--- trunk/COonPt/firstTry.tex	2013/02/22 18:33:25	3862
+++ trunk/COonPt/firstTry.tex	2013/02/27 21:15:17	3866
@@ -68,7 +68,7 @@ Notre Dame, Indiana 46556}
 \begin{doublespace}
 
 \begin{abstract}
-
+We examine potential surface reconstructions of Pt and Au (557) under various CO coverages using molecular dynamics in order to find possible mechanisms and dynamics for the restructuring. The metal-CO interactions were parameterized as part of this work so that a large scale treatment of this system could be undertaken. The relative binding strengths of the metal-CO interactions were found to play a large role with regards to step edge stability and adatom diffusion. A small correlation between coverage and the size of the diffusion constant was also determined. These results appear sufficient to explain the reconstructions observed on the Pt systems and the lack of reconstructions on the Au systems.
 \end{abstract}
 
 \newpage
@@ -100,15 +100,15 @@ This work an effort to understand the mechanism and ti
 reversible restructuring under exposure to moderate pressures of
 carbon monoxide.\cite{Tao:2010}
 
-This work an effort to understand the mechanism and timescale for
+This work is an attempt to understand the mechanism and timescale for
 surface restructuring using molecular simulations.  Since the dynamics
-of the process is of particular interest, we utilize classical force
+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 observe the process of interest.
+computational efficiency necessary to simulate the process of interest.
 
-Since restructuring occurs as a result of specific interactions of the
-catalyst with adsorbates, two metal systems exposed to carbon monoxide
-were examined in this work. The Pt(557) surface has already been shown
+Restructuring can occur as a result of specific interactions of the
+catalyst with adsorbates. In this work, two metal systems exposed 
+to carbon monoxide were examined. The Pt(557) surface has already been shown
 to reconstruct under certain conditions. The Au(557) surface, because
 of a weaker interaction with CO, is less likely to undergo this kind
 of reconstruction.  MORE HERE ON PT AND AU PREVIOUS WORK.
@@ -133,7 +133,7 @@ Au-Au and Pt-Pt interactions, while modeling the CO us
 Coulomb potential.  For this work, we have used classical molecular
 dynamics with potential energy surfaces that are specifically tuned
 for transition metals.  In particular, we used the EAM potential for
-Au-Au and Pt-Pt interactions, while modeling the CO using a rigid
+Au-Au and Pt-Pt interactions\cite{EAM}, while modeling the CO using a rigid
 three-site model developed by Straub and Karplus for studying
 photodissociation of CO from myoglobin.\cite{Straub} The Au-CO and
 Pt-CO cross interactions were parameterized as part of this work.
@@ -164,8 +164,8 @@ $\phi_{ij}(r_{ij})$ is an pairwise term that is meant 
 V_i =  F[ \bar{\rho}_i ]  + \sum_{j \neq i} \phi_{ij}(r_{ij})
 \end{equation*}
 where $F[ \bar{\rho}_i ]$ is an energy embedding functional, and
-$\phi_{ij}(r_{ij})$ is an pairwise term that is meant to represent the
-overlap of the two positively charged cores.  
+$\phi_{ij}(r_{ij})$ is a pairwise term that is meant to represent the
+repulsive overlap of the two positively charged cores.  
 
 % The {\it modified} embedded atom method (MEAM) adds angular terms to
 % the electron density functions and an angular screening factor to the
@@ -176,7 +176,7 @@ The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen 
 % metals,\cite{Lee:2001qf} and also interfaces.\cite{Beurden:2002ys})
 % MEAM presents significant additional computational costs, however.
 
-The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen potentials
+The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen (QSC) potentials
 have all been widely used by the materials simulation community for
 simulations of bulk and nanoparticle
 properties,\cite{Chui:2003fk,Wang:2005qy,Medasani:2007uq}
@@ -190,14 +190,14 @@ Since previous explanations for the surface rearrangem
 parameterized.\cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}  
 
 \subsection{Carbon Monoxide model}
-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 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 
+Previous explanations for the surface rearrangements center on
+the large linear quadrupole moment of carbon monoxide.  
+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 which places a massless M
+site at the center of mass position along the CO bond.  The geometry used along
+with the interaction parameters are reproduced in Table~\ref{tab:CO}. 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 
@@ -218,6 +218,7 @@ mechanical predictions (-2.46 D~\AA)\cite{QuadrupoleCO
 \textbf{M} & 0.0 & -  &  -  &    1.6 \\
 \hline
 \end{tabular}
+\label{tab:CO}
 \end{table}
 
 \subsection{Cross-Interactions between the metals and carbon monoxide}
@@ -230,13 +231,15 @@ position on Pt(111). This resulting binding energies a
 clean metal surfaces. Parameters reported by Korzeniewski {\it et
   al.}\cite{Pons:1986} were a starting point for our fits, which were
 modified to ensure that the Pt-CO interaction favored the atop binding
-position on Pt(111). This resulting binding energies are on the higher
-side of the experimentally-reported values. Following Korzeniewski
+position on Pt(111). These parameters are reproduced in Table~\ref{tab:co_parameters}
+This resulted in binding energies that are slightly higher
+than the experimentally-reported values as shown in Table~\ref{tab:co_energies}. Following Korzeniewski
 {\it et al.},\cite{Pons:1986} the Pt-C interaction was fit to a deep
 Lennard-Jones interaction to mimic strong, but short-ranged partial
 binding between the Pt $d$ orbitals and the $\pi^*$ orbital on CO. The
-Pt-O interaction was parameterized to a Morse potential with a large
-range parameter ($r_o$).  In most cases, this contributes a weak
+Pt-O interaction was parameterized to a Morse potential at a larger
+minimum distance, ($r_o$).  This was chosen so that the C would be preferred
+over O as the binder to the surface. In most cases, this parameterization contributes a weak
 repulsion which favors the atop site.  The resulting potential-energy
 surface suitably recovers the calculated Pt-C separation length
 (1.6~\AA)\cite{Beurden:2002ys} and affinity for the atop binding
@@ -245,10 +248,10 @@ The Au-C and Au-O cross-interactions were fit using Le
 %where did you actually get the functionals for citation?
 %scf calculations, so initial relaxation was of the four layers, but two layers weren't kept fixed, I don't think
 %same cutoff for slab and slab + CO ? seems low, although feibelmen had values around there...
-The Au-C and Au-O cross-interactions were fit using Lennard-Jones and
+The Au-C and Au-O cross-interactions were also fit using Lennard-Jones and
 Morse potentials, respectively, to reproduce Au-CO binding energies.
-
-The fits were refined against gas-surface DFT calculations with a
+The limited experimental data for CO adsorption on Au lead us to refine our fits against DFT.
+Adsorption energies were obtained from gas-surface DFT calculations with a
 periodic supercell plane-wave basis approach, as implemented in the
 {\sc Quantum ESPRESSO} package.\cite{QE-2009} Electron cores are
 described with the projector augmented-wave (PAW)
@@ -257,25 +260,25 @@ Ionic relaxations were performed until the energy diff
 computed with the PBE implementation of the generalized gradient
 approximation (GGA) for gold, carbon, and oxygen that was constructed
 by Rappe, Rabe, Kaxiras, and Joannopoulos.\cite{Perdew_GGA,RRKJ_PP}
-Ionic relaxations were performed until the energy difference between
-subsequent steps was less than $10^{-8}$ Ry.  In testing the CO-Au
-interaction, Au(111) supercells were constructed of four layers of 4
+In testing the Au-CO interaction, Au(111) supercells were constructed of four layers of 4
 Au x 2 Au surface planes and separated from vertical images by six
-layers of vacuum space. The surface atoms were all allowed to relax.
-Supercell calculations were performed nonspin-polarized with a 4 x 4 x
-4 Monkhorst-Pack {\bf k}-point sampling of the first Brillouin
+layers of vacuum space. The surface atoms were all allowed to relax 
+before CO was added to the system. Electronic relaxations were 
+performed until the energy difference between subsequent steps 
+was less than $10^{-8}$ Ry.   Nonspin-polarized supercell calculations 
+were performed with a 4~x~4~x~4 Monkhorst-Pack {\bf k}-point sampling of the first Brillouin
 zone.\cite{Monkhorst:1976,PhysRevB.13.5188} The relaxed gold slab was
 then used in numerous single point calculations with CO at various
 heights (and angles relative to the surface) to allow fitting of the
 empirical force field.
 
 %Hint at future work
-The parameters employed in this work are shown in Table 2 and the
-binding energies on the 111 surfaces are displayed in Table 3.  To
-speed up the computations, charge transfer and polarization are not
-being treated in this model, although these effects are likely to
-affect binding energies and binding site
-preferences.\cite{Deshlahra:2012}
+The parameters employed for the metal-CO cross-interactions in this work 
+are shown in Table~\ref{co_parameters} and the binding energies on the 
+(111) surfaces are displayed in Table~\ref{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 added in
+a future work.\cite{Deshlahra:2012,StreitzMintmire}
 
 %Table  of Parameters
 %Pt Parameter Set 9
@@ -295,6 +298,7 @@ preferences.\cite{Deshlahra:2012}
 
 \hline
 \end{tabular}
+\label{tab:co_parameters}
 \end{table}
 
 %Table of energies
@@ -312,6 +316,7 @@ preferences.\cite{Deshlahra:2012}
   \textbf{Au-CO} & -0.39 & -0.40 \bibpunct{}{}{,}{n}{}{,}  (Ref. \protect\cite{TPD_Gold}) \\
   \hline
 \end{tabular}
+\label{tab:co_energies}
 \end{table}
 
 \subsection{Pt(557) and Au(557) metal interfaces}