some more fixups

doc/src/Errors_messages.rst

@@ -301,7 +301,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    Specified bond type is not valid.
 
 *Bad fix ID in fix append/atoms command*
-   The value of the fix_id for keyword spatial must start with 'f_'.
+   The value of the fix_id for keyword spatial must start with "f\_".
 
 *Bad grid of processors*
    The 3d grid of processors defined by the processors command does not

doc/src/compute_chunk_atom.rst

@@ -270,14 +270,14 @@ 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.
 
-If the style begins with "c_", a compute ID must follow which has been
+If the style begins with "c\_", a compute ID must follow which has been
 previously defined in the input script.  If no bracketed integer is
 appended, the per-atom vector calculated by the compute is used.  If a
 bracketed integer is appended, the Ith column of the per-atom array
 calculated by the compute is used.  Users can also write code for
 their own compute styles and :doc:`add them to LAMMPS <Modify>`.
 
-If the style begins with "f_", a fix ID must follow which has been
+If the style begins with "f\_", a fix ID must follow which has been
 previously defined in the input script.  If no bracketed integer is
 appended, the per-atom vector calculated by the fix is used.  If a
 bracketed integer is appended, the Ith column of the per-atom array
@@ -286,7 +286,7 @@ their values on certain timesteps, which must be compatible with the
 timestep on which this compute accesses the fix, else an error
 results.  Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
 
-If a value begins with "v_", a variable name for an *atom* or
+If a value begins with "v\_", a variable name for an *atom* or
 *atomfile* style :doc:`variable <variable>` must follow which has been
 previously defined in the input script.  Variables of style *atom* can
 reference thermodynamic keywords and various per-atom attributes, or

doc/src/compute_global_atom.rst

@@ -133,7 +133,7 @@ simple rounded down to convert the value to integer indices.  The
 final values should range from 1 to N (inclusive), since they are used
 to access values from N-length vectors.
 
-If *index* begins with "c_", a compute ID must follow which has been
+If *index* begins with "c\_", a compute ID must follow which has been
 previously defined in the input script.  The compute must generate
 per-atom quantities.  See the individual :doc:`compute <compute>` doc
 page for details.  If no bracketed integer is appended, the per-atom
@@ -144,7 +144,7 @@ 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.
 
-If *index* begins with "f_", a fix ID must follow which has been
+If *index* begins with "f\_", a fix ID must follow which has been
 previously defined in the input script.  The Fix must generate
 per-atom quantities.  See the individual :doc:`fix <fix>` doc page for
 details.  Note that some fixes only produce their values on certain
@@ -157,7 +157,7 @@ own fix style 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.
 
-If *index* begins with "v_", a variable name must follow which has
+If *index* 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
@@ -171,7 +171,7 @@ This section explains the kinds of *input* values that can be used.
 Note that inputs reference global values, as contrasted with the
 *index* parameter which must reference per-atom values.
 
-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.  The compute must generate a
 global vector or array.  See the individual :doc:`compute <compute>` doc
 page for details.  If no bracketed integer is appended, the vector
@@ -181,7 +181,7 @@ used.  Users can also write code for their own compute styles and :doc:`add them
 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.  The fix must generate a
 global vector or array.  See the individual :doc:`fix <fix>` doc page
 for details.  Note that some fixes only produce their values on
@@ -194,7 +194,7 @@ own fix style 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.
 
-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 a
 :doc:`vector-style variable <variable>`.  Vector-style variables can
 reference thermodynamic keywords and various other attributes of

doc/src/compute_reduce.rst

@@ -122,7 +122,7 @@ 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
 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>` doc page for details.  If no bracketed integer
@@ -133,7 +133,7 @@ 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.
 
-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>` doc page for
 details.  Note that some fixes only produce their values on certain
@@ -145,7 +145,7 @@ is used.  Users can also write code for their own fix style and :doc:`add them t
 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

doc/src/compute_slice.rst

@@ -55,7 +55,7 @@ vector.  Each listed input must be a global vector or column of a
 global array calculated by another :doc:`compute <compute>` or
 :doc:`fix <fix>`.
 
-If an input value begins with "c_", a compute ID must follow which has
+If an input value begins with "c\_", a compute ID must follow which has
 been previously defined in the input script and which generates a
 global vector or array.  See the individual :doc:`compute <compute>` doc
 page for details.  If no bracketed integer is appended, the vector
@@ -63,7 +63,7 @@ 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>`.
 
-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 and which generates a global
 vector or array.  See the individual :doc:`fix <fix>` doc page for
 details.  Note that some fixes only produce their values on certain
@@ -73,7 +73,7 @@ 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>`.
 
-If an input value begins with "v_", a variable name must follow which
+If an input value begins with "v\_", a variable name must follow which
 has been previously defined in the input script.  Only vector-style
 variables can be referenced.  See the :doc:`variable <variable>` command
 for details.  Note that variables of style *vector* define a formula

doc/src/dump_image.rst

@@ -193,7 +193,7 @@ atoms rendered in the image.  They can be any atom attribute defined
 for the :doc:`dump custom <dump>` command, including *type* and
 *element*\ .  This includes per-atom quantities calculated by a
 :doc:`compute <compute>`, :doc:`fix <fix>`, or :doc:`variable <variable>`,
-which are prefixed by "c_", "f_", or "v_" respectively.  Note that the
+which are prefixed by "c\_", "f\_", or "v\_" respectively.  Note that the
 *diameter* setting can be overridden with a numeric value applied to
 all atoms by the optional *adiam* keyword.
 

doc/src/dump_modify.rst

@@ -461,7 +461,7 @@ The *refresh* keyword only applies to the dump *custom*\ , *cfg*\ ,
 *image*\ , and *movie* styles.  It allows an "incremental" dump file to
 be written, by refreshing a compute that is used as a threshold for
 determining which atoms are included in a dump snapshot.  The
-specified *c_ID* gives the ID of the compute.  It is prefixed by "c_"
+specified *c_ID* gives the ID of the compute.  It is prefixed by "c\_"
 to indicate a compute, which is the only current option.  At some
 point, other options may be added, e.g. fixes or variables.
 

doc/src/fix_ave_atom.rst

@@ -121,7 +121,7 @@ an input value from that compute.
    which can be provided by the :doc:`compute property/atom <compute_property_atom>` command via its xu,yu,zu
    attributes.
 
-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.  If no bracketed term is
 appended, the per-atom vector calculated by the compute is used.  If a
 bracketed term containing an index I is appended, the Ith column of
@@ -130,7 +130,7 @@ write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
 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.  If no bracketed term is
 appended, the per-atom vector calculated by the fix is used.  If a
 bracketed term containing an index I is appended, the Ith column of
@@ -141,7 +141,7 @@ write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.  See
 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 as an :doc:`atom-style variable <variable>` Variables of style *atom* can reference
 thermodynamic keywords, or invoke other computes, fixes, or variables
 when they are evaluated, so this is a very general means of generating

doc/src/fix_ave_chunk.rst

@@ -265,7 +265,7 @@ of atoms to calculate their temperature.  The compute allows the
 center-of-mass velocity of each chunk to be subtracted before
 calculating the temperature; this fix does not.
 
-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.  If no bracketed integer is
 appended, the per-atom vector calculated by the compute is used.  If a
 bracketed integer is appended, the Ith column of the per-atom array
@@ -274,7 +274,7 @@ 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.
 
-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.  If no bracketed integer is
 appended, the per-atom vector calculated by the fix is used.  If a
 bracketed integer is appended, the Ith column of the per-atom array
@@ -285,7 +285,7 @@ own fix 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.
 
-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.  Variables of style
 *atom* can reference thermodynamic keywords and various per-atom
 attributes, or invoke other computes, fixes, or variables when they

doc/src/fix_ave_correlate.rst

@@ -169,7 +169,7 @@ default, then *Nfreq* >= (\ *Nrepeat*\ -1)\*\ *Nevery* is required.
 
 ----------
 
-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.  If no bracketed term is
 appended, the global scalar calculated by the compute is used.  If a
 bracketed term is appended, the Ith element of the global vector
@@ -185,7 +185,7 @@ or :doc:`fix temp/rescale <fix_temp_rescale>`.  See the doc pages for
 these commands which give the IDs of these computes.  Users can also
 write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
 
-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.  If no bracketed term is
 appended, the global scalar calculated by the fix is used.  If a
 bracketed term is appended, the Ith element of the global vector
@@ -197,7 +197,7 @@ Note that some fixes only produce their values on certain timesteps,
 which must be compatible with *Nevery*\ , else an error will result.
 Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
 
-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.  Only equal-style or
 vector-style variables can be referenced; the latter requires a
 bracketed term to specify the Ith element of the vector calculated by

doc/src/fix_ave_histo.rst

@@ -176,7 +176,7 @@ 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
 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.  If *mode* = scalar, then if
 no bracketed term is appended, the global scalar calculated by the
 compute is used.  If a bracketed term is appended, the Ith element of
@@ -196,7 +196,7 @@ or :doc:`fix temp/rescale <fix_temp_rescale>`.  See the doc pages for
 these commands which give the IDs of these computes.  Users can also
 write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
 
-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.  If *mode* = scalar, then if
 no bracketed term is appended, the global scalar calculated by the fix
 is used.  If a bracketed term is appended, the Ith element of the
@@ -212,7 +212,7 @@ Note that some fixes only produce their values on certain timesteps,
 which must be compatible with *Nevery*\ , else an error will result.
 Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
 
-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.  If *mode* = scalar, then
 only equal-style or vector-style variables can be used, which both
 produce global values.  In this mode, a vector-style variable requires

doc/src/fix_ave_time.rst

@@ -155,7 +155,7 @@ averaging is done; values are simply generated on timesteps
 
 ----------
 
-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.  If *mode* = scalar, then if
 no bracketed term is appended, the global scalar calculated by the
 compute is used.  If a bracketed term is appended, the Ith element of
@@ -173,7 +173,7 @@ not in your input script, but by :doc:`thermodynamic output <thermo_style>` or o
 the doc pages for these commands which give the IDs of these computes.
 Users can also write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
 
-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.  If *mode* = scalar, then if
 no bracketed term is appended, the global scalar calculated by the fix
 is used.  If a bracketed term is appended, the Ith element of the
@@ -188,7 +188,7 @@ Note that some fixes only produce their values on certain timesteps,
 which must be compatible with *Nevery*\ , else an error will result.
 Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
 
-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.  If *mode* = scalar, then
 only equal-style or vector-style variables can be used, which both
 produce global values.  In this mode, a vector-style variable requires

doc/src/fix_controller.rst

@@ -152,7 +152,7 @@ The process variable *pvar* can be specified as the output of a
 :doc:`variable <variable>`.  In each case, the compute, fix, or variable
 must produce a global quantity, not a per-atom or local quantity.
 
-If *pvar* begins with "c_", a compute ID must follow which has been
+If *pvar* begins with "c\_", a compute ID must follow which has been
 previously defined in the input script and which generates a global
 scalar or vector.  See the individual :doc:`compute <compute>` doc page
 for details.  If no bracketed integer is appended, the scalar
@@ -160,7 +160,7 @@ calculated by the compute is used.  If a bracketed integer is
 appended, the Ith value of the vector calculated by the compute is
 used.  Users can also write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
 
-If *pvar* begins with "f_", a fix ID must follow which has been
+If *pvar* begins with "f\_", a fix ID must follow which has been
 previously defined in the input script and which generates a global
 scalar or vector.  See the individual :doc:`fix <fix>` doc page for
 details.  Note that some fixes only produce their values on certain
@@ -170,7 +170,7 @@ is appended, the scalar calculated by the fix is used.  If a bracketed
 integer is appended, the Ith value of the vector calculated by the fix
 is used.  Users can also write code for their own fix style and :doc:`add them to LAMMPS <Modify>`.
 
-If *pvar* begins with "v_", a variable name must follow which has been
+If *pvar* begins with "v\_", a variable name must follow which has been
 previously defined in the input script.  Only equal-style variables
 can be referenced.  See the :doc:`variable <variable>` command for
 details.  Note that variables of style *equal* define a formula which
@@ -183,7 +183,7 @@ The target value *setpoint* for the process variable must be a numeric
 value, in whatever units *pvar* is defined for.
 
 The control variable *cvar* must be the name of an :doc:`internal-style variable <variable>` previously defined in the input script.  Note
-that it is not specified with a "v_" prefix, just the name of the
+that it is not specified with a "v\_" prefix, just the name of the
 variable.  It must be an internal-style variable, because this fix
 updates its value directly.  Note that other commands can use an
 equal-style versus internal-style variable interchangeably.

doc/src/fix_rx.rst

@@ -189,7 +189,7 @@ Note that the species tags that are defined in the reaction equations
 are used by the :doc:`fix eos/table/rx <fix_eos_table_rx>` command to
 define the thermodynamic properties of each species.  Furthermore, the
 number of species molecules (i.e., concentration) can be specified
-either with the :doc:`set <set>` command using the "d_" prefix or by
+either with the :doc:`set <set>` command using the "d\_" prefix or by
 reading directly the concentrations from a data file.  For the latter
 case, the :doc:`read_data <read_data>` command with the fix keyword
 should be specified, where the fix-ID will be the "fix rx`ID with a <SPECIES">`_ suffix, e.g.

doc/src/fix_vector.rst

@@ -86,7 +86,7 @@ sufficient size.
 
 ----------
 
-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.  If no bracketed term is
 appended, the global scalar calculated by the compute is used.  If a
 bracketed term is appended, the Ith element of the global vector
@@ -100,7 +100,7 @@ or :doc:`fix temp/rescale <fix_temp_rescale>`.  See the doc pages for
 these commands which give the IDs of these computes.  Users can also
 write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
 
-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.  If no bracketed term is
 appended, the global scalar calculated by the fix is used.  If a
 bracketed term is appended, the Ith element of the global vector
@@ -110,7 +110,7 @@ Note that some fixes only produce their values on certain timesteps,
 which must be compatible with *Nevery*\ , else an error will result.
 Users can also write code for their own fix styles and :doc:`add them to LAMMPS <Modify>`.
 
-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.  An equal-style or
 vector-style variable can be referenced; the latter requires a
 bracketed term to specify the Ith element of the vector calculated by

doc/src/pair_resquared.rst

@@ -141,7 +141,7 @@ interactions are computed by another hybrid pair potential), then you
 still need to insure the epsilon a,b,c coefficients are assigned to
 that type in a "pair_coeff I J" command.
 
-For large uniform molecules it has been shown that the epsilon_\*_\*
+For large uniform molecules it has been shown that the :math:`\epsilon_{*,*}`
 energy parameters are approximately representable in terms of local
 contact curvatures :ref:`(Everaers) <Everaers3>`:
 

doc/src/variable.rst

@@ -1092,8 +1092,8 @@ column of an per-atom array.  See the doc pages for individual fixes
 to see what kind of values they produce.
 
 The different kinds of fix references are exactly the same as the
-compute references listed in the above table, where "c_" is replaced
-by "f_".  Again, there is typically no ambiguity (see exception below)
+compute references listed in the above table, where "c\_" is replaced
+by "f\_".  Again, there is typically no ambiguity (see exception below)
 as to what a reference means, since fixes only produce either global
 or per-atom quantities, never both.
 
@@ -1199,7 +1199,7 @@ formula immediately without using the variable command to define a
 named variable.
 
 More generally, there is a difference between referencing a variable
-with a leading $ sign (e.g. $x or ${abc}) versus with a leading "v_"
+with a leading $ sign (e.g. $x or ${abc}) versus with a leading "v\_"
 (e.g. v_x or v_abc).  The former can be used in any input script
 command, including a variable command.  The input script parser
 evaluates the reference variable immediately and substitutes its value
@@ -1208,7 +1208,7 @@ into the command.  As explained on the :doc:`Commands parse <Commands_parse>` do
 this $((xlo+xhi)/2+sqrt(v_area)) in an input script command evaluates
 the string between the parenthesis as an equal-style variable formula.
 
-Referencing a variable with a leading "v_" is an optional or required
+Referencing a variable with a leading "v\_" is an optional or required
 kind of argument for some commands (e.g. the :doc:`fix ave/chunk <fix_ave_chunk>` or :doc:`dump custom <dump>` or
 :doc:`thermo_style <thermo_style>` commands) if you wish it to evaluate
 a variable periodically during a run.  It can also be used in a