Merge remote-tracking branch 'github/develop' into collected-small-changes

doc/src/angle_style.rst

@@ -10,7 +10,7 @@ Syntax
 
    angle_style style
 
-* style = *none* or *hybrid* or *charmm* or *class2* or *cosine* or         *cosine/squared* or *harmonic*
+* style = *none* or *zero* or *hybrid* or *amoeba* or *charmm* or *class2* or *class2/p6* or *cosine* or *cosine/buck6d* or *cosine/delta* or *cosine/periodic* or *cosine/shift* or *cosine/shift/exp* or *cosine/squared* or *cross* or *dipole* or *fourier* or *fourier/simple* or *gaussian* or *harmonic* or *mm3* or *quartic* or *spica* or *table*
 
 Examples
 """"""""

doc/src/angle_zero.rst

@@ -8,7 +8,10 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   angle_style zero *nocoeff*
+   angle_style zero keyword
+
+* zero or more keywords may be appended
+* keyword = *nocoeff*
 
 Examples
 """"""""

doc/src/balance.rst

@@ -6,7 +6,7 @@ balance command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    balance thresh style args ... keyword args ...
 

doc/src/bond_style.rst

@@ -10,7 +10,7 @@ Syntax
 
    bond_style style args
 
-* style = *none* or *hybrid* or *class2* or *fene* or *fene/expand* or         *harmonic* or *morse* or *nonlinear* or *quartic*
+* style = *none* or *zero* or *hybrid* or *bpm/rotational* or *bpm/spring* or *class2* or *fene* or *fene/expand* or *fene/nm* or *gaussian* or *gromos* or *harmonic* or *harmonic/shift* or *harmonic/shift/cut* or *morse* or *nonlinear* or *oxdna/fene* or *oxdena2/fene* or *oxrna2/fene* or *quartic* or *special* or *table*
 
 * args = none for any style except *hybrid*
 

doc/src/bond_zero.rst

@@ -8,7 +8,10 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   bond_style zero [nocoeff]
+   bond_style zero keyword
+
+* zero or more keywords may be appended
+* keyword = *nocoeff*
 
 Examples
 """"""""

doc/src/boundary.rst

@@ -6,7 +6,7 @@ boundary command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    boundary x y z
 

doc/src/box.rst

@@ -6,7 +6,7 @@ box command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    box keyword value ...
 

doc/src/clear.rst

@@ -6,18 +6,18 @@ clear command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    clear
 
 Examples
 """"""""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
-   (commands for 1st simulation)
+   # (commands for 1st simulation)
    clear
-   (commands for 2nd simulation)
+   # (commands for 2nd simulation)
 
 Description
 """""""""""

doc/src/comm_modify.rst

@@ -10,8 +10,8 @@ Syntax
 
    comm_modify keyword value ...
 
-* zero or more keyword/value pairs may be appended
+* one or more keyword/value pairs may be appended
-* keyword = *mode* or *cutoff* or *cutoff/multi* or *multi/reduce* or *group* or *vel*
+* keyword = *mode* or *cutoff* or *cutoff/multi* or *group* or *reduce/multi* or *vel*
 
   .. parsed-literal::
 

doc/src/compute.rst

@@ -6,7 +6,7 @@ compute command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID style args
 
@@ -33,8 +33,8 @@ they are calculated from information about atoms on the current
 timestep or iteration, though a compute may internally store some
 information about a previous state of the system.  Defining a compute
 does not perform a computation.  Instead computes are invoked by other
-LAMMPS commands as needed, e.g. to calculate a temperature needed for
+LAMMPS commands as needed (e.g., to calculate a temperature needed for
-a thermostat fix or to generate thermodynamic or dump file output.
+a thermostat fix or to generate thermodynamic or dump file output).
 See the :doc:`Howto output <Howto_output>` page for a summary of
 various LAMMPS output options, many of which involve computes.
 
@@ -45,15 +45,15 @@ underscores.
 
 Computes calculate one of three styles of quantities: global,
 per-atom, or local.  A global quantity is one or more system-wide
-values, e.g. the temperature of the system.  A per-atom quantity is
+values (e.g., the temperature of the system).  A per-atom quantity is
-one or more values per atom, e.g. the kinetic energy of each atom.
+one or more values per atom (e.g., the kinetic energy of each atom).
 Per-atom values are set to 0.0 for atoms not in the specified compute
 group.  Local quantities are calculated by each processor based on the
-atoms it owns, but there may be zero or more per atom, e.g. a list of
+atoms it owns, but there may be zero or more per atom (e.g., a list of
-bond distances.  Computes that produce per-atom quantities have the
+bond distances).  Computes that produce per-atom quantities have the
-word "atom" in their style, e.g. *ke/atom*\ .  Computes that produce
+word "atom" in their style (e.g., *ke/atom*\ ).  Computes that produce
-local quantities have the word "local" in their style,
+local quantities have the word "local" in their style
-e.g. *bond/local*\ .  Styles with neither "atom" or "local" in their
+(e.g., *bond/local*\ ).  Styles with neither "atom" or "local" in their
 style produce global quantities.
 
 Note that a single compute can produce either global or per-atom or
@@ -64,8 +64,8 @@ compute page will explain.
 Global, per-atom, and local quantities each come in three kinds: a
 single scalar value, a vector of values, or a 2d array of values.  The
 doc page for each compute describes the style and kind of values it
-produces, e.g. a per-atom vector.  Some computes produce more than one
+produces (e.g., a per-atom vector).  Some computes produce more than one
-kind of a single style, e.g. a global scalar and a global vector.
+kind of a single style (e.g., a global scalar and a global vector).
 
 When a compute quantity is accessed, as in many of the output commands
 discussed below, it can be referenced via the following bracket
@@ -80,14 +80,14 @@ notation, where ID is the ID of the compute:
 +-------------+--------------------------------------------+
 
 In other words, using one bracket reduces the dimension of the
-quantity once (vector -> scalar, array -> vector).  Using two brackets
+quantity once (vector :math:`\to` scalar, array :math:`\to` vector).  Using two
-reduces the dimension twice (array -> scalar).  Thus a command that
+brackets reduces the dimension twice (array :math:`\to` scalar).  Thus a
-uses scalar compute values as input can also process elements of a
+command that uses scalar compute values as input can also process elements of a
 vector or array.
 
 Note that commands and :doc:`variables <variable>` which use compute
-quantities typically do not allow for all kinds, e.g. a command may
+quantities typically do not allow for all kinds (e.g., a command may
-require a vector of values, not a scalar.  This means there is no
+require a vector of values, not a scalar).  This means there is no
 ambiguity about referring to a compute quantity as c_ID even if it
 produces, for example, both a scalar and vector.  The doc pages for
 various commands explain the details.
@@ -111,14 +111,14 @@ ways:
 
 The results of computes that calculate global quantities can be either
 "intensive" or "extensive" values.  Intensive means the value is
-independent of the number of atoms in the simulation,
+independent of the number of atoms in the simulation
-e.g. temperature.  Extensive means the value scales with the number of
+(e.g., temperature).  Extensive means the value scales with the number of
-atoms in the simulation, e.g. total rotational kinetic energy.
+atoms in the simulation (e.g., total rotational kinetic energy).
 :doc:`Thermodynamic output <thermo_style>` will normalize extensive
 values by the number of atoms in the system, depending on the
 "thermo_modify norm" setting.  It will not normalize intensive values.
-If a compute value is accessed in another way, e.g. by a
+If a compute value is accessed in another way (e.g., by a
-:doc:`variable <variable>`, you may want to know whether it is an
+:doc:`variable <variable>`), you may want to know whether it is an
 intensive or extensive value.  See the page for individual
 computes for further info.
 
@@ -187,8 +187,8 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`cluster/atom <compute_cluster_atom>` - cluster ID for each atom
 * :doc:`cna/atom <compute_cna_atom>` - common neighbor analysis (CNA) for each atom
 * :doc:`cnp/atom <compute_cnp_atom>` - common neighborhood parameter (CNP) for each atom
-* :doc:`com <compute_com>` - center-of-mass of group of atoms
+* :doc:`com <compute_com>` - center of mass of group of atoms
-* :doc:`com/chunk <compute_com_chunk>` - center-of-mass for each chunk
+* :doc:`com/chunk <compute_com_chunk>` - center of mass for each chunk
 * :doc:`contact/atom <compute_contact_atom>` - contact count for each spherical particle
 * :doc:`coord/atom <compute_coord_atom>` - coordination number for each atom
 * :doc:`damage/atom <compute_damage_atom>` - Peridynamic damage for each atom
@@ -198,10 +198,10 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`dipole <compute_dipole>` - dipole vector and total dipole
 * :doc:`dipole/chunk <compute_dipole_chunk>` - dipole vector and total dipole for each chunk
 * :doc:`displace/atom <compute_displace_atom>` - displacement of each atom
-* :doc:`dpd <compute_dpd>` -
+* :doc:`dpd <compute_dpd>` - total values of internal conductive energy, internal mechanical energy, chemical energy, and harmonic average of internal temperature
-* :doc:`dpd/atom <compute_dpd_atom>` -
+* :doc:`dpd/atom <compute_dpd_atom>` - per-particle values of internal conductive energy, internal mechanical energy, chemical energy, and internal temperature
 * :doc:`edpd/temp/atom <compute_edpd_temp_atom>` - per-atom temperature for each eDPD particle in a group
-* :doc:`efield/atom <compute_efield_atom>` -
+* :doc:`efield/atom <compute_efield_atom>` - electric field at each atom
 * :doc:`entropy/atom <compute_entropy_atom>` - pair entropy fingerprint of each atom
 * :doc:`erotate/asphere <compute_erotate_asphere>` - rotational energy of aspherical particles
 * :doc:`erotate/rigid <compute_erotate_rigid>` - rotational energy of rigid bodies
@@ -213,7 +213,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`fep/ta <compute_fep_ta>` - compute free energies for a test area perturbation
 * :doc:`force/tally <compute_tally>` - force between two groups of atoms via the tally callback mechanism
 * :doc:`fragment/atom <compute_cluster_atom>` - fragment ID for each atom
-* :doc:`global/atom <compute_global_atom>` -
+* :doc:`global/atom <compute_global_atom>` - assign global values to each atom from arrays of global values
 * :doc:`group/group <compute_group_group>` - energy/force between two groups of atoms
 * :doc:`gyration <compute_gyration>` - radius of gyration of group of atoms
 * :doc:`gyration/chunk <compute_gyration_chunk>` - radius of gyration for each chunk
@@ -232,7 +232,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`ke/atom/eff <compute_ke_atom_eff>` - per-atom translational and radial kinetic energy in the electron force field model
 * :doc:`ke/eff <compute_ke_eff>` - kinetic energy of a group of nuclei and electrons in the electron force field model
 * :doc:`ke/rigid <compute_ke_rigid>` - translational kinetic energy of rigid bodies
-* :doc:`mliap <compute_mliap>` - gradients of energy and forces w.r.t. model parameters and related quantities for training machine learning interatomic potentials
+* :doc:`mliap <compute_mliap>` - gradients of energy and forces with respect to model parameters and related quantities for training machine learning interatomic potentials
 * :doc:`momentum <compute_momentum>` - translational momentum
 * :doc:`msd <compute_msd>` - mean-squared displacement of group of atoms
 * :doc:`msd/chunk <compute_msd_chunk>` - mean-squared displacement for each chunk
@@ -254,35 +254,35 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`property/chunk <compute_property_chunk>` - extract various per-chunk attributes
 * :doc:`property/local <compute_property_local>` - convert local attributes to localvectors/arrays
 * :doc:`ptm/atom <compute_ptm_atom>` - determines the local lattice structure based on the Polyhedral Template Matching method
-* :doc:`rdf <compute_rdf>` - radial distribution function g(r) histogram of group of atoms
+* :doc:`rdf <compute_rdf>` - radial distribution function :math:`g(r)` histogram of group of atoms
 * :doc:`reduce <compute_reduce>` - combine per-atom quantities into a single global value
 * :doc:`reduce/chunk <compute_reduce_chunk>` - reduce per-atom quantities within each chunk
 * :doc:`reduce/region <compute_reduce>` - same as compute reduce, within a region
 * :doc:`rigid/local <compute_rigid_local>` - extract rigid body attributes
 * :doc:`saed <compute_saed>` - electron diffraction intensity on a mesh of reciprocal lattice nodes
 * :doc:`slice <compute_slice>` - extract values from global vector or array
-* :doc:`smd/contact/radius <compute_smd_contact_radius>` -
+* :doc:`smd/contact/radius <compute_smd_contact_radius>` - contact radius for Smooth Mach Dynamics
 * :doc:`smd/damage <compute_smd_damage>` - damage status of SPH particles in Smooth Mach Dynamics
-* :doc:`smd/hourglass/error <compute_smd_hourglass_error>` -
+* :doc:`smd/hourglass/error <compute_smd_hourglass_error>` - error associated with approximated relative separation in Smooth Mach Dynamics
 * :doc:`smd/internal/energy <compute_smd_internal_energy>` - per-particle enthalpy in Smooth Mach Dynamics
 * :doc:`smd/plastic/strain <compute_smd_plastic_strain>` - equivalent plastic strain per particle in Smooth Mach Dynamics
 * :doc:`smd/plastic/strain/rate <compute_smd_plastic_strain_rate>` - time rate of the equivalent plastic strain in Smooth Mach Dynamics
 * :doc:`smd/rho <compute_smd_rho>` - per-particle mass density in Smooth Mach Dynamics
 * :doc:`smd/tlsph/defgrad <compute_smd_tlsph_defgrad>` - deformation gradient in Smooth Mach Dynamics
 * :doc:`smd/tlsph/dt <compute_smd_tlsph_dt>` - CFL-stable time increment per particle in Smooth Mach Dynamics
-* :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>` -
+* :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>` - number of particles inside the smoothing kernel radius for Smooth Mach Dynamics
-* :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>` -
+* :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>` - current shape of the volume of a particle for Smooth Mach Dynamics
-* :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>` -
+* :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>` - Green--Lagrange strain tensor for Smooth Mach Dynamics
-* :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>` -
+* :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>` - rate of strain for Smooth Mach Dynamics
 * :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>` - per-particle Cauchy stress tensor for SPH particles
-* :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>` -
+* :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>` - coordinates of vertices corresponding to the triangle elements of a mesh for Smooth Mach Dynamics
 * :doc:`smd/ulsph/effm <compute_smd_ulsph_effm>` - per-particle effective shear modulus
-* :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>` -
+* :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>` - number of neighbor particles inside the smoothing kernel radius for Smooth Mach Dynamics
-* :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>` -
+* :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>` - logarithmic strain tensor for Smooth Mach Dynamics
-* :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>` -
+* :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>` - logarithmic strain rate for Smooth Mach Dynamics
 * :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>` - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics
 * :doc:`smd/vol <compute_smd_vol>` - per-particle volumes and their sum in Smooth Mach Dynamics
-* :doc:`snap <compute_sna_atom>` - gradients of SNAP energy and forces w.r.t. linear coefficients and related quantities for fitting SNAP potentials
+* :doc:`snap <compute_sna_atom>` - gradients of SNAP energy and forces with respect to linear coefficients and related quantities for fitting SNAP potentials
 * :doc:`sna/atom <compute_sna_atom>` - bispectrum components for each atom
 * :doc:`sna/grid <compute_sna_atom>` - global array of bispectrum components on a regular grid
 * :doc:`sna/grid/local <compute_sna_atom>` - local array of bispectrum components on a regular grid
@@ -308,7 +308,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`temp/cs <compute_temp_cs>` - temperature based on the center-of-mass velocity of atom pairs that are bonded to each other
 * :doc:`temp/deform <compute_temp_deform>` - temperature excluding box deformation velocity
 * :doc:`temp/deform/eff <compute_temp_deform_eff>` - temperature excluding box deformation velocity in the electron force field model
-* :doc:`temp/drude <compute_temp_drude>` - temperature of Core-Drude pairs
+* :doc:`temp/drude <compute_temp_drude>` - temperature of Core--Drude pairs
 * :doc:`temp/eff <compute_temp_eff>` - temperature of a group of nuclei and electrons in the electron force field model
 * :doc:`temp/partial <compute_temp_partial>` - temperature excluding one or more dimensions of velocity
 * :doc:`temp/profile <compute_temp_profile>` - temperature excluding a binned velocity profile
@@ -324,7 +324,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`vcm/chunk <compute_vcm_chunk>` - velocity of center-of-mass for each chunk
 * :doc:`viscosity/cos <compute_viscosity_cos>` - velocity profile under cosine-shaped acceleration
 * :doc:`voronoi/atom <compute_voronoi_atom>` - Voronoi volume and neighbors for each atom
-* :doc:`xrd <compute_xrd>` - x-ray diffraction intensity on a mesh of reciprocal lattice nodes
+* :doc:`xrd <compute_xrd>` - X-ray diffraction intensity on a mesh of reciprocal lattice nodes
 
 Restrictions
 """"""""""""
@@ -333,7 +333,9 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`uncompute <uncompute>`, :doc:`compute_modify <compute_modify>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/histo <fix_ave_histo>`
+:doc:`uncompute <uncompute>`, :doc:`compute_modify <compute_modify>`,
+:doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/time <fix_ave_time>`,
+:doc:`fix ave/histo <fix_ave_histo>`
 
 Default
 """""""

doc/src/compute_ackland_atom.rst

@@ -6,7 +6,7 @@ compute ackland/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID ackland/atom keyword/value
 
@@ -17,7 +17,7 @@ Syntax
 
   .. parsed-literal::
 
-       *legacy* yes/no = use (\ *yes*\ ) or do not use (\ *no*\ ) legacy ackland algorithm implementation
+       *legacy* args = *yes* or *no* = use (\ *yes*\ ) or do not use (\ *no*\ ) legacy Ackland algorithm implementation
 
 Examples
 """"""""

doc/src/compute_adf.rst

@@ -6,7 +6,7 @@ compute adf command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID adf Nbin itype1 jtype1 ktype1 Rjinner1 Rjouter1 Rkinner1 Rkouter1 ...
 
@@ -16,10 +16,10 @@ Syntax
 * itypeN = central atom type for Nth ADF histogram (see asterisk form below)
 * jtypeN = J atom type for Nth ADF histogram (see asterisk form below)
 * ktypeN = K atom type for Nth ADF histogram (see asterisk form below)
-* RjinnerN =  inner radius of J atom shell for Nth ADF histogram (distance units)
+* RjinnerN = inner radius of J atom shell for Nth ADF histogram (distance units)
-* RjouterN =  outer radius of J atom shell for Nth ADF histogram (distance units)
+* RjouterN = outer radius of J atom shell for Nth ADF histogram (distance units)
 * RkinnerN = inner radius of K atom shell for Nth ADF histogram (distance units)
-* RkouterN =  outer radius of K atom shell for Nth ADF histogram (distance units)
+* RkouterN = outer radius of K atom shell for Nth ADF histogram (distance units)
 * zero or one keyword/value pairs may be appended
 * keyword = *ordinate*
 
@@ -177,8 +177,8 @@ Output info
 """""""""""
 
 This compute calculates a global array with the number of rows =
-*Nbins*, and the number of columns = 1 + 2\*Ntriples, where Ntriples is the
+*Nbins* and the number of columns = :math:`1 + 2 \times` *Ntriples*, where *Ntriples*
-number of I,J,K triples specified.  The first column has the bin
+is the number of I,J,K triples specified.  The first column has the bin
 coordinate (angle-related ordinate at midpoint of bin). Each subsequent column has
 the two ADF values for a specific set of (\ *itypeN*,\ *jtypeN*,\ *ktypeN*\ )
 interactions, as described above.  These values can be used
@@ -192,10 +192,10 @@ The first column of array values is the angle-related ordinate, either
 the angle in degrees or radians, or the cosine of the angle.  Each
 subsequent pair of columns gives the first and second kinds of ADF
 for a specific set of (\ *itypeN*,\ *jtypeN*,\ *ktypeN*\ ). The values
-in the first ADF column are normalized numbers >= 0.0,
+in the first ADF column are normalized numbers :math:`\ge 0.0`,
 whose integral w.r.t. the ordinate is 1,
 i.e. the first ADF is a normalized probability distribution.
-The values in the second ADF column are also numbers >= 0.0.
+The values in the second ADF column are also numbers :math:`\ge 0.0`.
 They are the cumulative density distribution of angles per atom.
 By definition, this ADF is monotonically increasing from zero to
 a maximum value equal to the average total number of

doc/src/compute_angle.rst

@@ -6,7 +6,7 @@ compute angle command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID angle
 
@@ -35,12 +35,12 @@ the hybrid sub-styles.
 Output info
 """""""""""
 
-This compute calculates a global vector of length N where N is the number of
+This compute calculates a global vector of length *N*, where *N* is the number
-sub_styles defined by the :doc:`angle_style hybrid <angle_style>` command,
+of sub_styles defined by the :doc:`angle_style hybrid <angle_style>` command,
-which can be accessed by indices 1-N.  These values can be used by any command
+which can be accessed by indices 1 through *N*.  These values can be used by
-that uses global scalar or vector values from a compute as input.  See the
+any command that uses global scalar or vector values from a compute as input.
-:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
+See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
-options.
+output options.
 
 The vector values are "extensive" and will be in energy
 :doc:`units <units>`.

doc/src/compute_angle_local.rst

@@ -6,7 +6,7 @@ compute angle/local command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID angle/local value1 value2 ... keyword args ...
 
@@ -47,7 +47,7 @@ interactions.  The number of datums generated, aggregated across all
 processors, equals the number of angles in the system, modified by the
 group parameter as explained below.
 
-The value *theta* is the angle for the 3 atoms in the interaction.
+The value *theta* is the angle for the three atoms in the interaction.
 
 The value *eng* is the interaction energy for the angle.
 
@@ -65,8 +65,8 @@ Note that the value of theta for each angle which stored in the
 internal variable is in radians, not degrees.
 
 As an example, these commands can be added to the bench/in.rhodo
-script to compute the cosine and cosine\^2 of every angle in the system
+script to compute the cosine and cosine-squared of every angle in the
-and output the statistics in various ways:
+system and output the statistics in various ways:
 
 .. code-block:: LAMMPS
 
@@ -83,19 +83,20 @@ and output the statistics in various ways:
 
    fix 10 all ave/histo 10 10 100 -1 1 20 c_2[3] mode vector file tmp.histo
 
-The :doc:`dump local <dump>` command will output the energy, angle,
+The :doc:`dump local <dump>` command will output the potential energy
-cosine(angle), cosine\^2(angle) for every angle in the system.  The
+(:math:`\phi`), the angle (:math:`\theta`), :math:`\cos(\theta`), and
-:doc:`thermo_style <thermo_style>` command will print the average of
+:math:`\cos^2(\theta)` for every angle :math:`\theta` in the system.
-those quantities via the :doc:`compute reduce <compute_reduce>` command
+The :doc:`thermo_style <thermo_style>` command will print the
-with thermo output.  And the :doc:`fix ave/histo <fix_ave_histo>`
+average of those quantities via the :doc:`compute reduce <compute_reduce>`
-command will histogram the cosine(angle) values and write them to a
+command with thermo output.  And the :doc:`fix ave/histo <fix_ave_histo>`
+command will histogram the :math:`\cos(\theta)` values and write them to a
 file.
 
 ----------
 
 The local data stored by this command is generated by looping over all
 the atoms owned on a processor and their angles.  An angle will only
-be included if all 3 atoms in the angle are in the specified compute
+be included if all three atoms in the angle are in the specified compute
 group.  Any angles that have been broken (see the
 :doc:`angle_style <angle_style>` command) by setting their angle type to
 0 are not included.  Angles that have been turned off (see the :doc:`fix shake <fix_shake>` or :doc:`delete_bonds <delete_bonds>` commands) by

doc/src/compute_angmom_chunk.rst

@@ -6,7 +6,7 @@ compute angmom/chunk command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID angmom/chunk chunkID
 
@@ -72,13 +72,13 @@ 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 :doc:`compute chunk/atom <compute_chunk_atom>` command.  The number of columns = 3 for the three
-3 for the 3 xyz components of the angular momentum for each chunk.
+(*x*, *y*, *z*) components of the angular momentum 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
 options.
 
-The array values are "intensive".  The array values will be in
+The array values are "intensive."  The array values will be in
 mass-velocity-distance :doc:`units <units>`.
 
 Restrictions

doc/src/compute_ave_sphere_atom.rst

@@ -9,7 +9,7 @@ Accelerator Variants: *ave/sphere/atom/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID ave/sphere/atom keyword values ...
 
@@ -37,13 +37,13 @@ Description
 
 Define a computation that calculates the local mass density and
 temperature for each atom based on its neighbors inside a spherical
-cutoff.  If an atom has M neighbors, then its local mass density is
+cutoff.  If an atom has :math:`M` neighbors, then its local mass density is
-calculated as the sum of its mass and its M neighbor masses, divided
+calculated as the sum of its mass and its :math:`M` neighbor masses, divided
 by the volume of the cutoff sphere (or circle in 2d).  The local
 temperature of the atom is calculated as the temperature of the
-collection of M+1 atoms, after subtracting the center-of-mass velocity
+collection of :math:`M+1` atoms, after subtracting the center-of-mass velocity
-of the M+1 atoms from each of the M+1 atom's velocities.  This is
+of the :math:`M+1` atoms from each of the :math:`M+1` atom's velocities.  This
-effectively the thermal velocity of the neighborhood of the central
+is effectively the thermal velocity of the neighborhood of the central
 atom, similar to :doc:`compute temp/com <compute_temp_com>`.
 
 The optional keyword *cutoff* defines the distance cutoff used when

doc/src/compute_basal_atom.rst

@@ -6,7 +6,7 @@ compute basal/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID basal/atom
 
@@ -47,12 +47,12 @@ in examples/PACKAGES/basal.
 Output info
 """""""""""
 
-This compute calculates a per-atom array with 3 columns, which can be
+This compute calculates a per-atom array with three columns, which can be
-accessed by indices 1-3 by any command that uses per-atom values from
+accessed by indices 1--3 by any command that uses per-atom values from
 a compute as input.  See the :doc:`Howto output <Howto_output>` doc page
 for an overview of LAMMPS output options.
 
-The per-atom vector values are unitless since the 3 columns represent
+The per-atom vector values are unitless since the three columns represent
 components of a unit vector.
 
 Restrictions

doc/src/compute_body_local.rst

@@ -6,7 +6,7 @@ compute body/local command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID body/local input1 input2 ...
 
@@ -33,7 +33,7 @@ Description
 """""""""""
 
 Define a computation that calculates properties of individual body
-sub-particles.  The number of datums generated, aggregated across all
+sub-particles.  The number of data generated, aggregated across all
 processors, equals the number of body sub-particles plus the number of
 non-body particles in the system, modified by the group parameter as
 explained below.  See the :doc:`Howto body <Howto_body>` page for
@@ -41,8 +41,8 @@ more details on using body particles.
 
 The local data stored by this command is generated by looping over all
 the atoms.  An atom will only be included if it is in the group.  If
-the atom is a body particle, then its N sub-particles will be looped
+the atom is a body particle, then its :math:`N` sub-particles will be looped
-over, and it will contribute N datums to the count of datums.  If it
+over, and it will contribute :math:`N` data to the count of data.  If it
 is not a body particle, it will contribute 1 datum.
 
 For both body particles and non-body particles, the *id* keyword
@@ -64,8 +64,8 @@ by the :doc:`atom_style body <atom_style>`, determines how many fields
 exist and what they are.  See the :doc:`Howto_body <Howto_body>` doc
 page for details of the different styles.
 
-Here is an example of how to output body information using the :doc:`dump local <dump>` command with this compute.  If fields 1,2,3 for the
+Here is an example of how to output body information using the :doc:`dump local <dump>` command with this compute.  If fields 1, 2, and 3 for the
-body sub-particles are x,y,z coordinates, then the dump file will be
+body sub-particles are (*x*, *y*, *z*) coordinates, then the dump file will be
 formatted similar to the output of a :doc:`dump atom or custom <dump>`
 command.
 
@@ -79,7 +79,7 @@ Output info
 
 This compute calculates a local vector or local array depending on the
 number of keywords.  The length of the vector or number of rows in the
-array is the number of datums as described above.  If a single keyword
+array is the number of data as described above.  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

doc/src/compute_bond.rst

@@ -6,7 +6,7 @@ compute bond command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID bond
 
@@ -35,10 +35,13 @@ 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`
-number of sub_styles defined by the :doc:`bond_style hybrid <bond_style>` command, which can be accessed by indices 1-N.
+is the number of sub_styles defined by the
+:doc:`bond_style hybrid <bond_style>` command,
+which can be accessed by indices 1 through :math:`N`.
 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.
 
 The vector values are "extensive" and will be in energy

doc/src/compute_bond_local.rst

@@ -6,7 +6,7 @@ compute bond/local command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID bond/local value1 value2 ... keyword args ...
 
@@ -35,8 +35,8 @@ Syntax
 
 .. parsed-literal::
 
-     *set* args = dist name
+     *set* args = *dist* name
-       dist = only currently allowed arg
+       *dist* = only currently allowed arg
        name = name of variable to set with distance (dist)
 
 Examples
@@ -49,7 +49,7 @@ Examples
 
    compute 1 all bond/local dist fx fy fz
 
-   compute 1 all angle/local dist v_distsq set dist d
+   compute 1 all bond/local dist v_distsq set dist d
 
 Description
 """""""""""
@@ -82,32 +82,34 @@ relative to the center of mass (COM) velocity of the 2 atoms in the
 bond.
 
 The value *engvib* is the vibrational kinetic energy of the two atoms
-in the bond, which is simply 1/2 m1 v1\^2 + 1/2 m2 v2\^2, where v1 and
+in the bond, which is simply :math:`\frac12 m_1 v_1^2 + \frac12 m_2 v_2^2,`
-v2 are the magnitude of the velocity of the 2 atoms along the bond
+where :math:`v_1` and :math:`v_2` are the magnitude of the velocity of the two
-direction, after the COM velocity has been subtracted from each.
+atoms along the bond direction, after the COM velocity has been subtracted from
-
-The value *engrot* is the rotational kinetic energy of the two atoms
-in the bond, which is simply 1/2 m1 v1\^2 + 1/2 m2 v2\^2, where v1 and
-v2 are the magnitude of the velocity of the 2 atoms perpendicular to
-the bond direction, after the COM velocity has been subtracted from
 each.
 
-The value *engtrans* is the translational kinetic energy associated
+The value *engrot* is the rotational kinetic energy of the two atoms
-with the motion of the COM of the system itself, namely 1/2 (m1+m2)
+in the bond, which is simply :math:`\frac12 m_1 v_1^2 + \frac12 m_2 v_2^2,`
-Vcm\^2 where Vcm = magnitude of the velocity of the COM.
+where :math:`v_1` and :math:`v_2` are the magnitude of the velocity of the two
+atoms perpendicular to the bond direction, after the COM velocity has been
+subtracted from each.
 
-Note that these 3 kinetic energy terms are simply a partitioning of
+The value *engtrans* is the translational kinetic energy associated
-the summed kinetic energy of the 2 atoms themselves.  I.e. total KE =
+with the motion of the COM of the system itself, namely :math:`\frac12(m_1+m_2)
-1/2 m1 v1\^2 + 1/2 m2 v2\^2 = engvib + engrot + engtrans, where v1,v2
+V_{\mathrm{cm}}^2`, where `Vcm` = magnitude of the velocity of the COM.
-are the magnitude of the velocities of the 2 atoms, without any
+
-adjustment for the COM velocity.
+Note that these three kinetic energy terms are simply a partitioning of
+the summed kinetic energy of the two atoms themselves.  That is, the total
+kinetic energy is
+:math:`\frac12 m_1 v_1^2 + \frac12 m_2 v_2^2` = engvib + engrot + engtrans,
+where :math:`v_1` and :math:`v_2` are the magnitude of the velocities of the
+two atoms, without any adjustment for the COM velocity.
 
 The value *omega* is the magnitude of the angular velocity of the
 two atoms around their COM position.
 
 The value *velvib* is the magnitude of the relative velocity of the
 two atoms in the bond towards each other.  A negative value means the
-2 atoms are moving toward each other; a positive value means they are
+two atoms are moving toward each other; a positive value means they are
 moving apart.
 
 The value *v_name* can be used together with the *set* keyword to
@@ -121,7 +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 distance\^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
@@ -138,12 +140,12 @@ 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, distance,
+The :doc:`dump local <dump>` command will output the energy, length,
-distance\^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>`
+with thermo output, and the :doc:`fix ave/histo <fix_ave_histo>`
-command will histogram the distance\^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_born_matrix.rst

@@ -6,20 +6,26 @@ compute born/matrix command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID born/matrix keyword value ...
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * born/matrix = style name of this compute command
-* zero or more keyword/value pairs may be appended
+* zero or more keywords or keyword/value pairs may be appended
 
   .. parsed-literal::
 
-     keyword = *numdiff*
+     keyword = *numdiff* or *pair* or *bond* or *angle* or *dihedral* or *improper*
        *numdiff* values = delta virial-ID
          delta = magnitude of strain (dimensionless)
          virial-ID = ID of pressure compute for virial (string)
+         (*numdiff* cannot be used with any other keyword)
+       *pair* = compute pair-wise contributions
+       *bond* = compute bonding contributions
+       *angle* = compute angle contributions
+       *dihedral* = compute dihedral contributions
+       *improper* = compute improper contributions
 
 Examples
 """"""""
@@ -36,8 +42,8 @@ Description
 .. versionadded:: 4May2022
 
 Define a compute that calculates
-:math:`\frac{\partial{}^2U}{\partial\varepsilon_{i}\partial\varepsilon_{j}}` the
+:math:`\frac{\partial{}^2U}{\partial\varepsilon_{i}\partial\varepsilon_{j}},` the
-second derivatives of the potential energy :math:`U` w.r.t. strain
+second derivatives of the potential energy :math:`U` with respect to the strain
 tensor :math:`\varepsilon` elements. These values are related to:
 
 .. math::
@@ -69,14 +75,14 @@ whose 21 independent elements are output in this order:
 
 .. math::
 
-    \begin{matrix}
+    \begin{bmatrix}
        C_{1}  & C_{7}   & C_{8}  & C_{9}  & C_{10} & C_{11} \\
        C_{7}  & C_{2}   & C_{12} & C_{13} & C_{14} & C_{15} \\
        \vdots & C_{12}  & C_{3}  & C_{16} & C_{17} & C_{18} \\
        \vdots & C_{13}  & C_{16} & C_{4}  & C_{19} & C_{20} \\
        \vdots & \vdots  & \vdots & C_{19} & C_{5}  & C_{21} \\
        \vdots & \vdots  & \vdots & \vdots & C_{21} & C_{6}
-    \end{matrix}
+    \end{bmatrix}
 
 in this matrix the indices of :math:`C_{k}` value are the corresponding element
 :math:`k` in the global vector output by this compute. Each term comes from the sum
@@ -169,14 +175,14 @@ requiring that it use the virial keyword e.g.
 **Output info:**
 
 This compute calculates a global vector with 21 values that are
-the second derivatives of the potential energy w.r.t. strain.
+the second derivatives of the potential energy with respect to strain.
 The values are in energy units.
 The values are ordered as explained above. These values can be used
 by any command that uses global values from a compute as input. See
 the :doc:`Howto output <Howto_output>` doc page for an overview of
 LAMMPS output options.
 
-The array values calculated by this compute are all "extensive".
+The array values calculated by this compute are all "extensive."
 
 Restrictions
 """"""""""""
@@ -188,7 +194,7 @@ the :doc:`Build package <Build_package>` page for more info.
 
 The Born term can be decomposed as a product of two terms. The first one is a
 general term which depends on the configuration. The second one is specific to
-every interaction composing your force field (non-bonded, bonds, angle...).
+every interaction composing your force field (non-bonded, bonds, angle, ...).
 Currently not all LAMMPS interaction styles implement the *born_matrix* method
 giving first and second order derivatives and LAMMPS will exit with an error if
 this compute is used with such interactions unless the *numdiff* option is

doc/src/compute_centro_atom.rst

@@ -6,17 +6,17 @@ compute centro/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID centro/atom lattice keyword value ...
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
-  centro/atom = style name of this compute command
+* centro/atom = style name of this compute command
-  lattice = *fcc* or *bcc* or N = # of neighbors per atom to include
+* lattice = *fcc* or *bcc* or N = # of neighbors per atom to include
 * zero or more keyword/value pairs may be appended
 * keyword = *axes*
 
-.. parsed-literal::
+  .. parsed-literal::
 
      *axes* value = *no* or *yes*
        *no* = do not calculate 3 symmetry axes
@@ -83,12 +83,13 @@ atoms with smallest contributions to the centrosymmetry parameter,
 i.e. the two most symmetric pairs of atoms.  The third vector is
 normal to the first two by the right-hand rule.  All three vectors are
 normalized to unit length.  For FCC crystals, the first two vectors
-will lie along a <110> direction, while the third vector will lie
+will lie along a :math:`\langle110\rangle` direction, while the third vector
-along either a <100> or <111> direction.  For HCP crystals, the first
+will lie along either a :math:`\langle100\rangle` or :math:`\langle111\rangle`
-two vectors will lie along <1000> directions, while the third vector
+direction.  For HCP crystals, the first two vectors will lie along
-will lie along <0001>.  This provides a simple way to measure local
+:math:`\langle1000\rangle` directions, while the third vector
-orientation in HCP structures.  In general, the *axes* keyword can be
+will lie along :math:`\langle0001\rangle`.  This provides a simple way to
-used to estimate the orientation of symmetry axes in the neighborhood
+measure local orientation in HCP structures.  In general, the *axes* keyword
+can be used to estimate the orientation of symmetry axes in the neighborhood
 of any atom.
 
 Only atoms within the cutoff of the pairwise neighbor list are
@@ -96,7 +97,7 @@ considered as possible neighbors.  Atoms not in the compute group are
 included in the :math:`N` neighbors used in this calculation.
 
 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
 *centro/atom* style.
@@ -111,11 +112,11 @@ options.
 
 If the *axes* keyword setting is *yes*, then a per-atom array is
 calculated. The first column is the centrosymmetry parameter.  The
-next three columns are the x, y, and z components of the first
+next three columns are the *x*, *y*, and *z* components of the first
 symmetry axis, followed by the second, and third symmetry axes in
-columns 5-7 and 8-10.
+columns 5--7 and 8--10.
 
-The centrosymmetry values are unitless values >= 0.0.  Their magnitude
+The centrosymmetry values are unitless values :math:`\ge 0.0`. Their magnitude
 depends on the lattice style due to the number of contributing neighbor
 pairs in the summation in the formula above.  And it depends on the
 local defects surrounding the central atom, as described above.  For

doc/src/compute_chunk_atom.rst

@@ -6,7 +6,7 @@ compute chunk/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID chunk/atom style args keyword values ...
 
@@ -150,14 +150,14 @@ The *binning* styles perform a spatial binning of atoms, and assign an
 atom the chunk ID corresponding to the bin number it is in.  *Nchunk*
 is set to the number of bins, which can change if the simulation box
 size changes.  This also depends on the setting of the *units*
-keyword; e.g. for *reduced* units the number of chunks may not change
+keyword (e.g., for *reduced* units the number of chunks may not change
-even if the box size does.
+even if the box size does).
 
 The *bin/1d*, *bin/2d*, and *bin/3d* styles define bins as 1d layers
 (slabs), 2d pencils, or 3d boxes.  The *dim*, *origin*, and *delta*
 settings are specified 1, 2, or 3 times.  For 2d or 3d bins, there is
-no restriction on specifying dim = x before dim = y or z, or dim = y
+no restriction on specifying dim = *x* before dim = *y* or *z*, or dim = *y*
-before dim = z.  Bins in a particular *dim* have a bin size in that
+before dim = *z*.  Bins in a particular *dim* have a bin size in that
 dimension given by *delta*\ .  In each dimension, bins are defined
 relative to a specified *origin*, which may be the lower/upper edge of
 the simulation box (in that dimension), or its center point, or a
@@ -170,10 +170,11 @@ boxes aligned with the xyz coordinate axes.  For triclinic
 (non-orthogonal) simulation boxes, the bin faces are parallel to the
 tilted faces of the simulation box.  See the :doc:`Howto triclinic <Howto_triclinic>` page for a discussion of the
 geometry of triclinic boxes in LAMMPS.  As described there, a tilted
-simulation box has edge vectors a,b,c.  In that nomenclature, bins in
+simulation box has edge vectors :math:`\vec a`, :math:`\vec b`, and
-the x dimension have faces with normals in the "b" cross "c"
+:math:`\vec c`.  In that nomenclature, bins in
-direction.  Bins in y have faces normal to the "a" cross "c"
+the *x* dimension have faces with normals in the :math:`\vec b \times \vec c`
-direction.  And bins in z have faces normal to the "a" cross "b"
+direction, bins in *y* have faces normal to the :math:`\vec a \times \vec c`
+direction, and bins in *z* have faces normal to the :math:`\vec a \times \vec b`
 direction.  Note that in order to define the size and position of
 these bins in an unambiguous fashion, the *units* option must be set
 to *reduced* when using a triclinic simulation box, as noted below.
@@ -181,46 +182,46 @@ to *reduced* when using a triclinic simulation box, as noted below.
 The meaning of *origin* and *delta* for triclinic boxes is as follows.
 Consider a triclinic box with bins that are 1d layers or slabs in the
 x dimension.  No matter how the box is tilted, an *origin* of 0.0
-means start layers at the lower "b" cross "c" plane of the simulation
+means start layers at the lower :math:`\vec b \times \vec c` plane of the
-box and an *origin* of 1.0 means to start layers at the upper "b"
+simulation box and an *origin* of 1.0 means to start layers at the upper
-cross "c" face of the box.  A *delta* value of 0.1 in *reduced* units
+:math:`\vec b \times \vec c` face of the box.  A *delta* value of 0.1 in
-means there will be 10 layers from 0.0 to 1.0, regardless of the
+*reduced* units means there will be 10 layers from 0.0 to 1.0, regardless of
-current size or shape of the simulation box.
+the current size or shape of the simulation box.
 
 The *bin/sphere* style defines a set of spherical shell bins around
 the origin (\ *xorig*,\ *yorig*,\ *zorig*\ ), using *nsbin* bins with radii
 equally spaced between *srmin* and *srmax*\ .  This is effectively a 1d
 vector of bins.  For example, if *srmin* = 1.0 and *srmax* = 10.0 and
-*nsbin* = 9, then the first bin spans 1.0 < r < 2.0, and the last bin
+*nsbin* = 9, then the first bin spans :math:`1.0 < r < 2.0`, and the last bin
-spans 9.0 < r 10.0.  The geometry of the bins is the same whether the
+spans :math:`9.0 < r < 10.0`.  The geometry of the bins is the same whether the
-simulation box is orthogonal or triclinic; i.e. the spherical shells
+simulation box is orthogonal or triclinic (i.e., the spherical shells
 are not tilted or scaled differently in different dimensions to
-transform them into ellipsoidal shells.
+transform them into ellipsoidal shells).
 
 The *bin/cylinder* style defines bins for a cylinder oriented along
 the axis *dim* with the axis coordinates in the other two radial
-dimensions at (\ *c1*,\ *c2*\ ).  For dim = x, c1/c2 = y/z; for dim = y,
+dimensions at (\ *c1*,\ *c2*\ ).  For dim = *x*, :math:`c_1/c_2 = y/z`;
-c1/c2 = x/z; for dim = z, c1/c2 = x/y.  This is effectively a 2d array
+for dim = *y*, :math:`c_1/c_2 = x/z`; for dim = *z*,
-of bins.  The first dimension is along the cylinder axis, the second
+:math:`c_1/c_2 = x/y`.  This is effectively a 2d array of bins.  The first
-dimension is radially outward from the cylinder axis.  The bin size
+dimension is along the cylinder axis, the second dimension is radially outward
-and positions along the cylinder axis are specified by the *origin*
+from the cylinder axis.  The bin size and positions along the cylinder axis are
-and *delta* values, the same as for the *bin/1d*, *bin/2d*, and
+specified by the *origin* and *delta* values, the same as for the *bin/1d*,
-*bin/3d* styles.  There are *ncbin* concentric circle bins in the
+*bin/2d*, and *bin/3d* styles.  There are *ncbin* concentric circle bins in the
 radial direction from the cylinder axis with radii equally spaced
 between *crmin* and *crmax*\ .  For example, if *crmin* = 1.0 and
-*crmax* = 10.0 and *ncbin* = 9, then the first bin spans 1.0 < r <
+*crmax* = 10.0 and *ncbin* = 9, then the first bin spans :math:`1.0 < r < 2.0`
-2.0, and the last bin spans 9.0 < r 10.0.  The geometry of the bins in
+and the last bin spans :math:`9.0 < r < 10.0`.  The geometry of the bins in
 the radial dimensions is the same whether the simulation box is
-orthogonal or triclinic; i.e. the concentric circles are not tilted or
+orthogonal or triclinic (i.e., the concentric circles are not tilted or
 scaled differently in the two different dimensions to transform them
-into ellipses.
+into ellipses).
 
 The created bins (and hence the chunk IDs) are numbered consecutively
 from 1 to the number of bins = *Nchunk*\ .  For *bin2d* and *bin3d*, the
 numbering varies most rapidly in the first dimension (which could be
-x, y, or z), next rapidly in the second dimension, and most slowly in the
+*x*, *y*, or *z*), next rapidly in the second dimension, and most slowly in the
 third dimension.  For *bin/sphere*, the bin with smallest radii is chunk
-1 and the bni with largest radii is chunk Nchunk = *ncbin*\ .  For
+1 and the bin with largest radii is chunk Nchunk = *ncbin*\ .  For
 *bin/cylinder*, the numbering varies most rapidly in the dimension
 along the cylinder axis and most slowly in the radial direction.
 
@@ -236,8 +237,8 @@ assigned to the atom.
 ----------
 
 The *type* style uses the atom type as the chunk ID.  *Nchunk* is set
-to the number of atom types defined for the simulation, e.g. via the
+to the number of atom types defined for the simulation (e.g., via the
-:doc:`create_box <create_box>` or :doc:`read_data <read_data>` commands.
+:doc:`create_box <create_box>` or :doc:`read_data <read_data>` commands).
 
 ----------
 
@@ -264,8 +265,8 @@ on a quantity calculated and stored by a compute, fix, or variable.
 In each case, it must be a per-atom quantity.  In each case the
 referenced floating point values are converted to an integer chunk ID
 as follows.  The floating point value is truncated (rounded down) to
-an integer value.  If the integer value is <= 0, then a chunk ID of 0
+an integer value.  If the integer value is :math:`\le 0`, then a chunk ID of 0
-is assigned to the atom.  If the integer value is > 0, it becomes the
+is assigned to the atom.  If the integer value is :math:`> 0`, it becomes the
 chunk ID to the atom.  *Nchunk* is set to the largest chunk ID.  Note
 that this excludes atoms which are not in the specified group or
 optional region.
@@ -362,7 +363,7 @@ If *limit* is set to *Nc* = 0, then no limit is imposed on *Nchunk*,
 though the *compress* keyword can still be used to reduce *Nchunk*, as
 described below.
 
-If *Nc* > 0, then the effect of the *limit* keyword depends on whether
+If *Nc* :math:`>` 0, then the effect of the *limit* keyword depends on whether
 the *compress* keyword is also used with a setting of *yes*, and
 whether the *compress* keyword is specified before the *limit* keyword
 or after.
@@ -374,7 +375,7 @@ First, here is what occurs if *compress yes* is not set.  If *limit*
 is set to *Nc max*, then *Nchunk* is reset to the smaller of *Nchunk*
 and *Nc*\ .  If *limit* is set to *Nc exact*, then *Nchunk* is reset to
 *Nc*, whether the original *Nchunk* was larger or smaller than *Nc*\ .
-If *Nchunk* shrank due to the *limit* setting, then atom chunk IDs >
+If *Nchunk* shrank due to the *limit* setting, then atom chunk IDs :math:`>`
 *Nchunk* will be reset to 0 or *Nchunk*, depending on the setting of
 the *discard* keyword.  If *Nchunk* grew, there will simply be some
 chunks with no atoms assigned to them.
@@ -384,22 +385,22 @@ If *compress yes* is set, and the *compress* keyword comes before the
 described below, which resets *Nchunk*\ .  The *limit* keyword is then
 applied to the new *Nchunk* value, exactly as described in the
 preceding paragraph.  Note that in this case, all atoms will end up
-with chunk IDs <= *Nc*, but their original values (e.g. molecule ID or
+with chunk IDs :math:`\le` *Nc*, but their original values (e.g., molecule ID
-compute/fix/variable) may have been > *Nc*, because of the compression
+or compute/fix/variable) may have been :math:`>` *Nc*, because of the
-operation.
+compression operation.
 
 If *compress yes* is set, and the *compress* keyword comes after the
 *limit* keyword, then the *limit* value of *Nc* is applied first to
-the uncompressed value of *Nchunk*, but only if *Nc* < *Nchunk*
+the uncompressed value of *Nchunk*, but only if *Nc* :math:`<` *Nchunk*
 (whether *Nc max* or *Nc exact* is used).  This effectively means all
-atoms with chunk IDs > *Nc* have their chunk IDs reset to 0 or *Nc*,
+atoms with chunk IDs :math:`>` *Nc* have their chunk IDs reset to 0 or *Nc*,
 depending on the setting of the *discard* keyword.  The compression
 operation is then performed, which may shrink *Nchunk* further.  If
-the new *Nchunk* < *Nc* and *limit* = *Nc exact* is specified, then
+the new *Nchunk* :math:`<` *Nc* and *limit* = *Nc exact* is specified, then
 *Nchunk* is reset to *Nc*, which results in extra chunks with no atoms
 assigned to them.  Note that in this case, all atoms will end up with
-chunk IDs <= *Nc*, and their original values (e.g. molecule ID or
+chunk IDs :math:`\le` *Nc*, and their original values (e.g., molecule ID or
-compute/fix/variable value) will also have been <= *Nc*\ .
+compute/fix/variable value) will also have been :math:`\le` *Nc*\ .
 
 ----------
 
@@ -601,7 +602,8 @@ 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. Angstroms for units = real or metal.
+:doc:`units <units>` command (e.g., :math:`\mathrm{\mathring A}`
+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
@@ -615,8 +617,8 @@ scaled by the lattice spacing or reduced value of the *x* dimension.
 
 Note that for the *bin/cylinder* style, the radii *crmin* and *crmax*
 are scaled by the lattice spacing or reduced value of the first
-dimension perpendicular to the cylinder axis.  E.g. y for an x-axis
+dimension perpendicular to the cylinder axis (e.g., *y* for an *x*-axis
-cylinder, x for a y-axis cylinder, and x for a z-axis cylinder.
+cylinder, *x* for a *y*-axis cylinder, and *x* for a *z*-axis cylinder).
 
 ----------
 

doc/src/compute_chunk_spread_atom.rst

@@ -6,7 +6,7 @@ compute chunk/spread/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID chunk/spread/atom chunkID input1 input2 ...
 
@@ -18,10 +18,10 @@ Syntax
 
   .. parsed-literal::
 
-       c_ID = global vector calculated by a compute with ID
+     c_ID = global vector calculated by a compute with ID
-       c_ID[I] = Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
+     c_ID[I] = Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
-       f_ID = global vector calculated by a fix with ID
+     f_ID = global vector calculated by a fix with ID
-       f_ID[I] = Ith column of global array calculated by a fix with ID, I can include wildcard (see below)
+     f_ID[I] = Ith column of global array calculated by a fix with ID, I can include wildcard (see below)
 
 Examples
 """"""""

doc/src/compute_cluster_atom.rst

@@ -14,7 +14,7 @@ compute aggregate/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID cluster/atom cutoff
    compute ID group-ID fragment/atom keyword value ...
@@ -69,9 +69,9 @@ fragments or not, based on the *yes* or *no* setting.  If the setting
 is *no* (the default), their fragment IDs are set to 0.
 
 An aggregate is defined by combining the rules for clusters and
-fragments, i.e. a set of atoms, where each of it is within the cutoff
+fragments (i.e., a set of atoms, where each of them is within the cutoff
 distance from one or more atoms within a fragment that is part of
-the same cluster. This measure can be used to track molecular assemblies
+the same cluster). This measure can be used to track molecular assemblies
 like micelles.
 
 For computes *cluster/atom* and *aggregate/atom* a neighbor list
@@ -92,9 +92,9 @@ style computes.
    does not apply when using long-range coulomb (\ *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 clusters for
+   dump file and use the :doc:`rerun <rerun>` command to compute the clusters
-   snapshots in the dump file.  The rerun script can use a
+   for 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.
 
@@ -114,7 +114,7 @@ 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 will be an ID > 0, as explained above.
+The per-atom vector values will be an ID :math:`> 0`, as explained above.
 
 Restrictions
 """"""""""""
@@ -129,5 +129,5 @@ Related commands
 Default
 """""""
 
-The default for fragment/atom is single no.
+The default for fragment/atom is single=no.
 

doc/src/compute_cna_atom.rst

@@ -6,7 +6,7 @@ compute cna/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID cna/atom cutoff
 
@@ -44,20 +44,22 @@ performed on mono-component systems.
 
 The CNA calculation can be sensitive to the specified cutoff value.
 You should insure the appropriate nearest neighbors of an atom are
-found within the cutoff distance for the presumed crystal structure.
+found within the cutoff distance for the presumed crystal structure
-E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest
+(e.g., 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest
-neighbors for perfect BCC crystals.  These formulas can be used to
+neighbors for perfect BCC crystals).  These formulas can be used to
 obtain a good cutoff distance:
 
 .. math::
 
-  r_{c}^{fcc} = & \frac{1}{2} \left(\frac{\sqrt{2}}{2} + 1\right) \mathrm{a} \simeq 0.8536 \:\mathrm{a} \\
+  r_{c}^{\mathrm{fcc}} = & \frac{1}{2} \left(\frac{\sqrt{2}}{2} + 1\right) a
-  r_{c}^{bcc} = & \frac{1}{2}(\sqrt{2} + 1) \mathrm{a} \simeq 1.207 \:\mathrm{a} \\
+    \approx 0.8536 a \\
-  r_{c}^{hcp} = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) \mathrm{a}
+  r_{c}^{\mathrm{bcc}} = & \frac{1}{2}(\sqrt{2} + 1) a
+    \approx 1.207 a \\
+  r_{c}^{\mathrm{hcp}} = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) a
 
-where a is the lattice constant for the crystal structure concerned
+where :math:`a` is the lattice constant for the crystal structure concerned
-and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a
+and in the HCP case, :math:`x = (c/a) / 1.633`, where 1.633 is the ideal
-for HCP crystals.
+:math:`c/a` for HCP crystals.
 
 Also note that since the CNA calculation in LAMMPS uses the neighbors
 of an owned atom to find the nearest neighbors of a ghost atom, the

doc/src/compute_cnp_atom.rst

@@ -6,7 +6,7 @@ compute cnp/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID cnp/atom cutoff
 
@@ -28,7 +28,7 @@ Define a computation that calculates the Common Neighborhood
 Parameter (CNP) for each atom in the group.  In solid-state systems
 the CNP is a useful measure of the local crystal structure
 around an atom and can be used to characterize whether the
-atom is part of a perfect lattice, a local defect (e.g. a dislocation
+atom is part of a perfect lattice, a local defect (e.g., a dislocation
 or stacking fault), or at a surface.
 
 The value of the CNP parameter will be 0.0 for atoms not in the
@@ -40,7 +40,7 @@ This parameter is computed using the following formula from
 
 .. math::
 
-   Q_{i} = \frac{1}{n_i}\sum_{j = 1}^{n_i} \left | \sum_{k = 1}^{n_{ij}}  \vec{R}_{ik} + \vec{R}_{jk} \right | ^{2}
+   Q_{i} = \frac{1}{n_i}\sum_{j = 1}^{n_i} \left\lVert \sum_{k = 1}^{n_{ij}}  \vec{R}_{ik} + \vec{R}_{jk} \right\rVert^{2}
 
 where the index *j* goes over the :math:`n_i` nearest neighbors of atom
 *i*, and the index *k* goes over the :math:`n_{ij}` common nearest neighbors
@@ -58,13 +58,15 @@ obtain a good cutoff distance:
 
 .. math::
 
-  r_{c}^{fcc} = & \frac{1}{2} \left(\frac{\sqrt{2}}{2} + 1\right) \mathrm{a} \simeq 0.8536 \:\mathrm{a} \\
+  r_{c}^{\mathrm{fcc}} = & \frac{1}{2} \left(\frac{\sqrt{2}}{2} + 1\right) a
-  r_{c}^{bcc} = & \frac{1}{2}(\sqrt{2} + 1) \mathrm{a} \simeq 1.207 \:\mathrm{a} \\
+    \approx 0.8536 a \\
-  r_{c}^{hcp} = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) \mathrm{a}
+  r_{c}^{\mathrm{bcc}} = & \frac{1}{2}(\sqrt{2} + 1) a
+    \approx 1.207 a \\
+  r_{c}^{\mathrm{hcp}} = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) a
 
-where a is the lattice constant for the crystal structure concerned
+where :math:`a` is the lattice constant for the crystal structure concerned
-and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a
+and in the HCP case, :math:`x = (c/a) / 1.633`, where 1.633 is the ideal
-for HCP crystals.
+:math:`c/a` for HCP crystals.
 
 Also note that since the CNP calculation in LAMMPS uses the neighbors
 of an owned atom to find the nearest neighbors of a ghost atom, the
@@ -81,7 +83,7 @@ cutoff is the argument used with the compute cnp/atom command.  LAMMPS
 will issue a warning if this is not the case.
 
 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
 *cnp/atom* style.
@@ -103,9 +105,9 @@ values:
    BCC lattice = 0.0
    HCP lattice = 4.4
 
-   FCC (111) surface ~ 13.0
+   FCC (111) surface = 13.0
-   FCC (100) surface ~ 26.5
+   FCC (100) surface = 26.5
-   FCC dislocation core ~ 11
+   FCC dislocation core = 11
 
 Restrictions
 """"""""""""

doc/src/compute_com.rst

@@ -6,7 +6,7 @@ compute com command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID com
 
@@ -28,7 +28,7 @@ of atoms, including all effects due to atoms passing through periodic
 boundaries.
 
 A vector of three quantities is calculated by this compute, which
-are the x,y,z coordinates of the center of mass.
+are the :math:`(x,y,z)` coordinates of the center of mass.
 
 .. note::
 
@@ -38,17 +38,18 @@ are the x,y,z coordinates of the center of mass.
    "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.
 
 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 vector values will be in
+The vector values are "intensive."  The vector values will be in
 distance :doc:`units <units>`.
 
 Restrictions

doc/src/compute_com_chunk.rst

@@ -6,7 +6,7 @@ compute com/chunk command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID com/chunk chunkID
 
@@ -34,7 +34,7 @@ molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_c
 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 x,y,z coordinates of the center-of-mass
+This compute calculates the :math:`(x,y,z)` coordinates of the center of mass
 for each chunk, which includes all effects due to atoms passing through
 periodic boundaries.
 
@@ -54,7 +54,8 @@ non-zero chunk IDs.
    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 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 com/chunk
 calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
@@ -70,13 +71,13 @@ 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 :doc:`compute chunk/atom <compute_chunk_atom>` command.  The number of columns is
-3 for the x,y,z center-of-mass coordinates of each chunk.  These
+3 for the :math:`(x,y,z)` center-of-mass coordinates of 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>` doc
 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 :doc:`units <units>`.
 
 Restrictions

doc/src/compute_contact_atom.rst

@@ -6,7 +6,7 @@ compute contact/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID contact/atom group2-ID
 
@@ -44,11 +44,11 @@ accessed by 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 will be a number >= 0.0, as explained
+The per-atom vector values will be a number :math:`\ge 0.0`, as explained
 above.
 
 The optional *group2-ID* argument allows to specify from which group atoms
-contribute to the coordination number. Default setting is group 'all'.
+contribute to the coordination number. Default setting is group 'all.'
 
 Restrictions
 """"""""""""

doc/src/compute_coord_atom.rst

@@ -9,23 +9,23 @@ Accelerator Variants: *coord/atom/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. 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::
 
-       *cutoff* args = cutoff [group group2-ID] typeN
+     *cutoff* args = cutoff [*group* group2-ID] typeN
-         cutoff = distance within which to count coordination neighbors (distance units)
+       cutoff = distance within which to count coordination neighbors (distance units)
-         group *group2-ID* = select group-ID to restrict which atoms to consider for coordination number (optional)
+       *group* group2-ID = select group-ID to restrict which atoms to consider for coordination number (optional)
-         typeN = atom type for Nth coordination count (see asterisk form below)
+       typeN = atom type for Nth coordination count (see asterisk form below)
-       *orientorder* args = orientorderID threshold
+     *orientorder* args = orientorderID threshold
-         orientorderID = ID of an orientorder/atom compute
+       orientorderID = ID of an orientorder/atom compute
-         threshold = minimum value of the product of two "connected" atoms
+       threshold = minimum value of the product of two "connected" atoms
 
 Examples
 """"""""
@@ -54,7 +54,7 @@ neighboring atoms, unless selected by type, type range, or group option,
 are included in the coordination number tally.
 
 The optional *group* keyword allows to specify from which group atoms
-contribute to the coordination number. Default setting is group 'all'.
+contribute to the coordination number. Default setting is group 'all.'
 
 The *typeN* keywords allow specification of which atom types
 contribute to each coordination number.  One coordination number is
@@ -65,15 +65,15 @@ includes atoms of all types (same as the "\*" format, see below).
 The *typeN* keywords can be specified in one of two ways.  An explicit
 numeric value can be used, as in the second 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 number of
+takes the form "\*" or "\*n" or "m\*" or "m\*n".  If :math:`N` is the number of
 atom types, then an asterisk with no numeric values means all types
-from 1 to N.  A leading asterisk means all types from 1 to n
+from 1 to :math:`N`.  A leading asterisk means all types from 1 to n
-(inclusive).  A trailing asterisk means all types from 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).
 
 The *orientorder* cstyle calculates the number of "connected" neighbor
-atoms J around each central atom I.  For this *cstyle*, connected is
+atoms *j* around each central atom *i*\ .  For this *cstyle*, connected is
 defined by the orientational order parameter calculated by the
 :doc:`compute orientorder/atom <compute_orientorder_atom>` command.
 This *cstyle* thus allows one to apply the ten Wolde's criterion to
@@ -84,16 +84,16 @@ The ID of the previously specified :doc:`compute orientorder/atom <compute_orien
 calculate components of the *Ybar_lm* vector for each atoms, as
 described in its documentation.  Note that orientorder/atom compute
 defines its own criteria for identifying neighboring atoms.  If the
-scalar product (*Ybar_lm(i)*,*Ybar_lm(j)*), calculated by the
+scalar product (*Ybar_lm(i)*, *Ybar_lm(j)*), calculated by the
 orientorder/atom compute is larger than the specified *threshold*,
-then I and J are connected, and the coordination value of I is
+then *i* and *j* are connected, and the coordination value of *i* is
 incremented by one.
 
 For all *cstyle* settings, all coordination values will be 0.0 for
 atoms not in the specified compute group.
 
 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.
 
@@ -127,7 +127,7 @@ For *cstyle* cutoff, this compute can calculate a per-atom vector or
 array.  If single *type1* keyword is specified (or if none are
 specified), this compute calculates a per-atom vector.  If multiple
 *typeN* keywords are specified, this compute calculates a per-atom
-array, with N columns.
+array, with :math:`N` columns.
 
 For *cstyle* orientorder, this compute calculates a per-atom vector.
 
@@ -135,7 +135,7 @@ 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
 page for an overview of LAMMPS output options.
 
-The per-atom vector or array values will be a number >= 0.0, as
+The per-atom vector or array values will be a number :math:`\ge 0.0`, as
 explained above.
 
 Restrictions

doc/src/compute_damage_atom.rst

@@ -6,7 +6,7 @@ compute damage/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID damage/atom
 
@@ -48,7 +48,7 @@ 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 (damage) >= 0.0.
+The per-atom vector values are unitless numbers (damage) :math:`\ge 0.0`.
 
 Restrictions
 """"""""""""

doc/src/compute_dihedral.rst

@@ -6,7 +6,7 @@ compute dihedral command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID dihedral
 
@@ -34,10 +34,12 @@ 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`
-number of sub_styles defined by the :doc:`dihedral_style hybrid <dihedral_style>` command.  which can be accessed by indices
+is the number of sub_styles defined by the
-1-N.  These values can be used by any command that uses global scalar
+:doc:`dihedral_style hybrid <dihedral_style>` command, which can be accessed by
-or vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
+the indices 1 through :math:`N`.  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/src/compute_dihedral_local.rst

@@ -6,7 +6,7 @@ compute dihedral/local command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID dihedral/local value1 value2 ... keyword args ...
 
@@ -35,7 +35,6 @@ Examples
 .. code-block:: LAMMPS
 
    compute 1 all dihedral/local phi
-
    compute 1 all dihedral/local phi v_cos set phi p
 
 Description
@@ -46,25 +45,26 @@ interactions.  The number of datums generated, aggregated across all
 processors, equals the number of dihedral angles in the system, modified
 by the group parameter as explained below.
 
-The value *phi* is the dihedral angle, as defined in the diagram on
+The value *phi* (:math:`\phi`) is the dihedral angle, as defined in the diagram
-the :doc:`dihedral_style <dihedral_style>` doc page.
+on the :doc:`dihedral_style <dihedral_style>` doc page.
 
-The value *v_name* can be used together with the *set* keyword to
+The value *v_name* can be used together with the *set* keyword to compute a
-compute a user-specified function of the dihedral angle phi.  The
+user-specified function of the dihedral angle :math:`\phi`.  The *name*
-*name* specified for the *v_name* value is the name of an :doc:`equal-style variable <variable>` which should evaluate a formula based on a
+specified for the *v_name* value is the name of an
-variable which will store the angle phi.  This other variable must
+:doc:`equal-style variable <variable>` which should evaluate a formula based on
+a variable which will store the angle :math:`\phi`.  This other variable must
 be an :doc:`internal-style variable <variable>` defined in the input
 script; its initial numeric value can be anything.  It must be an
 internal-style variable, because this command resets its value
 directly.  The *set* keyword is used to identify the name of this
-other variable associated with phi.
+other variable associated with :math:`\phi`.
 
-Note that the value of phi for each angle which stored in the internal
+Note that the value of :math:`\phi` for each angle which stored in the internal
 variable is in radians, not degrees.
 
 As an example, these commands can be added to the bench/in.rhodo
-script to compute the cosine and cosine\^2 of every dihedral angle in
+script to compute the :math:`\cos\phi` and :math:`\cos^2\phi` of every dihedral
-the system and output the statistics in various ways:
+angle in the system and output the statistics in various ways:
 
 .. code-block:: LAMMPS
 
@@ -81,19 +81,18 @@ the system and output the statistics in various ways:
 
    fix 10 all ave/histo 10 10 100 -1 1 20 c_2[2] mode vector file tmp.histo
 
-The :doc:`dump local <dump>` command will output the angle,
+The :doc:`dump local <dump>` command will output the angle (:math:`\phi`),
-cosine(angle), cosine\^2(angle) for every dihedral in the system.  The
+:math:`\cos(\phi)`, and :math:`\cos^2(\phi)` for every dihedral in the system.
-:doc:`thermo_style <thermo_style>` command will print the average of
+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 cosine(angle) values and write them to a
+command will histogram the cosine(angle) values and write them to a file.
-file.
 
 ----------
 
 The local data stored by this command is generated by looping over all
 the atoms owned on a processor and their dihedrals.  A dihedral will
-only be included if all 4 atoms in the dihedral are in the specified
+only be included if all four atoms in the dihedral are in the specified
 compute group.
 
 Note that as atoms migrate from processor to processor, there will be
@@ -101,7 +100,8 @@ 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, dihedral output from the :doc:`compute property/local <compute_property_local>` command can be combined
+For example, dihedral 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.
 
@@ -120,9 +120,10 @@ This compute calculates a local vector or local array depending on the
 number of values.  The length of the vector or number of rows in the
 array is the number of dihedrals.  If a single value is specified, a
 local vector is produced.  If two or more values are specified, a
-local array is produced where the number of columns = the number of
+local array is produced where the number of columns is equal to the number of
 values.  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
+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 *phi* will be in degrees.

doc/src/compute_dilatation_atom.rst

@@ -6,12 +6,12 @@ compute dilatation/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID dilatation/atom
 
 * ID, group-ID are documented in compute command
-* dilation/atom = style name of this compute command
+* dilatation/atom = style name of this compute command
 
 Examples
 """"""""
@@ -30,13 +30,13 @@ for an overview of LAMMPS commands for Peridynamics modeling.
 For small deformation, dilatation of is the measure of the volumetric
 strain.
 
-The dilatation "theta" for each peridynamic particle I is calculated
+The dilatation :math:`\theta` for each peridynamic particle :math:`i` is
-as a sum over its neighbors with unbroken bonds, where the
+calculated as a sum over its neighbors with unbroken bonds, where the
-contribution of the IJ pair is a function of the change in bond length
+contribution of the :math:`ij` pair is a function of the change in bond length
 (versus the initial length in the reference state), the volume
 fraction of the particles and an influence function.  See the
-`PDLAMMPS user guide <http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for a formal
+`PDLAMMPS user guide <http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for
-definition of dilatation.
+a formal definition of dilatation.
 
 This command can only be used with a subset of the Peridynamic :doc:`pair styles <pair_peri>`: peri/lps, peri/ves and peri/eps.
 
@@ -51,13 +51,14 @@ 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 (theta) >= 0.0.
+The per-atom vector values are unitless numbers :math:`(\theta \ge 0.0)`.
 
 Restrictions
 """"""""""""
 
 This compute is part of the PERI package.  It is only enabled if
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+LAMMPS was built with that package.  See the
+:doc:`Build package <Build_package>` page for more info.
 
 Related commands
 """"""""""""""""

doc/src/compute_dipole.rst

@@ -6,13 +6,13 @@ compute dipole command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
-   compute ID group-ID dipole charge-correction
+   compute ID group-ID dipole arg
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * dipole = style name of this compute command
-* charge-correction = *mass* or *geometry*, use COM or geometric center for charged chunk correction (optional)
+* arg = *mass* or *geometry* = use COM or geometric center for charged chunk correction (optional)
 
 Examples
 """"""""
@@ -43,7 +43,7 @@ and per-atom dipole moments, if present, contribute to the computed dipole.
    :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
+   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.
 
 Output info
@@ -54,8 +54,9 @@ the computed dipole moment and a global vector of length 3 with the
 dipole vector.  See the :doc:`Howto output <Howto_output>` page for
 an overview of LAMMPS output options.
 
-The computed values are "intensive".  The array values will be in
+The computed values are "intensive."  The array values will be in
-dipole units, i.e. charge units times distance :doc:`units <units>`.
+dipole units (i.e., charge :doc:`units <units>` times distance
+:doc:`units <units>`).
 
 Restrictions
 """"""""""""

doc/src/compute_dipole_chunk.rst

@@ -6,14 +6,14 @@ compute dipole/chunk command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
-   compute ID group-ID dipole/chunk chunkID charge-correction
+   compute ID group-ID dipole/chunk chunkID arg
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * dipole/chunk = style name of this compute command
 * chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
-* charge-correction = *mass* or *geometry*, use COM or geometric center for charged chunk correction (optional)
+* arg = *mass* or *geometry* = use COM or geometric center for charged chunk correction (optional)
 
 Examples
 """"""""
@@ -38,8 +38,8 @@ or atoms in a spatial bin.  See the :doc:`compute chunk/atom
 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 x,y,z coordinates of the dipole vector and
+This compute calculates the :math:`(x,y,z)` coordinates of the dipole vector
-the total dipole moment for each chunk, which includes all effects due
+and the total dipole moment for each chunk, which includes all effects due
 to atoms passing through periodic boundaries. For chunks with a net
 charge the resulting dipole is made position independent by subtracting
 the position vector of the center of mass or geometric center times the
@@ -62,7 +62,7 @@ chunk IDs.
    "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
+   (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 com/chunk
@@ -80,14 +80,15 @@ 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 = 4 for
+chunk/atom <compute_chunk_atom>` command.  The number of columns is 4 for
-the x,y,z dipole vector components and the total dipole of each
+the :math:`(x,y,z)` dipole vector components and the total dipole of 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 options.
 
-The array values are "intensive".  The array values will be in
+The array values are "intensive."  The array values will be in
-dipole units, i.e. charge units times distance :doc:`units <units>`.
+dipole units (i.e., charge :doc:`units <units>` times distance
+:doc:`units <units>`).
 
 Restrictions
 """"""""""""

doc/src/compute_displace_atom.rst

@@ -6,7 +6,7 @@ compute displace/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID displace/atom
 
@@ -35,9 +35,9 @@ atom in the group from its original (reference) coordinates, including
 all effects due to atoms passing through periodic boundaries.
 
 A vector of four quantities per atom is calculated by this compute.
-The first 3 elements of the vector are the dx,dy,dz displacements.
+The first three elements of the vector are the :math:`(dx,dy,dz)`
-The fourth component is the total displacement, i.e. sqrt(dx\*dx + dy\*dy +
+displacements.  The fourth component is the total displacement
-dz\*dz).
+(i.e., :math:`\sqrt{dx^2 + dy^2 + dz^2}`).
 
 The displacement of an atom is from its original position at the time
 the compute command was issued.  The value of the displacement will be
@@ -50,7 +50,7 @@ the compute command was issued.  The value of the displacement will be
    <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
+   can reset the image flags (e.g., to 0) before invoking this compute
    by using the :doc:`set image <set>` command.
 
 .. note::
@@ -60,7 +60,7 @@ the compute command was issued.  The value of the displacement will be
    you should use the same ID for this compute, as in the original run.
    This is so that the fix this compute creates to store per-atom
    quantities will also have the same ID, and thus be initialized
-   correctly with time=0 atom coordinates from the restart file.
+   correctly with time = 0 atom coordinates from the restart file.
 
 ----------
 
@@ -95,14 +95,15 @@ something like the following commands:
                    refresh c_dsp delay 100
 
 The :doc:`dump_modify thresh <dump_modify>` command will only output
-atoms that have displaced more than 0.6 Angstroms on each snapshot
+atoms that have displaced more than :math:`0.6~\mathrm{\mathring A}` on each
-(assuming metal units).  The dump_modify *refresh* option triggers a
+snapshot (assuming metal units).  The dump_modify *refresh* option triggers a
 call to this compute at the end of every dump.
 
-The *refresh* argument for this compute is the ID of an :doc:`atom-style variable <variable>` which calculates a Boolean value (0 or 1)
+The *refresh* argument for this compute is the ID of an
+:doc:`atom-style variable <variable>` which calculates a Boolean value (0 or 1)
 based on the same criterion used by dump_modify thresh.  This compute
-evaluates the atom-style variable.  For each atom that returns 1
+evaluates the atom-style variable.  For each atom that returns 1 (true),
-(true), the original (reference) coordinates of the atom (stored by
+the original (reference) coordinates of the atom (stored by
 this compute) are updated.
 
 The effect of these commands is that a particular atom will only be
@@ -125,8 +126,8 @@ would be empty.
 Output info
 """""""""""
 
-This compute calculates a per-atom array with 4 columns, which can be
+This compute calculates a per-atom array with four columns, which can be
-accessed by indices 1-4 by any command that uses per-atom values from
+accessed by indices 1--4 by any command that uses per-atom 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_dpd.rst

@@ -6,7 +6,7 @@ compute dpd command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID dpd
 
@@ -24,9 +24,9 @@ Description
 """""""""""
 
 Define a computation that accumulates the total internal conductive
-energy (:math:`U^{cond}`), the total internal mechanical energy
+energy (:math:`U^{\text{cond}}`), the total internal mechanical energy
-(:math:`U^{mech}`), the total chemical energy (:math:`U^{chem}`)
+(:math:`U^{\text{mech}}`), the total chemical energy (:math:`U^\text{chem}`)
-and the *harmonic* average of the internal temperature (:math:`\theta_{avg}`)
+and the *harmonic* average of the internal temperature (:math:`\theta_\text{avg}`)
 for the entire system of particles.  See the
 :doc:`compute dpd/atom <compute_dpd_atom>` command if you want
 per-particle internal energies and internal temperatures.
@@ -36,22 +36,24 @@ relations:
 
 .. math::
 
-   U^{cond} = & \displaystyle\sum_{i=1}^{N} u_{i}^{cond} \\
+   U^\text{cond} = & \sum_{i=1}^{N} u_{i}^\text{cond} \\
-   U^{mech} = & \displaystyle\sum_{i=1}^{N} u_{i}^{mech} \\
+   U^\text{mech} = & \sum_{i=1}^{N} u_{i}^\text{mech} \\
-   U^{chem} = & \displaystyle\sum_{i=1}^{N} u_{i}^{chem} \\
+   U^\text{chem} = & \sum_{i=1}^{N} u_{i}^\text{chem} \\
-          U = & \displaystyle\sum_{i=1}^{N} (u_{i}^{cond} + u_{i}^{mech} + u_{i}^{chem}) \\
+               U = & \sum_{i=1}^{N} (u_{i}^\text{cond}
-   \theta_{avg} = & (\frac{1}{N}\displaystyle\sum_{i=1}^{N} \frac{1}{\theta_{i}})^{-1} \\
+                     + u_{i}^\text{mech} + u_{i}^\text{chem}) \\
+   \theta_{avg} = & \biggl(\frac{1}{N}\sum_{i=1}^{N}
+                          \frac{1}{\theta_{i}}\biggr)^{-1} \\
 
-where :math:`N` is the number of particles in the system
+where :math:`N` is the number of particles in the system.
 
 ----------
 
 Output info
 """""""""""
 
-This compute calculates a global vector of length 5 (:math:`U^{cond}`,
+This compute calculates a global vector of length 5 (:math:`U^\text{cond}`,
-:math:`U^{mech}`, :math:`U^{chem}`, :math:`\theta_{avg}`, :math:`N`),
+:math:`U^\text{mech}`, :math:`U^\text{chem}`, :math:`\theta_\text{avg}`,
-which can be accessed by indices 1-5.
+:math:`N`), which can be accessed by indices 1 through 5.
 See the :doc:`Howto output <Howto_output>` page for an overview of
 LAMMPS output options.
 
@@ -61,7 +63,8 @@ Restrictions
 """"""""""""
 
 This command is part of the DPD-REACT package.  It is only enabled if
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+LAMMPS was built with that package.
+See the :doc:`Build package <Build_package>` page for more info.
 
 This command also requires use of the :doc:`atom_style dpd <atom_style>`
 command.

doc/src/compute_dpd_atom.rst

@@ -6,7 +6,7 @@ compute dpd/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID dpd/atom
 
@@ -23,29 +23,28 @@ Examples
 Description
 """""""""""
 
-Define a computation that accesses the per-particle internal
+Define a computation that accesses the per-particle internal conductive energy
-conductive energy (:math:`u^{cond}`), internal mechanical
+(:math:`u^\text{cond}`), internal mechanical energy (:math:`u^\text{mech}`),
-energy (:math:`u^{mech}`), internal chemical energy (:math:`u^{chem}`)
+internal chemical energy (:math:`u^\text{chem}`) and internal temperatures
-and internal temperatures (:math:`\theta`) for each particle in a group.
+(:math:`\theta`) for each particle in a group.
 See the :doc:`compute dpd <compute_dpd>` command if you want the total
 internal conductive energy, the total internal mechanical energy, the
-total chemical energy and
+total chemical energy and average internal temperature of the entire system or
-average internal temperature of the entire system or group of dpd
+group of dpd particles.
-particles.
 
 Output info
 """""""""""
 
-This compute calculates a per-particle array with 4 columns (:math:`u^{cond}`,
+This compute calculates a per-particle array with four columns
-:math:`u^{mech}`, :math:`u^{chem}`, :math:`\theta`), which can be accessed
+(:math:`u^\text{cond}`, :math:`u^\text{mech}`, :math:`u^\text{chem}`,
-by indices 1-4 by any
+:math:`\theta`), which can be accessed by indices 1--4 by any
 command that uses per-particle values from a compute as input.  See
 the :doc:`Howto output <Howto_output>` page for an overview of
 LAMMPS output options.
 
-The per-particle array values will be in energy (:math:`u^{cond}`,
+The per-particle array values will be in energy (:math:`u^\text{cond}`,
-:math:`u^{mech}`, :math:`u^{chem}`)
+:math:`u^\text{mech}`, :math:`u^\text{chem}`)
-and temperature (:math:`theta`) :doc:`units <units>`.
+and temperature (:math:`\theta`) :doc:`units <units>`.
 
 Restrictions
 """"""""""""

doc/src/compute_edpd_temp_atom.rst

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

doc/src/compute_efield_atom.rst

@@ -6,12 +6,19 @@ compute efield/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
-   compute ID group-ID efield/atom
+   compute ID group-ID efield/atom keyword val
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * efield/atom = style name of this compute command
+* zero or more keyword/value pairs may be appended
+* keyword = *pair* or *kspace*
+
+  .. parsed-literal::
+
+     *pair* args = *yes* or *no*
+     *kspace* args = *yes* or *no*
 
 Examples
 """"""""
@@ -23,10 +30,10 @@ Examples
 
 Used in input scripts:
 
-   .. parsed-literal::
+.. parsed-literal::
 
-      examples/PACKAGES/dielectric/in.confined
+   examples/PACKAGES/dielectric/in.confined
-      examples/PACKAGES/dielectric/in.nopbc
+   examples/PACKAGES/dielectric/in.nopbc
 
 Description
 """""""""""

doc/src/compute_entropy_atom.rst

@@ -6,24 +6,23 @@ compute entropy/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID entropy/atom sigma cutoff keyword value ...
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * entropy/atom = style name of this compute command
-* sigma = width of gaussians used in the g(r) smoothing
+* sigma = width of Gaussians used in the :math:`g(r)` smoothing
-* cutoff = cutoff for the g(r) calculation
+* cutoff = cutoff for the :math:`g(r)` calculation
 * one or more keyword/value pairs may be appended
 
 .. parsed-literal::
 
    keyword = *avg* or *local*
-     *avg* values = *yes* or *no* cutoff2
+     *avg* args = neigh cutoff2
-       *yes* = average the pair entropy over neighbors
+       neigh value = *yes* or *no* = whether to average the pair entropy over neighbors
-       *no* = do not average the pair entropy over neighbors
        cutoff2 = cutoff for the averaging over neighbors
-     *local* values = *yes* or *no* = use the local density around each atom to normalize the g(r)
+     *local* arg = *yes* or *no* = use the local density around each atom to normalize the g(r)
 
 Examples
 """"""""
@@ -53,31 +52,32 @@ This parameter for atom i is computed using the following formula from
 
    s_S^i=-2\pi\rho k_B \int\limits_0^{r_m} \left [ g(r) \ln g(r) - g(r) + 1 \right ] r^2 dr
 
-where r is a distance, g(r) is the radial distribution function of atom
+where :math:`r` is a distance, :math:`g(r)` is the radial distribution function
-i and rho is the density of the system. The g(r) computed for each
+of atom :math:`i`, and :math:`\rho` is the density of the system.
-atom i can be noisy and therefore it is smoothed using:
+The :math:`g(r)` computed for each atom :math:`i` can be noisy and therefore it
+is smoothed using
 
 .. math::
 
    g_m^i(r) = \frac{1}{4 \pi \rho r^2} \sum\limits_{j} \frac{1}{\sqrt{2 \pi \sigma^2}} e^{-(r-r_{ij})^2/(2\sigma^2)}
 
-where the sum in j goes through the neighbors of atom i, and :math:`\sigma`
+where the sum over :math:`j` goes through the neighbors of atom :math:`i` and
-is a parameter to control the smoothing.
+:math:`\sigma` is a parameter to control the smoothing.
 
 The input parameters are *sigma* the smoothing parameter :math:`\sigma`,
-and the *cutoff* for the calculation of g(r).
+and the *cutoff* for the calculation of :math:`g(r)`.
 
 If the keyword *avg* has the setting *yes*, then this compute also
-averages the parameter over the neighbors  of atom i according to:
+averages the parameter over the neighbors  of atom :math:`i` according to
 
 .. math::
 
-  \left< s_S^i \right>  = \frac{\sum_j s_S^j + s_S^i}{N + 1}
+  \left< s_S^i \right>  = \frac{\sum_j s_S^j + s_S^i}{N + 1},
 
-where the sum j goes over the neighbors of atom i and N is the number
+where the sum over :math:`j` goes over the neighbors of atom :math:`i` and
-of neighbors. This procedure provides a sharper distinction between
+:math:`N` is the number of neighbors. This procedure provides a sharper
-order and disorder environments. In this case the input parameter
+distinction between order and disorder environments. In this case the input
-*cutoff2* is the cutoff for the averaging over the neighbors and
+parameter *cutoff2* is the cutoff for the averaging over the neighbors and
 must also be specified.
 
 If the *avg yes* option is used, the effective cutoff of the neighbor
@@ -90,14 +90,14 @@ to increase the skin of the neighbor list with:
 
 See :doc:`neighbor <neighbor>` for details.
 
-If the *local yes* option is used, the g(r) is normalized by the
+If the *local yes* option is used, the :math:`g(r)` is normalized by the
 local density around each atom, that is to say the density around each
 atom  is the number of neighbors within the neighbor list cutoff divided
 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 Angstroms),
+constant :math:`4.05~\mathrm{\mathring A}`),
 
 .. parsed-literal::
 
@@ -114,7 +114,8 @@ Output info
 
 By default, this compute calculates the pair entropy value for each
 atom as a per-atom vector, which can be accessed by 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
+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 pair entropy values have units of the Boltzmann constant. They are

doc/src/compute_erotate_asphere.rst

@@ -6,7 +6,7 @@ compute erotate/asphere command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID erotate/asphere
 
@@ -30,9 +30,9 @@ ellipsoids, or line segments, or triangles.  See the
 for descriptions of these options.
 
 For all 3 types of particles, the rotational kinetic energy is
-computed as 1/2 I w\^2, where I is the inertia tensor for the
+computed as :math:`\frac12 I \omega^2`, where :math:`I` is the inertia tensor
-aspherical particle and w is its angular velocity, which is computed
+for the aspherical particle and :math:`\omega` is its angular velocity, which
-from its angular momentum if needed.
+is computed from its angular momentum if needed.
 
 .. note::
 
@@ -48,7 +48,7 @@ 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 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
@@ -65,7 +65,7 @@ This compute requires that triangular particles atoms store a size and
 shape and quaternion orientation and angular momentum as defined by
 the :doc:`atom_style tri <atom_style>` command.
 
-All particles in the group must be finite-size.  They cannot be point
+All particles in the group must be of finite size.  They cannot be point
 particles.
 
 Related commands

doc/src/compute_erotate_rigid.rst

@@ -6,7 +6,7 @@ compute erotate/rigid command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID erotate/rigid fix-ID
 
@@ -25,18 +25,20 @@ Description
 """""""""""
 
 Define a computation that calculates the rotational kinetic energy of
-a collection of rigid bodies, as defined by one of the :doc:`fix rigid <fix_rigid>` command variants.
+a collection of rigid bodies, as defined by one of the
+:doc:`fix rigid <fix_rigid>` command variants.
 
-The rotational energy of each rigid body is computed as 1/2 I Wbody\^2,
+The rotational energy of each rigid body is computed as
-where I is the inertia tensor for the rigid body, and Wbody is its
+:math:`\frac12 I \omega_\text{body}^2`,
-angular velocity vector.  Both I and Wbody are in the frame of
+where :math:`I` is the inertia tensor for the rigid body and
-reference of the rigid body, i.e. I is diagonalized.
+:math:`\omega_\text{body}` is its angular velocity vector.
+Both :math:`I` and :math:`\omega_\text{body}` are in the frame of
+reference of the rigid body (i.e., :math:`I` is diagonal).
 
 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
 compute command is ignored.  The rotational energy of all the rigid
-bodies defined by the fix rigid command in included in the
+bodies defined by the fix rigid command in included in the calculation.
-calculation.
 
 Output info
 """""""""""
@@ -46,14 +48,15 @@ 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
 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
 """"""""""""
 
 This compute is part of the RIGID package.  It is only enabled if
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+LAMMPS was built with that package.  See the
+:doc:`Build package <Build_package>` page for more info.
 
 Related commands
 """"""""""""""""

doc/src/compute_erotate_sphere.rst

@@ -6,7 +6,7 @@ compute erotate/sphere command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID erotate/sphere
 
@@ -26,8 +26,9 @@ Description
 Define a computation that calculates the rotational kinetic energy of
 a group of spherical particles.
 
-The rotational energy is computed as 1/2 I w\^2, where I is the moment
+The rotational energy is computed as :math:`\frac12 I \omega^2`,
-of inertia for a sphere and w is the particle's angular velocity.
+where :math:`I` is the moment of inertia for a sphere and :math:`\omega`
+is the particle's angular velocity.
 
 .. note::
 
@@ -43,7 +44,7 @@ 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 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_erotate_sphere_atom.rst

@@ -6,7 +6,7 @@ compute erotate/sphere/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID erotate/sphere/atom
 
@@ -26,8 +26,9 @@ Description
 Define a computation that calculates the rotational kinetic energy for
 each particle in a group.
 
-The rotational energy is computed as 1/2 I w\^2, where I is the moment
+The rotational energy is computed as :math:`\frac12 I \omega^2`, where
-of inertia for a sphere and w is the particle's angular velocity.
+:math:`I` is the moment of inertia for a sphere and :math:`\omega` is the
+particle's angular velocity.
 
 .. note::
 
@@ -36,8 +37,7 @@ of inertia for a sphere and w is the particle's angular velocity.
    as in 3d.
 
 The value of the rotational kinetic energy will be 0.0 for atoms not
-in the specified compute group or for point particles with a radius =
+in the specified compute group or for point particles with a radius of 0.0.
-0.0.
 
 Output info
 """""""""""

doc/src/compute_event_displace.rst

@@ -6,7 +6,7 @@ compute event/displace command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID event/displace threshold
 
@@ -27,10 +27,9 @@ Description
 Define a computation that flags an "event" if any particle in the
 group has moved a distance greater than the specified threshold
 distance when compared to a previously stored reference state
-(i.e. the previous event).  This compute is typically used in
+(i.e., the previous event).  This compute is typically used in
 conjunction with the :doc:`prd <prd>` and :doc:`tad <tad>` commands,
-to detect if a transition
+to detect if a transition to a new minimum energy basin has occurred.
-to a new minimum energy basin has occurred.
 
 This value calculated by the compute is equal to 0 if no particle has
 moved far enough, and equal to 1 if one or more particles have moved
@@ -51,7 +50,7 @@ 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 options.
 
-The scalar value calculated by this compute is "intensive".  The
+The scalar value calculated by this compute is "intensive."  The
 scalar value will be a 0 or 1 as explained above.
 
 Restrictions

doc/src/compute_fabric.rst

@@ -6,9 +6,9 @@ compute fabric command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
-   compute ID group-ID fabric cutoff attribute1 attribute2 ... keyword values ...
+   compute ID group-ID fabric cutoff attribute ... keyword values ...
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * fabric = style name of this compute command
@@ -20,6 +20,7 @@ Syntax
        *radius* = cutoffs determined based on atom diameters (atom style sphere)
 
 * one or more attributes may be appended
+* attribute = *contact* or *branch* or *force/normal* or *force/tangential*
 
   .. parsed-literal::
 
@@ -63,7 +64,7 @@ tangential force tensor. The contact tensor is calculated as
 
 .. math::
 
-   C_{ab}  =  \frac{15}{2} (\phi_{ab} - \mathrm{tr}(\phi) \delta_{ab})
+   C_{ab}  =  \frac{15}{2} (\phi_{ab} - \mathrm{Tr}(\phi) \delta_{ab})
 
 where :math:`a` and :math:`b` are the :math:`x`, :math:`y`, :math:`z`
 directions, :math:`\delta_{ab}` is the Kronecker delta function, and
@@ -75,13 +76,14 @@ the tensor :math:`\phi` is defined as
 
 where :math:`n` loops over the :math:`N_p` pair interactions in the simulation,
 :math:`r_{a}` is the :math:`a` component of the radial vector between the
-two pairwise interacting particles, and :math:`r` is the magnitude of the radial vector.
+two pairwise interacting particles, and :math:`r` is the magnitude of the
+radial vector.
 
 The branch tensor is calculated as
 
 .. math::
 
-   B_{ab}  =  \frac{15}{6 \mathrm{tr}(D)} (D_{ab} - \mathrm{tr}(D) \delta_{ab})
+   B_{ab}  =  \frac{15}{6 \mathrm{Tr}(D)} (D_{ab} - \mathrm{Tr}(D) \delta_{ab})
 
 where the tensor :math:`D` is defined as
 
@@ -91,14 +93,15 @@ where the tensor :math:`D` is defined as
                 \frac{1}{N_c (r^2 + C_{cd} r_c r_d)}
                 \frac{r_{a} r_{b}}{r}
 
-where :math:`N_c` is the total number of contacts in the system and the subscripts
+where :math:`N_c` is the total number of contacts in the system and the
-:math:`c` and :math:`d` indices are summed according to Einstein notation.
+subscripts :math:`c` and :math:`d` indices are summed according to Einstein
+notation.
 
 The normal force fabric tensor is calculated as
 
 .. math::
 
-   F^n_{ab}  =  \frac{15}{6 \mathrm{tr}(N)} (N_{ab} - \mathrm{tr}(N) \delta_{ab})
+   F^n_{ab}  =  \frac{15}{6\, \mathrm{Tr}(N)} (N_{ab} - \mathrm{Tr}(N) \delta_{ab})
 
 where the tensor :math:`N` is defined as
 
@@ -116,7 +119,7 @@ as
 
 .. math::
 
-   F^t_{ab}  =  \frac{15}{9 \mathrm{tr}(N)} (T_{ab} - \mathrm{tr}(T) \delta_{ab})
+   F^t_{ab}  =  \frac{15}{9\, \mathrm{Tr}(N)} (T_{ab} - \mathrm{Tr}(T) \delta_{ab})
 
 where the tensor :math:`T` is defined as
 
@@ -133,21 +136,23 @@ Interactions between two atoms are only included in calculations if the atom typ
 are in the two lists. Each list consists of a series of type
 ranges separated by commas. The range can be specified as a
 single numeric value, or a wildcard asterisk can be used to specify a range
-of values.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  For
+of values.  This takes the form "\*" or "\*n" or "m\*" or "m\*n".  For
-example, if M = the number of atom types, then an asterisk with no numeric
+example, if :math:`M` is the number of atom types, then an asterisk with no
-values means all types from 1 to M.  A leading asterisk means all types
+numeric values means all types from 1 to :math:`M`.  A leading asterisk means
-from 1 to n (inclusive).  A trailing asterisk means all types from n to M
+all types from 1 to n (inclusive).  A trailing asterisk means all types from
-(inclusive).  A middle asterisk means all types from m to n (inclusive).
+m to :math:`M` (inclusive).  A middle asterisk means all types from m to n
-Multiple *type/include* keywords may be added.
+(inclusive).  Multiple *type/include* keywords may be added.
 
 Output info
 """""""""""
 
-This compute calculates a local vector of doubles and a scalar. The vector stores the
+This compute calculates a local vector of doubles and a scalar. The vector
-unique components of the first requested tensor in the order xx, yy, zz, xy, xz, yz
+stores the unique components of the first requested tensor in the order
-followed by the same components for all subsequent tensors. The length of the vector
+:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`
-is therefore six times the number of requested tensors. The scalar output is the
+followed by the same components for all subsequent tensors.
-number of pairwise interactions included in the calculation of the fabric tensor.
+The length of the vector is therefore six times the number of requested
+tensors. The scalar output is the number of pairwise interactions included in
+the calculation of the fabric tensor.
 
 Restrictions
 """"""""""""
@@ -164,7 +169,7 @@ following fixes which add rigid-body constraints: :doc:`fix shake
 <fix_shake>`, :doc:`fix rattle <fix_shake>`, :doc:`fix rigid
 <fix_rigid>`, :doc:`fix rigid/small <fix_rigid>`. It does not support
 granular pair styles that extend beyond the contact of atomic radii
-(e.g. JKR and DMT).
+(e.g., JKR and DMT).
 
 Related commands
 """"""""""""""""

doc/src/compute_fep.rst

@@ -6,7 +6,7 @@ compute fep command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID fep temp attribute args ... keyword value ...
 
@@ -19,12 +19,12 @@ Syntax
   .. parsed-literal::
 
        *pair* args = pstyle pparam I J v_delta
-         pstyle = pair style name, e.g. lj/cut
+         pstyle = pair style name (e.g., *lj/cut*)
          pparam = parameter to perturb
          I,J = type pair(s) to set parameter for
          v_delta = variable with perturbation to apply (in the units of the parameter)
        *atom* args = aparam I v_delta
-         aparam = parameter to perturb
+         aparam = *charge* = parameter to perturb
          I = type to set parameter for
          v_delta = variable with perturbation to apply (in the units of the parameter)
 
@@ -37,8 +37,8 @@ Syntax
          *no* = ignore tail correction to pair energies (usually small in fep)
          *yes* = include tail correction to pair energies
        *volume* value = *no* or *yes*
-         *no* = ignore volume changes (e.g. in *NVE* or *NVT* trajectories)
+         *no* = ignore volume changes (e.g., in *NVE* or *NVT* trajectories)
-         *yes* = include volume changes (e.g. in *NpT* trajectories)
+         *yes* = include volume changes (e.g., in *NPT* trajectories)
 
 Examples
 """"""""
@@ -84,7 +84,7 @@ It is possible but not necessary that the coupling parameter (or a
 function thereof) appears as a multiplication factor of the potential
 energy. Therefore, this compute can apply perturbations to interaction
 parameters that are not directly proportional to the potential energy
-(e.g. :math:`\sigma` in Lennard-Jones potentials).
+(e.g., :math:`\sigma` in Lennard-Jones potentials).
 
 This command can be combined with :doc:`fix adapt <fix_adapt>` to
 perform multistage free-energy perturbation calculations along
@@ -92,9 +92,9 @@ stepwise alchemical transformations during a simulation run:
 
 .. math::
 
-   \Delta_0^1 A = \sum_{i=0}^{n-1} \Delta_{\lambda_i}^{\lambda_{i+1}} A = - kT
+   \Delta_0^1 A = \sum_{i=0}^{n-1} \Delta_{\lambda_i}^{\lambda_{i+1}} A = - k_B T
    \sum_{i=0}^{n-1} \ln \left< \exp \left( - \frac{U(\lambda_{i+1}) -
-   U(\lambda_i)}{kT} \right) \right>_{\lambda_i}
+   U(\lambda_i)}{k_B T} \right) \right>_{\lambda_i}
 
 This compute is suitable for the finite-difference thermodynamic
 integration (FDTI) method :ref:`(Mezei) <Mezei>`, which is based on an
@@ -107,7 +107,8 @@ perturbation method using a very small :math:`\delta`:
    A(\lambda)}{\partial\lambda} \right)_\lambda \mathrm{d}\lambda \approx
    \sum_{i=0}^{n-1} w_i \frac{A(\lambda_{i} + \delta) - A(\lambda_i)}{\delta}
 
-where :math:`w_i` are weights of a numerical quadrature. The :doc:`fix adapt <fix_adapt>` command can be used to define the stages of
+where :math:`w_i` are weights of a numerical quadrature. The
+:doc:`fix adapt <fix_adapt>` command can be used to define the stages of
 :math:`\lambda` at which the derivative is calculated and averaged.
 
 The compute fep calculates the exponential Boltzmann term and also the
@@ -125,14 +126,14 @@ the derivative of the potential energy with respect to :math:`\lambda`:
 
 Another technique to calculate free energy differences is the
 acceptance ratio method :ref:`(Bennet) <Bennet>`, which can be implemented
-by calculating the potential energy differences with :math:`\delta` = 1.0 on
+by calculating the potential energy differences with :math:`\delta = 1.0` on
 both the forward and reverse routes:
 
 .. math::
 
-   \left< \frac{1}{1 + \exp\left[\left(U_1 - U_0 - \Delta_0^1A \right) /kT
+   \left< \frac{1}{1 + \exp\left[\left(U_1 - U_0 - \Delta_0^1A \right) /k_B T
    \right]} \right>_0 = \left< \frac{1}{1 + \exp\left[\left(U_0 - U_1 +
-   \Delta_0^1A \right) /kT \right]} \right>_1
+   \Delta_0^1A \right) /k_B T \right]} \right>_1
 
 The value of the free energy difference is determined by numerical
 root finding to establish the equality.
@@ -226,17 +227,17 @@ the pair\_\*.cpp file associated with the potential.
 
 Similar to the :doc:`pair_coeff <pair_coeff>` command, I and J can be
 specified in one of two ways.  Explicit numeric values can be used for
-each, as in the first example above.  I <= J is required.  LAMMPS sets
+each, as in the first example above.  I :math:`\le` J is required.  LAMMPS sets
 the coefficients for the symmetric J,I interaction to the same
 values. A wild-card asterisk can be used in place of or in conjunction
 with the I,J arguments to set the coefficients for multiple pairs of
-atom types.  This takes the form "\*" or "\*n" or "n\*" or "m\*n".  If N =
+atom types.  This takes the form "\*" or "\*n" or "m\*" or "m\*n".  If
-the number of atom types, then an asterisk with no numeric values
+:math:`N` is the number of atom types, then an asterisk with no numeric values
-means all types from 1 to N.  A leading asterisk means all types from
+means all types from 1 to :math:`N`.   A leading asterisk means all types from
-1 to n (inclusive).  A trailing asterisk means all types from n to N
+1 to n (inclusive).  A trailing asterisk means all types from m to N
 (inclusive).  A middle asterisk means all types from m to n
-(inclusive).  Note that only type pairs with I <= J are considered; if
+(inclusive).  Note that only type pairs with I :math:`\le` J are considered; if
-asterisks imply type pairs where J < I, they are ignored.
+asterisks imply type pairs where J :math:`<` I, they are ignored.
 
 If :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is being
 used, then the *pstyle* will be a sub-style name.  You must specify
@@ -275,8 +276,8 @@ trajectories during which the volume fluctuates or changes :ref:`(Allen and Tild
 
 .. math::
 
-   \Delta_0^1 A = - kT \sum_{i=0}^{n-1} \ln \frac{\left< V \exp \left( -
+   \Delta_0^1 A = - k_B T \sum_{i=0}^{n-1} \ln \frac{\left< V \exp \left( -
-   \frac{U(\lambda_{i+1}) - U(\lambda_i)}{kT} \right)
+   \frac{U(\lambda_{i+1}) - U(\lambda_i)}{k_B T} \right)
    \right>_{\lambda_i}}{\left< V \right>_{\lambda_i}}
 
 ----------
@@ -286,8 +287,8 @@ Output info
 
 This compute calculates a global vector of length 3 which contains the
 energy difference ( :math:`U_1-U_0` ) as c_ID[1], the
-Boltzmann factor :math:`\exp(-(U_1-U_0)/kT)`, or
+Boltzmann factor :math:`\exp(-(U_1-U_0)/k_B T)`, or
-:math:`V \exp(-(U_1-U_0)/kT)`, as c_ID[2] and the
+:math:`V \exp(-(U_1-U_0)/k_B T)`, as c_ID[2] and the
 volume of the simulation box :math:`V` as c_ID[3]. :math:`U_1` is the
 pair potential energy obtained with the perturbed parameters and
 :math:`U_0` is the pair potential energy obtained with the
@@ -298,7 +299,7 @@ These output results can be used by any command that uses a global
 scalar or vector from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
 options. For example, the computed values can be averaged using :doc:`fix ave/time <fix_ave_time>`.
 
-The values calculated by this compute are "extensive".
+The values calculated by this compute are "extensive."
 
 Restrictions
 """"""""""""

doc/src/compute_fep_ta.rst

@@ -6,7 +6,7 @@ compute fep/ta command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID fep/ta temp plane scale_factor keyword value ...
 
@@ -20,9 +20,9 @@ Syntax
 
   .. parsed-literal::
 
-       *tail* value = *no* or *yes*
+     *tail* value = *no* or *yes*
-         *no* = ignore tail correction to pair energies (usually small in fep)
+       *no* = ignore tail correction to pair energies (usually small in fep)
-         *yes* = include tail correction to pair energies
+       *yes* = include tail correction to pair energies
 
 Examples
 """"""""
@@ -42,11 +42,12 @@ in a single simulation:
 .. math::
 
    \gamma = \lim_{\Delta \mathcal{A} \to 0} \left( \frac{\Delta A_{0 \to 1 }}{\Delta \mathcal{A}}\right)_{N,V,T}
-   = - \frac{kT}{\Delta \mathcal{A}} \ln \left< \exp(-(U_1 - U_0)/kT) \right>_0
+   = - \frac{k_B T}{\Delta \mathcal{A}} \ln \left\langle \exp\left(\frac{-(U_1 - U_0)}{k_B T}\right) \right\rangle_0
 
 During the perturbation, both axes of *plane* are scaled by multiplying
-:math:`\sqrt{scale\_factor}`, while the other axis divided by
+:math:`\sqrt{\mathrm{scale\_factor}}`, while the other axis divided by
-*scale_factor* such that the overall volume of the system is maintained.
+:math:`\mathrm{scale\_factor}` such that the overall volume of the system is
+maintained.
 
 The *tail* keyword controls the calculation of the tail correction to
 "van der Waals" pair energies beyond the cutoff, if this has been
@@ -60,8 +61,8 @@ Output info
 """""""""""
 
 This compute calculates a global vector of length 3 which contains the
-energy difference ( :math:`U_1-U_0` ) as c_ID[1], the Boltzmann factor
+energy difference :math:`(U_1-U_0)` as c_ID[1], the Boltzmann factor
-:math:`\exp(-(U_1-U_0)/kT)`, as c_ID[2] and the change in the *plane*
+:math:`\exp\bigl(-(U_1-U_0)/k_B T\bigr)`, as c_ID[2] and the change in the *plane*
 area :math:`\Delta \mathcal{A}` as c_ID[3]. :math:`U_1` is the potential
 energy of the perturbed state and :math:`U_0` is the potential energy of
 the reference state.  The energies include kspace terms if these are

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_modify.rst

@@ -37,24 +37,27 @@ Description
 Modify one or more parameters of a previously defined compute.  Not
 all compute styles support all parameters.
 
-The *extra/dof* or *extra* keyword refers to how many
+The *extra/dof* or *extra* keyword refers to how many degrees of freedom are
-degrees-of-freedom are subtracted (typically from 3N) as a normalizing
+subtracted (typically from :math:`3N`) as a normalizing
 factor in a temperature computation.  Only computes that compute a
-temperature use this option.  The default is 2 or 3 for :doc:`2d or 3d systems <dimension>` which is a correction factor for an ensemble
+temperature use this option.  The default is 2 or 3 for
-of velocities with zero total linear momentum. For compute
+:doc:`2d or 3d systems <dimension>`, which is a correction factor for an
+ensemble of velocities with zero total linear momentum. For compute
 temp/partial, if one or more velocity components are excluded, the
 value used for *extra* is scaled accordingly. You can use a negative
 number for the *extra* parameter if you need to add
 degrees-of-freedom.  See the :doc:`compute temp/asphere <compute_temp_asphere>` command for an example.
 
 The *dynamic/dof* or *dynamic* keyword determines whether the number
-of atoms N in the compute group and their associated degrees of
+of atoms :math:`N` in the compute group and their associated degrees of
-freedom are re-computed each time a temperature is computed.  Only
+freedom (DOF) are re-computed each time a temperature is computed.  Only
 compute styles that calculate a temperature use this option.  By
-default, N and their DOF are assumed to be constant.  If you are
+default, :math:`N` and their DOF are assumed to be constant.  If you are
-adding atoms or molecules to the system (see the :doc:`fix pour <fix_pour>`, :doc:`fix deposit <fix_deposit>`, and :doc:`fix gcmc <fix_gcmc>` commands) or expect atoms or molecules to be lost
+adding atoms or molecules to the system (see the :doc:`fix pour <fix_pour>`,
-(e.g. due to exiting the simulation box or via :doc:`fix evaporate <fix_evaporate>`), then this option should be used to
+:doc:`fix deposit <fix_deposit>`, and :doc:`fix gcmc <fix_gcmc>` commands) or
-insure the temperature is correctly normalized.
+expect atoms or molecules to be lost (e.g., due to exiting the simulation box
+or via :doc:`fix evaporate <fix_evaporate>`), then this option should be used
+to ensure the temperature is correctly normalized.
 
 .. note::
 
@@ -75,4 +78,4 @@ Default
 """""""
 
 The option defaults are extra/dof = 2 or 3 for 2d or 3d systems and
-dynamic/dof = no.
+dynamic/dof = *no*.

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

@@ -6,14 +6,14 @@ compute pair/local command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID pair/local value1 value2 ... keyword args ...
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * pair/local = style name of this compute command
 * one or more values may be appended
-* value = *dist* or *dx* or *dy* or *dz* or *eng* or *force* or *fx* or *fy* or *fz* or *pN*
+* value = *dist* or *dx* or *dy* or *dz* or *eng* or *force* or *fx* or *fy* or *fz* or *p1* or *p2* or ...
 
   .. parsed-literal::
 
@@ -22,7 +22,7 @@ Syntax
        *eng* = pairwise energy
        *force* = pairwise force
        *fx*,\ *fy*,\ *fz* = components of pairwise force
-       *pN* = pair style specific quantities for allowed N values
+       *p1*, *p2*, ... = pair style specific quantities for allowed N values
 
 * zero or more keyword/arg pairs may be appended
 * keyword = *cutoff*
@@ -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.
-pair styles do not define any additional quantities, so N = 0.  An
+Most pair styles do not define any additional quantities, so :math:`N = 0`.
-example of ones that do are the :doc:`granular pair styles <pair_gran>`
+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 +38,37 @@ 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, :math:`T` is the
-is the dimensionality of the system (2 or 3 for 2d/3d), and *V* is the
+temperature, *d* is the dimensionality of the system (2 for 2d, 3 for
-system volume (or area in 2d).  The second term is the virial, equal to
+3d), and *V* is the system volume (or area in 2d).  The second term is
--dU/dV, computed for all pairwise as well as 2-body, 3-body, 4-body,
+the virial, equal to :math:`-dU/dV`, computed for all pairwise as well
-many-body, and long-range interactions, where :math:`r_i` and
+as 2-body, 3-body, 4-body, many-body, and long-range interactions, where
-:math:`f_i` are the position and force vector of atom *i*, and the black
+:math:`\vec r_i` and :math:`\vec f_i` are the position and force vector
-dot indicates a dot product.  This is computed in parallel for each
+of atom *i*, and the dot indicates the dot product (scalar product).
-sub-domain and then summed over all parallel processes. Thus N'
+This is computed in parallel for each sub-domain and then summed over
-necessarily includes atoms from neighboring sub-domains (so-called ghost
+all parallel processes. Thus :math:`N'` necessarily includes atoms from
-atoms) and the position and force vectors of ghost atoms are thus
+neighboring sub-domains (so-called ghost atoms) and the position and
-included in the summation.  Only when running in serial and without
+force vectors of ghost atoms are thus included in the summation.  Only
-periodic boundary conditions is N' = N = the number of atoms in the
+when running in serial and without periodic boundary conditions is
-system.  :doc:`Fixes <fix>` that impose constraints (e.g. the :doc:`fix
+:math:`N' = N` the number of atoms in the system.  :doc:`Fixes <fix>`
-shake <fix_shake>` command) may also contribute to the virial term.
+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 +92,30 @@ 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 +128,16 @@ 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/compute_reduce.rst

@@ -10,7 +10,7 @@ compute reduce/region command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID style arg mode input1 input2 ... keyword args ...
 
@@ -25,11 +25,11 @@ Syntax
 
 * mode = *sum* or *min* or *max* or *ave* or *sumsq* or *avesq* or *sumabs* or *aveabs*
 * one or more inputs can be listed
-* input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name
+* input = *x* or *y* or *z* or *vx* or *vy* or *vz* or *fx* or *fy* or *fz* or c_ID or c_ID[N] or f_ID or f_ID[N] or v_name
 
   .. parsed-literal::
 
-       x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
+       *x*,\ *y*,\ *z*,\ *vx*,\ *vy*,\ *vz*,\ *fx*,\ *fy*,\ *fz* = atom attribute (position, velocity, force component)
        c_ID = per-atom or local vector calculated by a compute with ID
        c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID, I can include wildcard (see below)
        f_ID = per-atom or local vector calculated by a fix with ID
@@ -76,10 +76,10 @@ then divides by the number of values in the vector.  The *sumsq*
 option sums the square of the values in the vector into a global
 total.  The *avesq* setting does the same as *sumsq*, then divides the
 sum of squares by the number of values.  The last two options can be
-useful for calculating the variance of some quantity, e.g. variance =
+useful for calculating the variance of some quantity (e.g., variance =
-sumsq - ave\^2.  The *sumabs* option sums the absolute values in the
+sumsq :math:`-` ave\ :math:`^2`).  The *sumabs* option sums the absolute
-vector into a global total.  The *aveabs* setting does the same as
+values in the vector into a global total.  The *aveabs* setting does the same
-*sumabs*, then divides the sum of absolute values by the number of
+as *sumabs*, then divides the sum of absolute values by the number of
 values.
 
 Each listed input is operated on independently.  For per-atom inputs,
@@ -97,20 +97,21 @@ component) or can be the result of a :doc:`compute <compute>` or
 :doc:`fix <fix>` or the evaluation of an atom-style
 :doc:`variable <variable>`.
 
-Note that for values from a compute or fix, the bracketed index I can
+Note that for values from a compute or fix, the bracketed index :math:`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
+specify multiple values.  This takes the form "\*" or "\*n" or "m\*" or
-"m\*n".  If N = the size of the vector (for *mode* = scalar) or the
+"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 leading
+with no numeric values means all indices from 1 to :math:`N`.  A leading
 asterisk means all indices from 1 to n (inclusive).  A trailing
-asterisk means all indices from n to N (inclusive).  A middle asterisk
+asterisk means all indices from m to :math:`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 reduce commands are
+had been listed one by one. For example, the following two compute reduce
-equivalent, since the :doc:`compute stress/atom <compute_stress_atom>`
+commands are equivalent, since the
-command creates a per-atom array with 6 columns:
+:doc:`compute stress/atom <compute_stress_atom>` command creates a per-atom
+array with six columns:
 
 .. code-block:: LAMMPS
 
@@ -121,12 +122,13 @@ command creates a per-atom array with 6 columns:
 
 ----------
 
-The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
+The atom attribute values (*x*, *y*, *z*, *vx*, *vy*, *vz*, *fx*, *fy*, and
-self-explanatory.  Note that other atom attributes can be used as
+*fz*) are self-explanatory.  Note that other atom attributes can be used as
-inputs to this fix by using the :doc:`compute property/atom <compute_property_atom>` command and then specifying
+inputs to this fix by using the
+:doc:`compute property/atom <compute_property_atom>` command and then specifying
 an input value from that compute.
 
-If a value begins with "c\_", a compute ID must follow which has been
+If a value begins with "c\_," a compute ID must follow which has been
 previously defined in the input script.  Computes can generate
 per-atom or local quantities.  See the individual
 :doc:`compute <compute>` page for details.  If no bracketed integer
@@ -134,10 +136,10 @@ 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 I can be specified with a wildcard asterisk
+discussion above for how :math:`I` can be specified with a wildcard asterisk
 to effectively specify multiple values.
 
-If a value begins with "f\_", a fix ID must follow which has been
+If a value begins with "f\_," a fix ID must follow which has been
 previously defined in the input script.  Fixes can generate per-atom
 or local quantities.  See the individual :doc:`fix <fix>` page for
 details.  Note that some fixes only produce their values on certain
@@ -145,27 +147,27 @@ timesteps, which must be compatible with when compute reduce
 references the values, else an error results.  If no bracketed integer
 is appended, the vector calculated by the fix is used.  If a bracketed
 integer is appended, the Ith column of the array calculated by the fix
-is used.  Users can also write code for their own fix style and :doc:`add them to LAMMPS <Modify>`.  See the discussion above for how I can
+is used.  Users can also write code for their own fix style and
-be specified with a wildcard asterisk to effectively specify multiple
+:doc:`add them to LAMMPS <Modify>`.  See the discussion above for how
-values.
+:math:`I` can be specified with a wildcard asterisk to effectively specify
+multiple values.
 
-If a value begins with "v\_", a variable name must follow which has
+If a value begins with "v\_," a variable name must follow which has
 been previously defined in the input script.  It must be an
 :doc:`atom-style variable <variable>`.  Atom-style variables can
 reference thermodynamic keywords and various per-atom attributes, or
 invoke other computes, fixes, or variables when they are evaluated, so
-this is a very general means of generating per-atom quantities to
+this is a very general means of generating per-atom quantities to reduce.
-reduce.
 
 ----------
 
 If the *replace* keyword is used, two indices *vec1* and *vec2* are
-specified, where each index ranges from 1 to the # of input values.
+specified, where each index ranges from 1 to the number of input values.
 The replace keyword can only be used if the *mode* is *min* or *max*\ .
 It works as follows.  A min/max is computed as usual on the *vec2*
-input vector.  The index N of that value within *vec2* is also stored.
+input vector.  The index :math:`N` of that value within *vec2* is also stored.
 Then, instead of performing a min/max on the *vec1* input vector, the
-stored index is used to select the Nth element of the *vec1* vector.
+stored index is used to select the :math:`N`\ th element of the *vec1* vector.
 
 Thus, for example, if you wish to use this compute to find the bond
 with maximum stretch, you can do it as follows:
@@ -178,8 +180,10 @@ with maximum stretch, you can do it as follows:
    thermo_style custom step temp c_3[1] c_3[2] c_3[3]
 
 The first two input values in the compute reduce command are vectors
-with the IDs of the 2 atoms in each bond, using the :doc:`compute property/local <compute_property_local>` command.  The last input
+with the IDs of the 2 atoms in each bond, using the
-value is bond distance, using the :doc:`compute bond/local <compute_bond_local>` command.  Instead of taking the
+:doc:`compute property/local <compute_property_local>` command.  The last input
+value is bond distance, using the
+:doc:`compute bond/local <compute_bond_local>` command.  Instead of taking the
 max of the two atom ID vectors, which does not yield useful
 information in this context, the *replace* keywords will extract the
 atom IDs for the two atoms in the bond of maximum stretch.  These atom
@@ -192,10 +196,13 @@ value.  If multiple inputs are specified, this compute produces a
 global vector of values, the length of which is equal to the number of
 inputs specified.
 
-As discussed below, for the *sum*, *sumabs* and *sumsq* modes, the value(s)
+As discussed below, for the *sum*, *sumabs*, and *sumsq* modes, the value(s)
-produced by this compute are all "extensive", meaning their value
+produced by this compute are all "extensive," meaning their value
 scales linearly with the number of atoms involved.  If normalized
-values are desired, this compute can be accessed by the :doc:`thermo_style custom <thermo_style>` command with :doc:`thermo_modify norm yes <thermo_modify>` set as an option.  Or it can be accessed by a
+values are desired, this compute can be accessed by the
+:doc:`thermo_style custom <thermo_style>` command with
+:doc:`thermo_modify norm yes <thermo_modify>` set as an option.
+Or it can be accessed by a
 :doc:`variable <variable>` that divides by the appropriate atom count.
 
 ----------
@@ -203,17 +210,17 @@ values are desired, this compute can be accessed by the :doc:`thermo_style custo
 Output info
 """""""""""
 
-This compute calculates a global scalar if a single input value is
+This compute calculates a global scalar if a single input value is specified
-specified or a global vector of length N where N is the number of
+or a global vector of length :math:`N`, where :math:`N` is the number of
-inputs, and which can be accessed by indices 1 to N.  These values can
+inputs, and which can be accessed by indices 1 to :math:`N`.  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.
 
 All the scalar or vector values calculated by this compute are
-"intensive", except when the *sum*, *sumabs* or *sumsq* modes are used on
+"intensive," except when the *sum*, *sumabs*, or *sumsq* modes are used on
 per-atom or local vectors, in which case the calculated values are
-"extensive".
+"extensive."
 
 The scalar or vector values will be in whatever :doc:`units <units>` the
 quantities being reduced are in.

doc/src/compute_reduce_chunk.rst

@@ -61,7 +61,7 @@ per-atom values for each chunk.
 
 Note that only atoms in the specified group contribute to the
 reduction operation.  If the *chunkID* compute returns a 0 for the
-chunk ID of an atom (i.e. the atom is not in a chunk defined by the
+chunk ID of an atom (i.e., the atom is not in a chunk defined by the
 :doc:`compute chunk/atom <compute_chunk_atom>` command), that atom will
 also not contribute to the reduction operation.  An input that is a
 compute or fix may define its own group which affects the quantities
@@ -74,17 +74,18 @@ of an atom-style :doc:`variable <variable>`.
 
 Note that for 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
+specify multiple values.  This takes the form "\*" or "\*n" or "m\*" or
-"m\*n".  If N = the size of the vector (for *mode* = scalar) or the
+"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 leading
+with no numeric values means all indices from 1 to :math:`N`.  A leading
 asterisk means all indices from 1 to n (inclusive).  A trailing
-asterisk means all indices from n to N (inclusive).  A middle asterisk
+asterisk means all indices from n to :math:`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 reduce/chunk
+had been listed one by one.  For example, the following two compute reduce/chunk
-commands are equivalent, since the :doc:`compute property/chunk <compute_property_chunk>` command creates a per-atom
+commands are equivalent, since the
+:doc:`compute property/chunk <compute_property_chunk>` command creates a per-atom
 array with 3 columns:
 
 .. code-block:: LAMMPS
@@ -101,13 +102,13 @@ The commands below can be added to the examples/in.micelle script.
 
 Imagine a collection of polymer chains or small molecules with
 hydrophobic end groups.  All the hydrophobic (HP) atoms are assigned
-to a group called "phobic".
+to a group called "phobic."
 
 These commands will assign a unique cluster ID to all HP atoms within
 a specified distance of each other.  A cluster will contain all HP
-atoms in a single molecule, but also the HP atoms in nearby molecules,
+atoms in a single molecule, but also the HP atoms in nearby molecules
-e.g. molecules that have clumped to form a micelle due to the
+(e.g., molecules that have clumped to form a micelle due to the
-attraction induced by the hydrophobicity.  The output of the
+attraction induced by the hydrophobicity).  The output of the
 chunk/reduce command will be a cluster ID per chunk (molecule).
 Molecules with the same cluster ID are in the same micelle.
 
@@ -136,7 +137,7 @@ atoms of that atom's molecule belong to.
 
 The result from compute chunk/spread/atom can be used to define a new
 set of chunks, where all the atoms in all the molecules in the same
-micelle are assigned to the same chunk, i.e. one chunk per micelle.
+micelle are assigned to the same chunk (i.e., one chunk per micelle).
 
 .. code-block:: LAMMPS
 
@@ -144,9 +145,8 @@ micelle are assigned to the same chunk, i.e. one chunk per micelle.
 
 Further analysis on a per-micelle basis can now be performed using any
 of the per-chunk computes listed on the :doc:`Howto chunk <Howto_chunk>`
-doc page.  E.g. count the number of atoms in each micelle, calculate
+doc page (e.g., count the number of atoms in each micelle, calculate
-its center or mass, shape (moments of inertia), radius of gyration,
+its center or mass, shape/moments of inertia, and radius of gyration).
-etc.
 
 .. code-block:: LAMMPS
 
@@ -155,7 +155,7 @@ etc.
 
 Each snapshot in the tmp.micelle file will have one line per micelle
 with its count of atoms, plus a first line for a chunk with all the
-solvent atoms.  By the time 50000 steps have elapsed there are a
+solvent atoms.  By the time 50000 steps have elapsed, there are a
 handful of large micelles.
 
 ----------

doc/src/compute_rigid_local.rst

@@ -108,7 +108,8 @@ The *mass* attribute is the total mass of the rigid body.
 
 There are two options for outputting the coordinates of the center of
 mass (COM) of the body.  The *x*, *y*, *z* attributes write the COM
-"unscaled", in the appropriate distance :doc:`units <units>` (Angstroms,
+"unscaled", in the appropriate distance :doc:`units <units>`
+(:math:`\mathrm{\mathring A}`,
 sigma, etc).  Use *xu*, *yu*, *zu* if you want the COM "unwrapped" by
 the image flags for each body.  Unwrapped means that if the body
 COM has passed through a periodic boundary one or more times, the value

doc/src/compute_saed.rst

@@ -86,19 +86,20 @@ will defined using the *c* values for the spacing along each reciprocal
 lattice axis. Note that manual mapping of the reciprocal space mesh is
 good for comparing diffraction results from  multiple simulations; however
 it can reduce the likelihood that Bragg reflections will be satisfied
-unless small spacing parameters <0.05 Angstrom\^(-1) are implemented.
+unless small spacing parameters (:math:`<0.05~\mathrm{\mathring A}^-1`)
-Meshes with manual spacing do not require a periodic boundary.
+are implemented.  Meshes with manual spacing do not require a periodic
+boundary.
 
 The limits of the reciprocal lattice mesh are determined by the use of
 the *Kmax*, *Zone*, and *dR_Ewald* parameters.  The rectilinear mesh
 created about the origin of reciprocal space is terminated at the
 boundary of a sphere of radius *Kmax* centered at the origin.  If
-*Zone* parameters z1=z2=z3=0 are used, diffraction intensities are
+*Zone* parameters *z1* = *z2* = *z3* = 0 are used, diffraction intensities are
 computed throughout the entire spherical volume - note this can
 greatly increase the cost of computation.  Otherwise, *Zone*
-parameters will denote the z1=h, z2=k, and z3=l (in a global since)
+parameters will denote the :math:`z1=h`, :math:`z2=k`, and :math:`z3=\ell`
-zone axis of an intersecting Ewald sphere.  Diffraction intensities
+(in a global sense) zone axis of an intersecting Ewald sphere.  Diffraction
-will only be computed at the intersection of the reciprocal lattice
+intensities will only be computed at the intersection of the reciprocal lattice
 mesh and a *dR_Ewald* thick surface of the Ewald sphere.  See the
 example 3D intensity data and the intersection of a [010] zone axis
 in the below image.

doc/src/compute_stress_atom.rst

@@ -10,7 +10,7 @@ compute centroid/stress/atom command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID style temp-ID keyword ...
 

doc/src/compute_stress_mop.rst

@@ -10,7 +10,7 @@ compute stress/mop/profile command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID style dir args keywords ...
 
@@ -28,6 +28,9 @@ Syntax
        origin = *lower* or *center* or *upper* or coordinate value (distance units) is the position of the first plane
        delta = value (distance units) is the distance between planes
 
+Examples
+""""""""
+
 .. code-block:: LAMMPS
 
    compute 1 all stress/mop x lower total
@@ -49,7 +52,7 @@ components are computed in directions *dir*,\ *x*\ ; *dir*,\ *y*\ ; and
 *dir*,\ *z*\ ; where *dir* is the direction normal to the plane, while
 in compute *stress/mop/profile* the profile of the stress is computed.
 
-Contrary to methods based on histograms of atomic stress (i.e. using
+Contrary to methods based on histograms of atomic stress (i.e., using
 :doc:`compute stress/atom <compute_stress_atom>`), the method of planes is
 compatible with mechanical balance in heterogeneous systems and at
 interfaces :ref:`(Todd) <mop-todd>`.
@@ -57,9 +60,9 @@ interfaces :ref:`(Todd) <mop-todd>`.
 The stress tensor is the sum of a kinetic term and a configurational
 term, which are given respectively by Eq. (21) and Eq. (16) in
 :ref:`(Todd) <mop-todd>`. For the kinetic part, the algorithm considers that
-atoms have crossed the plane if their positions at times t-dt and t are
+atoms have crossed the plane if their positions at times :math:`t-\Delta t`
-one on either side of the plane, and uses the velocity at time t-dt/2
+and :math:`t` are one on either side of the plane, and uses the velocity at
-given by the velocity-Verlet algorithm.
+time :math:`t-\Delta t/2` given by the velocity Verlet algorithm.
 
 Between one and three keywords can be used to indicate which
 contributions to the stress must be computed: kinetic stress (kin),
@@ -74,11 +77,9 @@ command, since those are contributions to the global system pressure.
 NOTE 3: The local stress profile generated by compute *stress/mop/profile*
 is similar to that obtained by compute
 :doc:`stress/cartesian <compute_stress_profile>`.
-A key difference
+A key difference is that compute *stress/mop/profile* considers particles
-is that compute *stress/mop/profile* considers particles
+crossing a set of planes, while compute *stress/cartesian* computes averages
-crossing a set of planes,
+for a set of small volumes.  More information
-while compute *stress/cartesian* computes averages for a set of
-small volumes.  More information
 on the similarities and differences can be found in
 :ref:`(Ikeshoji)<Ikeshoji2>`.
 

doc/src/compute_stress_profile.rst

@@ -15,7 +15,7 @@ compute stress/spherical command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID style args
 
@@ -26,8 +26,9 @@ Syntax
 .. parsed-literal::
 
   *stress/cartesian* args = dim bin_width
-    dim = x, y, or z. One or two dim/bin_width pairs may be appended
+    dim = *x* or *y* or *z*
     bin_width = width of the bin
+    one or two dim/bin_width pairs may be appended
   *stress/cylinder* args = zlo zh Rmax bin_width keyword
     zlo = minimum z-boundary for cylinder
     zhi = maximum z-boundary for cylinder
@@ -63,7 +64,7 @@ gives the total stress tensor :math:`P = P^k+P^v`. These computes can
 for example be used to calculate the diagonal components of the local
 stress tensor of interfaces with flat, cylindrical, or spherical
 symmetry. These computes obeys momentum balance through fluid
-interfaces. They use the Irving-Kirkwood contour, which is the straight
+interfaces. They use the Irving--Kirkwood contour, which is the straight
 line between particle pairs.
 
 The *stress/cartesian* computes the stress profile along one or two
@@ -83,27 +84,28 @@ center of the local volume in the first and second dimensions, number
 density, :math:`P^k_{xx}`, :math:`P^k_{yy}`, :math:`P^k_{zz}`,
 :math:`P^v_{xx}`, :math:`P^v_{yy}`, and :math:`P^v_{zz}`. There are 8
 columns when one dimension is specified and 9 columns when two
-dimensions are specified. The number of bins/rows are
+dimensions are specified. The number of bins (rows) is
-(L1/bin_width1)*(L2/bin_width2), L1 and L2 are the sizes of the
+:math:`(L_1/b_1)(L_2/b_2)`, where :math:`L_1` and :math:`L_2` are the lengths
-simulation box in the specified dimensions, and bin_width1 and
+of the simulation box in the specified dimensions and :math:`b_1` and
-bin_width2 are the specified bin widths. When only one dimension is
+:math:`b_2` are the specified bin widths. When only one dimension is
-specified the number of bins/rows are L1/bin_width.
+specified, the number of bins (rows) is :math:`L_1/b_1`.
 
 The default output columns for *stress/cylinder* are the radius to the
 center of the cylindrical shell, number density, :math:`P^k_{rr}`,
 :math:`P^k_{\phi\phi}`, :math:`P^k_{zz}`, :math:`P^v_{rr}`,
 :math:`P^v_{\phi\phi}`, and :math:`P^v_{zz}`. When the keyword *ke* is
-set to no, the kinetic contributions are not calculated, and
+set to *no*, the kinetic contributions are not calculated, and
-consequently there are only 5 columns the radius to the center of the
+consequently there are only 5 columns: the position of the center of the
-cylindrical shell, number density, :math:`P^v_{rr}`,
+cylindrical shell, the number density, :math:`P^v_{rr}`,
-:math:`P^v_{\phi\phi}`, :math:`P^v_{zz}`. The number of bins/rows are
+:math:`P^v_{\phi\phi}`, and :math:`P^v_{zz}`. The number of bins (rows) is
-Rmax/bin_width.
+:math:`R_\text{max}/b`, where :math:`b` is the specified bin width.
 
-The output columns for *stress/spherical* are the radius to the center
+The output columns for *stress/spherical* are the position of the center
-of the spherical shell, number density, :math:`P^k_{rr}`,
+of the spherical shell, the number density, :math:`P^k_{rr}`,
 :math:`P^k_{\theta\theta}`, :math:`P^k_{\phi\phi}`, :math:`P^v_{rr}`,
 :math:`P^v_{\theta\theta}`, and :math:`P^v_{\phi\phi}`. There are 8
-columns and the number of bins/rows are Rmax/bin_width.
+columns and the number of bins (rows) is :math:`R_\text{max}/b`, where
+:math:`b` is the specified bin width.
 
 This array can be output with :doc:`fix ave/time <fix_ave_time>`,
 
@@ -112,12 +114,13 @@ This array can be output with :doc:`fix ave/time <fix_ave_time>`,
   compute p all stress/cartesian x 0.1
   fix 2 all ave/time 100 1 100 c_p[*] file dump_p.out mode vector
 
-The values calculated by this compute are "intensive".  The stress
+The values calculated by this compute are "intensive."  The stress
 values will be in pressure :doc:`units <units>`. The number density
 values are in inverse volume :doc:`units <units>`.
 
 NOTE 1: The local stress does not include any Lennard-Jones tail
-corrections to the stress added by the :doc:`pair_modify tail yes <pair_modify>`
+corrections to the stress added by the
+:doc:`pair_modify tail yes <pair_modify>`
 command, since those are contributions to the global system pressure.
 
 NOTE 2: The local stress profiles generated by these computes are
@@ -134,11 +137,11 @@ Restrictions
 """"""""""""
 
 These computes calculate the stress tensor contributions for pair
-styles only (i.e. no bond, angle, dihedral, etc. contributions, and in
+styles only (i.e., no bond, angle, dihedral, etc. contributions, and in
 the presence of bonded interactions, the result will be incorrect due to
 exclusions for special bonds) and requires pairwise force calculations
-not available for most many-body pair styles. K-space calculations are
+not available for most many-body pair styles.
-also excluded.
+Note that :math:`k`-space calculations are also excluded.
 
 These computes are part of the EXTRA-COMPUTE package.  They are only
 enabled if LAMMPS was built with that package.  See the :doc:`Build

doc/src/compute_tally.rst

@@ -26,7 +26,7 @@ compute stress/tally command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID style group2-ID
 
@@ -57,8 +57,8 @@ accumulated directly during the non-bonded force computation. The
 computes *force/tally*, *pe/tally*, *stress/tally*, and
 *heat/flux/tally* are primarily provided as example how to program
 additional, more sophisticated computes using the tally callback
-mechanism. Compute *pe/mol/tally* is one such style, that can
+mechanism. Compute *pe/mol/tally* is one such style, that can---through using
-- through using this mechanism - separately tally intermolecular
+this mechanism---separately tally intermolecular
 and intramolecular energies. Something that would otherwise be
 impossible without integrating this as a core functionality into
 the base classes of LAMMPS.
@@ -92,7 +92,7 @@ Although, the *heat/flux/virial/tally* compute
 does not include the convective term,
 it can be used to obtain the total heat flux over control surfaces,
 when there are no particles crossing over,
-such as is often in solid-solid and solid-liquid interfaces.
+such as is often in solid--solid and solid--liquid interfaces.
 This would be identical to the method of planes method.
 Note that the *heat/flux/virial/tally* compute is distinctly different
 from the *heat/flux* and *heat/flux/tally* computes,
@@ -152,7 +152,7 @@ Output info
   atom scalar (the contributions of the single atom to the global
   scalar).
 
-- Compute *pe/mol/tally* calculates a global 4-element vector containing
+- Compute *pe/mol/tally* calculates a global four-element vector containing
   (in this order): *evdwl* and *ecoul* for intramolecular pairs and
   *evdwl* and *ecoul* for intermolecular pairs. Since molecules are
   identified by their molecule IDs, the partitioning does not have to be
@@ -165,24 +165,24 @@ Output info
 
 - Compute *stress/tally* calculates a global scalar
   (average of the diagonal elements of the stress tensor) and a per atom
-  vector (the 6 elements of stress tensor contributions from the
+  vector (the six elements of stress tensor contributions from the
   individual atom).
 
 - As in :doc:`compute heat/flux <compute_heat_flux>`,
   compute *heat/flux/tally* calculates a global vector of length 6,
-  where the first 3 components are the :math:`x`, :math:`y`, :math:`z`
+  where the first three components are the :math:`x`, :math:`y`, :math:`z`
   components of the full heat flow vector,
-  and the next 3 components are the corresponding components
+  and the next three components are the corresponding components
-  of just the convective portion of the flow, i.e. the
+  of just the convective portion of the flow (i.e., the
-  first term in the equation for :math:`\mathbf{Q}`.
+  first term in the equation for :math:`\mathbf{Q}`).
 
 - Compute *heat/flux/virial/tally* calculates a global scalar (heat flow)
-  and a per atom 3-element vector
+  and a per atom three-element vector
   (contribution to the force acting over atoms in the first group
   from individual atoms in both groups).
 
 Both the scalar and vector values calculated by this compute are
-"extensive".
+"extensive."
 
 Restrictions
 """"""""""""

doc/src/compute_tdpd_cc_atom.rst

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

doc/src/compute_temp.rst

@@ -9,7 +9,7 @@ Accelerator Variants: *temp/kk*
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID temp
 
@@ -29,19 +29,27 @@ Description
 
 Define a computation that calculates the temperature of a group of
 atoms.  A compute of this style can be used by any command that
-computes a temperature, e.g. :doc:`thermo_modify <thermo_modify>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix npt <fix_nh>`, etc.
+computes a temperature (e.g., :doc:`thermo_modify <thermo_modify>`,
+:doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix npt <fix_nh>`)
 
-The temperature is calculated by the formula KE = dim/2 N k T, where
+The temperature is calculated by the formula
-KE = total kinetic energy of the group of atoms (sum of 1/2 m v\^2),
-dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
-in the group, k = Boltzmann constant, and T = temperature.
 
-A kinetic energy tensor, stored as a 6-element vector, is also
+.. math::
+
+   \text{KE} = \frac{\text{dim}}{2} N k_B T,
+
+where KE = total kinetic energy of the group of atoms (sum of
+:math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the simulation,
+:math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann
+constant, and :math:`T` is the absolute temperature.
+
+A kinetic energy tensor, stored as a six-element vector, is also
 calculated by this compute for use in the computation of a pressure
 tensor.  The formula for the components of the tensor is the same as
-the above formula, except that v\^2 is replaced by vx\*vy for the xy
+the above formula, except that :math:`v^2` is replaced by
-component, etc.  The 6 components of the vector are ordered xx, yy,
+:math:`v_x v_y` for the :math:`xy` component, and so on.
-zz, xy, xz, yz.
+The six components of the vector are ordered :math:`xx`, :math:`yy`,
+:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
 
 The number of atoms contributing to the temperature is assumed to be
 constant for the duration of the run; use the *dynamic* option of the
@@ -77,12 +85,13 @@ Output info
 """""""""""
 
 This compute calculates a global scalar (the temperature) and a global
-vector of length 6 (KE tensor), which can be accessed by indices 1-6.
+vector of length six (KE tensor), which can be accessed by indices 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
+vector values 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 "intensive".  The
+The scalar value calculated by this compute is "intensive."  The
 vector values are "extensive".
 
 The scalar value will be in temperature :doc:`units <units>`.  The