def case_8_(src_path, dst_path): opts = jigsawpy.jigsaw_jig_t() geom = jigsawpy.jigsaw_msh_t() mesh = jigsawpy.jigsaw_msh_t() #------------------------------------ make mesh using JIGSAW print("Call libJIGSAW: case 8a.") jigsawpy.loadmsh(os.path.join(src_path, "eight.msh"), geom) opts.hfun_hmax = 0.04 # set HFUN limits opts.mesh_kern = "delfront" # DELFRONT kernel opts.mesh_dims = +3 jigsawpy.lib.jigsaw(opts, geom, mesh) print("Saving case_8a.vtk file.") jigsawpy.savevtk(os.path.join(dst_path, "case_8a.vtk"), geom) print("Saving case_8b.vtk file.") jigsawpy.savevtk(os.path.join(dst_path, "case_8b.vtk"), mesh) return
def case_7_(src_path, dst_path): opts = jigsawpy.jigsaw_jig_t() geom = jigsawpy.jigsaw_msh_t() mesh = jigsawpy.jigsaw_msh_t() #------------------------------------ make mesh using JIGSAW print("Call libJIGSAW: case 7a.") jigsawpy.loadmsh(os.path.join(src_path, "wheel.msh"), geom) opts.hfun_hmax = 0.03 # set HFUN limits opts.mesh_kern = "delfront" # DELFRONT kernel opts.mesh_dims = +2 opts.geom_feat = True opts.mesh_top1 = True opts.mesh_top2 = True jigsawpy.lib.jigsaw(opts, geom, mesh) print("Saving case_7a.vtk file.") jigsawpy.savevtk(os.path.join(dst_path, "case_7a.vtk"), geom) print("Saving case_7b.vtk file.") jigsawpy.savevtk(os.path.join(dst_path, "case_7b.vtk"), mesh) return
def setinit(): init = jigsawpy.jigsaw_msh_t() #------------------------------------ set initial conditions print("BUILDING MESH INIT.") filename = os.path.join(HERE, "..", "delaware_60_30_5_2", "tmp", "mesh.msh") if os.path.isfile(filename): # load from init. jigsawpy.loadmsh(filename, init) else: raise Exception("File not found: first run delaware_60_30_5_2" " to form initial conditions!") geom = copy.deepcopy(GEOM[0]) spac = copy.deepcopy(SPAC[0]) zipnear(init, geom, spac, near=+1.E+01) return init
def case_6_(src_path, dst_path): opts = jigsawpy.jigsaw_jig_t() geom = jigsawpy.jigsaw_msh_t() mesh = jigsawpy.jigsaw_msh_t() #------------------------------------ setup files for JIGSAW opts.geom_file = \ os.path.join(src_path, "piece.msh") opts.jcfg_file = \ os.path.join(dst_path, "piece.jig") opts.mesh_file = \ os.path.join(dst_path, "piece.msh") #------------------------------------ make mesh using JIGSAW jigsawpy.loadmsh(opts.geom_file, geom) print("Saving case_6a.vtk file.") jigsawpy.savevtk(os.path.join(dst_path, "case_6a.vtk"), geom) opts.hfun_hmax = 0.03 # set HFUN limits opts.mesh_kern = "delfront" # DELFRONT kernel opts.mesh_dims = +2 jigsawpy.cmd.jigsaw(opts, mesh) print("Saving case_6b.vtk file.") jigsawpy.savevtk(os.path.join(dst_path, "case_6b.vtk"), mesh) #------------------------------------ make mesh using JIGSAW opts.hfun_hmax = 0.03 # set HFUN limits opts.mesh_kern = "delfront" # DELFRONT kernel opts.mesh_dims = +2 opts.geom_feat = True opts.mesh_top1 = True jigsawpy.cmd.jigsaw(opts, mesh) print("Saving case_6c.vtk file.") jigsawpy.savevtk(os.path.join(dst_path, "case_6c.vtk"), mesh) return
def geom(self): """ This is the global geom """ try: name = self.__geom_tmpfile.name geom = jigsaw_msh_t() loadmsh(name, geom) return geom except AttributeError: # jigsawpy.msh_t.jigsaw_msh_t if isinstance(self._geom, jigsaw_msh_t): self._logger.debug('self.geom:AttributeError:jigsaw_msh_t') self._geom.edge2 = geomesh.utils.edge2_from_msh_t(self._geom) geom = self._geom elif isinstance(self._geom, (Polygon, MultiPolygon)): msg = 'self.geom:AttributeError:(Polygon, MultiPolygon)' self._logger.debug(msg) geom = self._get_geom_from_shapely() # RasterCollection elif isinstance( self._geom, ( geomesh.Raster, geomesh.RasterCollection ) ): msg = 'self.geom:AttributeError:(Raster, RasterCollection)' self._logger.debug(msg) geom = self._get_geom_from_raster() else: self._logger.debug('self.geom:AttributeError:Undefined') msg = f"Undefined handler for geom type {self._geom}" raise NotImplementedError(msg) tmpfile = tempfile.NamedTemporaryFile( prefix=geomesh.tmpdir, suffix='.msh') savemsh(tmpfile.name, geom) self.__geom_tmpfile = tmpfile # spherical mesh if self._radii is not None: geom.radii = self._radii geom.mshID = self._mshID return geom
def read_msh(msh_file): mesh = jigsawpy.jigsaw_msh_t() jigsawpy.loadmsh(msh_file, mesh) nn = len(mesh.point) lon_mesh = np.zeros(nn) lat_mesh = np.zeros(nn) for i in range(nn): lon_mesh[i] = mesh.point[i][0][0] lat_mesh[i] = mesh.point[i][0][1] ne = len(mesh.tria3) ect = np.zeros((ne, 3)) for i in range(ne): ect[i, :] = mesh.tria3['index'][i][:] return lon_mesh, lat_mesh
def setspac(): spac = jigsawpy.jigsaw_msh_t() #------------------------------------ define spacing pattern print("BUILDING MESH SPAC.") filename = os.path.join(HERE, "..", "delaware_60_30_5_2", "tmp", "spac.msh") if os.path.isfile(filename): # load from init. jigsawpy.loadmsh(filename, spac) else: raise Exception("File not found: first run delaware_60_30_5_2" " to form initial conditions!") SPAC[0] = spac # save a "pointer" return spac
def case_4_(src_path, dst_path): # DEMO-4: generate a multi-resolution mesh, via local refin- # ement along coastlines and shallow ridges. Global grid # resolution is 150KM, background resolution is 67KM and the # min. adaptive resolution is 33KM. opts = jigsawpy.jigsaw_jig_t() topo = jigsawpy.jigsaw_msh_t() geom = jigsawpy.jigsaw_msh_t() mesh = jigsawpy.jigsaw_msh_t() hmat = jigsawpy.jigsaw_msh_t() #------------------------------------ setup files for JIGSAW opts.geom_file = \ os.path.join(src_path, "eSPH.msh") opts.jcfg_file = \ os.path.join(dst_path, "eSPH.jig") opts.mesh_file = \ os.path.join(dst_path, "mesh.msh") opts.hfun_file = \ os.path.join(dst_path, "spac.msh") #------------------------------------ define JIGSAW geometry geom.mshID = "ellipsoid-mesh" geom.radii = np.full(3, 6.371E+003, dtype=geom.REALS_t) jigsawpy.savemsh(opts.geom_file, geom) #------------------------------------ define spacing pattern jigsawpy.loadmsh(os.path.join(src_path, "topo.msh"), topo) hmat.mshID = "ellipsoid-grid" hmat.radii = geom.radii hmat.xgrid = topo.xgrid * np.pi / 180. hmat.ygrid = topo.ygrid * np.pi / 180. hfn0 = +150. # global spacing hfn2 = +33. # adapt. spacing hfn3 = +67. # arctic spacing hmat.value = np.sqrt(np.maximum(-topo.value, 0.0)) hmat.value = \ np.maximum(hmat.value, hfn2) hmat.value = \ np.minimum(hmat.value, hfn3) mask = hmat.ygrid < 40. * np.pi / 180. hmat.value[mask] = hfn0 #------------------------------------ set HFUN grad.-limiter hmat.slope = np.full( # |dH/dx| limits topo.value.shape, +0.050, dtype=hmat.REALS_t) jigsawpy.savemsh(opts.hfun_file, hmat) jigsawpy.cmd.marche(opts, hmat) #------------------------------------ make mesh using JIGSAW opts.hfun_scal = "absolute" opts.hfun_hmax = float("inf") # null HFUN limits opts.hfun_hmin = float(+0.00) opts.mesh_dims = +2 # 2-dim. simplexes opts.optm_qlim = +9.5E-01 # tighter opt. tol opts.optm_iter = +32 opts.optm_qtol = +1.0E-05 jigsawpy.cmd.tetris(opts, 3, mesh) scr2 = jigsawpy.triscr2( # "quality" metric mesh.point["coord"], mesh.tria3["index"]) #------------------------------------ save mesh for Paraview apos = jigsawpy.R3toS2(geom.radii, mesh.point["coord"][:]) apos = apos * 180. / np.pi zfun = interpolate.RectBivariateSpline(topo.ygrid, topo.xgrid, topo.value) mesh.value = zfun(apos[:, 1], apos[:, 0], grid=False) cell = mesh.tria3["index"] zmsk = \ mesh.value[cell[:, 0]] + \ mesh.value[cell[:, 1]] + \ mesh.value[cell[:, 2]] zmsk = zmsk / +3.0 mesh.tria3 = mesh.tria3[zmsk < +0.] print("Saving to ../cache/case_4a.vtk") jigsawpy.savevtk(os.path.join(dst_path, "case_4a.vtk"), mesh) print("Saving to ../cache/case_4b.vtk") jigsawpy.savevtk(os.path.join(dst_path, "case_4b.vtk"), hmat) return
def case_3_(src_path, dst_path): # DEMO-3: generate multi-resolution spacing, via local refi- # nement along coastlines and shallow ridges. Global grid # resolution is 150KM, background resolution is 67KM and the # min. adaptive resolution is 33KM. opts = jigsawpy.jigsaw_jig_t() topo = jigsawpy.jigsaw_msh_t() geom = jigsawpy.jigsaw_msh_t() hraw = jigsawpy.jigsaw_msh_t() hlim = jigsawpy.jigsaw_msh_t() #------------------------------------ setup files for JIGSAW opts.geom_file = \ os.path.join(src_path, "eSPH.msh") opts.jcfg_file = \ os.path.join(dst_path, "eSPH.jig") opts.hfun_file = \ os.path.join(dst_path, "spac.msh") #------------------------------------ define JIGSAW geometry geom.mshID = "ellipsoid-mesh" geom.radii = np.full(3, 6.371E+003, dtype=geom.REALS_t) jigsawpy.savemsh(opts.geom_file, geom) #------------------------------------ define spacing pattern jigsawpy.loadmsh(os.path.join(src_path, "topo.msh"), topo) hraw.mshID = "ellipsoid-grid" hraw.radii = geom.radii hraw.xgrid = topo.xgrid * np.pi / 180. hraw.ygrid = topo.ygrid * np.pi / 180. hfn0 = +150. # global spacing hfn2 = +33. # adapt. spacing hfn3 = +67. # arctic spacing hraw.value = np.sqrt(np.maximum(-topo.value, 0.0)) hraw.value = \ np.maximum(hraw.value, hfn2) hraw.value = \ np.minimum(hraw.value, hfn3) mask = hraw.ygrid < 40. * np.pi / 180. hraw.value[mask] = hfn0 #------------------------------------ set HFUN grad.-limiter hlim = copy.copy(hraw) hlim.slope = np.full( # |dH/dx| limits topo.value.shape, +0.050, dtype=hlim.REALS_t) jigsawpy.savemsh(opts.hfun_file, hlim) jigsawpy.cmd.marche(opts, hlim) #------------------------------------ save mesh for Paraview print("Saving to ../cache/case_3a.vtk") jigsawpy.savevtk(os.path.join(dst_path, "case_3a.vtk"), hraw) print("Saving to ../cache/case_3b.vtk") jigsawpy.savevtk(os.path.join(dst_path, "case_3b.vtk"), hlim) return
def case_4_(src_path, dst_path): # DEMO-4: generate a multi-resolution mesh, via local refin- # ement along coastlines and shallow ridges. Global grid # resolution is 150KM, background resolution is 67KM and the # min. adaptive resolution is 33KM. opts = jigsawpy.jigsaw_jig_t() topo = jigsawpy.jigsaw_msh_t() geom = jigsawpy.jigsaw_msh_t() mesh = jigsawpy.jigsaw_msh_t() hmat = jigsawpy.jigsaw_msh_t() #------------------------------------ setup files for JIGSAW opts.geom_file = \ os.path.join(dst_path, "geom.msh") opts.jcfg_file = \ os.path.join(dst_path, "opts.jig") opts.mesh_file = \ os.path.join(dst_path, "mesh.msh") opts.hfun_file = \ os.path.join(dst_path, "spac.msh") #------------------------------------ define JIGSAW geometry geom.mshID = "ellipsoid-mesh" geom.radii = np.full(3, 6.371E+003, dtype=geom.REALS_t) jigsawpy.savemsh(opts.geom_file, geom) #------------------------------------ define spacing pattern jigsawpy.loadmsh(os.path.join(src_path, "topo.msh"), topo) hmat.mshID = "ellipsoid-grid" hmat.radii = geom.radii hmat.xgrid = topo.xgrid * np.pi / 180. hmat.ygrid = topo.ygrid * np.pi / 180. hfn0 = +150. # global spacing hfn2 = +33. # adapt. spacing hfn3 = +67. # arctic spacing hmat.value = np.sqrt(np.maximum(-topo.value, 0.0)) hmat.value = \ np.maximum(hmat.value, hfn2) hmat.value = \ np.minimum(hmat.value, hfn3) mask = hmat.ygrid < 40. * np.pi / 180. hmat.value[mask] = hfn0 #------------------------------------ set HFUN grad.-limiter hmat.slope = np.full( # |dH/dx| limits topo.value.shape, +0.050, dtype=hmat.REALS_t) jigsawpy.savemsh(opts.hfun_file, hmat) jigsawpy.cmd.marche(opts, hmat) #------------------------------------ make mesh using JIGSAW opts.hfun_scal = "absolute" opts.hfun_hmax = float("inf") # null HFUN limits opts.hfun_hmin = float(+0.00) opts.mesh_dims = +2 # 2-dim. simplexes opts.optm_qlim = +9.5E-01 # tighter opt. tol opts.optm_iter = +32 opts.optm_qtol = +1.0E-05 # opts.optm_kern = "cvt+dqdx" rbar = np.mean(geom.radii) # bisect heuristic hbar = np.mean(hmat.value) nlev = round(math.log2(rbar / math.sin(.4 * math.pi) / hbar)) ttic = time.time() jigsawpy.cmd.tetris(opts, nlev - 1, mesh) ttoc = time.time() print("CPUSEC =", (ttoc - ttic)) print("BISECT =", +nlev) cost = jigsawpy.triscr2( # quality metrics! mesh.point["coord"], mesh.tria3["index"]) print("TRISCR =", np.min(cost), np.mean(cost)) cost = jigsawpy.pwrscr2(mesh.point["coord"], mesh.power, mesh.tria3["index"]) print("PWRSCR =", np.min(cost), np.mean(cost)) tbad = jigsawpy.centre2(mesh.point["coord"], mesh.power, mesh.tria3["index"]) print("OBTUSE =", +np.count_nonzero(np.logical_not(tbad))) ndeg = jigsawpy.trideg2(mesh.point["coord"], mesh.tria3["index"]) print("TOPOL. =", +np.count_nonzero(ndeg == +6) / ndeg.size) #------------------------------------ save mesh for Paraview apos = jigsawpy.R3toS2(geom.radii, mesh.point["coord"][:]) apos = apos * 180. / np.pi zfun = interpolate.RectBivariateSpline(topo.ygrid, topo.xgrid, topo.value) mesh.value = zfun(apos[:, 1], apos[:, 0], grid=False) cell = mesh.tria3["index"] zmsk = \ mesh.value[cell[:, 0]] + \ mesh.value[cell[:, 1]] + \ mesh.value[cell[:, 2]] zmsk = zmsk / +3.0 mesh.tria3 = mesh.tria3[zmsk < +0.] print("Saving to ../cache/case_4a.vtk") jigsawpy.savevtk(os.path.join(dst_path, "case_4a.vtk"), mesh) print("Saving to ../cache/case_4b.vtk") jigsawpy.savevtk(os.path.join(dst_path, "case_4b.vtk"), hmat) return
def getInitialMesh(topofile, meshfile, spacefile, outfile, dst_path, hfn): t0 = process_time() opts = jigsawpy.jigsaw_jig_t() topo = jigsawpy.jigsaw_msh_t() geom = jigsawpy.jigsaw_msh_t() mesh = jigsawpy.jigsaw_msh_t() hmat = jigsawpy.jigsaw_msh_t() jigsawpy.loadmsh(topofile, topo) print("Load topography grid (%0.02f seconds)" % (process_time() - t0)) t0 = process_time() opts.geom_file = os.path.join(dst_path, "topology.msh") opts.jcfg_file = os.path.join(dst_path, "config.jig") opts.mesh_file = meshfile opts.hfun_file = spacefile geom.mshID = "ellipsoid-mesh" geom.radii = np.full(3, 6.371e003, dtype=geom.REALS_t) jigsawpy.savemsh(opts.geom_file, geom) hmat.mshID = "ellipsoid-grid" hmat.radii = geom.radii hmat.xgrid = topo.xgrid * np.pi / 180.0 hmat.ygrid = topo.ygrid * np.pi / 180.0 # Set HFUN gradient-limiter hmat.value = np.full(topo.value.shape, hfn[0], dtype=hmat.REALS_t) hmat.value[topo.value > -1000] = hfn[1] hmat.value[topo.value > 0] = hfn[2] hmat.slope = np.full(topo.value.shape, +0.050, dtype=hmat.REALS_t) jigsawpy.savemsh(opts.hfun_file, hmat) jigsawpy.cmd.marche(opts, hmat) print("Build space function (%0.02f seconds)" % (process_time() - t0)) t0 = process_time() opts.hfun_scal = "absolute" opts.hfun_hmax = float("inf") # null HFUN limits opts.hfun_hmin = float(+0.00) opts.mesh_dims = +2 # 2-dim. simplexes opts.optm_qlim = +9.5e-01 # tighter opt. tol opts.optm_iter = +32 opts.optm_qtol = +1.0e-05 jigsawpy.cmd.tetris(opts, 3, mesh) print("Perform triangulation (%0.02f seconds)" % (process_time() - t0)) t0 = process_time() apos = jigsawpy.R3toS2(geom.radii, mesh.point["coord"][:]) apos = apos * 180.0 / np.pi zfun = interpolate.RectBivariateSpline(topo.ygrid, topo.xgrid, topo.value) mesh.value = zfun(apos[:, 1], apos[:, 0], grid=False) jigsawpy.savevtk(outfile, mesh) jigsawpy.savemsh(opts.mesh_file, mesh) print("Get unstructured mesh (%0.02f seconds)" % (process_time() - t0)) return
def waves_mesh(cfg): pwd = os.getcwd() src_path = pwd dst_path = pwd opts = jigsawpy.jigsaw_jig_t() hfun = jigsawpy.jigsaw_msh_t() mesh = jigsawpy.jigsaw_msh_t() init = jigsawpy.jigsaw_msh_t() #------------------------------------ setup files for JIGSAW opts.geom_file = \ str(Path(dst_path)/"geom.msh") # GEOM file opts.jcfg_file = \ str(Path(dst_path)/"jcfg.jig") # JCFG file opts.hfun_file = \ str(Path(dst_path)/"hfun.msh") # HFUN file opts.mesh_file = \ str(Path(dst_path)/"mesh.msh") # MESH file opts.init_file = \ str(Path(dst_path)/"init.msh") # INIT file #------------------------------------ define JIGSAW geometry if cfg['coastlines']: print('Defining coastline geometry') create_coastline_geometry(cfg['shpfiles'], opts.geom_file, cfg['sphere_radius']) else: geom = jigsawpy.jigsaw_msh_t() geom.mshID = 'ELLIPSOID-MESH' geom.radii = cfg['sphere_radius'] * np.ones(3, float) jigsawpy.savemsh(opts.geom_file, geom) #------------------------------------ define mesh size function print('Defining mesh size function') lon_min = -180.0 lon_max = 180.0 dlon = cfg['hfun_grid_spacing'] nlon = int((lon_max - lon_min) / dlon) + 1 lat_min = -90.0 lat_max = 90.0 nlat = int((lat_max - lat_min) / dlon) + 1 dlat = cfg['hfun_grid_spacing'] xlon = np.linspace(lon_min, lon_max, nlon) ylat = np.linspace(lat_min, lat_max, nlat) print(' hfun grid dimensions: {}, {}'.format(xlon.size, ylat.size)) define_hfunction.depth_threshold_refined = cfg['depth_threshold_refined'] define_hfunction.distance_threshold_refined = cfg[ 'distance_threshold_refined'] define_hfunction.depth_threshold_global = cfg['depth_threshold_global'] define_hfunction.distance_threshold_global = cfg[ 'distance_threshold_global'] define_hfunction.refined_res = cfg['refined_res'] define_hfunction.maxres = cfg['maxres'] hfunction = define_hfunction.cell_widthVsLatLon(xlon, ylat, cfg['shpfiles'], cfg['sphere_radius'], cfg['ocean_mesh']) hfunction = hfunction / km hfun.mshID = "ellipsoid-grid" hfun.radii = np.full(3, cfg['sphere_radius'], dtype=jigsawpy.jigsaw_msh_t.REALS_t) hfun.xgrid = np.radians(xlon) hfun.ygrid = np.radians(ylat) hfun.value = hfunction.astype(jigsawpy.jigsaw_msh_t.REALS_t) #------------------------------------ specify JIGSAW initial conditions print('Specifying initial fixed coordinate locations') create_initial_points(cfg['ocean_mesh'], xlon, ylat, hfunction, cfg['sphere_radius'], opts.init_file) jigsawpy.loadmsh(opts.init_file, init) jigsawpy.savevtk(str(Path(dst_path) / "init.vtk"), init) #------------------------------------ set HFUN grad.-limiter print('Limiting mesh size function gradients') hfun.slope = np.full( # |dH/dx| limits hfun.value.shape, cfg['hfun_slope_lim'], dtype=hfun.REALS_t) jigsawpy.savemsh(opts.hfun_file, hfun) jigsawpy.cmd.marche(opts, hfun) #------------------------------------ make mesh using JIGSAW opts.hfun_scal = "absolute" opts.hfun_hmax = float("inf") # null HFUN limits opts.hfun_hmin = float(+0.00) opts.mesh_dims = +2 # 2-dim. simplexes opts.mesh_eps1 = +.67 # relax edge error opts.mesh_rad2 = +1.2 opts.optm_qlim = +9.5E-01 # tighter opt. tol opts.optm_iter = +32 opts.optm_qtol = +1.0E-05 opts.verbosity = 2 #jigsawpy.cmd.tetris(opts, 3, mesh) jigsawpy.cmd.jigsaw(opts, mesh) if cfg['coastlines']: segment.segment(mesh) #------------------------------------ save mesh for Paraview print("Writing ex_h.vtk file.") jigsawpy.savevtk(str(Path(dst_path) / "_hfun.vtk"), hfun) jigsawpy.savevtk(str(Path(dst_path) / "waves_mesh.vtk"), mesh) jigsawpy.savemsh(str(Path(dst_path) / "waves_mesh.msh"), mesh) #------------------------------------ convert mesh to MPAS format jigsaw_to_netcdf(msh_filename='waves_mesh.msh', output_name='waves_mesh_triangles.nc', on_sphere=True, sphere_radius=cfg['sphere_radius']) write_netcdf( convert(xarray.open_dataset('waves_mesh_triangles.nc'), dir='./', logger=None), 'waves_mesh.nc') #------------------------------------ cull mesh to ocean bounary if os.path.exists('./cull_waves_mesh'): f = open('cull_waves_mesh.nml', 'w') f.write('&inputs\n') f.write(" waves_mesh_file = 'waves_mesh.nc'\n") f.write(" ocean_mesh_file = '" + cfg['ocean_mesh'] + "'\n") f.write("/\n") f.write('&output\n') f.write(" waves_mesh_culled_vtk = 'waves_mesh_culled.vtk'\n") f.write(" waves_mesh_culled_gmsh = 'waves_mesh_culled.msh'\n") f.write("/\n") f.close() subprocess.call('./cull_waves_mesh', shell=True) #------------------------------------ output ocean mesh polygons subprocess.call('paraview_vtk_field_extractor.py -f ' + cfg['ocean_mesh'] + ' --ignore_time -v areaCell -o ' + cfg['ocean_mesh'] + '.vtk', shell=True) return
def ex_9(): # DEMO-9: generate a 2-dim. grid for the Australian coastal # region, using scaled ocean-depth as a mesh-resolution # heuristic. A local stereographic projection is employed. dst_path = \ os.path.abspath( os.path.dirname(__file__)) src_path = \ os.path.join(dst_path, "..", "files") dst_path = \ os.path.join(dst_path, "..", "cache") opts = jigsawpy.jigsaw_jig_t() topo = jigsawpy.jigsaw_msh_t() geom = jigsawpy.jigsaw_msh_t() mesh = jigsawpy.jigsaw_msh_t() msph = jigsawpy.jigsaw_msh_t() hmat = jigsawpy.jigsaw_msh_t() proj = jigsawpy.jigsaw_prj_t() #------------------------------------ setup files for JIGSAW opts.geom_file = \ os.path.join(dst_path, "proj.msh") opts.jcfg_file = \ os.path.join(dst_path, "aust.jig") opts.mesh_file = \ os.path.join(dst_path, "mesh.msh") opts.hfun_file = \ os.path.join(dst_path, "spac.msh") #------------------------------------ define JIGSAW geometry jigsawpy.loadmsh(os.path.join(src_path, "aust.msh"), geom) jigsawpy.loadmsh(os.path.join(src_path, "topo.msh"), topo) xmin = np.min(geom.point["coord"][:, 0]) ymin = np.min(geom.point["coord"][:, 1]) xmax = np.max(geom.point["coord"][:, 0]) ymax = np.max(geom.point["coord"][:, 1]) zlev = topo.value xmsk = np.logical_and(topo.xgrid > xmin, topo.xgrid < xmax) ymsk = np.logical_and(topo.ygrid > ymin, topo.ygrid < ymax) zlev = zlev[:, xmsk] zlev = zlev[ymsk, :] #------------------------------------ define spacing pattern hmat.mshID = "ellipsoid-grid" hmat.radii = np.full(+3, +6371.0, dtype=jigsawpy.jigsaw_msh_t.REALS_t) hmat.xgrid = \ topo.xgrid[xmsk] * np.pi / 180. hmat.ygrid = \ topo.ygrid[ymsk] * np.pi / 180. hmin = +1.0E+01 hmax = +1.0E+02 hmat.value = \ np.sqrt(np.maximum(-zlev, 0.)) / 0.5 hmat.value = \ np.maximum(hmat.value, hmin) hmat.value = \ np.minimum(hmat.value, hmax) hmat.slope = np.full(hmat.value.shape, +0.1500, dtype=jigsawpy.jigsaw_msh_t.REALS_t) #------------------------------------ do stereographic proj. geom.point["coord"][:, :] *= np.pi / 180. proj.prjID = 'stereographic' proj.radii = +6.371E+003 proj.xbase = \ +0.500 * (xmin + xmax) * np.pi / 180. proj.ybase = \ +0.500 * (ymin + ymax) * np.pi / 180. jigsawpy.project(geom, proj, "fwd") jigsawpy.project(hmat, proj, "fwd") jigsawpy.savemsh(opts.geom_file, geom) jigsawpy.savemsh(opts.hfun_file, hmat) #------------------------------------ set HFUN grad.-limiter jigsawpy.cmd.marche(opts, hmat) #------------------------------------ make mesh using JIGSAW opts.hfun_scal = "absolute" opts.hfun_hmax = float("inf") # null HFUN limits opts.hfun_hmin = float(+0.00) opts.mesh_dims = +2 # 2-dim. simplexes opts.mesh_eps1 = +1.0E+00 # relax edge error opts.optm_iter = +32 opts.optm_qtol = +1.0E-05 jigsawpy.cmd.jigsaw(opts, mesh) #------------------------------------ do stereographic proj. msph = copy.deepcopy(mesh) jigsawpy.project(msph, proj, "inv") radii = np.full(+3, proj.radii, dtype=jigsawpy.jigsaw_msh_t.REALS_t) msph.vert3 = np.zeros((msph.vert2.size), dtype=jigsawpy.jigsaw_msh_t.VERT3_t) msph.vert3["coord"] = \ jigsawpy.S2toR3( radii, msph.point["coord"]) msph.vert2 = None #------------------------------------ save mesh for Paraview print("Saving to ../cache/case_9a.vtk") jigsawpy.savevtk(os.path.join(dst_path, "case_9a.vtk"), mesh) print("Saving to ../cache/case_9b.vtk") jigsawpy.savevtk(os.path.join(dst_path, "case_9b.vtk"), hmat) print("Saving to ../cache/case_9c.vtk") jigsawpy.savevtk(os.path.join(dst_path, "case_9c.vtk"), msph) return
def case_1_(src_path, dst_path): # DEMO-1: generate a uniform resolution (150KM) global grid. opts = jigsawpy.jigsaw_jig_t() topo = jigsawpy.jigsaw_msh_t() geom = jigsawpy.jigsaw_msh_t() mesh = jigsawpy.jigsaw_msh_t() #------------------------------------ setup files for JIGSAW opts.geom_file = \ os.path.join(dst_path, "geom.msh") opts.jcfg_file = \ os.path.join(dst_path, "opts.jig") opts.mesh_file = \ os.path.join(dst_path, "mesh.msh") #------------------------------------ define JIGSAW geometry geom.mshID = "ellipsoid-mesh" geom.radii = np.full(3, 6.371E+003, dtype=geom.REALS_t) jigsawpy.savemsh(opts.geom_file, geom) #------------------------------------ make mesh using JIGSAW opts.hfun_scal = "absolute" opts.hfun_hmax = +150. # uniform at 150km opts.mesh_dims = +2 # 2-dim. simplexes opts.optm_qlim = +9.5E-01 # tighter opt. tol opts.optm_iter = +32 opts.optm_qtol = +1.0E-05 # opts.optm_kern = "cvt+dqdx" rbar = np.mean(geom.radii) # bisect heuristic nlev = round(math.log2(rbar / math.sin(.4 * math.pi) / opts.hfun_hmax)) ttic = time.time() jigsawpy.cmd.tetris(opts, nlev - 1, mesh) ttoc = time.time() print("CPUSEC =", (ttoc - ttic)) print("BISECT =", +nlev) cost = jigsawpy.triscr2( # quality metrics! mesh.point["coord"], mesh.tria3["index"]) print("TRISCR =", np.min(cost), np.mean(cost)) cost = jigsawpy.pwrscr2(mesh.point["coord"], mesh.power, mesh.tria3["index"]) print("PWRSCR =", np.min(cost), np.mean(cost)) tbad = jigsawpy.centre2(mesh.point["coord"], mesh.power, mesh.tria3["index"]) print("OBTUSE =", +np.count_nonzero(np.logical_not(tbad))) ndeg = jigsawpy.trideg2(mesh.point["coord"], mesh.tria3["index"]) print("TOPOL. =", +np.count_nonzero(ndeg == +6) / ndeg.size) #------------------------------------ save mesh for Paraview jigsawpy.loadmsh(os.path.join(src_path, "topo.msh"), topo) #------------------------------------ a very rough land mask apos = jigsawpy.R3toS2(geom.radii, mesh.point["coord"][:]) apos = apos * 180. / np.pi zfun = interpolate.RectBivariateSpline(topo.ygrid, topo.xgrid, topo.value) mesh.value = zfun(apos[:, 1], apos[:, 0], grid=False) cell = mesh.tria3["index"] zmsk = \ mesh.value[cell[:, 0]] + \ mesh.value[cell[:, 1]] + \ mesh.value[cell[:, 2]] zmsk = zmsk / +3.0 mesh.tria3 = mesh.tria3[zmsk < +0.] print("Saving to ../cache/case_1a.vtk") jigsawpy.savevtk(os.path.join(dst_path, "case_1a.vtk"), mesh) return
def unstMesh(esph, infile, hfn0=100.0, hfn1=30.0, hfn2=15, tmp="tmp/"): opts = jigsawpy.jigsaw_jig_t() topo = jigsawpy.jigsaw_msh_t() geom = jigsawpy.jigsaw_msh_t() mesh = jigsawpy.jigsaw_msh_t() hmat = jigsawpy.jigsaw_msh_t() opts.geom_file = esph opts.jcfg_file = os.path.join(tmp, "topo.jig") opts.mesh_file = os.path.join(tmp, "mesh.msh") opts.hfun_file = os.path.join(tmp, "spac.msh") # define JIGSAW geometry geom.mshID = "ellipsoid-mesh" geom.radii = np.full(3, 6.371e003, dtype=geom.REALS_t) jigsawpy.savemsh(opts.geom_file, geom) # define spacing pattern jigsawpy.loadmsh(infile, topo) hmat.mshID = "ellipsoid-grid" hmat.radii = geom.radii hmat.xgrid = topo.xgrid * np.pi / 180.0 hmat.ygrid = topo.ygrid * np.pi / 180.0 # Define grid resolution for each elevation domain hmat.value = np.full(topo.value.shape, hfn0, dtype=hmat.REALS_t) hmat.value[topo.value > -1000.0] = hfn1 hmat.value[topo.value > 0.0] = hfn2 # Set HFUN gradient-limiter hmat.slope = np.full(topo.value.shape, +0.025, dtype=hmat.REALS_t) jigsawpy.savemsh(opts.hfun_file, hmat) jigsawpy.cmd.marche(opts, hmat) # Make mesh using JIGSAW opts.hfun_scal = "absolute" opts.hfun_hmax = float("inf") # null HFUN limits opts.hfun_hmin = float(+0.00) opts.mesh_dims = +2 # 2-dim. simplexes opts.optm_qlim = +9.5e-01 # tighter opt. tol opts.optm_iter = +32 opts.optm_qtol = +1.0e-05 jigsawpy.cmd.tetris(opts, 4, mesh) scr2 = jigsawpy.triscr2( # "quality" metric mesh.point["coord"], mesh.tria3["index"]) apos = jigsawpy.R3toS2(geom.radii, mesh.point["coord"][:]) apos = apos * 180.0 / np.pi zfun = interpolate.RectBivariateSpline(topo.ygrid, topo.xgrid, topo.value) mesh.value = zfun(apos[:, 1], apos[:, 0], grid=False) coords = (mesh.vert3["coord"] / 6.371e003) * 6378137.0 del scr2 return coords, mesh.tria3["index"], mesh.value
def case_6_(src_path, dst_path): # DEMO-6: generate a 2-dim. grid for the Australian coastal # region, using scaled ocean-depth as a mesh-resolution # heuristic. A local stereographic projection is employed. opts = jigsawpy.jigsaw_jig_t() topo = jigsawpy.jigsaw_msh_t() geom = jigsawpy.jigsaw_msh_t() mesh = jigsawpy.jigsaw_msh_t() hmat = jigsawpy.jigsaw_msh_t() proj = jigsawpy.jigsaw_prj_t() #------------------------------------ setup files for JIGSAW opts.geom_file = \ os.path.join(dst_path, "geom.msh") opts.jcfg_file = \ os.path.join(dst_path, "aust.jig") opts.mesh_file = \ os.path.join(dst_path, "mesh.msh") opts.hfun_file = \ os.path.join(dst_path, "spac.msh") #------------------------------------ define JIGSAW geometry jigsawpy.loadmsh(os.path.join(src_path, "aust.msh"), geom) jigsawpy.loadmsh(os.path.join(src_path, "topo.msh"), topo) xmin = np.min(geom.point["coord"][:, 0]) ymin = np.min(geom.point["coord"][:, 1]) xmax = np.max(geom.point["coord"][:, 0]) ymax = np.max(geom.point["coord"][:, 1]) zlev = topo.value xmsk = np.logical_and(topo.xgrid > xmin, topo.xgrid < xmax) ymsk = np.logical_and(topo.ygrid > ymin, topo.ygrid < ymax) zlev = zlev[:, xmsk] zlev = zlev[ymsk, :] #------------------------------------ define spacing pattern hmat.mshID = "ellipsoid-grid" hmat.radii = np.full(+3, +6371.0, dtype=jigsawpy.jigsaw_msh_t.REALS_t) hmat.xgrid = \ topo.xgrid[xmsk] * np.pi / 180. hmat.ygrid = \ topo.ygrid[ymsk] * np.pi / 180. hmin = +1.0E+01 hmax = +1.0E+02 hmat.value = \ np.sqrt(np.maximum(-zlev, 0.)) / 0.5 hmat.value = \ np.maximum(hmat.value, hmin) hmat.value = \ np.minimum(hmat.value, hmax) hmat.slope = np.full(hmat.value.shape, +0.1500, dtype=jigsawpy.jigsaw_msh_t.REALS_t) #------------------------------------ do stereographic proj. geom.point["coord"][:, :] *= np.pi / 180. proj.prjID = 'stereographic' proj.radii = +6.371E+003 proj.xbase = \ +0.500 * (xmin + xmax) * np.pi / 180. proj.ybase = \ +0.500 * (ymin + ymax) * np.pi / 180. jigsawpy.project(geom, proj, "fwd") jigsawpy.project(hmat, proj, "fwd") jigsawpy.savemsh(opts.geom_file, geom) jigsawpy.savemsh(opts.hfun_file, hmat) #------------------------------------ set HFUN grad.-limiter jigsawpy.cmd.marche(opts, hmat) #------------------------------------ make mesh using JIGSAW opts.hfun_scal = "absolute" opts.hfun_hmax = float("inf") # null HFUN limits opts.hfun_hmin = float(+0.00) opts.mesh_dims = +2 # 2-dim. simplexes opts.mesh_eps1 = +1. ttic = time.time() jigsawpy.cmd.jigsaw(opts, mesh) ttoc = time.time() print("CPUSEC =", (ttoc - ttic)) cost = jigsawpy.triscr2( # quality metrics! mesh.point["coord"], mesh.tria3["index"]) print("TRISCR =", np.min(cost), np.mean(cost)) cost = jigsawpy.pwrscr2(mesh.point["coord"], mesh.power, mesh.tria3["index"]) print("PWRSCR =", np.min(cost), np.mean(cost)) tbad = jigsawpy.centre2(mesh.point["coord"], mesh.power, mesh.tria3["index"]) print("OBTUSE =", +np.count_nonzero(np.logical_not(tbad))) #------------------------------------ save mesh for Paraview print("Saving to ../cache/case_6a.vtk") jigsawpy.savevtk(os.path.join(dst_path, "case_6a.vtk"), mesh) print("Saving to ../cache/case_6b.vtk") jigsawpy.savevtk(os.path.join(dst_path, "case_6b.vtk"), hmat) return
def case_7_(src_path, dst_path): # DEMO-7: generate a multi-part mesh of the (contiguous) USA # using state boundaries to partition the mesh. A local # stereographic projection is employed. The domain is meshed # using uniform resolution. opts = jigsawpy.jigsaw_jig_t() geom = jigsawpy.jigsaw_msh_t() mesh = jigsawpy.jigsaw_msh_t() proj = jigsawpy.jigsaw_prj_t() #------------------------------------ setup files for JIGSAW opts.geom_file = \ os.path.join(dst_path, "geom.msh") opts.jcfg_file = \ os.path.join(dst_path, "us48.jig") opts.mesh_file = \ os.path.join(dst_path, "mesh.msh") #------------------------------------ define JIGSAW geometry jigsawpy.loadmsh(os.path.join(src_path, "us48.msh"), geom) xmin = np.min(geom.point["coord"][:, 0]) ymin = np.min(geom.point["coord"][:, 1]) xmax = np.max(geom.point["coord"][:, 0]) ymax = np.max(geom.point["coord"][:, 1]) geom.point["coord"][:, :] *= np.pi / 180. proj.prjID = 'stereographic' proj.radii = +6.371E+003 proj.xbase = \ +0.500 * (xmin + xmax) * np.pi / 180. proj.ybase = \ +0.500 * (ymin + ymax) * np.pi / 180. jigsawpy.project(geom, proj, "fwd") jigsawpy.savemsh(opts.geom_file, geom) #------------------------------------ make mesh using JIGSAW opts.hfun_hmax = .005 opts.mesh_dims = +2 # 2-dim. simplexes opts.mesh_eps1 = +1 / 6. ttic = time.time() jigsawpy.cmd.jigsaw(opts, mesh) ttoc = time.time() print("CPUSEC =", (ttoc - ttic)) cost = jigsawpy.triscr2( # quality metrics! mesh.point["coord"], mesh.tria3["index"]) print("TRISCR =", np.min(cost), np.mean(cost)) cost = jigsawpy.pwrscr2(mesh.point["coord"], mesh.power, mesh.tria3["index"]) print("PWRSCR =", np.min(cost), np.mean(cost)) tbad = jigsawpy.centre2(mesh.point["coord"], mesh.power, mesh.tria3["index"]) print("OBTUSE =", +np.count_nonzero(np.logical_not(tbad))) #------------------------------------ save mesh for Paraview print("Saving to ../cache/case_7a.vtk") jigsawpy.savevtk(os.path.join(dst_path, "case_7a.vtk"), mesh) return
def case_5_(src_path, dst_path): # DEMO-5: generate struct. icosahedral and cubedsphere grids opts = jigsawpy.jigsaw_jig_t() topo = jigsawpy.jigsaw_msh_t() geom = jigsawpy.jigsaw_msh_t() icos = jigsawpy.jigsaw_msh_t() cube = jigsawpy.jigsaw_msh_t() #------------------------------------ setup files for JIGSAW opts.geom_file = \ os.path.join(dst_path, "geom.msh") opts.jcfg_file = \ os.path.join(dst_path, "opts.jig") opts.mesh_file = \ os.path.join(dst_path, "mesh.msh") #------------------------------------ define JIGSAW geometry geom.mshID = "ellipsoid-mesh" geom.radii = np.full(3, 1.000E+000, dtype=geom.REALS_t) jigsawpy.savemsh(opts.geom_file, geom) #------------------------------------ make mesh using JIGSAW opts.hfun_hmax = +1. opts.mesh_dims = +2 # 2-dim. simplexes opts.optm_iter = +512 opts.optm_qtol = +1.0E-06 # opts.optm_kern = "cvt+dqdx" ttic = time.time() jigsawpy.cmd.icosahedron(opts, +6, icos) ttoc = time.time() print("CPUSEC =", (ttoc - ttic)) ttic = time.time() jigsawpy.cmd.cubedsphere(opts, +6, cube) ttoc = time.time() print("CPUSEC =", (ttoc - ttic)) #------------------------------------ save mesh for Paraview jigsawpy.loadmsh(os.path.join(src_path, "topo.msh"), topo) #------------------------------------ a very rough land mask zfun = interpolate.RectBivariateSpline(topo.ygrid, topo.xgrid, topo.value) apos = jigsawpy.R3toS2(geom.radii, icos.point["coord"][:]) apos = apos * 180. / np.pi icos.value = zfun(apos[:, 1], apos[:, 0], grid=False) cell = icos.tria3["index"] zmsk = \ icos.value[cell[:, 0]] + \ icos.value[cell[:, 1]] + \ icos.value[cell[:, 2]] zmsk = zmsk / +3.0 icos.tria3 = icos.tria3[zmsk < +0.] print("Saving to ../cache/case_5a.vtk") jigsawpy.savevtk(os.path.join(dst_path, "case_5a.vtk"), icos) #------------------------------------ a very rough land mask apos = jigsawpy.R3toS2(geom.radii, cube.point["coord"][:]) apos = apos * 180. / np.pi cube.value = zfun(apos[:, 1], apos[:, 0], grid=False) cell = cube.quad4["index"] zmsk = \ cube.value[cell[:, 0]] + \ cube.value[cell[:, 1]] + \ cube.value[cell[:, 2]] + \ cube.value[cell[:, 3]] zmsk = zmsk / +4.0 cube.quad4 = cube.quad4[zmsk < +0.] print("Saving to ../cache/case_5b.vtk") jigsawpy.savevtk(os.path.join(dst_path, "case_5b.vtk"), cube) return
def case_1_(src_path, dst_path): # DEMO-1: generate a uniform resolution (150KM) global grid. opts = jigsawpy.jigsaw_jig_t() topo = jigsawpy.jigsaw_msh_t() geom = jigsawpy.jigsaw_msh_t() mesh = jigsawpy.jigsaw_msh_t() #------------------------------------ setup files for JIGSAW opts.geom_file = \ os.path.join(src_path, "eSPH.msh") opts.jcfg_file = \ os.path.join(dst_path, "eSPH.jig") opts.mesh_file = \ os.path.join(dst_path, "mesh.msh") #------------------------------------ define JIGSAW geometry geom.mshID = "ellipsoid-mesh" geom.radii = np.full( 3, 6.371E+003, dtype=geom.REALS_t) jigsawpy.savemsh(opts.geom_file, geom) #------------------------------------ make mesh using JIGSAW opts.hfun_scal = "absolute" opts.hfun_hmax = +150. # uniform at 150km opts.mesh_dims = +2 # 2-dim. simplexes opts.optm_qlim = +9.5E-01 # tighter opt. tol opts.optm_iter = +32 opts.optm_qtol = +1.0E-05 jigsawpy.cmd.tetris(opts, 3, mesh) scr2 = jigsawpy.triscr2( # "quality" metric mesh.point["coord"], mesh.tria3["index"]) #------------------------------------ save mesh for Paraview jigsawpy.loadmsh(os.path.join( src_path, "topo.msh"), topo) #------------------------------------ a very rough land mask apos = jigsawpy.R3toS2( geom.radii, mesh.point["coord"][:]) apos = apos * 180. / np.pi zfun = interpolate.RectBivariateSpline( topo.ygrid, topo.xgrid, topo.value) mesh.value = zfun( apos[:, 1], apos[:, 0], grid=False) cell = mesh.tria3["index"] zmsk = \ mesh.value[cell[:, 0]] + \ mesh.value[cell[:, 1]] + \ mesh.value[cell[:, 2]] zmsk = zmsk / +3.0 mesh.tria3 = mesh.tria3[zmsk < +0.] print("Saving to ../cache/case_1a.vtk") jigsawpy.savevtk(os.path.join( dst_path, "case_1a.vtk"), mesh) return
def case_3_(src_path, dst_path): opts = jigsawpy.jigsaw_jig_t() geom = jigsawpy.jigsaw_msh_t() mesh = jigsawpy.jigsaw_msh_t() #------------------------------------ setup files for JIGSAW opts.geom_file = \ os.path.join(src_path, "bunny.msh") opts.jcfg_file = \ os.path.join(dst_path, "bunny.jig") opts.mesh_file = \ os.path.join(dst_path, "bunny.msh") #------------------------------------ make mesh using JIGSAW jigsawpy.loadmsh( opts.geom_file, geom) print("Saving case_3a.vtk file.") jigsawpy.savevtk(os.path.join( dst_path, "case_3a.vtk"), geom) opts.mesh_kern = "delaunay" # DELAUNAY kernel opts.mesh_dims = +2 opts.optm_iter = +0 opts.hfun_hmax = 0.03 jigsawpy.cmd.jigsaw(opts, mesh) scr2 = jigsawpy.triscr2( # "quality" metric mesh.point["coord"], mesh.tria3["index"]) print("Saving case_3b.vtk file.") jigsawpy.savevtk(os.path.join( dst_path, "case_3b.vtk"), mesh) #------------------------------------ make mesh using JIGSAW opts.mesh_kern = "delfront" # DELFRONT kernel opts.mesh_dims = +2 opts.optm_iter = +0 opts.hfun_hmax = 0.03 jigsawpy.cmd.jigsaw(opts, mesh) scr2 = jigsawpy.triscr2( # "quality" metric mesh.point["coord"], mesh.tria3["index"]) print("Saving case_3c.vtk file.") jigsawpy.savevtk(os.path.join( dst_path, "case_3c.vtk"), mesh) return
def ex_3(): # DEMO-3: generate a grid based on the "HR" spacing pattern, # developed by the FESOM team at AWI. dst_path = \ os.path.abspath( os.path.dirname(__file__)) src_path = \ os.path.join(dst_path, "..", "files") dst_path = \ os.path.join(dst_path, "..", "cache") opts = jigsawpy.jigsaw_jig_t() topo = jigsawpy.jigsaw_msh_t() geom = jigsawpy.jigsaw_msh_t() hfun = jigsawpy.jigsaw_msh_t() mesh = jigsawpy.jigsaw_msh_t() #------------------------------------ setup files for JIGSAW opts.geom_file = \ os.path.join(src_path, "eSPH.msh") opts.jcfg_file = \ os.path.join(dst_path, "eSPH.jig") opts.mesh_file = \ os.path.join(dst_path, "mesh.msh") opts.hfun_file = \ os.path.join(dst_path, "spac.msh") #------------------------------------ define JIGSAW geometry geom.mshID = "ellipsoid-mesh" geom.radii = np.full( 3, 6.371E+003, dtype=geom.REALS_t) jigsawpy.savemsh(opts.geom_file, geom) #------------------------------------ define spacing pattern jigsawpy.loadmsh(os.path.join( src_path, "f_hr.msh"), hfun) hfun.value = +3. * hfun.value # for fast example jigsawpy.savemsh(opts.hfun_file, hfun) #------------------------------------ make mesh using JIGSAW opts.hfun_scal = "absolute" opts.hfun_hmax = float("inf") # null HFUN limits opts.hfun_hmin = float(+0.00) opts.mesh_dims = +2 # 2-dim. simplexes opts.optm_qlim = +9.5E-01 # tighter opt. tol opts.optm_iter = +32 opts.optm_qtol = +1.0E-05 jigsawpy.cmd.jigsaw(opts, mesh) #------------------------------------ save mesh for Paraview jigsawpy.loadmsh(os.path.join( src_path, "topo.msh"), topo) #------------------------------------ a very rough land mask apos = jigsawpy.R3toS2( geom.radii, mesh.point["coord"][:]) apos = apos * 180. / np.pi zfun = interpolate.RectBivariateSpline( topo.ygrid, topo.xgrid, topo.value) mesh.value = zfun( apos[:, 1], apos[:, 0], grid=False) cell = mesh.tria3["index"] zmsk = \ mesh.value[cell[:, 0]] + \ mesh.value[cell[:, 1]] + \ mesh.value[cell[:, 2]] zmsk = zmsk / +3.0 mesh.tria3 = mesh.tria3[zmsk < +0.] print("Saving to ../cache/case_3a.vtk") jigsawpy.savevtk(os.path.join( dst_path, "case_3a.vtk"), mesh) print("Saving to ../cache/case_3b.vtk") jigsawpy.savevtk(os.path.join( dst_path, "case_3b.vtk"), hfun) return
def case_2_(src_path, dst_path): # DEMO-2: generate a regionally-refined global grid with a # high-resolution 37.5km patch embedded in a uniform 150km # background grid. opts = jigsawpy.jigsaw_jig_t() topo = jigsawpy.jigsaw_msh_t() geom = jigsawpy.jigsaw_msh_t() hfun = jigsawpy.jigsaw_msh_t() mesh = jigsawpy.jigsaw_msh_t() #------------------------------------ setup files for JIGSAW opts.geom_file = \ os.path.join(dst_path, "geom.msh") opts.jcfg_file = \ os.path.join(dst_path, "opts.jig") opts.mesh_file = \ os.path.join(dst_path, "mesh.msh") opts.hfun_file = \ os.path.join(dst_path, "spac.msh") #------------------------------------ define JIGSAW geometry geom.mshID = "ellipsoid-mesh" geom.radii = np.full(3, 6.371E+003, dtype=geom.REALS_t) jigsawpy.savemsh(opts.geom_file, geom) #------------------------------------ define spacing pattern hfun.mshID = "ellipsoid-grid" hfun.radii = geom.radii hfun.xgrid = np.linspace(-1. * np.pi, +1. * np.pi, 360) hfun.ygrid = np.linspace(-.5 * np.pi, +.5 * np.pi, 180) xmat, ymat = \ np.meshgrid(hfun.xgrid, hfun.ygrid) hfun.value = +150. - 112.5 * np.exp(-(+1.5 * (xmat + 1.0)**2 + +1.5 * (ymat - 0.5)**2)**4) jigsawpy.savemsh(opts.hfun_file, hfun) #------------------------------------ make mesh using JIGSAW opts.hfun_scal = "absolute" opts.hfun_hmax = float("inf") # null HFUN limits opts.hfun_hmin = float(+0.00) opts.mesh_dims = +2 # 2-dim. simplexes opts.optm_qlim = +9.5E-01 # tighter opt. tol opts.optm_iter = +32 opts.optm_qtol = +1.0E-05 # opts.optm_kern = "cvt+dqdx" rbar = np.mean(geom.radii) # bisect heuristic hbar = np.mean(hfun.value) nlev = round(math.log2(rbar / math.sin(.4 * math.pi) / hbar)) ttic = time.time() jigsawpy.cmd.tetris(opts, nlev - 1, mesh) ttoc = time.time() print("CPUSEC =", (ttoc - ttic)) print("BISECT =", +nlev) cost = jigsawpy.triscr2( # quality metrics! mesh.point["coord"], mesh.tria3["index"]) print("TRISCR =", np.min(cost), np.mean(cost)) cost = jigsawpy.pwrscr2(mesh.point["coord"], mesh.power, mesh.tria3["index"]) print("PWRSCR =", np.min(cost), np.mean(cost)) tbad = jigsawpy.centre2(mesh.point["coord"], mesh.power, mesh.tria3["index"]) print("OBTUSE =", +np.count_nonzero(np.logical_not(tbad))) ndeg = jigsawpy.trideg2(mesh.point["coord"], mesh.tria3["index"]) print("TOPOL. =", +np.count_nonzero(ndeg == +6) / ndeg.size) #------------------------------------ save mesh for Paraview jigsawpy.loadmsh(os.path.join(src_path, "topo.msh"), topo) #------------------------------------ a very rough land mask apos = jigsawpy.R3toS2(geom.radii, mesh.point["coord"][:]) apos = apos * 180. / np.pi zfun = interpolate.RectBivariateSpline(topo.ygrid, topo.xgrid, topo.value) mesh.value = zfun(apos[:, 1], apos[:, 0], grid=False) cell = mesh.tria3["index"] zmsk = \ mesh.value[cell[:, 0]] + \ mesh.value[cell[:, 1]] + \ mesh.value[cell[:, 2]] zmsk = zmsk / +3.0 mesh.tria3 = mesh.tria3[zmsk < +0.] print("Saving to ../cache/case_2a.vtk") jigsawpy.savevtk(os.path.join(dst_path, "case_2a.vtk"), mesh) print("Saving to ../cache/case_2b.vtk") jigsawpy.savevtk(os.path.join(dst_path, "case_2b.vtk"), hfun) return
def open_msh(cls, path, crs=None): msh = jigsawpy.jigsaw_msh_t() jigsawpy.loadmsh(path, msh) return cls.from_msh_t(msh, crs)
def case_2_(src_path, dst_path): # DEMO-2: generate a regionally-refined global grid with a # high-resolution 37.5km patch embedded in a uniform 150km # background grid. opts = jigsawpy.jigsaw_jig_t() topo = jigsawpy.jigsaw_msh_t() geom = jigsawpy.jigsaw_msh_t() hfun = jigsawpy.jigsaw_msh_t() mesh = jigsawpy.jigsaw_msh_t() #------------------------------------ setup files for JIGSAW opts.geom_file = \ os.path.join(src_path, "eSPH.msh") opts.jcfg_file = \ os.path.join(dst_path, "eSPH.jig") opts.mesh_file = \ os.path.join(dst_path, "mesh.msh") opts.hfun_file = \ os.path.join(dst_path, "spac.msh") #------------------------------------ define JIGSAW geometry geom.mshID = "ellipsoid-mesh" geom.radii = np.full(3, 6.371E+003, dtype=geom.REALS_t) jigsawpy.savemsh(opts.geom_file, geom) #------------------------------------ define spacing pattern hfun.mshID = "ellipsoid-grid" hfun.radii = geom.radii hfun.xgrid = np.linspace(-1. * np.pi, +1. * np.pi, 360) hfun.ygrid = np.linspace(-.5 * np.pi, +.5 * np.pi, 180) xmat, ymat = \ np.meshgrid(hfun.xgrid, hfun.ygrid) hfun.value = +150. - 112.5 * np.exp(-(+1.5 * (xmat + 1.0)**2 + +1.5 * (ymat - 0.5)**2)**4) jigsawpy.savemsh(opts.hfun_file, hfun) #------------------------------------ make mesh using JIGSAW opts.hfun_scal = "absolute" opts.hfun_hmax = float("inf") # null HFUN limits opts.hfun_hmin = float(+0.00) opts.mesh_dims = +2 # 2-dim. simplexes opts.optm_qlim = +9.5E-01 # tighter opt. tol opts.optm_iter = +32 opts.optm_qtol = +1.0E-05 jigsawpy.cmd.tetris(opts, 3, mesh) scr2 = jigsawpy.triscr2( # "quality" metric mesh.point["coord"], mesh.tria3["index"]) #------------------------------------ save mesh for Paraview jigsawpy.loadmsh(os.path.join(src_path, "topo.msh"), topo) #------------------------------------ a very rough land mask apos = jigsawpy.R3toS2(geom.radii, mesh.point["coord"][:]) apos = apos * 180. / np.pi zfun = interpolate.RectBivariateSpline(topo.ygrid, topo.xgrid, topo.value) mesh.value = zfun(apos[:, 1], apos[:, 0], grid=False) cell = mesh.tria3["index"] zmsk = \ mesh.value[cell[:, 0]] + \ mesh.value[cell[:, 1]] + \ mesh.value[cell[:, 2]] zmsk = zmsk / +3.0 mesh.tria3 = mesh.tria3[zmsk < +0.] print("Saving to ../cache/case_2a.vtk") jigsawpy.savevtk(os.path.join(dst_path, "case_2a.vtk"), mesh) print("Saving to ../cache/case_2b.vtk") jigsawpy.savevtk(os.path.join(dst_path, "case_2b.vtk"), hfun) return
def case_6_(src_path, dst_path): # DEMO-6: generate a multi-part mesh of the (contiguous) USA # using state boundaries to partition the mesh. A local # stereographic projection is employed. The domain is meshed # using uniform resolution. opts = jigsawpy.jigsaw_jig_t() geom = jigsawpy.jigsaw_msh_t() mesh = jigsawpy.jigsaw_msh_t() proj = jigsawpy.jigsaw_prj_t() #------------------------------------ setup files for JIGSAW opts.geom_file = \ os.path.join(src_path, "proj.msh") opts.jcfg_file = \ os.path.join(dst_path, "us48.jig") opts.mesh_file = \ os.path.join(dst_path, "mesh.msh") #------------------------------------ define JIGSAW geometry jigsawpy.loadmsh(os.path.join(src_path, "us48.msh"), geom) xmin = np.min(geom.point["coord"][:, 0]) ymin = np.min(geom.point["coord"][:, 1]) xmax = np.max(geom.point["coord"][:, 0]) ymax = np.max(geom.point["coord"][:, 1]) geom.point["coord"][:, :] *= np.pi / 180. proj.prjID = 'stereographic' proj.radii = +6.371E+003 proj.xbase = \ +0.500 * (xmin + xmax) * np.pi / 180. proj.ybase = \ +0.500 * (ymin + ymax) * np.pi / 180. jigsawpy.project(geom, proj, "fwd") jigsawpy.savemsh(opts.geom_file, geom) #------------------------------------ make mesh using JIGSAW opts.hfun_hmax = .005 opts.mesh_dims = +2 # 2-dim. simplexes opts.mesh_eps1 = +1 / 6. jigsawpy.cmd.jigsaw(opts, mesh) #------------------------------------ save mesh for Paraview print("Saving to ../cache/case_6a.vtk") jigsawpy.savevtk(os.path.join(dst_path, "case_6a.vtk"), mesh) return
def case_5_(src_path, dst_path): opts = jigsawpy.jigsaw_jig_t() geom = jigsawpy.jigsaw_msh_t() mesh = jigsawpy.jigsaw_msh_t() hmat = jigsawpy.jigsaw_msh_t() #------------------------------------ setup files for JIGSAW opts.geom_file = \ os.path.join(src_path, "airfoil.msh") opts.jcfg_file = \ os.path.join(dst_path, "airfoil.jig") opts.mesh_file = \ os.path.join(dst_path, "airfoil.msh") opts.hfun_file = \ os.path.join(dst_path, "spacing.msh") #------------------------------------ compute HFUN over GEOM jigsawpy.loadmsh(opts.geom_file, geom) xgeo = geom.vert2["coord"][:, 0] ygeo = geom.vert2["coord"][:, 1] xpos = np.linspace(xgeo.min(), xgeo.max(), 80) ypos = np.linspace(ygeo.min(), ygeo.max(), 40) xmat, ymat = np.meshgrid(xpos, ypos) fun1 = \ +0.1 * (xmat - .40) ** 2 + \ +2.0 * (ymat - .55) ** 2 fun2 = \ +0.7 * (xmat - .75) ** 2 + \ +0.7 * (ymat - .45) ** 2 hfun = np.minimum(fun1, fun2) hmin = 0.01 hmax = 0.10 hfun = 0.4 * np.maximum(np.minimum(hfun, hmax), hmin) hmat.mshID = "euclidean-grid" hmat.ndims = +2 hmat.xgrid = np.array(xpos, dtype=hmat.REALS_t) hmat.ygrid = np.array(ypos, dtype=hmat.REALS_t) hmat.value = np.array(hfun, dtype=hmat.REALS_t) jigsawpy.savemsh(opts.hfun_file, hmat) #------------------------------------ make mesh using JIGSAW opts.hfun_scal = "absolute" opts.hfun_hmax = float("inf") # null HFUN limits opts.hfun_hmin = float(+0.00) opts.mesh_kern = "delfront" # DELFRONT kernel opts.mesh_dims = +2 opts.geom_feat = True opts.mesh_top1 = True jigsawpy.cmd.jigsaw(opts, mesh) print("Saving case_5a.vtk file.") jigsawpy.savevtk(os.path.join(dst_path, "case_5a.vtk"), hmat) print("Saving case_5b.vtk file.") jigsawpy.savevtk(os.path.join(dst_path, "case_5b.vtk"), mesh) return
def ex_8(): # DEMO-8: build regional meshes via stereographic projection dst_path = \ os.path.abspath( os.path.dirname(__file__)) src_path = \ os.path.join(dst_path, "..", "files") dst_path = \ os.path.join(dst_path, "..", "cache") opts = jigsawpy.jigsaw_jig_t() topo = jigsawpy.jigsaw_msh_t() geom = jigsawpy.jigsaw_msh_t() hfun = jigsawpy.jigsaw_msh_t() mesh = jigsawpy.jigsaw_msh_t() msph = jigsawpy.jigsaw_msh_t() proj = jigsawpy.jigsaw_prj_t() #------------------------------------ setup files for JIGSAW opts.geom_file = \ os.path.join(dst_path, "proj.msh") opts.jcfg_file = \ os.path.join(dst_path, "paci.jig") opts.mesh_file = \ os.path.join(dst_path, "mesh.msh") opts.hfun_file = \ os.path.join(dst_path, "spac.msh") #------------------------------------ define JIGSAW geometry jigsawpy.loadmsh(os.path.join( src_path, "paci.msh"), geom) jigsawpy.loadmsh(os.path.join( src_path, "topo.msh"), topo) xmin = np.min(geom.point["coord"][:, 0]) xmax = np.max(geom.point["coord"][:, 0]) xlon = np.linspace(xmin, xmax, 100) ymin = np.min(geom.point["coord"][:, 1]) ymax = np.max(geom.point["coord"][:, 1]) ylat = np.linspace(ymin, ymax, 100) #------------------------------------ define spacing pattern hfun.mshID = "ellipsoid-grid" hfun.radii = np.full( +3, 6.371E+003, dtype=jigsawpy.jigsaw_msh_t.REALS_t) hfun.xgrid = xlon * np.pi / 180. hfun.ygrid = ylat * np.pi / 180. hfun.value = np.full( (ylat.size, xlon.size), 200., dtype=jigsawpy.jigsaw_msh_t.REALS_t) #------------------------------------ do stereographic proj. geom.point["coord"][:, :] *= np.pi / 180. proj.prjID = 'stereographic' proj.radii = +6.371E+003 proj.xbase = \ +0.500 * (xmin + xmax) * np.pi / 180. proj.ybase = \ +0.500 * (ymin + ymax) * np.pi / 180. jigsawpy.project(geom, proj, "fwd") jigsawpy.project(hfun, proj, "fwd") jigsawpy.savemsh(opts.geom_file, geom) jigsawpy.savemsh(opts.hfun_file, hfun) #------------------------------------ make mesh using JIGSAW opts.hfun_scal = "absolute" opts.hfun_hmax = float("inf") # null HFUN limits opts.hfun_hmin = float(+0.00) opts.mesh_dims = +2 # 2-dim. simplexes opts.mesh_eps1 = +1.0E+00 # relax edge error opts.optm_iter = +32 opts.optm_qtol = +1.0E-05 jigsawpy.cmd.jigsaw(opts, mesh) #------------------------------------ do stereographic proj. msph = copy.deepcopy(mesh) jigsawpy.project(msph, proj, "inv") radii = np.full( +3, proj.radii, dtype=jigsawpy.jigsaw_msh_t.REALS_t) msph.vert3 = np.zeros( (msph.vert2.size), dtype=jigsawpy.jigsaw_msh_t.VERT3_t) msph.vert3["coord"] = \ jigsawpy.S2toR3( radii, msph.point["coord"]) msph.vert2 = None #------------------------------------ save mesh for Paraview print("Saving to ../cache/case_8a.vtk") jigsawpy.savevtk(os.path.join( dst_path, "case_8a.vtk"), mesh) print("Saving to ../cache/case_8b.vtk") jigsawpy.savevtk(os.path.join( dst_path, "case_8b.vtk"), hfun) print("Saving to ../cache/case_8c.vtk") jigsawpy.savevtk(os.path.join( dst_path, "case_8c.vtk"), msph) return