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11      <td>
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15        &nbsp;
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17      <td>
18        <H1>Tsunami Modelling Methodology Validation: GERALDTON</H1>
19      </td>
20    </tr>
21  </table>
22  <hr>
23
24  <a name="modifications"><h2><b>Modifying a simulation</b></h2></a>
25
26  Here we talk about how to change the simulation.  Reasons for modifying the simulation include the availability of
27  better elevation data, or a desire to run the simulation on a finer mesh in certain areas.
28  <p>
29  First we describe the usage of the script files you might change, then we walk through a few examples
30  of changes you might make.
31  <p>
32
33  <a name="project_files"><h3><b>The project scripts</b></h3></a>
34
35  In the <b>project</b> directory are the scripts that control the simulation.  These scripts are:
36  <table class="code">
37    <tr><td><font color="red">project.py</font></td><td>Defines the input data used, where to place output, etc.</td></tr>
38    <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>
39    <tr><td><font color="red">setup_model.py</font></td><td>Prepares the simulation before actually running it</td></tr>
40    <tr><td><font color="red">run_model.py</font></td><td>Runs the simulation</td></tr>
41  </table>
42
43  <a name="project.py"><h4><b>project.py</b></h4></a>
44
45    This file is the heart of the simulation. The project script introduces all files that are necessary to run all accompanying scripts.
46    By changing one of the variables in this script the output could be completely different.
47    For further details on changing parameters see <a href="#change">Making changes to a simulation</a>.
48
49  <a name="build_elevation.py"><h4><b>build_elevation.py</b></h4></a>
50
51  This script combines all input elevation files into a single elevation point file (PTS file).
52  We have provided you with the PTS file used to create the outputs on this DVD.
53  If you would like to change the elevation, see <a href="#change">Making changes to a simulation</a>.
54  <p>
55
56  <a name="setup_model.py"><h4><b>setup_model.py</b></h4></a>
57
58  This script is used to transform data into a specific format for <font color="red">run_model.py</font>,
59  if required, and to generate warning messages if you are missing data.
60  <p>
61
62  <a name="run_model.py"><h4><b>run_model.py</b></h4></a>
63
64  This script runs a tsunami inundation scenario.  It relies on the parameters set in <font color="red">project.py</font>
65  as well as the elevation and event input files (PTS and STS files respectively).
66  An STS file has been generated for each event listed in the <u>boundaries</u> directory. For further details on events see
67  <a href="#change">Making changes to a simulation</a>.
68  <p>
69
70  <a name="change"><h3><b>Making changes to a simulation</b></h3></a>
71
72  There are many parameters that you can change within the <font color="red">project.py</font> script,
73  but the following four parameters are those most commonly changed.
74  <p>
75
76  <a name="output"><h4><b>Output Folder Name</b></h4></a>
77
78  The <b>output folder name</b> should be unique between different runs on different data.
79  The list of items below will be used to create the folder in your <u>output</u> directory.
80  Your user name and time+date will be automatically added.  For example,
81  <pre><font color="brown">
82  output_comments = [setup, tide, event_number]</font></pre>
83  will result in a folder name like
84  <pre><font color="brown">
85  20090212_091046_run_final_0_27283_rwilson</font>
86Where 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>,
87<b>tide</b> = <u>0</u>, <b>event_number</b> = <u>27283</u>  - refer below for more information on these parameters </pre>
88  <p>
89  You can also add strings to this list
90  <pre><font color="brown">
91  output_comments = [setup, tide, event_number, 'large']</font></pre>
92  will result in a folder name like
93  <pre><font color="brown">
94  20090212_091046_run_final_0_27283_large_rwilson</font></pre>
95  <p>
96  <p>
97    <a name="setup"><h4><b>Setup</b></h4></a>
98
99  The <b>setup</b> parameter determines the type of run. This can be one of three values:
100  <pre><font color="brown">
101  'trial' <font color="black">- coarsest mesh, fast </font>
102  'basic' <font color="black">- coarse mesh</font>
103  'final' <font color="black">- fine mesh, slowest</font>
104  </pre></font>
105  Note: <b>'final'</b> must be used if determining the best estimate of inundation for your area of interest.
106  <p>
107  <a name="tide"><h4><b>Tide</b></h4></a>
108
109  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
110  the initial water level will be at Mean Sea Level.  If you increase the <b>tide</b> value the water level will become deeper.
111  This setting will also increase non tidal lakes and rivers inside the model.  To compensate a mask is used on land called
112  <b>initial conditions</b> which brings the internal water bodies back to 0.  Please note that within ANUGA the <b>tide</b> is modelled as a constant
113  change in sea level and does not vary with time.
114  <p>
115
116  <a name="elevation"><h4><b>Elevation</b></h4></a>
117
118  Elevation data can be changed in the <font color="red">project.py</font> script under ELEVATION DATA.
119  Elevation data can be read as either a point file, comma delimited, or as an ASCII grid file
120  (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.
121  <p>
122
123  A header for a CSV file has the format:
124
125    <pre><font color="brown">
126  x,y,elevation</font></pre>
127
128  <p>
129
130  An ASC file header has the format:
131
132    <pre><font color="brown">
133  ncols         868
134  nrows         856
135  xllcorner     418933.86055096
136  yllcorner     5151810.6668096
137  cellsize      250
138  NODATA_value  -9999</font></pre>
139
140  <p>
141
142  The header of a PRJ file has the format:
143
144    <pre><font color="brown">
145  Projection    UTM
146  Zone          56
147  Datum         D_GDA_1994
148  Zunits        NO
149  Units         METERS
150  Spheroid      GRS_1980
151  Xshift        500000
152  Yshift        10000000
153  Parameters</font></pre>
154
155  <p>
156
157  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>
158  depending on their format. Point files need to have their extension shown however the ascii grid files have the .asc extension assumed:
159
160    <pre><font color="brown">
161  point_filenames = ['point1.csv',
162                     'point2.csv',
163                     'point3.csv']
164
165  ascii_grid_filenames = ['grid1',
166                          'grid2',
167                          'grid3']</font></pre>
168
169  <p>
170
171  For further information on ANUGA file formats please see the ANUGA User Manual, section 6.1.
172  <p>
173
174  <a name="interior_regions"><h4><b>Interior regions</b></h4></a>
175
176  The user can specify a number of internal polygons within each of which the resolution of the mesh can be specified.
177  Mesh resolution is the maximum allowable area specified for each region, defining the largest area an individual
178  triangular element of the mesh can take (and therefore the minimum mesh resolution).
179  These polygons need to be nested within each other with no overlapping edges.
180  <p>
181  The <b>interior regions</b> can be changed in the <font color="red">project.py</font> script under INTERIOR REGIONS.
182  Interior regions can be read as either seperate CSV files for each polygon displayed as a listed paired with its
183  resolution and/or one CSV file for all polygons, where its resolution is defined within the csv under 'id'.
184  All file inputs should sit in <u>polygons</u> and must be projected in the correct UTM zone.
185  <p>
186  The format for a CSV file with ONE polygon has the format:
187  <pre><font color="brown">
188  easting,northing  </font><font color="black"> Note: NO Header  </font></pre>
189
190
191  The header for a CSV file with MANY polygons has the format:
192  <pre><font color="brown">
193  easting,northing,id,value</font></pre>
194  <p>
195  Where id = polygon number and value = maximum allowable area.
196  <p>
197  The <font color="red">project.py</font> script for this section looks like this:
198
199
200  <pre><font color="brown">
201  interior_regions_list = [['aos1.csv', 1500],
202                           ['aos2.csv', 1500],
203                           ['sw.csv', 30000]]
204  interior_regions_multiple_csv = 'PriorityAreas.csv'</font></pre>
205
206  <p>
207
208  For further information on ANUGA file formats please see the ANUGA User Manual, section 5.1.
209  <p>
210 
211    <a name="Mux_files"><h4><b>Obtaining time series of the offshore tsunami wave for other locations</b></h4></a> 
212 
213  Mux files containing time series of the tsunami wave at points along the 100 m depth contour around Western Australia were obtained from the URSGA model.
214  These time series form the seaward boundary condition for the ANUGA inundation model. To run an ANUGA simulation for a different area, tsunami time series for points
215  offshore the location of interest must be extracted and reformatted into netCDF (.sts) format from the mux files. This is handled by the <font color="red">build_urs_boundary.py</font> script, which is
216  called from within <font color="red">run_model.py</font>.
217  The points for which the time series are extracted are defined within the file <a href="data/western_australia/geraldton_tsunami_scenario/anuga/boundaries">urs_order.csv</a>.
218  This file must be modified as follows to run a model for a different area.
219  <p>
220  The file <a href="data/western_australia/geraldton_tsunami_scenario/anuga/boundaries">USRGA_gauges_all_WA.csv</a> contains a list of all the points for which timeseries exist within the mux files. This file can be loaded into a GIS environment and the points within the model selected.
221  Note that you should only choose approximately every fifth point, keeping the points in as close to a straight line as possible.
222  Choosing points too close to each other can cause problems with fitting the mesh to the model domain.
223  These points should be written into a .csv file in the following format (including header):
224 
225   <pre><font color="brown">
226  index, longitude, latitude</font></pre>
227
228  <p>
229  If the name of this .csv file is changed from urs_order, then this must be updated in <font color="red">project.py</font>
230   <p>
231  <hr>
232   <a rel="license" href="http://creativecommons.org/licenses/by-nc/3.0/"><img alt="Creative Commons License" style="border-width:0" src="http://i.creativecommons.org/l/by-nc/3.0/88x31.png" /></a><br />
233  © Commonwealth of Australia (Geoscience Australia, Department of Transport Western Australia and Landgate) 2010.
234  This material is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc/3.0/">Creative Commons Attribution-Noncommercial
235  3.0 Australia License</a>.   
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