| 1 | """Script for running a tsunami inundation scenario for Sydney, NSW, Australia. |
|---|
| 2 | |
|---|
| 3 | Source data such as elevation and boundary data is assumed to be available in |
|---|
| 4 | directories specified by project.py |
|---|
| 5 | The output sww file is stored in project.outputdir |
|---|
| 6 | |
|---|
| 7 | The scenario is defined by a triangular mesh created from project.polygon, |
|---|
| 8 | the elevation data and a simulated submarine landslide. |
|---|
| 9 | |
|---|
| 10 | Ole Nielsen and Duncan Gray, GA - 2005 and Adrian Hitchman and Jane Sexton, GA - 2006 |
|---|
| 11 | """ |
|---|
| 12 | |
|---|
| 13 | |
|---|
| 14 | #-------------------------------------------------------------------------------# Import necessary modules |
|---|
| 15 | #------------------------------------------------------------------------------- |
|---|
| 16 | |
|---|
| 17 | # Standard modules |
|---|
| 18 | import os |
|---|
| 19 | import time |
|---|
| 20 | |
|---|
| 21 | # Related major packages |
|---|
| 22 | from pyvolution.shallow_water import Domain, Reflective_boundary, Time_boundary, Dirichlet_boundary |
|---|
| 23 | from pyvolution.data_manager import convert_dem_from_ascii2netcdf, dem2pts |
|---|
| 24 | from pyvolution.combine_pts import combine_rectangular_points_files |
|---|
| 25 | from pyvolution.pmesh2domain import pmesh_to_domain_instance |
|---|
| 26 | from pyvolution.quantity import Quantity |
|---|
| 27 | from geospatial_data import * |
|---|
| 28 | from utilities.polygon import inside_polygon |
|---|
| 29 | from Numeric import allclose |
|---|
| 30 | |
|---|
| 31 | # Application specific imports |
|---|
| 32 | import project # Definition of file names and polygons |
|---|
| 33 | from smf import slump_tsunami # Function for submarine mudslide |
|---|
| 34 | |
|---|
| 35 | |
|---|
| 36 | #------------------------------------------------------------------------------- |
|---|
| 37 | # Preparation of topographic data |
|---|
| 38 | # |
|---|
| 39 | # Convert ASC 2 DEM 2 PTS using source data and store result in source data |
|---|
| 40 | # Do for coarse and fine data |
|---|
| 41 | # Fine pts file to be clipped to area of interest |
|---|
| 42 | #------------------------------------------------------------------------------- |
|---|
| 43 | # filenames |
|---|
| 44 | coarsedemname = project.coarsedemname |
|---|
| 45 | finedemname = project.finedemname |
|---|
| 46 | |
|---|
| 47 | |
|---|
| 48 | # coarse data |
|---|
| 49 | convert_dem_from_ascii2netcdf(coarsedemname, use_cache=True, verbose=True) |
|---|
| 50 | #dem2pts(coarsedemname, use_cache=True, verbose=True) |
|---|
| 51 | dem2pts(coarsedemname, |
|---|
| 52 | easting_min=project.eastingmin, |
|---|
| 53 | easting_max=project.eastingmax, |
|---|
| 54 | northing_min=project.northingmin, |
|---|
| 55 | northing_max= project.northingmax, |
|---|
| 56 | use_cache=True, |
|---|
| 57 | verbose=True) |
|---|
| 58 | |
|---|
| 59 | # fine data (clipping the points file to smaller area) |
|---|
| 60 | convert_dem_from_ascii2netcdf(finedemname, use_cache=True, verbose=True) |
|---|
| 61 | dem2pts(finedemname, |
|---|
| 62 | easting_min=project.eastingmin, |
|---|
| 63 | easting_max=project.eastingmax, |
|---|
| 64 | northing_min=project.northingmin, |
|---|
| 65 | northing_max= project.northingmax, |
|---|
| 66 | use_cache=True, |
|---|
| 67 | verbose=True) |
|---|
| 68 | |
|---|
| 69 | |
|---|
| 70 | # combining the coarse and fine data |
|---|
| 71 | combine_rectangular_points_files(project.finedemname + '.pts', |
|---|
| 72 | project.coarsedemname + '.pts', |
|---|
| 73 | project.combineddemname + '.pts') |
|---|
| 74 | |
|---|
| 75 | #------------------------------------------------------------------------------- |
|---|
| 76 | # Create the triangular mesh based on overall clipping polygon with a tagged |
|---|
| 77 | # boundary and interior regions defined in project.py along with |
|---|
| 78 | # resolutions (maximal area of per triangle) for each polygon |
|---|
| 79 | #------------------------------------------------------------------------------- |
|---|
| 80 | #from pmesh.create_mesh import create_mesh_from_regions |
|---|
| 81 | from pmesh.mesh_interface import create_mesh_from_regions |
|---|
| 82 | |
|---|
| 83 | meshname = project.meshname4+'.msh' |
|---|
| 84 | |
|---|
| 85 | interior_res1 = 1000 |
|---|
| 86 | interior_res2 = 1315 |
|---|
| 87 | |
|---|
| 88 | # Read in files containing polygon points (generated by GIS) |
|---|
| 89 | # and construct list of interior polygons into interior_regions. |
|---|
| 90 | |
|---|
| 91 | def get_polygon_from_file(filename): |
|---|
| 92 | """ Function to read in output from GIS determined polygon |
|---|
| 93 | """ |
|---|
| 94 | fid = open(filename) |
|---|
| 95 | lines = fid.readlines() |
|---|
| 96 | fid.close() |
|---|
| 97 | |
|---|
| 98 | polygon = [] |
|---|
| 99 | for line in lines[1:]: |
|---|
| 100 | fields = line.split(',') |
|---|
| 101 | x = float(fields[1]) |
|---|
| 102 | y = float(fields[2]) |
|---|
| 103 | polygon.append([x, y]) |
|---|
| 104 | |
|---|
| 105 | return polygon |
|---|
| 106 | |
|---|
| 107 | num_polygons = 4 |
|---|
| 108 | fileext = '.csv' |
|---|
| 109 | filename = project.polygonptsfile |
|---|
| 110 | |
|---|
| 111 | interior_regions = [] |
|---|
| 112 | bounding_polygon = project.diffpolygonall |
|---|
| 113 | count = 0 |
|---|
| 114 | for p in range(3, num_polygons+1): |
|---|
| 115 | thefilename = filename + str(p) + fileext |
|---|
| 116 | print 'reading in polygon points', thefilename |
|---|
| 117 | interior_polygon = get_polygon_from_file(thefilename) |
|---|
| 118 | interior_regions.append([interior_polygon, interior_res1]) |
|---|
| 119 | n = len(interior_polygon) |
|---|
| 120 | # check interior polygon falls in bounding polygon |
|---|
| 121 | if len(inside_polygon(interior_polygon, bounding_polygon, |
|---|
| 122 | closed = True, verbose = False)) <> len(interior_polygon): |
|---|
| 123 | print 'WARNING: interior polygon %d is outside bounding polygon' %(p) |
|---|
| 124 | count += 1 |
|---|
| 125 | # check for duplicate points in interior polygon |
|---|
| 126 | |
|---|
| 127 | print 'number of interior polygons: ', len(interior_regions) |
|---|
| 128 | if count == 0: print 'interior polygons OK' |
|---|
| 129 | |
|---|
| 130 | # original |
|---|
| 131 | #interior_regions = [] |
|---|
| 132 | #interior_regions = [[project.harbour_polygon_2, interior_res1], |
|---|
| 133 | # [project.botanybay_polygon_2, interior_res1]] |
|---|
| 134 | |
|---|
| 135 | # finer set |
|---|
| 136 | #interior_regions = [[project.newpoly1, interior_res1], |
|---|
| 137 | # #[project.parrariver, interior_res1], #remove for second run |
|---|
| 138 | # [project.south1, interior_res1], |
|---|
| 139 | # [project.finepolymanly, interior_res2], |
|---|
| 140 | # [project.finepolyquay, interior_res2]] |
|---|
| 141 | |
|---|
| 142 | |
|---|
| 143 | #FIXME: Fix caching of this one once the mesh_interface is ready |
|---|
| 144 | from caching import cache |
|---|
| 145 | |
|---|
| 146 | |
|---|
| 147 | #_ = cache(create_mesh_from_regions, |
|---|
| 148 | # project.diffpolygonall, |
|---|
| 149 | # {'boundary_tags': {'bottom': [0], |
|---|
| 150 | # 'right1': [1], 'right0': [2], |
|---|
| 151 | # 'right2': [3], 'top': [4], 'left1': [5], |
|---|
| 152 | # 'left2': [6], 'left3': [7]}, |
|---|
| 153 | # 'maximum_triangle_area': 150000, |
|---|
| 154 | # 'filename': meshname, |
|---|
| 155 | # 'interior_regions': interior_regions}, |
|---|
| 156 | # verbose = True) |
|---|
| 157 | |
|---|
| 158 | # for demo construction |
|---|
| 159 | _ = cache(create_mesh_from_regions, |
|---|
| 160 | project.demopoly, |
|---|
| 161 | {'boundary_tags': {'bottom': [0], 'right': [1], |
|---|
| 162 | 'top': [2], 'left': [3]}, |
|---|
| 163 | 'maximum_triangle_area': 100000, |
|---|
| 164 | 'filename': meshname, |
|---|
| 165 | 'interior_regions': interior_regions}, |
|---|
| 166 | verbose = True) |
|---|
| 167 | |
|---|
| 168 | #mesh_geo_reference: |
|---|
| 169 | #------------------------------------------------------------------------------- |
|---|
| 170 | # Setup computational domain |
|---|
| 171 | #------------------------------------------------------------------------------- |
|---|
| 172 | |
|---|
| 173 | domain = pmesh_to_domain_instance(meshname, Domain, |
|---|
| 174 | use_cache = True, |
|---|
| 175 | verbose = True) |
|---|
| 176 | |
|---|
| 177 | print 'Number of triangles = ', len(domain) |
|---|
| 178 | print 'The extent is ', domain.get_extent() |
|---|
| 179 | print domain.statistics() |
|---|
| 180 | |
|---|
| 181 | domain.set_name(project.basename4) |
|---|
| 182 | domain.set_datadir(project.outputdir) |
|---|
| 183 | domain.set_quantities_to_be_stored(['stage', 'xmomentum', 'ymomentum']) |
|---|
| 184 | |
|---|
| 185 | |
|---|
| 186 | #------------------------------------------------------------------------------- |
|---|
| 187 | # Set up scenario (tsunami_source is a callable object used with set_quantity) |
|---|
| 188 | #------------------------------------------------------------------------------- |
|---|
| 189 | |
|---|
| 190 | tsunami_source = slump_tsunami(length=30000.0, |
|---|
| 191 | depth=400.0, |
|---|
| 192 | slope=6.0, |
|---|
| 193 | thickness=176.0, |
|---|
| 194 | radius=3330, |
|---|
| 195 | dphi=0.23, |
|---|
| 196 | x0=project.slump_origin[0], |
|---|
| 197 | y0=project.slump_origin[1], |
|---|
| 198 | alpha=0.0, |
|---|
| 199 | domain=domain) |
|---|
| 200 | |
|---|
| 201 | #------------------------------------------------------------------------------- |
|---|
| 202 | # Setup initial conditions |
|---|
| 203 | #------------------------------------------------------------------------------- |
|---|
| 204 | |
|---|
| 205 | G = Geospatial_data(project.test_pts, project.test_elev) #points, attributes |
|---|
| 206 | domain.set_quantity('stage', 0) #tsunami_source) |
|---|
| 207 | domain.set_quantity('friction', 0.0) # supplied by Benfield, initial value 0.03 |
|---|
| 208 | domain.set_quantity('elevation', |
|---|
| 209 | filename = project.coarsedemname + '.pts', |
|---|
| 210 | use_cache = True, |
|---|
| 211 | verbose = True) |
|---|
| 212 | |
|---|
| 213 | from pyvolution.least_squares import fit_to_mesh_file, DEFAULT_ALPHA |
|---|
| 214 | |
|---|
| 215 | #Add elevation data to the mesh |
|---|
| 216 | #fit_to_mesh_file(mesh_file, point_file, mesh_output_file, DEFAULT_ALPHA, |
|---|
| 217 | # verbose=True, expand_search=True, precrop=True) |
|---|
| 218 | #pointname = project.coarsedemname + '.pts' |
|---|
| 219 | #mesh_elevname = project.meshelevname |
|---|
| 220 | #cache(fit_to_mesh_file,(meshname, |
|---|
| 221 | # pointname, |
|---|
| 222 | # mesh_elevname, |
|---|
| 223 | # DEFAULT_ALPHA), |
|---|
| 224 | # {'verbose': True, |
|---|
| 225 | # 'expand_search': True, |
|---|
| 226 | # 'precrop': True} |
|---|
| 227 | # ,dependencies = [meshname, pointname] |
|---|
| 228 | # #,evaluate = True |
|---|
| 229 | # ,verbose = False |
|---|
| 230 | # ) |
|---|
| 231 | |
|---|
| 232 | #------------------------------------------------------------------------------- |
|---|
| 233 | # Setup boundary conditions (all reflective) |
|---|
| 234 | #------------------------------------------------------------------------------- |
|---|
| 235 | |
|---|
| 236 | print 'Available boundary tags', domain.get_boundary_tags() |
|---|
| 237 | |
|---|
| 238 | Br = Reflective_boundary(domain) |
|---|
| 239 | Bd = Dirichlet_boundary([0, 0, 0]) |
|---|
| 240 | |
|---|
| 241 | # for demo |
|---|
| 242 | domain.set_boundary( {'bottom': Bd, 'right': Bd, 'left': Bd, 'top': Bd} ) |
|---|
| 243 | #domain.set_boundary( {'bottom': Br, 'right1': Br, 'right0': Br, |
|---|
| 244 | # 'right2': Br, 'top': Br, 'left1': Br, |
|---|
| 245 | # 'left2': Br, 'left3': Br} ) |
|---|
| 246 | |
|---|
| 247 | |
|---|
| 248 | #------------------------------------------------------------------------------- |
|---|
| 249 | # Evolve system through time |
|---|
| 250 | #------------------------------------------------------------------------------- |
|---|
| 251 | |
|---|
| 252 | import time |
|---|
| 253 | t0 = time.time() |
|---|
| 254 | thisfile = project.integraltimeseries+'.csv' |
|---|
| 255 | fid = open(thisfile, 'w') |
|---|
| 256 | |
|---|
| 257 | for t in domain.evolve(yieldstep = 10, finaltime = 600): |
|---|
| 258 | domain.write_time() |
|---|
| 259 | domain.write_boundary_statistics(tags = 'bottom') |
|---|
| 260 | stagestep = domain.get_quantity('stage') |
|---|
| 261 | s = '%.2f, %.2f\n' %(t, stagestep.get_integral()) |
|---|
| 262 | fid.write(s) |
|---|
| 263 | if allclose(t, 30): |
|---|
| 264 | slump = Quantity(domain) |
|---|
| 265 | slump.set_values(tsunami_source) |
|---|
| 266 | domain.set_quantity('stage', slump + stagestep) |
|---|
| 267 | |
|---|
| 268 | # save every two minutes leading up to interesting period |
|---|
| 269 | for t in domain.evolve(yieldstep = 120, finaltime = 660, # steps |
|---|
| 270 | skip_initial_step = True): |
|---|
| 271 | domain.write_time() |
|---|
| 272 | domain.write_boundary_statistics(tags = 'bottom') |
|---|
| 273 | # calculate integral |
|---|
| 274 | thisstagestep = domain.get_quantity('stage') |
|---|
| 275 | s = '%.2f, %.2f\n' %(t, thisstagestep.get_integral()) |
|---|
| 276 | fid.write(s) |
|---|
| 277 | |
|---|
| 278 | # save every thirty secs during interesting period |
|---|
| 279 | for t in domain.evolve(yieldstep = 30, finaltime = 3500, # steps |
|---|
| 280 | skip_initial_step = True): |
|---|
| 281 | domain.write_time() |
|---|
| 282 | domain.write_boundary_statistics(tags = 'bottom') #quantities = 'stage') |
|---|
| 283 | # calculate integral |
|---|
| 284 | thisstagestep = domain.get_quantity('stage') |
|---|
| 285 | s = '%.2f, %.2f\n' %(t, thisstagestep.get_integral()) |
|---|
| 286 | fid.write(s) |
|---|
| 287 | |
|---|
| 288 | # save every two mins for next 5000 secs |
|---|
| 289 | for t in domain.evolve(yieldstep = 120, finaltime = 10000, # about 42 steps |
|---|
| 290 | skip_initial_step = True): |
|---|
| 291 | domain.write_time() |
|---|
| 292 | domain.write_boundary_statistics(tags = 'bottom') #quantities = 'stage') |
|---|
| 293 | # calculate integral |
|---|
| 294 | thisstagestep = domain.get_quantity('stage') |
|---|
| 295 | s = '%.2f, %.2f\n' %(t, thisstagestep.get_integral()) |
|---|
| 296 | fid.write(s) |
|---|
| 297 | |
|---|
| 298 | # save every half hour to end of simulation |
|---|
| 299 | for t in domain.evolve(yieldstep = 1800, finaltime = 10*60*60, # 14 steps |
|---|
| 300 | skip_initial_step = True): |
|---|
| 301 | domain.write_time() |
|---|
| 302 | domain.write_boundary_statistics(tags = 'bottom') #quantities = 'stage' |
|---|
| 303 | # calculate integral |
|---|
| 304 | thisstagestep = domain.get_quantity('stage') |
|---|
| 305 | s = '%.2f, %.2f\n' %(t, thisstagestep.get_integral()) |
|---|
| 306 | fid.write(s) |
|---|
| 307 | |
|---|
| 308 | print 'That took %.2f seconds' %(time.time()-t0) |
|---|
| 309 | |
|---|
| 310 | |
|---|
| 311 | |
|---|
