| 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, geo_reference = 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 | self.beta = 1.0 |
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| 24 | #Store Points |
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| 25 | self.coordinates = array(coordinates) |
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| 26 | |
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| 27 | if geo_reference is None: |
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| 28 | self.geo_reference = Geo_reference() #Use defaults |
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| 29 | else: |
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| 30 | self.geo_reference = geo_reference |
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| 31 | |
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| 32 | #Register number of Elements |
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| 33 | self.number_of_elements = N = len(self.coordinates)-1 |
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| 34 | |
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| 35 | #Allocate space for neighbour and boundary structures |
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| 36 | self.neighbours = zeros((N, 2), Int) |
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| 37 | #self.neighbour_edges = zeros((N, 2), Int) |
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| 38 | self.neighbour_vertices = zeros((N, 2), Int) |
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| 39 | self.number_of_boundaries = zeros(N, Int) |
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| 40 | self.surrogate_neighbours = zeros((N, 2), Int) |
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| 41 | |
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| 42 | #Allocate space for geometric quantities |
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| 43 | self.vertices = zeros((N, 2), Float) |
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| 44 | self.centroids = zeros(N, Float) |
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| 45 | self.areas = zeros(N, Float) |
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| 46 | |
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| 47 | self.normals = zeros((N, 2), Float) |
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| 48 | |
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| 49 | for i in range(N): |
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| 50 | xl = self.coordinates[i] |
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| 51 | xr = self.coordinates[i+1] |
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| 52 | self.vertices[i,0] = xl |
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| 53 | self.vertices[i,1] = xr |
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| 54 | |
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| 55 | centroid = (xl+xr)/2 |
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| 56 | self.centroids[i] = centroid |
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| 57 | |
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| 58 | msg = 'Coordinates should be ordered, smallest to largest' |
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| 59 | assert xr>xl, msg |
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| 60 | |
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| 61 | #The normal vectors |
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| 62 | # - point outward from each edge |
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| 63 | # - are orthogonal to the edge |
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| 64 | # - have unit length |
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| 65 | # - Are enumerated by left vertex then right vertex normals |
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| 66 | |
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| 67 | nl = -1.0 |
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| 68 | nr = 1.0 |
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| 69 | self.normals[i,:] = [nl, nr] |
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| 70 | |
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| 71 | self.areas[i] = (xr-xl) |
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| 72 | |
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| 73 | ## print 'N', N |
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| 74 | ## print 'Centroid', self.centroids |
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| 75 | ## print 'Areas', self.areas |
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| 76 | ## print 'Vertex_Coordinates', self.vertices |
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| 77 | |
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| 78 | #Initialise Neighbours (-1 means that it is a boundary neighbour) |
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| 79 | self.neighbours[i, :] = [-1, -1] |
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| 80 | #Initialise edge ids of neighbours |
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| 81 | #Initialise vertex ids of neighbours |
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| 82 | #In case of boundaries this slot is not used |
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| 83 | #self.neighbour_edges[i, :] = [-1, -1] |
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| 84 | self.neighbour_vertices[i, :] = [-1, -1] |
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| 85 | |
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| 86 | self.build_vertexlist() |
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| 87 | |
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| 88 | #Build neighbour structure |
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| 89 | self.build_neighbour_structure() |
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| 90 | |
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| 91 | #Build surrogate neighbour structure |
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| 92 | self.build_surrogate_neighbour_structure() |
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| 93 | |
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| 94 | #Build boundary dictionary mapping (id, edge) to symbolic tags |
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| 95 | #Build boundary dictionary mapping (id, vertex) to symbolic tags |
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| 96 | self.build_boundary_dictionary(boundary) |
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| 97 | |
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| 98 | #Build tagged element dictionary mapping (tag) to array of elements |
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| 99 | self.build_tagged_elements_dictionary(tagged_elements) |
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| 100 | |
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| 101 | from quantity import Quantity, Conserved_quantity |
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| 102 | |
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| 103 | #List of quantity names entering |
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| 104 | #the conservation equations |
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| 105 | #(Must be a subset of quantities) |
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| 106 | if conserved_quantities is None: |
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| 107 | self.conserved_quantities = [] |
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| 108 | else: |
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| 109 | self.conserved_quantities = conserved_quantities |
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| 110 | |
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| 111 | if other_quantities is None: |
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| 112 | self.other_quantities = [] |
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| 113 | else: |
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| 114 | self.other_quantities = other_quantities |
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| 115 | |
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| 116 | |
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| 117 | #Build dictionary of Quantity instances keyed by quantity names |
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| 118 | self.quantities = {} |
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| 119 | |
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| 120 | #FIXME: remove later - maybe OK, though.... |
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| 121 | for name in self.conserved_quantities: |
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| 122 | self.quantities[name] = Conserved_quantity(self) |
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| 123 | for name in self.other_quantities: |
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| 124 | self.quantities[name] = Quantity(self) |
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| 125 | |
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| 126 | #Create an empty list for explicit forcing terms |
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| 127 | self.forcing_terms = [] |
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| 128 | |
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| 129 | #Defaults |
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| 130 | from config import max_smallsteps, beta_w, beta_h, epsilon, CFL |
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| 131 | self.beta_w = beta_w |
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| 132 | self.beta_h = beta_h |
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| 133 | self.epsilon = epsilon |
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| 134 | |
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| 135 | #FIXME: Maybe have separate orders for h-limiter and w-limiter? |
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| 136 | #Or maybe get rid of order altogether and use beta_w and beta_h |
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| 137 | self.default_order = 1 |
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| 138 | self.order = self.default_order |
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| 139 | self.smallsteps = 0 |
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| 140 | self.max_smallsteps = max_smallsteps |
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| 141 | self.number_of_steps = 0 |
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| 142 | self.number_of_first_order_steps = 0 |
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| 143 | self.CFL = CFL |
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| 144 | |
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| 145 | #Model time |
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| 146 | self.time = 0.0 |
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| 147 | self.finaltime = None |
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| 148 | self.min_timestep = self.max_timestep = 0.0 |
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| 149 | self.starttime = 0 #Physical starttime if any (0 is 1 Jan 1970 00:00:00) |
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| 150 | #Checkpointing and storage |
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| 151 | from config import default_datadir |
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| 152 | self.datadir = default_datadir |
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| 153 | self.filename = 'domain' |
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| 154 | self.checkpoint = False |
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| 155 | |
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| 156 | def __len__(self): |
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| 157 | return self.number_of_elements |
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| 158 | |
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| 159 | def build_vertexlist(self): |
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| 160 | """Build vertexlist index by vertex ids and for each entry (point id) |
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| 161 | build a list of (triangles, vertex_id) pairs that use the point |
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| 162 | as vertex. |
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| 163 | |
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| 164 | Preconditions: |
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| 165 | self.coordinates and self.triangles are defined |
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| 166 | |
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| 167 | Postcondition: |
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| 168 | self.vertexlist is built |
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| 169 | """ |
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| 170 | from Numeric import array |
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| 171 | |
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| 172 | vertexlist = [None]*len(self.coordinates) |
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| 173 | for i in range(self.number_of_elements): |
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| 174 | |
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| 175 | #a = self.triangles[i, 0] |
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| 176 | #b = self.triangles[i, 1] |
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| 177 | #c = self.triangles[i, 2] |
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| 178 | a = i |
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| 179 | b = i + 1 |
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| 180 | |
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| 181 | #Register the vertices v as lists of |
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| 182 | #(triangle_id, vertex_id) tuples associated with them |
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| 183 | #This is used for smoothing |
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| 184 | #for vertex_id, v in enumerate([a,b,c]): |
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| 185 | for vertex_id, v in enumerate([a,b]): |
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| 186 | if vertexlist[v] is None: |
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| 187 | vertexlist[v] = [] |
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| 188 | |
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| 189 | vertexlist[v].append( (i, vertex_id) ) |
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| 190 | |
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| 191 | self.vertexlist = vertexlist |
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| 192 | |
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| 193 | |
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| 194 | def build_neighbour_structure(self): |
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| 195 | """Update all registered triangles to point to their neighbours. |
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| 196 | |
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| 197 | Also, keep a tally of the number of boundaries for each triangle |
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| 198 | |
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| 199 | Postconditions: |
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| 200 | neighbours and neighbour_edges is populated |
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| 201 | neighbours and neighbour_vertices is populated |
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| 202 | number_of_boundaries integer array is defined. |
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| 203 | """ |
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| 204 | |
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| 205 | #Step 1: |
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| 206 | #Build dictionary mapping from segments (2-tuple of points) |
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| 207 | #to left hand side edge (facing neighbouring triangle) |
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| 208 | |
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| 209 | N = self.number_of_elements |
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| 210 | neighbourdict = {} |
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| 211 | #l_edge = 0 |
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| 212 | #r_edge = 1 |
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| 213 | l_vertex = 0 |
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| 214 | r_vertex = 1 |
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| 215 | for i in range(N): |
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| 216 | |
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| 217 | #Register all segments as keys mapping to current triangle |
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| 218 | #and segment id |
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| 219 | #a = self.triangles[i, 0] |
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| 220 | #b = self.triangles[i, 1] |
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| 221 | #c = self.triangles[i, 2] |
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| 222 | a = self.vertices[i,0] |
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| 223 | b = self.vertices[i,1] |
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| 224 | |
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| 225 | """ |
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| 226 | if neighbourdict.has_key((a,b)): |
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| 227 | 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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| 228 | raise msg |
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| 229 | if neighbourdict.has_key((b,c)): |
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| 230 | 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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| 231 | raise msg |
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| 232 | if neighbourdict.has_key((c,a)): |
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| 233 | 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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| 234 | raise msg |
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| 235 | """ |
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| 236 | #neighbourdict[a,b] = (i, 2) #(id, edge) |
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| 237 | #neighbourdict[b,c] = (i, 0) #(id, edge) |
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| 238 | #neighbourdict[c,a] = (i, 1) #(id, edge) |
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| 239 | #neighbourdict[a,b] = (i, 1) #(id, edge) |
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| 240 | #neighbourdict[b,a] = (i, 0) #(id, edge) |
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| 241 | #neighbourdict[a,l_edge] = (i, 0) #(id, edge) |
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| 242 | #neighbourdict[b,r_edge] = (i, 1) #(id, edge) |
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| 243 | neighbourdict[a,l_vertex] = (i, 0) #(id, vertex) |
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| 244 | neighbourdict[b,r_vertex] = (i, 1) #(id, vertex) |
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| 245 | |
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| 246 | |
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| 247 | #Step 2: |
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| 248 | #Go through triangles again, but this time |
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| 249 | #reverse direction of segments and lookup neighbours. |
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| 250 | for i in range(N): |
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| 251 | #a = self.triangles[i, 0] |
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| 252 | #b = self.triangles[i, 1] |
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| 253 | #c = self.triangles[i, 2] |
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| 254 | |
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| 255 | a = self.vertices[i,0] |
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| 256 | b = self.vertices[i,1] |
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| 257 | |
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| 258 | #self.number_of_boundaries[i] = 3 |
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| 259 | self.number_of_boundaries[i] = 2 |
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| 260 | #if neighbourdict.has_key((b,l_edge)): |
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| 261 | if neighbourdict.has_key((b,l_vertex)): |
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| 262 | #self.neighbours[i, 1] = neighbourdict[b,l_edge][0] |
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| 263 | #self.neighbour_edges[i, 1] = neighbourdict[b,l_edge][1] |
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| 264 | self.neighbours[i, 1] = neighbourdict[b,l_vertex][0] |
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| 265 | self.neighbour_vertices[i, 1] = neighbourdict[b,l_vertex][1] |
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| 266 | self.number_of_boundaries[i] -= 1 |
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| 267 | |
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| 268 | #if neighbourdict.has_key((a,r_edge)): |
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| 269 | if neighbourdict.has_key((a,r_vertex)): |
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| 270 | #self.neighbours[i, 0] = neighbourdict[a,r_edge][0] |
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| 271 | #self.neighbour_edges[i, 0] = neighbourdict[a,r_edge][1] |
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| 272 | self.neighbours[i, 0] = neighbourdict[a,r_vertex][0] |
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| 273 | self.neighbour_vertices[i, 0] = neighbourdict[a,r_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((b,a)): |
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| 277 | # self.neighbours[i, 1] = neighbourdict[b,a][0] |
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| 278 | # self.neighbour_edges[i, 1] = neighbourdict[b,a][1] |
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| 279 | # self.number_of_boundaries[i] -= 1 |
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| 280 | |
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| 281 | #if neighbourdict.has_key((c,b)): |
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| 282 | # self.neighbours[i, 0] = neighbourdict[c,b][0] |
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| 283 | # self.neighbour_edges[i, 0] = neighbourdict[c,b][1] |
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| 284 | # self.number_of_boundaries[i] -= 1 |
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| 285 | |
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| 286 | #if neighbourdict.has_key((a,b)): |
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| 287 | # self.neighbours[i, 0] = neighbourdict[a,b][0] |
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| 288 | # self.neighbour_edges[i, 0] = neighbourdict[a,b][1] |
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| 289 | # self.number_of_boundaries[i] -= 1 |
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| 290 | |
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| 291 | def build_surrogate_neighbour_structure(self): |
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| 292 | """Build structure where each triangle edge points to its neighbours |
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| 293 | if they exist. Otherwise point to the triangle itself. |
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| 294 | |
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| 295 | The surrogate neighbour structure is useful for computing gradients |
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| 296 | based on centroid values of neighbours. |
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| 297 | |
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| 298 | Precondition: Neighbour structure is defined |
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| 299 | Postcondition: |
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| 300 | Surrogate neighbour structure is defined: |
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| 301 | surrogate_neighbours: i0, i1, i2 where all i_k >= 0 point to |
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| 302 | triangles. |
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| 303 | |
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| 304 | """ |
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| 305 | |
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| 306 | N = self.number_of_elements |
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| 307 | for i in range(N): |
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| 308 | #Find all neighbouring volumes that are not boundaries |
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| 309 | #for k in range(3): |
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| 310 | for k in range(2): |
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| 311 | if self.neighbours[i, k] < 0: |
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| 312 | self.surrogate_neighbours[i, k] = i #Point this triangle |
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| 313 | else: |
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| 314 | self.surrogate_neighbours[i, k] = self.neighbours[i, k] |
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| 315 | |
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| 316 | def build_boundary_dictionary(self, boundary = None): |
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| 317 | """Build or check the dictionary of boundary tags. |
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| 318 | self.boundary is a dictionary of tags, |
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| 319 | keyed by volume id and edge: |
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| 320 | { (id, edge): tag, ... } |
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| 321 | |
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| 322 | Postconditions: |
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| 323 | self.boundary is defined. |
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| 324 | """ |
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| 325 | |
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| 326 | from config import default_boundary_tag |
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| 327 | |
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| 328 | if boundary is None: |
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| 329 | boundary = {} |
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| 330 | for vol_id in range(self.number_of_elements): |
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| 331 | #for edge_id in range(0, 3): |
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| 332 | #for edge_id in range(0, 2): |
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| 333 | for vertex_id in range(0, 2): |
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| 334 | #if self.neighbours[vol_id, edge_id] < 0: |
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| 335 | if self.neighbours[vol_id, vertex_id] < 0: |
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| 336 | #boundary[(vol_id, edge_id)] = default_boundary_tag |
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| 337 | boundary[(vol_id, vertex_id)] = default_boundary_tag |
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| 338 | else: |
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| 339 | #Check that all keys in given boundary exist |
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| 340 | #for vol_id, edge_id in boundary.keys(): |
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| 341 | for vol_id, vertex_id in boundary.keys(): |
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| 342 | #msg = 'Segment (%d, %d) does not exist' %(vol_id, edge_id) |
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| 343 | msg = 'Segment (%d, %d) does not exist' %(vol_id, vertex_id) |
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| 344 | a, b = self.neighbours.shape |
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| 345 | #assert vol_id < a and edge_id < b, msg |
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| 346 | assert vol_id < a and vertex_id < b, msg |
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| 347 | |
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| 348 | #FIXME: This assert violates internal boundaries (delete it) |
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| 349 | #msg = 'Segment (%d, %d) is not a boundary' %(vol_id, edge_id) |
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| 350 | #assert self.neighbours[vol_id, edge_id] < 0, msg |
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| 351 | |
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| 352 | #Check that all boundary segments are assigned a tag |
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| 353 | for vol_id in range(self.number_of_elements): |
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| 354 | #for edge_id in range(0, 3): |
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| 355 | #for edge_id in range(0, 2): |
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| 356 | for vertex_id in range(0, 2): |
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| 357 | #if self.neighbours[vol_id, edge_id] < 0: |
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| 358 | if self.neighbours[vol_id, vertex_id] < 0: |
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| 359 | #if not boundary.has_key( (vol_id, edge_id) ): |
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| 360 | if not boundary.has_key( (vol_id, vertex_id) ): |
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| 361 | msg = 'WARNING: Given boundary does not contain ' |
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| 362 | #msg += 'tags for edge (%d, %d). '\ |
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| 363 | # %(vol_id, edge_id) |
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| 364 | msg += 'tags for vertex (%d, %d). '\ |
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| 365 | %(vol_id, vertex_id) |
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| 366 | msg += 'Assigning default tag (%s).'\ |
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| 367 | %default_boundary_tag |
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| 368 | |
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| 369 | #FIXME: Print only as per verbosity |
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| 370 | #print msg |
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| 371 | |
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| 372 | #FIXME: Make this situation an error in the future |
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| 373 | #and make another function which will |
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| 374 | #enable default boundary-tags where |
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| 375 | #tags a not specified |
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| 376 | #boundary[ (vol_id, edge_id) ] =\ |
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| 377 | boundary[ (vol_id, vertex_id) ] =\ |
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| 378 | default_boundary_tag |
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| 379 | |
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| 380 | |
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| 381 | |
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| 382 | self.boundary = boundary |
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| 383 | |
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| 384 | def build_tagged_elements_dictionary(self, tagged_elements = None): |
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| 385 | """Build the dictionary of element tags. |
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| 386 | self.tagged_elements is a dictionary of element arrays, |
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| 387 | keyed by tag: |
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| 388 | { (tag): [e1, e2, e3..] } |
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| 389 | |
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| 390 | Postconditions: |
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| 391 | self.element_tag is defined |
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| 392 | """ |
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| 393 | from Numeric import array, Int |
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| 394 | |
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| 395 | if tagged_elements is None: |
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| 396 | tagged_elements = {} |
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| 397 | else: |
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| 398 | #Check that all keys in given boundary exist |
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| 399 | for tag in tagged_elements.keys(): |
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| 400 | tagged_elements[tag] = array(tagged_elements[tag]).astype(Int) |
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| 401 | |
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| 402 | msg = 'Not all elements exist. ' |
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| 403 | assert max(tagged_elements[tag]) < self.number_of_elements, msg |
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| 404 | #print "tagged_elements", tagged_elements |
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| 405 | self.tagged_elements = tagged_elements |
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| 406 | |
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| 407 | def get_boundary_tags(self): |
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| 408 | """Return list of available boundary tags |
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| 409 | """ |
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| 410 | |
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| 411 | tags = {} |
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| 412 | for v in self.boundary.values(): |
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| 413 | tags[v] = 1 |
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| 414 | |
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| 415 | return tags.keys() |
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| 416 | |
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| 417 | def get_vertex_coordinates(self, obj = False): |
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| 418 | """Return all vertex coordinates. |
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| 419 | Return all vertex coordinates for all triangles as an Nx6 array |
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| 420 | (ordered as x0, y0, x1, y1, x2, y2 for each triangle) |
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| 421 | |
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| 422 | if obj is True, the x/y pairs are returned in a 3*N x 2 array. |
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| 423 | FIXME, we might make that the default. |
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| 424 | FIXME Maybe use keyword: continuous = False for this condition? |
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| 425 | |
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| 426 | |
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| 427 | """ |
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| 428 | |
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| 429 | if obj is True: |
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| 430 | from Numeric import concatenate, reshape |
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| 431 | #V = self.vertex_coordinates |
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| 432 | V = self.vertices |
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| 433 | #return concatenate( (V[:,0:2], V[:,2:4], V[:,4:6]), axis=0) |
|---|
| 434 | |
|---|
| 435 | N = V.shape[0] |
|---|
| 436 | #return reshape(V, (3*N, 2)) |
|---|
| 437 | return reshape(V, (N, 2)) |
|---|
| 438 | else: |
|---|
| 439 | #return self.vertex_coordinates |
|---|
| 440 | return self.vertices |
|---|
| 441 | |
|---|
| 442 | def get_conserved_quantities(self, vol_id, vertex=None):#, edge=None): |
|---|
| 443 | """Get conserved quantities at volume vol_id |
|---|
| 444 | |
|---|
| 445 | If vertex is specified use it as index for vertex values |
|---|
| 446 | If edge is specified use it as index for edge values |
|---|
| 447 | If neither are specified use centroid values |
|---|
| 448 | If both are specified an exeception is raised |
|---|
| 449 | |
|---|
| 450 | Return value: Vector of length == number_of_conserved quantities |
|---|
| 451 | |
|---|
| 452 | """ |
|---|
| 453 | |
|---|
| 454 | from Numeric import zeros, Float |
|---|
| 455 | |
|---|
| 456 | #if not (vertex is None):# or edge is None): |
|---|
| 457 | # msg = 'Values for both vertex and edge was specified.' |
|---|
| 458 | # msg += 'Only one (or none) is allowed.' |
|---|
| 459 | # raise msg |
|---|
| 460 | |
|---|
| 461 | q = zeros( len(self.conserved_quantities), Float) |
|---|
| 462 | |
|---|
| 463 | for i, name in enumerate(self.conserved_quantities): |
|---|
| 464 | Q = self.quantities[name] |
|---|
| 465 | if vertex is not None: |
|---|
| 466 | q[i] = Q.vertex_values[vol_id, vertex] |
|---|
| 467 | #elif edge is not None: |
|---|
| 468 | # q[i] = Q.edge_values[vol_id, edge] |
|---|
| 469 | else: |
|---|
| 470 | q[i] = Q.centroid_values[vol_id] |
|---|
| 471 | |
|---|
| 472 | return q |
|---|
| 473 | |
|---|
| 474 | |
|---|
| 475 | def get_centroids(self): |
|---|
| 476 | """Return all coordinates of centroids |
|---|
| 477 | Return x coordinate of centroid for each element as a N array |
|---|
| 478 | """ |
|---|
| 479 | |
|---|
| 480 | return self.centroids |
|---|
| 481 | |
|---|
| 482 | def get_vertices(self): |
|---|
| 483 | """Return all coordinates of centroids |
|---|
| 484 | Return x coordinate of centroid for each element as a N array |
|---|
| 485 | """ |
|---|
| 486 | |
|---|
| 487 | return self.vertices |
|---|
| 488 | |
|---|
| 489 | def get_coordinate(self, elem_id, vertex=None): |
|---|
| 490 | """Return coordinate of centroid, |
|---|
| 491 | or left or right vertex. |
|---|
| 492 | Left vertex (vertex=0). Right vertex (vertex=1) |
|---|
| 493 | """ |
|---|
| 494 | |
|---|
| 495 | if vertex is None: |
|---|
| 496 | return self.centroids[elem_id] |
|---|
| 497 | else: |
|---|
| 498 | return self.vertices[elem_id,vertex] |
|---|
| 499 | |
|---|
| 500 | def get_area(self, elem_id): |
|---|
| 501 | """Return area of element id |
|---|
| 502 | """ |
|---|
| 503 | |
|---|
| 504 | return self.areas[elem_id] |
|---|
| 505 | |
|---|
| 506 | def get_quantity(self, name, location='vertices', indices = None): |
|---|
| 507 | """Get values for named quantity |
|---|
| 508 | |
|---|
| 509 | name: Name of quantity |
|---|
| 510 | |
|---|
| 511 | In case of location == 'centroids' the dimension values must |
|---|
| 512 | be a list of a Numerical array of length N, N being the number |
|---|
| 513 | of elements. Otherwise it must be of dimension Nx3. |
|---|
| 514 | |
|---|
| 515 | Indices is the set of element ids that the operation applies to. |
|---|
| 516 | |
|---|
| 517 | The values will be stored in elements following their |
|---|
| 518 | internal ordering. |
|---|
| 519 | """ |
|---|
| 520 | |
|---|
| 521 | return self.quantities[name].get_values( location, indices = indices) |
|---|
| 522 | |
|---|
| 523 | def get_centroid_coordinates(self): |
|---|
| 524 | """Return all centroid coordinates. |
|---|
| 525 | Return all centroid coordinates for all triangles as an Nx2 array |
|---|
| 526 | (ordered as x0, y0 for each triangle) |
|---|
| 527 | """ |
|---|
| 528 | return self.centroids |
|---|
| 529 | |
|---|
| 530 | def set_quantity(self, name, *args, **kwargs): |
|---|
| 531 | """Set values for named quantity |
|---|
| 532 | |
|---|
| 533 | |
|---|
| 534 | One keyword argument is documented here: |
|---|
| 535 | expression = None, # Arbitrary expression |
|---|
| 536 | |
|---|
| 537 | expression: |
|---|
| 538 | Arbitrary expression involving quantity names |
|---|
| 539 | |
|---|
| 540 | See Quantity.set_values for further documentation. |
|---|
| 541 | """ |
|---|
| 542 | |
|---|
| 543 | #FIXME (Ole): Allow new quantities here |
|---|
| 544 | #from quantity import Quantity, Conserved_quantity |
|---|
| 545 | #Create appropriate quantity object |
|---|
| 546 | ##if name in self.conserved_quantities: |
|---|
| 547 | ## self.quantities[name] = Conserved_quantity(self) |
|---|
| 548 | ##else: |
|---|
| 549 | ## self.quantities[name] = Quantity(self) |
|---|
| 550 | |
|---|
| 551 | |
|---|
| 552 | #Do the expression stuff |
|---|
| 553 | if kwargs.has_key('expression'): |
|---|
| 554 | expression = kwargs['expression'] |
|---|
| 555 | del kwargs['expression'] |
|---|
| 556 | |
|---|
| 557 | Q = self.create_quantity_from_expression(expression) |
|---|
| 558 | kwargs['quantity'] = Q |
|---|
| 559 | |
|---|
| 560 | |
|---|
| 561 | print "self.vertices1" |
|---|
| 562 | print self.vertices |
|---|
| 563 | |
|---|
| 564 | #Assign values |
|---|
| 565 | self.quantities[name].set_values(*args, **kwargs) |
|---|
| 566 | |
|---|
| 567 | print "self.vertices2" |
|---|
| 568 | print self.vertices |
|---|
| 569 | |
|---|
| 570 | def set_boundary(self, boundary_map): |
|---|
| 571 | """Associate boundary objects with tagged boundary segments. |
|---|
| 572 | |
|---|
| 573 | Input boundary_map is a dictionary of boundary objects keyed |
|---|
| 574 | by symbolic tags to matched against tags in the internal dictionary |
|---|
| 575 | self.boundary. |
|---|
| 576 | |
|---|
| 577 | As result one pointer to a boundary object is stored for each vertex |
|---|
| 578 | in the list self.boundary_objects. |
|---|
| 579 | More entries may point to the same boundary object |
|---|
| 580 | |
|---|
| 581 | Schematically the mapping is from two dictionaries to one list |
|---|
| 582 | where the index is used as pointer to the boundary_values arrays |
|---|
| 583 | within each quantity. |
|---|
| 584 | |
|---|
| 585 | self.boundary: (vol_id, edge_id): tag |
|---|
| 586 | boundary_map (input): tag: boundary_object |
|---|
| 587 | ---------------------------------------------- |
|---|
| 588 | self.boundary_objects: ((vol_id, edge_id), boundary_object) |
|---|
| 589 | |
|---|
| 590 | |
|---|
| 591 | Pre-condition: |
|---|
| 592 | self.boundary has been built. |
|---|
| 593 | |
|---|
| 594 | Post-condition: |
|---|
| 595 | self.boundary_objects is built |
|---|
| 596 | |
|---|
| 597 | If a tag from the domain doesn't appear in the input dictionary an |
|---|
| 598 | exception is raised. |
|---|
| 599 | However, if a tag is not used to the domain, no error is thrown. |
|---|
| 600 | FIXME: This would lead to implementation of a |
|---|
| 601 | default boundary condition |
|---|
| 602 | |
|---|
| 603 | Note: If a segment is listed in the boundary dictionary and if it is |
|---|
| 604 | not None, it *will* become a boundary - |
|---|
| 605 | even if there is a neighbouring triangle. |
|---|
| 606 | This would be the case for internal boundaries |
|---|
| 607 | |
|---|
| 608 | Boundary objects that are None will be skipped. |
|---|
| 609 | |
|---|
| 610 | FIXME: If set_boundary is called multiple times and if Boundary |
|---|
| 611 | object is changed into None, the neighbour structure will not be |
|---|
| 612 | restored!!! |
|---|
| 613 | """ |
|---|
| 614 | |
|---|
| 615 | self.boundary_objects = [] |
|---|
| 616 | |
|---|
| 617 | |
|---|
| 618 | |
|---|
| 619 | |
|---|
| 620 | |
|---|
| 621 | self.boundary_map = boundary_map #Store for use with eg. boundary_stats. |
|---|
| 622 | |
|---|
| 623 | #FIXME: Try to remove the sorting and fix test_mesh.py |
|---|
| 624 | x = self.boundary.keys() |
|---|
| 625 | x.sort() |
|---|
| 626 | |
|---|
| 627 | #Loop through edges that lie on the boundary and associate them with |
|---|
| 628 | #callable boundary objects depending on their tags |
|---|
| 629 | #for k, (vol_id, edge_id) in enumerate(x): |
|---|
| 630 | for k, (vol_id, vertex_id) in enumerate(x): |
|---|
| 631 | #tag = self.boundary[ (vol_id, edge_id) ] |
|---|
| 632 | tag = self.boundary[ (vol_id, vertex_id) ] |
|---|
| 633 | |
|---|
| 634 | if boundary_map.has_key(tag): |
|---|
| 635 | B = boundary_map[tag] #Get callable boundary object |
|---|
| 636 | |
|---|
| 637 | if B is not None: |
|---|
| 638 | #self.boundary_objects.append( ((vol_id, edge_id), B) ) |
|---|
| 639 | #self.neighbours[vol_id, edge_id] = -len(self.boundary_objects) |
|---|
| 640 | self.boundary_objects.append( ((vol_id, vertex_id), B) ) |
|---|
| 641 | self.neighbours[vol_id, vertex_id] = -len(self.boundary_objects) |
|---|
| 642 | else: |
|---|
| 643 | pass |
|---|
| 644 | #FIXME: Check and perhaps fix neighbour structure |
|---|
| 645 | |
|---|
| 646 | else: |
|---|
| 647 | msg = 'ERROR (domain.py): Tag "%s" has not been ' %tag |
|---|
| 648 | msg += 'bound to a boundary object.\n' |
|---|
| 649 | msg += 'All boundary tags defined in domain must appear ' |
|---|
| 650 | msg += 'in the supplied dictionary.\n' |
|---|
| 651 | msg += 'The tags are: %s' %self.get_boundary_tags() |
|---|
| 652 | raise msg |
|---|
| 653 | |
|---|
| 654 | |
|---|
| 655 | |
|---|
| 656 | def check_integrity(self): |
|---|
| 657 | #Mesh.check_integrity(self) |
|---|
| 658 | |
|---|
| 659 | for quantity in self.conserved_quantities: |
|---|
| 660 | msg = 'Conserved quantities must be a subset of all quantities' |
|---|
| 661 | assert quantity in self.quantities, msg |
|---|
| 662 | |
|---|
| 663 | ##assert hasattr(self, 'boundary_objects') |
|---|
| 664 | |
|---|
| 665 | def get_name(self): |
|---|
| 666 | return self.filename |
|---|
| 667 | |
|---|
| 668 | def set_name(self, name): |
|---|
| 669 | self.filename = name |
|---|
| 670 | |
|---|
| 671 | def get_datadir(self): |
|---|
| 672 | return self.datadir |
|---|
| 673 | |
|---|
| 674 | def set_datadir(self, name): |
|---|
| 675 | self.datadir = name |
|---|
| 676 | |
|---|
| 677 | #Main components of evolve |
|---|
| 678 | |
|---|
| 679 | def evolve(self, yieldstep = None, finaltime = None, |
|---|
| 680 | skip_initial_step = False): |
|---|
| 681 | """Evolve model from time=0.0 to finaltime yielding results |
|---|
| 682 | every yieldstep. |
|---|
| 683 | |
|---|
| 684 | Internally, smaller timesteps may be taken. |
|---|
| 685 | |
|---|
| 686 | Evolve is implemented as a generator and is to be called as such, e.g. |
|---|
| 687 | |
|---|
| 688 | for t in domain.evolve(timestep, yieldstep, finaltime): |
|---|
| 689 | <Do something with domain and t> |
|---|
| 690 | |
|---|
| 691 | """ |
|---|
| 692 | |
|---|
| 693 | from config import min_timestep, max_timestep, epsilon |
|---|
| 694 | |
|---|
| 695 | #FIXME: Maybe lump into a larger check prior to evolving |
|---|
| 696 | msg = 'Boundary tags must be bound to boundary objects before evolving system, ' |
|---|
| 697 | msg += 'e.g. using the method set_boundary.\n' |
|---|
| 698 | msg += 'This system has the boundary tags %s ' %self.get_boundary_tags() |
|---|
| 699 | assert hasattr(self, 'boundary_objects'), msg |
|---|
| 700 | |
|---|
| 701 | ##self.set_defaults() |
|---|
| 702 | |
|---|
| 703 | if yieldstep is None: |
|---|
| 704 | yieldstep = max_timestep |
|---|
| 705 | else: |
|---|
| 706 | yieldstep = float(yieldstep) |
|---|
| 707 | |
|---|
| 708 | self.order = self.default_order |
|---|
| 709 | |
|---|
| 710 | |
|---|
| 711 | self.yieldtime = 0.0 #Time between 'yields' |
|---|
| 712 | |
|---|
| 713 | #Initialise interval of timestep sizes (for reporting only) |
|---|
| 714 | # SEEMS WIERD |
|---|
| 715 | self.min_timestep = max_timestep |
|---|
| 716 | self.max_timestep = min_timestep |
|---|
| 717 | self.finaltime = finaltime |
|---|
| 718 | self.number_of_steps = 0 |
|---|
| 719 | self.number_of_first_order_steps = 0 |
|---|
| 720 | |
|---|
| 721 | #update ghosts |
|---|
| 722 | #self.update_ghosts() |
|---|
| 723 | |
|---|
| 724 | #Initial update of vertex and edge values |
|---|
| 725 | self.distribute_to_vertices_and_edges() |
|---|
| 726 | |
|---|
| 727 | #Initial update boundary values |
|---|
| 728 | self.update_boundary() |
|---|
| 729 | |
|---|
| 730 | #Or maybe restore from latest checkpoint |
|---|
| 731 | if self.checkpoint is True: |
|---|
| 732 | self.goto_latest_checkpoint() |
|---|
| 733 | |
|---|
| 734 | if skip_initial_step is False: |
|---|
| 735 | yield(self.time) #Yield initial values |
|---|
| 736 | |
|---|
| 737 | while True: |
|---|
| 738 | |
|---|
| 739 | #Compute fluxes across each element edge |
|---|
| 740 | self.compute_fluxes() |
|---|
| 741 | |
|---|
| 742 | #Update timestep to fit yieldstep and finaltime |
|---|
| 743 | self.update_timestep(yieldstep, finaltime) |
|---|
| 744 | |
|---|
| 745 | #Update conserved quantities |
|---|
| 746 | self.update_conserved_quantities() |
|---|
| 747 | |
|---|
| 748 | #update ghosts |
|---|
| 749 | #self.update_ghosts() |
|---|
| 750 | |
|---|
| 751 | #Update vertex and edge values |
|---|
| 752 | self.distribute_to_vertices_and_edges() |
|---|
| 753 | |
|---|
| 754 | #Update boundary values |
|---|
| 755 | self.update_boundary() |
|---|
| 756 | |
|---|
| 757 | #print 'timestep', self.timestep |
|---|
| 758 | |
|---|
| 759 | #Update time |
|---|
| 760 | self.time += self.timestep |
|---|
| 761 | self.yieldtime += self.timestep |
|---|
| 762 | self.number_of_steps += 1 |
|---|
| 763 | if self.order == 1: |
|---|
| 764 | self.number_of_first_order_steps += 1 |
|---|
| 765 | |
|---|
| 766 | #Yield results |
|---|
| 767 | if finaltime is not None and abs(self.time - finaltime) < epsilon: |
|---|
| 768 | |
|---|
| 769 | #FIXME: There is a rare situation where the |
|---|
| 770 | #final time step is stored twice. Can we make a test? |
|---|
| 771 | |
|---|
| 772 | # Yield final time and stop |
|---|
| 773 | yield(self.time) |
|---|
| 774 | break |
|---|
| 775 | |
|---|
| 776 | |
|---|
| 777 | if abs(self.yieldtime - yieldstep) < epsilon: |
|---|
| 778 | # Yield (intermediate) time and allow inspection of domain |
|---|
| 779 | |
|---|
| 780 | if self.checkpoint is True: |
|---|
| 781 | self.store_checkpoint() |
|---|
| 782 | self.delete_old_checkpoints() |
|---|
| 783 | |
|---|
| 784 | #Pass control on to outer loop for more specific actions |
|---|
| 785 | yield(self.time) |
|---|
| 786 | |
|---|
| 787 | # Reinitialise |
|---|
| 788 | self.yieldtime = 0.0 |
|---|
| 789 | self.min_timestep = max_timestep |
|---|
| 790 | self.max_timestep = min_timestep |
|---|
| 791 | self.number_of_steps = 0 |
|---|
| 792 | self.number_of_first_order_steps = 0 |
|---|
| 793 | |
|---|
| 794 | def distribute_to_vertices_and_edges(self): |
|---|
| 795 | """Extrapolate conserved quantities from centroid to |
|---|
| 796 | vertices and edge-midpoints for each volume |
|---|
| 797 | |
|---|
| 798 | Default implementation is straight first order, |
|---|
| 799 | i.e. constant values throughout each element and |
|---|
| 800 | no reference to non-conserved quantities. |
|---|
| 801 | """ |
|---|
| 802 | |
|---|
| 803 | for name in self.conserved_quantities: |
|---|
| 804 | Q = self.quantities[name] |
|---|
| 805 | if self.order == 1: |
|---|
| 806 | Q.extrapolate_first_order() |
|---|
| 807 | elif self.order == 2: |
|---|
| 808 | Q.extrapolate_second_order() |
|---|
| 809 | Q.limit() |
|---|
| 810 | else: |
|---|
| 811 | raise 'Unknown order' |
|---|
| 812 | #Q.interpolate_from_vertices_to_edges() |
|---|
| 813 | |
|---|
| 814 | |
|---|
| 815 | def update_boundary(self): |
|---|
| 816 | """Go through list of boundary objects and update boundary values |
|---|
| 817 | for all conserved quantities on boundary. |
|---|
| 818 | """ |
|---|
| 819 | |
|---|
| 820 | #FIXME: Update only those that change (if that can be worked out) |
|---|
| 821 | #FIXME: Boundary objects should not include ghost nodes. |
|---|
| 822 | #for i, ((vol_id, edge_id), B) in enumerate(self.boundary_objects): |
|---|
| 823 | # q = B.evaluate(vol_id, edge_id) |
|---|
| 824 | for i, ((vol_id, vertex_id), B) in enumerate(self.boundary_objects): |
|---|
| 825 | q = B.evaluate(vol_id, vertex_id) |
|---|
| 826 | |
|---|
| 827 | for j, name in enumerate(self.conserved_quantities): |
|---|
| 828 | Q = self.quantities[name] |
|---|
| 829 | Q.boundary_values[i] = q[j] |
|---|
| 830 | |
|---|
| 831 | def update_timestep(self, yieldstep, finaltime): |
|---|
| 832 | |
|---|
| 833 | from config import min_timestep |
|---|
| 834 | |
|---|
| 835 | # self.timestep is calculated from speed of characteristics |
|---|
| 836 | # Apply CFL condition here |
|---|
| 837 | timestep = self.CFL*self.timestep |
|---|
| 838 | |
|---|
| 839 | #Record maximal and minimal values of timestep for reporting |
|---|
| 840 | self.max_timestep = max(timestep, self.max_timestep) |
|---|
| 841 | self.min_timestep = min(timestep, self.min_timestep) |
|---|
| 842 | |
|---|
| 843 | #Protect against degenerate time steps |
|---|
| 844 | if timestep < min_timestep: |
|---|
| 845 | |
|---|
| 846 | #Number of consecutive small steps taken b4 taking action |
|---|
| 847 | self.smallsteps += 1 |
|---|
| 848 | |
|---|
| 849 | if self.smallsteps > self.max_smallsteps: |
|---|
| 850 | self.smallsteps = 0 #Reset |
|---|
| 851 | |
|---|
| 852 | if self.order == 1: |
|---|
| 853 | msg = 'WARNING: Too small timestep %.16f reached '\ |
|---|
| 854 | %timestep |
|---|
| 855 | msg += 'even after %d steps of 1 order scheme'\ |
|---|
| 856 | %self.max_smallsteps |
|---|
| 857 | print msg |
|---|
| 858 | timestep = min_timestep #Try enforcing min_step |
|---|
| 859 | |
|---|
| 860 | #raise msg |
|---|
| 861 | else: |
|---|
| 862 | #Try to overcome situation by switching to 1 order |
|---|
| 863 | self.order = 1 |
|---|
| 864 | |
|---|
| 865 | else: |
|---|
| 866 | self.smallsteps = 0 |
|---|
| 867 | if self.order == 1 and self.default_order == 2: |
|---|
| 868 | self.order = 2 |
|---|
| 869 | |
|---|
| 870 | |
|---|
| 871 | #Ensure that final time is not exceeded |
|---|
| 872 | if finaltime is not None and self.time + timestep > finaltime: |
|---|
| 873 | timestep = finaltime-self.time |
|---|
| 874 | |
|---|
| 875 | #Ensure that model time is aligned with yieldsteps |
|---|
| 876 | if self.yieldtime + timestep > yieldstep: |
|---|
| 877 | timestep = yieldstep-self.yieldtime |
|---|
| 878 | |
|---|
| 879 | self.timestep = timestep |
|---|
| 880 | |
|---|
| 881 | |
|---|
| 882 | def compute_forcing_terms(self): |
|---|
| 883 | """If there are any forcing functions driving the system |
|---|
| 884 | they should be defined in Domain subclass and appended to |
|---|
| 885 | the list self.forcing_terms |
|---|
| 886 | """ |
|---|
| 887 | |
|---|
| 888 | for f in self.forcing_terms: |
|---|
| 889 | f(self) |
|---|
| 890 | |
|---|
| 891 | |
|---|
| 892 | def update_conserved_quantities(self): |
|---|
| 893 | """Update vectors of conserved quantities using previously |
|---|
| 894 | computed fluxes specified forcing functions. |
|---|
| 895 | """ |
|---|
| 896 | |
|---|
| 897 | from Numeric import ones, sum, equal, Float |
|---|
| 898 | |
|---|
| 899 | N = self.number_of_elements |
|---|
| 900 | d = len(self.conserved_quantities) |
|---|
| 901 | |
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| 902 | timestep = self.timestep |
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| 903 | |
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| 904 | #Compute forcing terms |
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| 905 | self.compute_forcing_terms() |
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| 906 | |
|---|
| 907 | #Update conserved_quantities |
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| 908 | for name in self.conserved_quantities: |
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| 909 | Q = self.quantities[name] |
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| 910 | Q.update(timestep) |
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| 911 | |
|---|
| 912 | #Clean up |
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| 913 | #Note that Q.explicit_update is reset by compute_fluxes |
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| 914 | |
|---|
| 915 | #MH090605 commented out the following since semi_implicit_update is now re-initialized |
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| 916 | #at the end of the _update function in quantity_ext.c (This is called by the |
|---|
| 917 | #preceeding Q.update(timestep) statement above). |
|---|
| 918 | #For run_profile.py with N=128, the time of update_conserved_quantities is cut from 14.00 secs |
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| 919 | #to 8.35 secs |
|---|
| 920 | |
|---|
| 921 | #Q.semi_implicit_update[:] = 0.0 |
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| 922 | |
|---|
| 923 | if __name__ == "__main__": |
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| 924 | |
|---|
| 925 | points1 = [0.0, 1.0, 2.0, 3.0] |
|---|
| 926 | D1 = Domain(points1) |
|---|
| 927 | |
|---|
| 928 | print D1.get_coordinate(0) |
|---|
| 929 | print D1.get_coordinate(0,1) |
|---|
| 930 | print 'Number of Elements = ',D1.number_of_elements |
|---|
| 931 | |
|---|
| 932 | try: |
|---|
| 933 | print D1.get_coordinate(3) |
|---|
| 934 | except: |
|---|
| 935 | pass |
|---|
| 936 | else: |
|---|
| 937 | msg = 'Should have raised an out of bounds exception' |
|---|
| 938 | raise msg |
|---|
| 939 | |
|---|
| 940 | #points2 = [0.0, 1.0, 2.0, 3.0, 2.5] |
|---|
| 941 | #D2 = Domain(points2) |
|---|
| 942 | |
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