convert some more fixes

doc/src/Eqs/fix_gld1.tex

@@ -1,13 +0,0 @@
-\documentclass[12pt]{article}
-
-\usepackage{amsmath}
-
-\begin{document}
- 
-\begin{align*}
- &{\bf F}_{j}(t) = {\bf F}^C_j(t)-\int \limits_{0}^{t} \Gamma_j(t-s) {\bf v}_j(s)~\text{d}s + {\bf F}^R_j(t) \\
- &\Gamma_j(t-s) = \sum \limits_{k=1}^{N_k} \frac{c_k}{\tau_k} e^{-(t-s)/\tau_k} \\ 
- &\langle{\bf F}^R_j(t),{\bf F}^R_j(s)\rangle = \text{k$_\text{B}$T} ~\Gamma_j(t-s)
-\end{align*}
-
-\end{document}

doc/src/Eqs/fix_integration_spin_stdecomposition.tex

@@ -1,40 +0,0 @@
-\documentclass[preview]{standalone}
-\usepackage{varwidth}
-\usepackage[utf8x]{inputenc}
-\usepackage{amsmath,amssymb,amsthm,bm,tikz}
-\usetikzlibrary{automata,arrows,shapes,snakes}
-\begin{document}
-\begin{varwidth}{50in}
-\begin{tikzpicture}
-
-%Global
-\node (v1) at (0,6.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{v} \leftarrow \bm{v}+L_v.\Delta t/2$ };
-\node (s1) at (0,4.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{s} \leftarrow \bm{s}+L_s.\Delta t/2$ };
-\node (r)  at (0,3.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{r} \leftarrow \bm{r}+L_r.\Delta t$ };
-\node (s2) at (0,1.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{s} \leftarrow \bm{s}+L_s.\Delta t/2$ };
-\node (v2) at (0,0.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{v} \leftarrow \bm{v}+L_v.\Delta t/2$ };
-
-\draw[line width=2pt, ->] (v1) -- (s1);
-\draw[line width=2pt, ->] (s1) -- (r);
-\draw[line width=2pt, ->] (r) -- (s2);
-\draw[line width=2pt, ->] (s2) -- (v2);
-
-%Spin
-\node (s01) at (6,6.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_0 \leftarrow \bm{s}_0+L_{s_0}.\Delta t/4$ };
-\node (sN1) at (6,4.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N-1}\leftarrow\bm{s}_{\rm N-1}+L_{s_{\rm N-1}}.\Delta t/4$};
-\node (sN)  at (6,3.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N} \leftarrow \bm{s}_{\rm N}+L_{s_{\rm N}}.\Delta t/2$ };
-\node (sN2) at (6,1.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N-1}\leftarrow\bm{s}_{\rm N-1}+L_{s_{\rm N-1}}.\Delta t/4$};
-\node (s02) at (6,0.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_0 \leftarrow \bm{s}_0+L_{s_0}.\Delta t/4$ };
-
-\draw[line width=2pt,dashed, ->] (s01) -- (sN1);
-\draw[line width=2pt, ->] (sN1) -- (sN);
-\draw[line width=2pt, ->] (sN) -- (sN2);
-\draw[line width=2pt,dashed, ->] (sN2) -- (s02);
-
-%from Global to Spin
-\draw[line width=2pt, dashed, ->] (s1) -- (s01.west);
-\draw[line width=2pt, dashed, ->] (s1) -- (s02.west);
-
-\end{tikzpicture}
-\end{varwidth}
-\end{document}

doc/src/Eqs/fix_mvv_dpd.tex

@@ -1,21 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  v(t+\frac{\Delta t}{2}) = v(t) + \frac{\Delta t}{2}\cdot a(t),
-$$
-
-$$
-  r(t+\Delta t) = r(t) + \Delta t\cdot v(t+\frac{\Delta t}{2}),
-$$
-
-$$
-  a(t+\Delta t) = \frac{1}{m}\cdot F\left[ r(t+\Delta t), v(t) +\lambda \cdot \Delta t\cdot a(t)\right],
-$$
-
-$$
-  v(t+\Delta t) = v(t+\frac{\Delta t}{2}) + \frac{\Delta t}{2}\cdot a(t+\Delta t)
-$$
-
-\end{document}

doc/src/Eqs/fix_nphug.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-T_t - T = \frac{\left(\frac{1}{2}\left(P + P_0\right)\left(V_0 - V\right) + E_0 - E\right)}{N_{dof} k_B } = Delta
-$$
-
-\end{document}

doc/src/Eqs/fix_pimd.tex

@@ -1,17 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  Z = \int d{\bf q} d{\bf p} \cdot \textrm{exp} [ -\beta H_{eff} ]
-$$
-
-$$
-  H_{eff} = \bigg(\sum_{i=1}^P \frac{p_i^2}{2m_i}\bigg) + V_{eff}
-$$
-
-$$
-  V_{eff} = \sum_{i=1}^P \bigg[ \frac{mP}{2\beta^2 \hbar^2} (q_i - q_{i+1})^2 + \frac{1}{P} V(q_i)\bigg]
-$$
-
-\end{document}

doc/src/Eqs/fix_rhok.tex

@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
- U &=&  \frac{1}{2} K (|\rho_{\vec{k}}| - a)^2 \\
- \rho_{\vec{k}} &=& \sum_j^N \exp(-i\vec{k} \cdot \vec{r}_j )/\sqrt{N} \\
- \vec{k} &=& (2\pi n_x /L_x , 2\pi n_y  /L_y , 2\pi n_z/L_z ) 
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/fix_rx.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_rx_localTemp.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-\pagestyle{empty}
-\begin{document}
-
-\begin{eqnarray*}
-   \theta_i^{-1} = \frac{\sum_{j=1}\omega_{Lucy}\left(r_{ij}\right)\theta_j^{-1}}{\sum_{j=1}\omega_{Lucy}\left(r_{ij}\right)}
-\end{eqnarray*}                           
-
-\end{document}

doc/src/Eqs/fix_rx_localTemp2.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-\pagestyle{empty}
-\begin{document}
-
-\begin{eqnarray*}
-   \omega_{Lucy}\left(r_{ij}\right) = \left( 1 + \frac{3r_{ij}}{r_c} \right) \left( 1 - \frac{r_{ij}}{r_c} \right)^3
-\end{eqnarray*}                           
-
-\end{document}

doc/src/Eqs/fix_rx_reaction.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-\pagestyle{empty}
-\begin{document}
-
-\begin{eqnarray*}
-   \nu_{A}A + \nu_{B}B \rightarrow \nu_{C}C
-\end{eqnarray*}                           
-
-\end{document}

doc/src/Eqs/fix_rx_reactionRate.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-\pagestyle{empty}
-\begin{document}
-
-\begin{eqnarray*}
-   r = k(T)[A]^{\nu_{A}}[B]^{\nu_{B}}
-\end{eqnarray*}                           
-
-\end{document}

doc/src/fix_gld.rst

@@ -62,8 +62,12 @@ to be a Prony series.
 
 With this fix active, the force on the *j*\ th atom is given as
 
-.. image:: Eqs/fix_gld1.jpg
-   :align: center
+.. math::
+
+   {\bf F}_{j}(t) = & {\bf F}^C_j(t)-\int \limits_{0}^{t} \Gamma_j(t-s) {\bf v}_j(s)~\text{d}s + {\bf F}^R_j(t) \\
+   \Gamma_j(t-s) = & \sum \limits_{k=1}^{N_k} \frac{c_k}{\tau_k} e^{-(t-s)/\tau_k} \\ 
+   \langle{\bf F}^R_j(t),{\bf F}^R_j(s)\rangle = & \text{k$_\text{B}$T} ~\Gamma_j(t-s)
+
 
 Here, the first term is representative of all conservative (pairwise,
 bonded, etc) forces external to this fix, the second is the temporally
@@ -72,7 +76,7 @@ the colored Gaussian random force.
 
 The Prony series form of the memory kernel is chosen to enable an
 extended variable formalism, with a number of exemplary mathematical
-features discussed in :ref:`(Baczewski) <Baczewski>`. In particular, 3N\_k
+features discussed in :ref:`(Baczewski) <Baczewski>`. In particular, :math:`3N_k`
 extended variables are added to each atom, which effect the action of
 the memory kernel without having to explicitly evaluate the integral
 over time in the second term of the force. This also has the benefit

doc/src/fix_mvv_dpd.rst

@@ -50,10 +50,14 @@ The modified velocity-Verlet (MVV) algorithm aims to improve the
 stability of the time integrator by using an extrapolated version of
 the velocity for the force evaluation:
 
-.. image:: Eqs/fix_mvv_dpd.jpg
-   :align: center
+.. math::
 
-where the parameter <font size="4">&lambda;</font> depends on the
+   v(t+\frac{\Delta t}{2}) = & v(t) + \frac{\Delta t}{2}\cdot a(t) \\
+   r(t+\Delta t) = & r(t) + \Delta t\cdot v(t+\frac{\Delta t}{2}) \\
+   a(t+\Delta t) = & \frac{1}{m}\cdot F\left[ r(t+\Delta t), v(t) +\lambda \cdot \Delta t\cdot a(t)\right] \\
+   v(t+\Delta t) = & v(t+\frac{\Delta t}{2}) + \frac{\Delta t}{2}\cdot a(t+\Delta t)
+
+where the parameter :math:`\lambda` depends on the
 specific choice of DPD parameters, and needs to be tuned on a
 case-by-case basis.  Specification of a *lambda* value is optional.
 If specified, the setting must be from 0.0 to 1.0.  If not specified,

doc/src/fix_nphug.rst

@@ -88,21 +88,23 @@ Essentially, a Hugoniostat simulation is an NPT simulation in which the
 user-specified target temperature is replaced with a time-dependent
 target temperature Tt obtained from the following equation:
 
-.. image:: Eqs/fix_nphug.jpg
-   :align: center
+.. math::
 
-where T and Tt are the instantaneous and target temperatures,
-P and P0 are the instantaneous and reference pressures or axial stresses,
+   T_t - T = \frac{\left(\frac{1}{2}\left(P + P_0\right)\left(V_0 - V\right) + E_0 - E\right)}{N_{dof} k_B } = \Delta
+
+
+where *T* and :math:`T_t` are the instantaneous and target temperatures,
+*P* and :math:`P_0` are the instantaneous and reference pressures or axial stresses,
 depending on whether hydrostatic or uniaxial compression is being
-performed, V and V0 are the instantaneous and reference volumes,
-E and E0 are the instantaneous and reference internal energy (potential
-plus kinetic), Ndof is the number of degrees of freedom used in the
-definition of temperature, and kB is the Boltzmann constant. Delta is the
+performed, *V* and :math:`V_0` are the instantaneous and reference volumes,
+*E* and :math:`E_0` are the instantaneous and reference internal energy (potential
+plus kinetic), :math:`N_{dof}` is the number of degrees of freedom used in the
+definition of temperature, and :math:`k_B` is the Boltzmann constant. :math:`\Delta` is the
 negative deviation of the instantaneous temperature from the target temperature.
-When the system reaches a stable equilibrium, the value of Delta should
+When the system reaches a stable equilibrium, the value of :math:`\Delta` should
 fluctuate about zero.
 
-The values of E0, V0, and P0 are the instantaneous values at the start of
+The values of :math:`E_0`, :math:`V_0`, and :math:`P_0` are the instantaneous values at the start of
 the simulation. These can be overridden using the fix\_modify keywords *e0*\ ,
 *v0*\ , and *p0* described below.
 
@@ -179,19 +181,20 @@ instructions on how to use the accelerated styles effectively.
 
 **Restart, fix\_modify, output, run start/stop, minimize info:**
 
-This fix writes the values of E0, V0, and P0, as well as the
-state of all the thermostat and barostat
-variables to :doc:`binary restart files <restart>`.  See the
-:doc:`read_restart <read_restart>` command for info on how to re-specify
-a fix in an input script that reads a restart file, so that the
-operation of the fix continues in an uninterrupted fashion.
+This fix writes the values of :math:`E_0`, :math:`V_0`, and :math:`P_0`,
+as well as the state of all the thermostat and barostat variables to
+:doc:`binary restart files <restart>`.  See the :doc:`read_restart
+<read_restart>` command for info on how to re-specify a fix in an input
+script that reads a restart file, so that the operation of the fix
+continues in an uninterrupted fashion.
 
-The :doc:`fix_modify <fix_modify>` *e0*\ , *v0* and *p0* keywords
-can be used to define the values of E0, V0, and P0. Note the
-the values for *e0* and *v0* are extensive, and so must correspond
-to the total energy and volume of the entire system, not energy and
-volume per atom. If any of these quantities are not specified, then the
-instantaneous value in the system at the start of the simulation is used.
+The :doc:`fix_modify <fix_modify>` *e0*\ , *v0* and *p0* keywords can be
+used to define the values of :math:`E_0`, :math:`V_0`, and
+:math:`P_0`. Note the the values for *e0* and *v0* are extensive, and so
+must correspond to the total energy and volume of the entire system, not
+energy and volume per atom. If any of these quantities are not
+specified, then the instantaneous value in the system at the start of
+the simulation is used.
 
 The :doc:`fix_modify <fix_modify>` *temp* and *press* options are
 supported by these fixes.  You can use them to assign a
@@ -216,7 +219,7 @@ values are "intensive".
 
 The scalar is the cumulative energy change due to the fix.
 
-The vector stores three quantities unique to this fix (Delta, Us, and up),
+The vector stores three quantities unique to this fix (:math:`\Delta`, Us, and up),
 followed by all the internal Nose/Hoover thermostat and barostat
 variables defined for :doc:`fix npt <fix_nh>`. Delta is the deviation
 of the temperature from the target temperature, given by the above equation.

doc/src/fix_nve_spin.rst

@@ -47,7 +47,7 @@ By default a spin-lattice integration is performed (lattice = moving).
 The *nve/spin* fix applies a Suzuki-Trotter decomposition to
 the equations of motion of the spin lattice system, following the scheme:
 
-.. image:: Eqs/fix_integration_spin_stdecomposition.jpg
+.. image:: JPG/fix_integration_spin_stdecomposition.jpg
    :align: center
 
 according to the implementation reported in :ref:`(Omelyan) <Omelyan1>`.

doc/src/fix_pimd.rst

@@ -46,8 +46,11 @@ configurations from the canonical ensemble :ref:`(Feynman) <Feynman>`.
 The classical partition function and its components are given
 by the following equations:
 
-.. image:: Eqs/fix_pimd.jpg
-   :align: center
+.. math::
+
+   Z = & \int d{\bf q} d{\bf p} \cdot \textrm{exp} [ -\beta H_{eff} ] \\
+   H_{eff} = & \bigg(\sum_{i=1}^P \frac{p_i^2}{2m_i}\bigg) + V_{eff} \\
+   V_{eff} = & \sum_{i=1}^P \bigg[ \frac{mP}{2\beta^2 \hbar^2} (q_i - q_{i+1})^2 + \frac{1}{P} V(q_i)\bigg]
 
 The interested user is referred to any of the numerous references on
 this methodology, but briefly, each quantum particle in a path

doc/src/fix_rhok.rst

@@ -29,8 +29,12 @@ Description
 
 The fix applies a force to atoms given by the potential
 
-.. image:: Eqs/fix_rhok.jpg
-   :align: center
+.. math::
+
+   U  = &  \frac{1}{2} K (|\rho_{\vec{k}}| - a)^2 \\
+   \rho_{\vec{k}}  = & \sum_j^N \exp(-i\vec{k} \cdot \vec{r}_j )/\sqrt{N} \\
+   \vec{k}  = & (2\pi n_x /L_x , 2\pi n_y  /L_y , 2\pi n_z/L_z )
+
 
 as described in :ref:`(Pedersen) <Pedersen>`.
 

doc/src/fix_rx.rst

@@ -46,13 +46,17 @@ defined within the file associated with this command.
 
 For a general reaction such that
 
-.. image:: Eqs/fix_rx_reaction.jpg
-   :align: center
+.. math::
+
+   \nu_{A}A + \nu_{B}B \rightarrow \nu_{C}C
+
 
 the reaction rate equation is defined to be of the form
 
-.. image:: Eqs/fix_rx_reactionRate.jpg
-   :align: center
+.. math::
+
+   r = k(T)[A]^{\nu_{A}}[B]^{\nu_{B}}
+
 
 In the current implementation, the exponents are defined to be equal
 to the stoichiometric coefficients.  A given reaction set consisting
@@ -121,12 +125,14 @@ irreversible reaction.  After specifying the reaction, the reaction
 rate constant is determined through the temperature dependent
 Arrhenius equation:
 
-.. image:: Eqs/fix_rx.jpg
-   :align: center
+.. math::
+
+   k = AT^{n}e^{\frac{-E_{a}}{k_{B}T}}
+
 
 where *A* is the Arrhenius factor in time units or concentration/time
 units, *n* is the unitless exponent of the temperature dependence, and
-*E\_a* is the activation energy in energy units.  The temperature
+:math:`E_a` is the activation energy in energy units.  The temperature
 dependence can be removed by specifying the exponent as zero.
 
 The internal temperature of the coarse-grained particles can be used
@@ -136,13 +142,17 @@ be specified to compute a local-average particle internal temperature
 for use in the reaction rate constant expressions.  The local-average
 particle internal temperature is defined as:
 
-.. image:: Eqs/fix_rx_localTemp.jpg
-   :align: center
+.. math::
+
+   \theta_i^{-1} = \frac{\sum_{j=1}\omega_{Lucy}\left(r_{ij}\right)\theta_j^{-1}}{\sum_{j=1}\omega_{Lucy}\left(r_{ij}\right)}
+
 
 where the Lucy function is expressed as:
 
-.. image:: Eqs/fix_rx_localTemp2.jpg
-   :align: center
+.. math::
+
+   \omega_{Lucy}\left(r_{ij}\right) = \left( 1 + \frac{3r_{ij}}{r_c} \right) \left( 1 - \frac{r_{ij}}{r_c} \right)^3
+
 
 The self-particle interaction is included in the above equation.