[7839] | 1 | """Class Domain - 1D domains for finite-volume computations of |
---|
| 2 | the shallow water wave equation |
---|
| 3 | |
---|
| 4 | |
---|
| 5 | Copyright 2004 |
---|
| 6 | Ole Nielsen, Stephen Roberts, Duncan Gray, Christopher Zoppou |
---|
| 7 | Geoscience Australia |
---|
| 8 | """ |
---|
| 9 | |
---|
| 10 | import numpy |
---|
| 11 | from generic_boundary_conditions import * |
---|
| 12 | |
---|
| 13 | |
---|
| 14 | class Generic_domain: |
---|
| 15 | |
---|
| 16 | def __init__(self, |
---|
| 17 | coordinates, |
---|
| 18 | boundary = None, |
---|
| 19 | conserved_quantities = None, |
---|
| 20 | evolved_quantities = None, |
---|
| 21 | other_quantities = None, |
---|
| 22 | tagged_elements = None): |
---|
| 23 | """ |
---|
| 24 | Build 1D elements from x coordinates |
---|
| 25 | """ |
---|
| 26 | |
---|
| 27 | from config import timestepping_method |
---|
| 28 | from config import CFL |
---|
| 29 | |
---|
| 30 | #Store Points |
---|
| 31 | self.coordinates = numpy.array(coordinates, numpy.float) |
---|
| 32 | |
---|
| 33 | |
---|
| 34 | #Register number of Elements |
---|
| 35 | self.number_of_elements = N = len(self.coordinates)-1 |
---|
| 36 | |
---|
| 37 | self.beta = 1.0 |
---|
| 38 | self.set_limiter("minmod_kurganov") |
---|
| 39 | self.set_CFL(CFL) |
---|
| 40 | self.set_timestepping_method(timestepping_method) |
---|
| 41 | |
---|
| 42 | self.wet_nodes = numpy.zeros((N,2), numpy.int) # should this be here |
---|
| 43 | |
---|
| 44 | #Allocate space for neighbour and boundary structures |
---|
| 45 | self.neighbours = numpy.zeros((N, 2), numpy.int) |
---|
| 46 | #self.neighbour_edges = numpy.zeros((N, 2), numpy.int) |
---|
| 47 | self.neighbour_vertices = numpy.zeros((N, 2), numpy.int) |
---|
| 48 | self.number_of_boundaries = numpy.zeros(N, numpy.int) |
---|
| 49 | self.surrogate_neighbours = numpy.zeros((N, 2), numpy.int) |
---|
| 50 | |
---|
| 51 | #Allocate space for geometric quantities |
---|
| 52 | self.vertices = numpy.zeros((N, 2), numpy.float) |
---|
| 53 | self.centroids = numpy.zeros(N, numpy.float) |
---|
| 54 | self.areas = numpy.zeros(N, numpy.float) |
---|
| 55 | |
---|
| 56 | self.max_speed_array = numpy.zeros(N, numpy.float) |
---|
| 57 | |
---|
| 58 | |
---|
| 59 | self.normals = numpy.zeros((N, 2), numpy.float) |
---|
| 60 | |
---|
| 61 | for i in range(N): |
---|
| 62 | xl = self.coordinates[i] |
---|
| 63 | xr = self.coordinates[i+1] |
---|
| 64 | self.vertices[i,0] = xl |
---|
| 65 | self.vertices[i,1] = xr |
---|
| 66 | |
---|
| 67 | centroid = (xl+xr)/2.0 |
---|
| 68 | self.centroids[i] = centroid |
---|
| 69 | |
---|
| 70 | msg = 'Coordinates should be ordered, smallest to largest' |
---|
| 71 | assert xr>xl, msg |
---|
| 72 | |
---|
| 73 | #The normal vectors |
---|
| 74 | # - point outward from each edge |
---|
| 75 | # - are orthogonal to the edge |
---|
| 76 | # - have unit length |
---|
| 77 | # - Are enumerated by left vertex then right vertex normals |
---|
| 78 | |
---|
| 79 | nl = -1.0 |
---|
| 80 | nr = 1.0 |
---|
| 81 | self.normals[i,:] = [nl, nr] |
---|
| 82 | |
---|
| 83 | self.areas[i] = (xr-xl) |
---|
| 84 | |
---|
| 85 | # # print 'N', N |
---|
| 86 | # # print 'Centroid', self.centroids |
---|
| 87 | # # print 'Areas', self.areas |
---|
| 88 | # # print 'Vertex_Coordinates', self.vertices |
---|
| 89 | |
---|
| 90 | #Initialise Neighbours (-1 means that it is a boundary neighbour) |
---|
| 91 | self.neighbours[i, :] = [-1, -1] |
---|
| 92 | #Initialise edge ids of neighbours |
---|
| 93 | #Initialise vertex ids of neighbours |
---|
| 94 | #In case of boundaries this slot is not used |
---|
| 95 | #self.neighbour_edges[i, :] = [-1, -1] |
---|
| 96 | self.neighbour_vertices[i, :] = [-1, -1] |
---|
| 97 | |
---|
| 98 | self.build_vertexlist() |
---|
| 99 | |
---|
| 100 | #Build neighbour structure |
---|
| 101 | self.build_neighbour_structure() |
---|
| 102 | |
---|
| 103 | #Build surrogate neighbour structure |
---|
| 104 | self.build_surrogate_neighbour_structure() |
---|
| 105 | |
---|
| 106 | #Build boundary dictionary mapping (id, edge) to symbolic tags |
---|
| 107 | #Build boundary dictionary mapping (id, vertex) to symbolic tags |
---|
| 108 | self.build_boundary_dictionary(boundary) |
---|
| 109 | |
---|
| 110 | #Build tagged element dictionary mapping (tag) to array of elements |
---|
| 111 | self.build_tagged_elements_dictionary(tagged_elements) |
---|
| 112 | |
---|
| 113 | from quantity import Quantity |
---|
| 114 | #from quantity_domain import Quantity, Conserved_quantity |
---|
| 115 | |
---|
| 116 | #List of quantity names entering |
---|
| 117 | #the conservation equations |
---|
| 118 | #(Must be a subset of quantities) |
---|
| 119 | if conserved_quantities is None: |
---|
| 120 | self.conserved_quantities = [] |
---|
| 121 | else: |
---|
| 122 | self.conserved_quantities = conserved_quantities |
---|
| 123 | |
---|
| 124 | if evolved_quantities is None: |
---|
| 125 | self.evolved_quantities = self.conserved_quantities |
---|
| 126 | else: |
---|
| 127 | self.evolved_quantities = evolved_quantities |
---|
| 128 | |
---|
| 129 | if other_quantities is None: |
---|
| 130 | self.other_quantities = [] |
---|
| 131 | else: |
---|
| 132 | self.other_quantities = other_quantities |
---|
| 133 | |
---|
| 134 | |
---|
| 135 | #Build dictionary of Quantity instances keyed by quantity names |
---|
| 136 | self.quantities = {} |
---|
| 137 | |
---|
| 138 | #print self.conserved_quantities |
---|
| 139 | #print self.evolved_quantities |
---|
| 140 | |
---|
| 141 | |
---|
| 142 | #FIXME: remove later - maybe OK, though.... |
---|
| 143 | for name in self.evolved_quantities: |
---|
| 144 | self.quantities[name] = Quantity(self) |
---|
| 145 | for name in self.other_quantities: |
---|
| 146 | self.quantities[name] = Quantity(self) |
---|
| 147 | |
---|
| 148 | #Create an empty list for explicit forcing terms |
---|
| 149 | self.forcing_terms = [] |
---|
| 150 | |
---|
| 151 | #Defaults |
---|
| 152 | from config import max_smallsteps, beta_w, beta_h, epsilon, CFL |
---|
| 153 | self.beta_w = beta_w |
---|
| 154 | self.beta_h = beta_h |
---|
| 155 | self.epsilon = epsilon |
---|
| 156 | |
---|
| 157 | #FIXME: Maybe have separate orders for h-limiter and w-limiter? |
---|
| 158 | #Or maybe get rid of order altogether and use beta_w and beta_h |
---|
| 159 | self.default_order = 1 |
---|
| 160 | self.order = self.default_order |
---|
| 161 | |
---|
| 162 | self.default_time_order = 1 |
---|
| 163 | self.time_order = self.default_time_order |
---|
| 164 | |
---|
| 165 | self.smallsteps = 0 |
---|
| 166 | self.max_smallsteps = max_smallsteps |
---|
| 167 | self.number_of_steps = 0 |
---|
| 168 | self.number_of_first_order_steps = 0 |
---|
| 169 | |
---|
| 170 | #Model time |
---|
| 171 | self.time = 0.0 |
---|
| 172 | self.finaltime = None |
---|
| 173 | self.min_timestep = self.max_timestep = 0.0 |
---|
| 174 | self.starttime = 0 #Physical starttime if any (0 is 1 Jan 1970 00:00:00) |
---|
| 175 | #Checkpointing and storage |
---|
| 176 | from config import default_datadir |
---|
| 177 | self.set_datadir(default_datadir) |
---|
| 178 | self.filename = 'domain' |
---|
| 179 | self.checkpoint = False |
---|
| 180 | |
---|
| 181 | def __len__(self): |
---|
| 182 | return self.number_of_elements |
---|
| 183 | |
---|
| 184 | def build_vertexlist(self): |
---|
| 185 | """Build vertexlist index by vertex ids and for each entry (point id) |
---|
| 186 | build a list of (triangles, vertex_id) pairs that use the point |
---|
| 187 | as vertex. |
---|
| 188 | |
---|
| 189 | Preconditions: |
---|
| 190 | self.coordinates and self.triangles are defined |
---|
| 191 | |
---|
| 192 | Postcondition: |
---|
| 193 | self.vertexlist is built |
---|
| 194 | """ |
---|
| 195 | |
---|
| 196 | vertexlist = [None]*len(self.coordinates) |
---|
| 197 | for i in range(self.number_of_elements): |
---|
| 198 | |
---|
| 199 | #a = self.triangles[i, 0] |
---|
| 200 | #b = self.triangles[i, 1] |
---|
| 201 | #c = self.triangles[i, 2] |
---|
| 202 | a = i |
---|
| 203 | b = i + 1 |
---|
| 204 | |
---|
| 205 | #Register the vertices v as lists of |
---|
| 206 | #(triangle_id, vertex_id) tuples associated with them |
---|
| 207 | #This is used for smoothing |
---|
| 208 | #for vertex_id, v in enumerate([a,b,c]): |
---|
| 209 | for vertex_id, v in enumerate([a,b]): |
---|
| 210 | if vertexlist[v] is None: |
---|
| 211 | vertexlist[v] = [] |
---|
| 212 | |
---|
| 213 | vertexlist[v].append( (i, vertex_id) ) |
---|
| 214 | |
---|
| 215 | self.vertexlist = vertexlist |
---|
| 216 | |
---|
| 217 | |
---|
| 218 | def build_neighbour_structure(self): |
---|
| 219 | """Update all registered triangles to point to their neighbours. |
---|
| 220 | |
---|
| 221 | Also, keep a tally of the number of boundaries for each triangle |
---|
| 222 | |
---|
| 223 | Postconditions: |
---|
| 224 | neighbours and neighbour_edges is populated |
---|
| 225 | neighbours and neighbour_vertices is populated |
---|
| 226 | number_of_boundaries integer array is defined. |
---|
| 227 | """ |
---|
| 228 | |
---|
| 229 | #Step 1: |
---|
| 230 | #Build dictionary mapping from segments (2-tuple of points) |
---|
| 231 | #to left hand side edge (facing neighbouring triangle) |
---|
| 232 | |
---|
| 233 | N = self.number_of_elements |
---|
| 234 | neighbourdict = {} |
---|
| 235 | #l_edge = 0 |
---|
| 236 | #r_edge = 1 |
---|
| 237 | l_vertex = 0 |
---|
| 238 | r_vertex = 1 |
---|
| 239 | for i in range(N): |
---|
| 240 | |
---|
| 241 | #Register all segments as keys mapping to current triangle |
---|
| 242 | #and segment id |
---|
| 243 | #a = self.triangles[i, 0] |
---|
| 244 | #b = self.triangles[i, 1] |
---|
| 245 | #c = self.triangles[i, 2] |
---|
| 246 | a = self.vertices[i,0] |
---|
| 247 | b = self.vertices[i,1] |
---|
| 248 | |
---|
| 249 | """ |
---|
| 250 | if neighbourdict.has_key((a,b)): |
---|
| 251 | msg = "Edge 2 of triangle %d is duplicating edge %d of triangle %d.\n" %(i,neighbourdict[a,b][1],neighbourdict[a,b][0]) |
---|
| 252 | raise msg |
---|
| 253 | if neighbourdict.has_key((b,c)): |
---|
| 254 | msg = "Edge 0 of triangle %d is duplicating edge %d of triangle %d.\n" %(i,neighbourdict[b,c][1],neighbourdict[b,c][0]) |
---|
| 255 | raise msg |
---|
| 256 | if neighbourdict.has_key((c,a)): |
---|
| 257 | msg = "Edge 1 of triangle %d is duplicating edge %d of triangle %d.\n" %(i,neighbourdict[c,a][1],neighbourdict[c,a][0]) |
---|
| 258 | raise msg |
---|
| 259 | """ |
---|
| 260 | #neighbourdict[a,b] = (i, 2) #(id, edge) |
---|
| 261 | #neighbourdict[b,c] = (i, 0) #(id, edge) |
---|
| 262 | #neighbourdict[c,a] = (i, 1) #(id, edge) |
---|
| 263 | #neighbourdict[a,b] = (i, 1) #(id, edge) |
---|
| 264 | #neighbourdict[b,a] = (i, 0) #(id, edge) |
---|
| 265 | #neighbourdict[a,l_edge] = (i, 0) #(id, edge) |
---|
| 266 | #neighbourdict[b,r_edge] = (i, 1) #(id, edge) |
---|
| 267 | neighbourdict[a,l_vertex] = (i, 0) #(id, vertex) |
---|
| 268 | neighbourdict[b,r_vertex] = (i, 1) #(id, vertex) |
---|
| 269 | |
---|
| 270 | |
---|
| 271 | #Step 2: |
---|
| 272 | #Go through triangles again, but this time |
---|
| 273 | #reverse direction of segments and lookup neighbours. |
---|
| 274 | for i in range(N): |
---|
| 275 | #a = self.triangles[i, 0] |
---|
| 276 | #b = self.triangles[i, 1] |
---|
| 277 | #c = self.triangles[i, 2] |
---|
| 278 | |
---|
| 279 | a = self.vertices[i,0] |
---|
| 280 | b = self.vertices[i,1] |
---|
| 281 | |
---|
| 282 | #self.number_of_boundaries[i] = 3 |
---|
| 283 | self.number_of_boundaries[i] = 2 |
---|
| 284 | #if neighbourdict.has_key((b,l_edge)): |
---|
| 285 | if neighbourdict.has_key((b,l_vertex)): |
---|
| 286 | #self.neighbours[i, 1] = neighbourdict[b,l_edge][0] |
---|
| 287 | #self.neighbour_edges[i, 1] = neighbourdict[b,l_edge][1] |
---|
| 288 | self.neighbours[i, 1] = neighbourdict[b,l_vertex][0] |
---|
| 289 | self.neighbour_vertices[i, 1] = neighbourdict[b,l_vertex][1] |
---|
| 290 | self.number_of_boundaries[i] -= 1 |
---|
| 291 | |
---|
| 292 | #if neighbourdict.has_key((a,r_edge)): |
---|
| 293 | if neighbourdict.has_key((a,r_vertex)): |
---|
| 294 | #self.neighbours[i, 0] = neighbourdict[a,r_edge][0] |
---|
| 295 | #self.neighbour_edges[i, 0] = neighbourdict[a,r_edge][1] |
---|
| 296 | self.neighbours[i, 0] = neighbourdict[a,r_vertex][0] |
---|
| 297 | self.neighbour_vertices[i, 0] = neighbourdict[a,r_vertex][1] |
---|
| 298 | self.number_of_boundaries[i] -= 1 |
---|
| 299 | |
---|
| 300 | #if neighbourdict.has_key((b,a)): |
---|
| 301 | # self.neighbours[i, 1] = neighbourdict[b,a][0] |
---|
| 302 | # self.neighbour_edges[i, 1] = neighbourdict[b,a][1] |
---|
| 303 | # self.number_of_boundaries[i] -= 1 |
---|
| 304 | |
---|
| 305 | #if neighbourdict.has_key((c,b)): |
---|
| 306 | # self.neighbours[i, 0] = neighbourdict[c,b][0] |
---|
| 307 | # self.neighbour_edges[i, 0] = neighbourdict[c,b][1] |
---|
| 308 | # self.number_of_boundaries[i] -= 1 |
---|
| 309 | |
---|
| 310 | #if neighbourdict.has_key((a,b)): |
---|
| 311 | # self.neighbours[i, 0] = neighbourdict[a,b][0] |
---|
| 312 | # self.neighbour_edges[i, 0] = neighbourdict[a,b][1] |
---|
| 313 | # self.number_of_boundaries[i] -= 1 |
---|
| 314 | |
---|
| 315 | def build_surrogate_neighbour_structure(self): |
---|
| 316 | """Build structure where each triangle edge points to its neighbours |
---|
| 317 | if they exist. Otherwise point to the triangle itself. |
---|
| 318 | |
---|
| 319 | The surrogate neighbour structure is useful for computing gradients |
---|
| 320 | based on centroid values of neighbours. |
---|
| 321 | |
---|
| 322 | Precondition: Neighbour structure is defined |
---|
| 323 | Postcondition: |
---|
| 324 | Surrogate neighbour structure is defined: |
---|
| 325 | surrogate_neighbours: i0, i1, i2 where all i_k >= 0 point to |
---|
| 326 | triangles. |
---|
| 327 | |
---|
| 328 | """ |
---|
| 329 | |
---|
| 330 | N = self.number_of_elements |
---|
| 331 | for i in range(N): |
---|
| 332 | #Find all neighbouring volumes that are not boundaries |
---|
| 333 | #for k in range(3): |
---|
| 334 | for k in range(2): |
---|
| 335 | if self.neighbours[i, k] < 0: |
---|
| 336 | self.surrogate_neighbours[i, k] = i #Point this triangle |
---|
| 337 | else: |
---|
| 338 | self.surrogate_neighbours[i, k] = self.neighbours[i, k] |
---|
| 339 | |
---|
| 340 | def build_boundary_dictionary(self, boundary = None): |
---|
| 341 | """Build or check the dictionary of boundary tags. |
---|
| 342 | self.boundary is a dictionary of tags, |
---|
| 343 | keyed by volume id and edge: |
---|
| 344 | { (id, edge): tag, ... } |
---|
| 345 | |
---|
| 346 | Postconditions: |
---|
| 347 | self.boundary is defined. |
---|
| 348 | """ |
---|
| 349 | |
---|
| 350 | from config import default_boundary_tag |
---|
| 351 | |
---|
| 352 | if boundary is None: |
---|
| 353 | boundary = {} |
---|
| 354 | for vol_id in range(self.number_of_elements): |
---|
| 355 | #for edge_id in range(0, 3): |
---|
| 356 | #for edge_id in range(0, 2): |
---|
| 357 | for vertex_id in range(0, 2): |
---|
| 358 | #if self.neighbours[vol_id, edge_id] < 0: |
---|
| 359 | if self.neighbours[vol_id, vertex_id] < 0: |
---|
| 360 | #boundary[(vol_id, edge_id)] = default_boundary_tag |
---|
| 361 | boundary[(vol_id, vertex_id)] = default_boundary_tag |
---|
| 362 | else: |
---|
| 363 | #Check that all keys in given boundary exist |
---|
| 364 | #for vol_id, edge_id in boundary.keys(): |
---|
| 365 | for vol_id, vertex_id in boundary.keys(): |
---|
| 366 | #msg = 'Segment (%d, %d) does not exist' %(vol_id, edge_id) |
---|
| 367 | msg = 'Segment (%d, %d) does not exist' %(vol_id, vertex_id) |
---|
| 368 | a, b = self.neighbours.shape |
---|
| 369 | #assert vol_id < a and edge_id < b, msg |
---|
| 370 | assert vol_id < a and vertex_id < b, msg |
---|
| 371 | |
---|
| 372 | #FIXME: This assert violates internal boundaries (delete it) |
---|
| 373 | #msg = 'Segment (%d, %d) is not a boundary' %(vol_id, edge_id) |
---|
| 374 | #assert self.neighbours[vol_id, edge_id] < 0, msg |
---|
| 375 | |
---|
| 376 | #Check that all boundary segments are assigned a tag |
---|
| 377 | for vol_id in range(self.number_of_elements): |
---|
| 378 | #for edge_id in range(0, 3): |
---|
| 379 | #for edge_id in range(0, 2): |
---|
| 380 | for vertex_id in range(0, 2): |
---|
| 381 | #if self.neighbours[vol_id, edge_id] < 0: |
---|
| 382 | if self.neighbours[vol_id, vertex_id] < 0: |
---|
| 383 | #if not boundary.has_key( (vol_id, edge_id) ): |
---|
| 384 | if not boundary.has_key( (vol_id, vertex_id) ): |
---|
| 385 | msg = 'WARNING: Given boundary does not contain ' |
---|
| 386 | #msg += 'tags for edge (%d, %d). '\ |
---|
| 387 | # %(vol_id, edge_id) |
---|
| 388 | msg += 'tags for vertex (%d, %d). '\ |
---|
| 389 | %(vol_id, vertex_id) |
---|
| 390 | msg += 'Assigning default tag (%s).'\ |
---|
| 391 | %default_boundary_tag |
---|
| 392 | |
---|
| 393 | #FIXME: Print only as per verbosity |
---|
| 394 | #print msg |
---|
| 395 | |
---|
| 396 | #FIXME: Make this situation an error in the future |
---|
| 397 | #and make another function which will |
---|
| 398 | #enable default boundary-tags where |
---|
| 399 | #tags a not specified |
---|
| 400 | #boundary[ (vol_id, edge_id) ] =\ |
---|
| 401 | boundary[ (vol_id, vertex_id) ] =\ |
---|
| 402 | default_boundary_tag |
---|
| 403 | |
---|
| 404 | |
---|
| 405 | |
---|
| 406 | self.boundary = boundary |
---|
| 407 | |
---|
| 408 | def build_tagged_elements_dictionary(self, tagged_elements = None): |
---|
| 409 | """Build the dictionary of element tags. |
---|
| 410 | self.tagged_elements is a dictionary of element arrays, |
---|
| 411 | keyed by tag: |
---|
| 412 | { (tag): [e1, e2, e3..] } |
---|
| 413 | |
---|
| 414 | Postconditions: |
---|
| 415 | self.element_tag is defined |
---|
| 416 | """ |
---|
| 417 | |
---|
| 418 | if tagged_elements is None: |
---|
| 419 | tagged_elements = {} |
---|
| 420 | else: |
---|
| 421 | #Check that all keys in given boundary exist |
---|
| 422 | for tag in tagged_elements.keys(): |
---|
| 423 | tagged_elements[tag] = array(tagged_elements[tag]).astype(numpy.int) |
---|
| 424 | |
---|
| 425 | msg = 'Not all elements exist. ' |
---|
| 426 | assert max(tagged_elements[tag]) < self.number_of_elements, msg |
---|
| 427 | #print "tagged_elements", tagged_elements |
---|
| 428 | self.tagged_elements = tagged_elements |
---|
| 429 | |
---|
| 430 | |
---|
| 431 | def set_quantities_to_be_stored(self, q): |
---|
| 432 | """Specify which quantities will be stored in the sww file. |
---|
| 433 | |
---|
| 434 | q must be either: |
---|
| 435 | - the name of a quantity |
---|
| 436 | - a list of quantity names |
---|
| 437 | - None |
---|
| 438 | |
---|
| 439 | In the two first cases, the named quantities will be stored at each |
---|
| 440 | yieldstep |
---|
| 441 | (This is in addition to the quantities elevation and friction) |
---|
| 442 | If q is None, storage will be switched off altogether. |
---|
| 443 | """ |
---|
| 444 | |
---|
| 445 | |
---|
| 446 | if q is None: |
---|
| 447 | self.quantities_to_be_stored = [] |
---|
| 448 | self.store = False |
---|
| 449 | return |
---|
| 450 | |
---|
| 451 | if isinstance(q, basestring): |
---|
| 452 | q = [q] # Turn argument into a list |
---|
| 453 | |
---|
| 454 | #Check correcness |
---|
| 455 | for quantity_name in q: |
---|
| 456 | msg = 'Quantity %s is not a valid conserved quantity' %quantity_name |
---|
| 457 | assert quantity_name in self.conserved_quantities, msg |
---|
| 458 | |
---|
| 459 | self.quantities_to_be_stored = q |
---|
| 460 | |
---|
| 461 | |
---|
| 462 | |
---|
| 463 | |
---|
| 464 | |
---|
| 465 | def get_boundary_tags(self): |
---|
| 466 | """Return list of available boundary tags |
---|
| 467 | """ |
---|
| 468 | |
---|
| 469 | tags = {} |
---|
| 470 | for v in self.boundary.values(): |
---|
| 471 | tags[v] = 1 |
---|
| 472 | |
---|
| 473 | return tags.keys() |
---|
| 474 | |
---|
| 475 | def get_vertex_coordinates(self, obj = False): |
---|
| 476 | """Return all vertex coordinates. |
---|
| 477 | Return all vertex coordinates for all triangles as an Nx6 array |
---|
| 478 | (ordered as x0, y0, x1, y1, x2, y2 for each triangle) |
---|
| 479 | |
---|
| 480 | if obj is True, the x/y pairs are returned in a 3*N x 2 array. |
---|
| 481 | FIXME, we might make that the default. |
---|
| 482 | FIXME Maybe use keyword: continuous = False for this condition? |
---|
| 483 | |
---|
| 484 | |
---|
| 485 | """ |
---|
| 486 | |
---|
| 487 | if obj is True: |
---|
| 488 | |
---|
| 489 | #V = self.vertex_coordinates |
---|
| 490 | V = self.vertices |
---|
| 491 | #return concatenate( (V[:,0:2], V[:,2:4], V[:,4:6]), axis=0) |
---|
| 492 | |
---|
| 493 | N = V.shape[0] |
---|
| 494 | #return reshape(V, (3*N, 2)) |
---|
| 495 | return numpy.reshape(V, (N, 2)) |
---|
| 496 | else: |
---|
| 497 | #return self.vertex_coordinates |
---|
| 498 | return self.vertices |
---|
| 499 | |
---|
| 500 | def get_conserved_quantities(self, vol_id, vertex=None):#, edge=None): |
---|
| 501 | """Get conserved quantities at volume vol_id |
---|
| 502 | |
---|
| 503 | If vertex is specified use it as index for vertex values |
---|
| 504 | If edge is specified use it as index for edge values |
---|
| 505 | If neither are specified use centroid values |
---|
| 506 | If both are specified an exeception is raised |
---|
| 507 | |
---|
| 508 | Return value: Vector of length == number_of_conserved quantities |
---|
| 509 | |
---|
| 510 | """ |
---|
| 511 | |
---|
| 512 | #if not (vertex is None):# or edge is None): |
---|
| 513 | # msg = 'Values for both vertex and edge was specified.' |
---|
| 514 | # msg += 'Only one (or none) is allowed.' |
---|
| 515 | # raise msg |
---|
| 516 | |
---|
| 517 | q = numpy.zeros( len(self.conserved_quantities), numpy.float) |
---|
| 518 | |
---|
| 519 | for i, name in enumerate(self.conserved_quantities): |
---|
| 520 | Q = self.quantities[name] |
---|
| 521 | if vertex is not None: |
---|
| 522 | q[i] = Q.vertex_values[vol_id, vertex] |
---|
| 523 | #elif edge is not None: |
---|
| 524 | # q[i] = Q.edge_values[vol_id, edge] |
---|
| 525 | else: |
---|
| 526 | q[i] = Q.centroid_values[vol_id] |
---|
| 527 | |
---|
| 528 | return q |
---|
| 529 | |
---|
| 530 | |
---|
| 531 | def get_evolved_quantities(self, vol_id, vertex=None):#, edge=None): |
---|
| 532 | """Get evolved quantities at volume vol_id |
---|
| 533 | |
---|
| 534 | If vertex is specified use it as index for vertex values |
---|
| 535 | If edge is specified use it as index for edge values |
---|
| 536 | If neither are specified use centroid values |
---|
| 537 | If both are specified an exeception is raised |
---|
| 538 | |
---|
| 539 | Return value: Vector of length == number_of_evolved quantities |
---|
| 540 | |
---|
| 541 | """ |
---|
| 542 | |
---|
| 543 | |
---|
| 544 | |
---|
| 545 | #if not (vertex is None):# or edge is None): |
---|
| 546 | # msg = 'Values for both vertex and edge was specified.' |
---|
| 547 | # msg += 'Only one (or none) is allowed.' |
---|
| 548 | # raise msg |
---|
| 549 | |
---|
| 550 | q = numpy.zeros( len(self.evolved_quantities), numpy.float) |
---|
| 551 | |
---|
| 552 | for i, name in enumerate(self.evolved_quantities): |
---|
| 553 | Q = self.quantities[name] |
---|
| 554 | if vertex is not None: |
---|
| 555 | q[i] = Q.vertex_values[vol_id, vertex] |
---|
| 556 | #elif edge is not None: |
---|
| 557 | # q[i] = Q.edge_values[vol_id, edge] |
---|
| 558 | else: |
---|
| 559 | q[i] = Q.centroid_values[vol_id] |
---|
| 560 | |
---|
| 561 | return q |
---|
| 562 | |
---|
| 563 | |
---|
| 564 | def get_centroids(self): |
---|
| 565 | """Return all coordinates of centroids |
---|
| 566 | Return x coordinate of centroid for each element as a N array |
---|
| 567 | """ |
---|
| 568 | |
---|
| 569 | return self.centroids |
---|
| 570 | |
---|
| 571 | def get_vertices(self): |
---|
| 572 | """Return all coordinates of centroids |
---|
| 573 | Return x coordinate of centroid for each element as a N array |
---|
| 574 | """ |
---|
| 575 | |
---|
| 576 | return self.vertices |
---|
| 577 | |
---|
| 578 | def get_coordinate(self, elem_id, vertex=None): |
---|
| 579 | """Return coordinate of centroid, |
---|
| 580 | or left or right vertex. |
---|
| 581 | Left vertex (vertex=0). Right vertex (vertex=1) |
---|
| 582 | """ |
---|
| 583 | |
---|
| 584 | if vertex is None: |
---|
| 585 | return self.centroids[elem_id] |
---|
| 586 | else: |
---|
| 587 | return self.vertices[elem_id,vertex] |
---|
| 588 | |
---|
| 589 | def get_area(self, elem_id=None): |
---|
| 590 | """Return area of element id |
---|
| 591 | """ |
---|
| 592 | |
---|
| 593 | if elem_id is None: |
---|
| 594 | return sum(self.areas) |
---|
| 595 | else: |
---|
| 596 | return self.areas[elem_id] |
---|
| 597 | |
---|
| 598 | |
---|
| 599 | def get_quantity(self, name, location='vertices', indices = None): |
---|
| 600 | """Get values for named quantity |
---|
| 601 | |
---|
| 602 | name: Name of quantity |
---|
| 603 | |
---|
| 604 | In case of location == 'centroids' the dimension values must |
---|
| 605 | be a list of a numpyal array of length N, N being the number |
---|
| 606 | of elements. Otherwise it must be of dimension Nx3. |
---|
| 607 | |
---|
| 608 | Indices is the set of element ids that the operation applies to. |
---|
| 609 | |
---|
| 610 | The values will be stored in elements following their |
---|
| 611 | internal ordering. |
---|
| 612 | """ |
---|
| 613 | |
---|
| 614 | return self.quantities[name].get_values( location, indices = indices) |
---|
| 615 | |
---|
| 616 | def get_centroid_coordinates(self): |
---|
| 617 | """Return all centroid coordinates. |
---|
| 618 | Return all centroid coordinates for all triangles as an Nx2 array |
---|
| 619 | (ordered as x0, y0 for each triangle) |
---|
| 620 | """ |
---|
| 621 | return self.centroids |
---|
| 622 | |
---|
| 623 | |
---|
| 624 | def get_timestepping_method(self): |
---|
| 625 | return self.timestepping_method |
---|
| 626 | |
---|
| 627 | def set_timestepping_method(self,timestepping_method): |
---|
| 628 | |
---|
| 629 | if timestepping_method in ['euler', 'rk2', 'rk3']: |
---|
| 630 | self.timestepping_method = timestepping_method |
---|
| 631 | return |
---|
| 632 | |
---|
| 633 | msg = '%s is an incorrect timestepping type'% timestepping_method |
---|
| 634 | raise Exception, msg |
---|
| 635 | |
---|
| 636 | |
---|
| 637 | def set_quantity(self, name, *args, **kwargs): |
---|
| 638 | """Set values for named quantity |
---|
| 639 | |
---|
| 640 | |
---|
| 641 | One keyword argument is documented here: |
---|
| 642 | expression = None, # Arbitrary expression |
---|
| 643 | |
---|
| 644 | expression: |
---|
| 645 | Arbitrary expression involving quantity names |
---|
| 646 | |
---|
| 647 | See Quantity.set_values for further documentation. |
---|
| 648 | """ |
---|
| 649 | |
---|
| 650 | #FIXME (Ole): Allow new quantities here |
---|
| 651 | #from quantity import Quantity, Conserved_quantity |
---|
| 652 | #Create appropriate quantity object |
---|
| 653 | # #if name in self.conserved_quantities: |
---|
| 654 | # # self.quantities[name] = Conserved_quantity(self) |
---|
| 655 | # #else: |
---|
| 656 | # # self.quantities[name] = Quantity(self) |
---|
| 657 | |
---|
| 658 | |
---|
| 659 | #Do the expression stuff |
---|
| 660 | if kwargs.has_key('expression'): |
---|
| 661 | expression = kwargs['expression'] |
---|
| 662 | del kwargs['expression'] |
---|
| 663 | |
---|
| 664 | Q = self.create_quantity_from_expression(expression) |
---|
| 665 | kwargs['quantity'] = Q |
---|
| 666 | |
---|
| 667 | #Assign values |
---|
| 668 | self.quantities[name].set_values(*args, **kwargs) |
---|
| 669 | |
---|
| 670 | def set_boundary(self, boundary_map): |
---|
| 671 | """Associate boundary objects with tagged boundary segments. |
---|
| 672 | |
---|
| 673 | Input boundary_map is a dictionary of boundary objects keyed |
---|
| 674 | by symbolic tags to matched against tags in the internal dictionary |
---|
| 675 | self.boundary. |
---|
| 676 | |
---|
| 677 | As result one pointer to a boundary object is stored for each vertex |
---|
| 678 | in the list self.boundary_objects. |
---|
| 679 | More entries may point to the same boundary object |
---|
| 680 | |
---|
| 681 | Schematically the mapping is from two dictionaries to one list |
---|
| 682 | where the index is used as pointer to the boundary_values arrays |
---|
| 683 | within each quantity. |
---|
| 684 | |
---|
| 685 | self.boundary: (vol_id, edge_id): tag |
---|
| 686 | boundary_map (input): tag: boundary_object |
---|
| 687 | ---------------------------------------------- |
---|
| 688 | self.boundary_objects: ((vol_id, edge_id), boundary_object) |
---|
| 689 | |
---|
| 690 | |
---|
| 691 | Pre-condition: |
---|
| 692 | self.boundary has been built. |
---|
| 693 | |
---|
| 694 | Post-condition: |
---|
| 695 | self.boundary_objects is built |
---|
| 696 | |
---|
| 697 | If a tag from the domain doesn't appear in the input dictionary an |
---|
| 698 | exception is raised. |
---|
| 699 | However, if a tag is not used to the domain, no error is thrown. |
---|
| 700 | FIXME: This would lead to implementation of a |
---|
| 701 | default boundary condition |
---|
| 702 | |
---|
| 703 | Note: If a segment is listed in the boundary dictionary and if it is |
---|
| 704 | not None, it *will* become a boundary - |
---|
| 705 | even if there is a neighbouring triangle. |
---|
| 706 | This would be the case for internal boundaries |
---|
| 707 | |
---|
| 708 | Boundary objects that are None will be skipped. |
---|
| 709 | |
---|
| 710 | FIXME: If set_boundary is called multiple times and if Boundary |
---|
| 711 | object is changed into None, the neighbour structure will not be |
---|
| 712 | restored!!! |
---|
| 713 | """ |
---|
| 714 | |
---|
| 715 | self.boundary_objects = [] |
---|
| 716 | self.boundary_map = boundary_map #Store for use with eg. boundary_stats. |
---|
| 717 | |
---|
| 718 | #FIXME: Try to remove the sorting and fix test_mesh.py |
---|
| 719 | x = self.boundary.keys() |
---|
| 720 | x.sort() |
---|
| 721 | |
---|
| 722 | #Loop through edges that lie on the boundary and associate them with |
---|
| 723 | #callable boundary objects depending on their tags |
---|
| 724 | #for k, (vol_id, edge_id) in enumerate(x): |
---|
| 725 | for k, (vol_id, vertex_id) in enumerate(x): |
---|
| 726 | #tag = self.boundary[ (vol_id, edge_id) ] |
---|
| 727 | tag = self.boundary[ (vol_id, vertex_id) ] |
---|
| 728 | |
---|
| 729 | if boundary_map.has_key(tag): |
---|
| 730 | B = boundary_map[tag] #Get callable boundary object |
---|
| 731 | |
---|
| 732 | if B is not None: |
---|
| 733 | #self.boundary_objects.append( ((vol_id, edge_id), B) ) |
---|
| 734 | #self.neighbours[vol_id, edge_id] = -len(self.boundary_objects) |
---|
| 735 | self.boundary_objects.append( ((vol_id, vertex_id), B) ) |
---|
| 736 | self.neighbours[vol_id, vertex_id] = -len(self.boundary_objects) |
---|
| 737 | else: |
---|
| 738 | pass |
---|
| 739 | #FIXME: Check and perhaps fix neighbour structure |
---|
| 740 | |
---|
| 741 | else: |
---|
| 742 | msg = 'ERROR (domain.py): Tag "%s" has not been ' %tag |
---|
| 743 | msg += 'bound to a boundary object.\n' |
---|
| 744 | msg += 'All boundary tags defined in domain must appear ' |
---|
| 745 | msg += 'in the supplied dictionary.\n' |
---|
| 746 | msg += 'The tags are: %s' %self.get_boundary_tags() |
---|
| 747 | raise msg |
---|
| 748 | |
---|
| 749 | |
---|
| 750 | |
---|
| 751 | def check_integrity(self): |
---|
| 752 | #Mesh.check_integrity(self) |
---|
| 753 | |
---|
| 754 | #print self.quantities |
---|
| 755 | #print self.conserved_quantities |
---|
| 756 | |
---|
| 757 | for quantity in self.conserved_quantities: |
---|
| 758 | msg = 'Conserved quantities must be a subset of all quantities' |
---|
| 759 | assert quantity in self.quantities, msg |
---|
| 760 | |
---|
| 761 | for quantity in self.evolved_quantities: |
---|
| 762 | msg = 'Evolved quantities must be a subset of all quantities' |
---|
| 763 | assert quantity in self.quantities, msg |
---|
| 764 | |
---|
| 765 | # #assert hasattr(self, 'boundary_objects') |
---|
| 766 | |
---|
| 767 | def write_time(self): |
---|
| 768 | print self.timestepping_statistics() |
---|
| 769 | |
---|
| 770 | def timestepping_statistics(self): |
---|
| 771 | """Return string with time stepping statistics for printing or logging |
---|
| 772 | """ |
---|
| 773 | |
---|
| 774 | msg = '' |
---|
| 775 | if self.min_timestep == self.max_timestep: |
---|
| 776 | msg += 'Time = %.4f, delta t = %.8f, steps=%d (%d)'\ |
---|
| 777 | %(self.time, self.min_timestep, self.number_of_steps, |
---|
| 778 | self.number_of_first_order_steps) |
---|
| 779 | elif self.min_timestep > self.max_timestep: |
---|
| 780 | msg += 'Time = %.4f, steps=%d (%d)'\ |
---|
| 781 | %(self.time, self.number_of_steps, |
---|
| 782 | self.number_of_first_order_steps) |
---|
| 783 | else: |
---|
| 784 | msg += 'Time = %.4f, delta t in [%.8f, %.8f], steps=%d (%d)'\ |
---|
| 785 | %(self.time, self.min_timestep, |
---|
| 786 | self.max_timestep, self.number_of_steps, |
---|
| 787 | self.number_of_first_order_steps) |
---|
| 788 | |
---|
| 789 | return msg |
---|
| 790 | |
---|
| 791 | def get_name(self): |
---|
| 792 | return self.filename |
---|
| 793 | |
---|
| 794 | def set_name(self, name): |
---|
| 795 | self.filename = name |
---|
| 796 | |
---|
| 797 | def get_datadir(self): |
---|
| 798 | return self.datadir |
---|
| 799 | |
---|
| 800 | def set_datadir(self, name): |
---|
| 801 | self.datadir = name |
---|
| 802 | |
---|
| 803 | def set_CFL(self, cfl): |
---|
| 804 | if cfl > 1.0: |
---|
| 805 | print 'WARNING: Setting CFL condition to %f which is greater than 1' % cfl |
---|
| 806 | self.CFL = cfl |
---|
| 807 | |
---|
| 808 | def get_CFL(self): |
---|
| 809 | return self.CFL |
---|
| 810 | |
---|
| 811 | def set_filename(self, name): |
---|
| 812 | self.filename = name |
---|
| 813 | |
---|
| 814 | def get_filename(self): |
---|
| 815 | return self.filename |
---|
| 816 | |
---|
| 817 | def get_limiter(self): |
---|
| 818 | return self.limiter |
---|
| 819 | |
---|
| 820 | def set_limiter(self,limiter): |
---|
| 821 | |
---|
| 822 | possible_limiters = \ |
---|
| 823 | ['pyvolution', 'minmod_steve', 'minmod', 'minmod_kurganov', 'superbee', 'vanleer', 'vanalbada'] |
---|
| 824 | |
---|
| 825 | if limiter in possible_limiters: |
---|
| 826 | self.limiter = limiter |
---|
| 827 | return |
---|
| 828 | |
---|
| 829 | msg = '%s is an incorrect limiter type.\n'% limiter |
---|
| 830 | msg += 'Possible types are: '+ ", ".join(["%s" % el for el in possible_limiters]) |
---|
| 831 | raise Exception, msg |
---|
| 832 | |
---|
| 833 | |
---|
| 834 | #-------------------------- |
---|
| 835 | # Main components of evolve |
---|
| 836 | #-------------------------- |
---|
| 837 | |
---|
| 838 | def evolve(self, yieldstep = None, |
---|
| 839 | finaltime = None, |
---|
| 840 | duration = None, |
---|
| 841 | skip_initial_step = False): |
---|
| 842 | """Evolve model through time starting from self.starttime. |
---|
| 843 | |
---|
| 844 | |
---|
| 845 | yieldstep: numpy.interval between yields where results are stored, |
---|
| 846 | statistics written and domain inspected or |
---|
| 847 | possibly modified. If omitted the internal predefined |
---|
| 848 | max timestep is used. |
---|
| 849 | numpy.internally, smaller timesteps may be taken. |
---|
| 850 | |
---|
| 851 | duration: Duration of simulation |
---|
| 852 | |
---|
| 853 | finaltime: Time where simulation should end. This is currently |
---|
| 854 | relative time. So it's the same as duration. |
---|
| 855 | |
---|
| 856 | If both duration and finaltime are given an exception is thrown. |
---|
| 857 | |
---|
| 858 | |
---|
| 859 | skip_initial_step: Boolean flag that decides whether the first |
---|
| 860 | yield step is skipped or not. This is useful for example to avoid |
---|
| 861 | duplicate steps when multiple evolve processes are dove tailed. |
---|
| 862 | |
---|
| 863 | |
---|
| 864 | Evolve is implemented as a generator and is to be called as such, e.g. |
---|
| 865 | |
---|
| 866 | for t in domain.evolve(yieldstep, finaltime): |
---|
| 867 | <Do something with domain and t> |
---|
| 868 | |
---|
| 869 | |
---|
| 870 | All times are given in seconds |
---|
| 871 | |
---|
| 872 | """ |
---|
| 873 | |
---|
| 874 | from config import min_timestep, max_timestep, epsilon |
---|
| 875 | |
---|
| 876 | # FIXME: Maybe lump into a larger check prior to evolving |
---|
| 877 | msg = 'Boundary tags must be bound to boundary objects before ' |
---|
| 878 | msg += 'evolving system, ' |
---|
| 879 | msg += 'e.g. using the method set_boundary.\n' |
---|
| 880 | msg += 'This system has the boundary tags %s '\ |
---|
| 881 | %self.get_boundary_tags() |
---|
| 882 | assert hasattr(self, 'boundary_objects'), msg |
---|
| 883 | |
---|
| 884 | |
---|
| 885 | if yieldstep is None: |
---|
| 886 | yieldstep = max_timestep |
---|
| 887 | else: |
---|
| 888 | yieldstep = numpy.float(yieldstep) |
---|
| 889 | |
---|
| 890 | self._order_ = self.default_order |
---|
| 891 | |
---|
| 892 | |
---|
| 893 | if finaltime is not None and duration is not None: |
---|
| 894 | # print 'F', finaltime, duration |
---|
| 895 | msg = 'Only one of finaltime and duration may be specified' |
---|
| 896 | raise msg |
---|
| 897 | else: |
---|
| 898 | if finaltime is not None: |
---|
| 899 | self.finaltime = numpy.float(finaltime) |
---|
| 900 | if duration is not None: |
---|
| 901 | self.finaltime = self.starttime + numpy.float(duration) |
---|
| 902 | |
---|
| 903 | |
---|
| 904 | |
---|
| 905 | N = len(self) # Number of triangles |
---|
| 906 | self.yieldtime = 0.0 # Track time between 'yields' |
---|
| 907 | |
---|
| 908 | # Initialise interval of timestep sizes (for reporting only) |
---|
| 909 | self.min_timestep = max_timestep |
---|
| 910 | self.max_timestep = min_timestep |
---|
| 911 | self.number_of_steps = 0 |
---|
| 912 | self.number_of_first_order_steps = 0 |
---|
| 913 | |
---|
| 914 | |
---|
| 915 | # Update ghosts |
---|
| 916 | self.update_ghosts() |
---|
| 917 | |
---|
| 918 | # Initial update of vertex and edge values |
---|
| 919 | self.distribute_to_vertices_and_edges() |
---|
| 920 | |
---|
| 921 | # Update extrema if necessary (for reporting) |
---|
| 922 | self.update_extrema() |
---|
| 923 | |
---|
| 924 | # Initial update boundary values |
---|
| 925 | self.update_boundary() |
---|
| 926 | |
---|
| 927 | # Or maybe restore from latest checkpoint |
---|
| 928 | if self.checkpoint is True: |
---|
| 929 | self.goto_latest_checkpoint() |
---|
| 930 | |
---|
| 931 | if skip_initial_step is False: |
---|
| 932 | yield(self.time) # Yield initial values |
---|
| 933 | |
---|
| 934 | while True: |
---|
| 935 | |
---|
| 936 | # Evolve One Step, using appropriate timestepping method |
---|
| 937 | if self.get_timestepping_method() == 'euler': |
---|
| 938 | self.evolve_one_euler_step(yieldstep,finaltime) |
---|
| 939 | |
---|
| 940 | elif self.get_timestepping_method() == 'rk2': |
---|
| 941 | self.evolve_one_rk2_step(yieldstep,finaltime) |
---|
| 942 | |
---|
| 943 | elif self.get_timestepping_method() == 'rk3': |
---|
| 944 | self.evolve_one_rk3_step(yieldstep,finaltime) |
---|
| 945 | |
---|
| 946 | |
---|
| 947 | # Update extrema if necessary (for reporting) |
---|
| 948 | self.update_extrema() |
---|
| 949 | |
---|
| 950 | |
---|
| 951 | |
---|
| 952 | self.yieldtime += self.timestep |
---|
| 953 | self.number_of_steps += 1 |
---|
| 954 | if self._order_ == 1: |
---|
| 955 | self.number_of_first_order_steps += 1 |
---|
| 956 | |
---|
| 957 | |
---|
| 958 | # Yield results |
---|
| 959 | if finaltime is not None and self.time >= finaltime-epsilon: |
---|
| 960 | |
---|
| 961 | if self.time > finaltime: |
---|
| 962 | # FIXME (Ole, 30 April 2006): Do we need this check? |
---|
| 963 | # Probably not (Ole, 18 September 2008). Now changed to |
---|
| 964 | # Exception |
---|
| 965 | msg = 'WARNING (domain.py): time overshot finaltime. ' |
---|
| 966 | msg += 'Contact Ole.Nielsen@ga.gov.au' |
---|
| 967 | raise Exception, msg |
---|
| 968 | |
---|
| 969 | |
---|
| 970 | # Yield final time and stop |
---|
| 971 | self.time = finaltime |
---|
| 972 | yield(self.time) |
---|
| 973 | break |
---|
| 974 | |
---|
| 975 | if self.yieldtime >= yieldstep: |
---|
| 976 | # Yield (intermediate) time and allow inspection of domain |
---|
| 977 | |
---|
| 978 | if self.checkpoint is True: |
---|
| 979 | self.store_checkpoint() |
---|
| 980 | self.delete_old_checkpoints() |
---|
| 981 | |
---|
| 982 | # Pass control on to outer loop for more specific actions |
---|
| 983 | |
---|
| 984 | yield(self.time) |
---|
| 985 | |
---|
| 986 | # Reinitialise |
---|
| 987 | self.yieldtime = 0.0 |
---|
| 988 | self.min_timestep = max_timestep |
---|
| 989 | self.max_timestep = min_timestep |
---|
| 990 | self.number_of_steps = 0 |
---|
| 991 | self.number_of_first_order_steps = 0 |
---|
| 992 | #self.max_speed_array = 0.0 |
---|
| 993 | |
---|
| 994 | |
---|
| 995 | def evolve_one_euler_step(self, yieldstep, finaltime): |
---|
| 996 | """ |
---|
| 997 | One Euler Time Step |
---|
| 998 | Q^{n+1} = E(h) Q^n |
---|
| 999 | """ |
---|
| 1000 | |
---|
| 1001 | |
---|
| 1002 | # Compute fluxes across each element edge |
---|
| 1003 | self.compute_fluxes() |
---|
| 1004 | |
---|
| 1005 | # Update timestep to fit yieldstep and finaltime |
---|
| 1006 | self.update_timestep(yieldstep, finaltime) |
---|
| 1007 | |
---|
| 1008 | # Update conserved quantities |
---|
| 1009 | self.update_conserved_quantities() |
---|
| 1010 | |
---|
| 1011 | # Update ghosts |
---|
| 1012 | self.update_ghosts() |
---|
| 1013 | |
---|
| 1014 | # Update vertex and edge values |
---|
| 1015 | self.distribute_to_vertices_and_edges() |
---|
| 1016 | |
---|
| 1017 | # Update boundary values |
---|
| 1018 | self.update_boundary() |
---|
| 1019 | |
---|
| 1020 | # Update time |
---|
| 1021 | self.time += self.timestep |
---|
| 1022 | |
---|
| 1023 | |
---|
| 1024 | |
---|
| 1025 | |
---|
| 1026 | def evolve_one_rk2_step(self, yieldstep, finaltime): |
---|
| 1027 | """ |
---|
| 1028 | One 2nd order RK timestep |
---|
| 1029 | Q^{n+1} = 0.5 Q^n + 0.5 E(h)^2 Q^n |
---|
| 1030 | """ |
---|
| 1031 | |
---|
| 1032 | # Save initial conserved quantities values |
---|
| 1033 | self.backup_conserved_quantities() |
---|
| 1034 | |
---|
| 1035 | #-------------------------------------- |
---|
| 1036 | # First euler step |
---|
| 1037 | #-------------------------------------- |
---|
| 1038 | |
---|
| 1039 | # Compute fluxes across each element edge |
---|
| 1040 | self.compute_fluxes() |
---|
| 1041 | |
---|
| 1042 | # Update timestep to fit yieldstep and finaltime |
---|
| 1043 | self.update_timestep(yieldstep, finaltime) |
---|
| 1044 | |
---|
| 1045 | # Update conserved quantities |
---|
| 1046 | self.update_conserved_quantities() |
---|
| 1047 | |
---|
| 1048 | # Update ghosts |
---|
| 1049 | self.update_ghosts() |
---|
| 1050 | |
---|
| 1051 | # Update vertex and edge values |
---|
| 1052 | self.distribute_to_vertices_and_edges() |
---|
| 1053 | |
---|
| 1054 | # Update boundary values |
---|
| 1055 | self.update_boundary() |
---|
| 1056 | |
---|
| 1057 | # Update time |
---|
| 1058 | self.time += self.timestep |
---|
| 1059 | |
---|
| 1060 | #------------------------------------ |
---|
| 1061 | # Second Euler step |
---|
| 1062 | #------------------------------------ |
---|
| 1063 | |
---|
| 1064 | # Compute fluxes across each element edge |
---|
| 1065 | self.compute_fluxes() |
---|
| 1066 | |
---|
| 1067 | # Update conserved quantities |
---|
| 1068 | self.update_conserved_quantities() |
---|
| 1069 | |
---|
| 1070 | #------------------------------------ |
---|
| 1071 | # Combine initial and final values |
---|
| 1072 | # of conserved quantities and cleanup |
---|
| 1073 | #------------------------------------ |
---|
| 1074 | |
---|
| 1075 | # Combine steps |
---|
| 1076 | self.saxpy_conserved_quantities(0.5, 0.5) |
---|
| 1077 | |
---|
| 1078 | #----------------------------------- |
---|
| 1079 | # clean up vertex values |
---|
| 1080 | #----------------------------------- |
---|
| 1081 | |
---|
| 1082 | # Update ghosts |
---|
| 1083 | self.update_ghosts() |
---|
| 1084 | |
---|
| 1085 | # Update vertex and edge values |
---|
| 1086 | self.distribute_to_vertices_and_edges() |
---|
| 1087 | |
---|
| 1088 | # Update boundary values |
---|
| 1089 | self.update_boundary() |
---|
| 1090 | |
---|
| 1091 | |
---|
| 1092 | |
---|
| 1093 | def evolve_one_rk3_step(self, yieldstep, finaltime): |
---|
| 1094 | """ |
---|
| 1095 | One 3rd order RK timestep |
---|
| 1096 | Q^(1) = 3/4 Q^n + 1/4 E(h)^2 Q^n (at time t^n + h/2) |
---|
| 1097 | Q^{n+1} = 1/3 Q^n + 2/3 E(h) Q^(1) (at time t^{n+1}) |
---|
| 1098 | """ |
---|
| 1099 | |
---|
| 1100 | # Save initial initial conserved quantities values |
---|
| 1101 | self.backup_conserved_quantities() |
---|
| 1102 | |
---|
| 1103 | initial_time = self.time |
---|
| 1104 | |
---|
| 1105 | #-------------------------------------- |
---|
| 1106 | # First euler step |
---|
| 1107 | #-------------------------------------- |
---|
| 1108 | |
---|
| 1109 | # Compute fluxes across each element edge |
---|
| 1110 | self.compute_fluxes() |
---|
| 1111 | |
---|
| 1112 | # Update timestep to fit yieldstep and finaltime |
---|
| 1113 | self.update_timestep(yieldstep, finaltime) |
---|
| 1114 | |
---|
| 1115 | # Update conserved quantities |
---|
| 1116 | self.update_conserved_quantities() |
---|
| 1117 | |
---|
| 1118 | # Update ghosts |
---|
| 1119 | self.update_ghosts() |
---|
| 1120 | |
---|
| 1121 | # Update vertex and edge values |
---|
| 1122 | self.distribute_to_vertices_and_edges() |
---|
| 1123 | |
---|
| 1124 | # Update boundary values |
---|
| 1125 | self.update_boundary() |
---|
| 1126 | |
---|
| 1127 | # Update time |
---|
| 1128 | self.time += self.timestep |
---|
| 1129 | |
---|
| 1130 | #------------------------------------ |
---|
| 1131 | # Second Euler step |
---|
| 1132 | #------------------------------------ |
---|
| 1133 | |
---|
| 1134 | # Compute fluxes across each element edge |
---|
| 1135 | self.compute_fluxes() |
---|
| 1136 | |
---|
| 1137 | # Update conserved quantities |
---|
| 1138 | self.update_conserved_quantities() |
---|
| 1139 | |
---|
| 1140 | #------------------------------------ |
---|
| 1141 | #Combine steps to obtain intermediate |
---|
| 1142 | #solution at time t^n + 0.5 h |
---|
| 1143 | #------------------------------------ |
---|
| 1144 | |
---|
| 1145 | # Combine steps |
---|
| 1146 | self.saxpy_conserved_quantities(0.25, 0.75) |
---|
| 1147 | |
---|
| 1148 | # Update ghosts |
---|
| 1149 | self.update_ghosts() |
---|
| 1150 | |
---|
| 1151 | # Update vertex and edge values |
---|
| 1152 | self.distribute_to_vertices_and_edges() |
---|
| 1153 | |
---|
| 1154 | # Update boundary values |
---|
| 1155 | self.update_boundary() |
---|
| 1156 | |
---|
| 1157 | # Set substep time |
---|
| 1158 | self.time = initial_time + self.timestep*0.5 |
---|
| 1159 | |
---|
| 1160 | #------------------------------------ |
---|
| 1161 | # Third Euler step |
---|
| 1162 | #------------------------------------ |
---|
| 1163 | |
---|
| 1164 | # Compute fluxes across each element edge |
---|
| 1165 | self.compute_fluxes() |
---|
| 1166 | |
---|
| 1167 | # Update conserved quantities |
---|
| 1168 | self.update_conserved_quantities() |
---|
| 1169 | |
---|
| 1170 | #------------------------------------ |
---|
| 1171 | # Combine final and initial values |
---|
| 1172 | # and cleanup |
---|
| 1173 | #------------------------------------ |
---|
| 1174 | |
---|
| 1175 | # Combine steps |
---|
| 1176 | self.saxpy_conserved_quantities(2.0/3.0, 1.0/3.0) |
---|
| 1177 | |
---|
| 1178 | # Update ghosts |
---|
| 1179 | self.update_ghosts() |
---|
| 1180 | |
---|
| 1181 | # Update vertex and edge values |
---|
| 1182 | self.distribute_to_vertices_and_edges() |
---|
| 1183 | |
---|
| 1184 | # Update boundary values |
---|
| 1185 | self.update_boundary() |
---|
| 1186 | |
---|
| 1187 | # Set new time |
---|
| 1188 | self.time = initial_time + self.timestep |
---|
| 1189 | |
---|
| 1190 | |
---|
| 1191 | def backup_conserved_quantities(self): |
---|
| 1192 | N = len(self) # Number_of_triangles |
---|
| 1193 | |
---|
| 1194 | # Backup conserved_quantities centroid values |
---|
| 1195 | for name in self.conserved_quantities: |
---|
| 1196 | Q = self.quantities[name] |
---|
| 1197 | Q.backup_centroid_values() |
---|
| 1198 | |
---|
| 1199 | def saxpy_conserved_quantities(self,a,b): |
---|
| 1200 | N = len(self) #number_of_triangles |
---|
| 1201 | |
---|
| 1202 | # Backup conserved_quantities centroid values |
---|
| 1203 | for name in self.conserved_quantities: |
---|
| 1204 | Q = self.quantities[name] |
---|
| 1205 | Q.saxpy_centroid_values(a,b) |
---|
| 1206 | |
---|
| 1207 | |
---|
| 1208 | |
---|
| 1209 | |
---|
| 1210 | def distribute_to_vertices_and_edges(self): |
---|
| 1211 | """Extrapolate conserved quantities from centroid to |
---|
| 1212 | vertices and edge-midpoints for each volume |
---|
| 1213 | |
---|
| 1214 | Default implementation is straight first order, |
---|
| 1215 | i.e. constant values throughout each element and |
---|
| 1216 | no reference to non-conserved quantities. |
---|
| 1217 | """ |
---|
| 1218 | |
---|
| 1219 | for name in self.conserved_quantities: |
---|
| 1220 | Q = self.quantities[name] |
---|
| 1221 | if self.order == 1: |
---|
| 1222 | Q.extrapolate_first_order() |
---|
| 1223 | elif self.order == 2: |
---|
| 1224 | Q.extrapolate_second_order() |
---|
| 1225 | #Q.limit() |
---|
| 1226 | else: |
---|
| 1227 | raise 'Unknown order' |
---|
| 1228 | #Q.interpolate_from_vertices_to_edges() |
---|
| 1229 | |
---|
| 1230 | |
---|
| 1231 | def update_ghosts(self): |
---|
| 1232 | pass |
---|
| 1233 | |
---|
| 1234 | def update_boundary(self): |
---|
| 1235 | """Go through list of boundary objects and update boundary values |
---|
| 1236 | for all conserved quantities on boundary. |
---|
| 1237 | """ |
---|
| 1238 | |
---|
| 1239 | #FIXME: Update only those that change (if that can be worked out) |
---|
| 1240 | #FIXME: Boundary objects should not include ghost nodes. |
---|
| 1241 | #for i, ((vol_id, edge_id), B) in enumerate(self.boundary_objects): |
---|
| 1242 | # q = B.evaluate(vol_id, edge_id) |
---|
| 1243 | for i, ((vol_id, vertex_id), B) in enumerate(self.boundary_objects): |
---|
| 1244 | q = B.evaluate(vol_id, vertex_id) |
---|
| 1245 | #print 'q ',q |
---|
| 1246 | for j, name in enumerate(self.evolved_quantities): |
---|
| 1247 | #print 'name %s j = %f \n'%(name,j) |
---|
| 1248 | Q = self.quantities[name] |
---|
| 1249 | Q.boundary_values[i] = q[j] |
---|
| 1250 | #print 'Q=',Q |
---|
| 1251 | |
---|
| 1252 | def update_timestep(self, yieldstep, finaltime): |
---|
| 1253 | |
---|
| 1254 | from config import min_timestep, max_timestep |
---|
| 1255 | |
---|
| 1256 | # self.timestep is calculated from speed of characteristics |
---|
| 1257 | # Apply CFL condition here |
---|
| 1258 | timestep = min(self.CFL*self.flux_timestep, max_timestep) |
---|
| 1259 | |
---|
| 1260 | #Record maximal and minimal values of timestep for reporting |
---|
| 1261 | self.max_timestep = max(timestep, self.max_timestep) |
---|
| 1262 | self.min_timestep = min(timestep, self.min_timestep) |
---|
| 1263 | |
---|
| 1264 | #Protect against degenerate time steps |
---|
| 1265 | if timestep < min_timestep: |
---|
| 1266 | |
---|
| 1267 | #Number of consecutive small steps taken b4 taking action |
---|
| 1268 | self.smallsteps += 1 |
---|
| 1269 | |
---|
| 1270 | if self.smallsteps > self.max_smallsteps: |
---|
| 1271 | self.smallsteps = 0 #Reset |
---|
| 1272 | |
---|
| 1273 | if self.order == 1: |
---|
| 1274 | msg = 'WARNING: Too small timestep %.16f reached '\ |
---|
| 1275 | %timestep |
---|
| 1276 | msg += 'even after %d steps of 1 order scheme'\ |
---|
| 1277 | %self.max_smallsteps |
---|
| 1278 | print msg |
---|
| 1279 | timestep = min_timestep #Try enforcing min_step |
---|
| 1280 | |
---|
| 1281 | #raise msg |
---|
| 1282 | else: |
---|
| 1283 | #Try to overcome situation by switching to 1 order |
---|
| 1284 | print "changing Order 1" |
---|
| 1285 | self.order = 1 |
---|
| 1286 | |
---|
| 1287 | else: |
---|
| 1288 | self.smallsteps = 0 |
---|
| 1289 | if self.order == 1 and self.default_order == 2: |
---|
| 1290 | self.order = 2 |
---|
| 1291 | |
---|
| 1292 | |
---|
| 1293 | #Ensure that final time is not exceeded |
---|
| 1294 | if finaltime is not None and self.time + timestep > finaltime: |
---|
| 1295 | timestep = finaltime-self.time |
---|
| 1296 | |
---|
| 1297 | #Ensure that model time is aligned with yieldsteps |
---|
| 1298 | if self.yieldtime + timestep > yieldstep: |
---|
| 1299 | timestep = yieldstep-self.yieldtime |
---|
| 1300 | |
---|
| 1301 | self.timestep = timestep |
---|
| 1302 | |
---|
| 1303 | def update_extrema(self): |
---|
| 1304 | pass |
---|
| 1305 | |
---|
| 1306 | def compute_forcing_terms(self): |
---|
| 1307 | """If there are any forcing functions driving the system |
---|
| 1308 | they should be defined in Domain subclass and appended to |
---|
| 1309 | the list self.forcing_terms |
---|
| 1310 | """ |
---|
| 1311 | #Clears explicit_update needed for second order method |
---|
| 1312 | if self.time_order == 2: |
---|
| 1313 | for name in self.conserved_quantities: |
---|
| 1314 | Q = self.quantities[name] |
---|
| 1315 | Q.explicit_update[:] = 0.0 |
---|
| 1316 | |
---|
| 1317 | for f in self.forcing_terms: |
---|
| 1318 | f(self) |
---|
| 1319 | |
---|
| 1320 | |
---|
| 1321 | def update_derived_quantites(self): |
---|
| 1322 | pass |
---|
| 1323 | |
---|
| 1324 | #def update_conserved_quantities(self): |
---|
| 1325 | def update_conserved_quantities(self): |
---|
| 1326 | """Update vectors of conserved quantities using previously |
---|
| 1327 | computed fluxes specified forcing functions. |
---|
| 1328 | """ |
---|
| 1329 | |
---|
| 1330 | |
---|
| 1331 | timestep = self.timestep |
---|
| 1332 | |
---|
| 1333 | #Compute forcing terms |
---|
| 1334 | self.compute_forcing_terms() |
---|
| 1335 | |
---|
| 1336 | #Update conserved_quantities |
---|
| 1337 | for name in self.conserved_quantities: |
---|
| 1338 | Q = self.quantities[name] |
---|
| 1339 | Q.update(timestep) |
---|
| 1340 | |
---|
| 1341 | |
---|
| 1342 | |
---|
| 1343 | if __name__ == "__main__": |
---|
| 1344 | |
---|
| 1345 | points1 = [0.0, 1.0, 2.0, 3.0] |
---|
| 1346 | D1 = Domain(points1) |
---|
| 1347 | |
---|
| 1348 | print D1.get_coordinate(0) |
---|
| 1349 | print D1.get_coordinate(0,1) |
---|
| 1350 | print 'Number of Elements = ',D1.number_of_elements |
---|
| 1351 | |
---|
| 1352 | try: |
---|
| 1353 | print D1.get_coordinate(3) |
---|
| 1354 | except: |
---|
| 1355 | pass |
---|
| 1356 | else: |
---|
| 1357 | msg = 'Should have raised an out of bounds exception' |
---|
| 1358 | raise msg |
---|
| 1359 | |
---|
| 1360 | #points2 = [0.0, 1.0, 2.0, 3.0, 2.5] |
---|
| 1361 | #D2 = Domain(points2) |
---|