| 1 | """Class Domain - 1D domains for finite-volume computations of |
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| 2 | the shallow water wave equation |
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| 3 | |
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| 4 | |
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| 5 | Copyright 2004 |
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| 6 | Ole Nielsen, Stephen Roberts, Duncan Gray, Christopher Zoppou |
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| 7 | Geoscience Australia |
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| 8 | """ |
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| 9 | |
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| 10 | import numpy |
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| 11 | from generic_boundary_conditions import * |
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| 12 | |
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| 13 | |
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| 14 | class Generic_domain: |
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| 15 | |
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| 16 | def __init__(self, |
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| 17 | coordinates, |
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| 18 | boundary = None, |
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| 19 | conserved_quantities = [], |
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| 20 | evolved_quantities = [], |
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| 21 | other_quantities = [], |
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| 22 | tagged_elements = None): |
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| 23 | """ |
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| 24 | Build 1D elements from x coordinates |
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| 25 | """ |
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| 26 | |
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| 27 | from config import timestepping_method |
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| 28 | from config import CFL |
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| 29 | |
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| 30 | #Store Points |
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| 31 | self.coordinates = numpy.array(coordinates, numpy.float) |
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| 32 | |
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| 33 | |
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| 34 | #Register number of Elements |
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| 35 | self.number_of_elements = N = len(self.coordinates)-1 |
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| 36 | |
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| 37 | self.set_CFL(CFL) |
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| 38 | self.set_timestepping_method(timestepping_method) |
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| 39 | |
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| 40 | |
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| 41 | # work array for special vertices (like wet or dry cells |
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| 42 | self.special_vertices = numpy.zeros((N,2), numpy.int) # should this be here |
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| 43 | |
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| 44 | #Allocate space for neighbour and boundary structures |
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| 45 | self.neighbours = numpy.zeros((N, 2), numpy.int) |
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| 46 | #self.neighbour_edges = numpy.zeros((N, 2), numpy.int) |
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| 47 | self.neighbour_vertices = numpy.zeros((N, 2), numpy.int) |
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| 48 | self.number_of_boundaries = numpy.zeros(N, numpy.int) |
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| 49 | self.surrogate_neighbours = numpy.zeros((N, 2), numpy.int) |
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| 50 | |
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| 51 | #Allocate space for geometric quantities |
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| 52 | self.vertices = numpy.zeros((N, 2), numpy.float) |
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| 53 | self.centroids = numpy.zeros(N, numpy.float) |
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| 54 | self.areas = numpy.zeros(N, numpy.float) |
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| 55 | |
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| 56 | self.max_speed_array = numpy.zeros(N, numpy.float) |
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| 57 | |
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| 58 | |
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| 59 | self.normals = numpy.zeros((N, 2), numpy.float) |
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| 60 | |
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| 61 | |
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| 62 | xl = self.coordinates[0:-1] |
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| 63 | xr = self.coordinates[1: ] |
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| 64 | |
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| 65 | self.vertices[:,0] = xl |
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| 66 | self.vertices[:,1] = xr |
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| 67 | |
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| 68 | self.centroids[:] = (xl+xr)/2.0 |
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| 69 | |
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| 70 | msg = 'Coordinates should be ordered, smallest to largest' |
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| 71 | assert (xr>xl).all(), msg |
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| 72 | |
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| 73 | #The normal vectors |
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| 74 | # - point outward from each edge |
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| 75 | # - are orthogonal to the edge |
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| 76 | # - have unit length |
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| 77 | # - Are enumerated by left vertex then right vertex normals |
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| 78 | |
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| 79 | |
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| 80 | self.normals[:,0] = -1.0 |
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| 81 | self.normals[:,1] = 1.0 |
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| 82 | |
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| 83 | self.areas[:] = (xr-xl) |
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| 84 | |
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| 85 | #Initialise Neighbours (-1 means that it is a boundary neighbour) |
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| 86 | |
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| 87 | self.neighbours[:, :] = -1 |
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| 88 | |
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| 89 | #Initialise edge ids of neighbours |
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| 90 | self.neighbour_vertices[:, :] = -1 |
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| 91 | |
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| 92 | |
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| 93 | # for i in range(N): |
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| 94 | # xl = self.coordinates[i] |
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| 95 | # xr = self.coordinates[i+1] |
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| 96 | # self.vertices[i,0] = xl |
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| 97 | # self.vertices[i,1] = xr |
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| 98 | # |
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| 99 | # centroid = (xl+xr)/2.0 |
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| 100 | # self.centroids[i] = centroid |
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| 101 | # |
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| 102 | # msg = 'Coordinates should be ordered, smallest to largest' |
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| 103 | # assert xr>xl, msg |
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| 104 | # |
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| 105 | # #The normal vectors |
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| 106 | # # - point outward from each edge |
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| 107 | # # - are orthogonal to the edge |
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| 108 | # # - have unit length |
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| 109 | # # - Are enumerated by left vertex then right vertex normals |
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| 110 | # |
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| 111 | # nl = -1.0 |
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| 112 | # nr = 1.0 |
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| 113 | # self.normals[i,:] = [nl, nr] |
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| 114 | # |
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| 115 | # self.areas[i] = (xr-xl) |
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| 116 | # |
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| 117 | ## # print 'N', N |
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| 118 | ## # print 'Centroid', self.centroids |
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| 119 | ## # print 'Areas', self.areas |
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| 120 | ## # print 'Vertex_Coordinates', self.vertices |
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| 121 | # |
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| 122 | # #Initialise Neighbours (-1 means that it is a boundary neighbour) |
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| 123 | # self.neighbours[i, :] = [-1, -1] |
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| 124 | # #Initialise edge ids of neighbours |
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| 125 | # #Initialise vertex ids of neighbours |
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| 126 | # #In case of boundaries this slot is not used |
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| 127 | # #self.neighbour_edges[i, :] = [-1, -1] |
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| 128 | # self.neighbour_vertices[i, :] = [-1, -1] |
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| 129 | |
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| 130 | self.build_vertexlist() |
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| 131 | |
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| 132 | #Build neighbour structure |
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| 133 | self.build_neighbour_structure() |
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| 134 | |
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| 135 | #Build surrogate neighbour structure |
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| 136 | self.build_surrogate_neighbour_structure() |
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| 137 | |
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| 138 | #Build boundary dictionary mapping (id, vertex) to symbolic tags |
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| 139 | self.build_boundary_dictionary(boundary) |
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| 140 | |
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| 141 | #Build tagged element dictionary mapping (tag) to array of elements |
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| 142 | self.build_tagged_elements_dictionary(tagged_elements) |
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| 143 | |
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| 144 | from quantity import Quantity |
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| 145 | #from quantity_domain import Quantity, Conserved_quantity |
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| 146 | |
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| 147 | #List of quantity names entering |
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| 148 | #the conservation equations |
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| 149 | #(Must be a subset of quantities) |
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| 150 | if conserved_quantities is None: |
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| 151 | self.conserved_quantities = [] |
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| 152 | else: |
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| 153 | self.conserved_quantities = conserved_quantities |
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| 154 | |
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| 155 | if evolved_quantities is None: |
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| 156 | self.evolved_quantities = self.conserved_quantities |
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| 157 | else: |
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| 158 | self.evolved_quantities = evolved_quantities |
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| 159 | |
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| 160 | if other_quantities is None: |
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| 161 | self.other_quantities = [] |
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| 162 | else: |
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| 163 | self.other_quantities = other_quantities |
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| 164 | |
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| 165 | |
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| 166 | #Build dictionary of Quantity instances keyed by quantity names |
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| 167 | self.quantities = {} |
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| 168 | |
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| 169 | #print self.conserved_quantities |
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| 170 | #print self.evolved_quantities |
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| 171 | |
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| 172 | |
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| 173 | #FIXME: remove later - maybe OK, though.... |
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| 174 | for name in self.evolved_quantities: |
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| 175 | self.quantities[name] = Quantity(self) |
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| 176 | for name in self.other_quantities: |
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| 177 | self.quantities[name] = Quantity(self) |
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| 178 | |
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| 179 | #Create an empty list for explicit forcing terms |
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| 180 | self.forcing_terms = [] |
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| 181 | |
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| 182 | #Defaults |
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| 183 | from config import max_smallsteps, beta_w, beta_h, epsilon, CFL |
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| 184 | self.beta_w = beta_w |
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| 185 | self.beta_h = beta_h |
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| 186 | self.epsilon = epsilon |
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| 187 | |
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| 188 | #FIXME: Maybe have separate orders for h-limiter and w-limiter? |
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| 189 | #Or maybe get rid of order altogether and use beta_w and beta_h |
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| 190 | self.default_order = 1 |
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| 191 | self.order = self.default_order |
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| 192 | |
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| 193 | self.default_time_order = 1 |
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| 194 | self.time_order = self.default_time_order |
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| 195 | |
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| 196 | self.smallsteps = 0 |
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| 197 | self.max_smallsteps = max_smallsteps |
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| 198 | self.number_of_steps = 0 |
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| 199 | self.number_of_first_order_steps = 0 |
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| 200 | |
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| 201 | #Model time |
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| 202 | self.time = 0.0 |
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| 203 | self.finaltime = None |
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| 204 | self.min_timestep = self.max_timestep = 0.0 |
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| 205 | self.starttime = 0 #Physical starttime if any (0 is 1 Jan 1970 00:00:00) |
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| 206 | #Checkpointing and storage |
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| 207 | from config import default_datadir |
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| 208 | self.set_datadir(default_datadir) |
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| 209 | self.filename = 'domain' |
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| 210 | self.checkpoint = False |
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| 211 | |
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| 212 | def __len__(self): |
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| 213 | return self.number_of_elements |
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| 214 | |
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| 215 | def build_vertexlist(self): |
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| 216 | """Build vertexlist index by vertex ids and for each entry (point id) |
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| 217 | build a list of (triangles, vertex_id) pairs that use the point |
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| 218 | as vertex. |
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| 219 | |
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| 220 | Preconditions: |
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| 221 | self.coordinates and self.triangles are defined |
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| 222 | |
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| 223 | Postcondition: |
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| 224 | self.vertexlist is built |
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| 225 | """ |
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| 226 | |
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| 227 | vertexlist = [None]*len(self.coordinates) |
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| 228 | for i in range(self.number_of_elements): |
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| 229 | |
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| 230 | #a = self.triangles[i, 0] |
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| 231 | #b = self.triangles[i, 1] |
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| 232 | #c = self.triangles[i, 2] |
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| 233 | a = i |
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| 234 | b = i + 1 |
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| 235 | |
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| 236 | #Register the vertices v as lists of |
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| 237 | #(triangle_id, vertex_id) tuples associated with them |
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| 238 | #This is used for smoothing |
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| 239 | #for vertex_id, v in enumerate([a,b,c]): |
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| 240 | for vertex_id, v in enumerate([a,b]): |
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| 241 | if vertexlist[v] is None: |
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| 242 | vertexlist[v] = [] |
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| 243 | |
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| 244 | vertexlist[v].append( (i, vertex_id) ) |
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| 245 | |
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| 246 | self.vertexlist = vertexlist |
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| 247 | |
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| 248 | |
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| 249 | def build_neighbour_structure(self): |
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| 250 | """Update all registered triangles to point to their neighbours. |
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| 251 | |
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| 252 | Also, keep a tally of the number of boundaries for each triangle |
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| 253 | |
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| 254 | Postconditions: |
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| 255 | neighbours and neighbour_edges is populated |
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| 256 | neighbours and neighbour_vertices is populated |
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| 257 | number_of_boundaries integer array is defined. |
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| 258 | """ |
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| 259 | |
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| 260 | #Step 1: |
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| 261 | #Build dictionary mapping from segments (2-tuple of points) |
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| 262 | #to left hand side edge (facing neighbouring triangle) |
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| 263 | |
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| 264 | N = self.number_of_elements |
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| 265 | neighbourdict = {} |
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| 266 | #l_edge = 0 |
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| 267 | #r_edge = 1 |
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| 268 | l_vertex = 0 |
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| 269 | r_vertex = 1 |
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| 270 | for i in range(N): |
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| 271 | |
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| 272 | #Register all segments as keys mapping to current triangle |
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| 273 | #and segment id |
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| 274 | #a = self.triangles[i, 0] |
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| 275 | #b = self.triangles[i, 1] |
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| 276 | #c = self.triangles[i, 2] |
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| 277 | a = self.vertices[i,0] |
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| 278 | b = self.vertices[i,1] |
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| 279 | |
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| 280 | """ |
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| 281 | if neighbourdict.has_key((a,b)): |
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| 282 | msg = "Edge 2 of triangle %d is duplicating edge %d of triangle %d.\n" %(i,neighbourdict[a,b][1],neighbourdict[a,b][0]) |
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| 283 | raise msg |
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| 284 | if neighbourdict.has_key((b,c)): |
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| 285 | msg = "Edge 0 of triangle %d is duplicating edge %d of triangle %d.\n" %(i,neighbourdict[b,c][1],neighbourdict[b,c][0]) |
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| 286 | raise msg |
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| 287 | if neighbourdict.has_key((c,a)): |
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| 288 | msg = "Edge 1 of triangle %d is duplicating edge %d of triangle %d.\n" %(i,neighbourdict[c,a][1],neighbourdict[c,a][0]) |
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| 289 | raise msg |
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| 290 | """ |
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| 291 | #neighbourdict[a,b] = (i, 2) #(id, edge) |
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| 292 | #neighbourdict[b,c] = (i, 0) #(id, edge) |
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| 293 | #neighbourdict[c,a] = (i, 1) #(id, edge) |
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| 294 | #neighbourdict[a,b] = (i, 1) #(id, edge) |
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| 295 | #neighbourdict[b,a] = (i, 0) #(id, edge) |
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| 296 | #neighbourdict[a,l_edge] = (i, 0) #(id, edge) |
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| 297 | #neighbourdict[b,r_edge] = (i, 1) #(id, edge) |
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| 298 | neighbourdict[a,l_vertex] = (i, 0) #(id, vertex) |
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| 299 | neighbourdict[b,r_vertex] = (i, 1) #(id, vertex) |
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| 300 | |
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| 301 | |
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| 302 | #Step 2: |
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| 303 | #Go through triangles again, but this time |
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| 304 | #reverse direction of segments and lookup neighbours. |
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| 305 | for i in range(N): |
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| 306 | #a = self.triangles[i, 0] |
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| 307 | #b = self.triangles[i, 1] |
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| 308 | #c = self.triangles[i, 2] |
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| 309 | |
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| 310 | a = self.vertices[i,0] |
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| 311 | b = self.vertices[i,1] |
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| 312 | |
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| 313 | #self.number_of_boundaries[i] = 3 |
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| 314 | self.number_of_boundaries[i] = 2 |
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| 315 | #if neighbourdict.has_key((b,l_edge)): |
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| 316 | if neighbourdict.has_key((b,l_vertex)): |
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| 317 | #self.neighbours[i, 1] = neighbourdict[b,l_edge][0] |
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| 318 | #self.neighbour_edges[i, 1] = neighbourdict[b,l_edge][1] |
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| 319 | self.neighbours[i, 1] = neighbourdict[b,l_vertex][0] |
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| 320 | self.neighbour_vertices[i, 1] = neighbourdict[b,l_vertex][1] |
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| 321 | self.number_of_boundaries[i] -= 1 |
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| 322 | |
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| 323 | #if neighbourdict.has_key((a,r_edge)): |
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| 324 | if neighbourdict.has_key((a,r_vertex)): |
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| 325 | #self.neighbours[i, 0] = neighbourdict[a,r_edge][0] |
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| 326 | #self.neighbour_edges[i, 0] = neighbourdict[a,r_edge][1] |
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| 327 | self.neighbours[i, 0] = neighbourdict[a,r_vertex][0] |
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| 328 | self.neighbour_vertices[i, 0] = neighbourdict[a,r_vertex][1] |
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| 329 | self.number_of_boundaries[i] -= 1 |
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| 330 | |
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| 331 | #if neighbourdict.has_key((b,a)): |
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| 332 | # self.neighbours[i, 1] = neighbourdict[b,a][0] |
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| 333 | # self.neighbour_edges[i, 1] = neighbourdict[b,a][1] |
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| 334 | # self.number_of_boundaries[i] -= 1 |
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| 335 | |
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| 336 | #if neighbourdict.has_key((c,b)): |
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| 337 | # self.neighbours[i, 0] = neighbourdict[c,b][0] |
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| 338 | # self.neighbour_edges[i, 0] = neighbourdict[c,b][1] |
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| 339 | # self.number_of_boundaries[i] -= 1 |
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| 340 | |
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| 341 | #if neighbourdict.has_key((a,b)): |
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| 342 | # self.neighbours[i, 0] = neighbourdict[a,b][0] |
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| 343 | # self.neighbour_edges[i, 0] = neighbourdict[a,b][1] |
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| 344 | # self.number_of_boundaries[i] -= 1 |
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| 345 | |
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| 346 | def build_surrogate_neighbour_structure(self): |
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| 347 | """Build structure where each triangle edge points to its neighbours |
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| 348 | if they exist. Otherwise point to the triangle itself. |
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| 349 | |
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| 350 | The surrogate neighbour structure is useful for computing gradients |
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| 351 | based on centroid values of neighbours. |
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| 352 | |
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| 353 | Precondition: Neighbour structure is defined |
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| 354 | Postcondition: |
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| 355 | Surrogate neighbour structure is defined: |
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| 356 | surrogate_neighbours: i0, i1, i2 where all i_k >= 0 point to |
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| 357 | triangles. |
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| 358 | |
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| 359 | """ |
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| 360 | |
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| 361 | N = self.number_of_elements |
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| 362 | for i in range(N): |
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| 363 | #Find all neighbouring volumes that are not boundaries |
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| 364 | #for k in range(3): |
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| 365 | for k in range(2): |
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| 366 | if self.neighbours[i, k] < 0: |
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| 367 | self.surrogate_neighbours[i, k] = i #Point this triangle |
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| 368 | else: |
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| 369 | self.surrogate_neighbours[i, k] = self.neighbours[i, k] |
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| 370 | |
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| 371 | def build_boundary_dictionary(self, boundary = None): |
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| 372 | """Build or check the dictionary of boundary tags. |
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| 373 | self.boundary is a dictionary of tags, |
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| 374 | keyed by volume id and edge: |
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| 375 | { (id, edge): tag, ... } |
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| 376 | |
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| 377 | Postconditions: |
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| 378 | self.boundary is defined. |
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| 379 | """ |
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| 380 | |
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| 381 | from config import default_boundary_tag |
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| 382 | |
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| 383 | if boundary is None: |
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| 384 | boundary = {} |
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| 385 | for vol_id in range(self.number_of_elements): |
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| 386 | #for edge_id in range(0, 3): |
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| 387 | #for edge_id in range(0, 2): |
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| 388 | for vertex_id in range(0, 2): |
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| 389 | #if self.neighbours[vol_id, edge_id] < 0: |
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| 390 | if self.neighbours[vol_id, vertex_id] < 0: |
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| 391 | #boundary[(vol_id, edge_id)] = default_boundary_tag |
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| 392 | boundary[(vol_id, vertex_id)] = default_boundary_tag |
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| 393 | else: |
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| 394 | #Check that all keys in given boundary exist |
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| 395 | #for vol_id, edge_id in boundary.keys(): |
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| 396 | for vol_id, vertex_id in boundary.keys(): |
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| 397 | #msg = 'Segment (%d, %d) does not exist' %(vol_id, edge_id) |
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| 398 | msg = 'Segment (%d, %d) does not exist' %(vol_id, vertex_id) |
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| 399 | a, b = self.neighbours.shape |
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| 400 | #assert vol_id < a and edge_id < b, msg |
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| 401 | assert vol_id < a and vertex_id < b, msg |
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| 402 | |
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| 403 | #FIXME: This assert violates internal boundaries (delete it) |
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| 404 | #msg = 'Segment (%d, %d) is not a boundary' %(vol_id, edge_id) |
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| 405 | #assert self.neighbours[vol_id, edge_id] < 0, msg |
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| 406 | |
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| 407 | #Check that all boundary segments are assigned a tag |
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| 408 | for vol_id in range(self.number_of_elements): |
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| 409 | #for edge_id in range(0, 3): |
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| 410 | #for edge_id in range(0, 2): |
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| 411 | for vertex_id in range(0, 2): |
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| 412 | #if self.neighbours[vol_id, edge_id] < 0: |
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| 413 | if self.neighbours[vol_id, vertex_id] < 0: |
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| 414 | #if not boundary.has_key( (vol_id, edge_id) ): |
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| 415 | if not boundary.has_key( (vol_id, vertex_id) ): |
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| 416 | msg = 'WARNING: Given boundary does not contain ' |
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| 417 | #msg += 'tags for edge (%d, %d). '\ |
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| 418 | # %(vol_id, edge_id) |
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| 419 | msg += 'tags for vertex (%d, %d). '\ |
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| 420 | %(vol_id, vertex_id) |
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| 421 | msg += 'Assigning default tag (%s).'\ |
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| 422 | %default_boundary_tag |
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| 423 | |
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| 424 | #FIXME: Print only as per verbosity |
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| 425 | #print msg |
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| 426 | |
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| 427 | #FIXME: Make this situation an error in the future |
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| 428 | #and make another function which will |
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| 429 | #enable default boundary-tags where |
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| 430 | #tags a not specified |
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| 431 | #boundary[ (vol_id, edge_id) ] =\ |
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| 432 | boundary[ (vol_id, vertex_id) ] =\ |
|---|
| 433 | default_boundary_tag |
|---|
| 434 | |
|---|
| 435 | |
|---|
| 436 | |
|---|
| 437 | self.boundary = boundary |
|---|
| 438 | |
|---|
| 439 | def build_tagged_elements_dictionary(self, tagged_elements = None): |
|---|
| 440 | """Build the dictionary of element tags. |
|---|
| 441 | self.tagged_elements is a dictionary of element arrays, |
|---|
| 442 | keyed by tag: |
|---|
| 443 | { (tag): [e1, e2, e3..] } |
|---|
| 444 | |
|---|
| 445 | Postconditions: |
|---|
| 446 | self.element_tag is defined |
|---|
| 447 | """ |
|---|
| 448 | |
|---|
| 449 | if tagged_elements is None: |
|---|
| 450 | tagged_elements = {} |
|---|
| 451 | else: |
|---|
| 452 | #Check that all keys in given boundary exist |
|---|
| 453 | for tag in tagged_elements.keys(): |
|---|
| 454 | tagged_elements[tag] = array(tagged_elements[tag]).astype(numpy.int) |
|---|
| 455 | |
|---|
| 456 | msg = 'Not all elements exist. ' |
|---|
| 457 | assert max(tagged_elements[tag]) < self.number_of_elements, msg |
|---|
| 458 | #print "tagged_elements", tagged_elements |
|---|
| 459 | self.tagged_elements = tagged_elements |
|---|
| 460 | |
|---|
| 461 | |
|---|
| 462 | def set_quantities_to_be_stored(self, q): |
|---|
| 463 | """Specify which quantities will be stored in the sww file. |
|---|
| 464 | |
|---|
| 465 | q must be either: |
|---|
| 466 | - the name of a quantity |
|---|
| 467 | - a list of quantity names |
|---|
| 468 | - None |
|---|
| 469 | |
|---|
| 470 | In the two first cases, the named quantities will be stored at each |
|---|
| 471 | yieldstep |
|---|
| 472 | (This is in addition to the quantities elevation and friction) |
|---|
| 473 | If q is None, storage will be switched off altogether. |
|---|
| 474 | """ |
|---|
| 475 | |
|---|
| 476 | |
|---|
| 477 | if q is None: |
|---|
| 478 | self.quantities_to_be_stored = [] |
|---|
| 479 | self.store = False |
|---|
| 480 | return |
|---|
| 481 | |
|---|
| 482 | if isinstance(q, basestring): |
|---|
| 483 | q = [q] # Turn argument into a list |
|---|
| 484 | |
|---|
| 485 | #Check correcness |
|---|
| 486 | for quantity_name in q: |
|---|
| 487 | msg = 'Quantity %s is not a valid conserved quantity' %quantity_name |
|---|
| 488 | assert quantity_name in self.conserved_quantities, msg |
|---|
| 489 | |
|---|
| 490 | self.quantities_to_be_stored = q |
|---|
| 491 | |
|---|
| 492 | |
|---|
| 493 | |
|---|
| 494 | |
|---|
| 495 | |
|---|
| 496 | def get_boundary_tags(self): |
|---|
| 497 | """Return list of available boundary tags |
|---|
| 498 | """ |
|---|
| 499 | |
|---|
| 500 | tags = {} |
|---|
| 501 | for v in self.boundary.values(): |
|---|
| 502 | tags[v] = 1 |
|---|
| 503 | |
|---|
| 504 | return tags.keys() |
|---|
| 505 | |
|---|
| 506 | def get_vertex_coordinates(self, obj = False): |
|---|
| 507 | """Return all vertex coordinates. |
|---|
| 508 | Return all vertex coordinates for all triangles as an Nx6 array |
|---|
| 509 | (ordered as x0, y0, x1, y1, x2, y2 for each triangle) |
|---|
| 510 | |
|---|
| 511 | if obj is True, the x/y pairs are returned in a 3*N x 2 array. |
|---|
| 512 | FIXME, we might make that the default. |
|---|
| 513 | FIXME Maybe use keyword: continuous = False for this condition? |
|---|
| 514 | |
|---|
| 515 | |
|---|
| 516 | """ |
|---|
| 517 | |
|---|
| 518 | if obj is True: |
|---|
| 519 | |
|---|
| 520 | #V = self.vertex_coordinates |
|---|
| 521 | V = self.vertices |
|---|
| 522 | #return concatenate( (V[:,0:2], V[:,2:4], V[:,4:6]), axis=0) |
|---|
| 523 | |
|---|
| 524 | N = V.shape[0] |
|---|
| 525 | #return reshape(V, (3*N, 2)) |
|---|
| 526 | return numpy.reshape(V, (N, 2)) |
|---|
| 527 | else: |
|---|
| 528 | #return self.vertex_coordinates |
|---|
| 529 | return self.vertices |
|---|
| 530 | |
|---|
| 531 | def get_conserved_quantities(self, vol_id, vertex=None):#, edge=None): |
|---|
| 532 | """Get conserved quantities at volume vol_id |
|---|
| 533 | |
|---|
| 534 | If vertex is specified use it as index for vertex values |
|---|
| 535 | If edge is specified use it as index for edge values |
|---|
| 536 | If neither are specified use centroid values |
|---|
| 537 | If both are specified an exeception is raised |
|---|
| 538 | |
|---|
| 539 | Return value: Vector of length == number_of_conserved quantities |
|---|
| 540 | |
|---|
| 541 | """ |
|---|
| 542 | |
|---|
| 543 | #if not (vertex is None):# or edge is None): |
|---|
| 544 | # msg = 'Values for both vertex and edge was specified.' |
|---|
| 545 | # msg += 'Only one (or none) is allowed.' |
|---|
| 546 | # raise msg |
|---|
| 547 | |
|---|
| 548 | q = numpy.zeros( len(self.conserved_quantities), numpy.float) |
|---|
| 549 | |
|---|
| 550 | for i, name in enumerate(self.conserved_quantities): |
|---|
| 551 | Q = self.quantities[name] |
|---|
| 552 | if vertex is not None: |
|---|
| 553 | q[i] = Q.vertex_values[vol_id, vertex] |
|---|
| 554 | #elif edge is not None: |
|---|
| 555 | # q[i] = Q.edge_values[vol_id, edge] |
|---|
| 556 | else: |
|---|
| 557 | q[i] = Q.centroid_values[vol_id] |
|---|
| 558 | |
|---|
| 559 | return q |
|---|
| 560 | |
|---|
| 561 | |
|---|
| 562 | def get_evolved_quantities(self, vol_id, vertex=None):#, edge=None): |
|---|
| 563 | """Get evolved quantities at volume vol_id |
|---|
| 564 | |
|---|
| 565 | If vertex is specified use it as index for vertex values |
|---|
| 566 | If edge is specified use it as index for edge values |
|---|
| 567 | If neither are specified use centroid values |
|---|
| 568 | If both are specified an exeception is raised |
|---|
| 569 | |
|---|
| 570 | Return value: Vector of length == number_of_evolved quantities |
|---|
| 571 | |
|---|
| 572 | """ |
|---|
| 573 | |
|---|
| 574 | |
|---|
| 575 | |
|---|
| 576 | #if not (vertex is None):# or edge is None): |
|---|
| 577 | # msg = 'Values for both vertex and edge was specified.' |
|---|
| 578 | # msg += 'Only one (or none) is allowed.' |
|---|
| 579 | # raise msg |
|---|
| 580 | |
|---|
| 581 | q = numpy.zeros( len(self.evolved_quantities), numpy.float) |
|---|
| 582 | |
|---|
| 583 | for i, name in enumerate(self.evolved_quantities): |
|---|
| 584 | Q = self.quantities[name] |
|---|
| 585 | if vertex is not None: |
|---|
| 586 | q[i] = Q.vertex_values[vol_id, vertex] |
|---|
| 587 | #elif edge is not None: |
|---|
| 588 | # q[i] = Q.edge_values[vol_id, edge] |
|---|
| 589 | else: |
|---|
| 590 | q[i] = Q.centroid_values[vol_id] |
|---|
| 591 | |
|---|
| 592 | return q |
|---|
| 593 | |
|---|
| 594 | |
|---|
| 595 | def get_centroids(self): |
|---|
| 596 | """Return all coordinates of centroids |
|---|
| 597 | Return x coordinate of centroid for each element as a N array |
|---|
| 598 | """ |
|---|
| 599 | |
|---|
| 600 | return self.centroids |
|---|
| 601 | |
|---|
| 602 | def get_vertices(self): |
|---|
| 603 | """Return all coordinates of centroids |
|---|
| 604 | Return x coordinate of centroid for each element as a N array |
|---|
| 605 | """ |
|---|
| 606 | |
|---|
| 607 | return self.vertices |
|---|
| 608 | |
|---|
| 609 | def get_coordinate(self, elem_id, vertex=None): |
|---|
| 610 | """Return coordinate of centroid, |
|---|
| 611 | or left or right vertex. |
|---|
| 612 | Left vertex (vertex=0). Right vertex (vertex=1) |
|---|
| 613 | """ |
|---|
| 614 | |
|---|
| 615 | if vertex is None: |
|---|
| 616 | return self.centroids[elem_id] |
|---|
| 617 | else: |
|---|
| 618 | return self.vertices[elem_id,vertex] |
|---|
| 619 | |
|---|
| 620 | def get_area(self, elem_id=None): |
|---|
| 621 | """Return area of element id |
|---|
| 622 | """ |
|---|
| 623 | |
|---|
| 624 | if elem_id is None: |
|---|
| 625 | return sum(self.areas) |
|---|
| 626 | else: |
|---|
| 627 | return self.areas[elem_id] |
|---|
| 628 | |
|---|
| 629 | |
|---|
| 630 | def get_quantity(self, name, location='vertices', indices = None): |
|---|
| 631 | """Get values for named quantity |
|---|
| 632 | |
|---|
| 633 | name: Name of quantity |
|---|
| 634 | |
|---|
| 635 | In case of location == 'centroids' the dimension values must |
|---|
| 636 | be a list of a numpyal array of length N, N being the number |
|---|
| 637 | of elements. Otherwise it must be of dimension Nx3. |
|---|
| 638 | |
|---|
| 639 | Indices is the set of element ids that the operation applies to. |
|---|
| 640 | |
|---|
| 641 | The values will be stored in elements following their |
|---|
| 642 | internal ordering. |
|---|
| 643 | """ |
|---|
| 644 | |
|---|
| 645 | return self.quantities[name].get_values( location, indices = indices) |
|---|
| 646 | |
|---|
| 647 | def get_centroid_coordinates(self): |
|---|
| 648 | """Return all centroid coordinates. |
|---|
| 649 | Return all centroid coordinates for all triangles as an Nx2 array |
|---|
| 650 | (ordered as x0, y0 for each triangle) |
|---|
| 651 | """ |
|---|
| 652 | return self.centroids |
|---|
| 653 | |
|---|
| 654 | |
|---|
| 655 | def get_timestepping_method(self): |
|---|
| 656 | return self.timestepping_method |
|---|
| 657 | |
|---|
| 658 | def set_timestepping_method(self,timestepping_method): |
|---|
| 659 | |
|---|
| 660 | if timestepping_method in ['euler', 'rk2', 'rk3']: |
|---|
| 661 | self.timestepping_method = timestepping_method |
|---|
| 662 | return |
|---|
| 663 | |
|---|
| 664 | if timestepping_method in [1, 2, 3]: |
|---|
| 665 | self.timestepping_method = ['euler', 'rk2', 'rk3'][timestepping_method-1] |
|---|
| 666 | return |
|---|
| 667 | |
|---|
| 668 | msg = '%s is an incorrect timestepping type'% timestepping_method |
|---|
| 669 | raise Exception, msg |
|---|
| 670 | |
|---|
| 671 | |
|---|
| 672 | def set_quantity(self, name, *args, **kwargs): |
|---|
| 673 | """Set values for named quantity |
|---|
| 674 | |
|---|
| 675 | |
|---|
| 676 | One keyword argument is documented here: |
|---|
| 677 | expression = None, # Arbitrary expression |
|---|
| 678 | |
|---|
| 679 | expression: |
|---|
| 680 | Arbitrary expression involving quantity names |
|---|
| 681 | |
|---|
| 682 | See Quantity.set_values for further documentation. |
|---|
| 683 | """ |
|---|
| 684 | |
|---|
| 685 | #FIXME (Ole): Allow new quantities here |
|---|
| 686 | #from quantity import Quantity, Conserved_quantity |
|---|
| 687 | #Create appropriate quantity object |
|---|
| 688 | # #if name in self.conserved_quantities: |
|---|
| 689 | # # self.quantities[name] = Conserved_quantity(self) |
|---|
| 690 | # #else: |
|---|
| 691 | # # self.quantities[name] = Quantity(self) |
|---|
| 692 | |
|---|
| 693 | |
|---|
| 694 | #Do the expression stuff |
|---|
| 695 | if kwargs.has_key('expression'): |
|---|
| 696 | expression = kwargs['expression'] |
|---|
| 697 | del kwargs['expression'] |
|---|
| 698 | |
|---|
| 699 | Q = self.create_quantity_from_expression(expression) |
|---|
| 700 | kwargs['quantity'] = Q |
|---|
| 701 | |
|---|
| 702 | #Assign values |
|---|
| 703 | self.quantities[name].set_values(*args, **kwargs) |
|---|
| 704 | |
|---|
| 705 | def set_boundary(self, boundary_map): |
|---|
| 706 | """Associate boundary objects with tagged boundary segments. |
|---|
| 707 | |
|---|
| 708 | Input boundary_map is a dictionary of boundary objects keyed |
|---|
| 709 | by symbolic tags to matched against tags in the internal dictionary |
|---|
| 710 | self.boundary. |
|---|
| 711 | |
|---|
| 712 | As result one pointer to a boundary object is stored for each vertex |
|---|
| 713 | in the list self.boundary_objects. |
|---|
| 714 | More entries may point to the same boundary object |
|---|
| 715 | |
|---|
| 716 | Schematically the mapping is from two dictionaries to one list |
|---|
| 717 | where the index is used as pointer to the boundary_values arrays |
|---|
| 718 | within each quantity. |
|---|
| 719 | |
|---|
| 720 | self.boundary: (vol_id, edge_id): tag |
|---|
| 721 | boundary_map (input): tag: boundary_object |
|---|
| 722 | ---------------------------------------------- |
|---|
| 723 | self.boundary_objects: ((vol_id, edge_id), boundary_object) |
|---|
| 724 | |
|---|
| 725 | |
|---|
| 726 | Pre-condition: |
|---|
| 727 | self.boundary has been built. |
|---|
| 728 | |
|---|
| 729 | Post-condition: |
|---|
| 730 | self.boundary_objects is built |
|---|
| 731 | |
|---|
| 732 | If a tag from the domain doesn't appear in the input dictionary an |
|---|
| 733 | exception is raised. |
|---|
| 734 | However, if a tag is not used to the domain, no error is thrown. |
|---|
| 735 | FIXME: This would lead to implementation of a |
|---|
| 736 | default boundary condition |
|---|
| 737 | |
|---|
| 738 | Note: If a segment is listed in the boundary dictionary and if it is |
|---|
| 739 | not None, it *will* become a boundary - |
|---|
| 740 | even if there is a neighbouring triangle. |
|---|
| 741 | This would be the case for internal boundaries |
|---|
| 742 | |
|---|
| 743 | Boundary objects that are None will be skipped. |
|---|
| 744 | |
|---|
| 745 | FIXME: If set_boundary is called multiple times and if Boundary |
|---|
| 746 | object is changed into None, the neighbour structure will not be |
|---|
| 747 | restored!!! |
|---|
| 748 | """ |
|---|
| 749 | |
|---|
| 750 | self.boundary_objects = [] |
|---|
| 751 | self.boundary_map = boundary_map #Store for use with eg. boundary_stats. |
|---|
| 752 | |
|---|
| 753 | #FIXME: Try to remove the sorting and fix test_mesh.py |
|---|
| 754 | x = self.boundary.keys() |
|---|
| 755 | x.sort() |
|---|
| 756 | |
|---|
| 757 | #Loop through edges that lie on the boundary and associate them with |
|---|
| 758 | #callable boundary objects depending on their tags |
|---|
| 759 | #for k, (vol_id, edge_id) in enumerate(x): |
|---|
| 760 | for k, (vol_id, vertex_id) in enumerate(x): |
|---|
| 761 | #tag = self.boundary[ (vol_id, edge_id) ] |
|---|
| 762 | tag = self.boundary[ (vol_id, vertex_id) ] |
|---|
| 763 | |
|---|
| 764 | if boundary_map.has_key(tag): |
|---|
| 765 | B = boundary_map[tag] #Get callable boundary object |
|---|
| 766 | |
|---|
| 767 | if B is not None: |
|---|
| 768 | #self.boundary_objects.append( ((vol_id, edge_id), B) ) |
|---|
| 769 | #self.neighbours[vol_id, edge_id] = -len(self.boundary_objects) |
|---|
| 770 | self.boundary_objects.append( ((vol_id, vertex_id), B) ) |
|---|
| 771 | self.neighbours[vol_id, vertex_id] = -len(self.boundary_objects) |
|---|
| 772 | else: |
|---|
| 773 | pass |
|---|
| 774 | #FIXME: Check and perhaps fix neighbour structure |
|---|
| 775 | |
|---|
| 776 | else: |
|---|
| 777 | msg = 'ERROR (domain.py): Tag "%s" has not been ' %tag |
|---|
| 778 | msg += 'bound to a boundary object.\n' |
|---|
| 779 | msg += 'All boundary tags defined in domain must appear ' |
|---|
| 780 | msg += 'in the supplied dictionary.\n' |
|---|
| 781 | msg += 'The tags are: %s' %self.get_boundary_tags() |
|---|
| 782 | raise Exception, msg |
|---|
| 783 | |
|---|
| 784 | |
|---|
| 785 | |
|---|
| 786 | def check_integrity(self): |
|---|
| 787 | #Mesh.check_integrity(self) |
|---|
| 788 | |
|---|
| 789 | #print self.quantities |
|---|
| 790 | #print self.conserved_quantities |
|---|
| 791 | |
|---|
| 792 | for quantity in self.conserved_quantities: |
|---|
| 793 | msg = 'Conserved quantities must be a subset of all quantities' |
|---|
| 794 | assert quantity in self.quantities, msg |
|---|
| 795 | |
|---|
| 796 | for quantity in self.evolved_quantities: |
|---|
| 797 | msg = 'Evolved quantities must be a subset of all quantities' |
|---|
| 798 | assert quantity in self.quantities, msg |
|---|
| 799 | |
|---|
| 800 | # #assert hasattr(self, 'boundary_objects') |
|---|
| 801 | |
|---|
| 802 | def write_time(self): |
|---|
| 803 | print self.timestepping_statistics() |
|---|
| 804 | |
|---|
| 805 | def timestepping_statistics(self): |
|---|
| 806 | """Return string with time stepping statistics for printing or logging |
|---|
| 807 | """ |
|---|
| 808 | |
|---|
| 809 | msg = '' |
|---|
| 810 | if self.min_timestep == self.max_timestep: |
|---|
| 811 | msg += 'Time = %.4f, delta t = %.8f, steps=%d (%d)'\ |
|---|
| 812 | %(self.time, self.min_timestep, self.number_of_steps, |
|---|
| 813 | self.number_of_first_order_steps) |
|---|
| 814 | elif self.min_timestep > self.max_timestep: |
|---|
| 815 | msg += 'Time = %.4f, steps=%d (%d)'\ |
|---|
| 816 | %(self.time, self.number_of_steps, |
|---|
| 817 | self.number_of_first_order_steps) |
|---|
| 818 | else: |
|---|
| 819 | msg += 'Time = %.4f, delta t in [%.8f, %.8f], steps=%d (%d)'\ |
|---|
| 820 | %(self.time, self.min_timestep, |
|---|
| 821 | self.max_timestep, self.number_of_steps, |
|---|
| 822 | self.number_of_first_order_steps) |
|---|
| 823 | |
|---|
| 824 | return msg |
|---|
| 825 | |
|---|
| 826 | def get_name(self): |
|---|
| 827 | return self.filename |
|---|
| 828 | |
|---|
| 829 | def set_name(self, name): |
|---|
| 830 | self.filename = name |
|---|
| 831 | |
|---|
| 832 | def get_datadir(self): |
|---|
| 833 | return self.datadir |
|---|
| 834 | |
|---|
| 835 | def set_datadir(self, name): |
|---|
| 836 | self.datadir = name |
|---|
| 837 | |
|---|
| 838 | def set_CFL(self, cfl): |
|---|
| 839 | if cfl > 1.0: |
|---|
| 840 | print 'WARNING: Setting CFL condition to %f which is greater than 1' % cfl |
|---|
| 841 | self.CFL = cfl |
|---|
| 842 | |
|---|
| 843 | def get_CFL(self): |
|---|
| 844 | return self.CFL |
|---|
| 845 | |
|---|
| 846 | def set_filename(self, name): |
|---|
| 847 | self.filename = name |
|---|
| 848 | |
|---|
| 849 | def get_filename(self): |
|---|
| 850 | return self.filename |
|---|
| 851 | |
|---|
| 852 | |
|---|
| 853 | def get_spatial_order(self): |
|---|
| 854 | return self.order |
|---|
| 855 | |
|---|
| 856 | def set_spatial_order(self, order): |
|---|
| 857 | |
|---|
| 858 | possible_orders = [1,2] |
|---|
| 859 | |
|---|
| 860 | if order in possible_orders: |
|---|
| 861 | self.order = order |
|---|
| 862 | return |
|---|
| 863 | |
|---|
| 864 | msg = '%s is an incorrect spatial order.\n'% limiter |
|---|
| 865 | msg += 'Possible orders are: '+ ", ".join(["%s" % el for el in possible_orders]) |
|---|
| 866 | raise Exception, msg |
|---|
| 867 | |
|---|
| 868 | |
|---|
| 869 | def get_beta(self): |
|---|
| 870 | |
|---|
| 871 | warn('limiter parameter beta associated with quantity not domain') |
|---|
| 872 | |
|---|
| 873 | def set_beta(self,beta): |
|---|
| 874 | """Set the same limiter beta parameter to all evolving quantities |
|---|
| 875 | """ |
|---|
| 876 | |
|---|
| 877 | for name in self.evolved_quantities: |
|---|
| 878 | Q = self.quantities[name] |
|---|
| 879 | Q.set_beta(beta) |
|---|
| 880 | |
|---|
| 881 | |
|---|
| 882 | def get_limiter(self): |
|---|
| 883 | |
|---|
| 884 | warn('limiter associated with quantity not domain') |
|---|
| 885 | |
|---|
| 886 | def set_limiter(self,limiter): |
|---|
| 887 | |
|---|
| 888 | for name in self.evolved_quantities: |
|---|
| 889 | Q = self.quantities[name] |
|---|
| 890 | Q.set_limiter(limiter) |
|---|
| 891 | |
|---|
| 892 | |
|---|
| 893 | |
|---|
| 894 | #-------------------------- |
|---|
| 895 | # Main components of evolve |
|---|
| 896 | #-------------------------- |
|---|
| 897 | |
|---|
| 898 | def evolve(self, yieldstep = None, |
|---|
| 899 | finaltime = None, |
|---|
| 900 | duration = None, |
|---|
| 901 | skip_initial_step = False): |
|---|
| 902 | """Evolve model through time starting from self.starttime. |
|---|
| 903 | |
|---|
| 904 | |
|---|
| 905 | yieldstep: numpy.interval between yields where results are stored, |
|---|
| 906 | statistics written and domain inspected or |
|---|
| 907 | possibly modified. If omitted the internal predefined |
|---|
| 908 | max timestep is used. |
|---|
| 909 | numpy.internally, smaller timesteps may be taken. |
|---|
| 910 | |
|---|
| 911 | duration: Duration of simulation |
|---|
| 912 | |
|---|
| 913 | finaltime: Time where simulation should end. This is currently |
|---|
| 914 | relative time. So it's the same as duration. |
|---|
| 915 | |
|---|
| 916 | If both duration and finaltime are given an exception is thrown. |
|---|
| 917 | |
|---|
| 918 | |
|---|
| 919 | skip_initial_step: Boolean flag that decides whether the first |
|---|
| 920 | yield step is skipped or not. This is useful for example to avoid |
|---|
| 921 | duplicate steps when multiple evolve processes are dove tailed. |
|---|
| 922 | |
|---|
| 923 | |
|---|
| 924 | Evolve is implemented as a generator and is to be called as such, e.g. |
|---|
| 925 | |
|---|
| 926 | for t in domain.evolve(yieldstep, finaltime): |
|---|
| 927 | <Do something with domain and t> |
|---|
| 928 | |
|---|
| 929 | |
|---|
| 930 | All times are given in seconds |
|---|
| 931 | |
|---|
| 932 | """ |
|---|
| 933 | |
|---|
| 934 | from config import min_timestep, max_timestep, epsilon |
|---|
| 935 | |
|---|
| 936 | # FIXME: Maybe lump into a larger check prior to evolving |
|---|
| 937 | msg = 'Boundary tags must be bound to boundary objects before ' |
|---|
| 938 | msg += 'evolving system, ' |
|---|
| 939 | msg += 'e.g. using the method set_boundary.\n' |
|---|
| 940 | msg += 'This system has the boundary tags %s '\ |
|---|
| 941 | %self.get_boundary_tags() |
|---|
| 942 | assert hasattr(self, 'boundary_objects'), msg |
|---|
| 943 | |
|---|
| 944 | |
|---|
| 945 | if yieldstep is None: |
|---|
| 946 | yieldstep = max_timestep |
|---|
| 947 | else: |
|---|
| 948 | yieldstep = numpy.float(yieldstep) |
|---|
| 949 | |
|---|
| 950 | self._order_ = self.default_order |
|---|
| 951 | |
|---|
| 952 | |
|---|
| 953 | if finaltime is not None and duration is not None: |
|---|
| 954 | # print 'F', finaltime, duration |
|---|
| 955 | msg = 'Only one of finaltime and duration may be specified' |
|---|
| 956 | raise msg |
|---|
| 957 | else: |
|---|
| 958 | if finaltime is not None: |
|---|
| 959 | self.finaltime = numpy.float(finaltime) |
|---|
| 960 | if duration is not None: |
|---|
| 961 | self.finaltime = self.starttime + numpy.float(duration) |
|---|
| 962 | |
|---|
| 963 | |
|---|
| 964 | |
|---|
| 965 | N = len(self) # Number of triangles |
|---|
| 966 | self.yieldtime = 0.0 # Track time between 'yields' |
|---|
| 967 | |
|---|
| 968 | # Initialise interval of timestep sizes (for reporting only) |
|---|
| 969 | self.min_timestep = max_timestep |
|---|
| 970 | self.max_timestep = min_timestep |
|---|
| 971 | self.number_of_steps = 0 |
|---|
| 972 | self.number_of_first_order_steps = 0 |
|---|
| 973 | |
|---|
| 974 | |
|---|
| 975 | # Update ghosts |
|---|
| 976 | self.update_ghosts() |
|---|
| 977 | |
|---|
| 978 | # Initial update of vertex and edge values |
|---|
| 979 | self.distribute_to_vertices_and_edges() |
|---|
| 980 | |
|---|
| 981 | # Update extrema if necessary (for reporting) |
|---|
| 982 | self.update_extrema() |
|---|
| 983 | |
|---|
| 984 | # Initial update boundary values |
|---|
| 985 | self.update_boundary() |
|---|
| 986 | |
|---|
| 987 | # Or maybe restore from latest checkpoint |
|---|
| 988 | if self.checkpoint is True: |
|---|
| 989 | self.goto_latest_checkpoint() |
|---|
| 990 | |
|---|
| 991 | if skip_initial_step is False: |
|---|
| 992 | yield(self.time) # Yield initial values |
|---|
| 993 | |
|---|
| 994 | while True: |
|---|
| 995 | |
|---|
| 996 | # Evolve One Step, using appropriate timestepping method |
|---|
| 997 | if self.get_timestepping_method() == 'euler': |
|---|
| 998 | self.evolve_one_euler_step(yieldstep,finaltime) |
|---|
| 999 | |
|---|
| 1000 | elif self.get_timestepping_method() == 'rk2': |
|---|
| 1001 | self.evolve_one_rk2_step(yieldstep,finaltime) |
|---|
| 1002 | |
|---|
| 1003 | elif self.get_timestepping_method() == 'rk3': |
|---|
| 1004 | self.evolve_one_rk3_step(yieldstep,finaltime) |
|---|
| 1005 | |
|---|
| 1006 | |
|---|
| 1007 | # Update extrema if necessary (for reporting) |
|---|
| 1008 | self.update_extrema() |
|---|
| 1009 | |
|---|
| 1010 | |
|---|
| 1011 | |
|---|
| 1012 | self.yieldtime += self.timestep |
|---|
| 1013 | self.number_of_steps += 1 |
|---|
| 1014 | if self._order_ == 1: |
|---|
| 1015 | self.number_of_first_order_steps += 1 |
|---|
| 1016 | |
|---|
| 1017 | |
|---|
| 1018 | # Yield results |
|---|
| 1019 | if finaltime is not None and self.time >= finaltime-epsilon: |
|---|
| 1020 | |
|---|
| 1021 | if self.time > finaltime: |
|---|
| 1022 | # FIXME (Ole, 30 April 2006): Do we need this check? |
|---|
| 1023 | # Probably not (Ole, 18 September 2008). Now changed to |
|---|
| 1024 | # Exception |
|---|
| 1025 | msg = 'WARNING (domain.py): time overshot finaltime. ' |
|---|
| 1026 | msg += 'Contact Ole.Nielsen@ga.gov.au' |
|---|
| 1027 | raise Exception, msg |
|---|
| 1028 | |
|---|
| 1029 | |
|---|
| 1030 | # Yield final time and stop |
|---|
| 1031 | self.time = finaltime |
|---|
| 1032 | yield(self.time) |
|---|
| 1033 | break |
|---|
| 1034 | |
|---|
| 1035 | if self.yieldtime >= yieldstep: |
|---|
| 1036 | # Yield (intermediate) time and allow inspection of domain |
|---|
| 1037 | |
|---|
| 1038 | if self.checkpoint is True: |
|---|
| 1039 | self.store_checkpoint() |
|---|
| 1040 | self.delete_old_checkpoints() |
|---|
| 1041 | |
|---|
| 1042 | # Pass control on to outer loop for more specific actions |
|---|
| 1043 | |
|---|
| 1044 | yield(self.time) |
|---|
| 1045 | |
|---|
| 1046 | # Reinitialise |
|---|
| 1047 | self.yieldtime = 0.0 |
|---|
| 1048 | self.min_timestep = max_timestep |
|---|
| 1049 | self.max_timestep = min_timestep |
|---|
| 1050 | self.number_of_steps = 0 |
|---|
| 1051 | self.number_of_first_order_steps = 0 |
|---|
| 1052 | #self.max_speed_array = 0.0 |
|---|
| 1053 | |
|---|
| 1054 | |
|---|
| 1055 | def evolve_one_euler_step(self, yieldstep, finaltime): |
|---|
| 1056 | """ |
|---|
| 1057 | One Euler Time Step |
|---|
| 1058 | Q^{n+1} = E(h) Q^n |
|---|
| 1059 | """ |
|---|
| 1060 | |
|---|
| 1061 | # Compute fluxes across each element edge |
|---|
| 1062 | self.compute_fluxes() |
|---|
| 1063 | |
|---|
| 1064 | |
|---|
| 1065 | # Update timestep to fit yieldstep and finaltime |
|---|
| 1066 | self.update_timestep(yieldstep, finaltime) |
|---|
| 1067 | |
|---|
| 1068 | # Update conserved quantities |
|---|
| 1069 | self.update_conserved_quantities() |
|---|
| 1070 | |
|---|
| 1071 | # Update ghosts |
|---|
| 1072 | self.update_ghosts() |
|---|
| 1073 | |
|---|
| 1074 | # Update vertex and edge values |
|---|
| 1075 | self.distribute_to_vertices_and_edges() |
|---|
| 1076 | |
|---|
| 1077 | # Update boundary values |
|---|
| 1078 | self.update_boundary() |
|---|
| 1079 | |
|---|
| 1080 | # Update time |
|---|
| 1081 | self.time += self.timestep |
|---|
| 1082 | |
|---|
| 1083 | |
|---|
| 1084 | |
|---|
| 1085 | |
|---|
| 1086 | def evolve_one_rk2_step(self, yieldstep, finaltime): |
|---|
| 1087 | """ |
|---|
| 1088 | One 2nd order RK timestep |
|---|
| 1089 | Q^{n+1} = 0.5 Q^n + 0.5 E(h)^2 Q^n |
|---|
| 1090 | """ |
|---|
| 1091 | |
|---|
| 1092 | |
|---|
| 1093 | # Save initial conserved quantities values |
|---|
| 1094 | self.backup_conserved_quantities() |
|---|
| 1095 | |
|---|
| 1096 | #-------------------------------------- |
|---|
| 1097 | # First euler step |
|---|
| 1098 | #-------------------------------------- |
|---|
| 1099 | |
|---|
| 1100 | # Compute fluxes across each element edge |
|---|
| 1101 | self.compute_fluxes() |
|---|
| 1102 | |
|---|
| 1103 | # Update timestep to fit yieldstep and finaltime |
|---|
| 1104 | self.update_timestep(yieldstep, finaltime) |
|---|
| 1105 | |
|---|
| 1106 | # Update conserved quantities |
|---|
| 1107 | self.update_conserved_quantities() |
|---|
| 1108 | |
|---|
| 1109 | # Update ghosts |
|---|
| 1110 | self.update_ghosts() |
|---|
| 1111 | |
|---|
| 1112 | # Update vertex and edge values |
|---|
| 1113 | self.distribute_to_vertices_and_edges() |
|---|
| 1114 | |
|---|
| 1115 | # Update boundary values |
|---|
| 1116 | self.update_boundary() |
|---|
| 1117 | |
|---|
| 1118 | # Update time |
|---|
| 1119 | self.time += self.timestep |
|---|
| 1120 | |
|---|
| 1121 | #------------------------------------ |
|---|
| 1122 | # Second Euler step |
|---|
| 1123 | #------------------------------------ |
|---|
| 1124 | |
|---|
| 1125 | # Compute fluxes across each element edge |
|---|
| 1126 | self.compute_fluxes() |
|---|
| 1127 | |
|---|
| 1128 | # Update conserved quantities |
|---|
| 1129 | self.update_conserved_quantities() |
|---|
| 1130 | |
|---|
| 1131 | #------------------------------------ |
|---|
| 1132 | # Combine initial and final values |
|---|
| 1133 | # of conserved quantities and cleanup |
|---|
| 1134 | #------------------------------------ |
|---|
| 1135 | |
|---|
| 1136 | # Combine steps |
|---|
| 1137 | self.saxpy_conserved_quantities(0.5, 0.5) |
|---|
| 1138 | |
|---|
| 1139 | #----------------------------------- |
|---|
| 1140 | # clean up vertex values |
|---|
| 1141 | #----------------------------------- |
|---|
| 1142 | |
|---|
| 1143 | # Update ghosts |
|---|
| 1144 | self.update_ghosts() |
|---|
| 1145 | |
|---|
| 1146 | # Update vertex and edge values |
|---|
| 1147 | self.distribute_to_vertices_and_edges() |
|---|
| 1148 | |
|---|
| 1149 | # Update boundary values |
|---|
| 1150 | self.update_boundary() |
|---|
| 1151 | |
|---|
| 1152 | |
|---|
| 1153 | |
|---|
| 1154 | def evolve_one_rk3_step(self, yieldstep, finaltime): |
|---|
| 1155 | """ |
|---|
| 1156 | One 3rd order RK timestep |
|---|
| 1157 | Q^(1) = 3/4 Q^n + 1/4 E(h)^2 Q^n (at time t^n + h/2) |
|---|
| 1158 | Q^{n+1} = 1/3 Q^n + 2/3 E(h) Q^(1) (at time t^{n+1}) |
|---|
| 1159 | """ |
|---|
| 1160 | |
|---|
| 1161 | # Save initial initial conserved quantities values |
|---|
| 1162 | self.backup_conserved_quantities() |
|---|
| 1163 | |
|---|
| 1164 | initial_time = self.time |
|---|
| 1165 | |
|---|
| 1166 | #-------------------------------------- |
|---|
| 1167 | # First euler step |
|---|
| 1168 | #-------------------------------------- |
|---|
| 1169 | |
|---|
| 1170 | # Compute fluxes across each element edge |
|---|
| 1171 | self.compute_fluxes() |
|---|
| 1172 | |
|---|
| 1173 | # Update timestep to fit yieldstep and finaltime |
|---|
| 1174 | self.update_timestep(yieldstep, finaltime) |
|---|
| 1175 | |
|---|
| 1176 | # Update conserved quantities |
|---|
| 1177 | self.update_conserved_quantities() |
|---|
| 1178 | |
|---|
| 1179 | # Update ghosts |
|---|
| 1180 | self.update_ghosts() |
|---|
| 1181 | |
|---|
| 1182 | # Update vertex and edge values |
|---|
| 1183 | self.distribute_to_vertices_and_edges() |
|---|
| 1184 | |
|---|
| 1185 | # Update boundary values |
|---|
| 1186 | self.update_boundary() |
|---|
| 1187 | |
|---|
| 1188 | # Update time |
|---|
| 1189 | self.time += self.timestep |
|---|
| 1190 | |
|---|
| 1191 | #------------------------------------ |
|---|
| 1192 | # Second Euler step |
|---|
| 1193 | #------------------------------------ |
|---|
| 1194 | |
|---|
| 1195 | # Compute fluxes across each element edge |
|---|
| 1196 | self.compute_fluxes() |
|---|
| 1197 | |
|---|
| 1198 | # Update conserved quantities |
|---|
| 1199 | self.update_conserved_quantities() |
|---|
| 1200 | |
|---|
| 1201 | #------------------------------------ |
|---|
| 1202 | #Combine steps to obtain intermediate |
|---|
| 1203 | #solution at time t^n + 0.5 h |
|---|
| 1204 | #------------------------------------ |
|---|
| 1205 | |
|---|
| 1206 | # Combine steps |
|---|
| 1207 | self.saxpy_conserved_quantities(0.25, 0.75) |
|---|
| 1208 | |
|---|
| 1209 | # Update ghosts |
|---|
| 1210 | self.update_ghosts() |
|---|
| 1211 | |
|---|
| 1212 | # Update vertex and edge values |
|---|
| 1213 | self.distribute_to_vertices_and_edges() |
|---|
| 1214 | |
|---|
| 1215 | # Update boundary values |
|---|
| 1216 | self.update_boundary() |
|---|
| 1217 | |
|---|
| 1218 | # Set substep time |
|---|
| 1219 | self.time = initial_time + self.timestep*0.5 |
|---|
| 1220 | |
|---|
| 1221 | #------------------------------------ |
|---|
| 1222 | # Third Euler step |
|---|
| 1223 | #------------------------------------ |
|---|
| 1224 | |
|---|
| 1225 | # Compute fluxes across each element edge |
|---|
| 1226 | self.compute_fluxes() |
|---|
| 1227 | |
|---|
| 1228 | # Update conserved quantities |
|---|
| 1229 | self.update_conserved_quantities() |
|---|
| 1230 | |
|---|
| 1231 | #------------------------------------ |
|---|
| 1232 | # Combine final and initial values |
|---|
| 1233 | # and cleanup |
|---|
| 1234 | #------------------------------------ |
|---|
| 1235 | |
|---|
| 1236 | # Combine steps |
|---|
| 1237 | self.saxpy_conserved_quantities(2.0/3.0, 1.0/3.0) |
|---|
| 1238 | |
|---|
| 1239 | # Update ghosts |
|---|
| 1240 | self.update_ghosts() |
|---|
| 1241 | |
|---|
| 1242 | # Update vertex and edge values |
|---|
| 1243 | self.distribute_to_vertices_and_edges() |
|---|
| 1244 | |
|---|
| 1245 | # Update boundary values |
|---|
| 1246 | self.update_boundary() |
|---|
| 1247 | |
|---|
| 1248 | # Set new time |
|---|
| 1249 | self.time = initial_time + self.timestep |
|---|
| 1250 | |
|---|
| 1251 | |
|---|
| 1252 | def backup_conserved_quantities(self): |
|---|
| 1253 | N = len(self) # Number_of_triangles |
|---|
| 1254 | |
|---|
| 1255 | # Backup conserved_quantities centroid values |
|---|
| 1256 | for name in self.conserved_quantities: |
|---|
| 1257 | Q = self.quantities[name] |
|---|
| 1258 | Q.backup_centroid_values() |
|---|
| 1259 | |
|---|
| 1260 | def saxpy_conserved_quantities(self,a,b): |
|---|
| 1261 | N = len(self) #number_of_triangles |
|---|
| 1262 | |
|---|
| 1263 | # Backup conserved_quantities centroid values |
|---|
| 1264 | for name in self.conserved_quantities: |
|---|
| 1265 | Q = self.quantities[name] |
|---|
| 1266 | Q.saxpy_centroid_values(a,b) |
|---|
| 1267 | |
|---|
| 1268 | |
|---|
| 1269 | |
|---|
| 1270 | |
|---|
| 1271 | def distribute_to_vertices_and_edges(self): |
|---|
| 1272 | """Extrapolate conserved quantities from centroid to |
|---|
| 1273 | vertices and edge-midpoints for each volume |
|---|
| 1274 | |
|---|
| 1275 | Default implementation is straight first order, |
|---|
| 1276 | i.e. constant values throughout each element and |
|---|
| 1277 | no reference to non-conserved quantities. |
|---|
| 1278 | """ |
|---|
| 1279 | |
|---|
| 1280 | for name in self.conserved_quantities: |
|---|
| 1281 | Q = self.quantities[name] |
|---|
| 1282 | if self.order == 1: |
|---|
| 1283 | Q.extrapolate_first_order() |
|---|
| 1284 | elif self.order == 2: |
|---|
| 1285 | Q.extrapolate_second_order() |
|---|
| 1286 | #Q.limit() |
|---|
| 1287 | else: |
|---|
| 1288 | raise 'Unknown order' |
|---|
| 1289 | #Q.interpolate_from_vertices_to_edges() |
|---|
| 1290 | |
|---|
| 1291 | |
|---|
| 1292 | def update_ghosts(self): |
|---|
| 1293 | pass |
|---|
| 1294 | |
|---|
| 1295 | def update_boundary(self): |
|---|
| 1296 | """Go through list of boundary objects and update boundary values |
|---|
| 1297 | for all conserved quantities on boundary. |
|---|
| 1298 | """ |
|---|
| 1299 | |
|---|
| 1300 | #FIXME: Update only those that change (if that can be worked out) |
|---|
| 1301 | #FIXME: Boundary objects should not include ghost nodes. |
|---|
| 1302 | #for i, ((vol_id, edge_id), B) in enumerate(self.boundary_objects): |
|---|
| 1303 | # q = B.evaluate(vol_id, edge_id) |
|---|
| 1304 | for i, ((vol_id, vertex_id), B) in enumerate(self.boundary_objects): |
|---|
| 1305 | q = B.evaluate(vol_id, vertex_id) |
|---|
| 1306 | #print 'q ',q |
|---|
| 1307 | for j, name in enumerate(self.evolved_quantities): |
|---|
| 1308 | #print 'name %s j = %f \n'%(name,j) |
|---|
| 1309 | Q = self.quantities[name] |
|---|
| 1310 | |
|---|
| 1311 | Q.boundary_values[i] = q[j] |
|---|
| 1312 | #print 'Q=',Q |
|---|
| 1313 | |
|---|
| 1314 | def update_timestep(self, yieldstep, finaltime): |
|---|
| 1315 | |
|---|
| 1316 | from config import min_timestep, max_timestep |
|---|
| 1317 | |
|---|
| 1318 | # self.timestep is calculated from speed of characteristics |
|---|
| 1319 | # Apply CFL condition here |
|---|
| 1320 | timestep = min(self.CFL*self.flux_timestep, max_timestep) |
|---|
| 1321 | |
|---|
| 1322 | #Record maximal and minimal values of timestep for reporting |
|---|
| 1323 | self.max_timestep = max(timestep, self.max_timestep) |
|---|
| 1324 | self.min_timestep = min(timestep, self.min_timestep) |
|---|
| 1325 | |
|---|
| 1326 | #Protect against degenerate time steps |
|---|
| 1327 | if timestep < min_timestep: |
|---|
| 1328 | |
|---|
| 1329 | #Number of consecutive small steps taken b4 taking action |
|---|
| 1330 | self.smallsteps += 1 |
|---|
| 1331 | |
|---|
| 1332 | if self.smallsteps > self.max_smallsteps: |
|---|
| 1333 | self.smallsteps = 0 #Reset |
|---|
| 1334 | |
|---|
| 1335 | if self.order == 1: |
|---|
| 1336 | msg = 'WARNING: Too small timestep %.16f reached '\ |
|---|
| 1337 | %timestep |
|---|
| 1338 | msg += 'even after %d steps of 1 order scheme'\ |
|---|
| 1339 | %self.max_smallsteps |
|---|
| 1340 | print msg |
|---|
| 1341 | timestep = min_timestep #Try enforcing min_step |
|---|
| 1342 | |
|---|
| 1343 | #raise msg |
|---|
| 1344 | else: |
|---|
| 1345 | #Try to overcome situation by switching to 1 order |
|---|
| 1346 | print "changing Order 1" |
|---|
| 1347 | self.order = 1 |
|---|
| 1348 | |
|---|
| 1349 | else: |
|---|
| 1350 | self.smallsteps = 0 |
|---|
| 1351 | if self.order == 1 and self.default_order == 2: |
|---|
| 1352 | self.order = 2 |
|---|
| 1353 | |
|---|
| 1354 | |
|---|
| 1355 | #Ensure that final time is not exceeded |
|---|
| 1356 | if finaltime is not None and self.time + timestep > finaltime: |
|---|
| 1357 | timestep = finaltime-self.time |
|---|
| 1358 | |
|---|
| 1359 | #Ensure that model time is aligned with yieldsteps |
|---|
| 1360 | if self.yieldtime + timestep > yieldstep: |
|---|
| 1361 | timestep = yieldstep-self.yieldtime |
|---|
| 1362 | |
|---|
| 1363 | self.timestep = timestep |
|---|
| 1364 | |
|---|
| 1365 | def update_extrema(self): |
|---|
| 1366 | pass |
|---|
| 1367 | |
|---|
| 1368 | def compute_forcing_terms(self): |
|---|
| 1369 | """If there are any forcing functions driving the system |
|---|
| 1370 | they should be defined in Domain subclass and appended to |
|---|
| 1371 | the list self.forcing_terms |
|---|
| 1372 | """ |
|---|
| 1373 | #Clears explicit_update needed for second order method |
|---|
| 1374 | if self.time_order == 2: |
|---|
| 1375 | for name in self.conserved_quantities: |
|---|
| 1376 | Q = self.quantities[name] |
|---|
| 1377 | Q.explicit_update[:] = 0.0 |
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| 1378 | |
|---|
| 1379 | for f in self.forcing_terms: |
|---|
| 1380 | f(self) |
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| 1381 | |
|---|
| 1382 | |
|---|
| 1383 | def update_derived_quantites(self): |
|---|
| 1384 | pass |
|---|
| 1385 | |
|---|
| 1386 | #def update_conserved_quantities(self): |
|---|
| 1387 | def update_conserved_quantities(self): |
|---|
| 1388 | """Update vectors of conserved quantities using previously |
|---|
| 1389 | computed fluxes specified forcing functions. |
|---|
| 1390 | """ |
|---|
| 1391 | |
|---|
| 1392 | |
|---|
| 1393 | # Stage = self.quantities['stage'] |
|---|
| 1394 | # Xmom = self.quantities['xmomentum'] |
|---|
| 1395 | # Bed = self.quantities['elevation'] |
|---|
| 1396 | # Height = self.quantities['height'] |
|---|
| 1397 | # Velocity = self.quantities['velocity'] |
|---|
| 1398 | # |
|---|
| 1399 | # #Arrays |
|---|
| 1400 | # w_C = Stage.centroid_values |
|---|
| 1401 | # uh_C = Xmom.centroid_values |
|---|
| 1402 | # z_C = Bed.centroid_values |
|---|
| 1403 | # h_C = Height.centroid_values |
|---|
| 1404 | # u_C = Velocity.centroid_values |
|---|
| 1405 | # |
|---|
| 1406 | # import numpy as np |
|---|
| 1407 | # print '== before forcing =======' |
|---|
| 1408 | # print 'w_C', np.any(np.isnan(w_C)) |
|---|
| 1409 | # print 'uh_C', np.any(np.isnan(uh_C)) |
|---|
| 1410 | # print 'z_C', np.any(np.isnan(z_C)) |
|---|
| 1411 | # print 'h_C', np.any(np.isnan(h_C)) |
|---|
| 1412 | # print 'u_C', np.any(np.isnan(u_C)) |
|---|
| 1413 | # print 'w_ex_update', np.any(np.isnan(Stage.explicit_update)) |
|---|
| 1414 | |
|---|
| 1415 | timestep = self.timestep |
|---|
| 1416 | |
|---|
| 1417 | |
|---|
| 1418 | |
|---|
| 1419 | #Compute forcing terms |
|---|
| 1420 | self.compute_forcing_terms() |
|---|
| 1421 | |
|---|
| 1422 | # print '==after forcing =======' |
|---|
| 1423 | # print 'w_C', np.any(np.isnan(w_C)) |
|---|
| 1424 | # print 'uh_C', np.any(np.isnan(uh_C)) |
|---|
| 1425 | # print 'z_C', np.any(np.isnan(z_C)) |
|---|
| 1426 | # print 'h_C', np.any(np.isnan(h_C)) |
|---|
| 1427 | # print 'u_C', np.any(np.isnan(u_C)) |
|---|
| 1428 | # print 'w_ex_update', np.any(np.isnan(Stage.explicit_update)) |
|---|
| 1429 | |
|---|
| 1430 | #Update conserved_quantities |
|---|
| 1431 | for name in self.conserved_quantities: |
|---|
| 1432 | Q = self.quantities[name] |
|---|
| 1433 | Q.update(timestep) |
|---|
| 1434 | |
|---|
| 1435 | # print '==after quantity update =======' |
|---|
| 1436 | # print 'w_C', np.any(np.isnan(w_C)) |
|---|
| 1437 | # print 'uh_C', np.any(np.isnan(uh_C)) |
|---|
| 1438 | # print 'z_C', np.any(np.isnan(z_C)) |
|---|
| 1439 | # print 'h_C', np.any(np.isnan(h_C)) |
|---|
| 1440 | # print 'u_C', np.any(np.isnan(u_C)) |
|---|
| 1441 | # print 'w_ex_update', np.any(np.isnan(Stage.explicit_update)) |
|---|
| 1442 | |
|---|
| 1443 | if __name__ == "__main__": |
|---|
| 1444 | |
|---|
| 1445 | points1 = [0.0, 1.0, 2.0, 3.0] |
|---|
| 1446 | D1 = Domain(points1) |
|---|
| 1447 | |
|---|
| 1448 | print D1.get_coordinate(0) |
|---|
| 1449 | print D1.get_coordinate(0,1) |
|---|
| 1450 | print 'Number of Elements = ',D1.number_of_elements |
|---|
| 1451 | |
|---|
| 1452 | try: |
|---|
| 1453 | print D1.get_coordinate(3) |
|---|
| 1454 | except: |
|---|
| 1455 | pass |
|---|
| 1456 | else: |
|---|
| 1457 | msg = 'Should have raised an out of bounds exception' |
|---|
| 1458 | raise msg |
|---|
| 1459 | |
|---|
| 1460 | #points2 = [0.0, 1.0, 2.0, 3.0, 2.5] |
|---|
| 1461 | #D2 = Domain(points2) |
|---|
