--- trunk/COonPt/firstTry.tex	2013/03/08 22:06:22	3870
+++ trunk/COonPt/firstTry.tex	2013/03/11 22:37:32	3872
@@ -112,8 +112,8 @@ This work is an attempt to understand the mechanism an
 reversible restructuring under exposure to moderate pressures of
 carbon monoxide.\cite{Tao:2010}
 
-This work is an attempt to understand the mechanism and timescale for
-surface restructuring by using molecular simulations.  Since the dynamics
+This work is an investigation into the mechanism and timescale for
+surface restructuring using molecular simulations.  Since the dynamics
 of the process are of particular interest, we employ classical force
 fields that represent a compromise between chemical accuracy and the
 computational efficiency necessary to simulate the process of interest.
@@ -123,16 +123,16 @@ and Piccolo et al.\cite{Piccolo:2004} have both observ
 to undergo a large scale reconstruction under certain conditions.\cite{Tao:2010} 
 The Au(557) surface, because of a weaker interaction with CO, is seen as less 
 likely to undergo this kind of reconstruction. However, Peters et al.\cite{Peters:2000} 
-and Piccolo et al.\cite{Piccolo:2004} have both observed CO induced 
-reconstruction of a Au(111) surface. Peters et al. saw a relaxing of the 
-22 x $\sqrt{3}$ cell. They argued that a very small number of Au atoms
-would become adatoms, limiting the stress of this reconstruction while 
-allowing the rest of the row to relax and approach the ideal (111) 
-configuration. They did not see the ``herringbone'' pattern being greatly 
+and Piccolo et al.\cite{Piccolo:2004} have both observed CO-induced 
+reconstruction of a Au(111) surface. Peters et al. saw a relaxation to the 
+22 x $\sqrt{3}$ cell. They argued that only a few Au atoms
+become adatoms, limiting the stress of this reconstruction while 
+allowing the rest to relax and approach the ideal (111) 
+configuration. They did not see the usual herringbone pattern being greatly 
 affected by this relaxation. Piccolo et al. on the other hand, did see a 
-disruption of the ``herringbone'' pattern as CO was adsorbed to the 
+disruption of the herringbone pattern as CO was adsorbed to the 
 surface. Both groups suggested that the preference CO shows for 
-low-coordinated Au particles was the primary driving force for these reconstructions.
+low-coordinated Au atoms was the primary driving force for the reconstruction.
 
 
 
@@ -209,14 +209,14 @@ up to the third nearest-neighbor were taken into accou
 dynamics.\cite{Shibata:2002hh} One of EAM's strengths
 is its sensitivity to small changes in structure. This arises
 from the original parameterization, where the interactions
-up to the third nearest-neighbor were taken into account.\cite{Voter95a}
+up to the third nearest neighbor were taken into account.\cite{Voter95a}
 Comparing that to the glue model of Ercolessi et al.\cite{Ercolessi88}
-which only parameterized up to the nearest-neighbor
+which is only parameterized up to the nearest-neighbor
 interactions, EAM is a suitable choice for systems where 
 the bulk properties are of secondary importance to low-index 
 surface structures. Additionally, the similarity of EAMs functional 
 treatment of the embedding energy to standard density functional 
-theory (DFT) approaches gives EAM, and conclusions derived, a firm theoretical footing.
+theory (DFT) makes fitting DFT-derived cross potentials with adsorbates somewhat easier.
 \cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}  
 
 
@@ -228,7 +228,7 @@ Karplus model, treats CO as a rigid three site molecul
 We used a model first proposed by Karplus and Straub to study
 the photodissociation of CO from myoglobin because it reproduces 
 the quadrupole moment well.\cite{Straub} The Straub and
-Karplus model, treats CO as a rigid three site molecule with a massless M
+Karplus model treats CO as a rigid three site molecule with a massless M
 site at the molecular center of mass. The geometry and interaction 
 parameters are reproduced in Table~\ref{tab:CO}. The effective 
 dipole moment, calculated from the assigned charges, is still
@@ -311,7 +311,7 @@ a future work.\cite{Deshlahra:2012,StreitzMintmire:199
 (111) surfaces are displayed in Table~\ref{tab:co_energies}.  Charge transfer
 and polarization are neglected in this model, although these effects are likely to
 affect binding energies and binding site preferences, and will be addressed in
-a future work.\cite{Deshlahra:2012,StreitzMintmire:1994}
+future work.
 
 %Table  of Parameters
 %Pt Parameter Set 9
@@ -353,15 +353,15 @@ Our Pt system has dimensions of 18~x~24~x~9 in a box o
 \end{table}
 
 \subsection{Pt(557) and Au(557) metal interfaces}
-Our Pt system has dimensions of 18~x~24~x~9 in a box of size
-54.482~x~50.046~x~120.88~\AA while our Au system has 
-dimensions of 18~x~24~x~8 in a box of size 57.4~x~51.9285~x~100~\AA.
+Our Pt system is an orthorhombic periodic box of dimensions
+54.482~x~50.046~x~120.88~\AA~while our Au system has 
+dimensions of 57.4~x~51.9285~x~100~\AA.
 The systems are arranged 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 oriented to expose two aligned
 (557) cuts along the extended {\it z}-axis.  Simulations of the 
 bare metal interfaces at temperatures ranging from 300~K to
-1200~K were performed to observe the relative
+1200~K were performed to confirm the relative
 stability of the surfaces without a CO overlayer.  
 
 The different bulk melting temperatures (1337~K for Au
@@ -373,32 +373,57 @@ coverage. Higher coverages resulted in CO double layer
 mobility on addition of CO. Each surface was then dosed with different concentrations of CO
 that was initially placed in the vacuum region.  Upon full adsorption,
 these concentrations correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface
-coverage. Higher coverages resulted in CO double layer formation, which introduces artifacts that are not relevant to (557) reconstruction.
+coverage. Higher coverages resulted in the formation of a double layer of CO,
+which introduces artifacts that are not relevant to (557) reconstruction.
 Because of the difference in binding energies, nearly all of the CO was bound to the Pt surface, while
 the Au surfaces often had a significant CO population in the gas
 phase.  These systems were allowed to reach thermal equilibrium (over
 5 ns) before being run in the microcanonical (NVE) ensemble for
 data collection. All of the systems examined had at least 40 ns in the
-data collection stage, although simulation times for some of the
-systems exceeded 200~ns.  Simulations were run using the open
+data collection stage, although simulation times for some Pt of the
+systems exceeded 200~ns.  Simulations were carried out using the open
 source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE}
 
-% Just results, leave discussion for discussion section
-% structure
-%	Pt: step wandering, double layers, no triangular motifs
-%	Au: step wandering, no double layers
-% dynamics
-% 	diffusion
-% 	time scale, formation, breakage
+
+
+
+% RESULTS
+%
 \section{Results}
 \subsection{Structural remodeling}
+The surfaces of both systems, upon dosage of CO, began 
+to undergo remodeling that was not observed in the bare 
+metal system. The surfaces to which no CO was exposed 
+did experience minor roughening of the step-edge, but the 
+(557) lattice was well-maintained throughout the simulation 
+time. The Au systems were limited to greater amounts of 
+roughening, i.e. breakup of the step-edge, and some step 
+wandering. The lower coverage Pt systems experienced 
+similar restructuring but to a greater extent when 
+compared to the Au systems. The 50\% coverage 
+Pt system formed double layers at numerous spots upon its surface.
+
+
+\subsubsection{Step wandering}
+The 0\% coverage surfaces for both metals showed 
+minimal movement at their respective run temperatures. 
+As the coverage increased, the mobility of the surface 
+also increased. Additionally, at the higher coverages 
+on both metals, there was a large increase in the amount 
+of observed step-wandering. Previous work by 
+Williams\cite{Williams:1993} highlighted the entropic 
+contribution to the repulsion felt between step-edges, 
+and situations were that repulsion could be negated, or 
+overcome, to allow for step coalescence or facet formation.
+
+\subsubsection{Double layers}
 Tao et al. have shown experimentally that the Pt(557) surface 
 undergoes two separate reconstructions upon CO 
 adsorption.\cite{Tao:2010} The first involves a doubling of 
 the step height and plateau length. Similar behavior has been 
 seen to occur on numerous surfaces at varying conditions: Ni(977), Si(111).
 \cite{Williams:1994,Williams:1991,Pearl} Of the two systems 
-we examined, the Pt system showed a larger amount of 
+we examined, the Pt system showed a greater propensity for
 reconstruction when compared to the Au system. The amount 
 of reconstruction is correlated to the amount of CO 
 adsorbed upon the surface.  This appears to be related to the 
@@ -421,10 +446,10 @@ Previous atomistic simulations of stepped surfaces wer
 the 40~ns time scale, experienced this reconstruction.
 
 \subsection{Dynamics}
-Previous atomistic simulations of stepped surfaces were largely 
-concerned with the energetics and structures at different conditions
+Previous atomistic simulations of stepped surfaces dealt largely
+with the energetics and structures at different conditions
 \cite{Williams:1991,Williams:1994}. Consequently, the most common 
-technique has been Monte Carlo. Monte Carlo gives an efficient 
+technique utilized to date has been Monte Carlo sampling. Monte Carlo gives an efficient 
 sampling of the equilibrium thermodynamic landscape at the expense 
 of ignoring the dynamics of the system. Previous work by Pearl and 
 Sibener\cite{Pearl}, using STM, has been able to show the coalescing 
@@ -438,42 +463,64 @@ diffusion, of the atoms making up the steps An ideal m
 %forcedSystems/stepSeparation
 The movement or wandering of a step-edge is a cooperative effect 
 arising from the individual movements, primarily through surface 
-diffusion, of the atoms making up the steps An ideal metal surface 
-displaying a low index facet, (111) or (100) is unlikely to experience 
+diffusion, of the atoms making up the steps. An ideal metal surface 
+displaying a low index facet, (111) or (100), is unlikely to experience 
 much surface diffusion because of the large energetic barrier that must 
 be overcome to lift an atom out of the surface. The presence of step-edges 
 on higher-index surfaces provide a source for mobile metal atoms. 
 Breaking away from the step-edge on a clean surface still imposes an 
-energetic penalty around $\sim$~40 kcal/mol, but is much less than lifting 
+energetic penalty around $\sim$~40 kcal/mol, but this is significantly easier than lifting 
 the same metal atom vertically out of the surface,  \textgreater~60 kcal/mol. 
 The penalty lowers significantly when CO is present in sufficient quantities 
-on the surface. For certain distributions of CO, the penalty can be as low as 
+on the surface. For certain distributions of CO, the penalty can fall as low as 
 $\sim$~20 kcal/mol. Once an adatom exists on the surface, the barrier for 
-diffusion is negligible ( \textless~4 kcal/mol) and these adatoms are well 
-able to explore the terrace before rejoining either the original step-edge or becoming a part 
-of a different edge. Atoms traversing separate terraces is a more difficult 
-process, but can be overcome through a joining and lifting stage which is 
-examined in the discussion section. By tracking the mobility of individual 
+diffusion is negligible ( \textless~4 kcal/mol) and these adatoms are 
+able to explore the terrace before rejoining either the original step-edge or 
+becoming a part of a different edge. It is a more difficult process for an atom 
+to traverse to a separate terrace although the presence of CO can lower the 
+energy barrier required to lift or lower the adatom. By tracking the mobility of individual 
 metal atoms on the Pt and Au surfaces we were able to determine the relative 
 diffusion constants, as well as how varying coverages of CO affect the diffusion. Close 
 observation of the mobile metal atoms showed that they were typically in 
 equilibrium with the step-edges, dynamically breaking apart and rejoining the edges. 
 At times, their motion was concerted and two or more adatoms would be 
-observed moving together across the surfaces. The primary challenge in 
-quantifying the overall surface mobility was in defining ``mobile" vs. ``static" atoms.
+observed moving together across the surfaces. 
 
-A particle was considered mobile once it had traveled more than 2~\AA~
+A particle was considered ``mobile'' once it had traveled more than 2~\AA~
 between saved configurations of the system (typically 10-100 ps). An atom that was 
-truly mobile would typically travel much greater distances than this, but the 2~\AA~ cutoff 
-was to prevent swamping the diffusion data with the in-place vibrational 
+truly mobile would typically travel much greater distances than this, but the 2~\AA~cutoff 
+was used to prevent swamping the diffusion data with the in-place vibrational 
 movement of buried atoms. Diffusion on  a surface is strongly affected by 
 local structures and in this work, the presence of single and double layer 
 step-edges causes the diffusion parallel to the step-edges to be different 
 from the diffusion perpendicular to these edges. Parallel and perpendicular
 diffusion constants are shown in Figure \ref{fig:diff}.
 
-\subsubsection{Double layer formation dynamics}
-The increased amounts of diffusion on Pt at the higher CO coverages plays a primary role in the formation of the double layers observed on Pt. However, this is not a complete explanation as seen by the 33\% Pt system which has higher diffusion constants but did not show any signs of undergoing the doubling. This difference will be explored more fully in the discussion. On the 50\% Pt system, three separate layers were formed over the extended run time of this system. Previous experimental work has given some insight into the upper bounds of the time required for step coalescing.\cite{Williams:1991,Pearl} In this system, as seen in Figure \ref{fig:reconstruct}, the first appearance of a double layer, a nodal site, appears at 19 ns into the simulation. Within 12 ns, nearly half of the step has formed the double layer and by 86 ns, the complete layer has been smoothed. The double layer could be considered ``complete" by 37 ns but is a bit rough or wavy. From the appearance of the first node to the first observed double layer, ignoring roughening, the process took $\sim$20 ns. Another $\sim$40 ns was necessary for the layer to completely straighten. The other two layers in this simulation form over a period of 22 ns and 42 ns respectively. Comparing this to the upper bounds of the image scan, it is likely that aspects of this reconstruction occur very quickly. A possible explanation for this rapid reconstruction is the elevated temperatures our systems were run at. It is likely that the process would take longer at lower temperatures and is an area of exploration for future work.
+\subsubsection{Dynamics of double layer formation}
+The increased diffusion on Pt at the higher 
+CO coverages plays a primary role in double layer formation. However, this is not 
+a complete explanation -- the 33\%~Pt system 
+has higher diffusion constants but did not show 
+any signs of edge doubling. On the 
+50\%~Pt system, three separate layers were formed over 
+150~ns of simulation time. Previous experimental 
+work gives insight into the upper bounds of the 
+time required for step coalescence.\cite{Williams:1991,Pearl} 
+In this system, as seen in Figure \ref{fig:reconstruct}, the first 
+appearance of a double layer, appears at 19~ns 
+into the simulation. Within 12~ns of this nucleation event, nearly half of the step has 
+formed the double layer and by 86 ns, the complete layer 
+has been flattened out. The double layer could be considered 
+``complete" by 37~ns but remains a bit rough. From the 
+appearance of the first nucleation event to the first observed double layer, the process took $\sim$20~ns. Another 
+$\sim$40~ns was necessary for the layer to completely straighten. 
+The other two layers in this simulation formed over periods of
+22~ns and 42~ns respectively. Comparing this to the upper 
+bounds of the image scan, it is likely that most aspects of this 
+reconstruction occur very rapidly. A possible explanation 
+for this rapid reconstruction is the elevated temperatures 
+under which our systems were simulated. It is probable that the process would 
+take longer at lower temperatures.
 
 %Evolution of surface
 \begin{figure}[H]
@@ -507,49 +554,46 @@ In this paper we have shown that we were able to accur
 
 %Discussion
 \section{Discussion}
-In this paper we have shown that we were able to accurately model the initial reconstruction of the
+We have shown that the classical potential models are able to model the initial reconstruction of the
 Pt(557) surface upon CO adsorption as shown by Tao et al. \cite{Tao:2010}. More importantly, we
-were able to observe the dynamic processes necessary for this reconstruction. 
+were able to observe features of the dynamic processes necessary for this reconstruction. 
 
 \subsection{Mechanism for restructuring}
 Since the Au surface showed no large scale restructuring throughout
 our simulation time our discussion will focus on the 50\% Pt-CO system
 which did undergo the doubling featured in Figure \ref{fig:reconstruct}.
-Comparing the results from this simulation to those reported previously by 
-Tao et al.\cite{Tao:2010} the similarities in the Pt-CO system are quite 
-strong. As shown in Figure \ref{fig:reconstruct}, the simulated Pt 
-system exposed to a large dosage of CO will restructure by doubling the terrace 
-widths and step heights. The restructuring occurs in a piecemeal fashion, one to two Pt atoms at a time and as such is a fairly stochastic event. 
-Looking at individual configurations of the system, the adatoms either 
+Similarities of our results to those reported previously by 
+Tao et al.\cite{Tao:2010} are quite 
+strong. The simulated Pt 
+system exposed to a large dosage of CO readily restructures by doubling the terrace 
+widths and step heights. The restructuring occurs in a piecemeal fashion, one to two Pt atoms at a time, but is rapid on experimental timescales. 
+The adatoms either 
 break away from the step-edge and stay on the lower terrace or they lift 
-up onto the higher terrace. Once ``free'', they will diffuse on the terrace 
+up onto a higher terrace. Once ``free'', they diffuse on the terrace 
 until reaching another step-edge or rejoining their original edge.  
 This combination of growth and decay of the step-edges is in a state of 
 dynamic equilibrium. However, once two previously separated edges 
-meet as shown in Figure 1.B, this meeting point tends to act as a focus 
-or growth point for the rest of the edge to meet up, akin to that of a zipper. 
-From the handful of cases where a double layer was formed during the 
-simulation, measuring from the initial appearance of a growth point, the 
-double layer tends to be fully formed within $\sim$35 ns.
+meet as shown in Figure 1.B, this nucleates the rest of the edge to meet up, forming a double layer.
+From simulations which exhibit a double layer, the time delay from the initial appearance of a nucleation point to a fully formed double layer is $\sim$35 ns.
 
 A number of possible mechanisms exist to explain the role of adsorbed 
 CO in restructuring the Pt surface. Quadrupolar repulsion between adjacent 
-CO molecules adsorbed on the surface is one likely possibility.  However, 
+CO molecules adsorbed on the surface is one possibility.  However, 
 the quadrupole-quadrupole interaction is short-ranged and is attractive for 
 some orientations.  If the CO molecules are ``locked'' in a specific orientation 
 relative to each other, through atop adsorption for example, this explanation 
-gains some weight.  The energetic repulsion between two CO located a 
-distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) with both in 
-a  vertical orientation is 8.62 kcal/mol. Moving the CO apart to the second 
+gains some credence.  The energetic repulsion between two CO located a 
+distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) and both in 
+a  vertical orientation, is 8.62 kcal/mol. Moving the CO apart to the second 
 nearest-neighbor distance of 4.8~\AA~or 5.54~\AA~drops the repulsion to 
 nearly 0 kcal/mol. Allowing the CO's to leave a purely vertical orientation 
 also quickly drops the repulsion, a minimum of 6.2 kcal/mol is reached at $\sim$24 degrees between the 2 CO when the carbons are locked at a distance of 2.77 \AA apart.
 As mentioned above, the energy barrier for surface diffusion 
-of a Pt adatom is only 4 kcal/mol. So this repulsion between CO can help 
+of a Pt adatom is only 4 kcal/mol. So this repulsion between neighboring CO molecules can 
 increase the surface diffusion. However, the residence time of CO on Pt was 
 examined and while the majority of the CO is on or near the surface throughout 
-the run, it is extremely mobile. This mobility suggests that the CO are more 
-likely to shift their positions without necessarily dragging the Pt along with them.
+the run, most molecules are mobile. This mobility suggests that the CO are more 
+likely to shift their positions without necessarily the Pt along with them.
 
 Another possible and more likely mechanism for the restructuring is in the
 destabilization of strong Pt-Pt interactions by CO adsorbed on surface
@@ -583,8 +627,8 @@ As shown in the results section, the diffusion paralle
 
 
 \subsection{Diffusion}
-As shown in the results section, the diffusion parallel to the step-edge tends to be 
-much larger than that perpendicular to the step-edge, likely because of the dynamic 
+The diffusion parallel to the step-edge tends to be 
+much larger than that perpendicular to the step-edge. The dynamic 
 equilibrium that is established between the step-edge and adatom interface. The coverage 
 of CO also appears to play a slight role in relative rates of diffusion, as shown in Figure \ref{fig:diff}.
 The 
@@ -612,13 +656,13 @@ more likely a growth point is to be formed. 
 
 
 %Peaks!
-\begin{figure}[H]
-\includegraphics[width=\linewidth]{doublePeaks_noCO.png}
-\caption{At the initial formation of this double layer  ( $\sim$ 37 ns) there is a degree
- of roughness inherent to the edge. The next $\sim$ 40 ns show the edge with 
- aspects of waviness and by 80 ns the double layer is completely formed and smooth. }
-\label{fig:peaks}
-\end{figure}
+%\begin{figure}[H]
+%\includegraphics[width=\linewidth]{doublePeaks_noCO.png}
+%\caption{At the initial formation of this double layer  ( $\sim$ 37 ns) there is a degree
+ %of roughness inherent to the edge. The next $\sim$ 40 ns show the edge with 
+ %aspects of waviness and by 80 ns the double layer is completely formed and smooth. }
+%\label{fig:peaks}
+%\end{figure}
 
 
 %Don't think I need this