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 | from generic_boundary_conditions import * |
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10 | #from coordinate_transforms.geo_reference import Geo_reference |
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11 | |
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12 | class Domain: |
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13 | |
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14 | def __init__(self, coordinates, boundary = None, |
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15 | conserved_quantities = None, other_quantities = None, |
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16 | tagged_elements = None): |
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17 | """ |
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18 | Build 1D elements from x coordinates |
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19 | """ |
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20 | |
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21 | from Numeric import array, zeros, Float, Int |
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22 | |
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23 | #Store Points |
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24 | self.coordinates = array(coordinates) |
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25 | |
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26 | ## if geo_reference is None: |
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27 | ## self. = Geo_reference() #Use defaults |
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28 | ## else: |
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29 | ## self.geo_reference = geo_reference |
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30 | |
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31 | #Register number of Elements |
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32 | self.number_of_elements = N = len(self.coordinates)-1 |
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33 | |
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34 | self.beta = 1.0 |
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35 | self.limiter = "minmod_kurganov" |
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36 | self.wet_nodes = zeros((N,2), Int) # should this be here |
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37 | |
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38 | #Allocate space for neighbour and boundary structures |
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39 | self.neighbours = zeros((N, 2), Int) |
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40 | #self.neighbour_edges = zeros((N, 2), Int) |
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41 | self.neighbour_vertices = zeros((N, 2), Int) |
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42 | self.number_of_boundaries = zeros(N, Int) |
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43 | self.surrogate_neighbours = zeros((N, 2), Int) |
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44 | |
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45 | #Allocate space for geometric quantities |
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46 | self.vertices = zeros((N, 2), Float) |
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47 | self.centroids = zeros(N, Float) |
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48 | self.areas = zeros(N, Float) |
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49 | |
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50 | self.normals = zeros((N, 2), Float) |
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51 | |
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52 | for i in range(N): |
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53 | xl = self.coordinates[i] |
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54 | xr = self.coordinates[i+1] |
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55 | self.vertices[i,0] = xl |
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56 | self.vertices[i,1] = xr |
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57 | |
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58 | centroid = (xl+xr)/2.0 |
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59 | self.centroids[i] = centroid |
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60 | |
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61 | msg = 'Coordinates should be ordered, smallest to largest' |
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62 | assert xr>xl, msg |
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63 | |
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64 | #The normal vectors |
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65 | # - point outward from each edge |
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66 | # - are orthogonal to the edge |
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67 | # - have unit length |
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68 | # - Are enumerated by left vertex then right vertex normals |
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69 | |
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70 | nl = -1.0 |
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71 | nr = 1.0 |
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72 | self.normals[i,:] = [nl, nr] |
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73 | |
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74 | self.areas[i] = (xr-xl) |
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75 | |
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76 | ## print 'N', N |
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77 | ## print 'Centroid', self.centroids |
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78 | ## print 'Areas', self.areas |
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79 | ## print 'Vertex_Coordinates', self.vertices |
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80 | |
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81 | #Initialise Neighbours (-1 means that it is a boundary neighbour) |
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82 | self.neighbours[i, :] = [-1, -1] |
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83 | #Initialise edge ids of neighbours |
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84 | #Initialise vertex ids of neighbours |
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85 | #In case of boundaries this slot is not used |
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86 | #self.neighbour_edges[i, :] = [-1, -1] |
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87 | self.neighbour_vertices[i, :] = [-1, -1] |
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88 | |
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89 | self.build_vertexlist() |
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90 | |
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91 | #Build neighbour structure |
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92 | self.build_neighbour_structure() |
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93 | |
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94 | #Build surrogate neighbour structure |
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95 | self.build_surrogate_neighbour_structure() |
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96 | |
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97 | #Build boundary dictionary mapping (id, edge) to symbolic tags |
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98 | #Build boundary dictionary mapping (id, vertex) to symbolic tags |
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99 | self.build_boundary_dictionary(boundary) |
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100 | |
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101 | #Build tagged element dictionary mapping (tag) to array of elements |
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102 | self.build_tagged_elements_dictionary(tagged_elements) |
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103 | |
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104 | from quantity import Quantity, Conserved_quantity |
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105 | #from quantity_domain import Quantity, Conserved_quantity |
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106 | |
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107 | #List of quantity names entering |
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108 | #the conservation equations |
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109 | #(Must be a subset of quantities) |
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110 | if conserved_quantities is None: |
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111 | self.conserved_quantities = [] |
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112 | else: |
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113 | self.conserved_quantities = conserved_quantities |
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114 | |
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115 | if other_quantities is None: |
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116 | self.other_quantities = [] |
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117 | else: |
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118 | self.other_quantities = other_quantities |
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119 | |
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120 | |
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121 | #Build dictionary of Quantity instances keyed by quantity names |
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122 | self.quantities = {} |
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123 | |
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124 | #FIXME: remove later - maybe OK, though.... |
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125 | for name in self.conserved_quantities: |
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126 | self.quantities[name] = Quantity(self) |
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127 | for name in self.other_quantities: |
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128 | self.quantities[name] = Quantity(self) |
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129 | |
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130 | #Create an empty list for explicit forcing terms |
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131 | self.forcing_terms = [] |
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132 | |
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133 | #Defaults |
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134 | from config import max_smallsteps, beta_w, beta_h, epsilon, CFL |
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135 | self.beta_w = beta_w |
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136 | self.beta_h = beta_h |
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137 | self.epsilon = epsilon |
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138 | |
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139 | #FIXME: Maybe have separate orders for h-limiter and w-limiter? |
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140 | #Or maybe get rid of order altogether and use beta_w and beta_h |
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141 | self.default_order = 1 |
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142 | self.order = self.default_order |
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143 | |
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144 | self.default_time_order = 1 |
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145 | self.time_order = self.default_time_order |
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146 | |
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147 | self.smallsteps = 0 |
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148 | self.max_smallsteps = max_smallsteps |
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149 | self.number_of_steps = 0 |
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150 | self.number_of_first_order_steps = 0 |
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151 | self.CFL = CFL |
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152 | |
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153 | #Model time |
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154 | self.time = 0.0 |
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155 | self.finaltime = None |
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156 | self.min_timestep = self.max_timestep = 0.0 |
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157 | self.starttime = 0 #Physical starttime if any (0 is 1 Jan 1970 00:00:00) |
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158 | #Checkpointing and storage |
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159 | from config import default_datadir |
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160 | self.datadir = default_datadir |
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161 | self.filename = 'domain' |
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162 | self.checkpoint = False |
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163 | |
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164 | def __len__(self): |
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165 | return self.number_of_elements |
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166 | |
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167 | def build_vertexlist(self): |
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168 | """Build vertexlist index by vertex ids and for each entry (point id) |
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169 | build a list of (triangles, vertex_id) pairs that use the point |
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170 | as vertex. |
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171 | |
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172 | Preconditions: |
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173 | self.coordinates and self.triangles are defined |
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174 | |
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175 | Postcondition: |
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176 | self.vertexlist is built |
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177 | """ |
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178 | from Numeric import array |
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179 | |
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180 | vertexlist = [None]*len(self.coordinates) |
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181 | for i in range(self.number_of_elements): |
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182 | |
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183 | #a = self.triangles[i, 0] |
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184 | #b = self.triangles[i, 1] |
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185 | #c = self.triangles[i, 2] |
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186 | a = i |
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187 | b = i + 1 |
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188 | |
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189 | #Register the vertices v as lists of |
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190 | #(triangle_id, vertex_id) tuples associated with them |
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191 | #This is used for smoothing |
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192 | #for vertex_id, v in enumerate([a,b,c]): |
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193 | for vertex_id, v in enumerate([a,b]): |
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194 | if vertexlist[v] is None: |
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195 | vertexlist[v] = [] |
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196 | |
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197 | vertexlist[v].append( (i, vertex_id) ) |
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198 | |
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199 | self.vertexlist = vertexlist |
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200 | |
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201 | |
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202 | def build_neighbour_structure(self): |
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203 | """Update all registered triangles to point to their neighbours. |
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204 | |
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205 | Also, keep a tally of the number of boundaries for each triangle |
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206 | |
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207 | Postconditions: |
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208 | neighbours and neighbour_edges is populated |
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209 | neighbours and neighbour_vertices is populated |
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210 | number_of_boundaries integer array is defined. |
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211 | """ |
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212 | |
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213 | #Step 1: |
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214 | #Build dictionary mapping from segments (2-tuple of points) |
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215 | #to left hand side edge (facing neighbouring triangle) |
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216 | |
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217 | N = self.number_of_elements |
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218 | neighbourdict = {} |
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219 | #l_edge = 0 |
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220 | #r_edge = 1 |
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221 | l_vertex = 0 |
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222 | r_vertex = 1 |
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223 | for i in range(N): |
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224 | |
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225 | #Register all segments as keys mapping to current triangle |
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226 | #and segment id |
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227 | #a = self.triangles[i, 0] |
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228 | #b = self.triangles[i, 1] |
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229 | #c = self.triangles[i, 2] |
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230 | a = self.vertices[i,0] |
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231 | b = self.vertices[i,1] |
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232 | |
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233 | """ |
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234 | if neighbourdict.has_key((a,b)): |
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235 | 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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236 | raise msg |
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237 | if neighbourdict.has_key((b,c)): |
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238 | 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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239 | raise msg |
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240 | if neighbourdict.has_key((c,a)): |
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241 | 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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242 | raise msg |
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243 | """ |
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244 | #neighbourdict[a,b] = (i, 2) #(id, edge) |
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245 | #neighbourdict[b,c] = (i, 0) #(id, edge) |
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246 | #neighbourdict[c,a] = (i, 1) #(id, edge) |
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247 | #neighbourdict[a,b] = (i, 1) #(id, edge) |
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248 | #neighbourdict[b,a] = (i, 0) #(id, edge) |
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249 | #neighbourdict[a,l_edge] = (i, 0) #(id, edge) |
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250 | #neighbourdict[b,r_edge] = (i, 1) #(id, edge) |
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251 | neighbourdict[a,l_vertex] = (i, 0) #(id, vertex) |
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252 | neighbourdict[b,r_vertex] = (i, 1) #(id, vertex) |
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253 | |
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254 | |
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255 | #Step 2: |
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256 | #Go through triangles again, but this time |
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257 | #reverse direction of segments and lookup neighbours. |
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258 | for i in range(N): |
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259 | #a = self.triangles[i, 0] |
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260 | #b = self.triangles[i, 1] |
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261 | #c = self.triangles[i, 2] |
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262 | |
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263 | a = self.vertices[i,0] |
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264 | b = self.vertices[i,1] |
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265 | |
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266 | #self.number_of_boundaries[i] = 3 |
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267 | self.number_of_boundaries[i] = 2 |
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268 | #if neighbourdict.has_key((b,l_edge)): |
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269 | if neighbourdict.has_key((b,l_vertex)): |
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270 | #self.neighbours[i, 1] = neighbourdict[b,l_edge][0] |
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271 | #self.neighbour_edges[i, 1] = neighbourdict[b,l_edge][1] |
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272 | self.neighbours[i, 1] = neighbourdict[b,l_vertex][0] |
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273 | self.neighbour_vertices[i, 1] = neighbourdict[b,l_vertex][1] |
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274 | self.number_of_boundaries[i] -= 1 |
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275 | |
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276 | #if neighbourdict.has_key((a,r_edge)): |
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277 | if neighbourdict.has_key((a,r_vertex)): |
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278 | #self.neighbours[i, 0] = neighbourdict[a,r_edge][0] |
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279 | #self.neighbour_edges[i, 0] = neighbourdict[a,r_edge][1] |
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280 | self.neighbours[i, 0] = neighbourdict[a,r_vertex][0] |
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281 | self.neighbour_vertices[i, 0] = neighbourdict[a,r_vertex][1] |
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282 | self.number_of_boundaries[i] -= 1 |
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283 | |
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284 | #if neighbourdict.has_key((b,a)): |
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285 | # self.neighbours[i, 1] = neighbourdict[b,a][0] |
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286 | # self.neighbour_edges[i, 1] = neighbourdict[b,a][1] |
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287 | # self.number_of_boundaries[i] -= 1 |
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288 | |
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289 | #if neighbourdict.has_key((c,b)): |
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290 | # self.neighbours[i, 0] = neighbourdict[c,b][0] |
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291 | # self.neighbour_edges[i, 0] = neighbourdict[c,b][1] |
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292 | # self.number_of_boundaries[i] -= 1 |
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293 | |
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294 | #if neighbourdict.has_key((a,b)): |
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295 | # self.neighbours[i, 0] = neighbourdict[a,b][0] |
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296 | # self.neighbour_edges[i, 0] = neighbourdict[a,b][1] |
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297 | # self.number_of_boundaries[i] -= 1 |
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298 | |
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299 | def build_surrogate_neighbour_structure(self): |
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300 | """Build structure where each triangle edge points to its neighbours |
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301 | if they exist. Otherwise point to the triangle itself. |
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302 | |
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303 | The surrogate neighbour structure is useful for computing gradients |
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304 | based on centroid values of neighbours. |
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305 | |
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306 | Precondition: Neighbour structure is defined |
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307 | Postcondition: |
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308 | Surrogate neighbour structure is defined: |
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309 | surrogate_neighbours: i0, i1, i2 where all i_k >= 0 point to |
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310 | triangles. |
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311 | |
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312 | """ |
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313 | |
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314 | N = self.number_of_elements |
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315 | for i in range(N): |
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316 | #Find all neighbouring volumes that are not boundaries |
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317 | #for k in range(3): |
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318 | for k in range(2): |
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319 | if self.neighbours[i, k] < 0: |
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320 | self.surrogate_neighbours[i, k] = i #Point this triangle |
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321 | else: |
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322 | self.surrogate_neighbours[i, k] = self.neighbours[i, k] |
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323 | |
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324 | def build_boundary_dictionary(self, boundary = None): |
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325 | """Build or check the dictionary of boundary tags. |
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326 | self.boundary is a dictionary of tags, |
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327 | keyed by volume id and edge: |
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328 | { (id, edge): tag, ... } |
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329 | |
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330 | Postconditions: |
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331 | self.boundary is defined. |
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332 | """ |
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333 | |
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334 | from config import default_boundary_tag |
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335 | |
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336 | if boundary is None: |
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337 | boundary = {} |
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338 | for vol_id in range(self.number_of_elements): |
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339 | #for edge_id in range(0, 3): |
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340 | #for edge_id in range(0, 2): |
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341 | for vertex_id in range(0, 2): |
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342 | #if self.neighbours[vol_id, edge_id] < 0: |
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343 | if self.neighbours[vol_id, vertex_id] < 0: |
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344 | #boundary[(vol_id, edge_id)] = default_boundary_tag |
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345 | boundary[(vol_id, vertex_id)] = default_boundary_tag |
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346 | else: |
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347 | #Check that all keys in given boundary exist |
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348 | #for vol_id, edge_id in boundary.keys(): |
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349 | for vol_id, vertex_id in boundary.keys(): |
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350 | #msg = 'Segment (%d, %d) does not exist' %(vol_id, edge_id) |
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351 | msg = 'Segment (%d, %d) does not exist' %(vol_id, vertex_id) |
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352 | a, b = self.neighbours.shape |
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353 | #assert vol_id < a and edge_id < b, msg |
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354 | assert vol_id < a and vertex_id < b, msg |
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355 | |
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356 | #FIXME: This assert violates internal boundaries (delete it) |
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357 | #msg = 'Segment (%d, %d) is not a boundary' %(vol_id, edge_id) |
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358 | #assert self.neighbours[vol_id, edge_id] < 0, msg |
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359 | |
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360 | #Check that all boundary segments are assigned a tag |
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361 | for vol_id in range(self.number_of_elements): |
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362 | #for edge_id in range(0, 3): |
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363 | #for edge_id in range(0, 2): |
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364 | for vertex_id in range(0, 2): |
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365 | #if self.neighbours[vol_id, edge_id] < 0: |
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366 | if self.neighbours[vol_id, vertex_id] < 0: |
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367 | #if not boundary.has_key( (vol_id, edge_id) ): |
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368 | if not boundary.has_key( (vol_id, vertex_id) ): |
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369 | msg = 'WARNING: Given boundary does not contain ' |
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370 | #msg += 'tags for edge (%d, %d). '\ |
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371 | # %(vol_id, edge_id) |
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372 | msg += 'tags for vertex (%d, %d). '\ |
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373 | %(vol_id, vertex_id) |
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374 | msg += 'Assigning default tag (%s).'\ |
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375 | %default_boundary_tag |
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376 | |
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377 | #FIXME: Print only as per verbosity |
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378 | #print msg |
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379 | |
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380 | #FIXME: Make this situation an error in the future |
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381 | #and make another function which will |
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382 | #enable default boundary-tags where |
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383 | #tags a not specified |
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384 | #boundary[ (vol_id, edge_id) ] =\ |
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385 | boundary[ (vol_id, vertex_id) ] =\ |
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386 | default_boundary_tag |
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387 | |
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388 | |
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389 | |
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390 | self.boundary = boundary |
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391 | |
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392 | def build_tagged_elements_dictionary(self, tagged_elements = None): |
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393 | """Build the dictionary of element tags. |
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394 | self.tagged_elements is a dictionary of element arrays, |
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395 | keyed by tag: |
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396 | { (tag): [e1, e2, e3..] } |
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397 | |
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398 | Postconditions: |
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399 | self.element_tag is defined |
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400 | """ |
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401 | from Numeric import array, Int |
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402 | |
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403 | if tagged_elements is None: |
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404 | tagged_elements = {} |
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405 | else: |
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406 | #Check that all keys in given boundary exist |
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407 | for tag in tagged_elements.keys(): |
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408 | tagged_elements[tag] = array(tagged_elements[tag]).astype(Int) |
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409 | |
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410 | msg = 'Not all elements exist. ' |
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411 | assert max(tagged_elements[tag]) < self.number_of_elements, msg |
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412 | #print "tagged_elements", tagged_elements |
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413 | self.tagged_elements = tagged_elements |
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414 | |
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415 | def get_boundary_tags(self): |
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416 | """Return list of available boundary tags |
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417 | """ |
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418 | |
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419 | tags = {} |
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420 | for v in self.boundary.values(): |
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421 | tags[v] = 1 |
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422 | |
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423 | return tags.keys() |
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424 | |
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425 | def get_vertex_coordinates(self, obj = False): |
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426 | """Return all vertex coordinates. |
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427 | Return all vertex coordinates for all triangles as an Nx6 array |
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428 | (ordered as x0, y0, x1, y1, x2, y2 for each triangle) |
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429 | |
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430 | if obj is True, the x/y pairs are returned in a 3*N x 2 array. |
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431 | FIXME, we might make that the default. |
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432 | FIXME Maybe use keyword: continuous = False for this condition? |
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433 | |
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434 | |
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435 | """ |
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436 | |
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437 | if obj is True: |
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438 | from Numeric import concatenate, reshape |
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439 | #V = self.vertex_coordinates |
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440 | V = self.vertices |
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441 | #return concatenate( (V[:,0:2], V[:,2:4], V[:,4:6]), axis=0) |
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442 | |
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443 | N = V.shape[0] |
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444 | #return reshape(V, (3*N, 2)) |
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445 | return reshape(V, (N, 2)) |
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446 | else: |
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447 | #return self.vertex_coordinates |
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448 | return self.vertices |
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449 | |
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450 | def get_conserved_quantities(self, vol_id, vertex=None):#, edge=None): |
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451 | """Get conserved quantities at volume vol_id |
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452 | |
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453 | If vertex is specified use it as index for vertex values |
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454 | If edge is specified use it as index for edge values |
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455 | If neither are specified use centroid values |
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456 | If both are specified an exeception is raised |
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457 | |
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458 | Return value: Vector of length == number_of_conserved quantities |
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459 | |
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460 | """ |
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461 | |
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462 | from Numeric import zeros, Float |
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463 | |
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464 | #if not (vertex is None):# or edge is None): |
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465 | # msg = 'Values for both vertex and edge was specified.' |
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466 | # msg += 'Only one (or none) is allowed.' |
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467 | # raise msg |
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468 | |
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469 | q = zeros( len(self.conserved_quantities), Float) |
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470 | |
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471 | for i, name in enumerate(self.conserved_quantities): |
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472 | Q = self.quantities[name] |
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473 | if vertex is not None: |
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474 | q[i] = Q.vertex_values[vol_id, vertex] |
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475 | #elif edge is not None: |
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476 | # q[i] = Q.edge_values[vol_id, edge] |
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477 | else: |
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478 | q[i] = Q.centroid_values[vol_id] |
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479 | |
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480 | return q |
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481 | |
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482 | |
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483 | def get_centroids(self): |
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484 | """Return all coordinates of centroids |
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485 | Return x coordinate of centroid for each element as a N array |
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486 | """ |
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487 | |
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488 | return self.centroids |
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489 | |
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490 | def get_vertices(self): |
---|
491 | """Return all coordinates of centroids |
---|
492 | Return x coordinate of centroid for each element as a N array |
---|
493 | """ |
---|
494 | |
---|
495 | return self.vertices |
---|
496 | |
---|
497 | def get_coordinate(self, elem_id, vertex=None): |
---|
498 | """Return coordinate of centroid, |
---|
499 | or left or right vertex. |
---|
500 | Left vertex (vertex=0). Right vertex (vertex=1) |
---|
501 | """ |
---|
502 | |
---|
503 | if vertex is None: |
---|
504 | return self.centroids[elem_id] |
---|
505 | else: |
---|
506 | return self.vertices[elem_id,vertex] |
---|
507 | |
---|
508 | def get_area(self, elem_id): |
---|
509 | """Return area of element id |
---|
510 | """ |
---|
511 | |
---|
512 | return self.areas[elem_id] |
---|
513 | |
---|
514 | def get_quantity(self, name, location='vertices', indices = None): |
---|
515 | """Get values for named quantity |
---|
516 | |
---|
517 | name: Name of quantity |
---|
518 | |
---|
519 | In case of location == 'centroids' the dimension values must |
---|
520 | be a list of a Numerical array of length N, N being the number |
---|
521 | of elements. Otherwise it must be of dimension Nx3. |
---|
522 | |
---|
523 | Indices is the set of element ids that the operation applies to. |
---|
524 | |
---|
525 | The values will be stored in elements following their |
---|
526 | internal ordering. |
---|
527 | """ |
---|
528 | |
---|
529 | return self.quantities[name].get_values( location, indices = indices) |
---|
530 | |
---|
531 | def get_centroid_coordinates(self): |
---|
532 | """Return all centroid coordinates. |
---|
533 | Return all centroid coordinates for all triangles as an Nx2 array |
---|
534 | (ordered as x0, y0 for each triangle) |
---|
535 | """ |
---|
536 | return self.centroids |
---|
537 | |
---|
538 | def set_quantity(self, name, *args, **kwargs): |
---|
539 | """Set values for named quantity |
---|
540 | |
---|
541 | |
---|
542 | One keyword argument is documented here: |
---|
543 | expression = None, # Arbitrary expression |
---|
544 | |
---|
545 | expression: |
---|
546 | Arbitrary expression involving quantity names |
---|
547 | |
---|
548 | See Quantity.set_values for further documentation. |
---|
549 | """ |
---|
550 | |
---|
551 | #FIXME (Ole): Allow new quantities here |
---|
552 | #from quantity import Quantity, Conserved_quantity |
---|
553 | #Create appropriate quantity object |
---|
554 | ##if name in self.conserved_quantities: |
---|
555 | ## self.quantities[name] = Conserved_quantity(self) |
---|
556 | ##else: |
---|
557 | ## self.quantities[name] = Quantity(self) |
---|
558 | |
---|
559 | |
---|
560 | #Do the expression stuff |
---|
561 | if kwargs.has_key('expression'): |
---|
562 | expression = kwargs['expression'] |
---|
563 | del kwargs['expression'] |
---|
564 | |
---|
565 | Q = self.create_quantity_from_expression(expression) |
---|
566 | kwargs['quantity'] = Q |
---|
567 | |
---|
568 | #Assign values |
---|
569 | self.quantities[name].set_values(*args, **kwargs) |
---|
570 | |
---|
571 | def set_boundary(self, boundary_map): |
---|
572 | """Associate boundary objects with tagged boundary segments. |
---|
573 | |
---|
574 | Input boundary_map is a dictionary of boundary objects keyed |
---|
575 | by symbolic tags to matched against tags in the internal dictionary |
---|
576 | self.boundary. |
---|
577 | |
---|
578 | As result one pointer to a boundary object is stored for each vertex |
---|
579 | in the list self.boundary_objects. |
---|
580 | More entries may point to the same boundary object |
---|
581 | |
---|
582 | Schematically the mapping is from two dictionaries to one list |
---|
583 | where the index is used as pointer to the boundary_values arrays |
---|
584 | within each quantity. |
---|
585 | |
---|
586 | self.boundary: (vol_id, edge_id): tag |
---|
587 | boundary_map (input): tag: boundary_object |
---|
588 | ---------------------------------------------- |
---|
589 | self.boundary_objects: ((vol_id, edge_id), boundary_object) |
---|
590 | |
---|
591 | |
---|
592 | Pre-condition: |
---|
593 | self.boundary has been built. |
---|
594 | |
---|
595 | Post-condition: |
---|
596 | self.boundary_objects is built |
---|
597 | |
---|
598 | If a tag from the domain doesn't appear in the input dictionary an |
---|
599 | exception is raised. |
---|
600 | However, if a tag is not used to the domain, no error is thrown. |
---|
601 | FIXME: This would lead to implementation of a |
---|
602 | default boundary condition |
---|
603 | |
---|
604 | Note: If a segment is listed in the boundary dictionary and if it is |
---|
605 | not None, it *will* become a boundary - |
---|
606 | even if there is a neighbouring triangle. |
---|
607 | This would be the case for internal boundaries |
---|
608 | |
---|
609 | Boundary objects that are None will be skipped. |
---|
610 | |
---|
611 | FIXME: If set_boundary is called multiple times and if Boundary |
---|
612 | object is changed into None, the neighbour structure will not be |
---|
613 | restored!!! |
---|
614 | """ |
---|
615 | |
---|
616 | self.boundary_objects = [] |
---|
617 | |
---|
618 | |
---|
619 | |
---|
620 | |
---|
621 | |
---|
622 | self.boundary_map = boundary_map #Store for use with eg. boundary_stats. |
---|
623 | |
---|
624 | #FIXME: Try to remove the sorting and fix test_mesh.py |
---|
625 | x = self.boundary.keys() |
---|
626 | x.sort() |
---|
627 | |
---|
628 | #Loop through edges that lie on the boundary and associate them with |
---|
629 | #callable boundary objects depending on their tags |
---|
630 | #for k, (vol_id, edge_id) in enumerate(x): |
---|
631 | for k, (vol_id, vertex_id) in enumerate(x): |
---|
632 | #tag = self.boundary[ (vol_id, edge_id) ] |
---|
633 | tag = self.boundary[ (vol_id, vertex_id) ] |
---|
634 | |
---|
635 | if boundary_map.has_key(tag): |
---|
636 | B = boundary_map[tag] #Get callable boundary object |
---|
637 | |
---|
638 | if B is not None: |
---|
639 | #self.boundary_objects.append( ((vol_id, edge_id), B) ) |
---|
640 | #self.neighbours[vol_id, edge_id] = -len(self.boundary_objects) |
---|
641 | self.boundary_objects.append( ((vol_id, vertex_id), B) ) |
---|
642 | self.neighbours[vol_id, vertex_id] = -len(self.boundary_objects) |
---|
643 | else: |
---|
644 | pass |
---|
645 | #FIXME: Check and perhaps fix neighbour structure |
---|
646 | |
---|
647 | else: |
---|
648 | msg = 'ERROR (domain.py): Tag "%s" has not been ' %tag |
---|
649 | msg += 'bound to a boundary object.\n' |
---|
650 | msg += 'All boundary tags defined in domain must appear ' |
---|
651 | msg += 'in the supplied dictionary.\n' |
---|
652 | msg += 'The tags are: %s' %self.get_boundary_tags() |
---|
653 | raise msg |
---|
654 | |
---|
655 | |
---|
656 | |
---|
657 | def check_integrity(self): |
---|
658 | #Mesh.check_integrity(self) |
---|
659 | |
---|
660 | for quantity in self.conserved_quantities: |
---|
661 | msg = 'Conserved quantities must be a subset of all quantities' |
---|
662 | assert quantity in self.quantities, msg |
---|
663 | |
---|
664 | ##assert hasattr(self, 'boundary_objects') |
---|
665 | |
---|
666 | def write_time(self): |
---|
667 | print self.timestepping_statistics() |
---|
668 | |
---|
669 | def timestepping_statistics(self): |
---|
670 | """Return string with time stepping statistics for printing or logging |
---|
671 | """ |
---|
672 | |
---|
673 | msg = '' |
---|
674 | if self.min_timestep == self.max_timestep: |
---|
675 | msg += 'Time = %.4f, delta t = %.8f, steps=%d (%d)'\ |
---|
676 | %(self.time, self.min_timestep, self.number_of_steps, |
---|
677 | self.number_of_first_order_steps) |
---|
678 | elif self.min_timestep > self.max_timestep: |
---|
679 | msg += 'Time = %.4f, steps=%d (%d)'\ |
---|
680 | %(self.time, self.number_of_steps, |
---|
681 | self.number_of_first_order_steps) |
---|
682 | else: |
---|
683 | msg += 'Time = %.4f, delta t in [%.8f, %.8f], steps=%d (%d)'\ |
---|
684 | %(self.time, self.min_timestep, |
---|
685 | self.max_timestep, self.number_of_steps, |
---|
686 | self.number_of_first_order_steps) |
---|
687 | |
---|
688 | return msg |
---|
689 | |
---|
690 | def get_name(self): |
---|
691 | return self.filename |
---|
692 | |
---|
693 | def set_name(self, name): |
---|
694 | self.filename = name |
---|
695 | |
---|
696 | def get_datadir(self): |
---|
697 | return self.datadir |
---|
698 | |
---|
699 | def set_datadir(self, name): |
---|
700 | self.datadir = name |
---|
701 | |
---|
702 | #Main components of evolve |
---|
703 | def evolve(self, yieldstep = None, finaltime = None, |
---|
704 | skip_initial_step = False): |
---|
705 | """Evolve model from time=0.0 to finaltime yielding results |
---|
706 | every yieldstep. |
---|
707 | |
---|
708 | Internally, smaller timesteps may be taken. |
---|
709 | |
---|
710 | Evolve is implemented as a generator and is to be called as such, e.g. |
---|
711 | |
---|
712 | for t in domain.evolve(timestep, yieldstep, finaltime): |
---|
713 | <Do something with domain and t> |
---|
714 | |
---|
715 | """ |
---|
716 | |
---|
717 | from config import min_timestep, max_timestep, epsilon |
---|
718 | |
---|
719 | #FIXME: Maybe lump into a larger check prior to evolving |
---|
720 | msg = 'Boundary tags must be bound to boundary objects before evolving system, ' |
---|
721 | msg += 'e.g. using the method set_boundary.\n' |
---|
722 | msg += 'This system has the boundary tags %s ' %self.get_boundary_tags() |
---|
723 | assert hasattr(self, 'boundary_objects'), msg |
---|
724 | |
---|
725 | ##self.set_defaults() |
---|
726 | |
---|
727 | if yieldstep is None: |
---|
728 | yieldstep = max_timestep |
---|
729 | else: |
---|
730 | yieldstep = float(yieldstep) |
---|
731 | |
---|
732 | self.order = self.default_order |
---|
733 | self.time_order = self.default_time_order |
---|
734 | |
---|
735 | self.yieldtime = 0.0 #Time between 'yields' |
---|
736 | |
---|
737 | #Initialise interval of timestep sizes (for reporting only) |
---|
738 | # SEEMS WIERD |
---|
739 | self.min_timestep = max_timestep |
---|
740 | self.max_timestep = min_timestep |
---|
741 | self.finaltime = finaltime |
---|
742 | self.number_of_steps = 0 |
---|
743 | self.number_of_first_order_steps = 0 |
---|
744 | |
---|
745 | #update ghosts |
---|
746 | #self.update_ghosts() |
---|
747 | |
---|
748 | #Initial update of vertex and edge values |
---|
749 | self.distribute_to_vertices_and_edges() |
---|
750 | |
---|
751 | #Initial update boundary values |
---|
752 | self.update_boundary() |
---|
753 | |
---|
754 | #Or maybe restore from latest checkpoint |
---|
755 | if self.checkpoint is True: |
---|
756 | self.goto_latest_checkpoint() |
---|
757 | |
---|
758 | if skip_initial_step is False: |
---|
759 | yield(self.time) #Yield initial values |
---|
760 | |
---|
761 | while True: |
---|
762 | if self.time_order == 1: |
---|
763 | #Compute fluxes across each element edge |
---|
764 | self.compute_fluxes() |
---|
765 | #Update timestep to fit yieldstep and finaltime |
---|
766 | self.update_timestep(yieldstep, finaltime) |
---|
767 | #Compute forcing terms |
---|
768 | self.compute_forcing_terms() |
---|
769 | #Update conserved quantities |
---|
770 | self.update_conserved_quantities(self.timestep) |
---|
771 | #update ghosts |
---|
772 | #self.update_ghosts() |
---|
773 | #Update vertex and edge values |
---|
774 | self.distribute_to_vertices_and_edges() |
---|
775 | #Update boundary values |
---|
776 | self.update_boundary() |
---|
777 | |
---|
778 | elif self.time_order == 2: |
---|
779 | |
---|
780 | self.compute_timestep() |
---|
781 | |
---|
782 | #Solve inhomogeneous operator for half a timestep |
---|
783 | self.solve_inhomogenous_second_order(yieldstep, finaltime) |
---|
784 | |
---|
785 | #Solve homogeneous operator for full timestep using |
---|
786 | #Harten second order timestepping |
---|
787 | self.solve_homogenous_second_order(yieldstep,finaltime) |
---|
788 | |
---|
789 | #Solve inhomogeneous operator for half a timestep |
---|
790 | self.solve_inhomogenous_second_order(yieldstep, finaltime) |
---|
791 | |
---|
792 | #Update time |
---|
793 | self.time += self.timestep |
---|
794 | self.yieldtime += self.timestep |
---|
795 | self.number_of_steps += 1 |
---|
796 | if self.order == 1: |
---|
797 | self.number_of_first_order_steps += 1 |
---|
798 | |
---|
799 | #Yield results |
---|
800 | if finaltime is not None and abs(self.time - finaltime) < epsilon: |
---|
801 | |
---|
802 | #FIXME: There is a rare situation where the |
---|
803 | #final time step is stored twice. Can we make a test? |
---|
804 | |
---|
805 | # Yield final time and stop |
---|
806 | yield(self.time) |
---|
807 | break |
---|
808 | |
---|
809 | |
---|
810 | if abs(self.yieldtime - yieldstep) < epsilon: |
---|
811 | # Yield (intermediate) time and allow inspection of domain |
---|
812 | |
---|
813 | if self.checkpoint is True: |
---|
814 | self.store_checkpoint() |
---|
815 | self.delete_old_checkpoints() |
---|
816 | |
---|
817 | #Pass control on to outer loop for more specific actions |
---|
818 | yield(self.time) |
---|
819 | |
---|
820 | # Reinitialise |
---|
821 | self.yieldtime = 0.0 |
---|
822 | self.min_timestep = max_timestep |
---|
823 | self.max_timestep = min_timestep |
---|
824 | self.number_of_steps = 0 |
---|
825 | self.number_of_first_order_steps = 0 |
---|
826 | |
---|
827 | def solve_inhomogenous_second_order(self,yieldstep, finaltime): |
---|
828 | |
---|
829 | #Update timestep to fit yieldstep and finaltime |
---|
830 | self.update_timestep(yieldstep, finaltime) |
---|
831 | #Compute forcing terms |
---|
832 | self.compute_forcing_terms() |
---|
833 | #Update conserved quantities |
---|
834 | self.update_conserved_quantities(0.5*self.timestep) |
---|
835 | #Update vertex and edge values |
---|
836 | self.distribute_to_vertices_and_edges() |
---|
837 | #Update boundary values |
---|
838 | self.update_boundary() |
---|
839 | |
---|
840 | def solve_homogenous_second_order(self,yieldstep,finaltime): |
---|
841 | """Use Shu Second order timestepping to update |
---|
842 | conserved quantities |
---|
843 | |
---|
844 | q^{n+1/2} = q^{n}+0.5*dt*F^{n} |
---|
845 | q^{n+1} = q^{n}+dt*F^{n+1/2} |
---|
846 | """ |
---|
847 | import copy |
---|
848 | from Numeric import zeros,Float |
---|
849 | |
---|
850 | N = self.number_of_elements |
---|
851 | |
---|
852 | self.compute_fluxes() |
---|
853 | #Update timestep to fit yieldstep and finaltime |
---|
854 | self.update_timestep(yieldstep, finaltime) |
---|
855 | #Compute forcing terms |
---|
856 | #NOT NEEDED FOR 2ND ORDER STRANG SPLIITING |
---|
857 | #ADDING THIS WILL NEED TO REMOVE ZEROING IN COMPUTE_FORCING |
---|
858 | #self.compute_forcing_terms() |
---|
859 | |
---|
860 | QC = zeros((N,len(self.conserved_quantities)),Float) |
---|
861 | QF = zeros((N,len(self.conserved_quantities)),Float) |
---|
862 | |
---|
863 | i = 0 |
---|
864 | for name in self.conserved_quantities: |
---|
865 | Q = self.quantities[name] |
---|
866 | #Store the centroid values at time t^n |
---|
867 | QC[:,i] = copy.copy(Q.centroid_values) |
---|
868 | QF[:,i] = copy.copy(Q.explicit_update) |
---|
869 | #Update conserved quantities |
---|
870 | Q.update(self.timestep) |
---|
871 | i+=1 |
---|
872 | |
---|
873 | #Update vertex and edge values |
---|
874 | self.distribute_to_vertices_and_edges() |
---|
875 | #Update boundary values |
---|
876 | self.update_boundary() |
---|
877 | |
---|
878 | self.compute_fluxes() |
---|
879 | self.update_timestep(yieldstep, finaltime) |
---|
880 | #Compute forcing terms |
---|
881 | #NOT NEEDED FOR 2ND ORDER STRANG SPLIITING |
---|
882 | #self.compute_forcing_terms() |
---|
883 | |
---|
884 | i = 0 |
---|
885 | for name in self.conserved_quantities: |
---|
886 | Q = self.quantities[name] |
---|
887 | Q.centroid_values = QC[:,i] |
---|
888 | Q.explicit_update = 0.5*(Q.explicit_update+QF[:,i]) |
---|
889 | #Update conserved quantities |
---|
890 | Q.update(self.timestep) |
---|
891 | i+=1 |
---|
892 | |
---|
893 | #Update vertex and edge values |
---|
894 | self.distribute_to_vertices_and_edges() |
---|
895 | #Update boundary values |
---|
896 | self.update_boundary() |
---|
897 | |
---|
898 | def solve_homogenous_second_order_harten(self,yieldstep,finaltime): |
---|
899 | """Use Harten Second order timestepping to update |
---|
900 | conserved quantities |
---|
901 | |
---|
902 | q^{n+1/2} = q^{n}+0.5*dt*F^{n} |
---|
903 | q^{n+1} = q^{n}+dt*F^{n+1/2} |
---|
904 | """ |
---|
905 | import copy |
---|
906 | from Numeric import zeros,Float |
---|
907 | |
---|
908 | N = self.number_of_elements |
---|
909 | |
---|
910 | self.compute_fluxes() |
---|
911 | #Update timestep to fit yieldstep and finaltime |
---|
912 | self.update_timestep(yieldstep, finaltime) |
---|
913 | #Compute forcing terms |
---|
914 | #NOT NEEDED FOR 2ND ORDER STRANG SPLIITING |
---|
915 | #ADDING THIS WILL NEED TO REMOVE ZEROING IN COMPUTE_FORCING |
---|
916 | #self.compute_forcing_terms() |
---|
917 | |
---|
918 | QC = zeros((N,len(self.conserved_quantities)),Float) |
---|
919 | |
---|
920 | i = 0 |
---|
921 | for name in self.conserved_quantities: |
---|
922 | Q = self.quantities[name] |
---|
923 | #Store the centroid values at time t^n |
---|
924 | QC[:,i] = copy.copy(Q.centroid_values) |
---|
925 | #Update conserved quantities |
---|
926 | Q.update(0.5*self.timestep) |
---|
927 | i+=1 |
---|
928 | |
---|
929 | #Update vertex and edge values |
---|
930 | self.distribute_to_vertices_and_edges() |
---|
931 | #Update boundary values |
---|
932 | self.update_boundary() |
---|
933 | |
---|
934 | self.compute_fluxes() |
---|
935 | self.update_timestep(yieldstep, finaltime) |
---|
936 | #Compute forcing terms |
---|
937 | #NOT NEEDED FOR 2ND ORDER STRANG SPLIITING |
---|
938 | #self.compute_forcing_terms() |
---|
939 | |
---|
940 | i = 0 |
---|
941 | for name in self.conserved_quantities: |
---|
942 | Q = self.quantities[name] |
---|
943 | Q.centroid_values = QC[:,i] |
---|
944 | #Update conserved quantities |
---|
945 | Q.update(self.timestep) |
---|
946 | i+=1 |
---|
947 | |
---|
948 | #Update vertex and edge values |
---|
949 | self.distribute_to_vertices_and_edges() |
---|
950 | #Update boundary values |
---|
951 | self.update_boundary() |
---|
952 | |
---|
953 | def distribute_to_vertices_and_edges(self): |
---|
954 | """Extrapolate conserved quantities from centroid to |
---|
955 | vertices and edge-midpoints for each volume |
---|
956 | |
---|
957 | Default implementation is straight first order, |
---|
958 | i.e. constant values throughout each element and |
---|
959 | no reference to non-conserved quantities. |
---|
960 | """ |
---|
961 | |
---|
962 | for name in self.conserved_quantities: |
---|
963 | Q = self.quantities[name] |
---|
964 | if self.order == 1: |
---|
965 | Q.extrapolate_first_order() |
---|
966 | elif self.order == 2: |
---|
967 | Q.extrapolate_second_order() |
---|
968 | #Q.limit() |
---|
969 | else: |
---|
970 | raise 'Unknown order' |
---|
971 | #Q.interpolate_from_vertices_to_edges() |
---|
972 | |
---|
973 | |
---|
974 | def update_boundary(self): |
---|
975 | """Go through list of boundary objects and update boundary values |
---|
976 | for all conserved quantities on boundary. |
---|
977 | """ |
---|
978 | |
---|
979 | #FIXME: Update only those that change (if that can be worked out) |
---|
980 | #FIXME: Boundary objects should not include ghost nodes. |
---|
981 | #for i, ((vol_id, edge_id), B) in enumerate(self.boundary_objects): |
---|
982 | # q = B.evaluate(vol_id, edge_id) |
---|
983 | for i, ((vol_id, vertex_id), B) in enumerate(self.boundary_objects): |
---|
984 | q = B.evaluate(vol_id, vertex_id) |
---|
985 | |
---|
986 | for j, name in enumerate(self.conserved_quantities): |
---|
987 | Q = self.quantities[name] |
---|
988 | Q.boundary_values[i] = q[j] |
---|
989 | |
---|
990 | def update_timestep(self, yieldstep, finaltime): |
---|
991 | |
---|
992 | from config import min_timestep |
---|
993 | |
---|
994 | # self.timestep is calculated from speed of characteristics |
---|
995 | # Apply CFL condition here |
---|
996 | timestep = self.CFL*self.timestep |
---|
997 | |
---|
998 | #Record maximal and minimal values of timestep for reporting |
---|
999 | self.max_timestep = max(timestep, self.max_timestep) |
---|
1000 | self.min_timestep = min(timestep, self.min_timestep) |
---|
1001 | |
---|
1002 | #Protect against degenerate time steps |
---|
1003 | if timestep < min_timestep: |
---|
1004 | |
---|
1005 | #Number of consecutive small steps taken b4 taking action |
---|
1006 | self.smallsteps += 1 |
---|
1007 | |
---|
1008 | if self.smallsteps > self.max_smallsteps: |
---|
1009 | self.smallsteps = 0 #Reset |
---|
1010 | |
---|
1011 | if self.order == 1: |
---|
1012 | msg = 'WARNING: Too small timestep %.16f reached '\ |
---|
1013 | %timestep |
---|
1014 | msg += 'even after %d steps of 1 order scheme'\ |
---|
1015 | %self.max_smallsteps |
---|
1016 | print msg |
---|
1017 | timestep = min_timestep #Try enforcing min_step |
---|
1018 | |
---|
1019 | #raise msg |
---|
1020 | else: |
---|
1021 | #Try to overcome situation by switching to 1 order |
---|
1022 | print "changing Order 1" |
---|
1023 | self.order = 1 |
---|
1024 | |
---|
1025 | else: |
---|
1026 | self.smallsteps = 0 |
---|
1027 | if self.order == 1 and self.default_order == 2: |
---|
1028 | self.order = 2 |
---|
1029 | |
---|
1030 | |
---|
1031 | #Ensure that final time is not exceeded |
---|
1032 | if finaltime is not None and self.time + timestep > finaltime: |
---|
1033 | timestep = finaltime-self.time |
---|
1034 | |
---|
1035 | #Ensure that model time is aligned with yieldsteps |
---|
1036 | if self.yieldtime + timestep > yieldstep: |
---|
1037 | timestep = yieldstep-self.yieldtime |
---|
1038 | |
---|
1039 | self.timestep = timestep |
---|
1040 | |
---|
1041 | |
---|
1042 | def compute_forcing_terms(self): |
---|
1043 | """If there are any forcing functions driving the system |
---|
1044 | they should be defined in Domain subclass and appended to |
---|
1045 | the list self.forcing_terms |
---|
1046 | """ |
---|
1047 | #Clears explicit_update needed for second order method |
---|
1048 | if self.time_order == 2: |
---|
1049 | for name in self.conserved_quantities: |
---|
1050 | Q = self.quantities[name] |
---|
1051 | Q.explicit_update[:] = 0.0 |
---|
1052 | |
---|
1053 | for f in self.forcing_terms: |
---|
1054 | f(self) |
---|
1055 | |
---|
1056 | |
---|
1057 | def update_derived_quantites(self): |
---|
1058 | pass |
---|
1059 | |
---|
1060 | #def update_conserved_quantities(self): |
---|
1061 | def update_conserved_quantities(self,timestep): |
---|
1062 | """Update vectors of conserved quantities using previously |
---|
1063 | computed fluxes specified forcing functions. |
---|
1064 | """ |
---|
1065 | |
---|
1066 | from Numeric import ones, sum, equal, Float |
---|
1067 | |
---|
1068 | N = self.number_of_elements |
---|
1069 | d = len(self.conserved_quantities) |
---|
1070 | |
---|
1071 | #timestep = self.timestep |
---|
1072 | |
---|
1073 | #Compute forcing terms |
---|
1074 | #self.compute_forcing_terms() |
---|
1075 | |
---|
1076 | #Update conserved_quantities |
---|
1077 | for name in self.conserved_quantities: |
---|
1078 | Q = self.quantities[name] |
---|
1079 | Q.update(timestep) |
---|
1080 | |
---|
1081 | #Clean up |
---|
1082 | #Note that Q.explicit_update is reset by compute_fluxes |
---|
1083 | |
---|
1084 | #MH090605 commented out the following since semi_implicit_update is now re-initialized |
---|
1085 | #at the end of the _update function in quantity_ext.c (This is called by the |
---|
1086 | #preceeding Q.update(timestep) statement above). |
---|
1087 | #For run_profile.py with N=128, the time of update_conserved_quantities is cut from 14.00 secs |
---|
1088 | #to 8.35 secs |
---|
1089 | |
---|
1090 | #Q.semi_implicit_update[:] = 0.0 |
---|
1091 | |
---|
1092 | if __name__ == "__main__": |
---|
1093 | |
---|
1094 | points1 = [0.0, 1.0, 2.0, 3.0] |
---|
1095 | D1 = Domain(points1) |
---|
1096 | |
---|
1097 | print D1.get_coordinate(0) |
---|
1098 | print D1.get_coordinate(0,1) |
---|
1099 | print 'Number of Elements = ',D1.number_of_elements |
---|
1100 | |
---|
1101 | try: |
---|
1102 | print D1.get_coordinate(3) |
---|
1103 | except: |
---|
1104 | pass |
---|
1105 | else: |
---|
1106 | msg = 'Should have raised an out of bounds exception' |
---|
1107 | raise msg |
---|
1108 | |
---|
1109 | #points2 = [0.0, 1.0, 2.0, 3.0, 2.5] |
---|
1110 | #D2 = Domain(points2) |
---|
1111 | |
---|