[1156] | 1 | // Python - C extension for quantity module. |
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| 2 | // |
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| 3 | // To compile (Python2.3): |
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| 4 | // gcc -c util_ext.c -I/usr/include/python2.3 -o util_ext.o -Wall -O |
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| 5 | // gcc -shared util_ext.o -o util_ext.so |
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| 6 | // |
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| 7 | // See the module quantity.py |
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| 8 | // |
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| 9 | // |
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| 10 | // Ole Nielsen, GA 2004 |
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| 11 | |
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| 12 | #include "Python.h" |
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[2547] | 13 | #include "arrayobject.h" |
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[1156] | 14 | #include "math.h" |
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| 15 | |
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| 16 | //Shared code snippets |
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| 17 | #include "util_ext.h" |
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| 18 | |
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| 19 | |
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| 20 | int _compute_gradients(int N, |
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| 21 | double* centroids, |
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| 22 | double* centroid_values, |
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| 23 | long* number_of_boundaries, |
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| 24 | long* surrogate_neighbours, |
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| 25 | double* a, |
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| 26 | double* b) { |
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| 27 | |
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| 28 | int i, k, k0, k1, k2, index3; |
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[1486] | 29 | double x0, x1, x2, y0, y1, y2, q0, q1, q2; //, det; |
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[1156] | 30 | |
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| 31 | |
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| 32 | for (k=0; k<N; k++) { |
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| 33 | index3 = 3*k; |
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| 34 | |
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| 35 | if (number_of_boundaries[k] < 2) { |
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| 36 | //Two or three true neighbours |
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| 37 | |
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| 38 | //Get indices of neighbours (or self when used as surrogate) |
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| 39 | //k0, k1, k2 = surrogate_neighbours[k,:] |
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| 40 | |
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| 41 | k0 = surrogate_neighbours[index3 + 0]; |
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| 42 | k1 = surrogate_neighbours[index3 + 1]; |
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| 43 | k2 = surrogate_neighbours[index3 + 2]; |
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| 44 | |
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| 45 | |
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| 46 | if (k0 == k1 || k1 == k2) return -1; |
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| 47 | |
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| 48 | //Get data |
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| 49 | q0 = centroid_values[k0]; |
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| 50 | q1 = centroid_values[k1]; |
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| 51 | q2 = centroid_values[k2]; |
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| 52 | |
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| 53 | x0 = centroids[k0*2]; y0 = centroids[k0*2+1]; |
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| 54 | x1 = centroids[k1*2]; y1 = centroids[k1*2+1]; |
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| 55 | x2 = centroids[k2*2]; y2 = centroids[k2*2+1]; |
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| 56 | |
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| 57 | //Gradient |
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| 58 | _gradient(x0, y0, x1, y1, x2, y2, q0, q1, q2, &a[k], &b[k]); |
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| 59 | |
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| 60 | } else if (number_of_boundaries[k] == 2) { |
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| 61 | //One true neighbour |
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| 62 | |
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| 63 | //#Get index of the one neighbour |
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| 64 | i=0; k0 = k; |
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| 65 | while (i<3 && k0==k) { |
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| 66 | k0 = surrogate_neighbours[index3 + i]; |
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| 67 | i++; |
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| 68 | } |
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| 69 | if (k0 == k) return -1; |
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| 70 | |
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| 71 | k1 = k; //self |
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| 72 | |
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| 73 | //Get data |
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| 74 | q0 = centroid_values[k0]; |
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| 75 | q1 = centroid_values[k1]; |
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| 76 | |
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| 77 | x0 = centroids[k0*2]; y0 = centroids[k0*2+1]; |
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| 78 | x1 = centroids[k1*2]; y1 = centroids[k1*2+1]; |
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| 79 | |
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[1486] | 80 | //Two point gradient |
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| 81 | _gradient2(x0, y0, x1, y1, q0, q1, &a[k], &b[k]); |
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| 82 | |
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| 83 | |
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| 84 | //Old (wrong code) |
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| 85 | //det = x0*y1 - x1*y0; |
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| 86 | //if (det != 0.0) { |
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| 87 | // a[k] = (y1*q0 - y0*q1)/det; |
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| 88 | // b[k] = (x0*q1 - x1*q0)/det; |
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| 89 | //} |
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[1156] | 90 | } |
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| 91 | // else: |
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| 92 | // #No true neighbours - |
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| 93 | // #Fall back to first order scheme |
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| 94 | // pass |
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| 95 | } |
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| 96 | return 0; |
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| 97 | } |
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| 98 | |
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| 99 | |
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| 100 | int _extrapolate(int N, |
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| 101 | double* centroids, |
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| 102 | double* centroid_values, |
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| 103 | double* vertex_coordinates, |
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| 104 | double* vertex_values, |
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| 105 | double* a, |
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| 106 | double* b) { |
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| 107 | |
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| 108 | int k, k2, k3, k6; |
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| 109 | double x, y, x0, y0, x1, y1, x2, y2; |
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| 110 | |
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| 111 | for (k=0; k<N; k++) { |
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| 112 | k6 = 6*k; |
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| 113 | k3 = 3*k; |
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| 114 | k2 = 2*k; |
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| 115 | |
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| 116 | //Centroid coordinates |
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| 117 | x = centroids[k2]; y = centroids[k2+1]; |
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| 118 | |
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| 119 | //vertex coordinates |
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| 120 | //x0, y0, x1, y1, x2, y2 = X[k,:] |
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| 121 | x0 = vertex_coordinates[k6 + 0]; |
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| 122 | y0 = vertex_coordinates[k6 + 1]; |
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| 123 | x1 = vertex_coordinates[k6 + 2]; |
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| 124 | y1 = vertex_coordinates[k6 + 3]; |
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| 125 | x2 = vertex_coordinates[k6 + 4]; |
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| 126 | y2 = vertex_coordinates[k6 + 5]; |
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| 127 | |
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| 128 | //Extrapolate |
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| 129 | vertex_values[k3+0] = centroid_values[k] + a[k]*(x0-x) + b[k]*(y0-y); |
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| 130 | vertex_values[k3+1] = centroid_values[k] + a[k]*(x1-x) + b[k]*(y1-y); |
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| 131 | vertex_values[k3+2] = centroid_values[k] + a[k]*(x2-x) + b[k]*(y2-y); |
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| 132 | |
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| 133 | } |
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| 134 | return 0; |
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| 135 | } |
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| 136 | |
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| 137 | |
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| 138 | |
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| 139 | |
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| 140 | int _interpolate(int N, |
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| 141 | double* vertex_values, |
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| 142 | double* edge_values) { |
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| 143 | |
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| 144 | int k, k3; |
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| 145 | double q0, q1, q2; |
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| 146 | |
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| 147 | |
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| 148 | for (k=0; k<N; k++) { |
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| 149 | k3 = 3*k; |
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| 150 | |
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| 151 | q0 = vertex_values[k3 + 0]; |
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| 152 | q1 = vertex_values[k3 + 1]; |
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| 153 | q2 = vertex_values[k3 + 2]; |
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| 154 | |
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| 155 | //printf("%f, %f, %f\n", q0, q1, q2); |
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| 156 | edge_values[k3 + 0] = 0.5*(q1+q2); |
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| 157 | edge_values[k3 + 1] = 0.5*(q0+q2); |
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| 158 | edge_values[k3 + 2] = 0.5*(q0+q1); |
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| 159 | } |
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| 160 | return 0; |
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| 161 | } |
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| 162 | |
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| 163 | int _update(int N, |
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| 164 | double timestep, |
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| 165 | double* centroid_values, |
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| 166 | double* explicit_update, |
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| 167 | double* semi_implicit_update) { |
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| 168 | //Update centroid values based on values stored in |
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| 169 | //explicit_update and semi_implicit_update as well as given timestep |
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| 170 | |
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| 171 | |
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| 172 | int k; |
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| 173 | double denominator, x; |
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| 174 | |
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| 175 | |
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| 176 | //Divide semi_implicit update by conserved quantity |
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| 177 | for (k=0; k<N; k++) { |
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| 178 | x = centroid_values[k]; |
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| 179 | if (x == 0.0) { |
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| 180 | semi_implicit_update[k] = 0.0; |
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| 181 | } else { |
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| 182 | semi_implicit_update[k] /= x; |
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| 183 | } |
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| 184 | } |
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| 185 | |
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| 186 | |
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| 187 | //Explicit updates |
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| 188 | for (k=0; k<N; k++) { |
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| 189 | centroid_values[k] += timestep*explicit_update[k]; |
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| 190 | } |
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| 191 | |
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| 192 | //Semi implicit updates |
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| 193 | for (k=0; k<N; k++) { |
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| 194 | denominator = 1.0 - timestep*semi_implicit_update[k]; |
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| 195 | if (denominator == 0.0) { |
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| 196 | return -1; |
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| 197 | } else { |
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| 198 | //Update conserved_quantities from semi implicit updates |
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| 199 | centroid_values[k] /= denominator; |
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| 200 | } |
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| 201 | } |
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[1506] | 202 | //MH080605 set semi_impliit_update[k] to 0.0 here, rather than in update_conserved_quantities.py |
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| 203 | for (k=0;k<N;k++) |
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| 204 | semi_implicit_update[k]=0.0; |
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[1156] | 205 | return 0; |
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| 206 | } |
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| 207 | |
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| 208 | |
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| 209 | ///////////////////////////////////////////////// |
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| 210 | // Gateways to Python |
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| 211 | PyObject *update(PyObject *self, PyObject *args) { |
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| 212 | |
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| 213 | PyObject *quantity; |
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| 214 | PyArrayObject *centroid_values, *explicit_update, *semi_implicit_update; |
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| 215 | |
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| 216 | double timestep; |
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| 217 | int N, err; |
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| 218 | |
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| 219 | |
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| 220 | // Convert Python arguments to C |
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| 221 | if (!PyArg_ParseTuple(args, "Od", &quantity, ×tep)) |
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| 222 | return NULL; |
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| 223 | |
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| 224 | centroid_values = get_consecutive_array(quantity, "centroid_values"); |
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| 225 | explicit_update = get_consecutive_array(quantity, "explicit_update"); |
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| 226 | semi_implicit_update = get_consecutive_array(quantity, "semi_implicit_update"); |
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| 227 | |
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| 228 | N = centroid_values -> dimensions[0]; |
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| 229 | |
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| 230 | err = _update(N, timestep, |
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| 231 | (double*) centroid_values -> data, |
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| 232 | (double*) explicit_update -> data, |
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| 233 | (double*) semi_implicit_update -> data); |
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| 234 | |
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| 235 | |
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| 236 | if (err != 0) { |
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| 237 | PyErr_SetString(PyExc_RuntimeError, |
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| 238 | "Zero division in semi implicit update - call Stephen :)"); |
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| 239 | return NULL; |
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| 240 | } |
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| 241 | |
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| 242 | //Release and return |
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| 243 | Py_DECREF(centroid_values); |
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| 244 | Py_DECREF(explicit_update); |
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| 245 | Py_DECREF(semi_implicit_update); |
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| 246 | |
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| 247 | return Py_BuildValue(""); |
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| 248 | } |
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| 249 | |
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| 250 | |
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| 251 | PyObject *interpolate_from_vertices_to_edges(PyObject *self, PyObject *args) { |
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| 252 | |
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| 253 | PyObject *quantity; |
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| 254 | PyArrayObject *vertex_values, *edge_values; |
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| 255 | |
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| 256 | int N, err; |
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| 257 | |
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| 258 | // Convert Python arguments to C |
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| 259 | if (!PyArg_ParseTuple(args, "O", &quantity)) |
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| 260 | return NULL; |
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| 261 | |
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| 262 | vertex_values = get_consecutive_array(quantity, "vertex_values"); |
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| 263 | edge_values = get_consecutive_array(quantity, "edge_values"); |
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| 264 | |
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| 265 | N = vertex_values -> dimensions[0]; |
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| 266 | |
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| 267 | err = _interpolate(N, |
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| 268 | (double*) vertex_values -> data, |
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| 269 | (double*) edge_values -> data); |
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| 270 | |
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| 271 | if (err != 0) { |
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| 272 | PyErr_SetString(PyExc_RuntimeError, "Interpolate could not be computed"); |
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| 273 | return NULL; |
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| 274 | } |
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| 275 | |
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| 276 | //Release and return |
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| 277 | Py_DECREF(vertex_values); |
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| 278 | Py_DECREF(edge_values); |
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| 279 | |
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| 280 | return Py_BuildValue(""); |
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| 281 | } |
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| 282 | |
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| 283 | |
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| 284 | PyObject *compute_gradients(PyObject *self, PyObject *args) { |
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| 285 | |
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| 286 | PyObject *quantity, *domain, *R; |
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| 287 | PyArrayObject |
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| 288 | *centroids, //Coordinates at centroids |
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| 289 | *centroid_values, //Values at centroids |
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| 290 | *number_of_boundaries, //Number of boundaries for each triangle |
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| 291 | *surrogate_neighbours, //True neighbours or - if one missing - self |
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| 292 | *a, *b; //Return values |
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| 293 | |
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| 294 | int dimensions[1], N, err; |
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| 295 | |
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| 296 | // Convert Python arguments to C |
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| 297 | if (!PyArg_ParseTuple(args, "O", &quantity)) |
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| 298 | return NULL; |
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| 299 | |
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| 300 | domain = PyObject_GetAttrString(quantity, "domain"); |
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| 301 | if (!domain) |
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| 302 | return NULL; |
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| 303 | |
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| 304 | //Get pertinent variables |
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| 305 | |
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| 306 | centroids = get_consecutive_array(domain, "centroid_coordinates"); |
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| 307 | centroid_values = get_consecutive_array(quantity, "centroid_values"); |
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| 308 | surrogate_neighbours = get_consecutive_array(domain, "surrogate_neighbours"); |
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| 309 | number_of_boundaries = get_consecutive_array(domain, "number_of_boundaries"); |
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| 310 | |
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| 311 | N = centroid_values -> dimensions[0]; |
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| 312 | |
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| 313 | //Release |
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| 314 | Py_DECREF(domain); |
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| 315 | |
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| 316 | //Allocate space for return vectors a and b (don't DECREF) |
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| 317 | dimensions[0] = N; |
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| 318 | a = (PyArrayObject *) PyArray_FromDims(1, dimensions, PyArray_DOUBLE); |
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| 319 | b = (PyArrayObject *) PyArray_FromDims(1, dimensions, PyArray_DOUBLE); |
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| 320 | |
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| 321 | |
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| 322 | |
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| 323 | err = _compute_gradients(N, |
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| 324 | (double*) centroids -> data, |
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| 325 | (double*) centroid_values -> data, |
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| 326 | (long*) number_of_boundaries -> data, |
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| 327 | (long*) surrogate_neighbours -> data, |
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| 328 | (double*) a -> data, |
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| 329 | (double*) b -> data); |
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| 330 | |
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| 331 | if (err != 0) { |
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| 332 | PyErr_SetString(PyExc_RuntimeError, "Gradient could not be computed"); |
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| 333 | return NULL; |
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| 334 | } |
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| 335 | |
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| 336 | //Release |
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| 337 | Py_DECREF(centroids); |
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| 338 | Py_DECREF(centroid_values); |
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| 339 | Py_DECREF(number_of_boundaries); |
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| 340 | Py_DECREF(surrogate_neighbours); |
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| 341 | |
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| 342 | //Build result, release and return |
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| 343 | R = Py_BuildValue("OO", PyArray_Return(a), PyArray_Return(b)); |
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| 344 | Py_DECREF(a); |
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| 345 | Py_DECREF(b); |
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| 346 | return R; |
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| 347 | } |
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| 348 | |
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| 349 | |
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| 350 | |
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| 351 | PyObject *extrapolate_second_order(PyObject *self, PyObject *args) { |
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| 352 | |
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| 353 | PyObject *quantity, *domain; |
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| 354 | PyArrayObject |
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| 355 | *centroids, //Coordinates at centroids |
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| 356 | *centroid_values, //Values at centroids |
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| 357 | *vertex_coordinates, //Coordinates at vertices |
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| 358 | *vertex_values, //Values at vertices |
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| 359 | *number_of_boundaries, //Number of boundaries for each triangle |
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| 360 | *surrogate_neighbours, //True neighbours or - if one missing - self |
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| 361 | *a, *b; //Gradients |
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| 362 | |
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| 363 | //int N, err; |
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| 364 | int dimensions[1], N, err; |
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| 365 | //double *a, *b; //Gradients |
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| 366 | |
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| 367 | // Convert Python arguments to C |
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| 368 | if (!PyArg_ParseTuple(args, "O", &quantity)) |
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| 369 | return NULL; |
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| 370 | |
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| 371 | domain = PyObject_GetAttrString(quantity, "domain"); |
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| 372 | if (!domain) |
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| 373 | return NULL; |
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| 374 | |
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| 375 | //Get pertinent variables |
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| 376 | centroids = get_consecutive_array(domain, "centroid_coordinates"); |
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| 377 | centroid_values = get_consecutive_array(quantity, "centroid_values"); |
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| 378 | surrogate_neighbours = get_consecutive_array(domain, "surrogate_neighbours"); |
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| 379 | number_of_boundaries = get_consecutive_array(domain, "number_of_boundaries"); |
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| 380 | vertex_coordinates = get_consecutive_array(domain, "vertex_coordinates"); |
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| 381 | vertex_values = get_consecutive_array(quantity, "vertex_values"); |
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| 382 | |
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| 383 | N = centroid_values -> dimensions[0]; |
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| 384 | |
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| 385 | //Release |
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| 386 | Py_DECREF(domain); |
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| 387 | |
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| 388 | //Allocate space for return vectors a and b (don't DECREF) |
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| 389 | dimensions[0] = N; |
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| 390 | a = (PyArrayObject *) PyArray_FromDims(1, dimensions, PyArray_DOUBLE); |
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| 391 | b = (PyArrayObject *) PyArray_FromDims(1, dimensions, PyArray_DOUBLE); |
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| 392 | |
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| 393 | //FIXME: Odd that I couldn't use normal arrays |
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| 394 | //Allocate space for return vectors a and b (don't DECREF) |
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| 395 | //a = (double*) malloc(N * sizeof(double)); |
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| 396 | //if (!a) return NULL; |
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| 397 | //b = (double*) malloc(N * sizeof(double)); |
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| 398 | //if (!b) return NULL; |
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| 399 | |
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| 400 | |
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| 401 | err = _compute_gradients(N, |
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| 402 | (double*) centroids -> data, |
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| 403 | (double*) centroid_values -> data, |
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| 404 | (long*) number_of_boundaries -> data, |
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| 405 | (long*) surrogate_neighbours -> data, |
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| 406 | (double*) a -> data, |
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| 407 | (double*) b -> data); |
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| 408 | |
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| 409 | if (err != 0) { |
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| 410 | PyErr_SetString(PyExc_RuntimeError, "Gradient could not be computed"); |
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| 411 | return NULL; |
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| 412 | } |
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| 413 | |
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| 414 | err = _extrapolate(N, |
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| 415 | (double*) centroids -> data, |
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| 416 | (double*) centroid_values -> data, |
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| 417 | (double*) vertex_coordinates -> data, |
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| 418 | (double*) vertex_values -> data, |
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| 419 | (double*) a -> data, |
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| 420 | (double*) b -> data); |
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| 421 | |
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| 422 | |
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| 423 | if (err != 0) { |
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| 424 | PyErr_SetString(PyExc_RuntimeError, |
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| 425 | "Internal function _extrapolate failed"); |
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| 426 | return NULL; |
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| 427 | } |
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| 428 | |
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| 429 | |
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| 430 | |
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| 431 | //Release |
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| 432 | Py_DECREF(centroids); |
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| 433 | Py_DECREF(centroid_values); |
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| 434 | Py_DECREF(number_of_boundaries); |
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| 435 | Py_DECREF(surrogate_neighbours); |
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| 436 | Py_DECREF(vertex_coordinates); |
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| 437 | Py_DECREF(vertex_values); |
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| 438 | Py_DECREF(a); |
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| 439 | Py_DECREF(b); |
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| 440 | |
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| 441 | return Py_BuildValue(""); |
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| 442 | } |
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| 443 | |
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| 444 | |
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| 445 | |
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| 446 | PyObject *limit(PyObject *self, PyObject *args) { |
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| 447 | |
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| 448 | PyObject *quantity, *domain, *Tmp; |
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| 449 | PyArrayObject |
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| 450 | *qv, //Conserved quantities at vertices |
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| 451 | *qc, //Conserved quantities at centroids |
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| 452 | *neighbours; |
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| 453 | |
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| 454 | int k, i, n, N, k3; |
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| 455 | double beta_w; //Safety factor |
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| 456 | double *qmin, *qmax, qn; |
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| 457 | |
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| 458 | // Convert Python arguments to C |
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| 459 | if (!PyArg_ParseTuple(args, "O", &quantity)) |
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| 460 | return NULL; |
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| 461 | |
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| 462 | domain = PyObject_GetAttrString(quantity, "domain"); |
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| 463 | if (!domain) |
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| 464 | return NULL; |
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| 465 | |
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| 466 | //neighbours = (PyArrayObject*) PyObject_GetAttrString(domain, "neighbours"); |
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| 467 | neighbours = get_consecutive_array(domain, "neighbours"); |
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| 468 | |
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| 469 | //Get safety factor beta_w |
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| 470 | Tmp = PyObject_GetAttrString(domain, "beta_w"); |
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| 471 | if (!Tmp) |
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| 472 | return NULL; |
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| 473 | |
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| 474 | beta_w = PyFloat_AsDouble(Tmp); |
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| 475 | |
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| 476 | Py_DECREF(Tmp); |
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| 477 | Py_DECREF(domain); |
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| 478 | |
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| 479 | |
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| 480 | qc = get_consecutive_array(quantity, "centroid_values"); |
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| 481 | qv = get_consecutive_array(quantity, "vertex_values"); |
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| 482 | |
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| 483 | |
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| 484 | N = qc -> dimensions[0]; |
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| 485 | |
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| 486 | //Find min and max of this and neighbour's centroid values |
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| 487 | qmin = malloc(N * sizeof(double)); |
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| 488 | qmax = malloc(N * sizeof(double)); |
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| 489 | for (k=0; k<N; k++) { |
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| 490 | k3=k*3; |
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| 491 | |
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| 492 | qmin[k] = ((double*) qc -> data)[k]; |
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| 493 | qmax[k] = qmin[k]; |
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| 494 | |
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| 495 | for (i=0; i<3; i++) { |
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| 496 | n = ((long*) neighbours -> data)[k3+i]; |
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| 497 | if (n >= 0) { |
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| 498 | qn = ((double*) qc -> data)[n]; //Neighbour's centroid value |
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| 499 | |
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| 500 | qmin[k] = min(qmin[k], qn); |
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| 501 | qmax[k] = max(qmax[k], qn); |
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| 502 | } |
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| 503 | } |
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| 504 | } |
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| 505 | |
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| 506 | // Call underlying routine |
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| 507 | _limit(N, beta_w, (double*) qc -> data, (double*) qv -> data, qmin, qmax); |
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| 508 | |
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| 509 | free(qmin); |
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| 510 | free(qmax); |
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| 511 | return Py_BuildValue(""); |
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| 512 | } |
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| 513 | |
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| 514 | |
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| 515 | |
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| 516 | // Method table for python module |
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| 517 | static struct PyMethodDef MethodTable[] = { |
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| 518 | {"limit", limit, METH_VARARGS, "Print out"}, |
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| 519 | {"update", update, METH_VARARGS, "Print out"}, |
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| 520 | {"compute_gradients", compute_gradients, METH_VARARGS, "Print out"}, |
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| 521 | {"extrapolate_second_order", extrapolate_second_order, |
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| 522 | METH_VARARGS, "Print out"}, |
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| 523 | {"interpolate_from_vertices_to_edges", |
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| 524 | interpolate_from_vertices_to_edges, |
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| 525 | METH_VARARGS, "Print out"}, |
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| 526 | {NULL, NULL, 0, NULL} // sentinel |
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| 527 | }; |
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| 528 | |
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| 529 | // Module initialisation |
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| 530 | void initquantity_ext(void){ |
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| 531 | Py_InitModule("quantity_ext", MethodTable); |
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| 532 | |
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| 533 | import_array(); //Necessary for handling of NumPY structures |
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| 534 | } |
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