Convert documentation of dihedral styles from images to mathjax

doc/src/Eqs/dihedral_charmm.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$  
-  E = K [ 1 + \cos (n \phi - d) ]
-$$
-
-\end{document}

doc/src/Eqs/dihedral_class2.tex

@@ -1,17 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-  E & = & E_d + E_{mbt} + E_{ebt} + E_{at} + E_{aat} + E_{bb13} \\
-  E_d & = & \sum_{n=1}^{3} K_n [ 1 - \cos (n \phi - \phi_n) ] \\
-  E_{mbt} & = & (r_{jk} - r_2) [ A_1 \cos (\phi) + A_2 \cos (2\phi) + A_3 \cos (3\phi) ] \\
-  E_{ebt} & = & (r_{ij} - r_1) [ B_1 \cos (\phi) + B_2 \cos (2\phi) + B_3 \cos (3\phi) ] + \\
-  & & (r_{kl} - r_3) [ C_1 \cos (\phi) + C_2 \cos (2\phi) + C_3 \cos (3\phi) ] \\
-  E_{at} & = & (\theta_{ijk} - \theta_1) [ D_1 \cos (\phi) + D_2 \cos (2\phi) + D_3 \cos (3\phi) ] + \\
-  & & (\theta_{jkl} - \theta_2) [ E_1 \cos (\phi) + E_2 \cos (2\phi) + E_3 \cos (3\phi) ] \\
-  E_{aat} & = & M (\theta_{ijk} - \theta_1) (\theta_{jkl} - \theta_2) \cos (\phi) \\
-  E_{bb13} & = & N (r_{ij} - r_1) (r_{kl} - r_3)
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/dihedral_cosine_shift_exp.tex

@@ -1,13 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-E=-U_{min} 
-\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1}
-\quad\mbox{with}\quad
-U(\theta,\theta_0)
-=-0.5 \left(1+\cos(\theta-\theta_0) \right)
-$$
-
-\end{document}

doc/src/Eqs/dihedral_fourier.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$  
-  E = \sum_{i=1,m} K_i  [ 1.0 + \cos ( n_i \phi - d_i ) ]
-$$
-
-\end{document}

doc/src/Eqs/dihedral_harmonic.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = K [ 1 + d  \cos (n \phi) ]
-$$
-
-\end{document}

doc/src/Eqs/dihedral_helix.tex

@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = A [1 - \cos(\theta)] + B [1 + \cos(3 \theta)] + 
-      C [1 + \cos(\theta + \frac{\pi}{4})]
-$$
-
-\end{document}

doc/src/Eqs/dihedral_multi_harmonic.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$  
-  E = \sum_{n=1,5} A_n  \cos^{n-1}(\phi)
-$$
-
-\end{document}

doc/src/Eqs/dihedral_nharmonic.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$  
-  E = \sum_{n=1,n} A_n  \cos^{n-1}(\phi)
-$$
-
-\end{document}

doc/src/Eqs/dihedral_opls.tex

@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = \frac{1}{2} K_1 [1 + \cos(\phi)] + \frac{1}{2} K_2 [1 - \cos(2 \phi)] +
-      \frac{1}{2} K_3 [1 + \cos(3 \phi)] + \frac{1}{2} K_4 [1 - \cos(4 \phi)]
-$$
-
-\end{document}

doc/src/Eqs/dihedral_quadratic.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = K (\phi - \phi_0)^2 
-$$
-
-\end{document}

doc/src/Eqs/dihedral_spherical.tex

@@ -1,15 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-\pagestyle{empty}
-\begin{eqnarray*}
-E(\phi,\theta_1,\theta_2) & = &\sum_{i=1}^N\nolimits\ C_i\ \Phi_i(\phi)\ \Theta_{1i}(\theta_1)\ \Theta_{2i}(\theta_2)\\
-\Phi_{i}(\phi)        & = &  u_i - \mathrm{cos}((\phi   - a_i)K_i) \\
-\Theta_{1i}(\theta_1) & = &  v_i - \mathrm{cos}((\theta_1-b_i)L_i) \\
-\Theta_{2i}(\theta_2) & = &  w_i - \mathrm{cos}((\theta_2-c_i)M_i)
-\end{eqnarray*}
-
-% Check using: http://quicklatex.com/  (24pt font)
-\pagestyle{empty}
-\end{document}
-

doc/src/Eqs/dihedral_table_cut.tex

@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-\pagestyle{empty}
-\begin{document}
-
-\begin{eqnarray*}
-        f(\theta) & = & K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\
-        f(\theta) & = & K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2
-\end{eqnarray*}
-
-\end{document}
-

doc/src/dihedral_charmm.rst

@@ -42,8 +42,10 @@ Description
 
 The *charmm* and *charmmfsw* dihedral styles use the potential
 
-.. image:: Eqs/dihedral_charmm.jpg
-   :align: center
+.. math::
+
+  E = K [ 1 + \cos (n \phi - d) ]
+
 
 See :ref:`(MacKerell) <dihedral-MacKerell>` for a description of the CHARMM
 force field.  This dihedral style can also be used for the AMBER force
@@ -66,9 +68,9 @@ The following coefficients must be defined for each dihedral type via the
 the data file or restart files read by the :doc:`read_data <read_data>`
 or :doc:`read_restart <read_restart>` commands:
 
-* K (energy)
-* n (integer >= 0)
-* d (integer value of degrees)
+* :math:`K` (energy)
+* :math:`n` (integer >= 0)
+* :math:`d` (integer value of degrees)
 * weighting factor (1.0, 0.5, or 0.0)
 
 The weighting factor is required to correct for double counting

doc/src/dihedral_class2.rst

@@ -36,114 +36,124 @@ Description
 
 The *class2* dihedral style uses the potential
 
-.. image:: Eqs/dihedral_class2.jpg
-   :align: center
+.. math::
 
-where Ed is the dihedral term, Embt is a middle-bond-torsion term,
-Eebt is an end-bond-torsion term, Eat is an angle-torsion term, Eaat
-is an angle-angle-torsion term, and Ebb13 is a bond-bond-13 term.
+  E & = & E_d + E_{mbt} + E_{ebt} + E_{at} + E_{aat} + E_{bb13} \\
+  E_d & = & \sum_{n=1}^{3} K_n [ 1 - \cos (n \phi - \phi_n) ] \\
+  E_{mbt} & = & (r_{jk} - r_2) [ A_1 \cos (\phi) + A_2 \cos (2\phi) + A_3 \cos (3\phi) ] \\
+  E_{ebt} & = & (r_{ij} - r_1) [ B_1 \cos (\phi) + B_2 \cos (2\phi) + B_3 \cos (3\phi) ] + \\
+  & & (r_{kl} - r_3) [ C_1 \cos (\phi) + C_2 \cos (2\phi) + C_3 \cos (3\phi) ] \\
+  E_{at} & = & (\theta_{ijk} - \theta_1) [ D_1 \cos (\phi) + D_2 \cos (2\phi) + D_3 \cos (3\phi) ] + \\
+  & & (\theta_{jkl} - \theta_2) [ E_1 \cos (\phi) + E_2 \cos (2\phi) + E_3 \cos (3\phi) ] \\
+  E_{aat} & = & M (\theta_{ijk} - \theta_1) (\theta_{jkl} - \theta_2) \cos (\phi) \\
+  E_{bb13} & = & N (r_{ij} - r_1) (r_{kl} - r_3)
 
-Theta1 and theta2 are equilibrium angles and r1 r2 r3 are equilibrium
-bond lengths.
+
+where :math:`E_d` is the dihedral term, :math:`E_{mbt}` is a middle-bond-torsion term,
+:math:`E_{ebt}` is an end-bond-torsion term, :math:`E_{at}` is an angle-torsion term, :math:`E_{aat}`
+is an angle-angle-torsion term, and :math:`E_{bb13}` is a bond-bond-13 term.
+
+:math:`\theta_1` and :math:`\theta_2` are equilibrium angles and :math:`r_1`, :math:`r_2`, and
+:math:`r_3` are equilibrium bond lengths.
 
 See :ref:`(Sun) <dihedral-Sun>` for a description of the COMPASS class2 force field.
 
-Coefficients for the Ed, Embt, Eebt, Eat, Eaat, and Ebb13 formulas
-must be defined for each dihedral type via the
-:doc:`dihedral_coeff <dihedral_coeff>` command as in the example above,
-or in the data file or restart files read by the
-:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
-commands.
+Coefficients for the :math:`E_d`, :math:`E_{mbt}`, :math:`E_{ebt}`,
+:math:`E_{at}`, :math:`E_{aat}`, and :math:`E_{bb13}` formulas must be
+defined for each dihedral type via the :doc:`dihedral_coeff <dihedral_coeff>`
+command as in the example above, or in the data file
+or restart files read by the :doc:`read_data <read_data>` or
+:doc:`read_restart <read_restart>` commands.
 
-These are the 6 coefficients for the Ed formula:
+These are the 6 coefficients for the :math:`E_d` formula:
 
-* K1 (energy)
-* phi1 (degrees)
-* K2 (energy)
-* phi2 (degrees)
-* K3 (energy)
-* phi3 (degrees)
+* :math:`K_1` (energy)
+* :math:`\phi_1` (degrees)
+* :math:`K_2` (energy)
+* :math:`\phi_2` (degrees)
+* :math:`K_3` (energy)
+* :math:`phi_3` (degrees)
 
-For the Embt formula, each line in a
+For the :math:`E_{mbt}` formula, each line in a
 :doc:`dihedral_coeff <dihedral_coeff>` command in the input script lists
-5 coefficients, the first of which is "mbt" to indicate they are
+5 coefficients, the first of which is *mbt* to indicate they are
 MiddleBondTorsion coefficients.  In a data file, these coefficients
-should be listed under a "MiddleBondTorsion Coeffs" heading and you
-must leave out the "mbt", i.e. only list 4 coefficients after the
+should be listed under a *MiddleBondTorsion Coeffs* heading and you
+must leave out the *mbt*, i.e. only list 4 coefficients after the
 dihedral type.
 
-* mbt
-* A1 (energy/distance)
-* A2 (energy/distance)
-* A3 (energy/distance)
-* r2 (distance)
+* *mbt*
+* :math:`A_1` (energy/distance)
+* :math:`A_2` (energy/distance)
+* :math:`A_3` (energy/distance)
+* :math:`r_2` (distance)
 
-For the Eebt formula, each line in a
+For the :math:`E_{ebt}` formula, each line in a
 :doc:`dihedral_coeff <dihedral_coeff>` command in the input script lists
-9 coefficients, the first of which is "ebt" to indicate they are
+9 coefficients, the first of which is *ebt* to indicate they are
 EndBondTorsion coefficients.  In a data file, these coefficients
-should be listed under a "EndBondTorsion Coeffs" heading and you must
-leave out the "ebt", i.e. only list 8 coefficients after the dihedral
+should be listed under a *EndBondTorsion Coeffs* heading and you must
+leave out the *ebt*, i.e. only list 8 coefficients after the dihedral
 type.
 
-* ebt
-* B1 (energy/distance)
-* B2 (energy/distance)
-* B3 (energy/distance)
-* C1 (energy/distance)
-* C2 (energy/distance)
-* C3 (energy/distance)
-* r1 (distance)
-* r3 (distance)
+* *ebt*
+* :math:`B_1` (energy/distance)
+* :math:`B_2` (energy/distance)
+* :math:`B_3` (energy/distance)
+* :math:`C_1` (energy/distance)
+* :math:`C_2` (energy/distance)
+* :math:`C_3` (energy/distance)
+* :math:`r_1` (distance)
+* :math:`r_3` (distance)
 
-For the Eat formula, each line in a
+For the :math:`E_{at}` formula, each line in a
 :doc:`dihedral_coeff <dihedral_coeff>` command in the input script lists
-9 coefficients, the first of which is "at" to indicate they are
+9 coefficients, the first of which is *at* to indicate they are
 AngleTorsion coefficients.  In a data file, these coefficients should
-be listed under a "AngleTorsion Coeffs" heading and you must leave out
-the "at", i.e. only list 8 coefficients after the dihedral type.
+be listed under a *AngleTorsion Coeffs* heading and you must leave out
+the *at*, i.e. only list 8 coefficients after the dihedral type.
 
-* at
-* D1 (energy/radian)
-* D2 (energy/radian)
-* D3 (energy/radian)
-* E1 (energy/radian)
-* E2 (energy/radian)
-* E3 (energy/radian)
-* theta1 (degrees)
-* theta2 (degrees)
+* *at*
+* :math:`D_1` (energy/radian)
+* :math:`D_2` (energy/radian)
+* :math:`D_3` (energy/radian)
+* :math:`E_1` (energy/radian)
+* :math:`E_2` (energy/radian)
+* :math:`E_3` (energy/radian)
+* :math:`\theta_1` (degrees)
+* :math:`\theta_2` (degrees)
 
-Theta1 and theta2 are specified in degrees, but LAMMPS converts them
-to radians internally; hence the units of D and E are in
+:math:`\theta_1` and :math:`\theta_2` are specified in degrees, but LAMMPS converts
+them to radians internally; hence the units of :math:`D` and :math:`E` are in
 energy/radian.
 
-For the Eaat formula, each line in a
+For the :math:`E_{aat}` formula, each line in a
 :doc:`dihedral_coeff <dihedral_coeff>` command in the input script lists
-4 coefficients, the first of which is "aat" to indicate they are
+4 coefficients, the first of which is *aat* to indicate they are
 AngleAngleTorsion coefficients.  In a data file, these coefficients
-should be listed under a "AngleAngleTorsion Coeffs" heading and you
-must leave out the "aat", i.e. only list 3 coefficients after the
+should be listed under a *AngleAngleTorsion Coeffs* heading and you
+must leave out the *aat*, i.e. only list 3 coefficients after the
 dihedral type.
 
-* aat
-* M (energy/radian\^2)
-* theta1 (degrees)
-* theta2 (degrees)
+* *aat*
+* :math:`M` (energy/radian\^2)
+* :math:`\theta_1` (degrees)
+* :math:`\theta_2` (degrees)
 
-Theta1 and theta2 are specified in degrees, but LAMMPS converts them
-to radians internally; hence the units of M are in energy/radian\^2.
+:math:`\theta_1` and :math:`\theta_2` are specified in degrees, but LAMMPS converts
+them to radians internally; hence the units of M are in energy/radian\^2.
 
-For the Ebb13 formula, each line in a
+For the :math:`E_{bb13}` formula, each line in a
 :doc:`dihedral_coeff <dihedral_coeff>` command in the input script lists
-4 coefficients, the first of which is "bb13" to indicate they are
+4 coefficients, the first of which is *bb13* to indicate they are
 BondBond13 coefficients.  In a data file, these coefficients should be
-listed under a "BondBond13 Coeffs" heading and you must leave out the
-"bb13", i.e. only list 3 coefficients after the dihedral type.
+listed under a *BondBond13 Coeffs* heading and you must leave out the
+*bb13*, i.e. only list 3 coefficients after the dihedral type.
 
-* bb13
-* N (energy/distance\^2)
-* r1 (distance)
-* r3 (distance)
+* *bb13*
+* :math:`N` (energy/distance\^2)
+* :math:`r_1` (distance)
+* :math:`r_3` (distance)
 
 
 ----------

doc/src/dihedral_cosine_shift_exp.rst

@@ -28,21 +28,24 @@ Description
 
 The *cosine/shift/exp* dihedral style uses the potential
 
-.. image:: Eqs/dihedral_cosine_shift_exp.jpg
-   :align: center
+.. math::
 
-where Umin, theta, and a are defined for each dihedral type.
+ E  =  -U_{min}\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1} \quad\mbox{with}\quad U(\theta,\theta_0)=-0.5 \left(1+\cos(\theta-\theta_0) \right)
 
-The potential is bounded between [-Umin:0] and the minimum is located
-at the angle theta0. The a parameter can be both positive or negative
+
+where :math:`U_{min}`, :math:`\theta`, and :math:`a` are defined for
+each dihedral type.
+
+The potential is bounded between :math:`\left[-U_{min}:0\right]` and the minimum is located
+at the angle :math:`\theta_0`. The a parameter can be both positive or negative
 and is used to control the spring constant at the equilibrium.
 
-The spring constant is given by k=a exp(a) Umin/ [2 (Exp(a)-1)].
-For a>3 k/Umin = a/2 to better than 5% relative error. For negative
+The spring constant is given by :math:`k=a e^a \frac{U_{min}}{2 \left(e^a-1\right)}`.
+For :math:`a>3` and  :math:`\frac{k}{U_{min}} = \frac{a}{2}` to better than 5% relative error. For negative
 values of the a parameter, the spring constant is essentially zero,
 and anharmonic terms takes over. The potential is furthermore well
-behaved in the limit a->0, where it has been implemented to linear
-order in a for a < 0.001.
+behaved in the limit :math:`a \rightarrow 0`, where it has been implemented to linear
+order in :math:`a` for :math:`a < 0.001`.
 
 The following coefficients must be defined for each dihedral type via
 the :doc:`dihedral_coeff <dihedral_coeff>` command as in the example
@@ -50,9 +53,9 @@ above, or in the data file or restart files read by the
 :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
 commands:
 
-* umin (energy)
-* theta (angle)
-* A (real number)
+* :math:`U_{min}` (energy)
+* :math:`\theta` (angle)
+* :math:`a` (real number)
 
 
 ----------

doc/src/dihedral_fourier.rst

@@ -31,27 +31,27 @@ Description
 
 The *fourier* dihedral style uses the potential:
 
-.. image:: Eqs/dihedral_fourier.jpg
-   :align: center
+.. math::
+
+  E = \sum_{i=1,m} K_i  [ 1.0 + \cos ( n_i \phi - d_i ) ]
+
 
 The following coefficients must be defined for each dihedral type via the
 :doc:`dihedral_coeff <dihedral_coeff>` command as in the example above, or in
 the data file or restart files read by the :doc:`read_data <read_data>`
 or :doc:`read_restart <read_restart>` commands:
 
-* m (integer >=1)
-* K1 (energy)
-* n1 (integer >= 0)
-* d1 (degrees)
+* :math:`m` (integer >=1)
+* :math:`K_1` (energy)
+* :math:`n_1` (integer >= 0)
+* :math:`d_1` (degrees)
 * [...]
-* Km (energy)
-* nm (integer >= 0)
-* dm (degrees)
-
+* :math:`K_m` (energy)
+* :math:`n_m` (integer >= 0)
+* :math:`d_m` (degrees)
 
 ----------
 
-
 Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available

doc/src/dihedral_harmonic.rst

@@ -34,17 +34,19 @@ Description
 
 The *harmonic* dihedral style uses the potential
 
-.. image:: Eqs/dihedral_harmonic.jpg
-   :align: center
+.. math::
+
+  E = K [ 1 + d  \cos (n \phi) ]
+
 
 The following coefficients must be defined for each dihedral type via the
 :doc:`dihedral_coeff <dihedral_coeff>` command as in the example above, or in
 the data file or restart files read by the :doc:`read_data <read_data>`
 or :doc:`read_restart <read_restart>` commands:
 
-* K (energy)
-* d (+1 or -1)
-* n (integer >= 0)
+* :math:`K` (energy)
+* :math:`d` (+1 or -1)
+* :math:`n` (integer >= 0)
 
 .. note::
 
@@ -55,9 +57,9 @@ or :doc:`read_restart <read_restart>` commands:
 
 * The LAMMPS convention is that the trans position = 180 degrees, while
   in some force fields trans = 0 degrees.
-* Some force fields reverse the sign convention on *d*\ .
-* Some force fields let *n* be positive or negative which corresponds to
-  *d* = 1 or -1 for the harmonic style.
+* Some force fields reverse the sign convention on :math:`d`.
+* Some force fields let :math:`n` be positive or negative which corresponds to
+  :math:`d = 1` or :math:`d = -1` for the harmonic style.
 
 
 

doc/src/dihedral_helix.rst

@@ -28,15 +28,19 @@ Description
 
 The *helix* dihedral style uses the potential
 
-.. image:: Eqs/dihedral_helix.jpg
-   :align: center
+.. math::
+
+  E = A [1 - \cos(\theta)] + B [1 + \cos(3 \theta)] + 
+      C [1 + \cos(\theta + \frac{\pi}{4})]
+
 
 This coarse-grain dihedral potential is described in :ref:`(Guo) <Guo>`.
 For dihedral angles in the helical region, the energy function is
 represented by a standard potential consisting of three minima, one
 corresponding to the trans (t) state and the other to gauche states
-(g+ and g-).  The paper describes how the A,B,C parameters are chosen
-so as to balance secondary (largely driven by local interactions) and
+(g+ and g-).  The paper describes how the :math:`A`, :math:`B` and,
+:math:`C` parameters are chosen so as to balance secondary (largely
+driven by local interactions) and
 tertiary structure (driven by long-range interactions).
 
 The following coefficients must be defined for each dihedral type via the
@@ -44,9 +48,9 @@ The following coefficients must be defined for each dihedral type via the
 the data file or restart files read by the :doc:`read_data <read_data>`
 or :doc:`read_restart <read_restart>` commands:
 
-* A (energy)
-* B (energy)
-* C (energy)
+* :math:`A` (energy)
+* :math:`B` (energy)
+* :math:`C` (energy)
 
 
 ----------

doc/src/dihedral_multi_harmonic.rst

@@ -28,19 +28,21 @@ Description
 
 The *multi/harmonic* dihedral style uses the potential
 
-.. image:: Eqs/dihedral_multi_harmonic.jpg
-   :align: center
+.. math::
+
+  E = \sum_{n=1,5} A_n  \cos^{n-1}(\phi)
+
 
 The following coefficients must be defined for each dihedral type via the
 :doc:`dihedral_coeff <dihedral_coeff>` command as in the example above, or in
 the data file or restart files read by the :doc:`read_data <read_data>`
 or :doc:`read_restart <read_restart>` commands:
 
-* A1 (energy)
-* A2 (energy)
-* A3 (energy)
-* A4 (energy)
-* A5 (energy)
+* :math:`A_1` (energy)
+* :math:`A_2` (energy)
+* :math:`A_3` (energy)
+* :math:`A_4` (energy)
+* :math:`A_5` (energy)
 
 
 ----------

doc/src/dihedral_nharmonic.rst

@@ -28,19 +28,21 @@ Description
 
 The *nharmonic* dihedral style uses the potential:
 
-.. image:: Eqs/dihedral_nharmonic.jpg
-   :align: center
+.. math::
+
+  E = \sum_{n=1,n} A_n  \cos^{n-1}(\phi)
+
 
 The following coefficients must be defined for each dihedral type via the
 :doc:`dihedral_coeff <dihedral_coeff>` command as in the example above, or in
 the data file or restart files read by the :doc:`read_data <read_data>`
 or :doc:`read_restart <read_restart>` commands:
 
-* n (integer >=1)
-* A1 (energy)
-* A2 (energy)
+* :math:`n` (integer >=1)
+* :math:`A_1` (energy)
+* :math:`A_2` (energy)
 * ...
-* An (energy)
+* :math:`A_n` (energy)
 
 
 ----------

doc/src/dihedral_opls.rst

@@ -36,8 +36,11 @@ Description
 
 The *opls* dihedral style uses the potential
 
-.. image:: Eqs/dihedral_opls.jpg
-   :align: center
+.. math::
+
+  E = \frac{1}{2} K_1 [1 + \cos(\phi)] + \frac{1}{2} K_2 [1 - \cos(2 \phi)] +
+      \frac{1}{2} K_3 [1 + \cos(3 \phi)] + \frac{1}{2} K_4 [1 - \cos(4 \phi)]
+
 
 Note that the usual 1/2 factor is not included in the K values.
 
@@ -49,10 +52,10 @@ The following coefficients must be defined for each dihedral type via the
 the data file or restart files read by the :doc:`read_data <read_data>`
 or :doc:`read_restart <read_restart>` commands:
 
-* K1 (energy)
-* K2 (energy)
-* K3 (energy)
-* K4 (energy)
+* :math:`K_1` (energy)
+* :math:`K_2` (energy)
+* :math:`K_3` (energy)
+* :math:`K_4` (energy)
 
 
 ----------

doc/src/dihedral_quadratic.rst

@@ -28,8 +28,10 @@ Description
 
 The *quadratic* dihedral style uses the potential:
 
-.. image:: Eqs/dihedral_quadratic.jpg
-   :align: center
+.. math::
+
+  E = K (\phi - \phi_0)^2 
+
 
 This dihedral potential can be used to keep a dihedral in a predefined
 value (cis=zero, right-hand convention is used).
@@ -40,8 +42,8 @@ above, or in the data file or restart files read by the
 :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
 commands:
 
-* K (energy/radian\^2)
-* phi0 (degrees)
+* :math:`K` (energy/radian\^2)
+* :math:`\phi_0` (degrees)
 
 
 ----------

doc/src/dihedral_spherical.rst

@@ -30,11 +30,17 @@ The *spherical* dihedral style uses the potential:
 .. image:: JPG/dihedral_spherical_angles.jpg
    :align: center
 
-.. image:: Eqs/dihedral_spherical.jpg
-   :align: center
+.. math::
+
+  E(\phi,\theta_1,\theta_2) & = & \sum_{i=1}^N\nolimits\ C_i\ \Phi_i(\phi)\ \Theta_{1i}(\theta_1)\ \Theta_{2i}(\theta_2) \\
+  \Phi_{i}(\phi)        & = &  u_i - \mathrm{cos}((\phi   - a_i)K_i) \\
+  \Theta_{1i}(\theta_1) & = &  v_i - \mathrm{cos}((\theta_1-b_i)L_i) \\
+  \Theta_{2i}(\theta_2) & = &  w_i - \mathrm{cos}((\theta_2-c_i)M_i)
+
 
 For this dihedral style, the energy can be any function that combines the
-4-body dihedral-angle (phi) and the two 3-body bond-angles (theta1, theta2).
+4-body dihedral-angle (:math:`\phi`) and the two 3-body bond-angles
+(:math:`\theta_1`, :math:`\theta_2`).
 For this reason, there is usually no need to define 3-body "angle" forces
 separately for the atoms participating in these interactions.
 It is probably more efficient to incorporate 3-body angle forces into
@@ -44,8 +50,9 @@ parameters can prevent singularities that occur with traditional
 force-fields whenever theta1 or theta2 approach 0 or 180 degrees.
 
 The last example above corresponds to an interaction with a single energy
-minima located near phi=93.9, theta1=74.4, theta2=48.1 degrees, and it remains
-numerically stable at all angles (phi, theta1, theta2). In this example,
+minima located near :math:`\phi=93.9`, :math:`\theta_1=74.4`,
+:math:`\theta_2=48.1` degrees, and it remains numerically stable at all
+angles (:math:`\phi`, :math:`\theta_1`, :math:`\theta_2`). In this example,
 the coefficients 49.1, and 25.2 can be physically interpreted as the
 harmonic spring constants for theta1 and theta2 around their minima.
 The coefficient 69.3 is the harmonic spring constant for phi after
@@ -56,28 +63,28 @@ The following coefficients must be defined for each dihedral type via the
 the Dihedral Coeffs section of a data file read by the
 :doc:`read_data <read_data>` command:
 
-* n (integer >= 1)
-* C1 (energy)
-* K1 (typically an integer)
-* a1 (degrees)
-* u1 (typically 0.0 or 1.0)
-* L1 (typically an integer)
-* b1 (degrees, typically 0.0 or 90.0)
-* v1 (typically 0.0 or 1.0)
-* M1 (typically an integer)
-* c1 (degrees, typically 0.0 or 90.0)
-* w1 (typically 0.0 or 1.0)
+* :math:`n` (integer >= 1)
+* :math:`C_1` (energy)
+* :math:`K_1` (typically an integer)
+* :math:`a_1` (degrees)
+* :math:`u_1` (typically 0.0 or 1.0)
+* :math:`L_1` (typically an integer)
+* :math:`b_1` (degrees, typically 0.0 or 90.0)
+* :math:`v_1` (typically 0.0 or 1.0)
+* :math:`M_1` (typically an integer)
+* :math:`c_1` (degrees, typically 0.0 or 90.0)
+* :math:`w_1` (typically 0.0 or 1.0)
 * [...]
-* Cn (energy)
-* Kn (typically an integer)
-* an (degrees)
-* un (typically 0.0 or 1.0)
-* Ln (typically an integer)
-* bn (degrees, typically 0.0 or 90.0)
-* vn (typically 0.0 or 1.0)
-* Mn (typically an integer)
-* cn (degrees, typically 0.0 or 90.0)
-* wn (typically 0.0 or 1.0)
+* :math:`C_n` (energy)
+* :math:`K_n` (typically an integer)
+* :math:`a_n` (degrees)
+* :math:`u_n` (typically 0.0 or 1.0)
+* :math:`L_n` (typically an integer)
+* :math:`b_n` (degrees, typically 0.0 or 90.0)
+* :math:`v_n` (typically 0.0 or 1.0)
+* :math:`M_n` (typically an integer)
+* :math:`c_n` (degrees, typically 0.0 or 90.0)
+* :math:`w_n` (typically 0.0 or 1.0)
 
 
 ----------

doc/src/dihedral_table_cut.rst

@@ -66,18 +66,21 @@ above.
 The cutoff dihedral style uses a tabulated dihedral interaction with a
 cutoff function:
 
-.. image:: Eqs/dihedral_table_cut.jpg
-   :align: center
+.. math::
+
+        f(\theta) & = & K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\
+        f(\theta) & = & K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2
+
 
 The cutoff specifies an prefactor to the cutoff function.  While this value
 would ordinarily equal 1 there may be situations where the value should change.
 
-The cutoff angle1 specifies the angle (in degrees) below which the dihedral
+The cutoff :math:`\theta_1` specifies the angle (in degrees) below which the dihedral
 interaction is unmodified, i.e. the cutoff function is 1.
 
-The cutoff function is applied between angle1 and angle2, which is the angle at
-which the cutoff function drops to zero.  The value of zero effectively "turns
-off" the dihedral interaction.
+The cutoff function is applied between :math:`\theta_1` and :math:`\theta_2`, which is
+the angle at which the cutoff function drops to zero.  The value of zero effectively
+"turns off" the dihedral interaction.
 
 The filename specifies a file containing tabulated energy and
 derivative values. The keyword specifies a section of the file.  The