resolve some issues in .rst files detected by pandoc

doc/src/Howto_github.rst

@@ -487,10 +487,10 @@ updates are back-ported from the *develop* branch to the *maintenance*
 branch and occasionally merged to *stable* as an update release.
 
 Furthermore, the naming of the release tags now follow the pattern
-"patch_<Day><Month><Year>" to simplify comparisons between releases.
+"patch\_<Day><Month><Year>" to simplify comparisons between releases.
-For stable releases additional "stable_<Day><Month><Year>" tags are
+For stable releases additional "stable\_<Day><Month><Year>" tags are
 applied and update releases are tagged with
-"stable_<Day><Month><Year>_update<Number>", Finally, all releases and
+"stable\_<Day><Month><Year>\_update<Number>", Finally, all releases and
 submissions are subject to automatic testing and code checks to make
 sure they compile with a variety of compilers and popular operating
 systems.  Some unit and regression testing is applied as well.

doc/src/fix_hyper_global.rst

@@ -131,14 +131,15 @@ timesteps is simply
    t_{hyper} = \sum_{i=1,N} B-i \cdot dt
 
 where *dt* is the timestep size defined by the :doc:`timestep <timestep>`
-command.  The effective time acceleration due to GHD is thus t_hyper /
+command.  The effective time acceleration due to GHD is thus
-N\*dt, where N\*dt is elapsed time for a normal MD run of N timesteps.
+:math:`t_{hyper} / N * dt`, where N\*dt is elapsed time for a normal MD run
+of N timesteps.
 
-Note that in GHD, the boost factor varies from timestep to timestep.
+Note that in GHD, the boost factor varies from timestep to timestep.  Likewise,
-Likewise, which bond has :math:`E^{max}` strain and thus which pair of
+which bond has :math:`E^{max}` strain and thus which pair of atoms the bias
-atoms the bias potential is added to, will also vary from timestep to timestep.
+potential is added to, will also vary from timestep to timestep.  This is in
-This is in contrast to local hyperdynamics (LHD) where the boost
+contrast to local hyperdynamics (LHD) where the boost factor is an input
-factor is an input parameter; see the :doc:`fix hyper/local <fix_hyper_local>` page for details.
+parameter; see the :doc:`fix hyper/local <fix_hyper_local>` page for details.
 
 ----------
 
@@ -178,7 +179,7 @@ time-accurate trajectory of the system.
 
 Note that if *Vmax* is set too small, the GHD simulation will run
 correctly.  There will just be fewer events because the hyper time
-(t_hyper equation above) will be shorter.
+(:math:`t_{hyper}` equation above) will be shorter.
 
 .. note::
 

doc/src/fix_hyper_local.rst

@@ -111,7 +111,7 @@ requirement, and thus a bias potential :math:`V^{max}_{ij}` will be
 applied to many bonds on the same timestep.
 
 In LHD, all bonds store a :math:`C_{ij}` prefactor which appears in
-the :math:`V^{max}_{ij}` and :math:`F^{max}_{ij}equations above.  Note
+the :math:`V^{max}_{ij}` and :math:`F^{max}_{ij}` equations above.  Note
 that the :math:`C_{ij}` factor scales the strength of the bias energy
 and forces whenever bond *ij* is the maximum strain bond in its neighborhood.
 
@@ -269,7 +269,7 @@ inverse of the alpha parameter discussed in
 
 The *Btarget* argument is the desired time boost factor (a value > 1)
 that all the atoms in the system will experience.  The elapsed time
-t_hyper for an LHD simulation running for *N* timesteps is simply
+:math:`t_{hyper}` for an LHD simulation running for *N* timesteps is simply
 
 .. math::
 
@@ -294,7 +294,7 @@ is the specified temperature of the system
 
 Note that if *Btarget* is set smaller than this, the LHD simulation
 will run correctly.  There will just be fewer events because the hyper
-time (t_hyper equation above) will be shorter.
+time (:math:`t_{hyper}` equation above) will be shorter.
 
 .. note::