fix bond/react, box/relax, ehex

doc/src/Eqs/fix_bond_react.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-\pagestyle{empty}
-\begin{document}
-
-\begin{eqnarray*}
-   k = AT^{n}e^{\frac{-E_{a}}{k_{B}T}}
-\end{eqnarray*}                           
-
-\end{document}

doc/src/Eqs/fix_box_relax1.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-E = U + P_t \left(V-V_0 \right) + E_{strain}
-$$
-
-\end{document}

doc/src/Eqs/fix_box_relax2.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-\mathbf P = P_t \mathbf I + {\mathbf S_t} \left( \mathbf h_0^{-1} \right)^t \mathbf h_{0d}
-$$
-
-\end{document}

doc/src/Eqs/fix_ehex_eom.tex

@@ -1,8 +0,0 @@
-\documentclass[12pt]{article}
-\usepackage{amsmath}
-\begin{document}
-   \begin{align*}
-     \dot{\mathbf r}_i &= \mathbf v_i,  \\
-     \dot{\mathbf v}_i &= \frac{\mathbf f_i}{m_i} + \frac{\mathbf g_i}{m_i}.
-   \end{align*}
-\end{document}

doc/src/Eqs/fix_ehex_f.tex

@@ -1,12 +0,0 @@
-\documentclass[12pt]{article}
-\usepackage{amsmath}
-\begin{document}
- \begin{equation*}
-      \mathbf g_i = 
-      \begin{cases} \frac{m_i}{2}   \frac{ F_{\Gamma_{k(\mathbf r_i)}}}{ K_{\Gamma_{k(\mathbf r_i)}}} 
-               \left(\mathbf v_i -  \mathbf v_{\Gamma_{k(\mathbf r_i)}} \right) &  \mbox{$k(\mathbf r_i)> 0$ (inside a reservoir),} \\
-                  0                                     &  \mbox{otherwise, } 
-      \end{cases}
-  \end{equation*}
-\end{document}
-

doc/src/fix_bond_react.rst

@@ -374,8 +374,10 @@ reacting molecules.
 The constraint of type 'arrhenius' imposes an additional reaction
 probability according to the temperature-dependent Arrhenius equation:
 
-.. image:: Eqs/fix_bond_react.jpg
-   :align: center
+.. math::
+
+   k = AT^{n}e^{\frac{-E_{a}}{k_{B}T}}
+
 
 The Arrhenius constraint has the following syntax:
 
@@ -385,8 +387,8 @@ The Arrhenius constraint has the following syntax:
    arrhenius *A* *n* *E_a* *seed*
 
 where 'arrhenius' is the required keyword, *A* is the pre-exponential
-factor, *n* is the exponent of the temperature dependence, *E\_a* is
-the activation energy (:doc:`units <units>` of energy), and *seed* is a
+factor, *n* is the exponent of the temperature dependence, :math:`E_a`
+is the activation energy (:doc:`units <units>` of energy), and *seed* is a
 random number seed. The temperature is defined as the instantaneous
 temperature averaged over all atoms in the reaction site, and is
 calculated in the same manner as for example

doc/src/fix_box_relax.rst

@@ -228,23 +228,28 @@ With this fix, the potential energy used by the minimizer is augmented
 by an additional energy provided by the fix. The overall objective
 function then is:
 
-.. image:: Eqs/fix_box_relax1.jpg
-   :align: center
+.. math::
 
-where *U* is the system potential energy, *P*\ \_t is the desired
-hydrostatic pressure, *V* and *V*\ \_0 are the system and reference
-volumes, respectively.  *E*\ \_\ *strain* is the strain energy expression
+   E = U + P_t \left(V-V_0 \right) + E_{strain}
+
+
+where *U* is the system potential energy, :math:`P_t` is the desired
+hydrostatic pressure, :math:`V` and :math:`V_0` are the system and reference
+volumes, respectively.  :math:`E_{strain}` is the strain energy expression
 proposed by Parrinello and Rahman :ref:`(Parrinello1981) <Parrinello1981>`.
 Taking derivatives of *E* w.r.t. the box dimensions, and setting these
 to zero, we find that at the minimum of the objective function, the
 global system stress tensor **P** will satisfy the relation:
 
-.. image:: Eqs/fix_box_relax2.jpg
-   :align: center
+.. math::
 
-where **I** is the identity matrix, **h**\ \_0 is the box dimension tensor of
-the reference cell, and **h**\ \_0\ *d* is the diagonal part of
-**h**\ \_0. **S**\ \_\ *t* is a symmetric stress tensor that is chosen by LAMMPS
+   \mathbf P = P_t \mathbf I + {\mathbf S_t} \left( \mathbf h_0^{-1} \right)^t \mathbf h_{0d}
+
+
+where **I** is the identity matrix, :math:`\mathbf{h_0}` is the box
+dimension tensor of the reference cell, and ::math:`\mathbf{h_{0d}}`
+is the diagonal part of :math:`\mathbf{h_0}`. :math:`\mathbf{S_t}`
+is a symmetric stress tensor that is chosen by LAMMPS
 so that the upper-triangular components of **P** equal the stress tensor
 specified by the user.
 

doc/src/fix_ehex.rst

@@ -78,13 +78,20 @@ additional thermostatting force to the equations of motion, such that
 the time evolution of coordinates and momenta of particle :math:`i`
 becomes :ref:`(Wirnsberger) <Wirnsberger>`
 
-.. image:: Eqs/fix_ehex_eom.jpg
-   :align: center
+.. math::
+
+     \dot{\mathbf r}_i &= \mathbf v_i,  \\
+     \dot{\mathbf v}_i &= \frac{\mathbf f_i}{m_i} + \frac{\mathbf g_i}{m_i}.
 
 The thermostatting force is given by
 
-.. image:: Eqs/fix_ehex_f.jpg
-   :align: center
+.. math::
+
+   \mathbf g_i = \begin{cases}
+   \frac{m_i}{2}   \frac{ F_{\Gamma_{k(\mathbf r_i)}}}{ K_{\Gamma_{k(\mathbf r_i)}}} 
+   \left(\mathbf v_i -  \mathbf v_{\Gamma_{k(\mathbf r_i)}} \right) &  \mbox{$k(\mathbf r_i)> 0$ (inside a reservoir),} \\
+    0                                     &  \mbox{otherwise, } 
+   \end{cases}
 
 where :math:`m_i` is the mass and :math:`k(\mathbf r_i)` maps the particle
 position to the respective reservoir. The quantity