convert wall fixes to embedded math

doc/src/Eqs/fix_wall_colloid.tex

@@ -1,14 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray}
-E &=& \epsilon \left[ \frac{\sigma^{6}}{7560} 
-  \left(\frac{6R-D}{D^{7}} + \frac{D+8R}{(D+2R)^{7}} \right) - 
-  \frac{}{} \right. \nonumber \\
-  &&\qquad \left. \frac{1}{6} \left(\frac{2R(D+R) + D(D+2R)
-    \left[ \ln D - \ln (D+2R) \right]}{D(D+2R)} \right) \right] 
-\qquad r < r_c \nonumber
-\end{eqnarray}
-
-\end{document}

doc/src/Eqs/fix_wall_ees.tex

@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$ 
-E = \epsilon \left[ \frac{2  \sigma_{LJ}^{12} \left(7 r^5+14 r^3 \sigma_{n}^2+3 r \sigma_{n}^4\right) }{945 \left(r^2-\sigma_{n}^2\right)^7} -\frac{ \sigma_{LJ}^6 \left(2 r \sigma_{n}^3+\sigma_{n}^2 \left(r^2-\sigma_{n}^2\right)\log{ \left[\frac{r-\sigma_{n}}{r+\sigma_{n}}\right]}\right) }{12 \sigma_{n}^5 \left(r^2-\sigma_{n}^2\right)} \right]\qquad \sigma_n < r < r_c
-$$
-
-
-\end{document}

doc/src/Eqs/fix_wall_harmonic.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- E = \epsilon \hspace{0.1cm} (r - r_c)^2 \qquad r < r_c
-$$
-
-\end{document}

doc/src/Eqs/fix_wall_lj1043.tex

@@ -1,12 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- E = 2 \pi \epsilon \left[ \frac{2}{5} \left(\frac{\sigma}{r}\right)^{10} - 
-                       \left(\frac{\sigma}{r}\right)^4 -
-                       \frac{\sqrt(2)\sigma^3}{3\left(r+\left(0.61/\sqrt(2)\right)\sigma\right)^3}\right]
-                       \qquad r < r_c
-$$
-
-\end{document}

doc/src/Eqs/fix_wall_lj93.tex

@@ -1,11 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- E = \epsilon \left[ \frac{2}{15} \left(\frac{\sigma}{r}\right)^{9} - 
-                       \left(\frac{\sigma}{r}\right)^3 \right]
-                       \qquad r < r_c
-$$
-
-\end{document}

doc/src/fix_wall.rst

@@ -104,35 +104,58 @@ wall-particle interactions depends on the style.
 
 For style *wall/lj93*\ , the energy E is given by the 9/3 potential:
 
-.. image:: Eqs/fix_wall_lj93.jpg
-   :align: center
+.. math::
+
+ E = \epsilon \left[ \frac{2}{15} \left(\frac{\sigma}{r}\right)^{9} - 
+                       \left(\frac{\sigma}{r}\right)^3 \right]
+                       \qquad r < r_c
+
 
 For style *wall/lj126*\ , the energy E is given by the 12/6 potential:
 
-.. image:: Eqs/pair_lj.jpg
-   :align: center
+.. math::
+
+ E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - 
+                       \left(\frac{\sigma}{r}\right)^6 \right]
+                       \qquad r < r_c
+
 
 For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential:
 
-.. image:: Eqs/fix_wall_lj1043.jpg
-   :align: center
+.. math::
+
+ E = 2 \pi \epsilon \left[ \frac{2}{5} \left(\frac{\sigma}{r}\right)^{10} - 
+                       \left(\frac{\sigma}{r}\right)^4 -
+                       \frac{\sqrt(2)\sigma^3}{3\left(r+\left(0.61/\sqrt(2)\right)\sigma\right)^3}\right]
+                       \qquad r < r_c
+
 
 For style *wall/colloid*\ , the energy E is given by an integrated form
 of the :doc:`pair_style colloid <pair_colloid>` potential:
 
-.. image:: Eqs/fix_wall_colloid.jpg
-   :align: center
+.. math::
+
+   E = & \epsilon \left[ \frac{\sigma^{6}}{7560} 
+   \left(\frac{6R-D}{D^{7}} + \frac{D+8R}{(D+2R)^{7}} \right) \right. \\
+    & \left. - \frac{1}{6} \left(\frac{2R(D+R) + D(D+2R)
+    \left[ \ln D - \ln (D+2R) \right]}{D(D+2R)} \right) \right] \qquad r < r_c 
+
 
 For style *wall/harmonic*\ , the energy E is given by a harmonic spring
 potential:
 
-.. image:: Eqs/fix_wall_harmonic.jpg
-   :align: center
+.. math::
+
+ E = \epsilon \quad (r - r_c)^2 \qquad r < r_c
+
 
 For style *wall/morse*\ , the energy E is given by a Morse potential:
 
-.. image:: Eqs/pair_morse.jpg
-   :align: center
+.. math::
+
+   E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right]
+       \qquad r < r_c
+
 
 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

doc/src/fix_wall_ees.rst

@@ -65,15 +65,16 @@ group by generating a force on the atom in a direction perpendicular to
 the wall and a torque parallel with the wall.  The energy of
 wall-particle interactions E is given by:
 
-.. image:: Eqs/fix_wall_ees.jpg
-   :align: center
+.. math::
+
+   E = \epsilon \left[ \frac{2  \sigma_{LJ}^{12} \left(7 r^5+14 r^3 \sigma_{n}^2+3 r \sigma_{n}^4\right) }{945 \left(r^2-\sigma_{n}^2\right)^7} -\frac{ \sigma_{LJ}^6 \left(2 r \sigma_{n}^3+\sigma_{n}^2 \left(r^2-\sigma_{n}^2\right)\log{ \left[\frac{r-\sigma_{n}}{r+\sigma_{n}}\right]}\right) }{12 \sigma_{n}^5 \left(r^2-\sigma_{n}^2\right)} \right]\qquad \sigma_n < r < r_c
+
 
 Introduced by Babadi and Ejtehadi in :ref:`(Babadi) <BabadiEjtehadi>`. Here,
 *r* is the distance from the particle to the wall at position *coord*\ ,
 and Rc is the *cutoff* distance at which the particle and wall no
-longer interact. Also, sigma\_n is the distance between center of
-ellipsoid and the nearest point of its surface to the wall. The energy
-of the wall is:
+longer interact. Also, :math:`\sigma_n` is the distance between center of
+ellipsoid and the nearest point of its surface to the wall as shown below.
 
 .. image:: JPG/fix_wall_ees_image.jpg
    :align: center
@@ -82,24 +83,30 @@ Details of using this command and specifications are the same as
 fix/wall command. You can also find an example in USER/ees/ under
 examples/ directory.
 
-The prefactor *epsilon* can be thought of as an
+The prefactor :math:`\epsilon` can be thought of as an
 effective Hamaker constant with energy units for the strength of the
-ellipsoid-wall interaction.  More specifically, the *epsilon* pre-factor
-= 8 \* pi\^2 \* rho\_wall \* rho\_ellipsoid \* epsilon
-\* sigma\_a \* sigma\_b \* sigma\_c, where epsilon is the LJ parameters for
-the constituent LJ particles and sigma\_a, sigma\_b, and sigma\_c are radii
-of ellipsoidal particles. Rho\_wall and rho\_ellipsoid are the number
-density of the constituent particles, in the wall and ellipsoid
-respectively, in units of 1/volume.
+ellipsoid-wall interaction.  More specifically, the :math:`\epsilon`
+pre-factor is
+
+.. math::
+
+   8 \pi^2 \quad \rho_{wall} \quad \rho_{ellipsoid} \quad \epsilon \quad \sigma_a \quad \sigma_b \quad \sigma_c
+
+
+where :math:`\epsilon` is the LJ energy parameter for the constituent LJ
+particles and :math:`\sigma_a`, :math:`\sigma_b`, and :math:`\sigma_c`
+are the radii of the ellipsoidal particles. :math:`\rho_{wall}` and
+:math:`\rho_{ellipsoid}` are the number density of the constituent
+particles, in the wall and ellipsoid respectively, in units of 1/volume.
 
 .. note::
 
-   You must insure that r is always bigger than sigma\_n for
+   You must insure that r is always bigger than :math:`\sigma_n` for
    all particles in the group, or LAMMPS will generate an error.  This
    means you cannot start your simulation with particles touching the wall
-   position *coord* (r = sigma\_n) or with particles penetrating the wall
-   (0 =< r < sigma\_n) or with particles on the wrong side of the
-   wall (r < 0).
+   position *coord* (:math:`r = \sigma_n`) or with particles penetrating
+   the wall (:math:`0 =< r < \sigma_n`) or with particles on the wrong
+   side of the wall (:math:`r < 0`).
 
 Fix *wall/region/ees* treats the surface of the geometric region defined
 by the *region-ID* as a bounding wall which interacts with nearby

doc/src/fix_wall_region.rst

@@ -132,38 +132,62 @@ style.
 
 For style *lj93*\ , the energy E is given by the 9/3 potential:
 
-.. image:: Eqs/fix_wall_lj93.jpg
-   :align: center
+.. math::
+
+ E = \epsilon \left[ \frac{2}{15} \left(\frac{\sigma}{r}\right)^{9} - 
+                       \left(\frac{\sigma}{r}\right)^3 \right]
+                       \qquad r < r_c
+
 
 For style *lj126*\ , the energy E is given by the 12/6 potential:
 
-.. image:: Eqs/pair_lj.jpg
-   :align: center
+.. math::
+
+ E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - 
+                       \left(\frac{\sigma}{r}\right)^6 \right]
+                       \qquad r < r_c
+
 
 For style *wall/lj1043*\ , the energy E is given by the 10/4/3 potential:
 
-.. image:: Eqs/fix_wall_lj1043.jpg
-   :align: center
+.. math::
+
+ E = 2 \pi \epsilon \left[ \frac{2}{5} \left(\frac{\sigma}{r}\right)^{10} - 
+                       \left(\frac{\sigma}{r}\right)^4 -
+                       \frac{\sqrt(2)\sigma^3}{3\left(r+\left(0.61/\sqrt(2)\right)\sigma\right)^3}\right]
+                       \qquad r < r_c
+
 
 For style *colloid*\ , the energy E is given by an integrated form of
 the :doc:`pair_style colloid <pair_colloid>` potential:
 
-.. image:: Eqs/fix_wall_colloid.jpg
-   :align: center
+.. math::
+
+   E = & \epsilon \left[ \frac{\sigma^{6}}{7560} 
+   \left(\frac{6R-D}{D^{7}} + \frac{D+8R}{(D+2R)^{7}} \right) \right. \\
+    & \left. - \frac{1}{6} \left(\frac{2R(D+R) + D(D+2R)
+    \left[ \ln D - \ln (D+2R) \right]}{D(D+2R)} \right) \right] \qquad r < r_c 
+
 
 For style *wall/harmonic*\ , the energy E is given by a harmonic spring
 potential (the distance parameter is ignored):
 
-.. image:: Eqs/fix_wall_harmonic.jpg
-   :align: center
+.. math::
+
+   E = \epsilon \quad (r - r_c)^2 \qquad r < r_c
+
 
 For style *wall/morse*\ , the energy E is given by the Morse potential:
 
-.. image:: Eqs/pair_morse.jpg
-   :align: center
+.. math::
 
-Unlike other styles, this requires three parameters (*D\_0*, *alpha*\ , *r\_0*
-in this order) instead of two like for the other wall styles.
+   E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right]
+       \qquad r < r_c
+
+
+Unlike other styles, this requires three parameters (:math:`D_0`,
+:math:`\alpha`, and :math:`r_0` in this order) instead of two like
+for the other wall styles.
 
 In all cases, *r* is the distance from the particle to the region
 surface, and Rc is the *cutoff* distance at which the particle and