| 1 | """Script for running tsunami inundation scenario for Dampier, WA, Australia. |
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| 2 | |
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| 3 | Source data such as elevation and boundary data is assumed to be available in |
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| 4 | directories specified by project.py |
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| 5 | The output sww file is stored in project.output_run_time_dir |
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| 6 | |
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| 7 | The scenario is defined by a triangular mesh created from project.polygon, |
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| 8 | the elevation data and a simulated tsunami generated with URS code. |
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| 9 | |
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| 10 | Ole Nielsen and Duncan Gray, GA - 2005 and Jane Sexton, Nick Bartzis, GA - 2006 |
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| 11 | """ |
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| 12 | |
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| 13 | #------------------------------------------------------------------------------ |
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| 14 | # Import necessary modules |
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| 15 | #------------------------------------------------------------------------------ |
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| 16 | |
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| 17 | # Standard modules |
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| 18 | from os import sep |
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| 19 | import os |
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| 20 | from os.path import dirname, basename |
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| 21 | from os import mkdir, access, F_OK |
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| 22 | from shutil import copy |
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| 23 | import time |
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| 24 | import sys |
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| 25 | |
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| 26 | # Related major packages |
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| 27 | from anuga.shallow_water import Domain |
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| 28 | from anuga.shallow_water import Dirichlet_boundary |
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| 29 | from anuga.shallow_water import File_boundary |
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| 30 | from anuga.shallow_water import Reflective_boundary |
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| 31 | from anuga.shallow_water import Field_boundary |
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| 32 | from Numeric import allclose |
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| 33 | from anuga.shallow_water.data_manager import export_grid, create_sts_boundary |
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| 34 | |
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| 35 | from anuga.pmesh.mesh_interface import create_mesh_from_regions |
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| 36 | from anuga.shallow_water.data_manager import start_screen_catcher, copy_code_files,store_parameters |
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| 37 | #from anuga_parallel.parallel_api import distribute, numprocs, myid, barrier |
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| 38 | from anuga_parallel.parallel_abstraction import get_processor_name |
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| 39 | from anuga.caching import myhash |
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| 40 | from anuga.damage_modelling.inundation_damage import add_depth_and_momentum2csv, inundation_damage |
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| 41 | from anuga.fit_interpolate.benchmark_least_squares import mem_usage |
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| 42 | from anuga.utilities.polygon import read_polygon, plot_polygons, polygon_area, is_inside_polygon |
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| 43 | from anuga.geospatial_data.geospatial_data import find_optimal_smoothing_parameter |
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| 44 | from Scientific.IO.NetCDF import NetCDFFile |
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| 45 | |
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| 46 | # Application specific imports |
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| 47 | import project # Definition of file names and polygons |
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| 48 | numprocs = 1 |
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| 49 | myid = 0 |
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| 50 | |
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| 51 | def run_model(**kwargs): |
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| 52 | |
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| 53 | |
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| 54 | #------------------------------------------------------------------------------ |
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| 55 | # Copy scripts to time stamped output directory and capture screen |
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| 56 | # output to file |
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| 57 | #------------------------------------------------------------------------------ |
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| 58 | print "Processor Name:",get_processor_name() |
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| 59 | |
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| 60 | #copy script must be before screen_catcher |
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| 61 | #print kwargs |
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| 62 | |
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| 63 | print 'output_dir',kwargs['output_dir'] |
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| 64 | if myid == 0: |
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| 65 | copy_code_files(kwargs['output_dir'],__file__, |
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| 66 | dirname(project.__file__)+sep+ project.__name__+'.py' ) |
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| 67 | |
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| 68 | store_parameters(**kwargs) |
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| 69 | |
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| 70 | # barrier() |
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| 71 | |
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| 72 | start_screen_catcher(kwargs['output_dir'], myid, numprocs) |
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| 73 | |
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| 74 | print "Processor Name:",get_processor_name() |
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| 75 | |
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| 76 | |
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| 77 | #----------------------------------------------------------------------- |
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| 78 | # Domain definitions |
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| 79 | #----------------------------------------------------------------------- |
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| 80 | |
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| 81 | # Read in boundary from ordered sts file |
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| 82 | urs_bounding_polygon=create_sts_boundary(os.path.join(project.boundaries_dir,project.scenario_name)) |
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| 83 | |
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| 84 | # Reading the landward defined points, this incorporates the original clipping |
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| 85 | # polygon minus the 100m contour |
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| 86 | landward_bounding_polygon = read_polygon(project.polygons_dir+'landward_bounding_polygon.txt') |
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| 87 | |
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| 88 | # Combine sts polyline with landward points |
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| 89 | bounding_polygon = urs_bounding_polygon + landward_bounding_polygon |
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| 90 | |
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| 91 | # counting segments |
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| 92 | N = len(urs_bounding_polygon)-1 |
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| 93 | boundary_tags={'back': [N+1,N+2,N+3], 'side': [N,N+4],'ocean': range(N)} |
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| 94 | |
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| 95 | |
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| 96 | #-------------------------------------------------------------------------- |
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| 97 | # Create the triangular mesh based on overall clipping polygon with a |
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| 98 | # tagged |
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| 99 | # boundary and interior regions defined in project.py along with |
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| 100 | # resolutions (maximal area of per triangle) for each polygon |
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| 101 | #-------------------------------------------------------------------------- |
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| 102 | |
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| 103 | #IMPORTANT don't cache create_mesh_from_region and Domain(mesh....) as it |
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| 104 | # causes problems with the ability to cache set quantity which takes alot of times |
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| 105 | if myid == 0: |
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| 106 | |
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| 107 | print 'start create mesh from regions' |
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| 108 | |
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| 109 | create_mesh_from_regions(bounding_polygon, |
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| 110 | boundary_tags=boundary_tags, |
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| 111 | maximum_triangle_area=project.res_poly_all, |
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| 112 | interior_regions=project.interior_regions, |
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| 113 | filename=project.meshes_dir_name+'.msh', |
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| 114 | use_cache=True, |
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| 115 | verbose=True) |
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| 116 | # barrier() |
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| 117 | |
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| 118 | ## covariance_value,alpha = find_optimal_smoothing_parameter (data_file= kwargs['elevation_file'], |
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| 119 | ## alpha_list=[0.001, 0.01, 0.1, 0.15, 0.2, 0.25, 0.3, 0.4, 0.5], |
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| 120 | ## mesh_file = project.meshes_dir_name+'.msh') |
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| 121 | ## print 'optimal alpha', covariance_value,alpha |
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| 122 | |
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| 123 | #------------------------------------------------------------------------- |
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| 124 | # Setup computational domain |
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| 125 | #------------------------------------------------------------------------- |
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| 126 | print 'Setup computational domain' |
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| 127 | |
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| 128 | domain = Domain(project.meshes_dir_name+'.msh', use_cache=False, verbose=True) |
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| 129 | print 'memory usage before del domain',mem_usage() |
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| 130 | |
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| 131 | print domain.statistics() |
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| 132 | print 'triangles',len(domain) |
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| 133 | |
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| 134 | kwargs['act_num_trigs']=len(domain) |
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| 135 | |
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| 136 | |
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| 137 | #------------------------------------------------------------------------- |
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| 138 | # Setup initial conditions |
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| 139 | #------------------------------------------------------------------------- |
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| 140 | if myid == 0: |
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| 141 | |
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| 142 | print 'Setup initial conditions' |
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| 143 | |
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| 144 | from polygon import Polygon_function |
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| 145 | #following sets the stage/water to be offcoast only |
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| 146 | IC = Polygon_function( [(project.poly_mainland, 0)], default = kwargs['tide'], |
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| 147 | geo_reference = domain.geo_reference) |
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| 148 | domain.set_quantity('stage', IC) |
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| 149 | #domain.set_quantity('stage',kwargs['tide'] ) |
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| 150 | domain.set_quantity('friction', kwargs['friction']) |
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| 151 | |
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| 152 | print 'Start Set quantity',kwargs['elevation_file'] |
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| 153 | |
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| 154 | domain.set_quantity('elevation', |
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| 155 | filename = kwargs['elevation_file'], |
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| 156 | use_cache = False, |
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| 157 | verbose = True, |
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| 158 | alpha = kwargs['alpha']) |
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| 159 | print 'Finished Set quantity' |
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| 160 | #barrier() |
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| 161 | |
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| 162 | ## #------------------------------------------------------ |
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| 163 | ## # Create x,y,z file of mesh vertex!!! |
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| 164 | ## #------------------------------------------------------ |
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| 165 | ## coord = domain.get_vertex_coordinates() |
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| 166 | ## depth = domain.get_quantity('elevation') |
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| 167 | ## |
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| 168 | ## # Write vertex coordinates to file |
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| 169 | ## filename=project.vertex_filename |
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| 170 | ## fid=open(filename,'w') |
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| 171 | ## fid.write('x (m), y (m), z(m)\n') |
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| 172 | ## for i in range(len(coord)): |
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| 173 | ## pt=coord[i] |
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| 174 | ## x=pt[0] |
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| 175 | ## y=pt[1] |
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| 176 | ## z=depth[i] |
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| 177 | ## fid.write('%.6f,%.6f,%.6f\n' %(x, y, z)) |
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| 178 | ## |
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| 179 | |
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| 180 | #------------------------------------------------------ |
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| 181 | # Distribute domain to implement parallelism !!! |
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| 182 | #------------------------------------------------------ |
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| 183 | |
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| 184 | if numprocs > 1: |
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| 185 | domain=distribute(domain) |
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| 186 | |
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| 187 | #------------------------------------------------------ |
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| 188 | # Set domain parameters |
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| 189 | #------------------------------------------------------ |
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| 190 | print 'domain id', id(domain) |
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| 191 | domain.set_name(kwargs['aa_scenario_name']) |
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| 192 | domain.set_datadir(kwargs['output_dir']) |
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| 193 | domain.set_default_order(2) # Apply second order scheme |
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| 194 | domain.set_minimum_storable_height(0.01) # Don't store anything less than 1cm |
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| 195 | domain.set_store_vertices_uniquely(False) |
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| 196 | domain.set_quantities_to_be_stored(['stage', 'xmomentum', 'ymomentum']) |
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| 197 | domain.tight_slope_limiters = 1 |
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| 198 | print 'domain id', id(domain) |
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| 199 | |
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| 200 | #------------------------------------------------------------------------- |
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| 201 | # Setup boundary conditions |
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| 202 | #------------------------------------------------------------------------- |
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| 203 | print 'Available boundary tags', domain.get_boundary_tags() |
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| 204 | print 'domain id', id(domain) |
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| 205 | |
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| 206 | boundary_urs_out=project.boundaries_dir_name |
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| 207 | |
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| 208 | print 'Available boundary tags', domain.get_boundary_tags() |
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| 209 | Bf = Field_boundary(boundary_urs_out+'.sts', # Change from file_boundary |
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| 210 | domain, mean_stage= project.tide, |
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| 211 | time_thinning=1, |
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| 212 | use_cache=True, |
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| 213 | verbose = True, |
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| 214 | boundary_polygon=bounding_polygon) |
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| 215 | |
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| 216 | |
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| 217 | Br = Reflective_boundary(domain) |
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| 218 | Bd = Dirichlet_boundary([kwargs['tide'],0,0]) |
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| 219 | |
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| 220 | fid = NetCDFFile(boundary_urs_out+'.sts', 'r') #Open existing file for read |
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| 221 | sts_time=fid.variables['time'][:]+fid.starttime |
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| 222 | tmin=min(sts_time) |
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| 223 | tmax=max(sts_time) |
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| 224 | fid.close() |
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| 225 | |
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| 226 | print 'Boundary end time ', tmax-tmin |
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| 227 | |
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| 228 | ## Bf = Field_boundary(kwargs['boundary_file'], |
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| 229 | ## domain, time_thinning=kwargs['time_thinning'], mean_stage=kwargs['tide'], |
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| 230 | ## use_cache=False, verbose=True) |
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| 231 | |
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| 232 | domain.set_boundary({'back': Br, |
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| 233 | 'side': Bd, |
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| 234 | 'ocean': Bf}) |
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| 235 | |
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| 236 | kwargs['input_start_time']=domain.starttime |
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| 237 | |
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| 238 | print'finish set boundary' |
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| 239 | |
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| 240 | #---------------------------------------------------------------------------- |
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| 241 | # Evolve system through time |
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| 242 | #-------------------------------------------------------------------- |
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| 243 | t0 = time.time() |
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| 244 | |
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| 245 | for t in domain.evolve(yieldstep = project.yieldstep, finaltime = kwargs['finaltime'] |
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| 246 | ,skip_initial_step = False): |
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| 247 | domain.write_time() |
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| 248 | domain.write_boundary_statistics(tags = 'ocean') |
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| 249 | |
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| 250 | if t >= tmax-tmin: |
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| 251 | print 'changed to tide boundary condition at ocean' |
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| 252 | domain.set_boundary({'ocean': Bd}) |
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| 253 | |
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| 254 | x, y = domain.get_maximum_inundation_location() |
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| 255 | q = domain.get_maximum_inundation_elevation() |
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| 256 | |
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| 257 | print 'Maximum runup observed at (%.2f, %.2f) with elevation %.2f' %(x,y,q) |
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| 258 | |
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| 259 | print 'That took %.2f seconds' %(time.time()-t0) |
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| 260 | |
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| 261 | #kwargs 'completed' must be added to write the final parameters to file |
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| 262 | kwargs['completed']=str(time.time()-t0) |
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| 263 | |
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| 264 | if myid==0: |
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| 265 | store_parameters(**kwargs) |
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| 266 | # barrier |
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| 267 | |
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| 268 | print 'memory usage before del domain1',mem_usage() |
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| 269 | |
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| 270 | |
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| 271 | #------------------------------------------------------------- |
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| 272 | if __name__ == "__main__": |
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| 273 | |
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| 274 | kwargs={} |
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| 275 | kwargs['est_num_trigs']=project.trigs_min |
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| 276 | kwargs['num_cpu']=numprocs |
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| 277 | kwargs['host']=project.host |
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| 278 | kwargs['res_factor']=project.res_factor |
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| 279 | kwargs['starttime']=project.starttime |
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| 280 | kwargs['yieldstep']=project.yieldstep |
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| 281 | kwargs['finaltime']=project.finaltime |
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| 282 | |
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| 283 | kwargs['output_dir']=project.output_run_time_dir |
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| 284 | kwargs['elevation_file']=project.combined_dir_name+'.pts' |
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| 285 | kwargs['boundary_file']=project.boundaries_in_dir_name + '.sww' |
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| 286 | kwargs['file_name']=project.home+'detail.csv' |
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| 287 | kwargs['aa_scenario_name']=project.scenario_name |
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| 288 | kwargs['ab_time']=project.time |
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| 289 | kwargs['res_factor']= project.res_factor |
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| 290 | kwargs['tide']=project.tide |
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| 291 | kwargs['user']=project.user |
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| 292 | kwargs['alpha'] = project.alpha |
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| 293 | kwargs['friction']=project.friction |
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| 294 | kwargs['time_thinning'] = project.time_thinning |
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| 295 | kwargs['dir_comment']=project.dir_comment |
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| 296 | kwargs['export_cellsize']=project.export_cellsize |
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| 297 | |
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| 298 | |
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| 299 | run_model(**kwargs) |
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| 300 | |
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| 301 | if myid==0: |
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| 302 | export_model(**kwargs) |
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| 303 | #barrier |
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