Index: /anuga_work/publications/boxing_day_validation_2008/patong_validation.tex
===================================================================
--- /anuga_work/publications/boxing_day_validation_2008/patong_validation.tex	(revision 7376)
+++ /anuga_work/publications/boxing_day_validation_2008/patong_validation.tex	(revision 7377)
@@ -14,5 +14,5 @@
 %----------title-------------%
 \title{Benchmarking Tsunami Models using the December 2004 Indian
-  Ocean Tsunami and its Impact at Patong Beach}
+  Ocean Tsunami and its Impact at Patong Bay}
 
 %-------authors-----------
@@ -35,14 +35,14 @@
 %------Abstract--------------
 \begin{abstract}
-In this paper a new benchmark for tsunami model validation is
-proposed. The benchmark is based upon the 2004 Indian Ocean tsunami,
-which affords a uniquely large amount of observational data for model
-comparison. Unlike the small number of existing benchmarks, the
+This paper proposes a new benchmark for tsunami model validation. 
+The benchmark is based upon the 2004 Indian Ocean tsunami,
+which affords a uniquely large amount of observational data for events of this kind. 
+Unlike the small number of existing benchmarks, the
 proposed test validates all three stages of tsunami evolution -
-generation, propagation and inundation. Specifically we use geodetic
+generation (FIXME (Jane): really?), propagation and inundation. Specifically we use geodetic
 measurements of the Sumatra--Andaman earthquake to validate the
 tsunami source, altimetry data from the \textsc{jason} satellite to
 test open ocean propagation, eye-witness accounts to assess near shore
-propagation and a detailed inundation survey of Patong Bay, Thailand
+propagation and a detailed inundation survey of Patong city, Thailand
 to compare model and observed inundation. Furthermore we utilise this
 benchmark to further validate the hydrodynamic modelling tool
@@ -62,17 +62,14 @@
 
 \section{Introduction}
-Tsunami are a potential hazard to coastal communities all over the
+Tsunami is a potential hazard to coastal communities all over the
 world. A number of recent large events have increased community and
 scientific awareness of the need for effective detection, forecasting,
-and emergency preparedness. Probabilistic, geological, hydrodynamic,
-and economic models are required to predict the location and
+and emergency preparedness. Probabilistic, geophysical and hydrodynamic 
+models are required to predict the location and
 likelihood of an event, the initial sea floor deformation and
-subsequent propagation and inundation of the tsunami, the
-effectiveness of hazard mitigation procedures and the economic impact
-of such measures and of the event itself. Here we focus on modelling of
-the physical processes. 
-%OLE: I commented this out 23 June 2009 as there was no reference.
-%For discussion on economic and decision based
-%models refer to~\cite{} and the references therein.
+subsequent propagation and inundation of the tsunami. Engineering, economic and social vulnerability models can then be used to estimate the
+impact of the event as well as the effectiveness of hazard mitigation 
+procedures. In this paper, we focus on modelling of
+the physical processes only. 
 
 Various approaches are currently used to assess the potential impact
@@ -126,5 +123,6 @@
 data also significantly increases the uncertainty of the validation
 experiment that may constrain the ability to make unequivocal
-statements~\cite{bates01}.
+statements~\cite{bates01}. FIXME (Jane): Because?
+FIXME (Phil): references to all of the paragraph above, please
 
 Currently, the extent of tsunami-related field data is limited. The
@@ -133,5 +131,7 @@
 tsunamis pose greatest threat. The resulting lack of data has limited
 the number of field data sets available to validate tsunami
-models. Synolakis et al~\cite{synolakis07} have developed a set of
+models. 
+
+Synolakis et al~\cite{synolakis07} have developed a set of
 standards, criteria and procedures for evaluating numerical models of
 tsunami. They propose three analytical solutions to help identify the
@@ -151,7 +151,8 @@
 provides a good test for real-time forecasting models since the tsunami
 was recorded at three tsunameters. The test requires matching the
-propagation model data with the DART recording to constrain the
+tsunami propagation model output with the DART recording to constrain the
 tsunami source model, and then using it to reproduce the tide gauge
-record at Hilo.
+record at Hilo, Hawaii. 
+FIXME (Jane): Are the tsunameters and the DART recordings the same thing? 
 
 In this paper we develop a field data benchmark to be used in
@@ -164,5 +165,5 @@
 of the tsunami source, altimetry data from the JASON satellite to test
 open ocean propagation, eye-witness accounts to assess near shore
-propagation, and a detailed inundation survey of Patong Bay, Thailand
+propagation, and a detailed inundation survey of Patong city, Thailand
 to compare model and observed inundation. A description of the data
 required to construct the benchmark is given in
@@ -170,15 +171,16 @@
 
 An associated aim of this paper is to illustrate the use of this new
-benchmark to validate an operational tsunami inundation model called
+benchmark to validate a dedicated inundation model called
 \textsc{anuga} used by Geoscience Australia. A description of
 \textsc{anuga} is given in Section~\ref{sec:models} and the validation
 results are given in Section~\ref{sec:results}.
 
-The numerical models used to model tsunami are extremely
-computationally intensive. Full resolution models of the entire
+The numerical models used to simulate tsunami impact 
+are computationally intensive and high resolution models of the entire
 evolution process will often take a number of days to
-run. Consequently the uncertainty in model predictions is difficult to
-quantify. However model uncertainty should not be ignored. Section
-~\ref{sec:sensitivity} provides a simple sensitivity analysis that can
+run. Consequently, the uncertainty in model predictions is difficult to
+quantify as it would require a very large number of runs. 
+However, model uncertainty should not be ignored. Section
+~\ref{sec:sensitivity} provides a simple analysis that can
 be used to investigate the sensitivity of model predictions to model
 parameters.
@@ -192,7 +194,7 @@
 seismometers, tide gauges, \textsc{gps} surveys, satellite overpasses,
 subsequent coastal field surveys of run-up and flooding, and
-measurements of coseismic displacements and bathymetry from ship-based
+measurements of coseismic displacements as well as bathymetry from ship-based
 expeditions, have now been made
-available. %~\cite{vigny05,amnon05,kawata05,liu05}.  
+available. %~\cite{vigny05,amnon05,kawata05,liu05}. FIXME (Ole): Refs?  
 In this section we present the corresponding data necessary to implement 
 the proposed benchmark for each of the three stages of the tsunami's evolution.
@@ -208,6 +210,6 @@
 by the 2004 Sumatra--Andaman earthquake.
 
-The 2004 Sumatra--Andaman tsunami was generated by a severe coseismic
-displacement of the sea floor as a result of one of the largest
+The 2004 Sumatra--Andaman tsunami was generated by a coseismic
+displacement of the sea floor resulting from one of the largest
 earthquakes on record. The mega-thrust earthquake started on the 26
 December 2004 at 0h58'53'' UTC (or just before 8 am local time)
@@ -248,4 +250,5 @@
 
 \subsection{Propagation}
+\label{sec:propagation data}
 Once generated, a tsunami will propagate outwards from the source until
 it encounters the shallow water bordering coastal regions. This period
@@ -258,32 +261,37 @@
 
 \subsubsection{Bathymetry Data}
-A number of raw data sets were obtained, analysed and checked for
-quality and subsequently gridded for easier visualisation and input
-into the tsunami models. The resulting grid data is relatively coarse
-in the deeper water and becomes progressively finer as the distance to
-Patong Bay decreases.
-
-The nested bathymetry grid was generated from: 
+The bathymetry data used in this study was derived from the following 
+sources:
 \begin{itemize}
 \item a two arc minute grid data set covering the Bay of Bengal,
   DBDB2, obtained from US Naval Research Labs;
 \item a 3 second arc grid covering the whole of the Andaman Sea based
-  on Thai Navy charts no. 45 and no. 362; and
+  on Thai Navy charts no. 45 and no. 362; and 
 \item a one second grid created from the digitised Thai Navy
   bathymetry chart, no. 358, which covers Patong Bay and the
-  immediately adjacent regions.
+  immediately adjacent regions. (FIXME (Ole): How was the grid created from these digitised points?)
 \end{itemize}
-
-The final bathymetry data set consists of four nested grids obtained
-via interpolation and resampling of the aforementioned data sets. The
-four grids are shown in Figure~\ref{fig:nested_grids}.  The coarsest
+FIXME (Jane): Refs for all these.
+
+%A number of raw data sets were obtained, analysed and checked for
+%quality and subsequently gridded for easier visualisation and input
+%into the tsunami models. 
+
+These sets were combined via 
+interpolation and resampling to produce four nested grids 
+which are relatively coarse in the deeper water and 
+progressively finer as the distance to
+Patong Beach decreases as shown in Figure~\ref{fig:nested_grids}.  
+
+The coarsest
 bathymetry was obtained by interpolating the DBDB2 grid to a 27 second
 arc grid. A subsection of this region was then replaced by nine second
 data which was generated by sub-sampling the three second of arc grid from
-NOAA. A subset of the nine second grid was replaced by the three second
+NOAA (FIXME (Jane): This was not mentioned in the dots above). 
+A subset of the nine second grid was replaced by the three second
 data. Finally, the one second grid was used to approximate the
 bathymetry in Patong Bay and the immediately adjacent regions. Any
 points that deviated from the general trend near the boundary were
-deleted.
+deleted as a quality check.
 
 The sub-sampling of larger grids was performed by using {\bf resample},
@@ -300,5 +308,5 @@
 \begin{center}
 \includegraphics[width=0.75\textwidth,keepaspectratio=true]{nested_grids}
-\caption{Nested grids of the elevation data.}
+\caption{Nested bathymetry grids.}
 \label{fig:nested_grids}
 \end{center}
@@ -306,9 +314,9 @@
 
 \subsubsection{JASON Satellite Altimetry}\label{sec:data_jason}
-During the 26 December 2004 event, the Jason satellite tracked from
+During the 26 December 2004 event, the \textsc{jason} satellite tracked from
 north to south and over the equator at 02:55 UTC nearly two hours
 after the earthquake \cite{gower05}. The satellite recorded the sea
 level anomaly compared to the average sea level from its previous five
-passes over the same region in the 20-30 days prior.  This data was
+passes over the same region in the 20-30 days prior. This data was
 used to validate the propagation stage in Section
 \ref{sec:resultsPropagation}.
@@ -334,6 +342,11 @@
 
 \subsection{Inundation}
+\label{sec:inundation data}
+FIXME (Ole): Technically propagation covers everything up to 
+the coastline and inundation everything on-shore. 
+This means that ANUGA covers the final part of the propagation and the inundation part. Should we adopt this distiction throughout the paper? 
+
 Inundation refers to the final stages of the evolution of a tsunami and
-covers the propagation of the tsunami in shallow coastal water and the
+covers the propagation of the tsunami in coastal waters and the
 subsequent run-up onto land. This process is typically the most
 difficult of the three stages to model due to thin layers of water
@@ -343,45 +356,48 @@
 data which is often not available. In the case of model validation
 high quality field measurements are also required. For the proposed
-benchmark the authors have obtained a high resolution bathymetry and
+benchmark a high resolution bathymetry (FIXME (Ole): Bathymetry ?) and
 topography data set and a high quality inundation survey map from the
-CCOP in Thailand (\cite{szczucinski06}) to validate model inundation.
-
-The datasets necessary for reproducing the results
-of the inundation stage are available on Sourceforge under the \textsc{anuga}
-project (\url{http://sourceforge.net/projects/anuga}). At the time of
-writing the direct link is \url{http://tinyurl.com/patong2004-data}.
-%
-%\url{http://sourceforge.net/project/showfiles.php?group_id=172848&package_id=319323&release_id=677531}.
-
-In this section we also present eye-witness accounts which can be used to qualitatively validate tsunami inundation.
+Coordinating Committee Co-ordinating Committee for Geoscience Programmes 
+in East and Southeast Asia (CCOP) (\cite{szczucinski06}) was obtained 
+to validate model inundation. See also acknowledgements at the end of this paper.
+
+In this section we also present eye-witness accounts which can be used 
+to qualitatively validate tsunami inundation.
 
 \subsubsection{Topography Data}
 A one second grid was used to approximate the topography in Patong
 Bay. This elevation data was again created from the digitised Thai
-Navy bathymetry chart, no 358. A visualisation of the elevation data
+Navy bathymetry chart, no 358.
+FIXME (Ole): I don't think so. The Navy chart is only offshore.
+
+ A visualisation of the elevation data
 set used in Patong Bay is shown in
-Figure~\ref{fig:patong_bathymetry}. The continuous topography is an
-interpolation of known elevation measured at the coloured dots.
+Figure~\ref{fig:patong_bathymetry}. The continuous topography 
+(FIXME(Jane): What is meant by this?) is an
+interpolation of known elevation measured at the coloured dots. FIXME ??
 
 \begin{figure}[ht]
 \begin{center}
 \includegraphics[width=8.0cm,keepaspectratio=true]{patong_bay_data.jpg}
-\caption{Visualisation of the elevation data set used in Patong Bay showing data points, contours, rivers and roads draped over the final model.}
+\caption{3D visualisation of the elevation data set used in Patong Bay showing data points, contours, rivers and roads draped over the final model.}
 \label{fig:patong_bathymetry}
 \end{center}
 \end{figure}
+FIXME (Jane): legend? Were the contours derived from the final dataset?
+This is not the entire mode, only the bay and the beach.
 
 \subsubsection{Buildings and Other Structures}
-Human-made build and structures can significantly effect tsunami
-inundation. The location and size and number of floors of the
-buildings in Patong Bay were extracted from a GIS data set provided by
-the CCOP in Thailand (see acknowledgements at the end of this paper). 
+Human-made buildings and structures can significantly affect tsunami
+inundation. The footprint and number of floors of the
+buildings in Patong Bay were extracted from a GIS data set which was also provided by the CCOP (see Section \ref{sec:inundation data} for details). 
 The heights of these
-buildings were estimated assuming that each floor has a height of 3 m.
+buildings were estimated assuming that each floor has a height of 3 m and they 
+were added to the topographic dataset. 
 
 \subsubsection{Inundation Survey}
-Tsunami run-up is often the cause of the largest financial and human
+Tsunami run-up is the cause of the largest financial and human
 losses, yet run-up data that can be used to validate model run-up
-predictions is scarce. Of the two field benchmarks proposed in~\cite{synolakis07},
+predictions is scarce. Of the two field benchmarks proposed 
+in~\cite{synolakis07},
 only the Okushiri benchmark facilitates comparison between
 modelled and observed run-up. One of the major strengths of the
@@ -390,6 +406,16 @@
 rather than at a series of discrete sites. The survey map is
 shown in Figure~\ref{fig:patongescapemap} and plots the maximum run-up
-of the 2004 tsunami in Patong Bay. Refer to Szczucinski et
+of the 2004 Indian Ocean tsunami in Patong city. Refer to Szczucinski et
 al~\cite{szczucinski06} for further details.
+
+\begin{figure}[ht]
+\begin{center}
+\includegraphics[width=8.0cm,keepaspectratio=true]{patongescapemap.jpg}
+\caption{Tsunami survey mapping the maximum observed inundation at
+  Patong beach courtesy of the CCOP \protect \cite{szczucinski06}.}
+\label{fig:patongescapemap}
+\end{center}
+\end{figure}
+
 
 \subsubsection{Eyewitness Accounts}\label{sec:eyewitness data}
@@ -402,5 +428,5 @@
 minutes after the source rupture (09:55am to 10:05am local time).
 
-Two videos were sourced from the internet\footnote{The footage is 
+Two videos were sourced\footnote{The footage is 
 widely available and can for example be obtained from 
 \url{http://www.archive.org/download/patong_bavarian/patong_bavaria.wmv}
@@ -410,5 +436,5 @@
 %http://wizbangblog.com/content/2005/01/01/wizbang-tsunami.php
 which include footage of the tsunami in Patong Bay on the day
-of the Indian Ocean Tsunami. Both videos show an already inundated
+of the 2004 Indian Ocean Tsunami. Both videos show an already inundated
 group of buildings. They also show what is to be assumed as the second
 and third waves approaching and further flooding of the buildings and
@@ -438,4 +464,5 @@
 were found to be in the range of 5 to 7 metres per second (+/- 2 m/s)
 in the north and 0.5 to 2 metres per second (+/- 1 m/s) in the south.
+FIXME (Jane): How were these error bounds derived?
 Water depths could also
 be estimated from the videos by the level at which water rose up the
@@ -446,13 +473,4 @@
 speeds in the range of 2 to 5 m/s.
 
-\begin{figure}[ht]
-\begin{center}
-\includegraphics[width=8.0cm,keepaspectratio=true]{patongescapemap.jpg}
-\caption{Tsunami survey mapping the maximum observed inundation at
-  Patong beach courtesy of the Thai Department of Mineral Resources
-  \protect \cite{szczucinski06}.}
-\label{fig:patongescapemap}
-\end{center}
-\end{figure}
 
 \subsection{Validation Check-List}
@@ -465,11 +483,11 @@
  \item reproduce the vertical deformation observed in north-western
    Sumatra and along the Nicobar--Andaman islands (see
-   Section~\ref{sec:gen_data}).
+   Section~\ref{sec:gen_data}),
  \item reproduce the \textsc{jason} satellite altimetry sea surface
-   anomalies (see Section~\ref{sec:data_jason}).
- \item reproduce the inundation survey map in Patong bay
-   (Figure~\ref{fig:patongescapemap}).
+   anomalies (see Section~\ref{sec:data_jason}),
+ \item reproduce the inundation survey map in Patong city
+   (Figure~\ref{fig:patongescapemap}),
  \item simulate a leading depression followed by two distinct crests
-   of decreasing magnitude.
+   of decreasing magnitude at the beach, and
  \item predict the water depths and flow speeds, at the locations of
    the eye-witness videos, that fall within the bounds obtained from
@@ -479,5 +497,5 @@
 Ideally, the model should also be compared to measured timeseries of
 waveheights and velocities but the authors are not aware of the
-availability of such data.
+availability of such data near Patong Bay.
 
 
@@ -493,5 +511,5 @@
 
 There are various approaches to modelling the expected crustal
-deformation from an earthquake at depth. Most approaches model the
+deformation from an earthquake. Most approaches model the
 earthquake as a dislocation in a linear elastic medium. Here we use
 the method of Wang et al~\cite{wang03}. One of the main advantages
@@ -509,6 +527,10 @@
 using a combination of Hankel's transform and Wang et al's
 implementation of the Thomson-Haskell propagator
-algorithm~\cite{wang03}. Once the Green's functions are calculated we
-use a slightly modified version of \textsc{edcmp} to calculate the sea
+algorithm~\cite{wang03}. Once the Green's functions are calculated 
+a slightly modified version of \textsc{edcmp}\footnote{For this study, 
+we have made minor modifications
+to \textsc{edcmp} in order for it to provide output in a file format
+compatible with the propagation code in the following section. Otherwise it
+is similar to the original code.} is used to calculate the sea
 floor deformation for a specific subfault. This second code
 discretises the subfault into a set of unit sources and sums the
@@ -517,14 +539,12 @@
 deformation caused by a two dimensional dislocation along the
 subfault. This step is possible because of the linearity of the
-governing equations. For this study, we have made minor modifications
-to \textsc{edcmp} in order for it to provide output in a file format
-compatible with the propagation code in the following section. Otherwise it
-is similar to the original code.
-
-In order to calculate the crustal deformation using these codes we
-need a model that describes the variation in elastic
+governing equations.
+
+In order to calculate the crustal deformation using these codes 
+a model that describes the variation in elastic
 properties with depth and a slip model of the earthquake to describe
-the dislocation. The elastic parameters used for this study are the
-same as those in Table 2 of Burbidge~\cite{burbidge08}. For the slip
+the dislocation is required. 
+The elastic parameters used for this study are the
+same as those in Table 2 of Burbidge et al~\cite{burbidge08}. For the slip
 model, there are many possible models for the 2004 Andaman--Sumatran
 earthquake to select from
@@ -532,5 +552,6 @@
 determined from various geological surveys of the site. Others solve
 an inverse problem which calibrates the source based upon the tsunami
-wave signal, the seismic signal and/or the run-up. The source
+wave signal, the seismic signal and/or even the run-up. 
+The source
 parameters used here to simulate the 2004 Indian Ocean tsunami were
 taken from the slip model G-M9.15 of Chlieh
@@ -550,9 +571,9 @@
 
 \subsection{Propagation}\label{sec:modelPropagation}
-We use the \textsc{ursga} model described below to simulate the
-propagation of the 2004 tsunami in the deep ocean ocean, based on a
+The \textsc{ursga} model described below was used to simulate the
+propagation of the 2004 Indian Ocean tsunami across the open ocean, based on a
 discrete representation of the initial deformation of the sea floor, as
 described in Section~\ref{sec:modelGeneration}. For the models shown
-here, we assume that the uplift is instantaneous and creates a wave of
+here, the uplift is assumed to be instantaneous and creates a wave of
 the same size and amplitude as the co-seismic sea floor deformation.
 
@@ -563,9 +584,11 @@
 spherical co-ordinates with friction and Coriolis terms. The code is
 based on Satake~\cite{satake95} with significant modifications made by
-the \textsc{urs} corporation~\cite{thio08} and Geoscience
-Australia~\cite{burbidge08}. The tsunami is propagated via the nested
-grid system. Coarse grids are used in the open ocean and the finest
-resolution grid is employed in the region of most
-interest. \textsc{Ursga} is not publicly available.
+the \textsc{urs} corporation, Thio et al~\cite{thio08} and Geoscience
+Australia, Burbidge et al~\cite{burbidge08}. 
+The tsunami was propagated via the nested
+grid system described in Section \ref{sec:propagation data} where 
+the coarse grids were used in the open ocean and the finest
+resolution grid was employed in the region closest to Patong bay. 
+\textsc{Ursga} is not publicly available.
 
 \subsection{Inundation}\label{sec:modelInundation}
@@ -578,17 +601,20 @@
 Geoscience Australia tsunami modelling methodology is based on a
 hybrid approach using models like \textsc{ursga} for tsunami
-propagation up to a 100 m depth contour.
+propagation up to an offshore depth contour, typically 100 m.
 %Specifically we use the \textsc{ursga} model to simulate the
 %propagation of the 2004 Indian Ocean tsunami in the deep ocean, based
 %on a discrete representation of the initial deformation of the sea
 %floor, described in Section~\ref{sec:modelGeneration}.
-The wave signal is then used as a time varying boundary condition for
+The wave signal and the velocity field is then used as a 
+time varying boundary condition for
 the \textsc{anuga} inundation simulation.
 % A description of \textsc{anuga} is the following section.
 
 \subsubsection{ANUGA}
-\textsc{Anuga} is an Open Source hydrodynamic inundation tool that
+\textsc{Anuga} is a Free and Open Source hydrodynamic inundation tool that
 solves the conserved form of the depth-integrated nonlinear shallow
-water wave equations. The scheme used by \textsc{anuga}, first
+water wave equations using a Finite-Volume scheme on an 
+unstructured triangular mesh. 
+The scheme, first
 presented by Zoppou and Roberts~\cite{zoppou99}, is a high-resolution
 Godunov-type method that uses the rotational invariance property of
@@ -598,16 +624,18 @@
 et al~\cite{kurganov01} for solving one-dimensional conservation
 equations. The numerical scheme is presented in detail in 
-Roberts and Zoppou~\cite{zoppou99,roberts00} and
+Roberts and Zoppou~\cite{zoppou00,roberts00} and
 Nielsen et al~\cite{nielsen05}. An important capability of the
-software is that it can model the process of wetting and drying as
-water enters and leaves an area. This means that it is suitable for
+finite-volume scheme is that discontinuities in all conserved quantities 
+are allowed at every edge in the mesh. This means that the tool is 
+well suited to adequately resolving hydraulic jumps, transcritical flows and 
+the process of wetting and drying. This means that \textsc{Anuga} 
+is suitable for
 simulating water flow onto a beach or dry land and around structures
-such as buildings. It is also capable of adequately resolving
-hydraulic jumps due to the ability of the finite-volume method to
-handle discontinuities. The numerical scheme can also handle
-transitions between sub-critical and super-critical flow regimes
-seamlessly. \textsc{Anuga} has been validated against a number of
-analytical solutions and the wave tank simulation of the 1993 Okushiri
+such as buildings. \textsc{Anuga} has been validated against 
+%a number of analytical solutions and  FIXME: These have not been published 
+the wave tank simulation of the 1993 Okushiri
 Island tsunami~\cite{nielsen05,roberts06}.
+FIXME (Ole): Add reference to Tom Baldock's Dam Break valiadation of ANUGA.
+
 
 %================Section===========================
@@ -629,5 +657,5 @@
 (arrows point down) during and immediately after the earthquake. Most
 of this data comes from uplifted or subsided coral heads. The length of
-vector increases with the magnitude of the displacement; the length
+the vector increases with the magnitude of the displacement; the length
 corresponding to 1 m of observed motion is shown in the top right
 corner of the figure. As can be seen, the source model detailed in
@@ -642,11 +670,13 @@
 points) is only 0.06 m, well below the typical error of the
 observations of between 0.25 and 1.0 m. However, the occasional point
-has quite a large error (over 1 m); for example a couple
-uplifted/subsided points appear to be on a wrong side of the predicted
+has quite a large error (over 1 m); for example a couple of
+uplifted/subsided points appear to be on a wrong 
+(FIXME (Jane): This is incorrect) side of the predicted
 pivot line~\ref{fig:surface_deformation}. The excellence of the fit is
 not surprising, since the original slip model was chosen
 by~\cite{chlieh07} to fit this (and the seismic data) well. 
 This does demonstrate, however, that \textsc{edgrn} and our modified version of
-\textsc{edstat} can reproduce the correct pattern of vertical
+\textsc{edstat} (FIXME(Jane): This has never been mentioned before) 
+can reproduce the correct pattern of vertical
 deformation very well when the slip distribution is well constrained
 and when reasonable values for the elastic properties are used.
@@ -665,5 +695,6 @@
   hand corner of the figure. The cross marks show the location of
   the pivot line (the region between the uplift and subsided region
-  where the uplift is zero) derived from remote sensing. All the
+  where the uplift is zero) derived from remote sensing 
+  (FIXME(Jane): How was that possible?). All the
   observational data are from the dataset collated
   by~\cite{chlieh07}.}
@@ -686,6 +717,17 @@
 shown in Figure~\ref{fig:computational_domain}.
 
+\begin{figure}[ht]
+\begin{center}
+%\includegraphics[width=5.0cm,keepaspectratio=true]{extent_of_ursga_model.jpg}
+%\includegraphics[width=5.0cm,keepaspectratio=true]{ursgaDomain.jpg}
+\includegraphics[width=5.0cm,keepaspectratio=true]{extent_of_ANUGA_model.jpg}
+\caption{Computational domain of the \textsc{ursga} simulation (inset: white and black squares and main: black square) and the \textsc{anuga} simulation (main and inset: red polygon).}
+\label{fig:computational_domain}
+\end{center}
+\end{figure}
+
+
 Figure \ref{fig:jasonComparison} provides a comparison of the
-\textsc{ursga}-predicted sea surface elevation with the JASON
+\textsc{ursga}-predicted sea surface elevation with the \textsc{jason}
 satellite altimetry data. The \textsc{ursga} model replicates the 
 amplitude and timing of the the wave observed at $2.5^0$ South,
@@ -696,10 +738,11 @@
 as can be seen in the satellite data. Also note
 that the \textsc{ursga} model prediction of the ocean surface
-elevation becomes out of phase with the JASON data at $3^0$ to $7^0$ North
+elevation becomes out of phase with the \textsc{jason} 
+data at $3^0$ to $7^0$ North
 latitude. Chlieh et al~\cite{chlieh07} also observed these misfits and
 suggest it is caused by a reflected wave from the Aceh Peninsula that
 is not resolved in the model due to insufficient resolution of the
 computational mesh and bathymetry data. This is also a limitation of
-the model presented here, but probably could be improved by nesting
+the model presented here which could be improved by nesting
 grids near Aceh.
 
@@ -708,37 +751,31 @@
 \includegraphics[width=12.0cm,keepaspectratio=true]{jasonComparison.jpg}
 \caption{Comparison of the \textsc{ursga}-predicted surface elevation
-  with the JASON satellite altimetry data. The \textsc{ursga} wave
+  with the \textsc{jason} satellite altimetry data. The \textsc{ursga} wave
   heights have been corrected for the time the satellite passed
-  overhead compared to JASON sea level anomaly.}
+  overhead compared to \textsc{jason} sea level anomaly.}
 \label{fig:jasonComparison}
 \end{center}
 \end{figure}
+FIXME (Jane): This graph does not look nice. The legend URS Model should 
+be URSGA model.
 
 \subsection{Inundation}
 After propagating the tsunami in the open ocean using \textsc{ursga},
 the approximated ocean and surface elevation and horisontal flow
-velocities were extracted and used to construct a boundary condition
+velocities were extracted and used to construct a boundary condition 
 for the \textsc{anuga} model. The interface between the \textsc{ursga}
-and \textsc{anuga} models was chosen to roughly follow the 100 m depth
+and \textsc{anuga} models was chosen to roughly follow the 100~m depth
 contour along the west coast of Phuket Island. The computational
 domain is shown in Figure~\ref{fig:computational_domain}.
-\begin{figure}[ht]
-\begin{center}
-%\includegraphics[width=5.0cm,keepaspectratio=true]{extent_of_ursga_model.jpg}
-%\includegraphics[width=5.0cm,keepaspectratio=true]{ursgaDomain.jpg}
-\includegraphics[width=5.0cm,keepaspectratio=true]{extent_of_ANUGA_model.jpg}
-\caption{Computational domain of the URSGA simulation (inset: white and black squares and main: black square) and the \textsc{anuga} simulation (main and inset: red polygon).}
-\label{fig:computational_domain}
-\end{center}
-\end{figure}
 
 The domain was discretised into 386,338 triangles. The resolution of
-the grid was increased in certain regions to efficiently increase the
-accuracy of the simulation. The grid resolution ranged between a
-maximum triangle area of $1\times 10^5$ m$^2$ near the Western ocean
+the grid was increased in regions inside the bay and on-shore to 
+efficiently increase the simulation accuracy for the impact area. 
+The grid resolution ranged between a
+maximum triangle area of $1\times 10^5$ m$^2$ near the western ocean
 boundary to $20$ m$^2$ in the small regions surrounding the inundation
 region in Patong Bay. Due to a lack of available data, friction was
 set to a constant throughout the computational domain. For the
-reference simulation a Manning's coefficient of 0.01 was chosen to
+reference simulation, a Manning's coefficient of 0.01 was chosen to
 represent a small resistance to the water flow. See Section
 \ref{sec:friction sensitivity} for details on model sensitivity to
@@ -747,9 +784,12 @@
 
 The boundary condition at each side of the domain towards the south
-and the north where no data was available was chosen as a transmissive
+and the north where no information about the incident wave or 
+its velocity field is available 
+was chosen as a transmissive
 boundary condition, effectively replicating the time dependent wave
-height present just inside the computational domain. Momentum was set
+height present just inside the computational domain. 
+The velocity field on these boundaries was set
 to zero. Other choices include applying the mean tide value as a
-Dirichlet type boundary condition. But experiments as well as the
+Dirichlet boundary condition. But experiments as well as the
 result of the verification reported here showed that this approach
 tends to underestimate the tsunami impact due to the tempering of the
@@ -761,5 +801,5 @@
 specified by the Thai Navy tide charts
 (\url{http://www.navy.mi.th/hydro/}) at the time the tsunami arrived
-at Patong Bay. Although the tsunami propagated for approximately 3
+at Patong Bay. Although the tsunami propagated for approximately three
 hours before it reach Patong Bay, the period of time during which the
 wave propagated through the \textsc{anuga} domain is much
@@ -767,5 +807,5 @@
 reasonable.
 
-Maximum onshore inundation elevation was computed from the model
+Maximum onshore inundation depth was computed from the model
 throughout the entire Patong Bay region. 
 Figure~\ref{fig:inundationcomparison1cm} (left) shows very good
@@ -790,6 +830,15 @@
 
 
+The datasets necessary for reproducing the results
+of the inundation stage are available on Sourceforge under the \textsc{anuga}
+project (\url{http://sourceforge.net/projects/anuga}).
+At the time of
+writing the direct link is \url{http://tinyurl.com/patong2004-data}.
+%%\url{http://sourceforge.net/project/showfiles.php?group_id=172848&package_id=319323&release_id=677531}.
+The scripts required are part of the \textsc{anuga} distribution also 
+available from Sourceforge \url{http://sourceforge.net/projects/anuga} under 
+the validation section.
+
 An animation of this simulation is available on the \textsc{anuga} website at \url{https://datamining.anu.edu.au/anuga} or directly from \url{http://tinyurl.com/patong2004}.
-
 %\url{https://datamining.anu.edu.au/anuga/attachment/wiki/AnugaPublications/patong_2004_indian_ocean_tsunami_ANUGA_animation.mov}.
 
@@ -826,5 +875,6 @@
 parameterisation of the source model, effect of humans structures on
 flow, as well as uncertainties in the elevation data, effects of
-erosion and deposition by the tsunami event, measurement errors, and
+erosion and deposition by the tsunami event, 
+measurement errors in the GPS survey recordings, and
 missing data in the field survey data itself. The impact of some of
 these sources of uncertainties are is investigated in
@@ -852,5 +902,6 @@
 \includegraphics[width=10.0cm,keepaspectratio=true]{gauge_bay_depth.jpg}
 \includegraphics[width=10.0cm,keepaspectratio=true]{gauge_bay_speed.jpg}
-\caption{Time series obtained from the two offshore locations shown in Figure \protect \ref{fig:gauge_locations}.}
+\caption{Time series obtained from the two offshore gauge locations, 
+7C and 10C, shown in Figure \protect \ref{fig:gauge_locations}.}
 \end{center}
 \label{fig:offshore_timeseries}
@@ -861,5 +912,6 @@
 \includegraphics[width=10.0cm,keepaspectratio=true]{gauges_hotels_depths.jpg}
 \includegraphics[width=10.0cm,keepaspectratio=true]{gauges_hotels_speed.jpg}
-\caption{Time series obtained from the two onshore locations shown in Figure \protect \ref{fig:gauge_locations}.}
+\caption{Time series obtained from the two onshore locations, North and South, 
+shown in Figure \protect \ref{fig:gauge_locations}.}
 \end{center}
 \label{fig:onshore_timeseries}
@@ -867,5 +919,5 @@
 
 
-The estimated max depths and flow rates given in Section
+The estimated depths and flow rates given in Section
 \ref{sec:eyewitness data} are shown together with the modelled depths
 and flow rates obtained from the model in Table \ref{tab:depth and
@@ -891,4 +943,5 @@
 \label{tab:depth and flow comparisons}
 \end{table} 
+FIXME (Jane): We should perhaps look at average data in area surrounding these points
 
 %can be estimated with landmarks found in
@@ -921,10 +974,11 @@
 model maximum inundation. The reference model is the one reported in 
 Figure~\ref{fig:inundationcomparison1cm} (right) with a friction coefficient of 0.01, 
-buildings included and the boundary condition produced by the URSGA model.
+buildings included and the boundary condition produced by the 
+\textsc{ursga} model.
 
 %========================Friction==========================%
 \subsection{Friction}
 \label{sec:friction sensitivity}
-The first study investigated the impact of surface roughness on the
+The first sensitivity study investigated the impact of surface roughness on the
 predicted run-up. According to Schoettle~\cite{schoettle2007}
 appropriate values of Manning's coefficient range from 0.007 to 0.03
@@ -949,8 +1003,10 @@
 severity is directly proportional to the boundary waveheight but small
 perturbations in the input wave height of 10 cm appear to have little
-effect on the final on-shore run-up. Obviously larger perturbations
-will have greater impact. However, this value is generally well
+effect on the final inundated area. Obviously larger perturbations
+will have greater impact. However, wave heights in the open ocean are 
+generally well
 predicted by the generation and propagation models such as
-\textsc{ursga}. See e.g.\ \cite{thomas2009}.
+\textsc{ursga} as demonstrated in Section \ref{sec:resultsPropagation} 
+and also in \cite{thomas2009}.
 
 
@@ -958,9 +1014,13 @@
 %========================Buildings==========================%
 \subsection{Buildings and Other Structures}
-The presence of buildings has the greatest influence on the maximum
-on-shore inundation extent. Figure~\ref{fig:sensitivity_nobuildings}
-shows the maximum run-up and associated flow speeds in the presence and absence of buildings. It
-is apparent that the inundation is much more severe when the presence
-of human made structures and buildings are ignored.
+The presence or absence of physical buildings in the elevation model was also 
+investigated.
+Figure~\ref{fig:sensitivity_nobuildings}
+shows the inundated area and the associated maximum flow speeds 
+in the presence and absence of buildings. It
+is apparent that densely built-up areas act as 
+dissipators greatly reducing the inundated area. However, flow speeds
+tend to increase in passages between buildings.
+ 
 
 \begin{table}
@@ -1001,9 +1061,9 @@
 
 This study also shows that the tsunami impact modelling methodology
-adopted is sane and able to predict inundation extents with reasonable
+adopted is credible and able to predict inundation extents with reasonable
 accuracy.  An associated aim of this paper was to further validate the
 hydrodynamic modelling tool \textsc{anuga} which is used to simulate
-the tsunami inundation and run rain-induced floods. Model predictions
-matched well geodetic measurements of the Sumatra--Andaman earthquake,
+the tsunami inundation. Model predictions
+matched well the geodetic measurements of the Sumatra--Andaman earthquake,
 altimetry data from the \textsc{jason}, eye-witness accounts of wave
 front arrival times and flow speeds and a detailed inundation survey
@@ -1013,5 +1073,6 @@
 small changes in friction, wave height at the 100 m depth contour and
 the presence of buildings and other structures on the model
-predictions. The presence of buildings has the greatest influence on
+predictions. Of these three, the presence of buildings was shown to 
+have the greatest influence on
 the simulated inundation extent. The value of friction and small
 perturbations in the waveheight at the \textsc{anuga} boundary have
@@ -1022,10 +1083,10 @@
 This project was undertaken at Geoscience Australia and the Department
 of Mathematics, The Australian National University. The authors would
-like to thank Niran Chaimanee from the CCOP, Thailand for providing
+like to thank Niran Chaimanee from the CCOP for providing
 the post 2004 tsunami survey data, building footprints, aerial
-photography and the elevation data for Patong beach, Prapasri Asawakun
+photography and the elevation data for Patong city, Prapasri Asawakun
 from the Suranaree University of Technology and Parida Kuneepong for
 supporting this work; and Drew Whitehouse from the Australian National
-University for preparing the animation of the inundation model.
+University for preparing the animation of the simulated impact.
 
 \clearpage
@@ -1041,5 +1102,5 @@
 \caption{Results from reference model as reported in Section \protect \ref{sec:results}, 
   i.e.\ including buildings and a friction value of 0.01. The seaward boundary condition is as
-  provided by the URSGA model. The left image shows the maximum
+  provided by the \textsc{ursga} model. The left image shows the maximum
   modelled depth while the right hand image shows the maximum modelled
   flow velocities.}
@@ -1058,5 +1119,5 @@
   \protect \ref{fig:reference_model} (left).  The left and right images 
   show the inundation results if the wave at the \textsc{anuga} boundary
-  is reduced or increased by 10cm respectively. The inundation
+  is reduced or increased by 10 cm respectively. The inundation
   severity varies in proportion to the boundary waveheight, but the
   model results are only slightly sensitive to this parameter for the
@@ -1065,4 +1126,5 @@
 \end{center}
 \end{figure}
+FIXME (Jane): How and why was the +/- 10 cm chosen?
 
 
@@ -1083,7 +1145,7 @@
 \includegraphics[width=6cm,keepaspectratio=true]{sensitivity_nobuildings_depth}
 \includegraphics[width=6cm,keepaspectratio=true]{sensitivity_nobuildings_speed}
-\caption{This figure shows the effect of having buildings as part of
+\caption{Model results show the effect of buildings in
   the elevation data set. 
-  The left hand image shows the inundation depth results for
+  The left hand image shows the maximum inundation depth results for
   a model entirely without buildings.  As expected, the absence of
   buildings will increase the inundation extent beyond what was
