--- trunk/COonPt/firstTry.tex	2012/12/13 22:42:37	3811
+++ trunk/COonPt/firstTry.tex	2012/12/14 05:35:49	3813
@@ -109,9 +109,8 @@ reconstruct under certain conditions. The Au(557) surf
 Since restructuring occurs as a result of specific interactions of the catalyst
 with adsorbates, two metals systems exposed to the same adsorbate, CO,
 were examined in this work. The Pt(557) surface has already been shown to 
-reconstruct under certain conditions. The Au(557) surface will provide a
-useful counterpoint
-
+reconstruct under certain conditions. The Au(557) surface, because of gold's
+weaker interaction with CO, is less likely to undergo such a large reconstruction.
 %Platinum molecular dynamics
 %gold molecular dynamics
 
@@ -200,10 +199,12 @@ site at the center of mass along the CO bond.  The geo
 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 along with the interaction
-parameters are reproduced in Table 1. The effective dipole moment is still
+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}.
+to the experimental (-2.63 D~\AA)\cite{QuadrupoleCO} and quantum 
+mechanical predictions (-2.46 D~\AA)\cite{QuadrupoleCOCalc}.
 %CO Table
 \begin{table}[H]
 \caption{Positions, $\sigma$, $\epsilon$ and charges for CO geometry and self-interactions\cite{Straub}. Distances are in \AA~, energies are in kcal/mol, and charges are in $e$.}
@@ -224,31 +225,68 @@ is the proper parameterization of all of the potential
 \subsection{Cross-Interactions}
 
 One hurdle that must be overcome in classical molecular simulations 
-is the proper parameterization of all of the potential interactions present
-in the system. CO adsorbed on a platinum surface has been the focus of
-many experimental \cite{Yeo, Hopster:1978, Ertl:1977, Kelemen:1979} and theoretical studies. 
-\cite{Beurden:2002ys,Pons:1986,Deshlahra:2009,Feibelman:2001,Mason:2004} 
-We started with parameters reported by Korzeniewski et al. \cite{Pons:1986} and then
+is the proper parameterization of the potential interactions present
+in the system. Since the adsorption of CO onto a platinum surface has been 
+the focus of many experimental \cite{Yeo, Hopster:1978, Ertl:1977, Kelemen:1979} 
+and theoretical studies \cite{Beurden:2002ys,Pons:1986,Deshlahra:2009,Feibelman:2001,Mason:2004}
+there is a large amount of data in the literature to fit too. We started with parameters 
+reported by Korzeniewski et al. \cite{Pons:1986} and then
 modified them to ensure that the Pt-CO interaction favored 
-an atop binding position for the CO upon the Pt surface. Following the method 
-laid out by Korzeniewski, the Pt-C interaction was fit to a strong 
-Lennard-Jones 12-6 interaction to mimic binding, while the Pt-O interaction
-was parameterized to a Morse potential. The resultant potential-energy
-surface suitably recovers the calculated Pt-CO bond length (1.1 \AA)\cite{Deshlahra:2012} and affinity
+an atop binding position for the CO upon the Pt surface. This 
+constraint led to the binding energies being on the higher side 
+of reported values. Following the method laid out by Korzeniewski, 
+the Pt-C interaction was fit to a strong Lennard-Jones 12-6 
+interaction to mimic binding, while the Pt-O interaction
+was parameterized to a Morse potential with a large $r_o$ 
+to contribute a weak repulsion. The resultant potential-energy
+surface suitably recovers the calculated Pt-C bond length ( 1.6\AA)\cite{Beurden:2002ys} and affinity
 for the atop binding position.\cite{Deshlahra:2012, Hopster:1978}
 
-The Au-C and Au-O interaction parameters were fit to a Lennard-Jones and Morse potential respectively. The binding energies were obtained from quantum calculations carried out using <functional> for gold. 
+%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 interaction parameters were also fit to a Lennard-Jones
+and Morse potential respectively, to reproduce Au-CO binding energies. 
+These energies were obtained from quantum calculations carried out using 
+the PBE GGA exchange-correlation functionals\cite{Perdew_GGA} for gold, carbon, and oxygen
+constructed by Rappe, Rabe, Kaxiras, and Joannopoulos. \cite{RRKJ_PP}.
+All calculations were run using the {\sc Quantum ESPRESSO} package. \cite{QE-2009}  
+First, a four layer slab of gold comprised of 32 atoms displaying a (111) surface was
+converged using a 4X4X4 grid of Monkhorst-Pack \emph{k}-points.\cite{Monkhorst:1976}
+The kinetic energy of the wavefunctions were truncated at 20 Ry while the 
+cutoff for the charge density and potential was set at 80 Ry. This relaxed
+gold slab was then used in numerous single point calculations  with CO at various heights
+to create a potential energy surface for the Au-CO interaction.
 
-Numerous single point calculations were performed at various distances of the CO
+%Hint at future work
+The fit parameter sets employed in this work are shown in Table 2 and their
+reproduction of the binding energies are displayed in Table 3. Currently,
+charge transfer is not being treated in this system, however, that is a goal
+for future work as the effect has been seen to affect binding energies and 
+binding site preferences. \cite{Deshlahra:2012}
 
 
 
+
 \subsection{Construction and Equilibration of 557 Metal interfaces}
 
-Our model systems are composed of approximately 4000 metal atoms cut along the 557 plane. The bare crystals were initially run in the Canonical ensemble at 1000K and 800K respectively for Pt and Au. The difference in temperature is necessary because of the two metals different melting points. Various amounts of CO were added to the simulation box and allowed to absorb to the metal surfaces over a short period of 100 ps. After further thermal relaxation the simulations were all run for at least 40 ns. A subset of the runs that showed interesting effects were allowed to run longer. The system
+Our model systems are composed of approximately 4000 metal atoms 
+cut along the 557 plane so that they are periodic in the {\it x} and {\it y} 
+directions exposing the 557 plane in the {\it z} direction. Runs at various
+temperatures ranging from 300~K to 1200~K were started with the intent
+of viewing relative stability of the surface when CO was not present in the
+system.  Owing to the different melting points (1337~K for Au and 2045~K for Pt),
+the bare crystal systems were initially run in the Canonical ensemble at
+800~K and 1000~K respectively for 100 ps. Various amounts of CO were
+placed in the vacuum region, which upon full adsorption to the surface
+corresponded to 5\%, 25\%, 33\%, and 50\% coverages. These systems
+were again allowed to reach thermal equilibrium before being run in the
+microcanonical ensemble. All of the systems examined in this work were
+run for at least 40 ns. A subset that were undergoing interesting effects
+have been allowed to continue running with one system approaching 200 ns.
+All simulations were run using the open source molecular dynamics package, OpenMD. \cite{Ewald, OOPSE}
 
 
-Our model systems are composed of approximately 4000 metal atoms cut along the 557 plane. This cut creates a stepped surface of 6x(111) surface plateaus separated by a single (100) atomic step height. The abundance of low-coordination atoms along the step edges acts as a suitable model for industrial catalysts which tend to have a high concentration of high-index sites. Experimental work has shown that such surfaces are notable for reconstructing upon adsorption\cite{}. Reconstructions have been seen for the Pt 557 surface that involve doubling of the step height and further formation of nano clusters with a triangular motif \cite{doi:10.1126/science.1182122}. To shed insight on whether this reconstruction is limited to the platinum surface, simulations of gold under similar conditions will also be examined. To properly observe these changes, our system size needs to be greater than the periodic phenomena we are examining. The large size and the long time scales needed precluded us from using quantum approaches. Thus, a forcefield describing the Metal-Metal, CO-CO, and CO-Metal interactions was parameterized and the simulations were run using OpenMD\cite{} an open-source molecular dynamics package.
 
 
 
