Index: /DVD_images/extra_files/BatemansBay/analysis.html
===================================================================
--- /DVD_images/extra_files/BatemansBay/analysis.html	(revision 7328)
+++ /DVD_images/extra_files/BatemansBay/analysis.html	(revision 7329)
@@ -27,5 +27,5 @@
   from SWW files, but are offered as an example of one way to do it.
   <p>
-  This page describes the scripts and shows how to use them.  Note that due to the ad-hoc nature of the scripts, 
+  This page describes the scripts and shows how to use them.  Note that due to the ad-hoc nature of the scripts,
   you <b>must</b> modify these scripts before they can be used to extract information from any SWW files you
   generate.
@@ -33,47 +33,53 @@
   <a name="export_results_max.py scripts"><h3><b>export_results_max.py</b></h3></a>
   The <font color="red">export_results_max.py</font> script can be used to create an ASC file that contains the maximum
-  of an ANUGA variable or expression for each point in a user-defined raster on the simulation region.
+  of an ANUGA variable or expression for each point in a user-defined ArcGIS grid on the simulation region.
   <p>
   You must change certain values within the <font color="red">export_results_max.py</font> file to get what you want:
   <ul>
-    <li> You must determine how many SWW files your simulation produced and create as many lines like this:
+    <li> List the output folder names here, with one for each simulation you have run:
 <pre><font color="brown">    time_dir1 = '20090505_150430_run_final_0.8_58292_None_kvanputt'
     time_dir2 = '20090505_150517_run_final_0_58292_None_kvanputt'</font></pre>
-         as necessary.  Then modify the line:
+         For information on  <a href="modifications.html#output">output_folder_name</a>.
+  <p>Then modify the line:
 <pre><font color="brown">    time_dirs = [time_dir1, time_dir2]</font></pre>
          to include each of the variables you defined above.
-         <p>   
-    <li> Your SWW output will have a name like <font color="red">batemans_bay.sww</font>. For a large model you 
+         <p>
+    <li> Your SWW output will have a name like <font color="red">batemans_bay.sww</font>. For a large model you
          may have more than one output file with extra filenames like <font color="red">batemans_bay_37860_0.sww</font>,
-         where the <b>37860</b> tells us that the timestep at the start of this file is 37860 sec. The  
+         where the <b>37860</b> tells us that the timestep at the start of this file is 37860 sec. The
          <font color="red">export_results_max.py</font> script needs to examine all SWW output files, so we specify
          all the files produced by the model run to create a maximum over the entire time.
-         We do this by specifying the start times of all the extra SWW files: 
-         <p>	
-<pre><font color="brown">    times = [37860]</font></pre>
+         We do this by specifying the start times of all the extra SWW files:
          <p>
-         Note we do not have to specify the first SWW file, only the extra file start times. If there are no extra SWW files,
-         just do:
-         <p>	
+<pre><font color="brown">    times = [37860] <font color="black"> or </font>
+    times = [20000, 40000, 60000]</font></pre>
+         <p>
+         <i>Note we do not have to specify the first SWW file, only the extra file start times. If there are no extra SWW files,
+         just do:</i>
+         <p>
 <pre><font color="brown">    times = []</font></pre>
          <p>
-    <li> Modify the <b>cellsize</b> value to set the size of the raster you require.  For example:
-<pre><font color="brown">    cellsize = 20		# raster cell size in metres</font></pre>
-         <p>	
-    <li> You can get the maximum of a variable or expression over the entire model time, or for a single time in the simulation. 
+    <li> Modify the <b>cellsize</b> value to set the size of the ArcGIS grid you require.  For example:
+<pre><font color="brown">    cellsize = 20		# ArcGIS grid cell size in metres</font></pre>
+         <p>
+         <i>Note: That this value should not go beyond the most refined part of the mesh
+         i.e. if mesh resolution is 500m<sup>2</sup>, cellsize = (500 </i>x<i> 2)<sup>1/2</sup> = 32m</i>
+         <p>
+    <li> You can get the maximum of a variable or expression over the entire model time, or for a single time in the simulation.
          Set <b>timestep</b> to the required time you want the maximum for, or set it to <b>None</b> to indicate that you want
-         the maximum values in the raster over all timesteps:
+         the maximum values over all timesteps:
 <pre><font color="brown">    timestep = None  # over all timesteps
     #timestep = 0</font></pre>
-         <p>         
-         Note that if you want the elevation use <b>timestep = 0</b>. Elevation does not change over time and you only need the 
-         first SWW file.		
          <p>
-    <li> If you want to clip the raster to one or more small regions then put the names of the regions of interest
+         <i>Note that if you want the elevation use <b>timestep = 0</b>. Elevation does not change over time and you only need the
+         first SWW file.</i>
+         <p>
+    <li> If you want to clip the ArcGIS grid to one or more small regions then put the names of the regions of interest
          into the <b>area</b> list:
 <pre><font color="brown">    area = ['Batemans_Bay', 'NW', 'South']</font></pre>
-         Note that the name strings you put into the <b>area</b> list must match the names used in the
+         <p>
+         <i>Note that the name strings you put into the <b>area</b> list must match the names used in the
          <font color="red">project.py</font> file.  That is, if you use a name such as 'NW', then the
-         <font color="red">project.py</font> file must have lines like:
+         <font color="red">project.py</font> file must have lines like:</i>
 <pre><font color="brown">    xminNW = 548000
     xmaxNW = 561000
@@ -85,9 +91,9 @@
 <pre><font color="brown">    area = ['All']		# no region of interest</font></pre>
          <p>
-    <li> Finally you must decide which variable or expression values you want sampled on your raster.
+    <li> Finally you must decide which variable or expression values you want sampled on your ArcGIS grid.
          Define a list <b>var</b> that contains strings defining the required variable or expression:
 <pre><font color="brown">    var = ['depth', 'speed']</font></pre>
-         Note that the strings you supply must be defined in the <b>var_equations</b> dictionary
-         prior to your definition of <b>var</b>:
+         <i>Note that the strings you supply must be defined in the <b>var_equations</b> dictionary
+         prior to your definition of <b>var</b>:</i>
 <pre><font color="brown">    var_equations = {'stage':     'stage',
                      'momentum':  '(xmomentum**2 + ymomentum**2)**0.5',
@@ -100,9 +106,9 @@
   <a name="get_timeseries.py"><h3><b>get_timeseries.py</b></h3></a>
   The <font color="red">get_timeseries.py</font> script is used to get timeseries data for a selection of variable
-  data at one or more gauge points in a simulation.
+  data at one or more timeseries gauge points in a simulation.
   <p>
   You must change certain values within the <font color="red">get_timeseries.py</font> file to get what you want:
   <ul>
-    <li> You must determine how many SWW files your simulation produced and create as many lines like this:
+    <li> Depending on how many simulations you have run will determine the number of output folder names you insert here:
 <pre><font color="brown">    time_dir1 = '20090505_150430_run_final_0.8_58292_None_kvanputt'
     time_dir2 = '20090505_150517_run_final_0_58292_None_kvanputt'</font></pre>
@@ -111,5 +117,5 @@
          to include each of the variables you defined above.
          <p>
-    <li> Make sure that the <b>gauges</b> list in <font color="red">projects.py</font> contains one or more CSV files
+    <li> Make sure that the <b>gauges</b> list specified in <font color="red">projects.py</font> contains one or more CSV files
          defining the gauges within the simulation that you want the timeseries data for.
          The gauge file must have this format:
Index: D_images/extra_files/BatemansBay/auxiliary_scripts.html
===================================================================
--- /DVD_images/extra_files/BatemansBay/auxiliary_scripts.html	(revision 7328)
+++ 	(revision )
@@ -1,132 +1,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
-<html>
-<head>
-  <title>Geoscience Australia</title>
-  <link rel="stylesheet" href="browser_files/style.css">
-  <link REL="SHORTCUT ICON" HREF="browser_files/favicon.ico">
-</head>
-<body>
-  <table cellspacing="10" border="0">
-    <tr>
-      <td>
-        <img src="browser_files/logo.jpg" alt="Australian Government, Geoscience Australia" width="327" height="80" border="0"/>
-      </td>
-      <td width="50">
-        &nbsp;
-      </td>
-      <td>
-        <H1>Tsunami Inundation Models for the BATEMANS BAY region</H1>
-      </td>
-    </tr>
-  </table>
-  <hr>
-
-  <a name="auxiliary scripts"<h2><b>Auxiliary Scripts</b></h2></a>
-  There are number of auxiliary scripts on this disk that you can use to extract information from the SWW files
-  produced by a simulation run.  These scripts are not meant to be the definitive answer on how to get information
-  from SWW files, but are offered as an example of one way to do it.
-  <p>
-  This page describes the scripts and shows how to use them.  Note that due to the ad-hoc nature of the scripts, 
-  you <b>must</b> modify these scripts before they can be used to extract information from any SWW files you
-  generate.
-
-  <a name="export_results_max.py scripts"<h3><b>export_results_max.py</b></h3></a>
-  The <font color="red">export_results_max.py</font> script can be used to create an ASC file that contains the maximum
-  of an ANUGA variable or expression for each point in a user-defined raster on the simulation region.
-  <p>
-  You must change certain values within the <font color="red">export_results_max.py</font> file to get what you want:
-  <ul>
-    <li> You must determine how many SWW files your simulation produced and create as many lines like this:
-<pre><font color="brown">    time_dir1 = '20090505_150430_run_final_0.8_58292_None_kvanputt'
-    time_dir2 = '20090505_150517_run_final_0_58292_None_kvanputt'
-    time_dir3 = '20090505_150711_run_final_0_58280_None_kvanputt'
-    time_dir4 = '20090505_150805_run_final_0.8_58280_None_kvanputt'
-    time_dir5 = '20090505_151322_run_final_0.8_64477_None_kvanputt'
-    time_dir6 = '20090505_151447_run_final_0_64477_None_kvanputt'</font></pre>
-         as necessary.  Then modify the line:
-<pre><font color="brown">    time_dirs = [time_dir1, time_dir2, time_dir3, time_dir4, time_dir5, time_dir6]</font></pre>
-         to include each of the variables you defined above.
-
-    <li> Modify the <b>cellsize</b> value to set the size of the raster you require.  For example:
-<pre><font color="brown">    cellsize = 20		# raster cell size in metres</font></pre>
-
-    <li> Now set the timestep at which you want the raster generated.  Either set the actual timestep required or use 
-         <b>None</b> to indicate that you want the maximum values in the raster over all timesteps:
-<pre><font color="brown">    timestep = 1000
-    #timestep = None		# over all timesteps</font></pre>
-         <p>
-         Note that if you specify a particular timestep here you may not need to include all SWW files in the 
-         <b>time_dirs</b> list above.  For example, if you wanted data from timestep 0 only then you would need
-         to include only the first SWW file in the list.
-
-    <li> If you want to clip the raster to one or more small regions then put the names of the regions of interest
-         into the <b>area</b> list:
-<pre><font color="brown">    area = ['Hobart', 'NW', 'South']</font></pre>
-         Note that the name strings you put into the <b>area</b> list must match the names used in the
-         <font color="red">project.py</font> file.  That is, if you use a name such as 'NW', then the
-         <font color="red">project.py</font> file must have lines like:
-<pre><font color="brown">    xminNW = 548000
-    xmaxNW = 561000
-    yminNW = 5250000
-    ymaxNW = 5258000</font></pre>
-         which set the maximum and minimum eastings and northings that define a rectangular region.
-         <p>
-         If you don't want to clip to a region of interest, then do this:
-<pre><font color="brown">    area = ['All']		# no region of interest</font></pre>
-
-    <li> Now you must decide which variable or expression values you want sampled on your raster.
-         Define a list <b>var</b> that contains strings defining the required variable/expression:
-<pre><font color="brown">    var = ['depth', 'speed']</font></pre>
-         Note that the strings you supply must be defined in the <b>var_equations</b> dictionary
-         prior to your definition of <b>var</b>:
-<pre><font color="brown">    var_equations = {'stage':     'stage',
-                     'momentum':  '(xmomentum**2 + ymomentum**2)**0.5',
-                     'depth':     'stage-elevation',
-                     'speed':     '(xmomentum**2 + ymomentum**2)**0.5/(stage-elevation+1.e-6)',
-                     'elevation': 'elevation' }</font></pre>
-         This dictionary maps your <b>var</b> strings to a variable or expression.
-  </ul>
-
-  <a name="get_runup.py"<h3><b>get_runup.py</b></h3></a>
-  The <font color="red">get_runup.py</font> script is used to get the maximum runup height in a specified region
-  or regions.
-  <p>
-  You must change certain values within the <font color="red">get_runup.py</font> file to get what you want:
-  <ul>
-    <li> You must determine how many SWW files your simulation produced and create as many lines like this:
-<pre><font color="brown">    time_dir1 = '20090505_150430_run_final_0.8_58292_None_kvanputt'
-    time_dir2 = '20090505_150517_run_final_0_58292_None_kvanputt'
-    time_dir3 = '20090505_150711_run_final_0_58280_None_kvanputt'
-    time_dir4 = '20090505_150805_run_final_0.8_58280_None_kvanputt'
-    time_dir5 = '20090505_151322_run_final_0.8_64477_None_kvanputt'
-    time_dir6 = '20090505_151447_run_final_0_64477_None_kvanputt'</font></pre>
-         as necessary.  Then modify the line:
-<pre><font color="brown">    time_dirs = [time_dir1, time_dir2, time_dir3, time_dir4, time_dir5, time_dir6]</font></pre>
-         to include each of the variables you defined above.
-
-    <li> Make sure that the <b>images</b> list in <font color="red">projects.py</font> contains one or more CSV files
-         defining the regions within the simulation that you want the maximum runup for.
-  </ul>
-
-  <a name="get_timeseries.py"<h3><b>get_timeseries.py</b></h3></a>
-  The <font color="red">get_timeseries.py</font> script is used to get timeseries data for a selection of variable
-  data at one or more gauge points in a simulation.
-  <p>
-  You must change certain values within the <font color="red">get_timeseries.py</font> file to get what you want:
-  <ul>
-    <li> You must determine how many SWW files your simulation produced and create as many lines like this:
-<pre><font color="brown">    time_dir1 = '20090505_150430_run_final_0.8_58292_None_kvanputt'
-    time_dir2 = '20090505_150517_run_final_0_58292_None_kvanputt'
-    time_dir3 = '20090505_150711_run_final_0_58280_None_kvanputt'
-    time_dir4 = '20090505_150805_run_final_0.8_58280_None_kvanputt'
-    time_dir5 = '20090505_151322_run_final_0.8_64477_None_kvanputt'
-    time_dir6 = '20090505_151447_run_final_0_64477_None_kvanputt'</font></pre>
-         as necessary.  Then modify the line:
-<pre><font color="brown">    time_dirs = [time_dir1, time_dir2, time_dir3, time_dir4, time_dir5, time_dir6]</font></pre>
-         to include each of the variables you defined above.
-
-    <li> Make sure that the <b>gauges</b> list in <font color="red">projects.py</font> contains one or more CSV files
-         defining the gauges within the simulation that you want the timeseries data for.
-  </ul>
-</body>
-</html>
Index: /DVD_images/extra_files/BatemansBay/index.html
===================================================================
--- /DVD_images/extra_files/BatemansBay/index.html	(revision 7328)
+++ /DVD_images/extra_files/BatemansBay/index.html	(revision 7329)
@@ -23,31 +23,29 @@
 
   <a name="introduction"><h3><b>Introduction</b></h3></a>
-
-  The information on this DVD and the associated report is intended to assist emergency managers in developing preparation and
-  response plans that can be used during a tsunami threat or emergency.
-  <p>
-  The Attorney General's Department (AGD) has supported Geoscience Australia (GA) in developing a range of products to support
-  the understanding of tsunami hazard through the Australian Probabilistic Tsunami Warning System Project. The work reported here is intended
-  to further build the capacity of the Jurisdictions in developing inundation models for prioritised locations. 
+  The information within this DVD is intended to assist emergency managers in tsunami planning and preparation
+  activities. The Australian Government Attorney Generals Department (AGD) has supported Geoscience Australia (GA) in developing a
+  range of products to support the understanding of tsunami hazard through the Australian Tsunami Warning System Project. The work
+  reported here is intended to further build the capacity of the New South Wales (NSW) State Government in developing inundation models for
+  prioritised locations.
   <p>
   While the associated report provides background, model results and interpretations, the DVD contains all data, scripts and
-  software necessary to reproduce and potentially augment the models underpinning the report. This will allow the Jurisdiction
+  instructions for installing software necessary to reproduce and potentially augment the models underpinning the report. This will allow the NSW State Government
   to rerun the models with minor modifications or new elevation data as needed and also potentially replicate the methodology
-  to other locations within the model extent, if desired.  
+  for other locations within the model extent, if desired.
   <p>
   The data provided on this DVD is:
   <ul>
-    <li> The Professional Opinion Report 2009/XX entitled <blink><i><a href="documents/not_there.pdf">Capacity Building for Tsunami Planning and Preparation: 
-         Inundation Models for Four East Coast Australian Communities</a> <b><font color="red">UNFINISHED</font></b></i></blink>
-    <li>  <a href="documents/Figures">Figures</a> of maximum inundation and maximum speed
-    <li> Generated <a href="data/new_south_wales/batemans_bay_tsunami_scenario_2009/anuga/outputs">Arc grids</a> of maximum inundation and maximum speed for the areas of interest
-    <li> Generated <a href="data/new_south_wales/batemans_bay_tsunami_scenario_2009/anuga/outputs">timeseries</a> from the models 
+    <li> The Professional Opinion Report 2009/09 entitled <blink><i><a href="documents/PO_2009_09.pdf">Capacity Building for Tsunami Planning and Preparation:
+         Inundation Models for two New South Wales communities</a></i></blink>
+    <li>  <a href="documents/Figures">Figures</a> of maximum inundation depth and maximum flow speed
+    <li> Generated <a href="data/new_south_wales/batemans_bay_tsunami_scenario_2009/anuga/outputs">ArcGIS grids</a> of maximum inundation depth and maximum flow speed for the areas of interest
+    <li> Generated <a href="data/new_south_wales/batemans_bay_tsunami_scenario_2009/anuga/outputs">timeseries</a> from the models
     <li> Combined <a href="data/new_south_wales/batemans_bay_tsunami_scenario_2009/anuga/topographies">elevation data</a> used by the simulation
-    <li> The <a href="data/new_south_wales/batemans_bay_tsunami_scenario_2009/anuga/outputs/elevation">Arc grid</a> of the resulting elevation generated by ANUGA
-    <li> The Python scripts used to run the models
+    <li> The <a href="data/new_south_wales/batemans_bay_tsunami_scenario_2009/anuga/outputs/elevation">ArcGIS grid</a> of the resulting elevation
+    generated by the model software; <a href="https://datamining.anu.edu.au/anuga">ANUGA</a>
+    <li> The <a href="project">Python scripts</a> used to run the models
   </ul>
   <p>
-  The tsunami wave data on this disk are all derived from events available in the Australian Tsunami
-  Hazard Map. As this dataset is very large, this DVD only contains the events
+  The input tsunami wave data on this disk are all derived from events available in the Probabilistic Tsunami Hazard Assessment (PTHA) for Australia. As this dataset is very large, this DVD only contains the events
   described in the report.
 
Index: /DVD_images/extra_files/BatemansBay/installation.html
===================================================================
--- /DVD_images/extra_files/BatemansBay/installation.html	(revision 7328)
+++ /DVD_images/extra_files/BatemansBay/installation.html	(revision 7329)
@@ -31,7 +31,7 @@
 
   The tsunami inundation simulations are based on the Open Source software package called ANUGA.
-  For more information about ANUGA visit <a href="https://datamining.anu.edu.au/anuga">https://datamining.anu.edu.au/anuga</a>. 
+  For more information about ANUGA visit <a href="https://datamining.anu.edu.au/anuga">https://datamining.anu.edu.au/anuga</a>.
   <p>
-  ANUGA has been developed and tested under the Windows XP and Linux (Ubuntu, Mint and Red Hat) operating systems.  
+  ANUGA has been developed and tested under the Windows XP and Linux (Ubuntu, Mint and Red Hat) operating systems.
   ANUGA may also be installed on a Windows Vista system and Debian Linux, but these have not been extensively tested.
   <p>
@@ -40,8 +40,10 @@
 
   <a name="installing"><h3><b>Installing ANUGA</b></h3></a>
-
+  <a href="http://sourceforge.net/projects/anuga/">Download Software</a><i>: please note Internet Explorer has the habit of renaming the
+  .tgz file to .gz - the remedy is to rename them back or use another browser such as Firefox.</i>
+  <p>
   You must install ANUGA according to the <a href="documents/anuga_installation_guide.pdf">Installation Guide</a>.
   As the installation procedure comprises a number of steps we suggest that it is carried out by someone with a
-  basic understanding of how to install software packages on the operating system of choice. 
+  basic understanding of how to install software packages on the operating system of choice.
 
   <a name="simulating"><h3><b>How to run a simulation</b></h3></a>
@@ -52,5 +54,5 @@
   can be used to get help.
   <p>
-  
+
   <p>
   <hr align="left" width="100">
@@ -61,22 +63,21 @@
   <hr align="left" width="100">
   <p>
-  Next, you must copy the entire contents of the DVD to a place in your filesystem. Let's assume
-  that you want to put the data into <b>C:\ANUGA</b>. You would do this in a Command Prompt window:
-  <table class="code"><tr><td>
-    C:<br>
-    cd \<br>
-    mkdir ANUGA<br>
+  Next, you must copy the entire contents of the DVD to a place in your file system. Let's assume
+  that you want to put the data into <b>C:\ANUGA</b>. You could drag all files from the DVD into this folder with Explorer.
+  Or through the Command Prompt window:
+  <pre><font color="brown">
+    C:
+    cd
+    mkdir ANUGA
     xcopy /e X:\ ANUGA
-  </td></tr></table>
-  <p>
-  Of course, you could just drag all files on the DVD (X:\ is the assumed drive letter) to the desired target directory with Explorer.
+  </font></pre>
+  X:\ is the assumed to be the CD drive letter.
   <p>
   <hr align="left" width="100">
   <p>
   Now you must create an environment variable <b>ANUGADATA</b> that points to the directory you just created:
-  <table class="code"><tr><td>
+  <pre><font color="brown">
     set ANUGADATA=C:\ANUGA
-  </td></tr></table>
-  <p>
+  </font></pre>
   Doing the above in a Command Prompt window is temporary - if you open another
   window you will not have the ANUGADATA environment variable defined. To make
@@ -84,17 +85,13 @@
   tool (<b>Advanced</b> tab).  See the <a href="documents/anuga_installation_guide.pdf">Installation Guide</a>
   if you don't know how to do this.
-  <p>
   <hr align="left" width="100">
-  <p>
   Next, you prepare and execute the model:
-  <table class="code"><tr><td>
-    cd C:\ANUGA<br>
-    cd project<br>
-    python setup_model.py<br >
+  <pre><font color="brown">
+    cd C:\ANUGA
+    cd project
+    python setup_model.py
     python run_model.py
-  </td></tr></table>
-  <p>
+  </font></pre>
   <hr align="left" width="100">
-  <p>
   This should all run to completion though it may take several days, depending on
   the hardware used.
@@ -105,8 +102,8 @@
   drilling down from that point until you find a directory called <b>outputs</b>.
   The latest directory in <b>outputs</b> should contain a file called <font color="red">screen_error.txt</font>
-  with an explanation of the error at the end. 
+  with an explanation of the error at the end.
   <p>
   Once the simulation has completed you may view the results using the ANUGA
-  viewer as described in the <a href="documents/anuga_installation_guide.pdf">Installation Guide</a> 
+  viewer as described in the <a href="documents/anuga_installation_guide.pdf">Installation Guide</a>
   and <a href="documents/anuga_user_manual.pdf">User Manual</a>.  You may also
   generate rasters suitable for GIS mapping or write dedicated scripts extracting timeseries at selected
@@ -138,8 +135,6 @@
   <a name="FAQ"><h3><b>Frequently Asked Questions</b></h3></a>
 
-  There is a <b>Frequently Asked Questions</b> (FAQ) page at
-  <a href="https://datamining.anu.edu.au/anuga/wiki/FrequentlyAskedQuestions">https://datamining.anu.edu.au/anuga/wiki/FrequentlyAskedQuestions</a>.
-  Look in there and search the mailing list archives before asking questions on the ANUGA user's mailing list.
-  Someone may already have asked your question!
+  Look in <b><a href="https://datamining.anu.edu.au/anuga/wiki/FrequentlyAskedQuestions">Frequently Asked Questions</a></b> (FAQ) and search the mailing list archives before asking questions on the ANUGA user's mailing list.
+  Someone may already have asked and answered your question!
   <p>
   Note that you can edit the FAQ pages, so it is helpful if you can update the FAQ with your question and its answer if you feel
Index: /DVD_images/extra_files/BatemansBay/modifications.html
===================================================================
--- /DVD_images/extra_files/BatemansBay/modifications.html	(revision 7328)
+++ /DVD_images/extra_files/BatemansBay/modifications.html	(revision 7329)
@@ -24,9 +24,9 @@
   <a name="modifications"><h2><b>Modifying a simulation</b></h2></a>
 
-  Here we talk about how you change a simulation.  Why would you need to change a simulation?  Well, 
+  Here we talk about how to change a simulation.  Why would you need to change a simulation?  Well,
   you might have some better elevation data, you want to run the simulation on a finer mesh in certain
   areas, or maybe you want to see the result for different events.
   <p>
-  First we describe the uses of the script files you might change, then we walk through a few examples 
+  First we describe the usage of the script files you might change, then we walk through a few examples
   of changes you might make.
   <p>
@@ -37,5 +37,5 @@
   <table class="code">
     <tr><td><font color="red">project.py</font></td><td>Defines the input data used, where to place output, etc.</td></tr>
-    <tr><td><font color="red">build_elevation.py</font></td><td>Builds a PTS file of all elevation data specified by <font color="red">project.py</font></td></tr>
+    <tr><td><font color="red">build_elevation.py</font></td><td>Combines the elevation data specified by <font color="red">project.py</font> into one file; with the extension .PTS</td></tr>
     <tr><td><font color="red">setup_model.py</font></td><td>Prepares the simulation before actually running it</td></tr>
     <tr><td><font color="red">run_model.py</font></td><td>Runs the simulation</td></tr>
@@ -48,40 +48,9 @@
     For further details on changing parameters see <a href="#change">Making changes to a simulation</a>.
 
-<!--  This file is the heart of the simulation.  Here we specify many things, including the tide level, the simulation
-  start and stop times, input data files, and so on.  Because we are using python as the programming language in
-  these files, we can use the power of the language to speed up our development.  We use this by <i>parameterising</i>
-  data as much as possible.
-  <p>
-  Parameters that you might change 
-  As an example, let's look at the <b>scenario_name</b> variable we define in <font color="red">project.py</font>:
-  <table class="code">
-    <tr><td>scenario_name = 'hobart'&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;# name of the scenario</td></tr>
-  </table>
-  <p>
-  We define this variable solely to quickly change other input filenames.  Where we want a different input files for
-  a different scenario, 
-  depending on whether we want a 'small' or 'large' model, we build the filenames using the <b>model</b> variable.
-  Some examples are:
-  <p>
-  <table class="code">
-    <tr height="25"><td>bounding_polygon_filename = 'bounding_polygon_'+ model + '.csv'</td></tr>
-    <tr height="25"><td>land_initial_conditions_filename = [['initial_conditions_' + model +'.csv', 0]]</td></tr>
-    <tr height="25"><td>landward_boundary_filename = 'landward_boundary_'+ model +'.csv'</td></tr>
-  </table>
-  <p>
-  We must, of course, ensure that there are input files <font color="red">bounding_polygon_small.csv</font>
-  and <font color="red">bounding_polygon_large.csv</font>, and so on.
-  <p>
-  Now, if we need to change the simulation model from 'small' to 'large', we need only change the
-  value of the <b>model</b> variable, and all the input files that depend on the model will change.
-  This speeds up development and make errors less likely.  If you want to add another model to the two 
-  we show above, just set <b>model</b> to 'medium' and create appropriate input files with the string
-  'medium' in the filename. -->
-
   <a name="build_elevation.py"><h4><b>build_elevation.py</b></h4></a>
 
-  This script combines all input elevation files into one PTS file.
+  This script combines all input elevation files into a single elevation point file (PTS file).
   We have provided you with the PTS file used to create the outputs on this DVD.
-  If you would like to change the elevation see <a href="#change">Making changes to a simulation</a>. 
+  If you would like to change the elevation, see <a href="#change">Making changes to a simulation</a>.
   <p>
 
@@ -95,6 +64,6 @@
 
   This script runs a tsunami inundation scenario.  It relies on the parameters set in <font color="red">project.py</font>
-  as well as the PTS and STS files.
-  An STS file has been generated for each event listed in the boundaries directory. For further details on events see
+  as well as the elevation and event input files (PTS and STS files respectively).
+  An STS file has been generated for each event listed in the <u>boundaries</u> directory. For further details on events see
   <a href="#change">Making changes to a simulation</a>.
   <p>
@@ -106,9 +75,41 @@
   <p>
 
+  <a name="output"><h4><b>Output Folder Name</b></h4></a>
+
+  The <b>output folder name</b> should be unique between different runs on different data.
+  The list of items below will be used to create the folder in your <u>output</u> directory.
+  Your user name and time+date will be automatically added.  For example,
+  <pre><font color="brown">
+  output_comments = [setup, tide, event_number]</font></pre>
+  will result in a folder name like
+  <pre><font color="brown">
+  20090212_091046_run_final_0_27283_rwilson</font>
+Where you (<u>rwilson</u>) ran a <u>run</u> script at <u>9:10.46</u> in the morning on the <u>2/12/09</u>, <b>setup</b> = <u>final</u>,
+<b>tide</b> = <u>0</u>, <b>event_number</b> = <u>27283</u>  - refer below for more information on these parameters </pre>
+  <p>
+  You can also add strings to this list
+  <pre><font color="brown">
+  output_comments = [setup, tide, event_number, 'large']</font></pre>
+  will result in a folder name like
+  <pre><font color="brown">
+  20090212_091046_run_final_0_27283_large_rwilson</font></pre>
+  <p>
+  <p>
+    <a name="setup"><h4><b>Setup</b></h4></a>
+
+  The <b>setup</b> parameter determines the type of run. This can be one of three values:
+  <pre><font color="brown">
+  'trial' <font color="black">- coarsest mesh, fast </font>
+  'basic' <font color="black">- coarse mesh</font>
+  'final' <font color="black">- fine mesh, slowest</font>
+  </pre></font>
+  Note: <b>'final'</b> must be used if determining the best estimate of inundation for your area of interest.
+  <p>
   <a name="tide"><h4><b>Tide</b></h4></a>
 
-  The <b>tide</b> parameter is used to change the mean stage of the simulation.  When <b>tide</b> is set to 0
+  The <b>tide</b> parameter is used to change the mean inital water level of the simulation.  When <b>tide</b> is set to 0
   the initial water level will be at Mean Sea Level.  If you increase the <b>tide</b> value the water level will become deeper.
-  However land is masked out using initial conditions.  Within ANUGA <b>tide</b> is modelled as a constant.
+  This setting will also increase non tidal lakes and rivers inside the model.  To compensate a mask is used on land called
+  <b>initial conditions</b> which brings the internal water bodies back to 0.  Within ANUGA <b>tide</b> is modelled as a constant.
   <p>
 
@@ -119,61 +120,64 @@
   As we said above, a new STS file must be generated for <font color="red">run_model.py</font> to work.
   <p>
-  The event numbers correspond to a quake ID from the probabilistic tsunami hazard map of Australia.
-  <table class="code">
-    <tr><td><pre>event_number = 51436    # 1 in 10000 yr event from New Hebrides</pre></td></tr>
-  </table>
+  The event numbers correspond to a quake ID from the Probabilistic Tsunami Hazard Map Assessment of Australia.
+
+  <pre><font color="brown">
+  event_number = 51436    # 1 in 10000 yr event from New Hebrides</font></pre>
+
   <p>
 
   <a name="elevation"><h4><b>Elevation</b></h4></a>
 
-  Elevation data can be changed in the <font color="red">project.py</font> elevation script.
+  Elevation data can be changed in the <font color="red">project.py</font> script under ELEVATION DATA.
   Elevation data can be read as either a point file, comma delimited, or as an ASCII grid file
-  (ASC) with an accompanying projection file (PRJ). All elevation input must be projected in the correct UTM zone.
+  (ASC) with an accompanying projection file (PRJ). All elevation input should sit in <u>topographies</u> and must be projected in the correct UTM zone.
   <p>
 
   A header for a CSV file has the format:
-  <table class="code">
-    <tr><td><pre>x,y,elevation</pre></td></tr>
-  </table>
+
+    <pre><font color="brown">
+  x,y,elevation</font></pre>
+
   <p>
 
   An ASC file header has the format:
-  <table class="code">
-    <tr><td><pre>ncols         868
-nrows         856
-xllcorner     418933.86055096
-yllcorner     5151810.6668096
-cellsize      250
-NODATA_value  -9999</pre></td></tr>
-  </table>
+
+    <pre><font color="brown">
+  ncols         868
+  nrows         856
+  xllcorner     418933.86055096
+  yllcorner     5151810.6668096
+  cellsize      250
+  NODATA_value  -9999</font></pre>
+
   <p>
 
   The header of a PRJ file has the format:
-  <table class="code">
-    <tr><td><pre>Projection    UTM
-Zone          55
-Datum         D_GDA_1994
-Zunits        NO
-Units         METERS
-Spheroid      GRS_1980
-Xshift        500000
-Yshift        10000000
-Parameters</pre></td></tr>
-  </table>
-  <p>
-
-  The elevation filenames must be listed in either <b>point_filenames</b> or <b>ascii_grid_filenames</b>
+
+    <pre><font color="brown">
+  Projection    UTM
+  Zone          56
+  Datum         D_GDA_1994
+  Zunits        NO
+  Units         METERS
+  Spheroid      GRS_1980
+  Xshift        500000
+  Yshift        10000000
+  Parameters</font></pre>
+
+  <p>
+
+  The elevation filenames in <font color="red">project.py</font> must be listed in either <b>point_filenames</b> or <b>ascii_grid_filenames</b>
   depending on their format. Point files need to have their extension shown however the ascii grid files have the .asc extension assumed:
-  <table class="code">
-    <tr><td><pre>point_filenames = ['SD100031996_jgriffin_clip.csv',
-                   'tomaga_offshore_AHD_MGA_1997.csv',
-                   'Batemans_BBHD_MGA_1995.csv',
-                   'moruya_AHD_MGA_2000.csv']
-
-ascii_grid_filenames = ['sd100031996_p',
-                        'sd100031996_p2',
-                        'sd100031996_p3',
-                        'sd100031996_p4']</pre></td></tr>
-  </table>
+
+    <pre><font color="brown">
+  point_filenames = ['point1.csv',
+                     'point2.csv',
+                     'point3.csv']
+
+  ascii_grid_filenames = ['grid1',
+                          'grid2',
+                          'grid3']</font></pre>
+
   <p>
 
@@ -183,6 +187,39 @@
   <a name="interior_regions"><h4><b>Interior regions</b></h4></a>
 
-  The <b>interior_regions</b> parameter allows you to change the mesh of the model.
+  The user can specify a number of internal polygons within each of which the resolution of the mesh can be specified.
+  Mesh resolution is the maximum allowable area specified for each region, defining the largest area an indivdual
+  triangular element of the mesh can take (and therefore the minimum mesh resolution).
+  These polygons need to be nested within each other with no overlapping edges.
+  <p>
+  The <b>interior regions</b> can be changed in the <font color="red">project.py</font> script under INTERIOR REGIONS.
+  Interior regions can be read as either seperate CSV files for each polygon displayed as a listed paired with its
+  resolution and/or one CSV file for all polygons, where its resolution is defined within the csv under 'id'.
+  All file inputs should sit in <u>polygons</u> and must be projected in the correct UTM zone.
+  <p>
+  The format for a CSV file with ONE polygon has the format:
+  <pre><font color="brown">
+  easting,northing  </font><font color="black"> Note: NO Header  </font></pre>
+
+
+  The header for a CSV file with MANY polygons has the format:
+  <pre><font color="brown">
+  easting,northing,id,value</font></pre>
+  <p>
+  Where id = polygon number and value = maximum allowable area.
+  <p>
+  The <font color="red">project.py</font> script for this section looks like this:
+
+
+  <pre><font color="brown">
+  interior_regions_list = [['aos1.csv', 1500],
+                           ['aos2.csv', 1500],
+                           ['sw.csv', 30000]]
+  interior_regions_multiple_csv = 'PriorityAreas.csv'</font></pre>
+
+  <p>
+
+  For further information on ANUGA file formats please see the ANUGA User Manual, section 5.1.
   <p>
 </body>
 </html>
+
