--- trunk/COonPt/firstTry.tex	2012/12/15 22:41:13	3817
+++ trunk/COonPt/firstTry.tex	2012/12/17 18:45:57	3820
@@ -1,8 +1,10 @@
 \documentclass[11pt]{article}
 \usepackage{amsmath}
 \usepackage{amssymb}
+\usepackage{times}
+\usepackage{mathptm}
 \usepackage{setspace}
-\usepackage{endfloat}
+\usepackage{float}
 \usepackage{caption}
 
 %\usepackage{tabularx}
@@ -11,7 +13,6 @@
 %\usepackage{booktabs}
 %\usepackage{bibentry}
 %\usepackage{mathrsfs}
-%\usepackage[ref]{overcite}
 \usepackage[square, comma, sort&compress]{natbib}
 \usepackage{url}
 \pagestyle{plain} \pagenumbering{arabic} \oddsidemargin 0.0cm
@@ -19,12 +20,11 @@
 9.0in \textwidth 6.5in \brokenpenalty=10000
 
 % double space list of tables and figures
-\AtBeginDelayedFloats{\renewcommand{\baselinestretch}{1.66}}
+%\AtBeginDelayedFloats{\renewcomand{\baselinestretch}{1.66}}
 \setlength{\abovecaptionskip}{20 pt}
 \setlength{\belowcaptionskip}{30 pt}
 
-%\renewcommand\citemid{\ } % no comma in optional reference note
-\bibpunct{[}{]}{,}{n}{}{;}
+\bibpunct{}{}{,}{s}{}{;}
 \bibliographystyle{achemso}
 
 \begin{document}
@@ -49,15 +49,18 @@
 %%
 
 %Title
-\title{Investigation of the Pt and Au 557 Surface Reconstructions
-  under a CO Atmosphere}
+\title{Molecular Dynamics simulations of the surface reconstructions
+  of Pt(557) and Au(557) under exposure to CO}
+
 \author{Joseph R. Michalka, Patrick W. McIntyre and J. Daniel
 Gezelter\footnote{Corresponding author. \ Electronic mail: gezelter@nd.edu} \\
 Department of Chemistry and Biochemistry,\\
 University of Notre Dame\\
 Notre Dame, Indiana 46556}
+
 %Date
-\date{Dec 15,  2012}
+\date{Dec 15, 2012}
+
 %authors
 
 % make the title
@@ -117,9 +120,6 @@ weaker interaction with CO, is less likely to undergo 
 
 
 
-
-
-
 \section{Simulation Methods}
 The challenge in modeling any solid/gas interface problem is the
 development of a sufficiently general yet computationally tractable
@@ -248,19 +248,31 @@ The Au-C and Au-O interaction parameters were also fit
 %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.
+The Au-C and Au-O cross-interactions were fit using Lennard-Jones and
+Morse potentials, respectively, to reproduce Au-CO binding energies.
 
+The fits were refined against gas-surface calculations using DFT 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)
+method,\cite{PhysRevB.50.17953,PhysRevB.59.1758} with plane waves
+included to an energy cutoff of 20 Ry. Electronic energies are
+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 0.0001 eV.  In testing the CO-Au
+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, and energies
+were converged to within 0.03 meV per Au atom with a 4 x 4 x 4
+Monkhorst-Pack\cite{Monkhorst:1976,PhysRevB.13.5188} {\bf k}-point
+sampling of the first Brillouin zone.  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 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,