def generate_channel1_domain(gpu=True):
#--------------------------------------------------------------------------
# Setup computational domain
#--------------------------------------------------------------------------
#points, vertices, boundary = anuga.rectangular_cross(10, 1,
# len1=10.0, len2=5.0) # Mesh
points, vertices, boundary = anuga.rectangular_cross(1,
4,
len1=0.1,
len2=0.1) # Mesh
if gpu:
domain = GPU_domain(points, vertices, boundary) # Create domain
for i in range(len(sys.argv)):
if sys.argv[i] == '-gpu':
domain.using_gpu = True
print " --> Enable GPU version"
elif sys.argv[i] == '-fs':
finaltime = float(sys.argv[i + 1])
print " --> Finaltime is reset as %f" % finaltime
elif sys.argv[i] == '-test':
domain.cotesting = True
print " --> Enable Cotesting"
elif sys.argv[i] == '-ustore':
domain.store = True
print " --> Disable storing"
else:
domain = anuga.Domain(points, vertices, boundary) # Create domain
domain.set_name('channel1') # Output name
#--------------------------------------------------------------------------
# Setup initial conditions
#--------------------------------------------------------------------------
def topography(x, y):
return -x / 10 # linear bed slope
domain.set_quantity('elevation', topography) # Use function for elevation
domain.set_quantity('friction', 0.01) # Constant friction
domain.set_quantity(
'stage', # Dry bed
expression='elevation')
#--------------------------------------------------------------------------
# Setup boundary conditions
#--------------------------------------------------------------------------
Bi = anuga.Dirichlet_boundary([0.4, 0, 0]) # Inflow
Br = anuga.Reflective_boundary(domain) # Solid reflective wall
domain.set_boundary({'left': Bi, 'right': Br, 'top': Br, 'bottom': Br})
return domain
def setUp(self):
def elevation_function(x, y):
return -x
""" Setup for all tests. """
mesh_file = tempfile.mktemp(".tsh")
points = [[0.0,0.0],[6.0,0.0],[6.0,6.0],[0.0,6.0]]
m = Mesh()
m.add_vertices(points)
m.auto_segment()
m.generate_mesh(verbose=False)
m.export_mesh_file(mesh_file)
# Create shallow water domain
domain = anuga.Domain(mesh_file)
os.remove(mesh_file)
domain.default_order = 2
# This test was made before tight_slope_limiters were introduced
# Since were are testing interpolation values this is OK
domain.tight_slope_limiters = 0
# Set some field values
domain.set_quantity('elevation', elevation_function)
domain.set_quantity('friction', 0.03)
domain.set_quantity('xmomentum', 3.0)
domain.set_quantity('ymomentum', 4.0)
######################
# Boundary conditions
B = anuga.Transmissive_boundary(domain)
domain.set_boundary( {'exterior': B})
# This call mangles the stage values.
domain.distribute_to_vertices_and_edges()
domain.set_quantity('stage', 1.0)
domain.set_name('datatest' + str(time.time()))
domain.smooth = True
domain.reduction = mean
self.domain = domain
def generate_domain():
#--------------------------------------------------------------------------
# Setup computational domain
#--------------------------------------------------------------------------
length = 10.
width = 5.
dx = dy = 1. # Resolution: Length of subdivisions on both axes
points, vertices, boundary = anuga.rectangular_cross(int(length / dx),
int(width / dy),
len1=length,
len2=width)
domain = anuga.Domain(points, vertices, boundary)
domain.set_name('channel2') # Output name
#--------------------------------------------------------------------------
# Setup initial conditions
#--------------------------------------------------------------------------
def topography(x, y):
return -x / 10 # linear bed slope
domain.set_quantity('elevation', topography) # Use function for elevation
domain.set_quantity('friction', 0.01) # Constant friction
domain.set_quantity('stage',
expression='elevation') # Dry initial condition
#--------------------------------------------------------------------------
# Setup boundary conditions
#--------------------------------------------------------------------------
Bi = anuga.Dirichlet_boundary([0.4, 0, 0]) # Inflow
Br = anuga.Reflective_boundary(domain) # Solid reflective wall
Bo = anuga.Dirichlet_boundary([-5, 0, 0]) # Outflow
domain.set_boundary({'left': Bi, 'right': Br, 'top': Br, 'bottom': Br})
import sys
if len(sys.argv) > 1 and "gpu" in sys.argv:
domain.using_gpu = True
else:
domain.using_gpu = False
print sys.argv, "gpu" in sys.argv
return domain
def test_estimate_time_mem(self):
points, vertices, boundary = anuga.rectangular_cross(10,
5,
len1=10.0,
len2=5.0) # Mesh
domain = anuga.Domain(points, vertices, boundary) # Create domain
tri_num = len(domain)
yieldstep = 360
finaltime = 3600
time, memory = estimate_time_mem(domain,
yieldstep,
finaltime,
use_test_constants=True,
log_results=False)
actual = system_constants[TEST_CON]['tri_a_T'] * tri_num ** 2 + \
system_constants[TEST_CON]['tri_b_T'] * tri_num + \
system_constants[TEST_CON]['tim_a_T'] * finaltime + \
(system_constants[TEST_CON]['fil_a_T'] * finaltime / yieldstep) + \
system_constants[TEST_CON]['cons_T']
self.assertEqual(time, actual)
'top': [7, 8, 9, 10, 11],
'outflow': [6]
},
#boundary_tags=None,
maximum_triangle_area=0.1,
breaklines=riverWalls.values(),
interior_regions=interior_regions,
filename=meshname,
use_cache=False,
verbose=True)
#------------------------------------------------------------------------------
# SETUP COMPUTATIONAL DOMAIN
#------------------------------------------------------------------------------
domain = anuga.Domain(meshname, use_cache=False, verbose=True)
domain.set_minimum_storable_height(0.0)
domain.riverwallData.create_riverwalls(riverWalls)
domain.set_name(outname)
print(domain.statistics())
#------------------------------------------------------------------------------
# APPLY MANNING'S ROUGHNESSES
#------------------------------------------------------------------------------
domain.set_quantity('friction', 0.025)
# Set a Initial Water Level over the Domain
domain.set_quantity('stage', 0)
extslope=0.04
buffslope=0.2
lakeslope=0.4
initbreachwidth=0.08
initbreachdepth=0.08
lakeregion=[[0,0],[0.28,0],[0.28,craterwidth],[0,craterwidth],[0,0]]
nextregion=[[0.28,0],[0.28,craterwidth],[4,craterwidth],[4,0],[0.28,0]]
endregion=[[4,craterwidth],[5,craterwidth],[5,0],[4,0],[4,craterwidth]]
meshname='lake.msh'
m = anuga.create_mesh_from_regions(domainpolygon, boundary_tags, maximum_triangle_area=low_res,interior_regions=interior_regions,filename=meshname, use_cache=False)
evolved_quantities = ['stage', 'xmomentum', 'ymomentum', 'concentration', 'sedvolx', 'sedvoly']
#evolved_quantities = ['stage', 'xmomentum', 'ymomentum', 'concentration']
domain = anuga.Domain(meshname, use_cache=False, evolved_quantities = evolved_quantities)
domain.g = anuga.g # make sure the domain inherits the package's gravity.
print 'Number of triangles = ', len(domain)
def find_nearest(array, value):
array = np.asarray(array)
idx = (np.abs(array - value)).argmin()
return idx
def topography(x, y):
maxx = np.max(x)
miny, maxy = np.min(y), np.max(y)
#sets slope of flume surface
z=(4.0-x)*(extslope)
# Domain
#-------------------------------------------------------------------------------
n = 75#50
m = 75#50
lenx = 8000.0
leny = 8000.0
origin = (-4000.0, -4000.0)
#===============================================================================
# Create Sequential Domain
#===============================================================================
if myid == 0:
points, elements, boundary = anuga.rectangular_cross(m, n, lenx, leny, origin)
domain = anuga.Domain(points, elements, boundary)
domain.set_name(output_file)
domain.set_datadir(output_dir)
domain.set_flow_algorithm(alg)
#-------------------------------------------------------------------------------
# Initial conditions
#-------------------------------------------------------------------------------
t = 0.0
D0 = 1000.
L = 2500.
R0 = 2000.
from anuga.coordinate_transforms.geo_reference import Geo_reference
import anuga.load_mesh.loadASCII as loadASCII
file_name = "output_skewed.msh"
myid = 0
verbose = True
# The parallel interface
#from anuga import distribute, myid, numprocs, finalize, barrier
#------------------------------------------------------------------------------
# Do the domain creation on processor 0
#------------------------------------------------------------------------------
print '##################### %i #########################' % myid
if anuga.myid == 0:
domain = anuga.Domain(mesh_filename=file_name)
else:
domain = None
#------------------------------------------------------------------------------
# Now produce parallel domain
#------------------------------------------------------------------------------
domain = anuga.distribute(domain, verbose=verbose)
if anuga.myid == 0:
# Print some stats about mesh and domain
print 'Number of triangles = ', len(domain)
print 'The extent is ', domain.get_extent()
domain.set_quantity('stage', -10)
def test_momentum_jet(self):
"""test_momentum_jet
Test that culvert_class can accept keyword use_momentum_jet
This does not yet imply that the values have been tested. FIXME
"""
length = 40.
width = 5.
dx = dy = 1 # Resolution: Length of subdivisions on both axes
points, vertices, boundary = rectangular_cross(int(length / dx),
int(width / dy),
len1=length,
len2=width)
domain = anuga.Domain(points, vertices, boundary)
domain.set_name('Test_culvert_shallow') # Output name
domain.set_default_order(2)
#----------------------------------------------------------------------
# Setup initial conditions
#----------------------------------------------------------------------
def topography(x, y):
"""Set up a weir
A culvert will connect either side
"""
# General Slope of Topography
z = -x / 1000
N = len(x)
for i in range(N):
# Sloping Embankment Across Channel
if 5.0 < x[i] < 10.1:
# Cut Out Segment for Culvert face
if 1.0 + (x[i] - 5.0) / 5.0 < y[i] < 4.0 - (x[i] -
5.0) / 5.0:
z[i] = z[i]
else:
z[i] += 0.5 * (x[i] - 5.0) # Sloping Segment U/S Face
if 10.0 < x[i] < 12.1:
z[i] += 2.5 # Flat Crest of Embankment
if 12.0 < x[i] < 14.5:
# Cut Out Segment for Culvert face
if 2.0 - (x[i] - 12.0) / 2.5 < y[i] < 3.0 + (x[i] -
12.0) / 2.5:
z[i] = z[i]
else:
z[i] += 2.5 - 1.0 * (x[i] - 12.0) # Sloping D/S Face
return z
domain.set_quantity('elevation', topography)
domain.set_quantity('friction', 0.01) # Constant friction
domain.set_quantity(
'stage', expression='elevation + 1.0') # Shallow initial condition
# Boyd culvert
culvert = Culvert_flow(
domain,
label='Culvert No. 1',
description='This culvert is a test unit 1.2m Wide by 0.75m High',
end_point0=[9.0, 2.5],
end_point1=[13.0, 2.5],
width=1.20,
height=0.75,
culvert_routine=boyd_generalised_culvert_model,
number_of_barrels=1,
use_momentum_jet=True,
update_interval=2,
verbose=False)
domain.forcing_terms.append(culvert)
# Call
culvert(domain)
#-----------------------------------------------------------------------
# Setup boundary conditions
#-----------------------------------------------------------------------
Br = anuga.Reflective_boundary(domain) # Solid reflective wall
domain.set_boundary({'left': Br, 'right': Br, 'top': Br, 'bottom': Br})
#-----------------------------------------------------------------------
# Evolve system through time
#-----------------------------------------------------------------------
ref_volume = domain.get_quantity('stage').get_integral()
for t in domain.evolve(yieldstep=0.1, finaltime=25):
new_volume = domain.get_quantity('stage').get_integral()
msg = (
'Total volume has changed: Is %.8f m^3 should have been %.8f m^3'
% (new_volume, ref_volume))
assert num.allclose(new_volume, ref_volume, rtol=1.0e-10), msg
def test_that_culvert_dry_bed_boyd_does_not_produce_flow(self):
"""test_that_culvert_in_dry_bed_boyd_does_not_produce_flow(self):
Test that culvert on a sloping dry bed doesn't produce flows
although there will be a 'pressure' head due to delta_w > 0
This one is using the 'Boyd' variant
"""
path = get_pathname_from_package('anuga.culvert_flows')
length = 40.
width = 5.
dx = dy = 1 # Resolution: Length of subdivisions on both axes
points, vertices, boundary = rectangular_cross(int(length / dx),
int(width / dy),
len1=length,
len2=width)
domain = anuga.Domain(points, vertices, boundary)
domain.set_name('Test_culvert_dry') # Output name
domain.set_default_order(2)
#----------------------------------------------------------------------
# Setup initial conditions
#----------------------------------------------------------------------
def topography(x, y):
"""Set up a weir
A culvert will connect either side
"""
# General Slope of Topography
z = -x / 1000
N = len(x)
for i in range(N):
# Sloping Embankment Across Channel
if 5.0 < x[i] < 10.1:
# Cut Out Segment for Culvert face
if 1.0 + (x[i] - 5.0) / 5.0 < y[i] < 4.0 - (x[i] -
5.0) / 5.0:
z[i] = z[i]
else:
z[i] += 0.5 * (x[i] - 5.0) # Sloping Segment U/S Face
if 10.0 < x[i] < 12.1:
z[i] += 2.5 # Flat Crest of Embankment
if 12.0 < x[i] < 14.5:
# Cut Out Segment for Culvert face
if 2.0 - (x[i] - 12.0) / 2.5 < y[i] < 3.0 + (x[i] -
12.0) / 2.5:
z[i] = z[i]
else:
z[i] += 2.5 - 1.0 * (x[i] - 12.0) # Sloping D/S Face
return z
domain.set_quantity('elevation', topography)
domain.set_quantity('friction', 0.01) # Constant friction
domain.set_quantity('stage',
expression='elevation') # Dry initial condition
filename = os.path.join(path, 'example_rating_curve.csv')
culvert = Culvert_flow(
domain,
label='Culvert No. 1',
description='This culvert is a test unit 1.2m Wide by 0.75m High',
end_point0=[9.0, 2.5],
end_point1=[13.0, 2.5],
width=1.20,
height=0.75,
culvert_routine=boyd_generalised_culvert_model,
number_of_barrels=1,
update_interval=2,
verbose=False)
domain.forcing_terms.append(culvert)
#-----------------------------------------------------------------------
# Setup boundary conditions
#-----------------------------------------------------------------------
# Inflow based on Flow Depth and Approaching Momentum
Br = anuga.Reflective_boundary(domain) # Solid reflective wall
domain.set_boundary({'left': Br, 'right': Br, 'top': Br, 'bottom': Br})
#-----------------------------------------------------------------------
# Evolve system through time
#-----------------------------------------------------------------------
ref_volume = domain.get_quantity('stage').get_integral()
for t in domain.evolve(yieldstep=1, finaltime=25):
new_volume = domain.get_quantity('stage').get_integral()
msg = 'Total volume has changed'
assert num.allclose(new_volume, ref_volume, rtol=1.0e-10), msg
pass
def run_simulation(parallel=False,
control_data=None,
test_points=None,
verbose=False):
success = True
##-----------------------------------------------------------------------
## Setup domain
##-----------------------------------------------------------------------
points, vertices, boundary = rectangular_cross(int(length / dx),
int(width / dy),
len1=length,
len2=width)
domain = anuga.Domain(points, vertices, boundary)
#rm *.swwdomain.set_name('output_parallel_inlet_operator') # Output name
domain.set_store(False)
domain.set_default_order(2)
##-----------------------------------------------------------------------
## Distribute domain
##-----------------------------------------------------------------------
if parallel:
domain = distribute(domain)
#domain.dump_triangulation("frac_op_domain.png")
##-----------------------------------------------------------------------
## Setup boundary conditions
##-----------------------------------------------------------------------
domain.set_quantity('elevation', topography)
domain.set_quantity('friction', 0.01) # Constant friction
domain.set_quantity('stage',
expression='elevation') # Dry initial condition
Bi = anuga.Dirichlet_boundary([5.0, 0.0, 0.0])
Br = anuga.Reflective_boundary(domain) # Solid reflective wall
domain.set_boundary({'left': Br, 'right': Br, 'top': Br, 'bottom': Br})
##-----------------------------------------------------------------------
## Determine triangle index coinciding with test points
##-----------------------------------------------------------------------
assert (test_points is not None)
assert (len(test_points) == samples)
tri_ids = []
for point in test_points:
try:
k = domain.get_triangle_containing_point(point)
if domain.tri_full_flag[k] == 1:
tri_ids.append(k)
else:
tri_ids.append(-1)
except:
tri_ids.append(-2)
if verbose: print 'P%d has points = %s' % (myid, tri_ids)
if not parallel: control_data = []
################ Define Fractional Operators ##########################
inlet0 = None
inlet1 = None
boyd_box0 = None
inlet0 = Inlet_operator(domain, line0, Q0, verbose=False, default=0.0)
inlet1 = Inlet_operator(domain, line1, Q1, verbose=False)
if inlet0 is not None and verbose: inlet0.print_statistics()
if inlet1 is not None and verbose: inlet1.print_statistics()
#if boyd_box0 is not None and verbose: boyd_box0.print_statistics()
##-----------------------------------------------------------------------
## Evolve system through time
##-----------------------------------------------------------------------
for t in domain.evolve(yieldstep=2.0, finaltime=40.0):
if myid == 0 and verbose:
domain.write_time()
#print domain.volumetric_balance_statistics()
stage = domain.get_quantity('stage')
#if boyd_box0 is not None and verbose : boyd_box0.print_timestepping_statistics()
#for i in range(samples):
# if tri_ids[i] >= 0:
# if verbose: print 'P%d tri %d, value = %s' %(myid, i, stage.centroid_values[tri_ids[i]])
sys.stdout.flush()
pass
domain.sww_merge(delete_old=True)
success = True
##-----------------------------------------------------------------------
## Assign/Test Control data
##-----------------------------------------------------------------------
if not parallel:
stage = domain.get_quantity('stage')
for i in range(samples):
assert (tri_ids[i] >= 0)
control_data.append(stage.centroid_values[tri_ids[i]])
if inlet0 is not None:
control_data.append(inlet0.inlet.get_average_stage())
control_data.append(inlet0.inlet.get_average_xmom())
control_data.append(inlet0.inlet.get_average_ymom())
control_data.append(inlet0.inlet.get_total_water_volume())
control_data.append(inlet0.inlet.get_average_depth())
if verbose: print 'P%d control_data = %s' % (myid, control_data)
else:
stage = domain.get_quantity('stage')
for i in range(samples):
if tri_ids[i] >= 0:
local_success = num.allclose(control_data[i],
stage.centroid_values[tri_ids[i]])
success = success and local_success
if verbose:
print 'P%d tri %d, control = %s, actual = %s, Success = %s' % (
myid, i, control_data[i],
stage.centroid_values[tri_ids[i]], local_success)
if inlet0 is not None:
inlet_master_proc = inlet0.inlet.get_master_proc()
average_stage = inlet0.inlet.get_global_average_stage()
average_xmom = inlet0.inlet.get_global_average_xmom()
average_ymom = inlet0.inlet.get_global_average_ymom()
average_volume = inlet0.inlet.get_global_total_water_volume()
average_depth = inlet0.inlet.get_global_average_depth()
if myid == inlet_master_proc:
if verbose:
print 'P%d average stage, control = %s, actual = %s' % (
myid, control_data[samples], average_stage)
print 'P%d average xmom, control = %s, actual = %s' % (
myid, control_data[samples + 1], average_xmom)
print 'P%d average ymom, control = %s, actual = %s' % (
myid, control_data[samples + 2], average_ymom)
print 'P%d average volume, control = %s, actual = %s' % (
myid, control_data[samples + 3], average_volume)
print 'P%d average depth, control = %s, actual = %s' % (
myid, control_data[samples + 4], average_depth)
assert (success)
return control_data
def runOkushiri(par, n):
# ------------------------------------------------------------------------------
# Setup computational domain
# ------------------------------------------------------------------------------
xleft = 0
xright = 5.448
ybottom = 0
ytop = 3.402
# rectangular cross mesh
points, vertices, boundary = anuga.rectangular_cross(
int(n), int(n), xright - xleft, ytop - ybottom, (xleft, ybottom))
newpoints = points.copy()
# make refinement in x direction
x = np.multiply([0., 0.1, 0.2, 0.335, 0.925, 1.], max(points[:, 0]))
y = [0., 3., 4.25, 4.7, 5.3, max(points[:, 0])]
f1 = interp1d(x, y, kind='quadratic')
newpoints[:, 0] = f1(points[:, 0])
# make refinement in y direction
x = np.multiply([0., .125, .3, .7, .9, 1.], max(points[:, 1]))
y = [0., 1.25, 1.75, 2.15, 2.65, max(points[:, 1])]
f2 = interp1d(x, y, kind='quadratic')
newpoints[:, 1] = f2(points[:, 1])
c = abs(newpoints[:, 0] - 5.0) + .5 * abs(newpoints[:, 1] - 1.95)
c = 0.125 * c
points[:, 0] = c * points[:, 0] + (1 - c) * newpoints[:, 0]
points[:, 1] = c * points[:, 1] + (1 - c) * newpoints[:, 1]
# create domain
domain = anuga.Domain(points, vertices, boundary)
# don't store .sww file
# domain.set_quantities_to_be_stored(None)
# ------------------------------------------------------------------------------
# Initial Conditions
# ------------------------------------------------------------------------------
domain.set_quantity('friction', 0.01) # 0.0
domain.set_quantity('stage', 0.0)
domain.set_quantity(
'elevation',
filename='/home/rehmemk/git/anugasgpp/Okushiri/data/bathymetry.pts',
alpha=0.02)
# ------------------------------------------------------------------------------
# Set simulation parameters
# ------------------------------------------------------------------------------
domain.set_name('output_okushiri') # Output name
domain.set_minimum_storable_height(0.001) # Don't store w < 0.001m
domain.set_flow_algorithm('DE0')
# ------------------------------------------------------------------------------
# Modify input wave
# ------------------------------------------------------------------------------
# rescale input parameter
try:
dummy = len(par)
except:
par = [par]
par = np.dot(2, par)
# load wave data
# shutil.copyfile('boundary_wave_header.txt', 'boundary_wave_input.txt')
data = np.loadtxt(
'/home/rehmemk/git/anugasgpp/Okushiri/data/boundary_wave_original.txt',
skiprows=1)
t = data[:, 0]
y = data[:, 1]
energy = np.trapz(y**2, t)
# define bumps [create input wave based on parameters]
def bump(c):
theta = c[0]
position = c[1]
weight = c[2]
ybump = weight * np.exp(-.5 * (t - position)**2 * theta**-2)
return ybump
nbump = len(par)
residual = y.copy()
c = np.zeros((nbump, 3))
for k in range(nbump):
maxid = np.argmax(np.abs(residual))
c0 = np.array([1.5, t[maxid], residual[maxid]])
def cost(c):
ybump = bump(c)
cost = np.sqrt(np.mean((ybump - residual)**2))
return cost
c[k, :] = fmin(cost, c0, disp=False)
residual -= bump(c[k, :])
# deform wave
ynew = residual.copy()
for k in range(nbump):
ynew += par[k] * bump(c[k, :])
energynew = np.trapz(ynew**2, t)
ynew = np.sqrt(energy / energynew) * ynew
# write data
data[:, 1] = ynew.copy()
import scipy
wave_function = scipy.interpolate.interp1d(t,
ynew,
kind='zero',
fill_value='extrapolate')
# MR: uncomment to plot input wave
# points = np.linspace(-10, 30, 10000)
# evals = np.zeros(len(points))
# for i in range(len(evals)):
# evals[i] = wave_function(points[i])
# plt.figure()
# # plt.plot(points, evals)
# # plt.plot(t, residual, 'r')
# for k in range(nbump):
# plt.plot(t, par[k]*bump(c[k, :]), label='bum {}'.format(k))
# plt.title('Okushiri Input Wave')
# plt.show()
# ------------------------------------------------------------------------------
# Setup boundary conditions
# ------------------------------------------------------------------------------
# Create boundary function from input wave [replaced by wave function]
# Create and assign boundary objects
Bts = anuga.Transmissive_momentum_set_stage_boundary(domain, wave_function)
Br = anuga.Reflective_boundary(domain)
domain.set_boundary({'left': Bts, 'right': Br, 'top': Br, 'bottom': Br})
# ------------------------------------------------------------------------------
# Evolve system through time
# ------------------------------------------------------------------------------
# area for gulleys
x1 = 4.85
x2 = 5.25
y1 = 2.05
y2 = 1.85
# gauges
gauges = [[4.521, 1.196], [4.521, 1.696], [4.521, 2.196]]
# index in gulley area
x = domain.centroid_coordinates[:, 0]
y = domain.centroid_coordinates[:, 1]
v = np.sqrt((x - x1) ** 2 + (y - y1) ** 2) + \
np.sqrt((x - x2) ** 2 + (y - y2) ** 2) < 0.5
dplotter = Domain_plotter(domain, min_depth=0.001)
k = 0
# original number of timesteps is 451
numTimeSteps = int(
np.loadtxt(
'/home/rehmemk/git/anugasgpp/Okushiri/data/numTimeSteps.txt'))
meanstage = np.nan * np.ones((1, numTimeSteps))
yieldstep = 0.05
finaltime = (numTimeSteps - 1) * yieldstep
meanlayer = 0
# Do the actual calculation
# for t in domain.evolve(yieldstep=yieldstep, finaltime=finaltime):
# # domain.write_time()
# # stage [=height of water]
# stage = domain.quantities['stage'].centroid_values[v]
# # averaging for smoothness
# meanstage[0, k] = np.mean(stage)
# # k is time
# k += 1
# # PLOTTING
# # Make movie of each timestep
# dplotter.save_depth_frame()
# anim = dplotter.make_depth_animation()
# anim.save('okushiri_%i.mp4' % n)
# meanlayer = meanstage - meanstage[0, 0]
# Plot the domain
plt.figure()
xya = np.loadtxt(
'/home/rehmemk/git/anugasgpp/Okushiri/plots/Benchmark_2_Bathymetry.xya',
skiprows=1,
delimiter=',')
X = xya[:, 0].reshape(393, 244)
Y = xya[:, 1].reshape(393, 244)
Z = xya[:, 2].reshape(393, 244)
# Remove the white part of the seismic
# Steves original code uses cmap('gist_earth')
from matplotlib.colors import LinearSegmentedColormap
interval = np.hstack([np.linspace(0.0, 0.3), np.linspace(0.5, 1.0)])
colors = plt.cm.seismic(interval)
my_cmap = LinearSegmentedColormap.from_list('name', colors)
# Multiply heights by 400 so that we getreal scale, not model scale
N1, N2 = np.shape(Z)
for n1 in range(N1):
for n2 in range(N2):
Z[n1, n2] *= 400
plt.contourf(X, Y, Z, 20, cmap=my_cmap)
# plt.title('Bathymetry')
cbar = plt.colorbar()
cbar.ax.tick_params(labelsize=colorbarfontsize)
# cbar.set_label('elevation', rotation=270)
import matplotlib.patches
from matplotlib.patches import Ellipse
# plt.plot(x1, y1, 'o')
# plt.plot(x2, y2, 'o')
ellipse = Ellipse(((x2 + x1) / 2., (y1 + y2) / 2.),
width=0.5,
height=0.2,
angle=-20,
edgecolor='k',
fill=False,
label='area of interest',
linewidth=4)
plt.gca().add_patch(ellipse)
# plt.plot(gauges[0][0], gauges[0][1], 'ok')
# plt.plot(gauges[1][0], gauges[1][1], 'ok')
# plt.plot(gauges[2][0], gauges[2][1], 'ok', markersize=8, label='gauge')
# plt.axis('off')
plt.legend(loc='upper left', fontsize=legendfontsize)
plt.gca().tick_params(axis='both', which='major', labelsize=tickfontsize)
plt.tight_layout()
# ---------------- hack to get ellpse shaped ellipse in legend------------
import matplotlib.patches as mpatches
from matplotlib.legend_handler import HandlerPatch
colors = ["k"]
texts = ["area of interest"]
class HandlerEllipse(HandlerPatch):
def create_artists(self, legend, orig_handle, xdescent, ydescent,
width, height, fontsize, trans):
center = 0.5 * width - 0.5 * xdescent, 0.5 * height - 0.5 * ydescent
p = mpatches.Ellipse(xy=center,
width=width + xdescent,
height=height + ydescent)
self.update_prop(p, orig_handle, legend)
p.set_transform(trans)
return [p]
c = [
mpatches.Circle((0.5, 0.5),
1,
facecolor='None',
edgecolor='k',
linewidth=3) for i in range(len(texts))
]
plt.legend(c,
texts,
bbox_to_anchor=(0., 1.),
loc='upper left',
ncol=1,
fontsize=16,
handler_map={mpatches.Circle: HandlerEllipse()})
# ----------------------------
plt.savefig('okushiri_domain.pdf')
# Plot the triangle mesh
plt.figure()
mittelblau = (0. / 255, 81. / 255, 158. / 255)
plt.triplot(dplotter.triang, linewidth=0.3, color=mittelblau)
plt.axis('off')
plt.tight_layout()
plt.savefig('okushiri_mesh_%i.pdf' % n)
# Plot the domain and the triangle mesh
plt.figure()
plt.tripcolor(dplotter.triang,
facecolors=dplotter.elev,
edgecolors='k',
cmap='gist_earth')
plt.colorbar()
plt.tight_layout()
plt.savefig('okushiri_domainandmesh_%i.pdf' % n)
# make video from sww file
# swwplotter = SWW_plotter('output_okushiri.sww', min_depth=0.001)
# lilo = len(swwplotter.time)
# for k in range(lilo):
# if k % 10 == 0:
# print ' '
# swwplotter.save_stage_frame(frame=k, vmin=-0.02, vmax=0.1)
# print '(', swwplotter.time[k], k, ')',
# print ' '
# swwanim = swwplotter.make_stage_animation()
# swwanim.save('okushiri_fromswwfile.mp4')
return meanlayer
#------------------------------------------------------------------------------
if myid == 0:
print '>>>>> DUNE EROSION TEST SCRIPT V2'
print '>>>>> Setting up Domain on processor 0...'
length = 36.
width = 5.
dx = dy = 0.1 # Resolution: Length of subdivisions on both axes
print '>>>>> Domain has L = %f, W = %f, dx=dy= %f' % (length, width, dx)
points, vertices, boundary = anuga.rectangular_cross(int(length / dx),
int(width / dy),
len1=length,
len2=width)
points = points + 1000.0
domain = anuga.Domain(points, vertices, boundary, geo_reference=geo)
domain.set_flow_algorithm('DE0')
domain.set_name('sanddune_testV2SR') # Output name
domain.set_store_vertices_uniquely(False)
domain.set_quantities_to_be_stored({
'elevation': 2,
'stage': 2,
'xmomentum': 2,
'ymomentum': 2
})
domain.set_quantity('elevation', topography) # elevation is a function
domain.set_quantity('friction', 0.01) # Constant friction
domain.set_quantity('stage',
expression='elevation') # Dry initial condition
def main():
try:
try:
usage = "usage: jezero.py -1*initialstage-in-m \n Note that -2260 flows but barely does anything. So range for jezero is ~2260 to 2200. \n"
parser = optparse.OptionParser(usage=usage)
(options, inargs) = parser.parse_args()
if not inargs: parser.error("need parameters")
jezerostage = -1.0 * float(inargs[0])
# Before doing anything else, set gravity to Mars
anuga.g = gravity
#domain parameters
poly_highres = anuga.read_polygon('JezeroData/PolyHi.csv')
poly_bound = anuga.read_polygon(
'JezeroData/PolyBoundBiggerPts.csv')
base_scale = 25600 #160 m #HIRES REGION
lowres = 10000 * base_scale # 10 km
boundary_tags = {'exterior': [0]}
# Define list of interior regions with associated resolutions
interior_regions = [[poly_highres, base_scale]]
meshname = 'JezeroData/jezero.msh'
mesh = anuga.create_mesh_from_regions(
poly_bound,
boundary_tags=boundary_tags,
maximum_triangle_area=lowres,
interior_regions=interior_regions,
verbose=True,
filename=meshname,
fail_if_polygons_outside=False)
evolved_quantities = [
'stage', 'xmomentum', 'ymomentum', 'concentration', 'sedvolx',
'sedvoly'
]
domain = anuga.Domain(meshname,
use_cache=False,
evolved_quantities=evolved_quantities)
domain.g = anuga.g # make sure the domain inherits the package's gravity.
domain.set_quantity("elevation",
filename="JezeroData/jbigger.pts",
use_cache=False,
verbose=True)
domain.smooth = True
name = "jezero" + str(jezerostage) + "_" + str(
grainD * 1000.0) + "mm"
domain.set_name(name)
# Choose between DE0 (less accurate), DE1 (more accurate, slower), DE2 (even more accurate, slower still)
domain.set_flow_algorithm('DE0')
domain.set_CFL(cfl=1.0)
domain.set_minimum_allowed_height(
0.01
) #raise the default minimum depth from 1 mm to 1 cm to speed the simulation (for computation)
domain.set_minimum_storable_height(
0.01
) #raise the default minimum depth from 1 mm to 1 cm to speed the simulation (for storage/visualization)
domain.set_maximum_allowed_speed(
1.0
) #maximum particle speed that is allowed in water shallower than minimum_allowed_height (back of the envelope suggests 1m/s should be below tau_crit)
np.seterr(invalid='ignore')
voltotal = np.sum(domain.quantities['elevation'].centroid_values *
domain.areas)
domain.set_quantity('concentration', 0.00) # Start with no esd
domain.set_quantity(
'friction', constantn
) # Constant Manning friction. Only used to initialize domain (calculated every time step).
domain.set_quantity('stage', -10000.0)
stagepolygon = anuga.read_polygon('JezeroData/stage.csv')
domain.set_quantity('stage', jezerostage, polygon=stagepolygon)
domain.set_quantities_to_be_stored({
'stage': 2,
'xmomentum': 2,
'ymomentum': 2,
'elevation': 2
})
np.seterr(invalid='warn')
Br = anuga.Reflective_boundary(domain)
domain.set_boundary({'exterior': Br})
# fixed_inflow = anuga.Inlet_operator(domain, stagepolygon, Q=1000.0)
operatezero = suspendedtransport_operator(domain)
operateone = bedloadtransport_operator(domain)
operatetwo = friction_operator(domain)
operatethree = AoR_operator(domain)
breachpoint = [[19080.340, 1097556.781]]
initialdomain = copy.deepcopy(domain)
initial = domain.get_quantity('elevation').get_values(
interpolation_points=breachpoint, location='centroids')
print str(initial)
ystep = 300.0
ftime = 86400.0 * 5.0
polyline = [[40000, 1090000], [15000, 1120000]]
count = 0
for t in domain.evolve(yieldstep=ystep, finaltime=ftime):
print domain.timestepping_statistics()
print 'xmom:' + str(
domain.get_quantity('xmomentum').get_values(
interpolation_points=breachpoint,
location='centroids'))
breacherosion = domain.get_quantity('elevation').get_values(
interpolation_points=breachpoint,
location='centroids') - initial
print 'erosion: ' + str(breacherosion)
volcurr = np.sum(
domain.quantities['elevation'].centroid_values *
domain.areas)
volsed = np.sum(
domain.quantities['concentration'].centroid_values *
domain.quantities['height'].centroid_values * domain.areas)
conservation = (volcurr + volsed - voltotal) / voltotal
print 'conservation: ' + '{:.8%}'.format(conservation)
count = count + 1
time, Q = anuga.get_flow_through_cross_section(
name + '.sww', polyline)
print Q
initname = "initial_" + name + ".asc"
finname = "final_" + name + ".asc"
fluxname = "flux_" + name + ".txt"
np.savetxt(fluxname, Q)
anuga.sww2dem(name + '.sww', initname, reduction=0)
anuga.sww2dem(name + '.sww', finname, reduction=(count - 1))
finalstats(domain, initialdomain)
np.save('XconcC.npy',
domain.quantities['concentration'].centroid_values)
np.save('XelevC.npy',
domain.quantities['elevation'].centroid_values)
np.save('XxmC.npy', domain.quantities['xmomentum'].centroid_values)
np.save('XymC.npy', domain.quantities['ymomentum'].centroid_values)
np.save('XstageC.npy', domain.quantities['stage'].centroid_values)
np.save('XconcV.npy',
domain.quantities['concentration'].vertex_values)
np.save('XelevV.npy', domain.quantities['elevation'].vertex_values)
np.save('XxmV.npy', domain.quantities['xmomentum'].vertex_values)
np.save('XymV.npy', domain.quantities['ymomentum'].vertex_values)
np.save('XstageV.npy', domain.quantities['stage'].vertex_values)
except optparse.OptionError, msg:
raise Usage(msg)
except Usage, err:
print >> sys.stderr, err.msg
# print >>sys.stderr, "for help use --help"
return 2
def run_culvert_flow_problem(depth):
"""Run flow with culvert given depth
"""
length = 40.
width = 5.
dx = dy = 1 # Resolution: Length of subdivisions on both axes
points, vertices, boundary = rectangular_cross(int(old_div(length, dx)),
int(old_div(width, dy)),
len1=length,
len2=width)
domain = anuga.Domain(points, vertices, boundary)
domain.set_name('Test_culvert_shallow') # Output name
domain.set_default_order(2)
#----------------------------------------------------------------------
# Setup initial conditions
#----------------------------------------------------------------------
def topography(x, y):
"""Set up a weir
A culvert will connect either side
"""
# General Slope of Topography
z = old_div(-x, 1000)
N = len(x)
for i in range(N):
# Sloping Embankment Across Channel
if 5.0 < x[i] < 10.1:
# Cut Out Segment for Culvert face
if 1.0 + (x[i] - 5.0) / 5.0 < y[i] < 4.0 - (x[i] - 5.0) / 5.0:
z[i] = z[i]
else:
z[i] += 0.5 * (x[i] - 5.0) # Sloping Segment U/S Face
if 10.0 < x[i] < 12.1:
z[i] += 2.5 # Flat Crest of Embankment
if 12.0 < x[i] < 14.5:
# Cut Out Segment for Culvert face
if 2.0 - (x[i] - 12.0) / 2.5 < y[i] < 3.0 + (x[i] -
12.0) / 2.5:
z[i] = z[i]
else:
z[i] += 2.5 - 1.0 * (x[i] - 12.0) # Sloping D/S Face
return z
domain.set_quantity('elevation', topography)
domain.set_quantity('friction', 0.01) # Constant friction
domain.set_quantity('stage', expression='elevation + %f' %
depth) # Shallow initial condition
# Boyd culvert
culvert = Culvert_flow(
domain,
label='Culvert No. 1',
description='This culvert is a test unit 1.2m Wide by 0.75m High',
end_point0=[9.0, 2.5],
end_point1=[13.0, 2.5],
width=1.20,
height=0.75,
culvert_routine=boyd_generalised_culvert_model,
number_of_barrels=1,
update_interval=2,
verbose=False)
domain.forcing_terms.append(culvert)
#-----------------------------------------------------------------------
# Setup boundary conditions
#-----------------------------------------------------------------------
# Inflow based on Flow Depth and Approaching Momentum
Br = anuga.Reflective_boundary(domain) # Solid reflective wall
domain.set_boundary({'left': Br, 'right': Br, 'top': Br, 'bottom': Br})
#-----------------------------------------------------------------------
# Evolve system through time
#-----------------------------------------------------------------------
#print 'depth', depth
ref_volume = domain.get_quantity('stage').get_integral()
for t in domain.evolve(yieldstep=0.1, finaltime=10):
new_volume = domain.get_quantity('stage').get_integral()
msg = (
'Total volume has changed: Is %.8f m^3 should have been %.8f m^3' %
(new_volume, ref_volume))
assert num.allclose(new_volume, ref_volume), msg
os.remove('Test_culvert_shallow.sww')
def test_that_culvert_runs_rating(self):
"""test_that_culvert_runs_rating
This test exercises the culvert and checks values outside rating curve
are dealt with
"""
path = get_pathname_from_package('anuga.culvert_flows')
path = os.path.join(path, 'tests', 'data')
length = 40.
width = 5.
dx = dy = 1 # Resolution: Length of subdivisions on both axes
points, vertices, boundary = rectangular_cross(int(length / dx),
int(width / dy),
len1=length,
len2=width)
domain = anuga.Domain(points, vertices, boundary)
domain.set_name('Test_culvert') # Output name
domain.set_default_order(2)
#----------------------------------------------------------------------
# Setup initial conditions
#----------------------------------------------------------------------
def topography(x, y):
"""Set up a weir
A culvert will connect either side
"""
# General Slope of Topography
z = -x / 1000
N = len(x)
for i in range(N):
# Sloping Embankment Across Channel
if 5.0 < x[i] < 10.1:
# Cut Out Segment for Culvert face
if 1.0 + (x[i] - 5.0) / 5.0 < y[i] < 4.0 - (x[i] -
5.0) / 5.0:
z[i] = z[i]
else:
z[i] += 0.5 * (x[i] - 5.0) # Sloping Segment U/S Face
if 10.0 < x[i] < 12.1:
z[i] += 2.5 # Flat Crest of Embankment
if 12.0 < x[i] < 14.5:
# Cut Out Segment for Culvert face
if 2.0 - (x[i] - 12.0) / 2.5 < y[i] < 3.0 + (x[i] -
12.0) / 2.5:
z[i] = z[i]
else:
z[i] += 2.5 - 1.0 * (x[i] - 12.0) # Sloping D/S Face
return z
domain.set_quantity('elevation', topography)
domain.set_quantity('friction', 0.01) # Constant friction
domain.set_quantity('stage',
expression='elevation') # Dry initial condition
filename = os.path.join(path, 'example_rating_curve.csv')
culvert = Culvert_flow(domain,
culvert_description_filename=filename,
end_point0=[9.0, 2.5],
end_point1=[13.0, 2.5],
width=1.00,
use_velocity_head=True,
verbose=False)
domain.forcing_terms.append(culvert)
#-----------------------------------------------------------------------
# Setup boundary conditions
#-----------------------------------------------------------------------
# Inflow based on Flow Depth and Approaching Momentum
Bi = anuga.Dirichlet_boundary([0.0, 0.0, 0.0])
Br = anuga.Reflective_boundary(domain) # Solid reflective wall
Bo = anuga.Dirichlet_boundary([-5, 0, 0]) # Outflow
# Upstream and downstream conditions that will exceed the rating curve
# I.e produce delta_h outside the range [0, 10] specified in the the
# file example_rating_curve.csv
Btus = anuga.Time_boundary(
domain, lambda t: [100 * num.sin(2 * pi * (t - 4) / 10), 0.0, 0.0])
Btds = anuga.Time_boundary(
domain,
lambda t: [-5 * (num.cos(2 * pi * (t - 4) / 20)), 0.0, 0.0])
domain.set_boundary({
'left': Btus,
'right': Btds,
'top': Br,
'bottom': Br
})
#-----------------------------------------------------------------------
# Evolve system through time
#-----------------------------------------------------------------------
min_delta_w = sys.maxint
max_delta_w = -min_delta_w
for t in domain.evolve(yieldstep=1, finaltime=25):
delta_w = culvert.inlet.stage - culvert.outlet.stage
if delta_w > max_delta_w: max_delta_w = delta_w
if delta_w < min_delta_w: min_delta_w = delta_w
pass
# Check that extreme values in rating curve have been exceeded
# so that we know that condition has been exercised
assert min_delta_w < 0
assert max_delta_w > 10
os.remove('Test_culvert.sww')
def OBSOLETE_XXXtest_that_culvert_rating_limits_flow_in_shallow_inlet_condition(
self):
"""test_that_culvert_rating_limits_flow_in_shallow_inlet_condition
Test that culvert on a sloping dry bed limits flows when very little water
is present at inlet
This one is using the rating curve variant
"""
path = get_pathname_from_package('anuga.culvert_flows')
length = 40.
width = 5.
dx = dy = 1 # Resolution: Length of subdivisions on both axes
points, vertices, boundary = rectangular_cross(int(length / dx),
int(width / dy),
len1=length,
len2=width)
domain = anuga.Domain(points, vertices, boundary)
domain.set_name('Test_culvert_shallow') # Output name
domain.set_default_order(2)
#----------------------------------------------------------------------
# Setup initial conditions
#----------------------------------------------------------------------
def topography(x, y):
"""Set up a weir
A culvert will connect either side
"""
# General Slope of Topography
z = -x / 1000
N = len(x)
for i in range(N):
# Sloping Embankment Across Channel
if 5.0 < x[i] < 10.1:
# Cut Out Segment for Culvert face
if 1.0 + (x[i] - 5.0) / 5.0 < y[i] < 4.0 - (x[i] -
5.0) / 5.0:
z[i] = z[i]
else:
z[i] += 0.5 * (x[i] - 5.0) # Sloping Segment U/S Face
if 10.0 < x[i] < 12.1:
z[i] += 2.5 # Flat Crest of Embankment
if 12.0 < x[i] < 14.5:
# Cut Out Segment for Culvert face
if 2.0 - (x[i] - 12.0) / 2.5 < y[i] < 3.0 + (x[i] -
12.0) / 2.5:
z[i] = z[i]
else:
z[i] += 2.5 - 1.0 * (x[i] - 12.0) # Sloping D/S Face
return z
domain.set_quantity('elevation', topography)
domain.set_quantity('friction', 0.01) # Constant friction
domain.set_quantity(
'stage', expression='elevation + 0.1') # Shallow initial condition
# Boyd culvert
culvert = Culvert_flow(
domain,
label='Culvert No. 1',
description='This culvert is a test unit 1.2m Wide by 0.75m High',
end_point0=[9.0, 2.5],
end_point1=[13.0, 2.5],
width=1.20,
height=0.75,
culvert_routine=boyd_generalised_culvert_model,
number_of_barrels=1,
update_interval=2,
verbose=False)
# Rating curve
#filename = os.path.join(path, 'example_rating_curve.csv')
#culvert = Culvert_flow(domain,
# culvert_description_filename=filename,
# end_point0=[9.0, 2.5],
# end_point1=[13.0, 2.5],
# trigger_depth=0.01,
# verbose=False)
domain.forcing_terms.append(culvert)
#-----------------------------------------------------------------------
# Setup boundary conditions
#-----------------------------------------------------------------------
# Inflow based on Flow Depth and Approaching Momentum
Br = anuga.Reflective_boundary(domain) # Solid reflective wall
domain.set_boundary({'left': Br, 'right': Br, 'top': Br, 'bottom': Br})
#-----------------------------------------------------------------------
# Evolve system through time
#-----------------------------------------------------------------------
print 'depth', 0.1
ref_volume = domain.get_quantity('stage').get_integral()
for t in domain.evolve(yieldstep=0.1, finaltime=25):
new_volume = domain.get_quantity('stage').get_integral()
msg = (
'Total volume has changed: Is %.8f m^3 should have been %.8f m^3'
% (new_volume, ref_volume))
assert num.allclose(new_volume, ref_volume, rtol=1.0e-10), msg
return
# Now try this again for a depth of 10 cm and for a range of other depths
for depth in [0.1, 0.2, 0.5, 1.0]:
print 'depth', depth
domain.set_time(0.0)
domain.set_quantity('elevation', topography)
domain.set_quantity('friction', 0.01) # Constant friction
domain.set_quantity('stage', expression='elevation + %f' % depth)
ref_volume = domain.get_quantity('stage').get_integral()
for t in domain.evolve(yieldstep=0.1, finaltime=25):
new_volume = domain.get_quantity('stage').get_integral()
msg = 'Total volume has changed: Is %.8f m^3 should have been %.8f m^3'\
% (new_volume, ref_volume)
assert num.allclose(new_volume, ref_volume, rtol=1.0e-10), msg
def generate_channel3_domain(gpu=True):
#-----------------------------------------------------------------------
# Setup computational domain
#-----------------------------------------------------------------------
length = 40.
width = 5.
dx = dy = .1 # Resolution: Length of subdivisions on both axes
points, vertices, boundary = anuga.rectangular_cross(int(length / dx),
int(width / dy),
len1=length,
len2=width)
if gpu:
domain = GPU_domain(points, vertices, boundary)
if '-gpu' in sys.argv:
domain.using_gpu = True
print " --> Enable GPU version"
for i in range(len(sys.argv)):
if sys.argv[i] == '-fs':
global finaltime
finaltime = float(sys.argv[i + 1])
print " --> Finaltime is reset as %f" % finaltime
else:
domain = anuga.Domain(points, vertices, boundary)
domain.set_name('channel3') # Output name
#print domain.statistics()
#-----------------------------------------------------------------------
# Setup initial conditions
#-----------------------------------------------------------------------
def topography(x, y):
"""Complex topography defined by a function of vectors x and y."""
z = -x / 10
N = len(x)
for i in range(N):
# Step
if 10 < x[i] < 12:
z[i] += 0.4 - 0.05 * y[i]
# Constriction
if 27 < x[i] < 29 and y[i] > 3:
z[i] += 2
# Pole
if (x[i] - 34)**2 + (y[i] - 2)**2 < 0.4**2:
z[i] += 2
return z
domain.set_quantity('elevation', topography) # elevation is a function
domain.set_quantity('friction', 0.01) # Constant friction
domain.set_quantity('stage',
expression='elevation') # Dry initial condition
#-----------------------------------------------------------------------
# Setup boundary conditions
#-----------------------------------------------------------------------
Bi = anuga.Dirichlet_boundary([0.4, 0, 0]) # Inflow
Br = anuga.Reflective_boundary(domain) # Solid reflective wall
Bo = anuga.Dirichlet_boundary([-5, 0, 0]) # Outflow
domain.set_boundary({'left': Bi, 'right': Bo, 'top': Br, 'bottom': Br})
return domain
def test_predicted_boyd_flow(self):
"""test_predicted_boyd_flow
Test that flows predicted by the boyd method are consistent with what what
is calculated in engineering codes.
The data was supplied by Petar Milevski
"""
# FIXME(Ole) this is nowhere near finished
path = get_pathname_from_package('anuga.culvert_flows')
length = 12.
width = 5.
dx = dy = 0.5 # Resolution: Length of subdivisions on both axes
points, vertices, boundary = rectangular_cross(int(length / dx),
int(width / dy),
len1=length,
len2=width)
domain = anuga.Domain(points, vertices, boundary)
domain.set_name('test_culvert') # Output name
domain.set_default_order(2)
#----------------------------------------------------------------------
# Setup initial conditions
#----------------------------------------------------------------------
def topography(x, y):
# General Slope of Topography
z = -x / 10
return z
domain.set_quantity('elevation', topography)
domain.set_quantity('friction', 0.01) # Constant friction
domain.set_quantity('stage', expression='elevation')
Q0 = domain.get_quantity('stage')
Q1 = Quantity(domain)
# Add depths to stage
head_water_depth = 0.169
tail_water_depth = 0.089
inlet_poly = [[0, 0], [6, 0], [6, 5], [0, 5]]
outlet_poly = [[6, 0], [12, 0], [12, 5], [6, 5]]
Q1.set_values(
Polygon_function([(inlet_poly, head_water_depth),
(outlet_poly, tail_water_depth)]))
domain.set_quantity('stage', Q0 + Q1)
culvert = Culvert_flow(domain,
label='Test culvert',
description='4 m test culvert',
end_point0=[4.0, 2.5],
end_point1=[8.0, 2.5],
width=1.20,
height=0.75,
culvert_routine=boyd_generalised_culvert_model,
number_of_barrels=1,
verbose=False)
domain.forcing_terms.append(culvert)
# Call
culvert(domain)
def main():
try:
try:
usage = "usage: lakeerode.py LakeRadius-in-meters [-m depthmultiplier] [-i initialbreachdepth]\n"
parser = optparse.OptionParser(usage=usage)
parser.add_option("-m",
dest="dm",
help="Depth Multiplier for lake")
parser.add_option("-i",
dest="initbreachdepth",
help="Initial breach depth for flood")
(options, inargs) = parser.parse_args()
if not inargs: parser.error("need parameters")
lakeradius = float(inargs[0])
dm = 1.0 #default
if (options.dm): dm = float(options.dm)
h = dm * 21.39 * math.pow(
(lakeradius / 1000), 0.62
) #max depth in meters to get V=0.01A**1.31 from Fassett and Head 2008
initbreachdepth = 15.0 #default
lakebelowconfining = 5
if (options.initbreachdepth):
initbreachdepth = float(options.initbreachdepth)
initbreachdepth = initbreachdepth + lakebelowconfining #set this to be a real initial head, not dependent on lakebelowconfining
extslope = -0.015
extslopeint = 0.015
#anuga critical parameter
anuga.g = gravity
#domain parameters
domainpolygon = [[0, 0], [0 * lakeradius, 2 * lakeradius],
[2 * lakeradius, 2 * lakeradius],
[2 * lakeradius, 1.2 * lakeradius],
[10 * lakeradius, 1.2 * lakeradius],
[10 * lakeradius, 0.8 * lakeradius],
[2 * lakeradius, 0.8 * lakeradius],
[2 * lakeradius, 0], [0, 0]]
outletregion = [[1.9 * lakeradius, 0.8 * lakeradius],
[1.9 * lakeradius, 1.2 * lakeradius],
[4.5 * lakeradius, 1.2 * lakeradius],
[4.5 * lakeradius, 0.8 * lakeradius]]
boundary_tags = {'exterior': [0]}
high_resolution = (lakeradius / 100)**2
base_resolution = high_resolution * 80.0
initbreachwidth = lakeradius / 50.0
interior_regions = [[outletregion, high_resolution]]
meshname = 'lake.msh'
m = anuga.create_mesh_from_regions(
domainpolygon,
boundary_tags,
maximum_triangle_area=base_resolution,
interior_regions=interior_regions,
filename=meshname,
use_cache=False)
evolved_quantities = [
'stage', 'xmomentum', 'ymomentum', 'concentration', 'sedvolx',
'sedvoly'
]
#evolved_quantities = ['stage', 'xmomentum', 'ymomentum', 'concentration']
domain = anuga.Domain(meshname,
use_cache=False,
evolved_quantities=evolved_quantities)
domain.g = anuga.g # make sure the domain inherits the package's gravity.
print 'Number of triangles = ', len(domain)
def find_nearest(array, value):
array = np.asarray(array)
idx = (np.abs(array - value)).argmin()
return idx
def topography(x, y):
xc = x - lakeradius
yc = y - lakeradius
#sets up lake
ellipsoid = -(h**2 * (1 -
((xc**2 + yc**2) / lakeradius**2)))**0.5
z = np.where(ellipsoid < 0, ellipsoid, 0.0)
#sets up exterior slope
z = np.where(
np.logical_and(x > lakeradius * 2, x <= lakeradius * 4),
(x - lakeradius * 2) * extslope +
abs(y - lakeradius) * extslopeint, z)
#setup flatlying area
z = np.where(x > lakeradius * 4, (lakeradius * 2) * extslope +
abs(y - lakeradius) * extslopeint, z)
# add gaussian noise, with zero mean and 0.1 m standard deviation.
#z=z+np.random.normal(0,0.1,z.shape)
# set up breach as a failure at the midpoint in a region
#mask1 = (x>=(lakeradius*2+(initbreachdepth/extslope)))
mask1 = (x >= lakeradius)
#mask2 = (x<=(lakeradius*2-(initbreachdepth/extslope)))
mask3 = (y >= ((lakeradius - (initbreachwidth / 2.0))))
mask4 = (y <= ((lakeradius + (initbreachwidth / 2.0))))
mask5 = (z > -initbreachdepth)
#mask=mask1 & mask2 & mask3 & mask4 & mask5
mask = mask1 & mask3 & mask4 & mask5
z[mask] = -initbreachdepth
return z
def initialstage(x, y):
clow = domain.get_quantity('elevation').get_values(
interpolation_points=[[2 * lakeradius, lakeradius]])
istage = clow + initbreachdepth - lakebelowconfining
#outsidelake. Force depth=0 (istage=topo) across rim.
#istage=np.where(x>lakeradius*2,topography(x,y),istage)
istage = np.where(x > lakeradius * 2, -10000, istage)
return istage
name = "Marslake" + str(lakeradius) + "_" + str(
grainD * 1000) + "mm"
domain.set_name(name)
# Choose between DE0 (less accurate), DE1 (more accurate, slower), DE2 (even more accurate, slower still)
domain.set_flow_algorithm('DE0')
domain.set_CFL(cfl=1)
domain.set_minimum_allowed_height(
0.01
) #raise the default minimum depth from 1 mm to 1 cm to speed the simulation (for computation)
domain.set_minimum_storable_height(
0.01
) #raise the default minimum depth from 1 mm to 1 cm to speed the simulation (for storage/visualization)
domain.set_maximum_allowed_speed(
1
) #maximum particle speed that is allowed in water shallower than minimum_allowed_height (back of the envelope suggests 1m/s should be below tau_crit)
np.seterr(invalid='ignore')
domain.set_quantity(
'elevation', topography,
location='centroids') # elevation is a function
voltotal = np.sum(domain.quantities['elevation'].centroid_values *
domain.areas)
domain.set_quantity('concentration', 0.00) # Start with no esd
domain.set_quantity(
'friction', 0.0545
) # Constant Manning friction. Only used to initialize domain (calculated every time step).
domain.set_quantity('stage', initialstage, location='centroids')
domain.set_quantities_to_be_stored({
'stage': 2,
'xmomentum': 2,
'ymomentum': 2,
'elevation': 2
})
np.seterr(invalid='warn')
# Setup boundary conditions
Br = anuga.Reflective_boundary(domain)
domain.set_boundary({'exterior': Br})
operatezero = suspendedtransport_operator(domain)
operateone = bedloadtransport_operator(domain)
operatetwo = friction_operator(domain)
operatethree = AoR_operator(domain)
initial = domain.get_quantity('elevation').get_values(
interpolation_points=[[2 * lakeradius, lakeradius]],
location='centroids')
initialdomain = copy.deepcopy(domain)
ystep = 300
ftime = 86400 * 10
count = 0
volthresh = 1000
for t in domain.evolve(yieldstep=ystep, finaltime=ftime):
print domain.timestepping_statistics()
print 'xmom:' + str(
domain.get_quantity('xmomentum').get_values(
interpolation_points=[[2 * lakeradius, lakeradius]],
location='centroids'))
volcurr = np.sum(
domain.quantities['elevation'].centroid_values *
domain.areas)
breacherosion = domain.get_quantity('elevation').get_values(
interpolation_points=[[2 * lakeradius, lakeradius]],
location='centroids') - initial
print 'erosion: ' + str(breacherosion)
volsed = np.sum(
domain.quantities['concentration'].centroid_values *
domain.quantities['height'].centroid_values * domain.areas)
conservation = (volcurr + volsed - voltotal) / voltotal
print 'conservation: ' + '{:.8%}'.format(conservation)
if (volsed < volthresh) & (count > 0):
print "No sediment moving...ending..."
break
count = count + 1
polyline = [[2 * lakeradius, lakeradius - 2 * initbreachwidth],
[2 * lakeradius, lakeradius + 2 * initbreachwidth]]
time, Q = anuga.get_flow_through_cross_section(
name + '.sww', polyline)
print Q
initname = "initial_" + str(lakeradius) + "_" + str(
grainD * 1000) + "mm" + ".asc"
finname = "final_" + str(lakeradius) + "_" + str(
grainD * 1000) + "mm" + ".asc"
fluxname = "flux_" + str(lakeradius) + "_" + str(
grainD * 1000) + "mm" + ".txt"
np.savetxt(fluxname, Q)
finalstats(domain, initialdomain, lakeradius)
np.save('XconcC.npy',
domain.quantities['concentration'].centroid_values)
np.save('XelevC.npy',
domain.quantities['elevation'].centroid_values)
np.save('XxmC.npy', domain.quantities['xmomentum'].centroid_values)
np.save('XymC.npy', domain.quantities['ymomentum'].centroid_values)
np.save('XstageC.npy', domain.quantities['stage'].centroid_values)
np.save('XconcV.npy',
domain.quantities['concentration'].vertex_values)
np.save('XelevV.npy', domain.quantities['elevation'].vertex_values)
np.save('XxmV.npy', domain.quantities['xmomentum'].vertex_values)
np.save('XymV.npy', domain.quantities['ymomentum'].vertex_values)
np.save('XstageV.npy', domain.quantities['stage'].vertex_values)
except optparse.OptionError, msg:
raise Usage(msg)
except Usage, err:
print >> sys.stderr, err.msg
# print >>sys.stderr, "for help use --help"
return 2
def run_simulation(parallel=False,
control_data=None,
test_points=None,
verbose=False):
success = True
##-----------------------------------------------------------------------
## Setup domain
##-----------------------------------------------------------------------
points, vertices, boundary = rectangular_cross(int(old_div(length, dx)),
int(old_div(width, dy)),
len1=length,
len2=width)
domain = anuga.Domain(points, vertices, boundary)
#domain.set_name() # Output name
domain.set_store(False)
domain.set_default_order(2)
##-----------------------------------------------------------------------
## Distribute domain
##-----------------------------------------------------------------------
if parallel:
domain = distribute(domain)
#domain.dump_triangulation("frac_op_domain.png")
##-----------------------------------------------------------------------
## Setup boundary conditions
##-----------------------------------------------------------------------
domain.set_quantity('elevation', topography)
domain.set_quantity('friction', 0.01) # Constant friction
domain.set_quantity('stage',
expression='elevation') # Dry initial condition
Bi = anuga.Dirichlet_boundary([5.0, 0.0, 0.0])
Br = anuga.Reflective_boundary(domain) # Solid reflective wall
domain.set_boundary({'left': Br, 'right': Br, 'top': Br, 'bottom': Br})
##-----------------------------------------------------------------------
## Determine triangle index coinciding with test points
##-----------------------------------------------------------------------
assert (test_points is not None)
assert (len(test_points) == samples)
tri_ids = []
for point in test_points:
try:
k = domain.get_triangle_containing_point(point)
if domain.tri_full_flag[k] == 1:
tri_ids.append(k)
else:
tri_ids.append(-1)
except:
tri_ids.append(-2)
if verbose: print('P%d has points = %s' % (myid, tri_ids))
if not parallel: control_data = []
################ Define Fractional Operators ##########################
inlet0 = None
inlet1 = None
boyd_box0 = None
inlet0 = Inlet_operator(domain, line0, Q0, verbose=False, label='Inlet_0')
inlet1 = Inlet_operator(domain, line1, Q1, verbose=False, label='Inlet_1')
# Enquiry point [ 19. 2.5] is contained in two domains in 4 proc case
boyd_box0 = Boyd_box_operator(domain,
end_points=[[9.0, 2.5], [19.0, 2.5]],
losses=1.5,
width=5.0,
apron=5.0,
use_momentum_jet=True,
use_velocity_head=False,
manning=0.013,
label='Boyd_Box_0',
verbose=False)
#if inlet0 is not None and verbose: inlet0.print_statistics()
#if inlet1 is not None and verbose: inlet1.print_statistics()
if boyd_box0 is not None and verbose:
print("++++", myid)
boyd_box0.print_statistics()
# if parallel:
# factory = Parallel_operator_factory(domain, verbose = True)
#
# inlet0 = factory.inlet_operator_factory(line0, Q0)
# inlet1 = factory.inlet_operator_factory(line1, Q1)
#
# boyd_box0 = factory.boyd_box_operator_factory(end_points=[[9.0, 2.5],[19.0, 2.5]],
# losses=1.5,
# width=1.5,
# apron=5.0,
# use_momentum_jet=True,
# use_velocity_head=False,
# manning=0.013,
# verbose=False)
#
# else:
# inlet0 = Inlet_operator(domain, line0, Q0)
# inlet1 = Inlet_operator(domain, line1, Q1)
#
# # Enquiry point [ 19. 2.5] is contained in two domains in 4 proc case
# boyd_box0 = Boyd_box_operator(domain,
# end_points=[[9.0, 2.5],[19.0, 2.5]],
# losses=1.5,
# width=1.5,
# apron=5.0,
# use_momentum_jet=True,
# use_velocity_head=False,
# manning=0.013,
# verbose=False)
#######################################################################
##-----------------------------------------------------------------------
## Evolve system through time
##-----------------------------------------------------------------------
for t in domain.evolve(yieldstep=2.0, finaltime=20.0):
if myid == 0 and verbose:
domain.write_time()
#print domain.volumetric_balance_statistics()
stage = domain.get_quantity('stage')
if boyd_box0 is not None and verbose:
if myid == boyd_box0.master_proc:
print('master_proc ', myid)
boyd_box0.print_timestepping_statistics()
#for i in range(samples):
# if tri_ids[i] >= 0:
# if verbose: print 'P%d tri %d, value = %s' %(myid, i, stage.centroid_values[tri_ids[i]])
sys.stdout.flush()
pass
domain.sww_merge(delete_old=True)
success = True
##-----------------------------------------------------------------------
## Assign/Test Control data
##-----------------------------------------------------------------------
if not parallel:
stage = domain.get_quantity('stage')
for i in range(samples):
assert (tri_ids[i] >= 0)
control_data.append(stage.centroid_values[tri_ids[i]])
if inlet0 is not None:
control_data.append(inlet0.inlet.get_average_stage())
control_data.append(inlet0.inlet.get_average_xmom())
control_data.append(inlet0.inlet.get_average_ymom())
control_data.append(inlet0.inlet.get_total_water_volume())
control_data.append(inlet0.inlet.get_average_depth())
if verbose: print('P%d control_data = %s' % (myid, control_data))
else:
stage = domain.get_quantity('stage')
for i in range(samples):
if tri_ids[i] >= 0:
local_success = num.allclose(control_data[i],
stage.centroid_values[tri_ids[i]])
success = success and local_success
if verbose:
print(
'P%d tri %d, control = %s, actual = %s, Success = %s' %
(myid, i, control_data[i],
stage.centroid_values[tri_ids[i]], local_success))
if inlet0 is not None:
inlet_master_proc = inlet0.inlet.get_master_proc()
average_stage = inlet0.inlet.get_global_average_stage()
average_xmom = inlet0.inlet.get_global_average_xmom()
average_ymom = inlet0.inlet.get_global_average_ymom()
average_volume = inlet0.inlet.get_global_total_water_volume()
average_depth = inlet0.inlet.get_global_average_depth()
if myid == inlet_master_proc:
if verbose:
print('P%d average stage, control = %s, actual = %s' %
(myid, control_data[samples], average_stage))
print('P%d average xmom, control = %s, actual = %s' %
(myid, control_data[samples + 1], average_xmom))
print('P%d average ymom, control = %s, actual = %s' %
(myid, control_data[samples + 2], average_ymom))
print('P%d average volume, control = %s, actual = %s' %
(myid, control_data[samples + 3], average_volume))
print('P%d average depth, control = %s, actual = %s' %
(myid, control_data[samples + 4], average_depth))
return control_data, success
verbose=verbose)
barrier()
# configure my logging
import anuga.utilities.log as log
#log.console_logging_level = log.INFO
#log.log_logging_level = log.DEBUG
log.log_filename = './run_okushiri.log'
#-------------------------
# Create Domain from mesh
#-------------------------
if myid == 0:
try:
domain = anuga.Domain(mesh_filename, use_cache=False, verbose=verbose)
except:
msg = 'ERROR reading in mesh file. Have you run create_okushiri.py?'
raise Exception(msg)
if verbose: print(domain.statistics())
#-------------------------
# Initial Conditions
#-------------------------
domain.set_quantity('friction', 0.0025)
domain.set_quantity('stage', 0.0)
if verbose: print('set stage')
if elevation_in_mesh is False:
# domain.set_quantity('elevation',
# filename=bathymetry_filename_stem+'.pts',
# Setup computational domain
#------------------------------------------------------------------------------
if myid == 0:
print '>>>>> DUNE EROSION TEST SCRIPT V2'
print '>>>>> Setting up Domain on processor 0...'
length = 36.
width = 5.
dx = dy = 0.1 # Resolution: Length of subdivisions on both axes
print '>>>>> Domain has L = %f, W = %f, dx=dy= %f' % (length, width, dx)
points, vertices, boundary = anuga.rectangular_cross(int(length / dx),
int(width / dy),
len1=length,
len2=width)
domain = anuga.Domain(points, vertices, boundary)
domain.set_flow_algorithm('DE0')
domain.set_name('sanddune_testV2SR') # Output name
domain.set_quantity('elevation', topography) # elevation is a function
domain.set_quantity('friction', 0.01) # Constant friction
domain.set_quantity('stage',
expression='elevation') # Dry initial condition
print domain.statistics()
# get the indices of triangles in each erosion poly so can setup nsbase_ in domain
poly1ind = (Region(domain, polygon=polygon1)).indices
poly2ind = (Region(domain, polygon=polygon2)).indices
print '>>>>> poly1ind is of length ', len(
poly1ind), ' and contains triangles', poly1ind[0], ' to ', poly1ind[-1]
print '>>>>> poly2ind is of length ', len(
def run(par,
n,
withNormalization,
withResidual,
wave_type='bumps',
minimum_allowed_height=1e-5):
# ------------------------------------------------------------------------------
# Setup computational domain
# ------------------------------------------------------------------------------
xleft = 0
xright = 5.448
ybottom = 0
ytop = 3.402
# rectangular cross mesh
points, vertices, boundary = anuga.rectangular_cross(
int(n), int(n), xright - xleft, ytop - ybottom, (xleft, ybottom))
newpoints = points.copy()
# make refinement in x direction
x = np.multiply([0., 0.1, 0.2, 0.335, 0.925, 1.], max(points[:, 0]))
y = [0., 3., 4.25, 4.7, 5.3, max(points[:, 0])]
f1 = interp1d(x, y, kind='linear')
newpoints[:, 0] = f1(points[:, 0])
# make refinement in y direction
x = np.multiply([0., .125, .3, .7, .9, 1.], max(points[:, 1]))
y = [0., 1.25, 1.75, 2.15, 2.65, max(points[:, 1])]
f2 = interp1d(x, y, kind='linear')
newpoints[:, 1] = f2(points[:, 1])
c = abs(newpoints[:, 0] - 5.0) + .5 * abs(newpoints[:, 1] - 1.95)
c = 0.125 * c
points[:, 0] = c * points[:, 0] + (1 - c) * newpoints[:, 0]
points[:, 1] = c * points[:, 1] + (1 - c) * newpoints[:, 1]
# create domain
domain = anuga.Domain(points, vertices, boundary)
# don't store .sww file
domain.set_quantities_to_be_stored(None)
# ------------------------------------------------------------------------------
# Initial Conditions
# ------------------------------------------------------------------------------
domain.set_quantity('friction', 0.01) # 0.0
domain.set_quantity('stage', 0.0)
domain.set_quantity(
'elevation',
filename='/home/rehmemk/git/anugasgpp/Okushiri/data/bathymetry.pts',
alpha=0.02)
# ------------------------------------------------------------------------------
# Set simulation parameters
# ------------------------------------------------------------------------------
domain.set_name('output_okushiri') # Output name
# domain.set_minimum_storable_height(0.001) # Don't store w < 0.001m
domain.set_minimum_storable_height(1.0) # Don't store w < 0.001m
domain.set_flow_algorithm('DE0')
# ------------------------------------------------------------------------------
# Modify input wave
# ------------------------------------------------------------------------------
# rescale input parameter
try:
dummy = len(par)
except:
par = [par]
par = np.dot(2, par)
if wave_type == 'bumps':
wave_function, _, _ = wave_functions.heights_wave(
par, withResidual, withNormalization)
elif wave_type == 'original':
wave_function = wave_functions.original_wave_interpolant()
elif wave_type == 'cubic':
wave_function, _, _ = wave_functions.cubic_heights_wave(
par, withResidual, withNormalization)
else:
print(f'Error. Wave type {wave_type} unknown')
# ------------------------------------------------------------------------------
# Setup boundary conditions
# ------------------------------------------------------------------------------
# Create boundary function from input wave [replaced by wave function]
# Create and assign boundary objects
Bts = anuga.Transmissive_momentum_set_stage_boundary(domain, wave_function)
Br = anuga.Reflective_boundary(domain)
domain.set_boundary({'left': Bts, 'right': Br, 'top': Br, 'bottom': Br})
# ------------------------------------------------------------------------------
# Evolve system through time
# ------------------------------------------------------------------------------
# this prevents problems w.r.t. divisions by zero
# It might decrease the acheivable accuracy
domain.set_minimum_allowed_height(minimum_allowed_height) # default 1e-5
# area for gulleys
x1 = 4.85
x2 = 5.25
y1 = 2.05
y2 = 1.85
# index in gulley area
x = domain.centroid_coordinates[:, 0]
y = domain.centroid_coordinates[:, 1]
v = np.sqrt((x - x1) ** 2 + (y - y1) ** 2) + \
np.sqrt((x - x2) ** 2 + (y - y2) ** 2) < 0.5
# three gauges and a point somewhere on the boundary that could be used for verification
# get id's of the corresponding triangles
gauge = [[4.521, 1.196], [4.521, 1.696], [4.521, 2.196]]
bdyloc = [0.00001, 2.5]
g5_id = domain.get_triangle_containing_point(gauge[0])
g7_id = domain.get_triangle_containing_point(gauge[1])
g9_id = domain.get_triangle_containing_point(gauge[2])
bc_id = domain.get_triangle_containing_point(bdyloc)
k = 0
# original number of timesteps is 451
numTimeSteps = 451
sumstage = np.nan * np.ones(numTimeSteps)
stage_g5 = np.nan * np.ones(numTimeSteps)
stage_g7 = np.nan * np.ones(numTimeSteps)
stage_g9 = np.nan * np.ones(numTimeSteps)
stage_bc = np.nan * np.ones(numTimeSteps)
yieldstep = 0.05
finaltime = (numTimeSteps - 1) * yieldstep
for t in domain.evolve(yieldstep=yieldstep, finaltime=finaltime):
# domain.write_time()
# stage [=height of water]
stage = domain.quantities['stage'].centroid_values[v]
stage_g5[k] = domain.quantities['stage'].centroid_values[g5_id]
stage_g7[k] = domain.quantities['stage'].centroid_values[g7_id]
stage_g9[k] = domain.quantities['stage'].centroid_values[g9_id]
stage_bc[k] = domain.quantities['stage'].centroid_values[bc_id]
# averaging for smoothness
sumstage[k] = np.sum(stage)
# k is time
k += 1
# number of triangles which are active for the designated runup area
numActiveTriangles = anuga.collect_value(np.count_nonzero(v))
averageStage = sumstage / numActiveTriangles
# normalizing to zero level
# averageStage -= averageStage[0]
return [averageStage, stage_g5, stage_g7, stage_g9, stage_bc]
