--- trunk/tengDissertation/Methodology.tex	2006/06/06 14:35:35	2800
+++ trunk/tengDissertation/Methodology.tex	2006/06/06 14:56:36	2801
@@ -150,25 +150,26 @@ from the true energy baseline for clarity.} \label{tim
 increasing time step. For each time step, the dotted line is total
 energy using the DLM integrator, and the solid line comes from the
 quaternion integrator. The larger time step plots are shifted up
-from the true energy baseline for clarity.} \label{timestep}
+from the true energy baseline for clarity.}
+\label{methodFig:timestep}
 \end{figure}
 
-In Fig.~\ref{timestep}, the resulting energy drift at various time
-steps for both the DLM and quaternion integration schemes is
-compared. All of the 1000 molecule water simulations started with
-the same configuration, and the only difference was the method for
-handling rotational motion. At time steps of 0.1 and 0.5 fs, both
-methods for propagating molecule rotation conserve energy fairly
-well, with the quaternion method showing a slight energy drift over
-time in the 0.5 fs time step simulation. At time steps of 1 and 2
-fs, the energy conservation benefits of the DLM method are clearly
-demonstrated. Thus, while maintaining the same degree of energy
-conservation, one can take considerably longer time steps, leading
-to an overall reduction in computation time.
+In Fig.~\ref{methodFig:timestep}, the resulting energy drift at
+various time steps for both the DLM and quaternion integration
+schemes is compared. All of the 1000 molecule water simulations
+started with the same configuration, and the only difference was the
+method for handling rotational motion. At time steps of 0.1 and 0.5
+fs, both methods for propagating molecule rotation conserve energy
+fairly well, with the quaternion method showing a slight energy
+drift over time in the 0.5 fs time step simulation. At time steps of
+1 and 2 fs, the energy conservation benefits of the DLM method are
+clearly demonstrated. Thus, while maintaining the same degree of
+energy conservation, one can take considerably longer time steps,
+leading to an overall reduction in computation time.
 
 \subsection{\label{methodSection:NVT}Nos\'{e}-Hoover Thermostatting}
 
-The Nos\'e-Hoover equations of motion are given by\cite{Hoover85}
+The Nos\'e-Hoover equations of motion are given by\cite{Hoover1985}
 \begin{eqnarray}
 \dot{{\bf r}} & = & {\bf v}, \\
 \dot{{\bf v}} & = & \frac{{\bf f}}{m} - \chi {\bf v} ,\\
@@ -284,7 +285,7 @@ Helmholtz free energy,\cite{melchionna93}
 
 The Nos\'e-Hoover algorithm is known to conserve a Hamiltonian for
 the extended system that is, to within a constant, identical to the
-Helmholtz free energy,\cite{melchionna93}
+Helmholtz free energy,\cite{Melchionna1993}
 \begin{equation}
 H_{\mathrm{NVT}} = V + K + f k_B T_{\mathrm{target}} \left(
 \frac{\tau_{T}^2 \chi^2(t)}{2} + \int_{0}^{t} \chi(t^\prime)
@@ -294,17 +295,13 @@ of the integration.
 $H_{\mathrm{NVT}}$, so the conserved quantity is maintained in the
 last column of the {\tt .stat} file to allow checks on the quality
 of the integration.
-
-Bond constraints are applied at the end of both the {\tt moveA} and
-{\tt moveB} portions of the algorithm.  Details on the constraint
-algorithms are given in section \ref{oopseSec:rattle}.
 
 \subsection{\label{methodSection:NPTi}Constant-pressure integration with
 isotropic box deformations (NPTi)}
 
 To carry out isobaric-isothermal ensemble calculations {\sc oopse}
 implements the Melchionna modifications to the
-Nos\'e-Hoover-Andersen equations of motion,\cite{melchionna93}
+Nos\'e-Hoover-Andersen equations of motion,\cite{Melchionna1993}
 
 \begin{eqnarray}
 \dot{{\bf r}} & = & {\bf v} + \eta \left( {\bf r} - {\bf R}_0 \right), \\