Add equation numbers in reference manual

[alexxy/gromacs.git] / docs / reference-manual / algorithms / shell-molecular-dynamics.rst

diff --git a/docs/reference-manual/algorithms/shell-molecular-dynamics.rst b/docs/reference-manual/algorithms/shell-molecular-dynamics.rst
index b4bcd25f6ff9a0d0651770fafb590b7104204f14..6fdf32d1989d09f6a269ffb41868fc69b40b176d 100644 (file)
--- a/docs/reference-manual/algorithms/shell-molecular-dynamics.rst
+++ b/docs/reference-manual/algorithms/shell-molecular-dynamics.rst
@@ -12,45 +12,47 @@ applications of shell models in |Gromacs| have been published for
 Optimization of the shell positions
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-The force 
-:math:`\mathbf{F}`\ :math:`_S` on a shell
+The force :math:`\mathbf{F}`\ :math:`_S` on a shell
 particle :math:`S` can be decomposed into two components
 
 .. math:: \mathbf{F}_S ~=~ \mathbf{F}_{bond} + \mathbf{F}_{nb}
+          :label: eqnshellforcedecomp
 
-where 
-:math:`\mathbf{F}_{bond}` denotes the
+where :math:`\mathbf{F}_{bond}` denotes the
 component representing the polarization energy, usually represented by a
-harmonic potential and
-:math:`\mathbf{F}_{nb}` is the sum of Coulomb
+harmonic potential and :math:`\mathbf{F}_{nb}` is the sum of Coulomb
 and van der Waals interactions. If we assume that
 :math:`\mathbf{F}_{nb}` is almost constant we
 can analytically derive the optimal position of the shell, i.e. where
-:math:`\mathbf{F}_S` = 0. If we have the
-shell S connected to atom A we have
+:math:`\mathbf{F}_S` = 0. If we have the shell S connected to atom A we have
 
 .. math:: \mathbf{F}_{bond} ~=~ k_b \left( \mathbf{x}_S - \mathbf{x}_A\right).
+          :label: eqnshell
 
-In an iterative solver, we have positions
-:math:`\mathbf{x}_S(n)` where :math:`n` is
+In an iterative solver, we have positions :math:`\mathbf{x}_S(n)` where :math:`n` is
 the iteration count. We now have at iteration :math:`n`
 
 .. math:: \mathbf{F}_{nb} ~=~ \mathbf{F}_S - k_b \left( \mathbf{x}_S(n) - \mathbf{x}_A\right)
+          :label: eqnshellsolv
 
-and the optimal position for the shells :math:`x_S(n+1)` thus follows
-from
+and the optimal position for the shells :math:`x_S(n+1)` thus follows from
 
 .. math:: \mathbf{F}_S - k_b \left( \mathbf{x}_S(n) - \mathbf{x}_A\right) + k_b \left( \mathbf{x}_S(n+1) - \mathbf{x}_A\right) = 0
+          :label: eqnshelloptpos
 
 if we write
 
 .. math:: \Delta \mathbf{x}_S = \mathbf{x}_S(n+1) - \mathbf{x}_S(n)
+          :label: eqnshelloptpos2
 
 we finally obtain
 
 .. math:: \Delta \mathbf{x}_S = \mathbf{F}_S/k_b
+          :label: eqnshelloptpos3
 
 which then yields the algorithm to compute the next trial in the
 optimization of shell positions
 
 .. math:: \mathbf{x}_S(n+1) ~=~ \mathbf{x}_S(n) + \mathbf{F}_S/k_b.
+          :label: eqnshelloptpos4
+