some more formatting and math conversion improvements

doc/src/Python_test.rst

@@ -38,7 +38,7 @@ If an error occurs, carefully go through the steps on the
 library and the :doc:`Python\_install <Python_install>` doc page about
 insuring Python can find the necessary two files it needs.
 
-**Test LAMMPS and Python in serial:**
+Test LAMMPS and Python in serial:
 -------------------------------------
 
 To run a LAMMPS test in serial, type these lines into Python
@@ -67,7 +67,7 @@ typed something like:
 
    lmp_g++ -in in.lj
 
-**Test LAMMPS and Python in parallel:**
+Test LAMMPS and Python in parallel:
 ---------------------------------------
 
 To run LAMMPS in parallel, assuming you have installed the
@@ -128,7 +128,7 @@ described in the PyPar documentation.  The last line of your Python
 script should be pypar.finalize(), to insure MPI is shut down
 correctly.
 
-**Running Python scripts:**
+Running Python scripts:
 ---------------------------
 
 Note that any Python script (not just for LAMMPS) can be invoked in

doc/src/fix_hyper_local.rst

@@ -155,17 +155,15 @@ simulation domain.
 
 To accomplish this, if :math:`B_{ij} < B_{target}`, the :math:`C_{ij}`
 prefactor for bond *ij* is incremented on the current timestep by an
-amount proportional to the inverse of the specified *alpha* and the
-difference (:math:`B_{ij} - B_{target}`).
-Conversely if :math:`B_{ij} > B_{target}`, :math:`C_{ij}` is decremented
-by the same amount.
-This procedure is termed "boostostatting" in :ref:`(Voter2013) <Voter2013lhd>`.
-It drives all of the individual :math:`C_{ij}` to
-values such that when :math:`V^{max}_{ij}` is applied as a bias to
-bond *ij*, the resulting boost factor :math:`B_{ij}` will be close
-to :math:`B_{target}` on average.
-Thus the LHD time acceleration factor for the overall system is
-effectively *Btarget*\ .
+amount proportional to the inverse of the specified :math:`\alpha` and
+the difference (:math:`B_{ij} - B_{target}`).  Conversely if
+:math:`B_{ij} > B_{target}`, :math:`C_{ij}` is decremented by the same
+amount.  This procedure is termed "boostostatting" in :ref:`(Voter2013)
+<Voter2013lhd>`.  It drives all of the individual :math:`C_{ij}` to
+values such that when :math:`V^{max}_{ij}` is applied as a bias to bond
+*ij*, the resulting boost factor :math:`B_{ij}` will be close to
+:math:`B_{target}` on average.  Thus the LHD time acceleration factor
+for the overall system is effectively *Btarget*\ .
 
 Note that in LHD, the boost factor :math:`B_{target}` is specified by the user.
 This is in contrast to global hyperdynamics (GHD) where the boost

doc/src/fix_lb_fluid.rst

@@ -125,9 +125,9 @@ functions,
 Full details of the lattice-Boltzmann algorithm used can be found in
 :ref:`Mackay et al. <fluid-Mackay>`.
 
-The fluid is coupled to the MD particles described by *group-ID*
-through a velocity dependent force.  The contribution to the fluid
-force on a given lattice mesh site j due to MD particle alpha is
+The fluid is coupled to the MD particles described by *group-ID* through
+a velocity dependent force.  The contribution to the fluid force on a
+given lattice mesh site j due to MD particle :math:`\alpha` is
 calculated as:
 
 .. math::

doc/src/fix_qbmsst.rst

@@ -45,12 +45,12 @@ Examples
    fix 1 all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 seed 35082 f_max 0.3 N_f 100 eta 1 beta 400 T_init 110 (liquid methane modeled with the REAX force field, real units)
    fix 2 all qbmsst z 72 q 40 tscale 0.05 damp 1 seed 47508 f_max 120.0 N_f 100 eta 1.0 beta 500 T_init 300 (quartz modeled with the BKS force field, metal units)
 
-Two example input scripts are given, including shocked alpha quartz
-and shocked liquid methane. The input script first equilibrate an
-initial state with the quantum thermal bath at the target temperature
-and then apply the qbmsst to simulate shock compression with quantum
-nuclear correction.  The following two figures plot related quantities
-for shocked alpha quartz.
+Two example input scripts are given, including shocked
+:math:`\alpha-\mathrm{quartz}` and shocked liquid methane.
+The input script first equilibrate an initial state with the quantum
+thermal bath at the target temperature and then apply the qbmsst to
+simulate shock compression with quantum nuclear correction.  The
+following two figures plot related quantities for shocked alpha quartz.
 
 .. image:: JPG/qbmsst_init.jpg
    :align: center

doc/src/fix_wall.rst

@@ -158,7 +158,7 @@ For style *wall/morse*\ , the energy E is given by a Morse potential:
 
 
 In all cases, *r* is the distance from the particle to the wall at
-position *coord*\ , and Rc is the *cutoff* distance at which the
+position *coord*\ , and :math:`r_c` is the *cutoff* distance at which the
 particle and wall no longer interact.  The energy of the wall
 potential is shifted so that the wall-particle interaction energy is
 0.0 at the cutoff distance.
@@ -185,10 +185,10 @@ box parameters and timestep and elapsed time.  Thus it is easy to
 specify a time-dependent wall position.  See examples below.
 
 For the *wall/lj93* and *wall/lj126* and *wall/lj1043* styles,
-*epsilon* and *sigma* are the usual Lennard-Jones parameters, which
+:math:`\epsilon` and :math:`\sigma` are the usual Lennard-Jones parameters, which
 determine the strength and size of the particle as it interacts with
-the wall.  Epsilon has energy units.  Note that this *epsilon* and
-*sigma* may be different than any *epsilon* or *sigma* values defined
+the wall.  Epsilon has energy units.  Note that this :math:`\epsilon` and
+:math:`\sigma` may be different than any :math:`\epsilon` or :math:`\sigma` values defined
 for a pair style that computes particle-particle interactions.
 
 The *wall/lj93* interaction is derived by integrating over a 3d
@@ -197,39 +197,39 @@ interaction is effectively a harder, more repulsive wall interaction.
 The *wall/lj1043* interaction is yet a different form of wall
 interaction, described in Magda et al in :ref:`(Magda) <Magda>`.
 
-For the *wall/colloid* style, *R* is the radius of the colloid
-particle, *D* is the distance from the surface of the colloid particle
-to the wall (r-R), and *sigma* is the size of a constituent LJ
-particle inside the colloid particle and wall.  Note that the cutoff
-distance Rc in this case is the distance from the colloid particle
-center to the wall.  The prefactor *epsilon* can be thought of as an
-effective Hamaker constant with energy units for the strength of the
-colloid-wall interaction.  More specifically, the *epsilon* pre-factor
-= 4 \* pi\^2 \* rho\_wall \* rho\_colloid \* epsilon \* sigma\^6, where epsilon
-and sigma are the LJ parameters for the constituent LJ
-particles. Rho\_wall and rho\_colloid are the number density of the
-constituent particles, in the wall and colloid respectively, in units
-of 1/volume.
+For the *wall/colloid* style, *R* is the radius of the colloid particle,
+*D* is the distance from the surface of the colloid particle to the wall
+(r-R), and :math:`\sigma` is the size of a constituent LJ particle
+inside the colloid particle and wall.  Note that the cutoff distance Rc
+in this case is the distance from the colloid particle center to the
+wall.  The prefactor :math:`\epsilon` can be thought of as an effective
+Hamaker constant with energy units for the strength of the colloid-wall
+interaction.  More specifically, the :math:`\epsilon` pre-factor is
+:math:`4\pi^2 \rho_{wall} \rho_{colloid} \epsilon \sigma^6`, where
+:math:`\epsilon` and :math:`\sigma` are the LJ parameters for the
+constituent LJ particles. :math:`\rho_{wall}` and :math:`\rho_{colloid}`
+are the number density of the constituent particles, in the wall and
+colloid respectively, in units of 1/volume.
 
 The *wall/colloid* interaction is derived by integrating over
-constituent LJ particles of size *sigma* within the colloid particle
-and a 3d half-lattice of Lennard-Jones 12/6 particles of size *sigma*
+constituent LJ particles of size :math:`\sigma` within the colloid particle
+and a 3d half-lattice of Lennard-Jones 12/6 particles of size :math:`\sigma`
 in the wall.  As mentioned in the preceding paragraph, the density of
 particles in the wall and colloid can be different, as specified by
-the *epsilon* pre-factor.
+the :math:`\epsilon` pre-factor.
 
-For the *wall/harmonic* style, *epsilon* is effectively the spring
+For the *wall/harmonic* style, :math:`\epsilon` is effectively the spring
 constant K, and has units (energy/distance\^2).  The input parameter
-*sigma* is ignored.  The minimum energy position of the harmonic
+:math:`\sigma` is ignored.  The minimum energy position of the harmonic
 spring is at the *cutoff*\ .  This is a repulsive-only spring since the
 interaction is truncated at the *cutoff*
 
 For the *wall/morse* style, the three parameters are in this order:
-*D\_0* the depth of the potential, *alpha* the width parameter, and
-*r\_0* the location of the minimum.  *D\_0* has energy units, *alpha*
-inverse distance units, and *r\_0* distance units.
+:math:`D_0` the depth of the potential, :math:`\alpha` the width parameter, and
+:math:`r_0` the location of the minimum.  :math:`D_0` has energy units, :math:`\alpha`
+inverse distance units, and :math:`r_0` distance units.
 
-For any wall, the *epsilon* and/or *sigma* and/or *alpha* parameter can
+For any wall, the :math:`\epsilon` and/or :math:`\sigma` and/or :math:`\alpha` parameter can
 be specified
 as an :doc:`equal-style variable <variable>`, in which case it should be
 specified as v\_name, where name is the variable name.  As with a
@@ -253,7 +253,7 @@ time.  Thus it is easy to specify a time-dependent wall interaction.
    the finite-size particles of radius R must be a distance larger than R
    from the wall position *coord*\ .  The *harmonic* style is a softer
    potential and does not blow up as r -> 0, but you must use a large
-   enough *epsilon* that particles always reamin on the correct side of
+   enough :math:`\epsilon` that particles always reamin on the correct side of
    the wall (r > 0).
 
 The *units* keyword determines the meaning of the distance units used

doc/src/pair_buck6d_coul_gauss.rst

@@ -87,9 +87,9 @@ is thus evaluated as:
 
 where C is an energy-conversion constant, :math:`q_i` and :math:`q_j`
 are the charges on the 2 atoms, epsilon is the dielectric constant which
-can be set by the :doc:`dielectric <dielectric>` command, alpha is ion
-pair dependent damping parameter and erf() is the error-function.  The
-cutoff Rc truncates the interaction distance.
+can be set by the :doc:`dielectric <dielectric>` command, :math:`\alpha`
+is the ion pair dependent damping parameter and erf() is the
+error-function.  The cutoff :math:`r_c` truncates the interaction distance.
 
 The style *buck6d/coul/gauss/dsf* computes the Coulomb interaction
 via the damped shifted force model described in :ref:`(Fennell) <Fennell>`

doc/src/pair_coul.rst

@@ -207,7 +207,7 @@ manipulation of adding and subtracting a self term (for i = j) to the
 first and second term on the right-hand-side, respectively, and a
 small enough :math:`\alpha` damping parameter, the second term shrinks and
 the potential becomes a rapidly-converging real-space summation.  With
-a long enough cutoff and small enough alpha parameter, the energy and
+a long enough cutoff and small enough :math:`\alpha` parameter, the energy and
 forces calculated by the Wolf summation method approach those of the
 Ewald sum.  So it is a means of getting effective long-range
 interactions with a short-range potential.

doc/src/pair_edip.rst

@@ -88,14 +88,14 @@ and three-body coefficients in the formula above:
 * B (distance units)
 * cutoffA (distance units)
 * cutoffC (distance units)
-* alpha
-* beta
-* eta
-* gamma (distance units)
-* lambda (energy units)
-* mu
-* tho
-* sigma (distance units)
+* :math:`\alpha`
+* :math:`\beta`
+* :math:`\eta`
+* :math:`\gamma` (distance units)
+* :math:`lambda` (energy units)
+* :math:`\mu`
+* :math:`\tau`
+* :math:`\sigma` (distance units)
 * Q0
 * u1
 * u2

doc/src/pair_lj.rst

@@ -295,7 +295,7 @@ a self term (for i = j) to the first and second term on the
 right-hand-side, respectively, and a small enough :math:`\alpha` damping
 parameter, the second term shrinks and the potential becomes a
 rapidly-converging real-space summation.  With a long enough cutoff and
-small enough alpha parameter, the energy and forces calculated by the
+small enough :math:`\alpha` parameter, the energy and forces calculated by the
 Wolf summation method approach those of the Ewald sum.  So it is a means
 of getting effective long-range interactions with a short-range
 potential.

doc/src/pair_local_density.rst

@@ -128,7 +128,7 @@ where :math:`\alpha` gives the type of atom *i*\ , :math:`\beta` the
 type of atom *j*\ , and the coefficients *a* and *b* filter for atom
 types as specified by the user. *a* is called the central atom filter as
 it determines to which atoms the potential applies; :math:`a_{\alpha} =
-1` if the LD potential applies to atom type alpha else zero. On the
+1` if the LD potential applies to atom type :math:`\alpha` else zero. On the
 other hand, *b* is called the neighbor atom filter because it specifies
 which atom types to use in the calculation of the LD; :math:`b_{\beta} =
 1` if atom type :math:`\beta` contributes to the LD and zero otherwise.
@@ -210,12 +210,15 @@ and potential.  In general, blank lines anywhere are ignored.
 ----------
 
 **Mixing, shift, table, tail correction, restart, info**\ :
-This pair style does not support automatic mixing. For atom type pairs alpha,
-beta and alpha != beta, even if LD potentials of type (alpha, alpha) and 
-(beta, beta) are provided, you will need to explicitly provide LD potential 
-types (alpha, beta) and (beta, alpha) if need be (Here, the notation (alpha,
-beta) means that alpha is the central atom to which the LD potential is applied
-and beta is the neighbor atom which contributes to the LD potential on alpha).
+This pair style does not support automatic mixing. For atom type pairs
+:math:`\alpha`, :math:`\beta` and :math:`\alpha` != :math:`\beta`, even
+if LD potentials of type (:math:`\alpha`, :math:`\alpha`) and
+(:math:`\beta`, :math:`\beta`) are provided, you will need to explicitly
+provide LD potential types (:math:`\alpha`, :math:`\beta`) and
+(:math:`\beta`, :math:`\alpha`) if need be (Here, the notation
+(:math:`\alpha`, :math:`\beta`) means that :math:`\alpha` is the central
+atom to which the LD potential is applied and :math:`\beta` is the
+neighbor atom which contributes to the LD potential on :math:`\alpha`).
 
 This pair style does not support the :doc:`pair_modify <pair_modify>`
 shift, table, and tail options.

doc/src/pair_morse.rst

@@ -70,9 +70,9 @@ above, or in the data file or restart files read by the
 :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
 commands:
 
-* D0 (energy units)
-* alpha (1/distance units)
-* r0 (distance units)
+* :math:`D_0` (energy units)
+* :math:`\alpha` (1/distance units)
+* :math:`r_0` (distance units)
 * cutoff (distance units)
 
 The last coefficient is optional.  If not specified, the global morse

doc/src/pair_peri.rst

@@ -91,11 +91,11 @@ For the *peri/pmb* style:
 * c (energy/distance/volume\^2 units)
 * horizon (distance units)
 * s00 (unitless)
-* alpha (unitless)
+* :math:`\alpha` (unitless)
 
 C is the effectively a spring constant for Peridynamic bonds, the
 horizon is a cutoff distance for truncating interactions, and s00 and
-alpha are used as a bond breaking criteria.  The units of c are such
+:math:`\alpha` are used as a bond breaking criteria.  The units of c are such
 that c/distance = stiffness/volume\^2, where stiffness is
 energy/distance\^2 and volume is distance\^3.  See the users guide for
 more details.
@@ -106,10 +106,10 @@ For the *peri/lps* style:
 * G (force/area units)
 * horizon (distance units)
 * s00 (unitless)
-* alpha (unitless)
+* :math:`\alpha` (unitless)
 
 K is the bulk modulus and G is the shear modulus.  The horizon is a
-cutoff distance for truncating interactions, and s00 and alpha are
+cutoff distance for truncating interactions, and s00 and :math:`\alpha` are
 used as a bond breaking criteria. See the users guide for more
 details.
 
@@ -119,12 +119,12 @@ For the *peri/ves* style:
 * G (force/area units)
 * horizon (distance units)
 * s00 (unitless)
-* alpha (unitless)
+* :math:`\alpha` (unitless)
 * m\_lambdai (unitless)
 * m\_taubi (unitless)
 
 K is the bulk modulus and G is the shear modulus. The horizon is a
-cutoff distance for truncating interactions, and s00 and alpha are
+cutoff distance for truncating interactions, and s00 and :math:`\alpha` are
 used as a bond breaking criteria. m\_lambdai and m\_taubi are the
 viscoelastic relaxation parameter and time constant,
 respectively. m\_lambdai varies within zero to one. For very small
@@ -138,11 +138,11 @@ For the *peri/eps* style:
 * G (force/area units)
 * horizon (distance units)
 * s00 (unitless)
-* alpha (unitless)
+* :math:`\alpha` (unitless)
 * m\_yield\_stress (force/area units)
 
 K is the bulk modulus and G is the shear modulus. The horizon is a
-cutoff distance and s00 and alpha are used as a bond breaking
+cutoff distance and s00 and :math:`\alpha` are used as a bond breaking
 criteria.  m\_yield\_stress is the yield stress of the material. For
 details please see the description in "(Mtchell2011a)".
 

doc/src/pair_snap.rst

@@ -113,9 +113,9 @@ by the following commands:
    variable zblz equal 73
    pair_style hybrid/overlay &
    zbl ${zblcutinner} ${zblcutouter} snap
-   pair_coeff \* \* zbl 0.0
+   pair_coeff * * zbl 0.0
    pair_coeff 1 1 zbl ${zblz}
-   pair_coeff \* \* snap Ta06A.snapcoeff Ta06A.snapparam Ta
+   pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta
 
 It is convenient to keep these commands in a separate file that can
 be inserted in any LAMMPS input script using the :doc:`include <include>`
@@ -164,8 +164,7 @@ into two passes.
 Detailed definitions for all the other keywords 
 are given on the :doc:`compute sna/atom <compute_sna_atom>` doc page. 
 
-If *quadraticflag* is set to 1, then the SNAP energy expression includes the quadratic term,
-0.5\*B\^t.alpha.B, where alpha is a symmetric *K* by *K* matrix.
+If *quadraticflag* is set to 1, then the SNAP energy expression includes the quadratic term, 0.5\*B\^t.alpha.B, where alpha is a symmetric *K* by *K* matrix.
 The SNAP element file should contain *K*\ (\ *K*\ +1)/2 additional coefficients
 for each element, the upper-triangular elements of alpha.
 

doc/src/pair_thole.rst

@@ -113,7 +113,7 @@ For pair\_style *thole*\ , the following coefficients must be defined for
 each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command
 as in the example above.
 
-* alpha (distance units\^3)
+* :math:`\alpha` (distance units\^3)
 * damp
 * cutoff (distance units)
 
@@ -126,10 +126,10 @@ For pair style *lj/cut/thole/long*\ , the following coefficients must be
 defined for each pair of atoms types via the :doc:`pair_coeff <pair_coeff>`
 command.
 
-* epsilon (energy units)
-* sigma (length units)
-* alpha (distance units\^3)
-* damps
+* :math:`\epsilon` (energy units)
+* :math:`\sigma` (length units)
+* :math:`\alpha` (distance units\^3)
+* damp
 * LJ cutoff (distance units)
 
 The last two coefficients are optional and default to the global values from
@@ -168,12 +168,9 @@ are defined using
 
 .. math::
 
-   \alpha_{ij} = \sqrt{\alpha_i\alpha_j}
-
-
-.. math::
-
-   a_{ij} = \frac 1 2 (a_i + a_j)
+   \alpha_{ij} = & \sqrt{\alpha_i\alpha_j} \\
+   & \\
+   a_{ij} = & \frac 1 2 (a_i + a_j)
 
 Restrictions
 """"""""""""