def init_geometry(self):
"""
Compile a grid with simple polygon cells from the
boundaries in bounds_shp
"""
g = unstructured_grid.UnstructuredGrid()
for geo in self.bounds['geom']:
pnts = np.array(geo)
A = pnts[:-1]
B = pnts[1:]
for a, b in zip(A, B):
na = g.add_or_find_node(x=a)
nb = g.add_or_find_node(x=b)
try:
j = g.add_edge(nodes=[na, nb])
except g.GridException:
pass
cycles = g.find_cycles(max_cycle_len=g.Nnodes())
polys = [geometry.Polygon(g.nodes['x'][cycle]) for cycle in cycles]
gc = unstructured_grid.UnstructuredGrid(
max_sides=max([len(cyc) for cyc in cycles]))
gc.copy_from_grid(g)
for cyc in cycles:
gc.add_cell(nodes=cyc)
self.g = gc
def set_grid(self):
g = ugrid.UnstructuredGrid(max_sides=4)
g.add_rectilinear([0, 0], [self.L, self.W], self.nx, self.ny)
g.orient_edges()
g.add_cell_field('cell_z_bed', self.z_bed(g.cells_center()))
super(TwoCell, self).set_grid(g)
def __init__(self,**kw):
super().__init__(**kw)
self.set_run_dir(self.run_dir,mode='pristine')
g=unstructured_grid.UnstructuredGrid(max_sides=4)
g.add_rectilinear([0,0],
[self.L,self.W],
nx=1+self.Lcells,ny=1+self.Wcells)
node_z_bed=-2*np.ones(g.Nnodes())
# node_z_bed=-2 + ((m_gate5.grid.nodes['x'][:,0] - 50) / 50).clip(0)
g.add_node_field('node_z_bed',node_z_bed)
super().__init__(grid=g,
run_start=np.datetime64("2010-01-01 00:00"),
run_stop =np.datetime64("2010-01-02 00:00"),
**kw)
self.set_bcs()
self.add_monitor_sections( [ dict(geom=geometry.LineString([[50,0],[50,20]]),
name='at_gate'),
dict(geom=geometry.LineString([[80,0],[80,20]]),
name='downstream') ] )
self.mdu['geometry','kmx']=self.n_layers
self.mdu['geometry','Layertype']=2 # 1: sigma, 2: z, 3: read pliz file
# Turn on salinity:
self.mdu['physics','salinity']=1
# Will come back to implement a 3D IC
self.mdu['physics','InitialSalinity']=15
self.mdu['physics','Idensform']=2
# Decrease imposed mixing to simplify tests
self.mdu['physics','Vicouv']=0.0 # Uniform horizontal eddy viscosity (m2/s)
self.mdu['physics','Dicouv']=0.0 # eddy diffusivity (m2/s)
self.mdu['physics','Vicoww']= 1e-6 # Uniform vertical eddy viscosity (m2/s)
self.mdu['physics','Dicoww']= 1e-6 # Uniform vertical eddy diffusivity (m2/s)
def make_2D_grid_Cartesian(self, L, nwide=3, show_grid=False):
"""
Setup unstructured grid for channel n cells wide
Grid is Cartesian with edge length = self.dx
"""
nlong = int(L / self.dx)
ncells = nlong * nwide
npoints = (nlong + 1) * (nwide + 1)
nedges = nwide * (nlong + 1) + (nwide + 1) * nlong
points = np.zeros((npoints, 2), np.float64)
cells = -1 * np.ones((ncells, 4), np.int32) # cell nodes
edges = -1 * np.ones((nedges, 2), np.int32) # edge nodes
ipt = 0
for i in range(nlong + 1):
x = self.dx * i
for j in range(nwide + 1):
y = self.dx * j
points[ipt, 0] = x
points[ipt, 1] = y
ipt += 1
icell = 0
for i in range(nlong):
for j in range(nwide):
i1 = icell + i
i2 = i1 + 1
i3 = icell + nwide + i + 1
i4 = i3 + 1
cells[icell, :] = [i3, i4, i2, i1]
icell += 1
iedge = 0
for i in range(nlong):
for j in range(nwide):
icell = i * nwide + j
i1 = icell + i
i2 = i1 + 1
i3 = icell + nwide + i + 1
i4 = i3 + 1
if j == 0:
edges[iedge, :] = [i1, i3] # bottom
iedge += 1
edges[iedge, :] = [i1, i2] # left
iedge += 1
edges[iedge, :] = [i2, i4] # top
iedge += 1
i = nlong - 1 # last column right edges
for j in range(nwide):
icell = i * nwide + j
i3 = icell + nwide + i + 1
i4 = i3 + 1
edges[iedge, :] = [i3, i4] # top
iedge += 1
self.grd = ugrid.UnstructuredGrid(edges=edges,
points=points,
cells=cells,
max_sides=4)
if show_grid:
self.grd.plot_edges()
plt.show()
return
def __init__(self, **kw):
self.set_run_dir(self.run_dir, mode='pristine')
g = unstructured_grid.UnstructuredGrid(max_sides=4)
# Sort of Pescadero Lagoon-ish
g.add_rectilinear([0, 0], [600, 100], nx=60, ny=5)
node_z_bed = -0.5 * np.ones(g.Nnodes())
g.add_node_field('node_z_bed', node_z_bed)
super().__init__(grid=g,
run_start=np.datetime64("2010-01-01 00:00"),
run_stop=np.datetime64("2010-01-03 00:00"),
**kw)
self.set_bcs()
self.config_layers()
self.mdu['output', 'MapFormat'] = 4 # ugrid
# Turn on salinity:
self.mdu['physics', 'salinity'] = 1
self.mdu['physics', 'temperature'] = 0
self.mdu['physics', 'InitialSalinity'] = 15
self.mdu['physics', 'Idensform'] = 2
self.add_monitor_points([
dict(geom=geometry.Point([10, 50]), name='flow_end'),
dict(geom=geometry.Point([10, 50]), name='stage_end')
])
def __init__(self, **kw):
super().__init__(run_start=np.datetime64("2010-01-01 00:00"),
run_stop=np.datetime64("2010-01-05 00:00"),
**kw)
self.set_run_dir(self.run_dir, mode='pristine')
g = unstructured_grid.UnstructuredGrid(max_sides=4)
# Sort of Pescadero Lagoon-ish
g.add_rectilinear([0, 0], [600, 100], nx=30, ny=5)
# Sloping bed to better understand uplift.
# node_z_bed=-0.5*np.ones(g.Nnodes())
# slopes from 0.5 at x=0 to -0.5 at x=600
node_z_bed = 0.5 - 1.0 * g.nodes['x'][:, 0] / 600.
g.add_node_field('node_z_bed', node_z_bed)
self.set_grid(g)
self.set_bcs()
self.mdu['geometry', 'BedLevType'] = 4
self.config_layers()
self.mdu['output', 'MapFormat'] = 4 # ugrid
# Turn on salinity:
self.mdu['physics', 'salinity'] = 0
self.mdu['physics', 'temperature'] = 0
self.mdu['physics', 'InitialSalinity'] = 15
self.mdu['physics', 'Idensform'] = 2
self.add_monitor_points([
dict(geom=geometry.Point([10, 50]), name='flow_end'),
dict(geom=geometry.Point([10, 50]), name='stage_end')
])
def thacker_grid():
thacker_2d_fn='thacker2d-%g.nc'%R
if not os.path.exists(thacker_2d_fn):
# Generate a radial grid
g=unstructured_grid.UnstructuredGrid(max_sides=4)
# Add guide rings
scale=R/20.0 # nominal edge length
nspoke0=4*8
g.add_quad_ring(0*scale,1*scale,nrows=2,nspokes=nspoke0//4,sides=3,stagger0=0.75)
g.add_quad_ring(1*scale,2*scale,nrows='stitch',nspokes=nspoke0//4,stagger0=0.25)
g.add_quad_ring(2*scale,3*scale,nrows=2,nspokes=nspoke0/2,sides=3,stagger0=0.5)
g.add_quad_ring(3*scale,4*scale,nrows='stitch',nspokes=nspoke0/2) # row of quads
g.add_quad_ring(4*scale,5*scale,nrows=2,nspokes=nspoke0) # row of quads
g.add_quad_ring(5*scale,6*scale,nrows='stitch',nspokes=nspoke0)
g.add_quad_ring(6*scale,10*scale,5,2*nspoke0)
g.add_quad_ring(10*scale,11*scale,'stitch',2*nspoke0)
g.add_quad_ring(11*scale,20*scale,11,4*nspoke0)
g.make_cells_from_edges()
g.edge_to_cells(recalc=True)
g.renumber()
g.write_ugrid(thacker_2d_fn,overwrite=True)
g=unstructured_grid.UnstructuredGrid.read_ugrid(thacker_2d_fn)
return g
def set_grid(self):
g = ugrid.UnstructuredGrid(max_sides=4)
g.add_rectilinear([-self.L / 2, 0], [self.L / 2, self.W], self.nx + 1,
self.ny)
g.orient_edges()
super(SubgridThacker1D, self).set_grid(g)
def test_sed_mpi():
model=base_model()
g=unstructured_grid.UnstructuredGrid(max_sides=4)
g.add_rectilinear([0,0],[1000,100],101,11)
g.add_cell_field('depth',-6*np.ones(g.Ncells()))
model.set_grid(g)
model.num_procs=4
model.config['dt']=3.
# slow down the settling velocities to get some advection mixed in
model.config['Ws01']= 0.0001 # constant settling velocity for fraction No.1 (m/s)
model.config['Ws02']= 0.0005 # constant settling velocity for fraction No.2
model.config['Ws03']=-0.0005 # constant settling velocity for fraction No.3
geom=np.array([ [1000,0],
[1000,100]])
Q_bc=sun_driver.FlowBC(name="Q_bc",
geom=geom,
Q=100.0)
model.add_bcs( [Q_bc,
sun_driver.ScalarBC(parent=Q_bc,scalar="S",value=2),
sun_driver.ScalarBC(parent=Q_bc,scalar="T",value=0)] )
point_bc=sun_driver.SourceSinkBC(name="bedPoint",
geom=np.array([500,20]),
Q=10)
model.add_bcs( [point_bc,
sun_driver.ScalarBC(parent=point_bc,scalar="S",value=3),
sun_driver.ScalarBC(parent=point_bc,scalar="T",value=3)] )
model.write()
# leave some dry layers at the surface
model.ic_ds.eta.values[:]=model.bcs[0].z
model.ic_ds.salt.values[:]=1.0
model.ic_ds.temp.values[:]=1.0
model.write_ic_ds()
for sed_idx in range(3):
name="sed%d"%(sed_idx+1)
model.bc_ds['boundary_'+name]=model.bc_ds['boundary_S'].copy()
model.bc_ds[name]=model.bc_ds['S'].copy()
model.bc_ds['point_'+name]=model.bc_ds['point_S'].copy()
model.bc_ds['boundary_'+name].values[:]=sed_idx*1.0
model.bc_ds[name].values[:]=0.0
model.bc_ds['point_'+name].values[:]=sed_idx*2.0
model.write_bc_ds()
model.partition()
model.sun_verbose_flag='-v'
model.run_simulation()
return model
def init():
# inserting a constraint
dt = unstructured_grid.UnstructuredGrid()
cdt = cdt_class(dt)
pnts = [[0, 0], [5, 0], [10, 0], [5, 5], [3, 0], [6, 2], [12, 4]]
for pnt in pnts:
dt.add_node(x=pnt)
return dt, cdt
def test_flip1_cgal():
plot = False
g = unstructured_grid.UnstructuredGrid()
cdt = shadow_cdt.ShadowCGALCDT(g)
pnts = [[0, 0], [8, 0], [10, 5], [5, 5], [3, 0]]
[g.add_node(x=pnt) for pnt in pnts]
def set_grid(self):
g = ugrid.UnstructuredGrid(max_sides=4)
g.add_rectilinear([0, 0], [self.L, self.W], self.nx, self.ny)
g.orient_edges()
g.add_node_field('node_z_bed', self.z_bed(g.nodes['x']))
g.add_cell_field('cell_z_bed', self.z_bed(g.cells_center()))
super(SwampyBump1D, self).set_grid(g)
def test_duplicate_edge():
ug=unstructured_grid.UnstructuredGrid(max_sides=4)
n1=ug.add_node(x=[0,0])
n2=ug.add_node(x=[1,0])
j1=ug.add_edge(nodes=[n1,n2])
with assert_raises(unstructured_grid.GridException) as cm:
j2=ug.add_edge(nodes=[n2,n1])
def base_grid():
g = ugrid.UnstructuredGrid(max_sides=4)
g.add_rectilinear([0, 0], [L, W], nx, ny)
# z=0 along lower edge, and 10 on the upper edge.
# node_depths=-g.nodes['x'][:,1]/10.
node_depths = dem(g.nodes['x'])
g.add_node_field('depth', node_depths)
return g
def import_ras_geometry(self,
hdf_fname,
twod_area_name,
max_cell_faces,
show_grid=False):
h = h5py.File(hdf_fname, 'r')
points_xy = h['Geometry/2D Flow Areas/' + twod_area_name +
'/FacePoints Coordinate']
npoints = len(points_xy)
points = np.zeros((npoints, 2), np.float64)
for n in range(npoints):
points[n, 0] = points_xy[n][0]
points[n, 1] = points_xy[n][1]
edge_nodes = h['Geometry/2D Flow Areas/' + twod_area_name +
'/Faces FacePoint Indexes']
nedges = len(edge_nodes)
edges = -1 * np.ones((nedges, 2), dtype=int)
for j in range(nedges):
edges[j][0] = edge_nodes[j][0]
edges[j][1] = edge_nodes[j][1]
cell_nodes = h['Geometry/2D Flow Areas/' + twod_area_name +
'/Cells FacePoint Indexes']
for i in range(len(cell_nodes)):
if cell_nodes[i][
2] < 0: # first ghost cell (which are sorted to end of list)
break
ncells = i # don't count ghost cells
cells = -1 * np.ones((ncells, max_cell_faces), dtype=int)
for i in range(ncells):
for k in range(max_cell_faces):
cells[i][k] = cell_nodes[i][k]
cell_center_xy = h['Geometry/2D Flow Areas/' + twod_area_name +
'/Cells Center Coordinate']
self.ras_xf = np.array([cell_center_xy[i][0] for i in range(ncells)])
self.ras_yf = np.array([cell_center_xy[i][1] for i in range(ncells)])
self.grd = ugrid.UnstructuredGrid(edges=edges,
points=points,
cells=cells,
max_sides=max_cell_faces)
if show_grid:
self.grd.plot_edges()
ax = plt.gca()
ax.plot(self.ras_xf, self.ras_yf, 'rs', ms=3, mfc='none')
plt.show()
return
def test_triangle_from_scratch():
ug=unstructured_grid.UnstructuredGrid(max_sides=4)
n1=ug.add_node(x=[0,0])
n2=ug.add_node(x=[1,0])
n3=ug.add_node(x=[1,1])
j1=ug.add_edge(nodes=[n1,n2])
j2=ug.add_edge(nodes=[n2,n3])
j3=ug.add_edge(nodes=[n3,n1])
c1=ug.toggle_cell_at_point([0.2,0.2])
def test_point_source_1d():
"""
Create a 1D water column, with a point source at the bed.
Verifies that all cells with valid thickness (dzz>0.001m)
have near unity salinity.
"""
g=unstructured_grid.UnstructuredGrid(max_sides=4)
g.add_rectilinear([0,0],[10,10],2,2)
g.add_cell_field('depth',-6*np.ones(g.Ncells()))
model=sun_driver.SuntansModel()
model.load_template('point_source_test.dat')
model.set_grid(g)
model.run_start=np.datetime64("2018-01-01 00:00")
model.run_stop =np.datetime64("2018-01-01 10:00")
source=sun_driver.SourceSinkBC(name='inflow',geom=np.array([5,5]),
z=-10,Q=1.0)
model.add_bcs(source)
model.add_bcs( [sun_driver.ScalarBC(parent=source,scalar="S",value=1),
sun_driver.ScalarBC(parent=source,scalar="T",value=1)] )
model.set_run_dir('rundata_point_1d', mode='pristine')
model.projection='EPSG:26910'
model.config['dt']=2.5
model.config['ntout']=1
model.config['Cmax']=30
model.config['Nkmax']=10
model.config['stairstep']=0
model.config['mergeArrays']=0
model.write()
model.ic_ds.eta.values[:]=-5.999
model.ic_ds.salt.values[:]=1.0
model.ic_ds.temp.values[:]=1.0
model.write_ic_ds()
model.partition()
model.sun_verbose_flag='-v'
model.run_simulation()
ds=xr.open_dataset(model.map_outputs()[0])
dzz=ds.dzz.values
dzz_thresh=0.001
salt=ds.salt.values
salt_errors=salt[dzz>=dzz_thresh] - 1.0
assert np.max( np.abs(salt_errors) )<0.001
def test_pickle():
ug=unstructured_grid.UnstructuredGrid(max_sides=4)
def cb(*a,**k):
pass
ug.subscribe_after('add_node',cb)
chk=ug.checkpoint()
n1=ug.add_node(x=[0,0])
n2=ug.add_node(x=[1,0])
j1=ug.add_edge(nodes=[n1,n2])
ug.write_pickle('blah.pkl')
ug2=unstructured_grid.UnstructuredGrid.from_pickle('blah.pkl')
def test_constraints_dim1_cgal():
g = unstructured_grid.UnstructuredGrid()
cdt = shadow_cdt.ShadowCGALCDT(g)
pnts = [[0, 0], [5, 0], [10, 0]]
nodes = [g.add_node(x=pnt) for pnt in pnts]
j0 = g.add_edge(nodes=[nodes[0], nodes[1]])
j1 = g.add_edge(nodes=[nodes[1], nodes[2]])
g.delete_edge(j0)
g.delete_edge(j1)
try:
g.add_edge(nodes=[nodes[0], nodes[2]])
assert False
except cdt.ConstraintCollinearNode:
pass #
def process_quad_patch(name, M=None):
center_idx = np.nonzero(centerlines['name'] == name)[0][0]
centerline = centerlines['geom'][center_idx]
if M is None:
M = centerlines['rows'][center_idx]
bound = bounds['geom'][bounds['name'] == name][0]
center = linestring_utils.resample_linearring(np.array(centerline),
scale,
closed_ring=0)
g = unstructured_grid.UnstructuredGrid(max_sides=6)
# Smooth the exterior
ext_points = np.array(bound.exterior)
ext_points = linestring_utils.resample_linearring(ext_points,
scale,
closed_ring=True)
from stompy import filters
ext_points[:, 0] = filters.lowpass_fir(ext_points[:, 0], 3)
ext_points[:, 1] = filters.lowpass_fir(ext_points[:, 1], 3)
smooth_bound = geometry.Polygon(ext_points)
L = smooth_bound.exterior.length
def profile(x, s, perp):
probe_left = geometry.LineString([x, x + L * perp])
probe_right = geometry.LineString([x, x - L * perp])
left_cross = smooth_bound.exterior.intersection(probe_left)
right_cross = smooth_bound.exterior.intersection(probe_right)
assert left_cross.type == 'Point', "Fix this for multiple intersections"
assert right_cross.type == 'Point', "Fix this for multiple intersections"
pnt_left = np.array(left_cross)
pnt_right = np.array(right_cross)
d_left = utils.dist(x, pnt_left)
d_right = utils.dist(x, pnt_right)
return np.interp(np.linspace(-1, 1, M), [-1, 0, 1],
[-d_right, 0, d_left])
g.add_rectilinear_on_line(center, profile)
g.renumber()
return g
def test_quad_from_scratch():
ug=unstructured_grid.UnstructuredGrid(max_sides=4)
n1=ug.add_node(x=[0,0])
n2=ug.add_node(x=[1,0])
n3=ug.add_node(x=[1,1])
n4=ug.add_node(x=[0,1])
j1=ug.add_edge(nodes=[n1,n2])
j2=ug.add_edge(nodes=[n2,n3])
j3=ug.add_edge(nodes=[n3,n4])
j4=ug.add_edge(nodes=[n4,n1])
c1=ug.toggle_cell_at_point([0.2,0.2])
# and remove it..
ug.toggle_cell_at_point([0.2,0.2])
def test_remove_constraint_cgal():
g = unstructured_grid.UnstructuredGrid()
cdt = shadow_cdt.ShadowCGALCDT(g)
# inserting a constraint
pnts = [[0, 0], [5, 0], [10, 0], [5, 5], [3, 0], [6, 2], [12, 4]]
nodes = [g.add_node(x=pnt) for pnt in pnts]
j0 = g.add_edge(nodes=[nodes[4], nodes[6]])
nodes.append(g.add_node(x=[7, 0.5]))
g.delete_edge(j0)
j1 = g.add_edge(nodes=[nodes[2], nodes[3]])
j2 = g.add_edge(nodes=[nodes[4], nodes[7]])
g.delete_edge(j1)
g.delete_edge(j2)
def test_fuzz1_cgal():
plot = False
# Fuzzing, regular
x = np.arange(5)
y = np.arange(5)
X, Y = np.meshgrid(x, y)
xys = np.array([X.ravel(), Y.ravel()]).T
if plot:
plt.figure(1).clf()
fig, ax = plt.subplots(num=1)
ax.plot(xys[:, 0], xys[:, 1], 'go', alpha=0.4)
ax.axis([-1, 5, -1, 5])
idxs = np.zeros(len(xys), 'i8') - 1
g = unstructured_grid.UnstructuredGrid()
cdt = shadow_cdt.ShadowCGALCDT(g)
# definitely slows down as the number of nodes gets larger.
# starting off with <1s per 100 operations, later more like 2s
for repeat in range(1):
print "Repeat: ", repeat
for step in range(1000):
if step % 200 == 0:
print " step: ", step
toggle = np.random.randint(len(idxs))
if idxs[toggle] < 0:
idxs[toggle] = g.add_node(x=xys[toggle])
else:
g.delete_node(idxs[toggle])
idxs[toggle] = -1
if plot:
del ax.lines[1:]
ax.texts = []
ax.collections = []
dt.plot_nodes(labeler=lambda n, nrec: str(n))
dt.plot_edges(alpha=0.5, lw=2)
dt.plot_cells(lw=7,
facecolor='#ddddff',
edgecolor='w',
zorder=-5)
plt.draw()
def run_node_insertion(cdt_class):
g = unstructured_grid.UnstructuredGrid()
cdt = cdt_class(g)
pnts = [[0, 0], [5, 0], [10, 0], [5, 5]]
nA = g.add_node(x=pnts[0]) # This tests insert into empty
g.add_node(x=pnts[1]) # adjacent_vertex
g.add_node(x=pnts[2]) # adjacent_vertex
g.add_node(x=pnts[3]) # adjacent_edge
g.add_node(x=[3, 0]) # colinear
g.add_node(x=[6, 2]) # into cell interior
nB = g.add_node(x=[12, 4]) # collinear cell interior
return g, cdt # helps with debugging
def base_model(force=True, num_procs=1, run_dir='run-dfm-test'):
if not force and dflow_model.DFlowModel.run_completed(run_dir):
model = dflow_model.DFlowModel.load(run_dir)
return model
g = unstructured_grid.UnstructuredGrid(max_sides=4)
ret = g.add_rectilinear([0, 0], [500, 500], 50, 50)
# sloping N-S from -3 at y=0 to +2 at y=500
g.add_node_field('depth', -3 + g.nodes['x'][:, 1] / 100)
model = dflow_model.DFlowModel()
model.load_template('dflow-template.mdu')
model.set_grid(g)
model.num_procs = num_procs
model.set_run_dir(run_dir, mode='pristine')
model.run_start = np.datetime64("2018-01-01 00:00")
model.run_stop = np.datetime64("2018-01-03 00:00")
dt = np.timedelta64(300, 's')
t = np.arange(model.run_start - 20 * dt, model.run_stop + 20 * dt, dt)
# 4h period
periodic_Q = 50 * np.sin(
(t - t[0]) / np.timedelta64(1, 's') * 2 * np.pi / (4 * 3600.))
Q = xr.DataArray(periodic_Q, dims=['time'], coords={'time': t})
inflow = dflow_model.FlowBC(name='inflow',
geom=np.array([[0, 0], [0, 500]]),
Q=Q)
model.add_bcs(inflow)
model.projection = 'EPSG:26910'
model.mdu['geometry', 'WaterLevIni'] = 0.0
model.mdu['output', 'WaqInterval'] = 1800
model.mdu['output', 'MapInterval'] = 1800
model.write()
if not model.is_completed():
model.partition()
model.run_model()
return model
def build_net(self):
"""
Build a pseudo grid that has edges for neighbors (like a dual, but including
a larger neighborhood.
"""
self.t_dual = self.g
# transit time network
self.t_net = unstructured_grid.UnstructuredGrid(extra_node_fields=[
('value', np.float64), ('dual_cell', np.int32),
('hydro_cell', np.int32)
],
extra_edge_fields=[
('Td', np.float64)
])
self.dual_to_net_node = {} # speed up the reverse lookup
cc = g.cells_center()
for c in np.nonzero(self.g.cell_clip_mask(self.clip))[0]:
n = self.t_net.add_node(x=cc[c],
value=np.nan,
dual_cell=c,
hydro_cell=c)
self.dual_to_net_node[c] = n
# Create the neighborhood connectivity
for n in range(self.t_net.Nnodes()):
c = self.t_net.nodes['dual_cell'][n]
# use nodes to get the neighborhood of cells
c_nodes = self.g.cell_to_nodes(c)
c_cells = []
for c_node in c_nodes:
c_cells += list(self.g.node_to_cells(c_node))
c_cells = set(c_cells)
for cnbr in c_cells:
if (cnbr == c) or (cnbr not in self.dual_to_net_node):
# if we clipped the original, this will have a few
# hits outside the clip, which we ignore.
continue
try:
self.t_net.add_edge(nodes=[n, self.dual_to_net_node[cnbr]])
except self.t_net.GridException:
pass # b/c the edge is already there - great.
def make_1D_grid_Cartesian_non_orthog(self, L, show_grid=False):
"""
Setup unstructured grid for channel 1 cell wide
Grid is Cartesian with edge length = self.dx
but then has random displacement of nodes to create non-orothgonality
"""
ncells = int(L / self.dx)
npoints = 2 * ncells + 2
nedges = 3 * ncells + 1
points = np.zeros((npoints, 2), np.float64)
# in future if only 3 edges, node4 will have value -1
cells = -1 * np.ones((ncells, 4), np.int32) # cell nodes
edges = -1 * np.ones((nedges, 2), np.int32) # edge nodes
max_displacement = 0.4
for i in range(ncells + 1): # set node x,y etc.
disp = 2 * max_displacement * random.random() - max_displacement
points[2 * i, 0] = self.dx * i + disp
disp = 2 * max_displacement * random.random() - max_displacement
points[2 * i, 1] = 0.0 + disp
disp = 2 * max_displacement * random.random() - max_displacement
points[2 * i + 1, 0] = self.dx * i + disp
disp = 2 * max_displacement * random.random() - max_displacement
points[2 * i + 1, 1] = self.dx + disp
if i < ncells:
cells[i, :] = [2 * (i + 1), 2 * (i + 1) + 1, 2 * i + 1, 2 * i]
# bottom of cell
edges[3 * i, :] = [2 * (i + 1), 2 * i]
# left of cell
edges[3 * i + 1, :] = [2 * i, 2 * i + 1]
# top of cell
edges[3 * i + 2, :] = [2 * i + 1, 2 * (i + 1) + 1]
# far right hand edge
edges[3 * ncells, :] = [2 * ncells, 2 * ncells + 1]
self.grd = ugrid.UnstructuredGrid(edges=edges,
points=points,
cells=cells,
max_sides=4)
if show_grid:
self.grd.plot_edges()
plt.show()
return
def make_sector_grid(self):
g=unstructured_grid.UnstructuredGrid(max_sides=4)
g.add_rectilinear([-R,-1], [R,1], nx=2*self.sector_grid_N-1, ny=2)
sector_angle=2*np.pi / 128
n=g.select_nodes_nearest([0,1]) # will delete this
n2=g.select_nodes_nearest([0,-1]) # and make triangles with this
nbrs=g.node_to_nodes(n)
g.delete_node_cascade(n)
for nbr in nbrs:
if nbr!=n2:
g.add_edge(nodes=[nbr,n2])
g.nodes['x'][:,1] = g.nodes['x'][:,1] * g.nodes['x'][:,0]*np.sin(sector_angle/2)
g.make_cells_from_edges()
g.renumber()
g.edge_to_cells(recalc=True)
g.cells_center(refresh=True)
return g
def make_1D_grid_equilat_tri(self, L, show_grid=False):
"""
Setup unstructured grid for channel of equilateral triangles
Edge length = self.dx
"""
n = int(L / self.dx)
ncells = 2 * n
npoints = 2 * n + 2
nedges = 4 * n + 1
points = np.zeros((npoints, 2), np.float64)
# in future if only 3 edges, node4 will have value -1
cells = -1 * np.ones((ncells, 3), np.int32) # cell nodes
edges = -1 * np.ones((nedges, 2), np.int32) # edge nodes
for i in range(n + 1): # set node x,y etc.
points[2 * i, 0] = self.dx * i
points[2 * i, 1] = 0.0
points[2 * i + 1, 0] = self.dx * i + 0.5 * self.dx
points[2 * i + 1, 1] = self.dx * np.sqrt(3.) / 2.
if i < n:
cells[2 * i, :] = [2 * (i + 1), 2 * i + 1, 2 * i]
cells[2 * i + 1, :] = [2 * (i + 1) + 1, 2 * i + 1, 2 * (i + 1)]
# bottom of cell
edges[4 * i, :] = [2 * (i + 1), 2 * i]
# left of cell
edges[4 * i + 1, :] = [2 * i, 2 * i + 1]
# top of cell
edges[4 * i + 2, :] = [2 * i + 1, 2 * (i + 1) + 1]
# diag of cell
edges[4 * i + 3, :] = [2 * (i + 1), 2 * i + 1]
# far right hand edge
edges[4 * n, :] = [npoints - 1, npoints - 2]
self.grd = ugrid.UnstructuredGrid(edges=edges,
points=points,
cells=cells,
max_sides=3)
if show_grid:
self.grd.plot_edges()
plt.show()
return
def test_undo_00():
ug=unstructured_grid.UnstructuredGrid()
n1=ug.add_node(x=[0,0])
n2=ug.add_node(x=[0,1])
n3=ug.add_node(x=[0.67,0.5])
e1=ug.add_edge(nodes=[n1,n2])
e2=ug.add_edge(nodes=[n1,n3])
cp=ug.checkpoint()
e3=ug.add_edge(nodes=[n2,n3])
c0=ug.add_cell(nodes=[n1,n2,n3])
assert ug.Ncells()==1
assert ug.Nedges()==3
assert ug.Nnodes()==3
ug.revert(cp)
assert ug.Ncells()==0
assert ug.Nedges()==2
assert ug.Nnodes()==3