| 1 |
# -*- coding: utf-8 -*- |
| 2 |
|
| 3 |
############################################################################## |
| 4 |
# |
| 5 |
# Copyright (c) 2003-2020 by The University of Queensland |
| 6 |
# http://www.uq.edu.au |
| 7 |
# |
| 8 |
# Primary Business: Queensland, Australia |
| 9 |
# Licensed under the Apache License, version 2.0 |
| 10 |
# http://www.apache.org/licenses/LICENSE-2.0 |
| 11 |
# |
| 12 |
# Development until 2012 by Earth Systems Science Computational Center (ESSCC) |
| 13 |
# Development 2012-2013 by School of Earth Sciences |
| 14 |
# Development from 2014 by Centre for Geoscience Computing (GeoComp) |
| 15 |
# Development from 2019 by School of Earth and Environmental Sciences |
| 16 |
# |
| 17 |
############################################################################## |
| 18 |
|
| 19 |
from __future__ import print_function, division |
| 20 |
|
| 21 |
__copyright__="""Copyright (c) 2003-2020 by The University of Queensland |
| 22 |
http://www.uq.edu.au |
| 23 |
Primary Business: Queensland, Australia""" |
| 24 |
__license__="""Licensed under the Apache License, version 2.0 |
| 25 |
http://www.apache.org/licenses/LICENSE-2.0""" |
| 26 |
__url__="https://launchpad.net/escript-finley" |
| 27 |
|
| 28 |
""" |
| 29 |
mesh generation using gmsh |
| 30 |
|
| 31 |
:var __author__: name of author |
| 32 |
:var __copyright__: copyrights |
| 33 |
:var __license__: licence agreement |
| 34 |
:var __url__: url entry point on documentation |
| 35 |
:var __version__: version |
| 36 |
:var __date__: date of the version |
| 37 |
""" |
| 38 |
|
| 39 |
__author__="Lutz Gross, l.gross@uq.edu.au" |
| 40 |
|
| 41 |
from . import design |
| 42 |
import tempfile |
| 43 |
import os |
| 44 |
from .primitives import Point, Spline, BezierCurve, BSpline, Line, Arc, CurveLoop, RuledSurface, PlaneSurface, SurfaceLoop, Volume, PropertySet, Ellipse |
| 45 |
from esys.escript import getMPIWorldMax, getMPIRankWorld, gmshGeo2Msh |
| 46 |
from .transformations import DEG |
| 47 |
|
| 48 |
class Design(design.AbstractDesign): |
| 49 |
""" |
| 50 |
Design for gmsh. |
| 51 |
""" |
| 52 |
DELAUNAY="Delauny" |
| 53 |
MESHADAPT="MeshAdapt" |
| 54 |
FRONTAL="Frontal" |
| 55 |
NETGEN="Frontal" |
| 56 |
TETGEN="Delauny" |
| 57 |
|
| 58 |
def __init__(self, dim=3, element_size=1., order=1, keep_files=False): |
| 59 |
""" |
| 60 |
Initializes the gmsh design. |
| 61 |
|
| 62 |
:param dim: spatial dimension |
| 63 |
:param element_size: global element size |
| 64 |
:param order: element order |
| 65 |
:param keep_files: flag to keep work files |
| 66 |
""" |
| 67 |
design.AbstractDesign.__init__(self,dim=dim,element_size=element_size,order=order,keep_files=keep_files) |
| 68 |
self.__mshname_set = False |
| 69 |
self.__scriptname="" |
| 70 |
self.setScriptFileName() |
| 71 |
self.setOptions() |
| 72 |
self.setFileFormat(self.GMSH) |
| 73 |
|
| 74 |
def setScriptFileName(self, name=None): |
| 75 |
""" |
| 76 |
Sets the filename for the gmsh input script. If no name is given a name |
| 77 |
with extension `geo` is generated. |
| 78 |
""" |
| 79 |
if self.__scriptname: |
| 80 |
os.unlink(self.__scriptname) |
| 81 |
if name == None: |
| 82 |
self.__scriptname_set=False |
| 83 |
tmp_f_id=tempfile.mkstemp(suffix=".geo") |
| 84 |
self.__scriptname=tmp_f_id[1] |
| 85 |
os.close(tmp_f_id[0]) |
| 86 |
else: |
| 87 |
self.__scriptname=name |
| 88 |
self.__scriptname_set=True |
| 89 |
|
| 90 |
def getScriptFileName(self): |
| 91 |
""" |
| 92 |
Returns the name of the gmsh script file. |
| 93 |
""" |
| 94 |
return self.__scriptname |
| 95 |
|
| 96 |
def setOptions(self, algorithm=None, optimize_quality=True, smoothing=1, |
| 97 |
curvature_based_element_size=False, algorithm2D=None, |
| 98 |
algorithm3D=None, generate_hexahedra=False, |
| 99 |
random_factor=None): |
| 100 |
""" |
| 101 |
Sets options for the mesh generator. |
| 102 |
|
| 103 |
:param algorithm: selects 2D meshing algorithm |
| 104 |
:type algorithm: in self.DELAUNAY, self.MESHADAPT, self.FRONTAL |
| 105 |
:param algorithm2D: must be equal to algorithm |
| 106 |
:type algorithm2D: in self.DELAUNAY, self.MESHADAPT, self.FRONTAL |
| 107 |
:param algorithm3D: selects 3D meshing algorithm |
| 108 |
:type algorithm3D: in self.DELAUNAY, self.FRONTAL |
| 109 |
:param curvature_based_element_size: switch for curvature based element size adaption |
| 110 |
:type curvature_based_element_size: ```bool``` |
| 111 |
:param smoothing: number of smoothing steps |
| 112 |
:type smoothing: non-negative ```int``` |
| 113 |
:param optimize_quality: switch for mesh quality optimization |
| 114 |
:type optimize_quality: ```bool``` |
| 115 |
:param generate_hexahedra: switch for using quadrangles/hexahedra elements everywhere. |
| 116 |
:type generate_hexahedra: ```bool``` |
| 117 |
:param random_factor: used in the 2D meshing algorithm (should be increased if RandomFactor * size(triangle)/size(model) approaches machine accuracy) |
| 118 |
:type random_factor: positive ```float``` |
| 119 |
""" |
| 120 |
if random_factor==None: random_factor=1.e-9 |
| 121 |
if not random_factor > 0: |
| 122 |
raise ValueError("random_factor must be positive.") |
| 123 |
smoothing=int(smoothing) |
| 124 |
if not smoothing > 0: |
| 125 |
raise ValueError("smoothing must be positive.") |
| 126 |
|
| 127 |
if algorithm3D is None: |
| 128 |
algorithm3D=self.FRONTAL |
| 129 |
if algorithm is None: |
| 130 |
if algorithm2D is None: |
| 131 |
algorithm2D=self.MESHADAPT |
| 132 |
else: |
| 133 |
if not algorithm2D is None: |
| 134 |
if not algorithm == algorithm2D: |
| 135 |
raise ValueError("argument algorithm (=%s) and algorithm2D (=%s) must have the same value if set."%(algorithm, algorithm2D)) |
| 136 |
algorithm2D = algorithm |
| 137 |
if not algorithm2D in [ self.DELAUNAY, self.MESHADAPT, self.FRONTAL ]: |
| 138 |
raise ValueError("illegal 2D meshing algorithm %s."%algorithm2D) |
| 139 |
if not algorithm3D in [ self.DELAUNAY, self.FRONTAL ]: |
| 140 |
raise ValueError("illegal 3D meshing algorithm %s."%algorithm3D) |
| 141 |
|
| 142 |
self.__curvature_based_element_size=curvature_based_element_size |
| 143 |
self.__algo2D=algorithm2D |
| 144 |
self.__algo3D=algorithm3D |
| 145 |
self.__optimize_quality=optimize_quality |
| 146 |
self.__smoothing=smoothing |
| 147 |
self.__generate_hexahedra=generate_hexahedra |
| 148 |
self.__random_factor=random_factor |
| 149 |
|
| 150 |
def getOptions(self, name=None): |
| 151 |
""" |
| 152 |
Returns the current options for the mesh generator. |
| 153 |
""" |
| 154 |
if name is None: |
| 155 |
return {"optimize_quality" : self.__optimize_quality , |
| 156 |
"smoothing" : self.__smoothing, |
| 157 |
"curvature_based_element_size" : self.__curvature_based_element_size, |
| 158 |
"generate_hexahedra" : self.__generate_hexahedra, |
| 159 |
"algorithm2D" : self.__algo2D, |
| 160 |
"algorithm3D" : self.__algo3D , |
| 161 |
"random_factor" : self.__random_factor } |
| 162 |
else: |
| 163 |
return self.getOption()[name] |
| 164 |
|
| 165 |
def __del__(self): |
| 166 |
""" |
| 167 |
Cleans up. |
| 168 |
""" |
| 169 |
try: |
| 170 |
if not self.keepFiles(): |
| 171 |
if not self.__scriptname_set: #i.e. it's a tempfile |
| 172 |
os.unlink(self.getScriptFileName()) |
| 173 |
if not self.__mshname_set: #i.e. it's a tempfile |
| 174 |
os.unlink(self.getMeshFileName()) |
| 175 |
except OSError: |
| 176 |
pass # The file might not have been created and there is nothing |
| 177 |
# to do about a "failure" here anyway |
| 178 |
|
| 179 |
def getScriptHandler(self): |
| 180 |
""" |
| 181 |
Returns a handler to the script file to generate the geometry. |
| 182 |
In the current implementation a script file name is returned. |
| 183 |
""" |
| 184 |
if getMPIRankWorld() == 0: |
| 185 |
open(self.getScriptFileName(),"w").write(self.getScriptString()) |
| 186 |
return self.getScriptFileName() |
| 187 |
|
| 188 |
def getMeshHandler(self): |
| 189 |
""" |
| 190 |
Returns a handle to a mesh meshing the design. In the current |
| 191 |
implementation a mesh file name in gmsh format is returned. |
| 192 |
""" |
| 193 |
|
| 194 |
verbosity = 3 |
| 195 |
ret = gmshGeo2Msh(self.getScriptHandler(), self.getMeshFileName(), |
| 196 |
self.getDim(), self.getElementOrder(), verbosity) |
| 197 |
if ret > 0: |
| 198 |
self.setKeepFilesOn() #no files to delete, so don't try to |
| 199 |
raise RuntimeError("Could not build mesh using gmsh.\n" + \ |
| 200 |
"Is gmsh available?") |
| 201 |
return self.getMeshFileName() |
| 202 |
|
| 203 |
def getScriptString(self): |
| 204 |
""" |
| 205 |
Returns the gmsh script to generate the mesh. |
| 206 |
""" |
| 207 |
h=self.getElementSize() |
| 208 |
out='// generated by esys.pycad\nGeneral.Terminal = 1;\nGeneral.ExpertMode = 1;\n' |
| 209 |
options=self.getOptions() |
| 210 |
if options["optimize_quality"]: |
| 211 |
out += "Mesh.Optimize = 1;\n" |
| 212 |
else: |
| 213 |
out += "Mesh.Optimize = 0;\n" |
| 214 |
|
| 215 |
if options["curvature_based_element_size"]: |
| 216 |
out += "Mesh.CharacteristicLengthFromCurvature = 1;\n" |
| 217 |
else: |
| 218 |
out += "Mesh.CharacteristicLengthFromCurvature = 0;\n" |
| 219 |
|
| 220 |
if options["generate_hexahedra"]: |
| 221 |
if self.getDim() == 2: |
| 222 |
out += "Mesh.SubdivisionAlgorithm = 1;\n" |
| 223 |
else: |
| 224 |
out += "Mesh.SubdivisionAlgorithm = 2;\n" |
| 225 |
else: |
| 226 |
out += "Mesh.SubdivisionAlgorithm = 0;\n" |
| 227 |
|
| 228 |
out += "Mesh.Smoothing = %d;\n"%options["smoothing"] |
| 229 |
out += "Mesh.RandomFactor = %.14e;\n"%options["random_factor"] |
| 230 |
if options["algorithm2D"] == self.MESHADAPT: |
| 231 |
out += "Mesh.Algorithm = 1; // = MeshAdapt\n" |
| 232 |
elif options["algorithm2D"] == self.DELAUNAY: |
| 233 |
out += "Mesh.Algorithm = 5; // = Delaunay\n" |
| 234 |
elif options["algorithm2D"] == self.FRONTAL: |
| 235 |
out += "Mesh.Algorithm = 6; // = Frontal\n" |
| 236 |
|
| 237 |
if options["algorithm3D"] == self.DELAUNAY: |
| 238 |
out += "Mesh.Algorithm3D = 1; // = Delaunay\n" |
| 239 |
elif options["algorithm3D"] == self.FRONTAL: |
| 240 |
out += "Mesh.Algorithm3D = 4; // = Frontal\n" |
| 241 |
|
| 242 |
for prim in self.getAllPrimitives(): |
| 243 |
p=prim.getUnderlyingPrimitive() |
| 244 |
if isinstance(p, Point): |
| 245 |
c=p.getCoordinates() |
| 246 |
#out+="Point(%s) = {%f , %f, %f , %f };\n"%(p.getID(),c[0],c[1],c[2], p.getLocalScale()*h) |
| 247 |
out += "Point(%s) = {%.14e, %.14e, %.14e, %.14e};\n"%(p.getID(),c[0],c[1],c[2], p.getLocalScale()*h) |
| 248 |
|
| 249 |
elif isinstance(p, Spline): |
| 250 |
out += "Spline(%s) = {%s};\n"%(p.getID(),self.__mkArgs(p.getControlPoints()))+self.__mkTransfiniteLine(p) |
| 251 |
|
| 252 |
elif isinstance(p, BezierCurve): |
| 253 |
out += "Bezier(%s) = {%s};\n"%(p.getID(),self.__mkArgs(p.getControlPoints()))+self.__mkTransfiniteLine(p) |
| 254 |
|
| 255 |
elif isinstance(p, BSpline): |
| 256 |
out += "BSpline(%s) = {%s};\n"%(p.getID(),self.__mkArgs(p.getControlPoints()))+self.__mkTransfiniteLine(p) |
| 257 |
|
| 258 |
elif isinstance(p, Line): |
| 259 |
out += "Line(%s) = {%s, %s};\n"%(p.getID(),p.getStartPoint().getDirectedID(),p.getEndPoint().getDirectedID())+self.__mkTransfiniteLine(p) |
| 260 |
|
| 261 |
elif isinstance(p, Arc): |
| 262 |
out += "Circle(%s) = {%s, %s, %s};\n"%(p.getID(),p.getStartPoint().getDirectedID(),p.getCenterPoint().getDirectedID(),p.getEndPoint().getDirectedID())+self.__mkTransfiniteLine(p) |
| 263 |
|
| 264 |
elif isinstance(p, Ellipse): |
| 265 |
out += "Ellipse(%s) = {%s, %s, %s, %s};\n"%(p.getID(),p.getStartPoint().getDirectedID(),p.getCenterPoint().getDirectedID(),p.getPointOnMainAxis().getDirectedID(), p.getEndPoint().getDirectedID())+self.__mkTransfiniteLine(p) |
| 266 |
|
| 267 |
elif isinstance(p, CurveLoop): |
| 268 |
out += "Line Loop(%s) = {%s};\n"%(p.getID(),self.__mkArgs(p.getCurves())) |
| 269 |
|
| 270 |
elif isinstance(p, RuledSurface): |
| 271 |
out += "Ruled Surface(%s) = {%s};\n"%(p.getID(),p.getBoundaryLoop().getDirectedID())+self.__mkTransfiniteSurface(p) |
| 272 |
|
| 273 |
elif isinstance(p, PlaneSurface): |
| 274 |
line = self.__mkArgs(p.getHoles()) |
| 275 |
if len(line) > 0: |
| 276 |
out += "Plane Surface(%s) = {%s, %s};\n"%(p.getID(),p.getBoundaryLoop().getDirectedID(), line)+self.__mkTransfiniteSurface(p) |
| 277 |
else: |
| 278 |
out += "Plane Surface(%s) = {%s};\n"%(p.getID(),p.getBoundaryLoop().getDirectedID())+self.__mkTransfiniteSurface(p) |
| 279 |
|
| 280 |
elif isinstance(p, SurfaceLoop): |
| 281 |
out += "Surface Loop(%s) = {%s};\n"%(p.getID(),self.__mkArgs(p.getSurfaces())) |
| 282 |
|
| 283 |
elif isinstance(p, Volume): |
| 284 |
line = self.__mkArgs(p.getHoles()) |
| 285 |
if len(line)>0: |
| 286 |
out += "Volume(%s) = {%s, %s};\n"%(p.getID(),p.getSurfaceLoop().getDirectedID(), line)+self.__mkTransfiniteVolume(p) |
| 287 |
else: |
| 288 |
out += "Volume(%s) = {%s};\n"%(p.getID(),p.getSurfaceLoop().getDirectedID())+self.__mkTransfiniteVolume(p) |
| 289 |
|
| 290 |
elif isinstance(p, PropertySet): |
| 291 |
if p.getNumItems() > 0: |
| 292 |
dim=p.getDim() |
| 293 |
line = "Physical " |
| 294 |
if dim==0: |
| 295 |
line += "Point" |
| 296 |
elif dim==1: |
| 297 |
line += "Line" |
| 298 |
elif dim==2: |
| 299 |
line += "Surface" |
| 300 |
else: |
| 301 |
line += "Volume" |
| 302 |
out += line+"(" + str(p.getID()) + ") = {"+self.__mkArgs(p.getItems(),useAbs=True)+"};\n" |
| 303 |
|
| 304 |
else: |
| 305 |
raise TypeError("unable to pass %s object to gmsh."%str(type(p))) |
| 306 |
return out |
| 307 |
|
| 308 |
def __mkArgs(self, args, useAbs=False): |
| 309 |
line = "" |
| 310 |
for i in args: |
| 311 |
id = i.getDirectedID() |
| 312 |
if useAbs: id=abs(id) |
| 313 |
if len(line) > 0: |
| 314 |
line += ", %s"%id |
| 315 |
else: |
| 316 |
line = "%s"%id |
| 317 |
return line |
| 318 |
|
| 319 |
def __mkTransfiniteLine(self, p): |
| 320 |
s = p.getElementDistribution() |
| 321 |
if not s == None: |
| 322 |
if s[2]: |
| 323 |
out="Transfinite Line{%d} = %d Using Bump %s;\n"%(p.getID(),s[0],s[1]) |
| 324 |
else: |
| 325 |
out="Transfinite Line{%d} = %d Using Progression %s;\n"%(p.getID(),s[0],s[1]) |
| 326 |
else: |
| 327 |
out="" |
| 328 |
return out |
| 329 |
|
| 330 |
def __mkTransfiniteSurface(self, p): |
| 331 |
out = "" |
| 332 |
o = p.getRecombination() |
| 333 |
s = p.getTransfiniteMeshing() |
| 334 |
if not s == None: |
| 335 |
out2 = "" |
| 336 |
if not s[0] is None: |
| 337 |
for q in s[0]: |
| 338 |
if len(out2)==0: |
| 339 |
out2 = "%s"%q.getID() |
| 340 |
else: |
| 341 |
out2 = "%s,%s"%(out2, q.getID()) |
| 342 |
if s[1] is None: |
| 343 |
out += "Transfinite Surface{%s} = {%s};\n"%(p.getID(),out2) |
| 344 |
else: |
| 345 |
out += "Transfinite Surface{%s} = {%s} %s;\n"%(p.getID(),out2,s[1]) |
| 346 |
if not o is None: |
| 347 |
out += "Recombine Surface {%s} = %f;\n"%(p.getID(), o/DEG) |
| 348 |
return out |
| 349 |
|
| 350 |
def __mkTransfiniteVolume(self, p): |
| 351 |
out="" |
| 352 |
s=p.getTransfiniteMeshing() |
| 353 |
if not s == None: |
| 354 |
if len(s)>0: |
| 355 |
out2="" |
| 356 |
for q in s[0]: |
| 357 |
if len(out2)==0: |
| 358 |
out2="%s"%q.getID() |
| 359 |
else: |
| 360 |
out2="%s,%s"%(out2,q.getID()) |
| 361 |
out+="Transfinite Volume{%s} = {%s};\n"%(p.getID(),out2) |
| 362 |
else: |
| 363 |
out+="Transfinite Volume{%s};\n"%(p.getID(),) |
| 364 |
return out |
| 365 |
|
Parent Directory
| 
Revision Log