--- trunk/COonPt/firstTry.tex	2012/12/19 21:37:51	3826
+++ trunk/COonPt/firstTry.tex	2012/12/20 03:00:21	3827
@@ -193,14 +193,14 @@ manner. We used a model first proposed by Karplus and 
 Since previous explanations for the surface rearrangements center on
 the large linear quadrupole moment of carbon monoxide, the model
 chosen for this molecule exhibits this property in an efficient
-manner. We used a model first proposed by Karplus and Straub to study
-the photodissociation of CO from myoglobin.\cite{Straub} The Straub
-and Karplus model is a rigid linear three site model which places a
-massless (M) site at the center of mass along the CO bond.  The
-geometry and interaction parameters are reproduced in Table 1. The
-effective dipole moment, calculated from the assigned charges, is
-still small (0.35 D) while the linear quadrupole (-2.40 D~\AA) is
-close to the experimental (-2.63 D~\AA)\cite{QuadrupoleCO} and quantum
+manner.  We used a model first proposed by Karplus and Straub to study
+the photodissociation of CO from myoglobin.\cite{Straub} The Straub and
+Karplus model is a rigid three site model which places a massless M
+site at the center of mass along the CO bond.  The geometry used along
+with the interaction parameters are reproduced in Table~1. The effective 
+dipole moment, calculated from the assigned charges, is still
+small (0.35 D) while the linear quadrupole (-2.40 D~\AA) is close
+to the experimental (-2.63 D~\AA)\cite{QuadrupoleCO} and quantum 
 mechanical predictions (-2.46 D~\AA)\cite{QuadrupoleCOCalc}.
 %CO Table
 \begin{table}[H]
@@ -316,7 +316,7 @@ Our model systems are composed of 3888 Pt atoms and XX
 
 \subsection{Pt(557) and Au(557) metal interfaces}
 
-Our model systems are composed of 3888 Pt atoms and XXXX Au atoms in a
+Our model systems are composed of 3888 Pt atoms and 3384 Au atoms in a
 FCC crystal that have been cut along the 557 plane so that they are
 periodic in the {\it x} and {\it y} directions, and have been rotated
 to expose two parallel 557 cuts along the positive and negative {\it
@@ -380,7 +380,7 @@ between saved configurations (XX ps). Restricting the 
 mobility is in defining ``mobile'' vs. ``static'' atoms.
 
 A particle was considered mobile once it had traveled more than 2~\AA~
-between saved configurations (XX ps). Restricting the transport
+between saved configurations (10-100 ps). Restricting the transport
 calculations to only mobile atoms eliminates all of the bulk metal as
 well as any surface atoms that remain fixed for a significant length
 of time.  Since diffusion on a surface is strongly affected by local
@@ -392,7 +392,7 @@ linear fits to the mean squared displacement) are show
 %While an ideal metallic surface is unlikely to experience much surface diffusion, high-index surfaces have large numbers of low-coordinated atoms which have a much easier time overcoming the energetic barriers limiting diffusion, leading to easier surface reconstructions. Surface movement was divided between the parallel ($\parallel$) and perpendicular ($\perp$) directions relative to the step edge. We were then able to calculate diffusion constants as a function of CO coverage. As can be seen in Table 4, the presence and amount of CO directly affects the diffusion constants of surface platinum atoms. The presence of two 50\% coverage systems is to show how the diffusion process is affected by time. The majority of the systems were run for approximately 50 ns while the half monolayer system has been running continuously. The lowered diffusion constant at longer run times will be examined in-depth in the discussion section.
 
 \begin{figure}[H]
-\includegraphics[scale=0.6]{DiffusionComparison_error.png}
+\includegraphics[scale=0.6]{DiffusionComparison_errorXY.pdf}
 \caption{Diffusion constants for mobile surface atoms along directions
   parallel ($\mathbf{D}_{\parallel}$) and perpendicular
   ($\mathbf{D}_{\perp}$) to the 557 step edges as a function of CO
@@ -418,11 +418,11 @@ linear fits to the mean squared displacement) are show
 %   \hline
 %   \textbf{Surface Coverage} & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$ & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$  \\
 %   \hline
-%   50\% & 4.32(2) & 1.185 $\pm$ 0.008 & 1.72 $\pm$ 0.02 & 0.455 $\pm$ 0.006 \\
-%   33\% & 5.18 $\pm$ 0.03 & 1.999 $\pm$ 0.005 & 1.95 $\pm$ 0.02 & 0.337 $\pm$ 0.004  \\
-%   25\% & 5.01 $\pm$ 0.02 & 1.574 $\pm$ 0.004 & 1.26 $\pm$ 0.03 & 0.377 $\pm$ 0.006 \\
-%   5\%   & 3.61 $\pm$ 0.02 & 0.355 $\pm$ 0.002 & 1.84 $\pm$ 0.03 & 0.169 $\pm$ 0.004 \\
-%   0\%   & 3.27 $\pm$ 0.02 & 0.147 $\pm$ 0.004 & 1.50 $\pm$ 0.02 & 0.194 $\pm$ 0.002  \\
+%   50\% & 4.32(2) & 1.185(8)  & 1.72(2) & 0.455(6) \\
+%   33\% & 5.18(3)  & 1.999(5)  & 1.95(2) & 0.337(4)   \\
+%   25\% & 5.01(2)  & 1.574(4)  & 1.26(3) & 0.377(6) \\
+%   5\%   & 3.61(2)  & 0.355(2)  & 1.84(3)  & 0.169(4)  \\
+%   0\%   & 3.27(2)  & 0.147(4)  & 1.50(2)  & 0.194(2)   \\
 %   \hline 
 % \end{tabular}
 % \end{table}
@@ -484,6 +484,10 @@ As shown in the results section, the diffusion paralle
 \includegraphics[width=\linewidth]{doublePeaks_noCO.png}
 \caption{}
 \end{figure}
+\begin{figure}[H]
+\includegraphics[width=\linewidth]{557_300K_cleanPDF.pdf}
+\caption{}
+\end{figure}
 \section{Conclusion}