. The computation includes all effects
 due to atoms passing through periodic boundaries.
 
-The three computed shape parameters are the asphericity, b, the acylindricity, c,
+The three computed shape parameters are the asphericity, :math:`b`,
-and the relative shape anisotropy, k:
+the acylindricity, :math:`c`, and the relative shape anisotropy, :math:`k`,
+viz.,
 
 .. math::
 
- c = & l_z - 0.5(l_y+l_x) \\
+ b &= l_z - \frac12(l_y+l_x) \\
- b = & l_y - l_x \\
+ c &= l_y - l_x \\
- k = & \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2}
+ k &= \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2}
 
-where :math:`l_x` <= :math:`l_y` <= :math:`l_z` are the three eigenvalues of the gyration tensor. A general description
+where :math:`l_x \le l_y \le l_z` are the three eigenvalues of the gyration
-of these parameters is provided in :ref:`(Mattice) <Mattice1>` while an application to polymer systems
+tensor. A general description of these parameters is provided in
+:ref:`(Mattice) <Mattice1>` while an application to polymer systems
 can be found in :ref:`(Theodorou) <Theodorou1>`.
-The asphericity  is always non-negative and zero only when the three principal
+The asphericity is always non-negative and zero only when the three principal
-moments are equal. This zero condition is met when the distribution of particles
+moments are equal. This zero condition is met when the distribution of
-is spherically symmetric (hence the name asphericity) but also whenever the particle
+particles is spherically symmetric (hence the name asphericity) but also
-distribution is symmetric with respect to the three coordinate axes, e.g.,
+whenever the particle distribution is symmetric with respect to the three
-when the particles are distributed uniformly on a cube, tetrahedron or other Platonic
+coordinate axes (e.g., when the particles are distributed uniformly on a cube,
-solid. The acylindricity is always non-negative and zero only when the two principal
+tetrahedron or other Platonic solid). The acylindricity is always non-negative
-moments are equal. This zero condition is met when the distribution of particles is
+and zero only when the two principal moments are equal. This zero condition is
-cylindrically symmetric (hence the name, acylindricity), but also whenever the particle
+met when the distribution of particles is cylindrically symmetric (hence the
-distribution is symmetric with respect to the two coordinate axes, e.g., when the
+name, acylindricity), but also whenever the particle distribution is symmetric
-particles are distributed uniformly on a regular prism. the relative shape anisotropy
+with respect to the two coordinate axes (e.g., when the
-is bounded between zero (if all points are spherically symmetric) and one
+particles are distributed uniformly on a regular prism).
-(if all points lie on a line).
+The relative shape anisotropy is bounded between zero (if all points are
+spherically symmetric) and one (if all points lie on a line).
 
 .. note::
 
@@ -60,22 +63,23 @@ is bounded between zero (if all points are spherically symmetric) and one
    See the :doc:`dump custom <dump>` command for a discussion of "unwrapped"
    coordinates. See the Atoms section of the :doc:`read_data <read_data>`
    command for a discussion of image flags and how they are set for each
-   atom.  You can reset the image flags (e.g. to 0) before invoking this
+   atom.  You can reset the image flags (e.g., to 0) before invoking this
    compute by using the :doc:`set image <set>` command.
 
 Output info
 """""""""""
 
-This compute calculates a global vector of
+This compute calculates a global vector of length 6, which can be accessed by
-length 6, which can be accessed by indices 1-6. The first three values are the
+indices 1--6. The first three values are the eigenvalues of the gyration tensor
-eigenvalues of the gyration tensor followed by the asphericity, the acylindricity
+followed by the asphericity, the acylindricity and the relative shape
-and the relative shape anisotropy.  The computed values can be used by any command
+anisotropy.  The computed values can be used by any command that uses global
-that uses global  vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
+vector values from a compute as input.  See the
+:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
 The vector values calculated by this compute are
-"intensive".  The first five vector values will be in
+"intensive."  The first five vector values will be in
-distance\^2 :doc:`units <units>` while the sixth one is dimensionless.
+distance\ :math:`2` :doc:`units <units>` while the sixth one is dimensionless.
 
 Restrictions
 """"""""""""

doc/src/compute_gyration_shape_chunk.rst

@@ -6,7 +6,7 @@ compute gyration/shape/chunk command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID gyration/shape/chunk compute-ID
 
@@ -28,28 +28,32 @@ Define a computation that calculates the eigenvalues of the gyration tensor and
 three shape parameters of multiple chunks of atoms. The computation includes
 all effects due to atoms passing through periodic boundaries.
 
-The three computed shape parameters are the asphericity, b, the acylindricity, c,
+The three computed shape parameters are the asphericity, :math:`b`,
-and the relative shape anisotropy, k:
+the acylindricity, :math:`c`, and the relative shape anisotropy, :math:`k`,
+viz.,
 
 .. math::
 
- c = & l_z - 0.5(l_y+l_x) \\
+ b &= l_z - \frac12(l_y+l_x) \\
- b = & l_y - l_x \\
+ c &= l_y - l_x \\
- k = & \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2}
+ k &= \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2}
 
-where :math:`l_x` <= :math:`l_y` <= :math:`l_z` are the three eigenvalues of the gyration tensor. A general description
+where :math:`l_x \le l_y \le l_z` are the three eigenvalues of the gyration
-of these parameters is provided in :ref:`(Mattice) <Mattice2>` while an application to polymer systems
+tensor. A general description of these parameters is provided in
-can be found in :ref:`(Theodorou) <Theodorou2>`. The asphericity  is always non-negative and zero
+:ref:`(Mattice) <Mattice2>` while an application to polymer systems
-only when the three principal moments are equal. This zero condition is met when the distribution
+can be found in :ref:`(Theodorou) <Theodorou2>`. The asphericity is always
-of particles is spherically symmetric (hence the name asphericity) but also whenever the particle
+non-negative and zero only when the three principal moments are equal.
-distribution is symmetric with respect to the three coordinate axes, e.g.,
+This zero condition is met when the distribution of particles is spherically
-when the particles are distributed uniformly on a cube, tetrahedron or other Platonic
+symmetric (hence the name asphericity) but also whenever the particle
-solid. The acylindricity is always non-negative and zero only when the two principal
+distribution is symmetric with respect to the three coordinate axes (e.g.,
-moments are equal. This zero condition is met when the distribution of particles is
+when the particles are distributed uniformly on a cube, tetrahedron, or other
-cylindrically symmetric (hence the name, acylindricity), but also whenever the particle
+Platonic solid). The acylindricity is always non-negative and zero only when
-distribution is symmetric with respect to the two coordinate axes, e.g., when the
+the two principal moments are equal. This zero condition is met when the
-particles are distributed uniformly on a regular prism. the relative shape anisotropy
+distribution of particles is cylindrically symmetric (hence the name,
-is bounded between zero (if all points are spherically symmetric) and one
+acylindricity), but also whenever the particle distribution is symmetric with
+respect to the two coordinate axes (e.g., when the particles are distributed
+uniformly on a regular prism). The relative shape anisotropy
+is bounded between 0 (if all points are spherically symmetric) and 1
 (if all points lie on a line).
 
 The tensor keyword must be specified in the compute gyration/chunk command.
@@ -61,22 +65,23 @@ The tensor keyword must be specified in the compute gyration/chunk command.
    See the :doc:`dump custom <dump>` command for a discussion of "unwrapped"
    coordinates. See the Atoms section of the :doc:`read_data <read_data>`
    command for a discussion of image flags and how they are set for each
-   atom.  You can reset the image flags (e.g. to 0) before invoking this
+   atom.  You can reset the image flags (e.g., to 0) before invoking this
    compute by using the :doc:`set image <set>` command.
 
 Output info
 """""""""""
 
 This compute calculates a global array with six columns,
-which can be accessed by indices 1-6. The first three columns are the
+which can be accessed by indices 1--6. The first three columns are the
-eigenvalues of the gyration tensor followed by the asphericity, the acylindricity
+eigenvalues of the gyration tensor followed by the asphericity, the
-and the relative shape anisotropy.  The computed values can be used by any command
+acylindricity and the relative shape anisotropy.  The computed values can be
-that uses global array values from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
+used by any command that uses global array values from a compute as input.
-options.
+See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
+output options.
 
 The array calculated by this compute is
-"intensive".  The first five columns will be in
+"intensive."  The first five columns will be in
-distance\^2 :doc:`units <units>` while the sixth one is dimensionless.
+distance\ :math:`^2` :doc:`units <units>` while the sixth one is dimensionless.
 
 Restrictions
 """"""""""""

doc/src/compute_heat_flux.rst

@@ -6,7 +6,7 @@ compute heat/flux command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID heat/flux ke-ID pe-ID stress-ID
 
@@ -28,13 +28,13 @@ Description
 
 Define a computation that calculates the heat flux vector based on
 contributions from atoms in the specified group.  This can be used by
-itself to measure the heat flux through a set of atoms (e.g. a region
+itself to measure the heat flux through a set of atoms (e.g., a region
 between two thermostatted reservoirs held at different temperatures),
 or to calculate a thermal conductivity using the equilibrium
 Green-Kubo formalism.
 
 For other non-equilibrium ways to compute a thermal conductivity, see
-the :doc:`Howto kappa <Howto_kappa>` doc page..  These include use of
+the :doc:`Howto kappa <Howto_kappa>` doc page.  These include use of
 the :doc:`fix thermal/conductivity <fix_thermal_conductivity>` command
 for the Muller-Plathe method.  Or the :doc:`fix heat <fix_heat>` command
 which can add or subtract heat from groups of atoms.
@@ -52,12 +52,12 @@ third calculates per-atom stress (\ *stress-ID*\ ).
    (or any group whose atoms are superset of the atoms in this compute's
    group).  LAMMPS does not check for this.
 
-In case of two-body interactions, the heat flux is defined as:
+In case of two-body interactions, the heat flux :math:`\mathbf{J}` is defined as
 
 .. math::
    \mathbf{J} &= \frac{1}{V} \left[ \sum_i e_i \mathbf{v}_i - \sum_{i} \mathbf{S}_{i} \mathbf{v}_i \right] \\
    &= \frac{1}{V} \left[ \sum_i e_i \mathbf{v}_i + \sum_{i<j} \left( \mathbf{F}_{ij} \cdot \mathbf{v}_j \right) \mathbf{r}_{ij} \right] \\
-   &= \frac{1}{V} \left[ \sum_i e_i \mathbf{v}_i + \frac{1}{2} \sum_{i<j} \left( \mathbf{F}_{ij} \cdot \left(\mathbf{v}_i + \mathbf{v}_j \right)  \right) \mathbf{r}_{ij} \right]
+   &= \frac{1}{V} \left[ \sum_i e_i \mathbf{v}_i + \frac{1}{2} \sum_{i<j} \bigl( \mathbf{F}_{ij} \cdot \left(\mathbf{v}_i + \mathbf{v}_j \right) \bigr) \mathbf{r}_{ij} \right]
 
 :math:`e_i` in the first term of the equation
 is the per-atom energy (potential and kinetic).
@@ -68,12 +68,12 @@ See :doc:`compute stress/atom <compute_stress_atom>`
 and :doc:`compute centroid/stress/atom <compute_stress_atom>`
 for possible definitions of atomic stress :math:`\mathbf{S}_i`
 in the case of bonded and many-body interactions.
-The tensor multiplies :math:`\mathbf{v}_i` as a 3x3 matrix-vector multiply
+The tensor multiplies :math:`\mathbf{v}_i` by a :math:`3\times3` matrix
 to yield a vector.
-Note that as discussed below, the 1/:math:`{V}` scaling factor in the
+Note that as discussed below, the :math:`1/V` scaling factor in the
-equation for :math:`\mathbf{J}` is NOT included in the calculation performed by
+equation for :math:`\mathbf{J}` is **not** included in the calculation
-these computes; you need to add it for a volume appropriate to the atoms
+performed by these computes; you need to add it for a volume appropriate to the
-included in the calculation.
+atoms included in the calculation.
 
 .. note::
 
@@ -103,7 +103,7 @@ included in the calculation.
    contribution when computed via :doc:`compute stress/atom <compute_stress_atom>`
    are highly unphysical and should not be used.
 
-The Green-Kubo formulas relate the ensemble average of the
+The Green--Kubo formulas relate the ensemble average of the
 auto-correlation of the heat flux :math:`\mathbf{J}`
 to the thermal conductivity :math:`\kappa`:
 
@@ -112,17 +112,18 @@ to the thermal conductivity :math:`\kappa`:
 
 ----------
 
-The heat flux can be output every so many timesteps (e.g. via the
+The heat flux can be output every so many timesteps (e.g., via the
 :doc:`thermo_style custom <thermo_style>` command).  Then as a
 post-processing operation, an auto-correlation can be performed, its
-integral estimated, and the Green-Kubo formula above evaluated.
+integral estimated, and the Green--Kubo formula above evaluated.
 
 The :doc:`fix ave/correlate <fix_ave_correlate>` command can calculate
 the auto-correlation.  The trap() function in the
 :doc:`variable <variable>` command can calculate the integral.
 
-An example LAMMPS input script for solid Ar is appended below.  The
+An example LAMMPS input script for solid argon is appended below.  The
-result should be: average conductivity ~0.29 in W/mK.
+result should be an average conductivity
+:math:`\approx 0.29~\mathrm{W/m \cdot K}`.
 
 ----------
 
@@ -130,22 +131,22 @@ Output info
 """""""""""
 
 This compute calculates a global vector of length 6.
-The first 3 components are the :math:`x`, :math:`y`, :math:`z`
+The first three components are the :math:`x`, :math:`y`, and :math:`z`
-components of the full heat flux vector,
+components of the full heat flux vector
-i.e. (:math:`J_x`, :math:`J_y`, :math:`J_z`).
+(i.e., :math:`J_x`, :math:`J_y`, and :math:`J_z`).
-The next 3 components are the :math:`x`, :math:`y`, :math:`z` components
+The next three components are the :math:`x`, :math:`y`, and :math:`z`
-of just the convective portion of the flux, i.e. the
+components of just the convective portion of the flux (i.e., the
-first term in the equation for :math:`\mathbf{J}`.
+first term in the equation for :math:`\mathbf{J}`).
-Each component can be
+Each component can be accessed by indices 1--6. These values can be used by any
-accessed by indices 1-6. These values can be used by any command that
+command that uses global vector values from a compute as input.
-uses global vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
+See the :doc:`Howto output <Howto_output>` documentation for an overview of
-options.
+LAMMPS output options.
 
-The vector values calculated by this compute are "extensive", meaning
+The vector values calculated by this compute are "extensive," meaning
 they scale with the number of atoms in the simulation.  They can be
 divided by the appropriate volume to get a flux, which would then be
 an "intensive" value, meaning independent of the number of atoms in
-the simulation.  Note that if the compute is "all", then the
+the simulation.  Note that if the compute is "all," then the
 appropriate volume to divide by is the simulation box volume.
 However, if a sub-group is used, it should be the volume containing
 those atoms.
@@ -172,6 +173,9 @@ none
 
 ----------
 
+Example Input File
+------------------
+
 .. code-block:: LAMMPS
 
    # Sample LAMMPS input script for thermal conductivity of solid Ar

doc/src/compute_hexorder_atom.rst

@@ -6,7 +6,7 @@ compute hexorder/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID hexorder/atom keyword values ...
 
@@ -102,7 +102,7 @@ Output info
 
 This compute calculates a per-atom array with 2 columns, giving the
 real and imaginary parts :math:`q_n`, a complex number restricted to the
-unit disk of the complex plane i.e. :math:`Re(q_n)^2 + Im(q_n)^2 <= 1`.
+unit disk of the complex plane (i.e., :math:`\Re(q_n)^2 + \Im(q_n)^2 \le 1`).
 
 These values can be accessed by any command that uses per-atom values
 from a compute as input.  See the :doc:`Howto output <Howto_output>` doc

doc/src/compute_hma.rst

@@ -6,20 +6,23 @@ compute hma command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID hma temp-ID keyword ...
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * hma = style name of this compute command
 * temp-ID = ID of fix that specifies the set temperature during canonical simulation
-* keyword = *anharmonic* *u* *p Pharm* *cv*
+* one or more keywords or keyword/argument pairs must be appended
+* keyword = *anharmonic* or *u* or *p* or *cv*
 
 .. parsed-literal::
 
      *anharmonic* = compute will return anharmonic property values
      *u* = compute will return potential energy
-     *p* = compute will return pressure.  the following keyword must be the difference between the harmonic pressure and lattice pressure as described below
+     *p* value = Pharm = compute will return pressure
+        Pharm = difference between the harmonic pressure and lattice pressure
+                as described below
      *cv* = compute will return the heat capacity
 
 Examples
@@ -74,44 +77,48 @@ A detailed description of this method can be found in (:ref:`Moustafa <hma-Moust
 
 .. math::
 
-   \left< U\right>_{HMA} = \frac{d}{2} (N-1) k_B T  + \left< U + \frac{1}{2} F\bullet\Delta r \right>
+   \left< U\right>_\text{HMA} = \frac{d}{2} (N-1) k_B T  + \left< U + \frac{1}{2} \vec F\cdot\Delta \vec r \right>
 
 where :math:`N` is the number of atoms in the system, :math:`k_B` is Boltzmann's
-constant, :math:`T` is the temperature, :math:`d` is the
+constant, :math:`T` is the temperature, :math:`d` is the dimensionality of the
-dimensionality of the system (2 or 3 for 2d/3d), :math:`F\bullet\Delta r` is the sum of dot products of the
+system (2 or 3 for 2d/3d), :math:`\vec F\cdot\Delta\vec r` is the sum of dot
-atomic force vectors and displacement (from lattice sites) vectors, and :math:`U` is the sum of
+products of the atomic force vectors and displacement (from lattice sites)
-pair, bond, angle, dihedral, improper, kspace (long-range), and fix energies.
+vectors, and :math:`U` is the sum of pair, bond, angle, dihedral, improper,
+kspace (long-range), and fix energies.
 
 The pressure is computed by the formula:
 
 .. math::
 
-   \left< P\right>_{HMA} = \Delta \hat P + \left< P_{vir} + \frac{\beta \Delta \hat P - \rho}{d(N-1)} F\bullet\Delta r \right>
+   \left< P\right>_{HMA} = \Delta \hat P + \left< P_\text{vir}
+   + \frac{\beta \Delta \hat P - \rho}{d(N-1)} \vec F\cdot\Delta \vec r \right>
 
-where :math:`\rho` is the number density of the system, :math:`\Delta \hat P` is the
+where :math:`\rho` is the number density of the system, :math:`\Delta \hat P`
-difference between the harmonic and lattice pressure, :math:`P_{vir}` is
+is the difference between the harmonic and lattice pressure,
-the virial pressure computed as the sum of pair, bond, angle, dihedral,
+:math:`P_\text{vir}` is the virial pressure computed as the sum of pair, bond,
-improper, kspace (long-range), and fix contributions to the force on each
+angle, dihedral, improper, kspace (long-range), and fix contributions to the
-atom, and :math:`k_B=1/k_B T`.  Although the method will work for any value of :math:`\Delta \hat P`
+force on each atom, and :math:`k_B=1/k_B T`.  Although the method will work for
+any value of :math:`\Delta \hat P`
 specified (use pressure :doc:`units <units>`), the precision of the resultant
 pressure is sensitive to :math:`\Delta \hat P`; the precision tends to be
-best when :math:`\Delta \hat P` is the actual the difference between the lattice
+best when :math:`\Delta \hat P` is the actual the difference between the
-pressure and harmonic pressure.
+lattice pressure and harmonic pressure.
 
 .. math::
 
-   \left<C_V \right>_{HMA} = \frac{d}{2} (N-1) k_B + \frac{1}{k_B T^2} \left( \left<
+   \left<C_V \right>_\text{HMA} = \frac{d}{2} (N-1) k_B
-   U_{HMA}^2 \right> - \left<U_{HMA}\right>^2 \right) + \frac{1}{4 T}
+    + \frac{1}{k_B T^2} \left( \left<U_\text{HMA}^2 \right>
-   \left< F\bullet\Delta r + \Delta r \bullet \Phi \bullet \Delta r \right>
+                         - \left<U_\text{HMA}\right>^2 \right) + \frac{1}{4 T}
+   \left<\vec F\cdot\Delta\vec r + \Delta r \cdot\Phi\cdot \Delta\vec r\right>
 
 where :math:`\Phi` is the Hessian matrix. The compute hma command
 computes the full expression for :math:`C_V` except for the
-:math:`\left<U_{HMA}^2\right>^2` in the variance term, which can be obtained by
+:math:`\left<U_\text{HMA}\right>^2` in the variance term, which can be obtained
-passing the *u* keyword; you must add this extra contribution to the :math:`C_V`
+by passing the *u* keyword; you must add this extra contribution to the
-value reported by this compute.  The variance term can cause significant
+:math:`C_V` value reported by this compute.  The variance term can cause
-round-off error when computing :math:`C_V`.  To address this, the *anharmonic*
+significant round-off error when computing :math:`C_V`.  To address this, the
-keyword can be passed and/or the output format can be specified with more
+*anharmonic* keyword can be passed and/or the output format can be specified
-digits.
+with more digits.
 
 .. code-block:: LAMMPS
 
@@ -124,8 +131,10 @@ When using this keyword, the compute must be first active (it must be included
 via a :doc:`thermo_style custom <thermo_style>` command) while the atoms are
 still at their lattice sites (before equilibration).
 
-The temp-ID specified with compute hma command should be same as the fix-ID of Nose-Hoover (:doc:`fix nvt <fix_nh>`) or
+The temp-ID specified with compute hma command should be same as the fix-ID of
-Berendsen (:doc:`fix temp/berendsen <fix_temp_berendsen>`) thermostat used for the simulation. While using this command, Langevin thermostat
+the Nose--Hoover (:doc:`fix nvt <fix_nh>`) or
+Berendsen (:doc:`fix temp/berendsen <fix_temp_berendsen>`) thermostat used for
+the simulation. While using this command, the Langevin thermostat
 (:doc:`fix langevin <fix_langevin>`)
 should be avoided as its extra forces interfere with the HMA implementation.
 
@@ -160,10 +169,10 @@ Output info
 
 This compute calculates a global vector that includes the n properties
 requested as arguments to the command (the potential energy, pressure and/or heat
-capacity).  The elements of the vector can be accessed by indices 1-n by any
+capacity).  The elements of the vector can be accessed by indices 1--n by any
 command that uses global vector values as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output options.
 
-The vector values calculated by this compute are "extensive".  The
+The vector values calculated by this compute are "extensive."  The
 scalar value will be in energy :doc:`units <units>`.
 
 Restrictions
@@ -180,7 +189,7 @@ Related commands
 :doc:`compute pe <compute_pe>`, :doc:`compute pressure <compute_pressure>`
 
 :doc:`dynamical matrix <dynamical_matrix>` provides a finite difference
-formulation of the hessian provided by Pair's single_hessian, which is used by
+formulation of the Hessian provided by Pair's single_hessian, which is used by
 this compute.
 
 Default

doc/src/compute_improper.rst

@@ -6,7 +6,7 @@ compute improper command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID improper
 
@@ -34,11 +34,13 @@ total energy contributed by one or more of the hybrid sub-styles.
 Output info
 """""""""""
 
-This compute calculates a global vector of length N where N is the
+This compute calculates a global vector of length :math:`N`, where :math:`N` is
-number of sub_styles defined by the :doc:`improper_style hybrid <improper_style>` command.  which can be accessed by indices
+the number of sub_styles defined by the
-1-N.  These values can be used by any command that uses global scalar
+:doc:`improper_style hybrid <improper_style>` command.
-or vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
+These styles can be accessed by the indices 1 through :math:`N`.
-options.
+These values can be used by any command that uses global scalar or vector
+values from a compute as input.  See the :doc:`Howto output <Howto_output>`
+page for an overview of LAMMPS output options.
 
 The vector values are "extensive" and will be in energy
 :doc:`units <units>`.

doc/src/compute_improper_local.rst

@@ -6,7 +6,7 @@ compute improper/local command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID improper/local value1 value2 ...
 
@@ -40,7 +40,7 @@ the individual improper styles listed on
 
 The local data stored by this command is generated by looping over all
 the atoms owned on a processor and their impropers.  An improper will
-only be included if all 4 atoms in the improper are in the specified
+only be included if all four atoms in the improper are in the specified
 compute group.
 
 Note that as atoms migrate from processor to processor, there will be
@@ -69,7 +69,8 @@ array is the number of impropers.  If a single keyword is specified, a
 local vector is produced.  If two or more keywords are specified, a
 local array is produced where the number of columns = the number of
 keywords.  The vector or array can be accessed by any command that
-uses local values from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
+uses local values from a compute as input.  See the
+:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
 The output for *chi* will be in degrees.

doc/src/compute_inertia_chunk.rst

@@ -6,7 +6,7 @@ compute inertia/chunk command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID inertia/chunk chunkID
 
@@ -27,16 +27,20 @@ Description
 Define a computation that calculates the inertia tensor for multiple
 chunks of atoms.
 
-In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+In LAMMPS, chunks are collections of atoms defined by a
+:doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
 to a single chunk (or no chunk).  The ID for this command is specified
 as chunkID.  For example, a single chunk could be the atoms in a
-molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
+molecule or atoms in a spatial bin.  See the
+:doc:`compute chunk/atom <compute_chunk_atom>` and
+:doc:`Howto chunk <Howto_chunk>`
 doc pages for details of how chunks can be defined and examples of how
 they can be used to measure properties of a system.
 
-This compute calculates the 6 components of the symmetric inertia
+This compute calculates the six components of the symmetric inertia
-tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz.  The
+tensor for each chunk, ordered
-calculation includes all effects due to atoms passing through periodic
+:math:`I_{xx},I_{yy},I_{zz},I_{xy},I_{yz},I_{xz}`.
+The calculation includes all effects due to atoms passing through periodic
 boundaries.
 
 Note that only atoms in the specified group contribute to the
@@ -55,7 +59,8 @@ non-zero chunk IDs.
    of "unwrapped" coordinates.  See the Atoms section of the
    :doc:`read_data <read_data>` command for a discussion of image flags and
    how they are set for each atom.  You can reset the image flags
-   (e.g. to 0) before invoking this compute by using the :doc:`set image <set>` command.
+   (e.g., to 0) before invoking this compute by using the
+   :doc:`set image <set>` command.
 
 The simplest way to output the results of the compute inertia/chunk
 calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
@@ -71,14 +76,16 @@ Output info
 """""""""""
 
 This compute calculates a global array where the number of rows = the
-number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  The number of columns =
+number of chunks *Nchunk* as calculated by the specified
-6 for the 6 components of the inertia tensor for each chunk, ordered
+:doc:`compute chunk/atom <compute_chunk_atom>` command.
-as listed above.  These values can be accessed by any command that
+The number of columns is 6, one for each of the 6 components of the inertia
-uses global array values from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
+tensor for each chunk, ordered as listed above.  These values can be accessed
+by any command that uses global array values from a compute as input.  See the
+:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The array values are "intensive".  The array values will be in
+The array values are "intensive."  The array values will be in
-mass\*distance\^2 :doc:`units <units>`.
+mass\*distance\ :math:`^2` :doc:`units <units>`.
 
 Restrictions
 """"""""""""

doc/src/compute_ke.rst

@@ -6,7 +6,7 @@ compute ke command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID ke
 
@@ -27,7 +27,8 @@ Define a computation that calculates the translational kinetic energy
 of a group of particles.
 
 The kinetic energy of each particle is computed as :math:`\frac{1}{2} m
-v^2`, where *m* and *v* are the mass and velocity of the particle.
+v^2`, where *m* and *v* are the mass and velocity of the particle,
+respectively.
 
 There is a subtle difference between the quantity calculated by this
 compute and the kinetic energy calculated by the *ke* or *etotal*
@@ -38,10 +39,10 @@ formula above.  For thermodynamic output, the *ke* keyword infers
 kinetic energy from the temperature of the system with
 :math:`\frac{1}{2} k_B T` of energy for each degree of freedom.  For the
 default temperature computation via the :doc:`compute temp
-<compute_temp>` command, these are the same.  But different computes
+<compute_temp>` command, these are the same.
-that calculate temperature can subtract out different non-thermal
+However, different computes that calculate temperature can subtract out
-components of velocity and/or include different degrees of freedom
+different non-thermal components of velocity and/or include different degrees
-(translational, rotational, etc).
+of freedom (translational, rotational, etc.).
 
 Output info
 """""""""""
@@ -51,7 +52,7 @@ can be used by any command that uses a global scalar value from a
 compute as input.  See the :doc:`Howto output <Howto_output>` doc page
 for an overview of LAMMPS output options.
 
-The scalar value calculated by this compute is "extensive".  The
+The scalar value calculated by this compute is "extensive."  The
 scalar value will be in energy :doc:`units <units>`.
 
 Restrictions

doc/src/compute_ke_atom.rst

@@ -6,7 +6,7 @@ compute ke/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID ke/atom
 
@@ -26,8 +26,8 @@ Description
 Define a computation that calculates the per-atom translational
 kinetic energy for each atom in a group.
 
-The kinetic energy is simply 1/2 m v\^2, where m is the mass and v is
+The kinetic energy is simply :math:`\frac12 m v^2`, where :math:`m` is the mass
-the velocity of each atom.
+and :math:`v` is the velocity of each atom.
 
 The value of the kinetic energy will be 0.0 for atoms not in the
 specified compute group.

doc/src/compute_ke_atom_eff.rst

@@ -6,7 +6,7 @@ compute ke/atom/eff command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID ke/atom/eff
 

doc/src/compute_ke_eff.rst

@@ -6,7 +6,7 @@ compute ke/eff command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID ke/eff
 
@@ -29,9 +29,9 @@ group of eFF particles (nuclei and electrons), as modeled with the
 
 The kinetic energy for each nucleus is computed as :math:`\frac{1}{2} m
 v^2` and the kinetic energy for each electron is computed as
-:math:`\frac{1}{2}(m_e v^2 + \frac{3}{4} m_e s^2)`, where *m*
+:math:`\frac{1}{2}(m_e v^2 + \frac{3}{4} m_e s^2)`, where :math:`m`
-corresponds to the nuclear mass, :math:`m_e` to the electron mass, *v*
+corresponds to the nuclear mass, :math:`m_e` to the electron mass, :math:`v`
-to the translational velocity of each particle, and *s* to the radial
+to the translational velocity of each particle, and :math:`s` to the radial
 velocity of the electron, respectively.
 
 There is a subtle difference between the quantity calculated by this

doc/src/compute_ke_rigid.rst

@@ -6,7 +6,7 @@ compute ke/rigid command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID ke/rigid fix-ID
 
@@ -25,11 +25,13 @@ Description
 """""""""""
 
 Define a computation that calculates the translational kinetic energy
-of a collection of rigid bodies, as defined by one of the :doc:`fix rigid <fix_rigid>` command variants.
+of a collection of rigid bodies, as defined by one of the
+:doc:`fix rigid <fix_rigid>` command variants.
 
-The kinetic energy of each rigid body is computed as 1/2 M Vcm\^2,
+The kinetic energy of each rigid body is computed as
-where M is the total mass of the rigid body, and Vcm is its
+:math:`\frac12 M V_\text{cm}^2`,
-center-of-mass velocity.
+where :math:`M` is the total mass of the rigid body, and :math:`V_\text{cm}`
+is its center-of-mass velocity.
 
 The *fix-ID* should be the ID of one of the :doc:`fix rigid <fix_rigid>`
 commands which defines the rigid bodies.  The group specified in the
@@ -42,10 +44,11 @@ Output info
 
 This compute calculates a global scalar (the summed KE of all the
 rigid bodies).  This value can be used by any command that uses a
-global scalar value from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
+global scalar value from a compute as input.  See the
+:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The scalar value calculated by this compute is "extensive".  The
+The scalar value calculated by this compute is "extensive."  The
 scalar value will be in energy :doc:`units <units>`.
 
 Restrictions

doc/src/compute_mesont.rst

@@ -6,30 +6,29 @@ compute mesont command
 Syntax
 """"""
 
+.. code-block:: LAMMPS
 
-.. parsed-literal::
+   compute ID group-ID mesont style
-
-   compute ID group-ID mesont mode
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * mesont = style name of the compute command
-* mode = one of estretch, ebend, etube (see details below)
+* style = *estretch* or *ebend* or *etube*
 
 Examples
 """"""""
 
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute 1 all mesont estretch
 
 Description
 """""""""""
 
-These computes define computations for the stretching (estretch), bending
+These computes define computations for the stretching (*estretch*), bending
-(ebend), and intertube (etube) per-node (atom) and total energies. The
+(*ebend*), and intertube (*etube*) per-node (atom) and total energies. The
-evaluated value is selected by a parameter passed to the compute: estretch,
+evaluated value is selected by the style parameter passed to the compute
-ebend, etube.
+(*estretch*, *ebend*,or *etube*).
 
 Output info
 """""""""""

doc/src/compute_mliap.rst

@@ -36,10 +36,10 @@ Description
 """""""""""
 
 Compute style *mliap* provides a general interface to the gradient
-of machine-learning interatomic potentials w.r.t. model parameters.
+of machine-learning interatomic potentials with respect to model parameters.
 It is used primarily for calculating the gradient of energy, force, and
-stress components w.r.t. model parameters, which is useful when training
+stress components with respect to model parameters, which is useful when
-:doc:`mliap pair_style <pair_mliap>` models to match target data.
+training :doc:`mliap pair_style <pair_mliap>` models to match target data.
 It provides separate
 definitions of the interatomic potential functional form (*model*)
 and the geometric quantities that characterize the atomic positions
@@ -58,8 +58,8 @@ The compute *mliap* command must be followed by two keywords
 
 The *model* keyword is followed by the model style (*linear*,
 *quadratic* or *mliappy*).  The *mliappy* model is only available if
-LAMMPS is built with the *mliappy* python module. There are
+LAMMPS is built with the *mliappy* Python module. There are
-:ref:`specific installation instructions <mliap>` for that.
+:ref:`specific installation instructions <mliap>` for that module.
 
 The *descriptor* keyword is followed by a descriptor style, and
 additional arguments.  The compute currently supports two descriptor
@@ -79,13 +79,13 @@ described in detail there.
    must match the value of *nelems* in the descriptor file.
 
 Compute *mliap* calculates a global array containing gradient information.
-The number of columns in the array is :math:`nelems \times nparams + 1`.
+The number of columns in the array is *nelems* :math:`\times` *nparams* + 1.
-The first row of the array contain the derivative of potential energy w.r.t. to
+The first row of the array contain the derivative of potential energy with
-each parameter and each element. The last six rows
+respect to. to each parameter and each element. The last six rows
 of the array contain the corresponding derivatives of the
 virial stress tensor, listed in Voigt notation: *pxx*, *pyy*, *pzz*,
-*pyz*, *pxz*, *pxy*. In between the energy and stress rows are
+*pyz*, *pxz*, and *pxy*. In between the energy and stress rows are
-the 3\*\ *N* rows containing the derivatives of the force components.
+the :math:`3N` rows containing the derivatives of the force components.
 See section below on output for a detailed description of how
 rows and columns are ordered.
 
@@ -107,19 +107,19 @@ layout in the global array.
 
 The optional keyword *gradgradflag* controls how the force
 gradient is calculated. A value of 1 requires that the model provide
-the matrix of double gradients of energy w.r.t. both parameters
+the matrix of double gradients of energy with respect to both parameters
 and descriptors. For the linear and quadratic models this matrix is
 sparse and so is easily calculated and stored. For other models, this
 matrix may be prohibitively expensive to calculate and store.
 A value of 0 requires that the descriptor provide the derivative
-of the descriptors w.r.t. the position of every neighbor atom.
+of the descriptors with respect to the position of every neighbor atom.
 This is not optimal for linear and quadratic models, but may be
 a better choice for more complex models.
 
 Atoms not in the group do not contribute to this compute.
 Neighbor atoms not in the group do not contribute to this compute.
 The neighbor list needed to compute this quantity is constructed each
-time the calculation is performed (i.e. each time a snapshot of atoms
+time the calculation is performed (i.e., each time a snapshot of atoms
 is dumped).  Thus it can be inefficient to compute/dump this quantity
 too frequently.
 
@@ -144,17 +144,20 @@ too frequently.
 Output info
 """""""""""
 
-Compute *mliap* evaluates a global array.
+Compute *mliap* evaluates a global array.  The columns are arranged into
-The columns are arranged into
 *nelems* blocks, listed in order of element *I*\ . Each block
 contains one column for each of the *nparams* model parameters.
 A final column contains the corresponding energy, force component
 on an atom, or virial stress component. The rows of the array appear
 in the following order:
 
-* 1 row: Derivatives of potential energy w.r.t. each parameter of each element.
+* 1 row: Derivatives of potential energy with respect to each parameter of each element.
-* 3\*\ *N* rows: Derivatives of force components. x, y, and z components of force on atom *i* appearing in consecutive rows. The atoms are sorted based on atom ID.
+* :math:`3N` rows: Derivatives of force components; the *x*, *y*, and *z*
-* 6 rows: Derivatives of virial stress tensor  w.r.t. each parameter of each element. The ordering of the rows follows Voigt notation: *pxx*, *pyy*, *pzz*, *pyz*, *pxz*, *pxy*.
+  components of the force on atom *i* appear in consecutive rows. The atoms are
+  sorted based on atom ID.
+* 6 rows: Derivatives of the virial stress tensor with respect to each
+  parameter of each element. The ordering of the rows follows Voigt notation:
+  *pxx*, *pyy*, *pzz*, *pyz*, *pxz*, *pxy*.
 
 These values can be accessed by any command that uses a global array
 from a compute as input.  See the :doc:`Howto output <Howto_output>` doc

doc/src/compute_momentum.rst

@@ -6,7 +6,7 @@ compute momentum command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID momentum
 
@@ -24,7 +24,8 @@ Description
 """""""""""
 
 Define a computation that calculates the translational momentum *p*
-of a group of particles.  It is computed as the sum :math:`\vec{p} = \sum_i m_i \cdot \vec{v}_i`
+of a group of particles.  It is computed as the sum
+:math:`\vec{p} = \sum_i m_i \cdot \vec{v}_i`
 over all particles in the compute group, where *m* and *v* are
 the mass and velocity vector of the particle, respectively.
 
@@ -36,7 +37,7 @@ length 3. This value can be used by any command that uses a global
 vector value from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
-The vector value calculated by this compute is "extensive". The vector
+The vector value calculated by this compute is "extensive." The vector
 value will be in mass\*velocity :doc:`units <units>`.
 
 Restrictions

doc/src/compute_msd.rst

@@ -6,7 +6,7 @@ compute msd command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID msd keyword values ...
 
@@ -34,12 +34,13 @@ Description
 Define a computation that calculates the mean-squared displacement
 (MSD) of the group of atoms, including all effects due to atoms
 passing through periodic boundaries.  For computation of the non-Gaussian
-parameter of mean-squared displacement, see the :doc:`compute msd/nongauss <compute_msd_nongauss>` command.
+parameter of mean-squared displacement, see the
+:doc:`compute msd/nongauss <compute_msd_nongauss>` command.
 
-A vector of four quantities is calculated by this compute.  The first 3
+A vector of four quantities is calculated by this compute.  The first three
-elements of the vector are the squared dx,dy,dz displacements, summed
+elements of the vector are the squared *dx*, *dy*, and *dz* displacements,
-and averaged over atoms in the group.  The fourth element is the total
+summed and averaged over atoms in the group.  The fourth element is the total
-squared displacement, i.e. (dx\*dx + dy\*dy + dz\*dz), summed and
+squared displacement (i.e., :math:`dx^2 + dy^2 + dz^2`), summed and
 averaged over atoms in the group.
 
 The slope of the mean-squared displacement (MSD) versus time is
@@ -100,12 +101,12 @@ Output info
 """""""""""
 
 This compute calculates a global vector of length 4, which can be
-accessed by indices 1-4 by any command that uses global vector values
+accessed by indices 1--4 by any command that uses global vector values
 from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
 page for an overview of LAMMPS output options.
 
-The vector values are "intensive".  The vector values will be in
+The vector values are "intensive."  The vector values will be in
-distance\^2 :doc:`units <units>`.
+distance\ :math:`^2` :doc:`units <units>`.
 
 Restrictions
 """"""""""""

doc/src/compute_msd_chunk.rst

@@ -6,7 +6,7 @@ compute msd/chunk command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID msd/chunk chunkID
 
@@ -27,19 +27,21 @@ Description
 Define a computation that calculates the mean-squared displacement
 (MSD) for multiple chunks of atoms.
 
-In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+In LAMMPS, chunks are collections of atoms defined by a
+:doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
 to a single chunk (or no chunk).  The ID for this command is specified
 as chunkID.  For example, a single chunk could be the atoms in a
-molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
+molecule or atoms in a spatial bin.  See the
+:doc:`compute chunk/atom <compute_chunk_atom>` and
+:doc:`Howto chunk <Howto_chunk>`
 doc pages for details of how chunks can be defined and examples of how
 they can be used to measure properties of a system.
 
 Four quantities are calculated by this compute for each chunk.  The
-first 3 quantities are the squared dx,dy,dz displacements of the
+first 3 quantities are the squared *dx*, *dy*, and *dz* displacements of the
-center-of-mass.  The fourth component is the total squared displacement,
+center-of-mass.  The fourth component is the total squared displacement
-i.e. (dx\*dx + dy\*dy + dz\*dz) of the center-of-mass.  These
+(i.e., :math:`dx^2 + dy^2 + dz^2`) of the center-of-mass.  These calculations
-calculations include all effects due to atoms passing through periodic
+include all effects due to atoms passing through periodic boundaries.
-boundaries.
 
 Note that only atoms in the specified group contribute to the
 calculation.  The :doc:`compute chunk/atom <compute_chunk_atom>` command
@@ -58,12 +60,14 @@ compute command was first invoked.
 
 .. note::
 
-   The number of chunks *Nchunk* calculated by the :doc:`compute chunk/atom <compute_chunk_atom>` command must remain constant each
+   The number of chunks *Nchunk* calculated by the
-   time this compute is invoked, so that the displacement for each chunk
+   :doc:`compute chunk/atom <compute_chunk_atom>` command must remain constant
+   each time this compute is invoked, so that the displacement for each chunk
    from its original position can be computed consistently.  If *Nchunk*
    does not remain constant, an error will be generated.  If needed, you
-   can enforce a constant *Nchunk* by using the *nchunk once* or *ids
+   can enforce a constant *Nchunk* by using the *nchunk once* or *ids once*
-   once* options when specifying the :doc:`compute chunk/atom <compute_chunk_atom>` command.
+   options when specifying the :doc:`compute chunk/atom <compute_chunk_atom>`
+   command.
 
 .. note::
 
@@ -84,7 +88,8 @@ compute command was first invoked.
    "unwrapped" coordinates.  See the Atoms section of the
    :doc:`read_data <read_data>` command for a discussion of image flags and
    how they are set for each atom.  You can reset the image flags
-   (e.g. to 0) before invoking this compute by using the :doc:`set image <set>` command.
+   (e.g., to 0) before invoking this compute by using the
+   :doc:`set image <set>` command.
 
 .. note::
 
@@ -109,14 +114,15 @@ Output info
 """""""""""
 
 This compute calculates a global array where the number of rows = the
-number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  The number of columns =
+number of chunks *Nchunk* as calculated by the specified
-4 for dx,dy,dz and the total displacement.  These values can be
+:doc:`compute chunk/atom <compute_chunk_atom>` command.
-accessed by any command that uses global array values from a compute
+The number of columns = 4 for *dx*, *dy*, *dz*, and the total displacement.
-as input.  See the :doc:`Howto output <Howto_output>` page for an
+These values can be accessed by any command that uses global array values from
+a compute as input.  See the :doc:`Howto output <Howto_output>` page for an
 overview of LAMMPS output options.
 
-The array values are "intensive".  The array values will be in
+The array values are "intensive."  The array values will be in
-distance\^2 :doc:`units <units>`.
+distance\ :math:`^2` :doc:`units <units>`.
 
 Restrictions
 """"""""""""

doc/src/compute_msd_nongauss.rst

@@ -6,7 +6,7 @@ compute msd/nongauss command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID msd/nongauss keyword values ...
 
@@ -35,21 +35,21 @@ Define a computation that calculates the mean-squared displacement
 including all effects due to atoms passing through periodic boundaries.
 
 A vector of three quantities is calculated by this compute.  The first
-element of the vector is the total squared dx,dy,dz displacements
+element of the vector is the total squared displacement,
-drsquared = (dx\*dx + dy\*dy + dz\*dz) of atoms, and the second is the
+:math:`dr^2 = dx^2 + dy^2 + dz^2`, of the atoms, and the second is the
-fourth power of these displacements drfourth = (dx\*dx + dy\*dy +
+fourth power of these displacements, :math:`dr^4 = (dx^2 + dy^2 + dz^2)^2`,
-dz\*dz)\*(dx\*dx + dy\*dy + dz\*dz), summed and averaged over atoms in the
+summed and averaged over atoms in the group.  The third component is the
-group.  The third component is the nonGaussian diffusion parameter NGP =
+non-Gaussian diffusion parameter NGP,
-3\*drfourth/(5\*drsquared\*drsquared), i.e.
 
 .. math::
 
- NGP(t) = 3<(r(t)-r(0))^4>/(5<(r(t)-r(0))^2>^2) - 1
+   \text{NGP}(t) = \frac{3\left\langle(r(t)-r(0))^4\right\rangle}
+                        {5\left\langle(r(t)-r(0))^2\right\rangle^2} - 1.
 
 The NGP is a commonly used quantity in studies of dynamical
-heterogeneity.  Its minimum theoretical value (-0.4) occurs when all
+heterogeneity.  Its minimum theoretical value :math:`(-0.4)` occurs when all
-atoms have the same displacement magnitude.  NGP=0 for Brownian
+atoms have the same displacement magnitude.  :math:`\text{NGP}=0` for Brownian
-diffusion, while NGP > 0 when some mobile atoms move faster than
+diffusion, while :math:`\text{NGP} > 0` when some mobile atoms move faster than
 others.
 
 If the *com* option is set to *yes* then the effect of any drift in
@@ -63,13 +63,13 @@ Output info
 """""""""""
 
 This compute calculates a global vector of length 3, which can be
-accessed by indices 1-3 by any command that uses global vector values
+accessed by indices 1--3 by any command that uses global vector values
 from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
 page for an overview of LAMMPS output options.
 
-The vector values are "intensive".  The first vector value will be in
+The vector values are "intensive."  The first vector value will be in
-distance\^2 :doc:`units <units>`, the second is in distance\^4 units, and
+distance\ :math:`^2` :doc:`units <units>`, the second is in
-the third is dimensionless.
+distance\ :math:`^4` units, and the third is dimensionless.
 
 Restrictions
 """"""""""""

doc/src/compute_nbond_atom.rst

@@ -6,7 +6,7 @@ compute nbond/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID nbond/atom
 

doc/src/compute_omega_chunk.rst

@@ -6,7 +6,7 @@ compute omega/chunk command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID omega/chunk chunkID
 
@@ -27,18 +27,23 @@ Description
 Define a computation that calculates the angular velocity (omega) of
 multiple chunks of atoms.
 
-In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+In LAMMPS, chunks are collections of atoms defined by a
+:doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
 to a single chunk (or no chunk).  The ID for this command is specified
 as chunkID.  For example, a single chunk could be the atoms in a
-molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
+molecule or atoms in a spatial bin.  See the
+:doc:`compute chunk/atom <compute_chunk_atom>` and
+:doc:`Howto chunk <Howto_chunk>`
 doc pages for details of how chunks can be defined and examples of how
 they can be used to measure properties of a system.
 
-This compute calculates the 3 components of the angular velocity
+This compute calculates the three components of the angular velocity
-vector for each chunk, via the formula L = Iw where L is the angular
+vector for each chunk via the formula
-momentum vector of the chunk, I is its moment of inertia tensor, and w
+:math:`\vec L = \mathrm{I}\cdot \vec\omega`, where :math:`\vec L` is the
-is omega = angular velocity of the chunk.  The calculation includes
+angular momentum vector of the chunk, :math:`\mathrm{I}` is its moment of
-all effects due to atoms passing through periodic boundaries.
+inertia tensor, and :math:`\omega` is the angular velocity of the chunk.
+The calculation includes all effects due to atoms passing through periodic
+boundaries.
 
 Note that only atoms in the specified group contribute to the
 calculation.  The :doc:`compute chunk/atom <compute_chunk_atom>` command
@@ -56,7 +61,8 @@ non-zero chunk IDs.
    of "unwrapped" coordinates.  See the Atoms section of the
    :doc:`read_data <read_data>` command for a discussion of image flags and
    how they are set for each atom.  You can reset the image flags
-   (e.g. to 0) before invoking this compute by using the :doc:`set image <set>` command.
+   (e.g., to 0) before invoking this compute by using the
+   :doc:`set image <set>` command.
 
 The simplest way to output the results of the compute omega/chunk
 calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
@@ -71,14 +77,14 @@ command, for example:
 Output info
 """""""""""
 
-This compute calculates a global array where the number of rows = the
+This compute calculates a global array where the number of rows is the
-number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  The number of columns =
+number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  The number of columns is 3 for the three
-3 for the 3 xyz components of the angular velocity for each chunk.
+(*x*, *y*, *z*) components of the angular velocity for each chunk.
 These values can be accessed by any command that uses global array
-values from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
+values from a compute as input.  See the :doc:`Howto output <Howto_output>`
-options.
+page for an overview of LAMMPS output options.
 
-The array values are "intensive".  The array values will be in
+The array values are "intensive."  The array values will be in
 velocity/distance :doc:`units <units>`.
 
 Restrictions

doc/src/compute_orientorder_atom.rst

@@ -9,7 +9,7 @@ Accelerator Variants: *orientorder/atom/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID orientorder/atom keyword values ...
 
@@ -42,30 +42,30 @@ Description
 """""""""""
 
 Define a computation that calculates a set of bond-orientational
-order parameters :math:`Q_l` for each atom in a group. These order parameters
+order parameters :math:`Q_\ell` for each atom in a group. These order parameters
 were introduced by :ref:`Steinhardt et al. <Steinhardt>` as a way to
 characterize the local orientational order in atomic structures.
-For each atom, :math:`Q_l` is a real number defined as follows:
+For each atom, :math:`Q_\ell` is a real number defined as follows:
 
 .. math::
 
-   \bar{Y}_{lm} = & \frac{1}{nnn}\sum_{j = 1}^{nnn} Y_{lm}( \theta( {\bf r}_{ij} ), \phi( {\bf r}_{ij} ) ) \\
+   \bar{Y}_{\ell m} = & \frac{1}{nnn}\sum_{j = 1}^{nnn} Y_{\ell m}\bigl( \theta( {\bf r}_{ij} ), \phi( {\bf r}_{ij} ) \bigr) \\
-   Q_l = & \sqrt{\frac{4 \pi}{2 l + 1} \sum_{m = -l}^{m = l} \bar{Y}_{lm} \bar{Y}^*_{lm}}
+   Q_\ell  = & \sqrt{\frac{4 \pi}{2 \ell  + 1} \sum_{m = -\ell }^{m = \ell } \bar{Y}_{\ell m} \bar{Y}^*_{\ell m}}
 
 The first equation defines the local order parameters as averages
-of the spherical harmonics :math:`Y_{lm}` for each neighbor.
+of the spherical harmonics :math:`Y_{\ell m}` for each neighbor.
 These are complex number components of the 3D analog of the 2D order
 parameter :math:`q_n`, which is implemented as LAMMPS compute
 :doc:`hexorder/atom <compute_hexorder_atom>`.
 The summation is over the *nnn* nearest
-neighbors of the central atom.
+neighbors of the central atom.  The angles :math:`\theta` and :math:`\phi` are
-The angles :math:`theta` and :math:`phi` are the standard spherical polar angles
+the standard spherical polar angles
 defining the direction of the bond vector :math:`r_{ij}`.
-The phase and sign of :math:`Y_{lm}` follow the standard conventions,
+The phase and sign of :math:`Y_{\ell m}` follow the standard conventions,
-so that :math:`{\rm sign}(Y_{ll}(0,0)) = (-1)^l`.
+so that :math:`\mathrm{sign}(Y_{\ell\ell}(0,0)) = (-1)^\ell`.
-The second equation defines :math:`Q_l`, which is a
+The second equation defines :math:`Q_\ell`, which is a
 rotationally invariant non-negative amplitude obtained by summing
-over all the components of degree *l*\ .
+over all the components of degree :math:`\ell`.
 
 The optional keyword *cutoff* defines the distance cutoff
 used when searching for neighbors. The default value, also
@@ -73,7 +73,7 @@ the maximum allowable value, is the cutoff specified
 by the pair style.
 
 The optional keyword *nnn* defines the number of nearest
-neighbors used to calculate :math:`Q_l`. The default value is 12.
+neighbors used to calculate :math:`Q_\ell`. The default value is 12.
 If the value is NULL, then all neighbors up to the
 specified distance cutoff are used.
 
@@ -84,32 +84,45 @@ degree of each order parameter. Because :math:`Q_2` and all odd-degree order
 parameters are zero for atoms in cubic crystals (see
 :ref:`Steinhardt <Steinhardt>`), the default order parameters are :math:`Q_4`,
 :math:`Q_6`, :math:`Q_8`, :math:`Q_{10}`, and :math:`Q_{12}`. For the FCC
-crystal with *nnn* =12, :math:`Q_4 = \sqrt{\frac{7}{192}} = 0.19094...`.
+crystal with *nnn* =12,
+
+.. math::
+   Q_4 = \sqrt{\frac{7}{192}} \approx 0.19094
+
 The numerical values of all order
-parameters up to :math:`Q_12` for a range of commonly encountered
+parameters up to :math:`Q_{12}` for a range of commonly encountered
 high-symmetry structures are given in Table I of :ref:`Mickel et al. <Mickel>`,
 and these can be reproduced with this compute.
 
-The optional keyword *wl* will output the third-order invariants :math:`W_l`
+The optional keyword *wl* will output the third-order invariants :math:`W_\ell`
 (see Eq. 1.4 in :ref:`Steinhardt <Steinhardt>`) for the same degrees as
-for the :math:`Q_l` parameters. For the FCC crystal with *nnn* =12,
+for the :math:`Q_\ell` parameters. For the FCC crystal with *nnn* = 12,
-:math:`W_4` = -sqrt(14/143).(49/4096)/Pi\^1.5 = -0.0006722136...
+
+.. math::
+
+   W_4 = -\sqrt{\frac{14}{143}} \left(\frac{49}{4096}\right) \pi^{-3/2} \approx -0.0006722136
 
 The optional keyword *wl/hat* will output the normalized third-order
-invariants :math:`\hat{W}_l` (see Eq. 2.2 in :ref:`Steinhardt <Steinhardt>`)
+invariants :math:`\hat{W}_\ell` (see Eq. 2.2 in :ref:`Steinhardt <Steinhardt>`)
-for the same degrees as for the :math:`Q_l` parameters. For the FCC crystal
+for the same degrees as for the :math:`Q_\ell` parameters. For the FCC crystal
-with *nnn* =12, :math:`\hat{W}_4 = -\frac{7}{3} \sqrt{\frac{2}{429}} = -0.159317...`
+with *nnn* =12,
-The numerical
+
-values of :math:`\hat{W}_l` for a range of commonly encountered high-symmetry
+.. math:: 
-structures are given in Table I of :ref:`Steinhardt <Steinhardt>`, and these
+
-can be reproduced with this keyword.
+   \hat{W}_4 = -\frac{7}{3} \sqrt{\frac{2}{429}} \approx -0.159317
+
+The numerical values of :math:`\hat{W}_\ell` for a range of commonly
+encountered high-symmetry structures are given in Table I of
+:ref:`Steinhardt <Steinhardt>`, and these can be reproduced with this keyword.
 
 The optional keyword *components* will output the components of the
-*normalized* complex vector :math:`\hat{Y}_{lm} = \bar{Y}_{lm}/|\bar{Y}_{lm}|` of degree *ldegree*\,
+*normalized* complex vector
-which must be included in the list of order parameters to be computed. This option can be used
+:math:`\hat{Y}_{\ell m} = \bar{Y}_{\ell m}/|\bar{Y}_{\ell m}|`
-in conjunction with :doc:`compute coord_atom <compute_coord_atom>` to
+of degree *ldegree*\, which must be included in the list of order parameters to
-calculate the ten Wolde's criterion to identify crystal-like
+be computed. This option can be used in conjunction with
-particles, as discussed in :ref:`ten Wolde <tenWolde2>`.
+:doc:`compute coord_atom <compute_coord_atom>` to calculate the ten Wolde's
+criterion to identify crystal-like particles, as discussed in
+:ref:`ten Wolde <tenWolde2>`.
 
 The optional keyword *chunksize* is only applicable when using the
 the KOKKOS package and is ignored otherwise. This keyword controls
@@ -119,12 +132,12 @@ if there are 32768 atoms in the simulation and the *chunksize*
 is set to 16384, the parameter calculation will be broken up
 into two passes.
 
-The value of :math:`Q_l` is set to zero for atoms not in the
+The value of :math:`Q_\ell` is set to zero for atoms not in the
 specified compute group, as well as for atoms that have less than
 *nnn* neighbors within the distance cutoff, unless *nnn* is NULL.
 
 The neighbor list needed to compute this quantity is constructed each
-time the calculation is performed (i.e. each time a snapshot of atoms
+time the calculation is performed (i.e., each time a snapshot of atoms
 is dumped).  Thus it can be inefficient to compute/dump this quantity
 too frequently.
 
@@ -155,19 +168,21 @@ Output info
 """""""""""
 
 This compute calculates a per-atom array with *nlvalues* columns,
-giving the :math:`Q_l` values for each atom, which are real numbers on the
+giving the :math:`Q_\ell` values for each atom, which are real numbers in the
-range :math:`0 <= Q_l <= 1`.
+range :math:`0 \le Q_\ell \le 1`.
 
-If the keyword *wl* is set to yes, then the :math:`W_l` values for each
+If the keyword *wl* is set to yes, then the :math:`W_\ell` values for each
 atom will be added to the output array, which are real numbers.
 
-If the keyword *wl/hat* is set to yes, then the :math:`\hat{W}_l`
+If the keyword *wl/hat* is set to yes, then the :math:`\hat{W}_\ell`
 values for each atom will be added to the output array, which are real numbers.
 
 If the keyword *components* is set, then the real and imaginary parts
-of each component of *normalized* :math:`\hat{Y}_{lm}` will be added to the
+of each component of *normalized* :math:`\hat{Y}_{\ell m}` will be added to the
-output array in the following order: :math:`{\rm Re}(\hat{Y}_{-m}), {\rm Im}(\hat{Y}_{-m}),
+output array in the following order:
-{\rm Re}(\hat{Y}_{-m+1}), {\rm Im}(\hat{Y}_{-m+1}), \dots , {\rm Re}(\hat{Y}_m), {\rm Im}(\hat{Y}_m)`.
+:math:`\Re(\hat{Y}_{-m}),` :math:`\Im(\hat{Y}_{-m}),`
+:math:`\Re(\hat{Y}_{-m+1}),` :math:`\Im(\hat{Y}_{-m+1}), \dotsc,`
+:math:`\Re(\hat{Y}_m),` :math:`\Im(\hat{Y}_m).`
 
 In summary, the per-atom array will contain *nlvalues* columns, followed by
 an additional *nlvalues* columns if *wl* is set to yes, followed by
@@ -193,7 +208,7 @@ Default
 """""""
 
 The option defaults are *cutoff* = pair style cutoff, *nnn* = 12,
-*degrees* = 5 4 6 8 10 12 i.e. :math:`Q_4`, :math:`Q_6`, :math:`Q_8`, :math:`Q_{10}`, and :math:`Q_{12}`,
+*degrees* = 5 4 6 8 10 12 (i.e., :math:`Q_4`, :math:`Q_6`, :math:`Q_8`, :math:`Q_{10}`, and :math:`Q_{12}`),
 *wl* = no, *wl/hat* = no, *components* off, and *chunksize* = 16384
 
 ----------

doc/src/compute_pair.rst

@@ -6,7 +6,7 @@ compute pair command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID pair pstyle [nstyle] [evalue]
 
@@ -74,7 +74,7 @@ Output info
 
 This compute calculates a global scalar which is *epair* or *evdwl* or
 *ecoul*\ .  If the pair style supports it, it also calculates a global
-vector of length >= 1, as determined by the pair style.  These values
+vector of length :math:`\ge` 1, as determined by the pair style.  These values
 can be used by any command that uses global scalar or vector values
 from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
 page for an overview of LAMMPS output options.

doc/src/compute_pair_local.rst

@@ -6,7 +6,7 @@ compute pair/local command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID pair/local value1 value2 ... keyword args ...
 
@@ -57,7 +57,7 @@ force cutoff distance for that interaction, as defined by the
 commands.
 
 The value *dist* is the distance between the pair of atoms.
-The values *dx*, *dy*, and *dz* are the xyz components of the
+The values *dx*, *dy*, and *dz* are the :math:`(x,y,z)` components of the
 *distance* between the pair of atoms. This value is always the
 distance from the atom of lower to the one with the higher id.
 
@@ -65,21 +65,21 @@ The value *eng* is the interaction energy for the pair of atoms.
 
 The value *force* is the force acting between the pair of atoms, which
 is positive for a repulsive force and negative for an attractive
-force.  The values *fx*, *fy*, and *fz* are the xyz components of
+force.  The values *fx*, *fy*, and *fz* are the :math:`(x,y,z)` components of
 *force* on atom I.
 
 A pair style may define additional pairwise quantities which can be
-accessed as *p1* to *pN*, where N is defined by the pair style.  Most
+accessed as *p1* to *pN*, where :math:`N` is defined by the pair style.  Most
-pair styles do not define any additional quantities, so N = 0.  An
+pair styles do not define any additional quantities, so :math:`N = 0`.  An
 example of ones that do are the :doc:`granular pair styles <pair_gran>`
 which calculate the tangential force between two particles and return
-its components and magnitude acting on atom I for N = 1,2,3,4.  See
+its components and magnitude acting on atom :math:`I` for
-individual pair styles for details.
+:math:`N \in \{1,2,3,4\}`.  See individual pair styles for details.
 
 When using *pN* with pair style *hybrid*, the output will be the Nth
 quantity from the sub-style that computes the pairwise interaction
 (based on atom types).  If that sub-style does not define a *pN*,
-the output will be 0.0.  The maximum allowed N is the maximum number
+the output will be 0.0.  The maximum allowed :math:`N` is the maximum number
 of quantities provided by any sub-style.
 
 When using *pN* with pair style *hybrid/overlay* the quantities
@@ -104,7 +104,9 @@ the pairwise cutoff defined by the :doc:`pair_style <pair_style>`
 command for the types of the two atoms is used.  For the *radius*
 setting, the sum of the radii of the two particles is used as a
 cutoff.  For example, this is appropriate for granular particles which
-only interact when they are overlapping, as computed by :doc:`granular pair styles <pair_gran>`.  Note that if a granular model defines atom
+only interact when they are overlapping, as computed by
+:doc:`granular pair styles <pair_gran>`.
+Note that if a granular model defines atom
 types such that all particles of a specific type are monodisperse
 (same diameter), then the two settings are effectively identical.
 
@@ -113,7 +115,8 @@ no consistent ordering of the entries within the local vector or array
 from one timestep to the next.  The only consistency that is
 guaranteed is that the ordering on a particular timestep will be the
 same for local vectors or arrays generated by other compute commands.
-For example, pair output from the :doc:`compute property/local <compute_property_local>` command can be combined
+For example, pair output from the
+:doc:`compute property/local <compute_property_local>` command can be combined
 with data from this command and output by the :doc:`dump local <dump>`
 command in a consistent way.
 
@@ -127,13 +130,13 @@ Here is an example of how to do this:
 
 .. note::
 
-   For pairs, if two atoms I,J are involved in 1-2, 1-3, 1-4
+   For pairs, if two atoms I,J are involved in 1--2, 1--3, and 1--4
    interactions within the molecular topology, their pairwise interaction
    may be turned off, and thus they may not appear in the neighbor list,
    and will not be part of the local data created by this command.  More
    specifically, this will be true of I,J pairs with a weighting factor
    of 0.0; pairs with a non-zero weighting factor are included.  The
-   weighting factors for 1-2, 1-3, and 1-4 pairwise interactions are set
+   weighting factors for 1--2, 1--3, and 1--4 pairwise interactions are set
    by the :doc:`special_bonds <special_bonds>` command.  An exception is if
    long-range Coulombics are being computed via the
    :doc:`kspace_style <kspace_style>` command, then atom pairs with

doc/src/compute_pe.rst

@@ -6,7 +6,7 @@ compute pe command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID pe keyword ...
 
@@ -27,19 +27,19 @@ Description
 """""""""""
 
 Define a computation that calculates the potential energy of the
-entire system of atoms.  The specified group must be "all".  See the
+entire system of atoms.  The specified group must be "all."  See the
 :doc:`compute pe/atom <compute_pe_atom>` command if you want per-atom
 energies.  These per-atom values could be summed for a group of atoms
 via the :doc:`compute reduce <compute_reduce>` command.
 
-The energy is calculated by the various pair, bond, etc potentials
+The energy is calculated by the various pair, bond, etc. potentials
 defined for the simulation.  If no extra keywords are listed, then the
 potential energy is the sum of pair, bond, angle, dihedral, improper,
-kspace (long-range), and fix energy.  I.e. it is as if all the
+:math:`k`-space (long-range), and fix energy (i.e., it is as though all the
-keywords were listed.  If any extra keywords are listed, then only
+keywords were listed).  If any extra keywords are listed, then only
 those components are summed to compute the potential energy.
 
-The Kspace contribution requires 1 extra FFT each timestep the energy
+The :math:`k`-space contribution requires 1 extra FFT each timestep the energy
 is calculated, if using the PPPM solver via the :doc:`kspace_style pppm <kspace_style>` command.  Thus it can increase the cost of the
 PPPM calculation if it is needed on a large fraction of the simulation
 timesteps.
@@ -73,7 +73,7 @@ value can be used by any command that uses a global scalar value from
 a compute as input.  See the :doc:`Howto output <Howto_output>` doc page
 for an overview of LAMMPS output options.
 
-The scalar value calculated by this compute is "extensive".  The
+The scalar value calculated by this compute is "extensive."  The
 scalar value will be in energy :doc:`units <units>`.
 
 Restrictions

doc/src/compute_pe_atom.rst

@@ -6,7 +6,7 @@ compute pe/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID pe/atom keyword ...
 
@@ -34,20 +34,20 @@ you want the potential energy of the entire system.
 The per-atom energy is calculated by the various pair, bond, etc
 potentials defined for the simulation.  If no extra keywords are
 listed, then the potential energy is the sum of pair, bond, angle,
-dihedral,improper, kspace (long-range), and fix energy.  I.e. it is as
+dihedral, improper, :math:`k`-space (long-range), and fix energy (i.e., it is as
-if all the keywords were listed.  If any extra keywords are listed,
+though all the keywords were listed).  If any extra keywords are listed,
 then only those components are summed to compute the potential energy.
 
 Note that the energy of each atom is due to its interaction with all
 other atoms in the simulation, not just with other atoms in the group.
 
-For an energy contribution produced by a small set of atoms (e.g. 4
+For an energy contribution produced by a small set of atoms (e.g., 4
 atoms in a dihedral or 3 atoms in a Tersoff 3-body interaction), that
-energy is assigned in equal portions to each atom in the set.
+energy is assigned in equal portions to each atom in the set (e.g., 1/4 of the
-E.g. 1/4 of the dihedral energy to each of the 4 atoms.
+dihedral energy to each of the four atoms).
 
 The :doc:`dihedral_style charmm <dihedral_charmm>` style calculates
-pairwise interactions between 1-4 atoms.  The energy contribution of
+pairwise interactions between 1--4 atoms.  The energy contribution of
 these terms is included in the pair energy, not the dihedral energy.
 
 The KSpace contribution is calculated using the method in
@@ -81,8 +81,9 @@ in the last 2 columns of thermo output:
 .. note::
 
    The per-atom energy does not include any Lennard-Jones tail
-   corrections to the energy added by the :doc:`pair_modify tail yes <pair_modify>` command, since those are contributions to the
+   corrections to the energy added by the
-   global system energy.
+   :doc:`pair_modify tail yes <pair_modify>` command, since those are
+   contributions to the global system energy.
 
 Output info
 """""""""""

doc/src/compute_plasticity_atom.rst

@@ -6,7 +6,7 @@ compute plasticity/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID plasticity/atom
 
@@ -24,16 +24,19 @@ Description
 """""""""""
 
 Define a computation that calculates the per-atom plasticity for each
-atom in a group.  This is a quantity relevant for :doc:`Peridynamics models <pair_peri>`.  See `this document <PDF/PDLammps_overview.pdf>`_
+atom in a group.  This is a quantity relevant for
+:doc:`Peridynamics models <pair_peri>`.
+See `this document <PDF/PDLammps_overview.pdf>`_
 for an overview of LAMMPS commands for Peridynamics modeling.
 
 The plasticity for a Peridynamic particle is the so-called consistency
-parameter (lambda).  For elastic deformation lambda = 0, otherwise
+parameter (:math:`\lambda`).  For elastic deformation, :math:`\lambda = 0`,
-lambda > 0 for plastic deformation.  For details, see
+otherwise :math:`\lambda > 0` for plastic deformation.  For details, see
 :ref:`(Mitchell) <Mitchell>` and the PDF doc included in the LAMMPS
 distribution in `doc/PDF/PDLammps_EPS.pdf <PDF/PDLammps_EPS.pdf>`_.
 
-This command can be invoked for one of the Peridynamic :doc:`pair styles <pair_peri>`: peri/eps.
+This command can be invoked for one of the Peridynamic
+:doc:`pair styles <pair_peri>`: peri/eps.
 
 The plasticity value will be 0.0 for atoms not in the specified
 compute group.
@@ -46,7 +49,7 @@ any command that uses per-atom values from a compute as input.  See
 the :doc:`Howto output <Howto_output>` page for an overview of
 LAMMPS output options.
 
-The per-atom vector values are unitless numbers (lambda) >= 0.0.
+The per-atom vector values are unitless numbers :math:`\lambda \ge 0.0`.
 
 Restrictions
 """"""""""""
@@ -70,5 +73,5 @@ none
 .. _Mitchell:
 
 **(Mitchell)** Mitchell, "A non-local, ordinary-state-based
-viscoelasticity model for peridynamics", Sandia National Lab Report,
+viscoelasticity model for peridynamics," Sandia National Lab Report,
 8064:1-28 (2011).

doc/src/compute_pressure.rst

@@ -6,7 +6,7 @@ compute pressure command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID pressure temp-ID keyword ...
 
@@ -29,7 +29,8 @@ Description
 """""""""""
 
 Define a computation that calculates the pressure of the entire system
-of atoms.  The specified group must be "all".  See the :doc:`compute stress/atom <compute_stress_atom>` command if you want per-atom
+of atoms.  The specified group must be "all."  See the
+:doc:`compute stress/atom <compute_stress_atom>` command if you want per-atom
 pressure (stress).  These per-atom values could be summed for a group
 of atoms via the :doc:`compute reduce <compute_reduce>` command.
 
@@ -37,35 +38,36 @@ The pressure is computed by the formula
 
 .. math::
 
-   P = \frac{N k_B T}{V} + \frac{\sum_{i}^{N'} r_i \bullet f_i}{dV}
+   P = \frac{N k_B T}{V} + \frac{1}{V d}\sum_{i=1}^{N'} \vec r_i \cdot \vec f_i
 
 where *N* is the number of atoms in the system (see discussion of DOF
-below), :math:`k_B` is the Boltzmann constant, *T* is the temperature, d
+below), :math:`k_B` is the Boltzmann constant, *T* is the temperature, *d*
-is the dimensionality of the system (2 or 3 for 2d/3d), and *V* is the
+is the dimensionality of the system (2 for 2d, 3 for 3d), and *V* is the
 system volume (or area in 2d).  The second term is the virial, equal to
--dU/dV, computed for all pairwise as well as 2-body, 3-body, 4-body,
+:math:`-dU/dV`, computed for all pairwise as well as 2-body, 3-body, 4-body,
-many-body, and long-range interactions, where :math:`r_i` and
+many-body, and long-range interactions, where :math:`\vec r_i` and
-:math:`f_i` are the position and force vector of atom *i*, and the black
+:math:`\vec f_i` are the position and force vector of atom *i*, and the
-dot indicates a dot product.  This is computed in parallel for each
+dot indicates the dot product (scalar product).  This is computed in parallel
-sub-domain and then summed over all parallel processes. Thus N'
+for each sub-domain and then summed over all parallel processes. Thus
-necessarily includes atoms from neighboring sub-domains (so-called ghost
+:math:`N'` necessarily includes atoms from neighboring sub-domains (so-called
-atoms) and the position and force vectors of ghost atoms are thus
+ghost atoms) and the position and force vectors of ghost atoms are thus
 included in the summation.  Only when running in serial and without
-periodic boundary conditions is N' = N = the number of atoms in the
+periodic boundary conditions is :math:`N' = N` the number of atoms in the
-system.  :doc:`Fixes <fix>` that impose constraints (e.g. the :doc:`fix
+system.  :doc:`Fixes <fix>` that impose constraints (e.g., the :doc:`fix
 shake <fix_shake>` command) may also contribute to the virial term.
 
 A symmetric pressure tensor, stored as a 6-element vector, is also
-calculated by this compute.  The 6 components of the vector are
+calculated by this compute.  The six components of the vector are
-ordered xx, yy, zz, xy, xz, yz.  The equation for the I,J components
+ordered :math:`xx,` :math:`yy,` :math:`zz,` :math:`xy,` :math:`xz,` :math:`yz.`
-(where I and J = x,y,z) is similar to the above formula, except that
+The equation for the :math:`(I,J)` components (where :math:`I` and :math:`J`
-the first term uses components of the kinetic energy tensor and the
+are :math:`x`, :math:`y`, or :math:`z`) is similar to the above formula,
+except that the first term uses components of the kinetic energy tensor and the
 second term uses components of the virial tensor:
 
 .. math::
 
-   P_{IJ} = \frac{\sum_{k}^{N} m_k v_{k_I} v_{k_J}}{V} +
+   P_{IJ} = \frac{1}{V}\sum_{k=1}^{N} m_k v_{k_I} v_{k_J} +
-   \frac{\sum_{k}^{N'} r_{k_I} f_{k_J}}{V}
+   \frac{1}{V}\sum_{k=1}^{N'} r_{k_I} f_{k_J}.
 
 If no extra keywords are listed, the entire equations above are
 calculated.  This includes a kinetic energy (temperature) term and the
@@ -89,27 +91,30 @@ command.  If the kinetic energy is not included in the pressure, than
 the temperature compute is not used and can be specified as NULL.
 Normally the temperature compute used by compute pressure should
 calculate the temperature of all atoms for consistency with the virial
-term, but any compute style that calculates temperature can be used,
+term, but any compute style that calculates temperature can be used
-e.g. one that excludes frozen atoms or other degrees of freedom.
+(e.g., one that excludes frozen atoms or other degrees of freedom).
 
 Note that if desired the specified temperature compute can be one that
 subtracts off a bias to calculate a temperature using only the thermal
-velocity of the atoms, e.g. by subtracting a background streaming
+velocity of the atoms (e.g., by subtracting a background streaming
-velocity.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.
+velocity).
+See the doc pages for individual :doc:`compute commands <compute>` to determine
+which ones include a bias.
 
-Also note that the N in the first formula above is really
+Also note that the :math:`N` in the first formula above is really
-degrees-of-freedom divided by d = dimensionality, where the DOF value
+degrees-of-freedom divided by :math:`d` = dimensionality, where the DOF value
-is calculated by the temperature compute.  See the various :doc:`compute temperature <compute>` styles for details.
+is calculated by the temperature compute.
+See the various :doc:`compute temperature <compute>` styles for details.
 
-A compute of this style with the ID of "thermo_press" is created when
+A compute of this style with the ID of thermo_press is created when
 LAMMPS starts up, as if this command were in the input script:
 
 .. code-block:: LAMMPS
 
    compute thermo_press all pressure thermo_temp
 
-where "thermo_temp" is the ID of a similarly defined compute of style
+where thermo_temp is the ID of a similarly defined compute of style
-"temp".  See the "thermo_style" command for more details.
+"temp."  See the :doc:`thermo_style <thermo_style>` command for more details.
 
 ----------
 
@@ -122,15 +127,16 @@ Output info
 
 This compute calculates a global scalar (the pressure) and a global
 vector of length 6 (pressure tensor), which can be accessed by indices
-1-6.  These values can be used by any command that uses global scalar
+1--6.  These values can be used by any command that uses global scalar
 or vector values from a compute as input.  See the :doc:`Howto output
 <Howto_output>` page for an overview of LAMMPS output options.
 
 The ordering of values in the symmetric pressure tensor is as follows:
-pxx, pyy, pzz, pxy, pxz, pyz.
+:math:`p_{xx},` :math:`p_{yy},` :math:`p_{zz},` :math:`p_{xy},`
+:math:`p_{xz},` :math:`p_{yz}.`
 
 The scalar and vector values calculated by this compute are
-"intensive".  The scalar and vector values will be in pressure
+"intensive."  The scalar and vector values will be in pressure
 :doc:`units <units>`.
 
 Restrictions

doc/src/compute_pressure_uef.rst

@@ -6,7 +6,7 @@ compute pressure/uef command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID pressure/uef temp-ID keyword ...
 
@@ -42,14 +42,14 @@ Restrictions
 """"""""""""
 
 This fix is part of the UEF package. It is only enabled if LAMMPS
-was built with that package. See the :doc:`Build package <Build_package>` page for more info.
+was built with that package. See the :doc:`Build package <Build_package>` page
+for more info.
 
 This command can only be used when :doc:`fix nvt/uef <fix_nh_uef>`
 or :doc:`fix npt/uef <fix_nh_uef>` is active.
 
 The kinetic contribution to the pressure tensor
-will be accurate only when
+will be accurate only when the compute specified by *temp-ID* is a
-the compute specified by *temp-ID* is a
 :doc:`compute temp/uef <compute_temp_uef>`.
 
 Related commands

doc/src/compute_property_atom.rst

@@ -6,7 +6,7 @@ compute property/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID property/atom input1 input2 ...
 
@@ -127,7 +127,7 @@ LAMMPS.
 The values are stored in a per-atom vector or array as discussed
 below.  Zeroes are stored for atoms not in the specified group or for
 quantities that are not defined for a particular particle in the group
-(e.g. *shapex* if the particle is not an ellipsoid).
+(e.g., *shapex* if the particle is not an ellipsoid).
 
 Attributes *i_name*, *d_name*, *i2_name*, *d2_name* refer to custom
 per-atom integer and floating-point vectors or arrays that have been
@@ -135,7 +135,7 @@ added via the :doc:`fix property/atom <fix_property_atom>` command.
 When that command is used specific names are given to each attribute
 which are the "name" portion of these attributes.  For arrays *i2_name*
 and *d2_name*, the column of the array must also be included following
-the name in brackets: e.g. d2_xyz[2], i2_mySpin[3].
+the name in brackets (e.g., d2_xyz[2] or i2_mySpin[3]).
 
 The additional quantities only accessible via this command, and not
 directly via the :doc:`dump custom <dump>` command, are as follows.
@@ -144,21 +144,21 @@ directly via the :doc:`dump custom <dump>` command, are as follows.
 number of explicit bonds assigned to an atom.  Note that if the
 :doc:`newton bond <newton>` command is set to *on*\ , which is the
 default, then every bond in the system is assigned to only one of the
-two atoms in the bond.  Thus a bond between atoms I,J may be tallied
+two atoms in the bond.  Thus a bond between atoms :math:`I` and :math:`J` may
-for either atom I or atom J.  If :doc:`newton bond off <newton>` is
+be tallied for either atom :math:`I` or atom :math:`J`.
-set, it will be tallied with both atom I and atom J.
+If :doc:`newton bond off <newton>` is set, it will be tallied with both atom
+:math:`I` and atom :math:`J`.
 
-*Shapex*, *shapey*, and *shapez* are defined for ellipsoidal particles
+The quantities *shapex*, *shapey*, and *shapez* are defined for ellipsoidal
-and define the 3d shape of each particle.
+particles and define the 3d shape of each particle.
 
-*Quatw*, *quati*, *quatj*, and *quatk* are defined for ellipsoidal
+The quantities *quatw*, *quati*, *quatj*, and *quatk* are defined for
-particles and body particles and store the 4-vector quaternion
+ellipsoidal particles and body particles and store the 4-vector quaternion
 representing the orientation of each particle.  See the :doc:`set <set>`
 command for an explanation of the quaternion vector.
 
-*End1x*, *end1y*, *end1z*, *end2x*, *end2y*, *end2z*, are
+*End1x*, *end1y*, *end1z*, *end2x*, *end2y*, *end2z*, are defined for line
-defined for line segment particles and define the end points of each
+segment particles and define the end points of each line segment.
-line segment.
 
 *Corner1x*, *corner1y*, *corner1z*, *corner2x*, *corner2y*,
 *corner2z*, *corner3x*, *corner3y*, *corner3z*, are defined for
@@ -179,12 +179,12 @@ per-atom values from a compute as input.  See the :doc:`Howto output
 <Howto_output>` page for an overview of LAMMPS output options.
 
 The vector or array values will be in whatever :doc:`units <units>` the
-corresponding attribute is in, e.g. velocity units for vx, charge
+corresponding attribute is in (e.g., velocity units for *vx*, charge
-units for q, etc.
+units for *q*).
 
-For the spin quantities, sp is in the units of the Bohr magneton, spx,
+For the spin quantities, *sp* is in the units of the Bohr magneton;
-spy, and spz are unitless quantities, and fmx, fmy and fmz are given
+*spx*, *spy*, and *spz* are unitless quantities; and *fmx*, *fmy*, and *fmz*
-in rad/THz.
+are given in rad/THz.
 
 Restrictions
 """"""""""""

doc/src/compute_property_chunk.rst

@@ -6,7 +6,7 @@ compute property/chunk command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID property/chunk chunkID input1 input2 ...
 
@@ -35,19 +35,24 @@ Description
 Define a computation that stores the specified attributes of chunks of
 atoms.
 
-In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
+In LAMMPS, chunks are collections of atoms defined by a
+:doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
 to a single chunk (or no chunk).  The ID for this command is specified
-as chunkID.  For example, a single chunk could be the atoms in a
+as chunkID.  For example, a single chunk could be the atoms in a molecule or
-molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
+atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>`
-doc pages for details of how chunks can be defined and examples of how
+and :doc:`Howto chunk <Howto_chunk>` doc pages for details of how chunks can be
-they can be used to measure properties of a system.
+defined and examples of how they can be used to measure properties of a system.
 
 This compute calculates and stores the specified attributes of chunks
-as global data so they can be accessed by other :doc:`output commands <Howto_output>` and used in conjunction with other
+as global data so they can be accessed by other
-commands that generate per-chunk data, such as :doc:`compute com/chunk <compute_com_chunk>` or :doc:`compute msd/chunk <compute_msd_chunk>`.
+:doc:`output commands <Howto_output>` and used in conjunction with other
+commands that generate per-chunk data, such as
+:doc:`compute com/chunk <compute_com_chunk>` or
+:doc:`compute msd/chunk <compute_msd_chunk>`.
 
 Note that only atoms in the specified group contribute to the
-calculation of the *count* attribute.  The :doc:`compute chunk/atom <compute_chunk_atom>` command defines its own group;
+calculation of the *count* attribute.  The 
+:doc:`compute chunk/atom <compute_chunk_atom>` command defines its own group;
 atoms will have a chunk ID = 0 if they are not in that group,
 signifying they are not assigned to a chunk, and will thus also not
 contribute to this calculation.  You can specify the "all" group for
@@ -59,7 +64,7 @@ The *count* attribute is the number of atoms in the chunk.
 The *id* attribute stores the original chunk ID for each chunk.  It
 can only be used if the *compress* keyword was set to *yes* for the
 :doc:`compute chunk/atom <compute_chunk_atom>` command referenced by
-chunkID.  This means that the original chunk IDs (e.g. molecule IDs)
+chunkID.  This means that the original chunk IDs (e.g., molecule IDs)
 will have been compressed to remove chunk IDs with no atoms assigned
 to them.  Thus a compressed chunk ID of 3 may correspond to an original
 chunk ID (molecule ID in this case) of 415.  The *id* attribute will
@@ -75,7 +80,7 @@ is the center point of the bin in the corresponding dimension.  Style
 Note that if the value of the *units* keyword used in the :doc:`compute chunk/atom command <compute_chunk_atom>` is *box* or *lattice*, the
 *coordN* attributes will be in distance :doc:`units <units>`.  If the
 value of the *units* keyword is *reduced*, the *coordN* attributes
-will be in unitless reduced units (0-1).
+will be in unitless reduced units (0--1).
 
 The simplest way to output the results of the compute property/chunk
 calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
@@ -105,7 +110,7 @@ accessed by any command that uses global values from a compute as
 input.  See the :doc:`Howto output <Howto_output>` page for an
 overview of LAMMPS output options.
 
-The vector or array values are "intensive".  The values will be
+The vector or array values are "intensive."  The values will be
 unitless or in the units discussed above.
 
 Restrictions

doc/src/compute_property_local.rst

@@ -6,37 +6,65 @@ compute property/local command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID property/local attribute1 attribute2 ... keyword args ...
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * property/local = style name of this compute command
-* one or more attributes may be appended
+* one or more attributes of the same type (neighbor, pair, bond, angle,
+  dihedral, or improper) may be appended
 
   .. parsed-literal::
 
-       possible attributes = natom1 natom2 ntype1 ntype2
+     possible attributes = natom1, natom2, ntype1, ntype2,
-                             patom1 patom2 ptype1 ptype2
+                           patom1, patom2, ptype1, ptype2,
-                             batom1 batom2 btype
+                           batom1, batom2, btype,
-                             aatom1 aatom2 aatom3 atype
+                           aatom1, aatom2, aatom3, atype,
-                             datom1 datom2 datom3 datom4 dtype
+                           datom1, datom2, datom3, datom4, dtype,
-                             iatom1 iatom2 iatom3 iatom4 itype
+                           iatom1, iatom2, iatom3, iatom4, itype
+
+  * Neighbor attributes
 
   .. parsed-literal::
 
-          natom1, natom2 = IDs of 2 atoms in each pair (within neighbor cutoff)
+     natom1, natom2 = store IDs of 2 atoms in each pair (within neighbor cutoff)
-          ntype1, ntype2 = type of 2 atoms in each pair (within neighbor cutoff)
+     ntype1, ntype2 = store types of 2 atoms in each pair (within neighbor cutoff)
-          patom1, patom2 = IDs of 2 atoms in each pair (within force cutoff)
+
-          ptype1, ptype2 = type of 2 atoms in each pair (within force cutoff)
+  * Pair attributes
-          batom1, batom2 = IDs of 2 atoms in each bond
+
-          btype = bond type of each bond
+  .. parsed-literal::
-          aatom1, aatom2, aatom3 = IDs of 3 atoms in each angle
+
-          atype = angle type of each angle
+     patom1, patom2 = store IDs of 2 atoms in each pair (within force cutoff)
-          datom1, datom2, datom3, datom4 = IDs of 4 atoms in each dihedral
+     ptype1, ptype2 = store types of 2 atoms in each pair (within force cutoff)
-          dtype = dihedral type of each dihedral
+
-          iatom1, iatom2, iatom3, iatom4 = IDs of 4 atoms in each improper
+  * Bond attributes
-          itype = improper type of each improper
+
+  .. parsed-literal::
+
+     batom1, batom2 = store IDs of 2 atoms in each bond
+     btype = store bond type of each bond
+
+  * Angle attributes
+
+  .. parsed-literal::
+
+     aatom1, aatom2, aatom3 = store IDs of 3 atoms in each angle
+     atype = store angle type of each angle
+
+  * Dihedral attributes
+
+  .. parsed-literal::
+
+     datom1, datom2, datom3, datom4 = store IDs of 4 atoms in each dihedral
+     dtype = store dihedral type of each dihedral
+
+  * Improper attributes
+
+  .. parsed-literal::
+
+     iatom1, iatom2, iatom3, iatom4 = store IDs of 4 atoms in each improper
+     itype = store improper type of each improper
 
 * zero or more keyword/arg pairs may be appended
 * keyword = *cutoff*
@@ -66,7 +94,7 @@ If multiple attributes are specified then they must all generate the
 same amount of information, so that the resulting local array has the
 same number of rows for each column.  This means that only bond
 attributes can be specified together, or angle attributes, etc.  Bond
-and angle attributes can not be mixed in the same compute
+and angle attributes cannot be mixed in the same compute
 property/local command.
 
 If the inputs are pair attributes, the local data is generated by
@@ -113,21 +141,21 @@ same for local vectors or arrays generated by other compute commands.
 For example, output from the :doc:`compute bond/local <compute_bond_local>` command can be combined with bond
 atom indices from this command and output by the :doc:`dump local <dump>` command in a consistent way.
 
-The *natom1* and *natom2*, or *patom1* and *patom2* attributes refer
+The *natom1* and *natom2* or *patom1* and *patom2* attributes refer
 to the atom IDs of the 2 atoms in each pairwise interaction computed
 by the :doc:`pair_style <pair_style>` command.  The *ntype1* and
-*ntype2*, or *ptype1* and *ptype2* attributes refer to the atom types
+*ntype2* or *ptype1* and *ptype2* attributes refer to the atom types
 of the 2 atoms in each pairwise interaction.
 
 .. note::
 
-   For pairs, if two atoms I,J are involved in 1-2, 1-3, 1-4
+   For pairs, if two atoms :math:`I,J` are involved in 1--2, 1--3, 1--4
    interactions within the molecular topology, their pairwise interaction
    may be turned off, and thus they may not appear in the neighbor list,
    and will not be part of the local data created by this command.  More
-   specifically, this may be true of I,J pairs with a weighting factor of
+   specifically, this may be true of :math:`I,J` pairs with a weighting factor
-   0.0; pairs with a non-zero weighting factor are included.  The
+   of 0.0; pairs with a non-zero weighting factor are included.  The
-   weighting factors for 1-2, 1-3, and 1-4 pairwise interactions are set
+   weighting factors for 1--2, 1--3, and 1--4 pairwise interactions are set
    by the :doc:`special_bonds <special_bonds>` command.
 
 The *batom1* and *batom2* attributes refer to the atom IDs of the 2
@@ -136,7 +164,7 @@ the type of the bond, from 1 to Nbtypes = # of bond types.  The number
 of bond types is defined in the data file read by the
 :doc:`read_data <read_data>` command.
 
-The attributes that start with "a", "d", "i", refer to similar values
+The attributes that start with "a," "d," and "i" refer to similar values
 for :doc:`angles <angle_style>`, :doc:`dihedrals <dihedral_style>`, and
 :doc:`impropers <improper_style>`.
 
@@ -149,7 +177,8 @@ the array is the number of bonds, angles, etc.  If a single input is
 specified, a local vector is produced.  If two or more inputs are
 specified, a local array is produced where the number of columns = the
 number of inputs.  The vector or array can be accessed by any command
-that uses local values from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
+that uses local values from a compute as input.  See the
+:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options.
 
 The vector or array values will be integers that correspond to the

doc/src/compute_ptm_atom.rst

@@ -6,13 +6,13 @@ compute ptm/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID ptm/atom structures threshold group2-ID
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * ptm/atom = style name of this compute command
-* structures = structure types to search for
+* structures = *default* or *all* or any hyphen-separated combination of *fcc*, *hcp*, *bcc*, *ico*, *sc*, *dcub*, *dhex*, or *graphene* = structure types to search for
 * threshold = lattice distortion threshold (RMSD)
 * group2-ID determines which group is used for neighbor selection (optional, default "all")
 
@@ -43,9 +43,10 @@ Currently, there are seven lattice structures PTM recognizes:
 * dhex (diamond hexagonal) = 7
 * graphene = 8
 
-The value of the PTM structure will be 0 for unknown types and -1 for atoms not in the specified
+The value of the PTM structure will be 0 for unknown types and :math:`-1` for
-compute group.  The choice of structures to search for can be specified using the "structures"
+atoms not in the specified compute group.  The choice of structures to search
-argument, which is a hyphen-separated list of structure keywords.
+for can be specified using the "structures" argument, which is a
+hyphen-separated list of structure keywords.
 Two convenient pre-set options are provided:
 
 * default: fcc-hcp-bcc-ico
@@ -63,21 +64,25 @@ The deviation is calculated as:
 
 .. math::
 
-   \text{RMSD}(\mathbf{u}, \mathbf{v}) = \min_{s, \mathbf{Q}} \sqrt{\frac{1}{N} \sum\limits_{i=1}^{N}
+   \text{RMSD}(\mathbf{u}, \mathbf{v})
-   {\left|\left| s[\vec{u_i} - \overline{\mathbf{u}}] - \mathbf{Q} \vec{v_i} \right|\right|}^2}
+    = \min_{s, \mathbf{Q}} \sqrt{\frac{1}{N} \sum\limits_{i=1}^{N}
+   {\left\lVert s[\vec{u_i} - \mathbf{\bar{u}}]
+                 - \mathbf{Q} \cdot \vec{v_i} \right\rVert}^2}
 
-Here, u and v contain the coordinates of the local and ideal structures respectively,
+Here, :math:`\vec u` and :math:`\vec v` contain the coordinates of the local
-s is a scale factor, and Q is a rotation.  The best match is identified by the
+and ideal structures respectively, :math:`s` is a scale factor, and
-lowest RMSD value, using the optimal scaling, rotation, and correspondence between the
+:math:`\mathbf Q` is a rotation.  The best match is identified by the lowest
+RMSD value, using the optimal scaling, rotation, and correspondence between the
 points.
 
-The 'threshold' keyword sets an upper limit on the maximum permitted deviation before
+The *threshold* keyword sets an upper limit on the maximum permitted deviation
-a local structure is identified as disordered.  Typical values are in the range 0.1-0.15,
+before a local structure is identified as disordered.  Typical values are in
-but larger values may be desirable at higher temperatures.
+the range 0.1--0.15, but larger values may be desirable at higher temperatures.
-A value of 0 is equivalent to infinity and can be used if no threshold is desired.
+A value of 0 is equivalent to infinity and can be used if no threshold is
+desired.
 
 The neighbor list needed to compute this quantity is constructed each
-time the calculation is performed (e.g. each time a snapshot of atoms
+time the calculation is performed (e.g., each time a snapshot of atoms
 is dumped).  Thus it can be inefficient to compute/dump this quantity
 too frequently or to have multiple compute/dump commands, each with a
 *ptm/atom* style. By default the compute processes **all** neighbors
@@ -102,11 +107,12 @@ Results are stored in the per-atom array in the following order:
 * qy
 * qz
 
-The type is a number from -1 to 8.  The rmsd is a positive real number.
+The type is a number from :math:`-1` to 8. The rmsd is a positive real number.
 The interatomic distance is computed from the scale factor in the RMSD equation.
-The (qw,qx,qy,qz) parameters represent the orientation of the local structure
+The :math:`(qw,qx,qy,qz)` parameters represent the orientation of the local
-in quaternion form.  The reference coordinates for each template (from which the
+structure in quaternion form.  The reference coordinates for each template
-orientation is determined) can be found in the *ptm_constants.h* file in the PTM source directory.
+(from which the orientation is determined) can be found in the
+*ptm_constants.h* file in the PTM source directory.
 For atoms that are not within the compute group-ID, all values are set to zero.
 
 Restrictions

doc/src/compute_rdf.rst

@@ -6,7 +6,7 @@ compute rdf command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID rdf Nbin itype1 jtype1 itype2 jtype2 ... keyword/value ...
 
@@ -38,7 +38,7 @@ Description
 """""""""""
 
 Define a computation that calculates the radial distribution function
-(RDF), also called g(r), and the coordination number for a group of
+(RDF), also called :math:`g(r)`, and the coordination number for a group of
 particles.  Both are calculated in histogram form by binning pairwise
 distances into *Nbin* bins from 0.0 to the maximum force cutoff
 defined by the :doc:`pair_style <pair_style>` command or the cutoff
@@ -58,27 +58,27 @@ shell of distances in 3d and a thin ring of distances in 2d.
    using long-range coulomb interactions (\ *coul/long*, *coul/msm*,
    *coul/wolf* or similar.  One way to get around this would be to set
    special_bond scaling factors to very tiny numbers that are not exactly
-   zero (e.g. 1.0e-50). Another workaround is to write a dump file, and
+   zero (e.g., :math:`1.0 \times 10^{-50}`).  Another workaround is to write a
-   use the :doc:`rerun <rerun>` command to compute the RDF for snapshots in
+   dump file, and use the :doc:`rerun <rerun>` command to compute the RDF for
-   the dump file.  The rerun script can use a
+   snapshots in the dump file.  The rerun script can use a
    :doc:`special_bonds <special_bonds>` command that includes all pairs in
    the neighbor list.
 
 By default the RDF is computed out to the maximum force cutoff defined
 by the :doc:`pair_style <pair_style>` command.  If the *cutoff* keyword
-is used, then the RDF is computed accurately out to the *Rcut* > 0.0
+is used, then the RDF is computed accurately out to the *Rcut* :math:`> 0.0`
 distance specified.
 
 .. note::
 
    Normally, you should only use the *cutoff* keyword if no pair
-   style is defined, e.g. the :doc:`rerun <rerun>` command is being used to
+   style is defined (e.g., the :doc:`rerun <rerun>` command is being used to
-   post-process a dump file of snapshots.  Or if you really want the RDF
+   post-process a dump file of snapshots) or if you really want the RDF
    for distances beyond the pair_style force cutoff and cannot easily
    post-process a dump file to calculate it.  This is because using the
    *cutoff* keyword incurs extra computation and possibly communication,
-   which may slow down your simulation.  If you specify a *Rcut* <= force
+   which may slow down your simulation.  If you specify *Rcut* :math:`\le`
-   cutoff, you will force an additional neighbor list to be built at
+   force cutoff, you will force an additional neighbor list to be built at
    every timestep this command is invoked (or every reneighboring
    timestep, whichever is less frequent), which is inefficient.  LAMMPS
    will warn you if this is the case.  If you specify a *Rcut* > force
@@ -92,56 +92,56 @@ distance specified.
 
 The *itypeN* and *jtypeN* arguments are optional.  These arguments
 must come in pairs.  If no pairs are listed, then a single histogram
-is computed for g(r) between all atom types.  If one or more pairs are
+is computed for :math:`g(r)` between all atom types.  If one or more pairs are
 listed, then a separate histogram is generated for each
 *itype*,\ *jtype* pair.
 
 The *itypeN* and *jtypeN* settings can be specified in one of two
 ways.  An explicit numeric value can be used, as in the fourth example
 above.  Or a wild-card asterisk can be used to specify a range of atom
-types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N = the
+types.  This takes the form "\*" or "\*n" or "m\*" or "m\*n".  If 
-number of atom types, then an asterisk with no numeric values means
+:math:`N` is the number of atom types, then an asterisk with no numeric values
-all types from 1 to N.  A leading asterisk means all types from 1 to n
+means all types from 1 to :math:`N`. A leading asterisk means all types from 1
-(inclusive).  A trailing asterisk means all types from n to N
+to n (inclusive).  A trailing asterisk means all types from m to :math:`N`
-(inclusive).  A middle asterisk means all types from m to n
+(inclusive).  A middle asterisk means all types from m to n (inclusive).
-(inclusive).
 
 If both *itypeN* and *jtypeN* are single values, as in the fourth example
-above, this means that a g(r) is computed where atoms of type *itypeN*
+above, this means that a :math:`g(r)` is computed where atoms of type *itypeN*
 are the central atom, and atoms of type *jtypeN* are the distribution
 atom.  If either *itypeN* and *jtypeN* represent a range of values via
 the wild-card asterisk, as in the fifth example above, this means that a
-g(r) is computed where atoms of any of the range of types represented
+:math:`g(r)` is computed where atoms of any of the range of types represented
 by *itypeN* are the central atom, and atoms of any of the range of
 types represented by *jtypeN* are the distribution atom.
 
 Pairwise distances are generated by looping over a pairwise neighbor
 list, just as they would be in a :doc:`pair_style <pair_style>`
-computation.  The distance between two atoms I and J is included in a
+computation.  The distance between two atoms :math:`I` and :math:`J` is
-specific histogram if the following criteria are met:
+included in a specific histogram if the following criteria are met:
 
-* atoms I,J are both in the specified compute group
+* atoms :math:`I` and :math:`J` are both in the specified compute group
-* the distance between atoms I,J is less than the maximum force cutoff
+* the distance between atoms :math:`I` and :math:`J` is less than the maximum
-* the type of the I atom matches itypeN (one or a range of types)
+  force cutoff
-* the type of the J atom matches jtypeN (one or a range of types)
+* the type of the :math:`I` atom matches *itypeN* (one or a range of types)
+* the type of the :math:`J` atom matches *jtypeN* (one or a range of types)
 
 It is OK if a particular pairwise distance is included in more than
 one individual histogram, due to the way the *itypeN* and *jtypeN*
 arguments are specified.
 
-The g(r) value for a bin is calculated from the histogram count by
+The :math:`g(r)` value for a bin is calculated from the histogram count by
 scaling it by the idealized number of how many counts there would be
 if atoms of type *jtypeN* were uniformly distributed.  Thus it
 involves the count of *itypeN* atoms, the count of *jtypeN* atoms, the
 volume of the entire simulation box, and the volume of the bin's thin
 shell in 3d (or the area of the bin's thin ring in 2d).
 
-A coordination number coord(r) is also calculated, which is the number
+A coordination number :math:`\mathrm{coord}(r)` is also calculated, which is
-of atoms of type *jtypeN* within the current bin or closer, averaged
+the number of atoms of type *jtypeN* within the current bin or closer, averaged
 over atoms of type *itypeN*\ .  This is calculated as the area- or
-volume-weighted sum of g(r) values over all bins up to and including
+volume-weighted sum of :math:`g(r)` values over all bins up to and including
 the current bin, multiplied by the global average volume density of
-atoms of type jtypeN.
+atoms of type *jtypeN*.
 
 The simplest way to output the results of the compute rdf calculation
 to a file is to use the :doc:`fix ave/time <fix_ave_time>` command, for
@@ -155,41 +155,43 @@ example:
 Output info
 """""""""""
 
-This compute calculates a global array with the number of rows =
+This compute calculates a global array in which the number of rows is
-*Nbins*, and the number of columns = 1 + 2\*Npairs, where Npairs is the
+*Nbins* and the number of columns is :math:`1 + 2N_\text{pairs}`, where
-number of I,J pairings specified.  The first column has the bin
+:math:`N_\text{pairs}` is the number of :math:`I,J` pairings specified.
-coordinate (center of the bin), Each successive set of 2 columns has
+The first column has the bin coordinate (center of the bin), and each
-the g(r) and coord(r) values for a specific set of *itypeN* versus
+successive set of two columns has the :math:`g(r)` and :math:`\text{coord}(r)`
-*jtypeN* interactions, as described above.  These values can be used
+values for a specific set of *itypeN* versus *jtypeN* interactions,
+as described above.  These values can be used
 by any command that uses a global values from a compute as input.  See
 the :doc:`Howto output <Howto_output>` page for an overview of
 LAMMPS output options.
 
-The array values calculated by this compute are all "intensive".
+The array values calculated by this compute are all "intensive."
 
 The first column of array values will be in distance
-:doc:`units <units>`.  The g(r) columns of array values are normalized
+:doc:`units <units>`.  The :math:`g(r)` columns of array values are normalized
-numbers >= 0.0.  The coordination number columns of array values are
+numbers :math:`\ge 0.0`.  The coordination number columns of array values are
-also numbers >= 0.0.
+also numbers :math:`\ge 0.0`.
 
 Restrictions
 """"""""""""
 
 The RDF is not computed for distances longer than the force cutoff,
-since processors (in parallel) don't know about atom coordinates for
+since processors (in parallel) do not know about atom coordinates for
 atoms further away than that distance.  If you want an RDF for larger
 distances, you can use the :doc:`rerun <rerun>` command to post-process
 a dump file and set the cutoff for the potential to be longer in the
 rerun script.  Note that in the rerun context, the force cutoff is
 arbitrary, since you are not running dynamics and thus are not changing
-your model.  The definition of g(r) used by LAMMPS is only appropriate
+your model.  The definition of :math:`g(r)` used by LAMMPS is only appropriate
 for characterizing atoms that are uniformly distributed throughout the
 simulation cell. In such cases, the coordination number is still
 correct and meaningful.  As an example, if a large simulation cell
-contains only one atom of type *itypeN* and one of *jtypeN*, then g(r)
+contains only one atom of type *itypeN* and one of *jtypeN*, then :math:`g(r)`
 will register an arbitrarily large spike at whatever distance they
-happen to be at, and zero everywhere else.  Coord(r) will show a step
+happen to be at, and zero everywhere else.
-change from zero to one at the location of the spike in g(r).
+The function :math:`\text{coord}(r)` will show a step
+change from zero to one at the location of the spike in :math:`g(r)`.
 
 .. note::
 
@@ -198,7 +200,7 @@ change from zero to one at the location of the spike in g(r).
    parameters need to be re-computed in every step and include collective
    communication operations. This will reduce performance and limit
    parallel efficiency and scaling. For systems, where only the type
-   of atoms changes (e.g. when using :doc:`fix atom/swap <fix_atom_swap>`),
+   of atoms changes (e.g., when using :doc:`fix atom/swap <fix_atom_swap>`),
    you need to explicitly request the dynamic normalization updates
    via :doc:`compute_modify dynamic yes <compute_modify>`
 

doc/src/set.rst

@@ -14,8 +14,8 @@ Syntax
 * ID = atom ID range or type range or mol ID range or group ID or region ID
 * one or more keyword/value pairs may be appended
 * keyword = *type* or *type/fraction* or *type/ratio* or *type/subset*
-  or *mol* or *x* or *y* or *z* or *charge* or *dipole* or
+  or *mol* or *x* or *y* or *z* or *vx* or *vy* or *vz* or *charge* or
-  *dipole/random* or *quat* or *spin* or *spin/random* or
+  *dipole* or *dipole/random* or *quat* or *spin* or *spin/random* or
   *quat* or *quat/random* or *diameter* or *shape* or
   *length* or *tri* or *theta* or *theta/random* or *angmom* or
   *omega* or *mass* or *density* or *density/disc* or