def calc_mld(files,start,x0=0.0,y0=0.0):
""" Caclulate density-based MLD from a bunch of VTU files
"""
mld = []
times = []
dates = []
for file in files:
try:
os.stat(file)
except:
print("No such file: %s" % file)
sys.exit(1)
# open vtu and derive the field indices of the edge at (x=0,y=0) ordered by depth
u=vtktools.vtu(file)
pos = u.GetLocations()
ind = get_1d_indices(pos, x0, y0)
# from this we can derive the 1D profile of any field like this:
depth = vtktools.arr([-pos[i,2] for i in ind])
# handle time for different types of plots
time = u.GetScalarField('Time')
times.append(time[0]) # seconds
dates.append( date2num(start + timedelta(seconds=time[0])) ) # integer datetime
# grab density profile and calculate MLD_den (using 2 different deviation parameters
d = u.GetScalarField('Density')
den = vtktools.arr( [d[i] * 1000 for i in ind] )
mld.append( calc_mld_den(den, depth) ) #den0 = 0.03 is default
return mld, times, dates
def calc_mld_tke_files(files,start,x0=0.0,y0=0.0):
""" Caclulate tke-based MLD from a bunch of VTU files
"""
mld = []
times = []
dates = []
for file in files:
try:
os.stat(file)
except:
print "No such file: %s" % file
sys.exit(1)
# open vtu and derive the field indices of the edge at (x=0,y=0) ordered by depth
u=vtktools.vtu(file)
pos = u.GetLocations()
ind = get_1d_indices(pos, x0, y0)
# from this we can derive the 1D profile of any field like this:
depth = vtktools.arr([-pos[i,2] for i in ind])
# handle time for different types of plots
time = u.GetScalarField('Time')
times.append(time[0]) # seconds
dates.append( date2num(start + timedelta(seconds=time[0])) ) # integer datetime
# grab density profile and calculate MLD
d = u.GetScalarField('GLSTurbulentKineticEnergy')
tke = vtktools.arr( [d[i] for i in ind] )
mld.append( calc_mld_tke(tke, depth) )
return mld, times, dates
def calc_mld(files, start, x0=0.0, y0=0.0):
""" Caclulate density-based MLD from a bunch of VTU files
"""
mld = []
times = []
dates = []
for file in files:
try:
os.stat(file)
except:
print("No such file: %s" % file)
sys.exit(1)
# open vtu and derive the field indices of the edge at (x=0,y=0) ordered by depth
u = vtktools.vtu(file)
pos = u.GetLocations()
ind = get_1d_indices(pos, x0, y0)
# from this we can derive the 1D profile of any field like this:
depth = vtktools.arr([-pos[i, 2] for i in ind])
# handle time for different types of plots
time = u.GetScalarField('Time')
times.append(time[0]) # seconds
dates.append(date2num(start +
timedelta(seconds=time[0]))) # integer datetime
# grab density profile and calculate MLD_den (using 2 different deviation parameters
d = u.GetScalarField('Density')
den = vtktools.arr([d[i] * 1000 for i in ind])
mld.append(calc_mld_den(den, depth)) #den0 = 0.03 is default
return mld, times, dates
def plot_2d_data(data,depths,time_secs,start_date,file_path,axis_label,finish_date=None,mld_data=None,max_depth=150,interval=3,minimum=None,maximum=None,spacing=None,colour_scale=cm.jet,dates=None):
"""
"""
# turn given 2d-arrays into numpy arrays (in case they are not already)
data = vtktools.arr(data)
time_secs = vtktools.arr(time_secs)
depths = vtktools.arr(depths)
# convert time profiles in seconds into months
start = datetime.strptime(start_date, "%Y-%m-%d %H:%M:%S")
if (dates == None):
dates = time_secs
i = 0
for time in time_secs:
t = float(time[0].item())
dates[i,:] = date2num(start + timedelta(seconds=t))
i += 1
# see if finishing date is given, default to last time given
if (finish_date != None):
finish = datetime.strptime(finish_date, "%Y-%m-%d %H:%M:%S")
else:
finish = dates[-1][0]
# define min/max and spacing of data if not given (so we see all of the data)
if (minimum == None):
minimum = data.min()
minimum = minimum - (0.1*minimum)
if (maximum == None):
maximum = data.max()
maximum = maximum + (0.1*maximum)
if (spacing == None):
spacing = (maximum - minimum) /256.
# plot 2d colour graph...
fig = figure(figsize=(15,8),dpi=90)
ax = fig.add_axes([.1,.18,.9,.7])
cs=ax.contour(dates, depths, data, arange(minimum,maximum,spacing),cmap=colour_scale)
cs=ax.contourf(dates, depths, data, arange(minimum,maximum,spacing),cmap=colour_scale)
pp=colorbar(cs,format='%.2f')
if(mld_data!=None):
ax.plot(dates[:,0],mld_data,'w', alpha=0.7)
dateFmt = mpl.dates.DateFormatter('%m/%Y')
ax.xaxis.set_major_formatter(dateFmt)
monthsLoc = mpl.dates.MonthLocator(interval=interval)
ax.xaxis.set_major_locator(monthsLoc)
labels = ax.get_xticklabels()
for label in labels:
label.set_rotation(30)
ax.set_ylim(max_depth, 0)
ax.set_xlim(start,finish)
pp.set_label(axis_label)
xlabel('Date (mm/yyyy)')
ylabel('Depth (m)')
form = file_path.split('.')[-1].strip()
savefig(file_path, dpi=90,format=form)
close(fig)
def botella_p1(NN):
#Botella and Peyret (1998) Table 9.
filelist_not_sorted = glob.glob('driven_cavity-%d/*.vtu' % NN)
vtu_nos_not_sorted = [
int(file.split('.vtu')[0].split('_')[-1])
for file in filelist_not_sorted
]
filelist = [
filelist_not_sorted[i] for i in numpy.argsort(vtu_nos_not_sorted)
]
file = filelist[-1]
print file
try:
os.stat(file)
except:
print "No such file: %s" % file
sys.exit(1)
u = vtktools.vtu(file)
pts = vtktools.arr([[0.5, 0.0000, 0.0, 0.110591],
[0.5, 0.0547, 0.0, 0.109689],
[0.5, 0.0625, 0.0, 0.109200],
[0.5, 0.0703, 0.0, 0.108566],
[0.5, 0.1016, 0.0, 0.104187],
[0.5, 0.1719, 0.0, 0.081925],
[0.5, 0.2813, 0.0, 0.040377],
[0.5, 0.4531, 0.0, 0.004434],
[0.5, 0.5000, 0.0, 0.000000],
[0.5, 0.6172, 0.0, -0.000827],
[0.5, 0.7344, 0.0, 0.012122],
[0.5, 0.8516, 0.0, 0.034910],
[0.5, 0.9531, 0.0, 0.050329],
[0.5, 0.9609, 0.0, 0.050949],
[0.5, 0.9688, 0.0, 0.051514],
[0.5, 0.9766, 0.0, 0.052009],
[0.5, 1.0000, 0.0, 0.052987]])
velocity = u.ProbeData(pts, "Velocity")
(ilen, jlen) = velocity.shape
pressure = u.ProbeData(pts, "Pressure")
pts0 = vtktools.arr([[
0.5, 0.5, 0.0
]]) # We're going to subtract off the pressure at the centre point
press0 = u.ProbeData(pts0, "Pressure")
norm = 0.0
for i in range(ilen):
diff = pts[i][3] - (pressure[i][0] - press0[0][0])
norm = norm + diff * diff
norm = math.sqrt(norm / ilen)
print "botella_p1_norm:", norm
return norm
def botella_p2(NN):
#Botella and Peyret (1998) Table 10.
filelist_not_sorted = glob.glob('driven_cavity-%d/*.vtu' % NN)
vtu_nos_not_sorted = [
int(file.split('.vtu')[0].split('_')[-1])
for file in filelist_not_sorted
]
filelist = [
filelist_not_sorted[i] for i in numpy.argsort(vtu_nos_not_sorted)
]
file = filelist[-1]
print file
try:
os.stat(file)
except:
print "No such file: %s" % file
sys.exit(1)
u = vtktools.vtu(file)
pts = vtktools.arr([[1.0000, 0.5, 0.0, 0.077455],
[0.9688, 0.5, 0.0, 0.078837],
[0.9609, 0.5, 0.0, 0.078685],
[0.9531, 0.5, 0.0, 0.078148],
[0.9453, 0.5, 0.0, 0.077154],
[0.9063, 0.5, 0.0, 0.065816],
[0.8594, 0.5, 0.0, 0.049029],
[0.8047, 0.5, 0.0, 0.034552],
[0.5000, 0.5, 0.0, 0.000000],
[0.2344, 0.5, 0.0, 0.044848],
[0.2266, 0.5, 0.0, 0.047260],
[0.1563, 0.5, 0.0, 0.069511],
[0.0938, 0.5, 0.0, 0.084386],
[0.0781, 0.5, 0.0, 0.086716],
[0.0703, 0.5, 0.0, 0.087653],
[0.0625, 0.5, 0.0, 0.088445],
[0.0000, 0.5, 0.0, 0.090477]])
velocity = u.ProbeData(pts, "Velocity")
(ilen, jlen) = velocity.shape
pressure = u.ProbeData(pts, "Pressure")
pts0 = vtktools.arr([[
0.5, 0.5, 0.0
]]) # We're going to subtract off the pressure at the centre point
press0 = u.ProbeData(pts0, "Pressure")
norm = 0.0
for i in range(ilen):
diff = pts[i][3] - (pressure[i][0] - press0[0][0])
norm = norm + diff * diff
norm = math.sqrt(norm / ilen)
print "botella_p2_norm:", norm
return norm
def botella_p1(NN):
#Botella and Peyret (1998) Table 9.
filelist_not_sorted = glob.glob('driven_cavity-%d/*.vtu'%NN)
vtu_nos_not_sorted = [int(file.split('.vtu')[0].split('_')[-1]) for file in filelist_not_sorted]
filelist = [filelist_not_sorted[i] for i in numpy.argsort(vtu_nos_not_sorted)]
file = filelist[-1]
print file
try:
os.stat(file)
except:
print "No such file: %s" % file
sys.exit(1)
u=vtktools.vtu(file)
pts=vtktools.arr([
[0.5, 0.0000, 0.0, 0.110591],
[0.5, 0.0547, 0.0, 0.109689],
[0.5, 0.0625, 0.0, 0.109200],
[0.5, 0.0703, 0.0, 0.108566],
[0.5, 0.1016, 0.0, 0.104187],
[0.5, 0.1719, 0.0, 0.081925],
[0.5, 0.2813, 0.0, 0.040377],
[0.5, 0.4531, 0.0, 0.004434],
[0.5, 0.5000, 0.0, 0.000000],
[0.5, 0.6172, 0.0, -0.000827],
[0.5, 0.7344, 0.0, 0.012122],
[0.5, 0.8516, 0.0, 0.034910],
[0.5, 0.9531, 0.0, 0.050329],
[0.5, 0.9609, 0.0, 0.050949],
[0.5, 0.9688, 0.0, 0.051514],
[0.5, 0.9766, 0.0, 0.052009],
[0.5, 1.0000, 0.0, 0.052987]])
velocity = u.ProbeData(pts, "Velocity")
(ilen, jlen) = velocity.shape
pressure = u.ProbeData(pts, "Pressure")
pts0=vtktools.arr([[0.5, 0.5, 0.0]]) # We're going to subtract off the pressure at the centre point
press0 = u.ProbeData(pts0, "Pressure")
norm=0.0
for i in range(ilen):
diff = pts[i][3] - (pressure[i][0]-press0[0][0])
norm = norm + diff*diff
norm = math.sqrt(norm/ilen)
print "botella_p1_norm:", norm
return norm
def botella_p2(NN):
#Botella and Peyret (1998) Table 10.
filelist_not_sorted = glob.glob('driven_cavity-%d/*.vtu'%NN)
vtu_nos_not_sorted = [int(file.split('.vtu')[0].split('_')[-1]) for file in filelist_not_sorted]
filelist = [filelist_not_sorted[i] for i in numpy.argsort(vtu_nos_not_sorted)]
file = filelist[-1]
print file
try:
os.stat(file)
except:
print "No such file: %s" % file
sys.exit(1)
u=vtktools.vtu(file)
pts=vtktools.arr([
[1.0000, 0.5, 0.0, 0.077455],
[0.9688, 0.5, 0.0, 0.078837],
[0.9609, 0.5, 0.0, 0.078685],
[0.9531, 0.5, 0.0, 0.078148],
[0.9453, 0.5, 0.0, 0.077154],
[0.9063, 0.5, 0.0, 0.065816],
[0.8594, 0.5, 0.0, 0.049029],
[0.8047, 0.5, 0.0, 0.034552],
[0.5000, 0.5, 0.0, 0.000000],
[0.2344, 0.5, 0.0, 0.044848],
[0.2266, 0.5, 0.0, 0.047260],
[0.1563, 0.5, 0.0, 0.069511],
[0.0938, 0.5, 0.0, 0.084386],
[0.0781, 0.5, 0.0, 0.086716],
[0.0703, 0.5, 0.0, 0.087653],
[0.0625, 0.5, 0.0, 0.088445],
[0.0000, 0.5, 0.0, 0.090477]])
velocity = u.ProbeData(pts, "Velocity")
(ilen, jlen) = velocity.shape
pressure = u.ProbeData(pts, "Pressure")
pts0=vtktools.arr([[0.5, 0.5, 0.0]]) # We're going to subtract off the pressure at the centre point
press0 = u.ProbeData(pts0, "Pressure")
norm=0.0
for i in range(ilen):
diff = pts[i][3] - (pressure[i][0]-press0[0][0])
norm = norm + diff*diff
norm = math.sqrt(norm/ilen)
print "botella_p2_norm:", norm
return norm
def plot_1d_comparison(data_dict,style_dict,time_dict,start_date,finish_date,file_path,axis_label,interval=3):
"""
"""
start_time = date2num(datetime.strptime(start_date, "%Y-%m-%d %H:%M:%S"))
finish_time = date2num(datetime.strptime(finish_date, "%Y-%m-%d %H:%M:%S"))
# plot 1d graph...
fig = figure(figsize=(15,8),dpi=90)
ax = fig.add_axes([.05,.12,.9,.85])
max_value = 0.0
for key, data_arr in data_dict.iteritems():
ax.plot(time_dict[key],data_arr,style_dict[key], label=key)
data_arr = vtktools.arr(data_arr)
if data_arr.max() > max_value:
max_value = data_arr.max()
max_value += max_value * 0.1
dateFmt = mpl.dates.DateFormatter('%m/%Y')
ax.xaxis.set_major_formatter(dateFmt)
monthsLoc = mpl.dates.MonthLocator(interval=interval)
ax.xaxis.set_major_locator(monthsLoc)
labels = ax.get_xticklabels()
for label in labels:
label.set_rotation(30)
ax.set_ylim(max_value, 0)
ax.set_xlim(start_time,finish_time)
xlabel('Date (mm/yyyy)')
ylabel(axis_label)
legend(loc=0)
form = file_path.split('.')[-1].strip()
savefig(file_path, dpi=90,format=form)
close(fig)
def MLD(filelist):
x0 = 0.
tke0 = 1.0e-5
last_mld = 0
times = []
depths = []
Dm = []
for file in filelist:
try:
os.stat(file)
except:
print "No such file: %s" % file
sys.exit(1)
u=vtktools.vtu(file)
time = u.GetScalarField('Time')
tt = time[0]
kk = u.GetScalarField('GLSTurbulentKineticEnergy')
pos = u.GetLocations()
# ignore first 4 hours of simulaiton
if (tt < 14400):
continue
xyzkk = []
for i in range(0,len(kk)):
if( abs(pos[i,0] - x0) < 0.1 ):
xyzkk.append((pos[i,0],-pos[i,1],pos[i,2],(kk[i])))
xyzkkarr = vtktools.arr(xyzkk)
III = argsort(xyzkkarr[:,1])
xyzkkarrsort = xyzkkarr[III,:]
# march down the column, grabbing the last value above tk0 and the first
# one less than tke0. Interpolate between to get the MLD
kea = 1000
keb = 0
zza = 0
zzb = 0
for values in xyzkkarrsort:
if (values[3] > tke0):
kea = values[3]
zza = -values[1]
if (values[3] < tke0):
keb = values[3]
zzb = -values[1]
break
# the MLD is somewhere between these two values - let's estimate half way!
mld = (zzb+zza)/2.
if (last_mld == mld):
continue
times.append(tt/3600)
depths.append(-1.0*mld)
last_mld = mld
Dm.append(1.05*0.00988211768*(1.0/sqrt(0.01))*sqrt(tt))
return times, depths, Dm
def MLD(filelist):
x0 = 0.
tke0 = 1.0e-5
last_mld = 0
times = []
depths = []
Dm = []
for file in filelist:
try:
os.stat(file)
except:
print("No such file: %s" % file)
sys.exit(1)
u=vtktools.vtu(file)
time = u.GetScalarField('Time')
tt = time[0]
kk = u.GetScalarField('GLSTurbulentKineticEnergy')
pos = u.GetLocations()
# ignore first 4 hours of simulaiton
if (tt < 14400):
continue
xyzkk = []
for i in range(0,len(kk)):
if( abs(pos[i,0] - x0) < 0.1 ):
xyzkk.append((pos[i,0],-pos[i,1],pos[i,2],(kk[i])))
xyzkkarr = vtktools.arr(xyzkk)
III = argsort(xyzkkarr[:,1])
xyzkkarrsort = xyzkkarr[III,:]
# march down the column, grabbing the last value above tk0 and the first
# one less than tke0. Interpolate between to get the MLD
kea = 1000
keb = 0
zza = 0
zzb = 0
for values in xyzkkarrsort:
if (values[3] > tke0):
kea = values[3]
zza = -values[1]
if (values[3] < tke0):
keb = values[3]
zzb = -values[1]
break
# the MLD is somewhere between these two values - let's estimate half way!
mld = (zzb+zza)/2.
if (last_mld == mld):
continue
times.append(tt/3600)
depths.append(-1.0*mld)
last_mld = mld
Dm.append(1.05*0.00988211768*(1.0/sqrt(0.01))*sqrt(tt))
return times, depths, Dm
def plot_tracer(vtu_file, line=None):
u=vtktools.vtu(vtu_file)
pos = u.GetLocations()
time = u.GetScalarField('Time')[0]
t = u.GetScalarField('Tracer')
ind = get_1d_indices(pos)
distance = vtktools.arr([pos[i,0] for i in ind])
tracer = vtktools.arr( [t[i] for i in ind] )
if (line):
line.set_ydata(tracer) # update the data
draw()
else:
line, = plot(distance,tracer,color='k')
return line
def erturk_u(NN):
#Erturk et al 2005. Table VI
filelist_not_sorted = glob.glob('driven_cavity-%d/*.vtu' % NN)
vtu_nos_not_sorted = [
int(file.split('.vtu')[0].split('_')[-1])
for file in filelist_not_sorted
]
filelist = [
filelist_not_sorted[i] for i in numpy.argsort(vtu_nos_not_sorted)
]
file = filelist[-1]
print file
try:
os.stat(file)
except:
print "No such file: %s" % file
sys.exit(1)
u = vtktools.vtu(file)
pts = vtktools.arr([[0.5, 0.000, 0.000, 0.0000],
[0.5, 0.000, 0.000, 0.0000],
[0.5, 0.020, 0.000, -0.0757],
[0.5, 0.040, 0.000, -0.1392],
[0.5, 0.060, 0.000, -0.1951],
[0.5, 0.080, 0.000, -0.2472],
[0.5, 0.100, 0.000, -0.2960],
[0.5, 0.120, 0.000, -0.3381],
[0.5, 0.140, 0.000, -0.3690],
[0.5, 0.160, 0.000, -0.3854],
[0.5, 0.180, 0.000, -0.3869],
[0.5, 0.200, 0.000, -0.3756],
[0.5, 0.500, 0.000, -0.0620],
[0.5, 0.900, 0.000,
0.3838], [0.5, 0.910, 0.000, 0.3913],
[0.5, 0.920, 0.000,
0.3993], [0.5, 0.930, 0.000, 0.4101],
[0.5, 0.940, 0.000,
0.4276], [0.5, 0.950, 0.000, 0.4582],
[0.5, 0.960, 0.000,
0.5102], [0.5, 0.970, 0.000, 0.5917],
[0.5, 0.980, 0.000,
0.7065], [0.5, 0.990, 0.000, 0.8486],
[0.5, 1.000, 0.000, 1.0000]])
velocity = u.ProbeData(pts, "Velocity")
(ilen, jlen) = velocity.shape
norm = 0.0
for i in range(ilen):
diff = pts[i][3] - velocity[i][0]
norm = norm + diff * diff
norm = math.sqrt(norm / ilen)
print "erturk_u_norm:", norm
return norm
def MLD(filelist):
x0 = 0.
tke0 = 1.0e-5
last_mld = 0
times = []
depths = []
for file in filelist:
try:
os.stat(file)
except:
print "No such file: %s" % file
sys.exit(1)
u = vtktools.vtu(file)
time = u.GetScalarField('Time')
tt = time[0]
kk = u.GetScalarField('GLSTurbulentKineticEnergy')
pos = u.GetLocations()
if (tt < 100):
continue
xyzkk = []
for i in range(0, len(kk)):
if (abs(pos[i, 0] - x0) < 0.1):
xyzkk.append((pos[i, 0], -pos[i, 1], pos[i, 2], (kk[i])))
xyzkkarr = vtktools.arr(xyzkk)
III = argsort(xyzkkarr[:, 1])
xyzkkarrsort = xyzkkarr[III, :]
# march down the column, grabbing the last value above tk0 and the first
# one less than tke0. Interpolate between to get the MLD
kea = 1000
keb = 0
zza = 0
zzb = 0
for values in xyzkkarrsort:
if (values[3] > tke0):
kea = values[3]
zza = -values[1]
if (values[3] < tke0):
keb = values[3]
zzb = -values[1]
break
mld = zza
if (last_mld == mld):
continue
times.append(tt / 3600)
depths.append(-1.0 * mld)
last_mld = mld
return times, depths
def getDistanceMeshDensity(file):
v = vtktools.vtu(file)
l = [0.0] * v.ugrid.GetNumberOfPoints()
a = vtktools.arr(l)
for i in range(v.ugrid.GetNumberOfPoints()):
neighbours = v.GetPointPoints(i)
sum = 0.0
for neighbour in neighbours:
sum = sum + v.GetDistance(i, neighbour)
a[i] = sum / len(neighbours)
return a
def MLD(filelist):
x0 = 0.
tke0 = 1.0e-5
last_mld = 0
times = []
depths = []
for file in filelist:
try:
os.stat(file)
except:
print("No such file: %s" % file)
sys.exit(1)
u=vtktools.vtu(file)
time = u.GetScalarField('Time')
tt = time[0]
kk = u.GetScalarField('GLSTurbulentKineticEnergy')
pos = u.GetLocations()
if (tt < 100):
continue
xyzkk = []
for i in range(0,len(kk)):
if( abs(pos[i,0] - x0) < 0.1 ):
xyzkk.append((pos[i,0],-pos[i,1],pos[i,2],(kk[i])))
xyzkkarr = vtktools.arr(xyzkk)
III = argsort(xyzkkarr[:,1])
xyzkkarrsort = xyzkkarr[III,:]
# march down the column, grabbing the last value above tk0 and the first
# one less than tke0. Interpolate between to get the MLD
kea = 1000
keb = 0
zza = 0
zzb = 0
for values in xyzkkarrsort:
if (values[3] > tke0):
kea = values[3]
zza = -values[1]
if (values[3] < tke0):
keb = values[3]
zzb = -values[1]
break
mld = zza
if (last_mld == mld):
continue
times.append(tt/3600)
depths.append(-1.0*mld)
last_mld = mld
return times, depths
def getDistanceMeshDensity(file):
v = vtktools.vtu(file)
l = [0.0] * v.ugrid.GetNumberOfPoints()
a = vtktools.arr(l)
for i in range(v.ugrid.GetNumberOfPoints()):
neighbours = v.GetPointPoints(i)
sum = 0.0
for neighbour in neighbours:
sum = sum + v.GetDistance(i, neighbour)
a[i] = sum / len(neighbours)
return a
def getData(file, xmin=float('nan'), xmax=float('nan'), ymin=float('nan'), ymax=float('nan'), step_x=1,step_y=1):
u=vtktools.vtu(file)
print numpy.isnan(xmin), numpy.isnan(xmax), numpy.isnan(ymin), numpy.isnan(ymax)
if numpy.isnan(xmin):
xmin=u.ugrid.GetBounds()[0]
print 'xmin = ', xmin
if numpy.isnan(ymin):
ymin=u.ugrid.GetBounds()[2]
print 'ymin = ', ymin
if numpy.isnan(xmax):
xmax=u.ugrid.GetBounds()[1]
print 'xmax = ', xmax
if numpy.isnan(ymax):
ymax=u.ugrid.GetBounds()[3]
print 'ymax = ', ymax
Xlist = numpy.arange(xmin,xmax,step_x)# x coordinates
Ylist = numpy.arange(ymin,ymax,step_y)# y coordinates
[X0,Y0] = scipy.meshgrid(Xlist,Ylist)
X0=X0.transpose()
Y0=Y0.transpose()
print Xlist.shape, Ylist.shape, X0.shape, Y0.shape
Z0 = 0.0*Y0 # This is 2d so z is an array of zeros.
X = numpy.reshape(X0,(numpy.size(X0),))
Y = numpy.reshape(Y0,(numpy.size(Y0),))
Z = numpy.reshape(Z0,(numpy.size(Z0),))
pts = zip(X,Y,Z)
pts = vtktools.arr(pts)
# create arrays of velocity and temperature values at the desired points
sol = u.ProbeData(pts, 'solution')
print sol.shape, Xlist.shape, Ylist.shape
#temperature_structured = u.ProbeData(pts, 'Temperature')
numpy.savetxt("pts.dat", zip(X,Y,sol))
sol = sol.reshape((numpy.size(Xlist),numpy.size(Ylist)))
x=[]
y=[]
z=[]
for i in range(len(Xlist)):
for j in range(len(Ylist)):
#print i,j
x.append(X0[i,j])
y.append(Y0[i,j])
z.append(sol[i,j])
numpy.savetxt("pts2.dat", numpy.array(zip(x, y, z)))
#data = scipy.interpolate.RectBivariateSpline(Xlist,Ylist,sol)
# return Xlist, Ylist, sol
return Xlist,Ylist,sol
def erturk_u(NN):
#Erturk et al 2005. Table VI
filelist_not_sorted = glob.glob('driven_cavity-%d/*.vtu'%NN)
vtu_nos_not_sorted = [int(file.split('.vtu')[0].split('_')[-1]) for file in filelist_not_sorted]
filelist = [filelist_not_sorted[i] for i in numpy.argsort(vtu_nos_not_sorted)]
file = filelist[-1]
print file
try:
os.stat(file)
except:
print "No such file: %s" % file
sys.exit(1)
u=vtktools.vtu(file)
pts=vtktools.arr([[0.5, 0.000, 0.000, 0.0000],
[0.5, 0.000, 0.000, 0.0000],
[0.5, 0.020, 0.000, -0.0757],
[0.5, 0.040, 0.000, -0.1392],
[0.5, 0.060, 0.000, -0.1951],
[0.5, 0.080, 0.000, -0.2472],
[0.5, 0.100, 0.000, -0.2960],
[0.5, 0.120, 0.000, -0.3381],
[0.5, 0.140, 0.000, -0.3690],
[0.5, 0.160, 0.000, -0.3854],
[0.5, 0.180, 0.000, -0.3869],
[0.5, 0.200, 0.000, -0.3756],
[0.5, 0.500, 0.000, -0.0620],
[0.5, 0.900, 0.000, 0.3838],
[0.5, 0.910, 0.000, 0.3913],
[0.5, 0.920, 0.000, 0.3993],
[0.5, 0.930, 0.000, 0.4101],
[0.5, 0.940, 0.000, 0.4276],
[0.5, 0.950, 0.000, 0.4582],
[0.5, 0.960, 0.000, 0.5102],
[0.5, 0.970, 0.000, 0.5917],
[0.5, 0.980, 0.000, 0.7065],
[0.5, 0.990, 0.000, 0.8486],
[0.5, 1.000, 0.000, 1.0000]])
velocity = u.ProbeData(pts, "Velocity")
(ilen, jlen) = velocity.shape
norm=0.0
for i in range(ilen):
diff = pts[i][3] - velocity[i][0]
norm = norm + diff*diff
norm = math.sqrt(norm/ilen)
print "erturk_u_norm:", norm
return norm
def erturk_v(NN):
#Erturk et al 2005. Table VII
filelist_not_sorted = glob.glob('driven_cavity-%d/*.vtu'%NN)
vtu_nos_not_sorted = [int(file.split('.vtu')[0].split('_')[-1]) for file in filelist_not_sorted]
filelist = [filelist_not_sorted[i] for i in numpy.argsort(vtu_nos_not_sorted)]
file = filelist[-1]
print file
try:
os.stat(file)
except:
print "No such file: %s" % file
sys.exit(1)
u=vtktools.vtu(file)
pts=vtktools.arr([
[0.000, 0.5, 0.0, 0.0000],
[0.015, 0.5, 0.0, 0.1019],
[0.030, 0.5, 0.0, 0.1792],
[0.045, 0.5, 0.0, 0.2349],
[0.060, 0.5, 0.0, 0.2746],
[0.075, 0.5, 0.0, 0.3041],
[0.090, 0.5, 0.0, 0.3273],
[0.105, 0.5, 0.0, 0.3460],
[0.120, 0.5, 0.0, 0.3605],
[0.135, 0.5, 0.0, 0.3705],
[0.150, 0.5, 0.0, 0.3756],
[0.500, 0.5, 0.0, 0.0258],
[0.850, 0.5, 0.0, -0.4028],
[0.865, 0.5, 0.0, -0.4407],
[0.880, 0.5, 0.0, -0.4803],
[0.895, 0.5, 0.0, -0.5132],
[0.910, 0.5, 0.0, -0.5263],
[0.925, 0.5, 0.0, -0.5052],
[0.940, 0.5, 0.0, -0.4417],
[0.955, 0.5, 0.0, -0.3400],
[0.970, 0.5, 0.0, -0.2173],
[0.985, 0.5, 0.0, -0.0973],
[1.000, 0.5, 0.0, 0.0000]])
velocity = u.ProbeData(pts, "Velocity")
(ilen, jlen) = velocity.shape
norm=0.0
for i in range(ilen):
diff = pts[i][3] - velocity[i][1]
norm = norm + diff*diff
norm = math.sqrt(norm/ilen)
print "erturk_v_norm:", norm
return norm
def erturk_v(NN):
#Erturk et al 2005. Table VII
filelist_not_sorted = glob.glob('driven_cavity-%d/*.vtu'%NN)
vtu_nos_not_sorted = [int(file.split('.vtu')[0].split('_')[-1]) for file in filelist_not_sorted]
filelist = [filelist_not_sorted[i] for i in numpy.argsort(vtu_nos_not_sorted)]
file = filelist[-1]
print file
try:
os.stat(file)
except:
print "No such file: %s" % file
sys.exit(1)
u=vtktools.vtu(file)
pts=vtktools.arr([
[0.000, 0.5, 0.0, 0.0000],
[0.015, 0.5, 0.0, 0.1019],
[0.030, 0.5, 0.0, 0.1792],
[0.045, 0.5, 0.0, 0.2349],
[0.060, 0.5, 0.0, 0.2746],
[0.075, 0.5, 0.0, 0.3041],
[0.090, 0.5, 0.0, 0.3273],
[0.105, 0.5, 0.0, 0.3460],
[0.120, 0.5, 0.0, 0.3605],
[0.135, 0.5, 0.0, 0.3705],
[0.150, 0.5, 0.0, 0.3756],
[0.500, 0.5, 0.0, 0.0258],
[0.850, 0.5, 0.0, -0.4028],
[0.865, 0.5, 0.0, -0.4407],
[0.880, 0.5, 0.0, -0.4803],
[0.895, 0.5, 0.0, -0.5132],
[0.910, 0.5, 0.0, -0.5263],
[0.925, 0.5, 0.0, -0.5052],
[0.940, 0.5, 0.0, -0.4417],
[0.955, 0.5, 0.0, -0.3400],
[0.970, 0.5, 0.0, -0.2173],
[0.985, 0.5, 0.0, -0.0973],
[1.000, 0.5, 0.0, 0.0000]])
velocity = u.ProbeData(pts, "Velocity")
(ilen, jlen) = velocity.shape
norm=0.0
for i in range(ilen):
diff = pts[i][3] - velocity[i][1]
norm = norm + diff*diff
norm = math.sqrt(norm/ilen)
print "erturk_v_norm:", norm
return norm
def calc_mld(files, mld_depths):
for file in files:
try:
os.stat(file)
except:
print "No such file: %s" % file
sys.exit(1)
num = int(file.split(".vtu")[0].split('_')[-1])
u = vtktools.vtu(file)
pos = u.GetLocations()
time = u.GetScalarField('Time')
tt = time[0]
# grab the data e need from the VTUs and shove in an array
den = u.GetScalarField('Density')
xyz_data = []
for i in range(0, len(den)):
if (x0 - 0.1 < pos[i, 0] < x0 + 0.1
and y0 - 0.1 < pos[i, 1] < y0 + 0.1):
xyz_data.append(
(pos[i, 0], pos[i, 1], -pos[i, 2] + z0, 1000 * den[i]))
# sorted the array based on depth
xyz_data = vtktools.arr(xyz_data)
III = argsort(xyz_data[:, 2])
xyz_data_sorted = xyz_data[III, :]
# Surface values
sden = xyz_data_sorted[0, 3]
# grab any values where the UML condition is met for temperature, density and TKE
uml_den = ((xyz_data_sorted[:, 3]) <= (sden + den0)).nonzero()
# ...on density
if ((size(uml_den) > 0)):
LL = uml_den[-1][-1]
zz = xyz_data_sorted[:, 2]
if (LL + 1 < size(zz)):
zza = zz[LL + 1]
kea = xyz_data_sorted[LL + 1, 3]
else:
zza = zz[LL]
kea = xyz_data_sorted[LL, 3]
zzb = zz[LL]
keb = xyz_data_sorted[LL, 3]
tt = tt / (24 * 60 * 60)
time = start_datetime + timedelta(days=tt)
key = '%04d/%02d/%02d' % (time.year, time.month, time.day)
mld_depths[key] = (zza - (zzb - zza) * (((sden + den0) - kea) /
(kea - keb)))
def botella_v(NN):
#Botella and Peyret (1998) Table 10.
filelist_not_sorted = glob.glob('driven_cavity-%d/*.vtu' % NN)
vtu_nos_not_sorted = [
int(file.split('.vtu')[0].split('_')[-1])
for file in filelist_not_sorted
]
filelist = [
filelist_not_sorted[i] for i in numpy.argsort(vtu_nos_not_sorted)
]
file = filelist[-1]
print file
try:
os.stat(file)
except:
print "No such file: %s" % file
sys.exit(1)
u = vtktools.vtu(file)
pts = vtktools.arr([[1.0000, 0.5, 0.0, 0.0000000],
[0.9688, 0.5, 0.0, -0.2279225],
[0.9609, 0.5, 0.0, -0.2936869],
[0.9531, 0.5, 0.0, -0.3553213],
[0.9453, 0.5, 0.0, -0.4103754],
[0.9063, 0.5, 0.0, -0.5264392],
[0.8594, 0.5, 0.0, -0.4264545],
[0.8047, 0.5, 0.0, -0.3202137],
[0.5000, 0.5, 0.0, 0.0257995],
[0.2344, 0.5, 0.0, 0.3253592],
[0.2266, 0.5, 0.0, 0.3339924],
[0.1563, 0.5, 0.0, 0.3769189],
[0.0938, 0.5, 0.0, 0.3330442],
[0.0781, 0.5, 0.0, 0.3099097],
[0.0703, 0.5, 0.0, 0.2962703],
[0.0625, 0.5, 0.0, 0.2807056],
[0.0000, 0.5, 0.0, 0.0000000]])
velocity = u.ProbeData(pts, "Velocity")
(ilen, jlen) = velocity.shape
norm = 0.0
for i in range(ilen):
diff = pts[i][3] - velocity[i][1]
norm = norm + diff * diff
norm = math.sqrt(norm / ilen)
print "botella_v_norm:", norm
return norm
def getElementMeshDensity(file):
v = vtktools.vtu(file)
l = [0.0] * v.ugrid.GetNumberOfPoints()
a = vtktools.arr(l)
c = v.ugrid.GetCell(1)
for i in range(v.ugrid.GetNumberOfPoints()):
eles = v.GetPointCells(i)
sum = 0.0
for ele in eles:
points = v.ugrid.GetCell(ele).GetPoints().GetData()
sum = sum + c.ComputeVolume(points.GetTuple3(1), points.GetTuple3(2),
points.GetTuple3(3), points.GetTuple3(4))
a[i] = sum / len(eles)
return a
def calc_mld(files,mld_depths):
for file in files:
try:
os.stat(file)
except:
print "No such file: %s" % file
sys.exit(1)
num = int(file.split(".vtu")[0].split('_')[-1])
u=vtktools.vtu(file)
pos = u.GetLocations()
time = u.GetScalarField('Time')
tt = time[0]
# grab the data e need from the VTUs and shove in an array
den = u.GetScalarField('Density')
xyz_data = []
for i in range(0,len(den)):
if (x0-0.1 < pos[i,0] < x0+0.1 and y0-0.1 < pos[i,1] < y0+0.1):
xyz_data.append((pos[i,0],pos[i,1],-pos[i,2]+z0,1000*den[i]))
# sorted the array based on depth
xyz_data = vtktools.arr(xyz_data)
III = argsort(xyz_data[:,2])
xyz_data_sorted = xyz_data[III,:]
# Surface values
sden = xyz_data_sorted[0,3]
# grab any values where the UML condition is met for temperature, density and TKE
uml_den = ((xyz_data_sorted[:,3]) <= (sden+den0)).nonzero()
# ...on density
if( (size(uml_den) > 0 ) ):
LL = uml_den[-1][-1]
zz = xyz_data_sorted[:,2]
if (LL+1 < size(zz)):
zza = zz[LL+1]
kea = xyz_data_sorted[LL+1,3]
else:
zza = zz[LL]
kea = xyz_data_sorted[LL,3]
zzb = zz[LL]
keb = xyz_data_sorted[LL,3]
tt = tt/(24*60*60)
time = start_datetime + timedelta(days=tt)
key = '%04d/%02d/%02d' % (time.year, time.month, time.day)
mld_depths[key] = (zza-(zzb-zza)*(((sden+den0)-kea)/(kea-keb)))
def botella_u(NN):
#Botella and Peyret (1998) Table 9. NB.our velocity at the lid is reverse theirs therefore minus signs in u below
filelist_not_sorted = glob.glob('driven_cavity-%d/*.vtu' % NN)
vtu_nos_not_sorted = [
int(file.split('.vtu')[0].split('_')[-1])
for file in filelist_not_sorted
]
filelist = [
filelist_not_sorted[i] for i in numpy.argsort(vtu_nos_not_sorted)
]
file = filelist[-1]
print file
try:
os.stat(file)
except:
print "No such file: %s" % file
sys.exit(1)
u = vtktools.vtu(file)
pts = vtktools.arr([[0.5, 0.0000, 0.0, 0.0000000],
[0.5, 0.0547, 0.0, -0.1812881],
[0.5, 0.0625, 0.0, -0.2023300],
[0.5, 0.0703, 0.0, -0.2228955],
[0.5, 0.1016, 0.0, -0.3004561],
[0.5, 0.1719, 0.0, -0.3885691],
[0.5, 0.2813, 0.0, -0.2803696],
[0.5, 0.4531, 0.0, -0.1081999],
[0.5, 0.5000, 0.0, -0.0620561],
[0.5, 0.6172, 0.0, 0.0570178],
[0.5, 0.7344, 0.0, 0.1886747],
[0.5, 0.8516, 0.0, 0.3372212],
[0.5, 0.9531, 0.0, 0.4723329],
[0.5, 0.9609, 0.0, 0.5169277],
[0.5, 0.9688, 0.0, 0.5808359],
[0.5, 0.9766, 0.0, 0.6644227],
[0.5, 1.0000, 0.0, 1.0000000]])
velocity = u.ProbeData(pts, "Velocity")
(ilen, jlen) = velocity.shape
norm = 0.0
for i in range(ilen):
diff = pts[i][3] - velocity[i][0]
norm = norm + diff * diff
norm = math.sqrt(norm / ilen)
print "botella_u_norm:", norm
return norm
def getElementMeshDensity(file):
v = vtktools.vtu(file)
l = [0.0] * v.ugrid.GetNumberOfPoints()
a = vtktools.arr(l)
c = v.ugrid.GetCell(1)
for i in range(v.ugrid.GetNumberOfPoints()):
eles = v.GetPointCells(i)
sum = 0.0
for ele in eles:
points = v.ugrid.GetCell(ele).GetPoints().GetData()
sum = sum + c.ComputeVolume(
points.GetTuple3(1), points.GetTuple3(2), points.GetTuple3(3),
points.GetTuple3(4))
a[i] = sum / len(eles)
return a
def botella_v(NN):
#Botella and Peyret (1998) Table 10.
filelist_not_sorted = glob.glob('driven_cavity-%d/*.vtu'%NN)
vtu_nos_not_sorted = [int(file.split('.vtu')[0].split('_')[-1]) for file in filelist_not_sorted]
filelist = [filelist_not_sorted[i] for i in numpy.argsort(vtu_nos_not_sorted)]
file = filelist[-1]
print file
try:
os.stat(file)
except:
print "No such file: %s" % file
sys.exit(1)
u=vtktools.vtu(file)
pts=vtktools.arr([
[1.0000, 0.5, 0.0, 0.0000000],
[0.9688, 0.5, 0.0, -0.2279225],
[0.9609, 0.5, 0.0, -0.2936869],
[0.9531, 0.5, 0.0, -0.3553213],
[0.9453, 0.5, 0.0, -0.4103754],
[0.9063, 0.5, 0.0, -0.5264392],
[0.8594, 0.5, 0.0, -0.4264545],
[0.8047, 0.5, 0.0, -0.3202137],
[0.5000, 0.5, 0.0, 0.0257995],
[0.2344, 0.5, 0.0, 0.3253592],
[0.2266, 0.5, 0.0, 0.3339924],
[0.1563, 0.5, 0.0, 0.3769189],
[0.0938, 0.5, 0.0, 0.3330442],
[0.0781, 0.5, 0.0, 0.3099097],
[0.0703, 0.5, 0.0, 0.2962703],
[0.0625, 0.5, 0.0, 0.2807056],
[0.0000, 0.5, 0.0, 0.0000000]])
velocity = u.ProbeData(pts, "Velocity")
(ilen, jlen) = velocity.shape
norm=0.0
for i in range(ilen):
diff = pts[i][3] - velocity[i][1]
norm = norm + diff*diff
norm = math.sqrt(norm/ilen)
print "botella_v_norm:", norm
return norm
def botella_u(NN):
#Botella and Peyret (1998) Table 9. NB.our velocity at the lid is reverse theirs therefore minus signs in u below
filelist_not_sorted = glob.glob('driven_cavity-%d/*.vtu'%NN)
vtu_nos_not_sorted = [int(file.split('.vtu')[0].split('_')[-1]) for file in filelist_not_sorted]
filelist = [filelist_not_sorted[i] for i in numpy.argsort(vtu_nos_not_sorted)]
file = filelist[-1]
print file
try:
os.stat(file)
except:
print "No such file: %s" % file
sys.exit(1)
u=vtktools.vtu(file)
pts=vtktools.arr([
[0.5, 0.0000, 0.0, 0.0000000],
[0.5, 0.0547, 0.0, -0.1812881],
[0.5, 0.0625, 0.0, -0.2023300],
[0.5, 0.0703, 0.0, -0.2228955],
[0.5, 0.1016, 0.0, -0.3004561],
[0.5, 0.1719, 0.0, -0.3885691],
[0.5, 0.2813, 0.0, -0.2803696],
[0.5, 0.4531, 0.0, -0.1081999],
[0.5, 0.5000, 0.0, -0.0620561],
[0.5, 0.6172, 0.0, 0.0570178],
[0.5, 0.7344, 0.0, 0.1886747],
[0.5, 0.8516, 0.0, 0.3372212],
[0.5, 0.9531, 0.0, 0.4723329],
[0.5, 0.9609, 0.0, 0.5169277],
[0.5, 0.9688, 0.0, 0.5808359],
[0.5, 0.9766, 0.0, 0.6644227],
[0.5, 1.0000, 0.0, 1.0000000]])
velocity = u.ProbeData(pts, "Velocity")
(ilen, jlen) = velocity.shape
norm=0.0
for i in range(ilen):
diff = pts[i][3] - velocity[i][0]
norm = norm + diff*diff
norm = math.sqrt(norm/ilen)
print "botella_u_norm:", norm
return norm
def csv_reader(filename, coords, t):
import sys
import vtktools
vtu = vtktools.vtu(filename[:-10] + '_' + str(t) + '.pvtu')
vtu.ApplyProjection('x', 'y', '0') # Set the third component to zero.
#Xlist = arange(0.0,4.001,0.01)# x co-ordinates of the desired array shape
#Ylist = arange(0.0,2.001,0.01)# y co-ordinates of the desired array shape
#[X,Y] = meshgrid(Xlist,Ylist)
#Z = 0.0*X # This is 2d so z is an array of zeros.
#X = reshape(X,(size(X),))
#Y = reshape(Y,(size(Y),))
#Z = reshape(Z,(size(Z),))
#zip(X,Y,Z)
#pts = zip(X,Y,Z)
print "coords: ", coords
pts = vtktools.arr([coords])
# create arrays of velocity and temperature values at the desired points
fs = vtu.ProbeData(pts, 'FreeSurface')
return fs[0]
def csv_reader(filename, coords, t):
import sys
import vtktools
vtu=vtktools.vtu(filename[:-10]+'_'+str(t)+'.pvtu')
vtu.ApplyProjection('x', 'y', '0') # Set the third component to zero.
#Xlist = arange(0.0,4.001,0.01)# x co-ordinates of the desired array shape
#Ylist = arange(0.0,2.001,0.01)# y co-ordinates of the desired array shape
#[X,Y] = meshgrid(Xlist,Ylist)
#Z = 0.0*X # This is 2d so z is an array of zeros.
#X = reshape(X,(size(X),))
#Y = reshape(Y,(size(Y),))
#Z = reshape(Z,(size(Z),))
#zip(X,Y,Z)
#pts = zip(X,Y,Z)
print "coords: ", coords
pts = vtktools.arr([coords])
# create arrays of velocity and temperature values at the desired points
fs = vtu.ProbeData(pts, 'FreeSurface')
return fs[0]
def find_sub_arc_isotherm_depth(
u, temp, a_t_dist
): #Take in vtu, temp, arc-trench distance, return isotherm depth
import vtktools
import numpy as np
import matplotlib.pyplot as plt
from scipy.interpolate import interp1d
max_x = 301000 #maximum x distance from trench to be considered
wedge_pts = []
X = np.array([i for i in np.arange(0, max_x, 1000)])
Y = np.array([i for i in np.arange(0, -201000, -1000)])
for i in np.arange(0, max_x, 1000):
for j in np.arange(0, -201000, -1000):
wedge_pts.append([i, j, 0.0])
dom = vtktools.arr(np.array(wedge_pts))
temp_struct = u.ProbeData(dom, 'Temperature')
CS = plt.contour(X,
Y,
np.reshape(temp_struct, (301, 201)).T, [temp],
colors="w",
linewidth=200)
plt.clf()
x = []
y = []
for i in range(2):
p = CS.collections[0].get_paths()[i]
v = p.vertices
x.extend(v[:, 0])
y.extend(v[:, 1])
x_new = []
y_new = []
for i in range(len(y)):
if y[i] > -100000:
x_new.append(x[i])
y_new.append(y[i])
f = interp1d(x_new, y_new)
return f(a_t_dist)
def find_sub_arc_isotherm_depth(u,temp,a_t_dist):#Take in vtu, temp, arc-trench distance, return isotherm depth import vtktools import numpy as np import matplotlib.pyplot as plt from scipy.interpolate import interp1d max_x=301000#maximum x distance from trench to be considered wedge_pts=[] X=np.array([i for i in np.arange(0,max_x,1000)]) Y=np.array([i for i in np.arange(0,-201000,-1000)]) for i in np.arange(0,max_x,1000): for j in np.arange(0,-201000,-1000): wedge_pts.append([i,j,0.0]) dom=vtktools.arr(np.array(wedge_pts)) temp_struct=u.ProbeData(dom,'Temperature') CS=plt.contour(X,Y,np.reshape(temp_struct,(301,201)).T,[temp],colors="w",linewidth=200) plt.clf() x=[] y=[] for i in range(2): p=CS.collections[0].get_paths()[i] v=p.vertices x.extend(v[:,0]) y.extend(v[:,1]) x_new=[] y_new=[] for i in range(len(y)): if y[i] >-100000: x_new.append(x[i]) y_new.append(y[i]) f=interp1d(x_new,y_new) return f(a_t_dist)
print ' Map data into probe...', 'VTK version ::', vtk.vtkVersion.GetVTKMajorVersion(
), '.', vtk.vtkVersion.GetVTKMinorVersion()
if vtk.vtkVersion.GetVTKMajorVersion() <= 5:
probe.SetInput(polydata)
probe.SetSource(ugrid)
else:
probe.SetInputData(polydata)
probe.SetSourceData(ugrid)
probe.Update()
print ' Check point Validity'
valid_ids = probe.GetOutput().GetPointData().GetArray(
'vtkValidPointMask')
validPoints = vtktools.arr(
[valid_ids.GetTuple1(i) for i in range(NrbPoints)])
print ' ... ', len(validPoints) - np.sum(
validPoints), 'invalid points'
# Extract data
print ' Extract Data'
values = probe.GetOutput().GetPointData().GetArray(fieldname)
for j in range(len(coordinates)):
# If valid point, extract using probe,
# Otherwise extract the cell:
# If no cell associated - then it is really a non-valid point outside the domain
# Otherwise: do the average over the cell values - this provide the tracer value.
if validPoints[j] == 1:
tmp = values.GetValue(j)
if tmp < 0.: # This is because a negative values of concentration makes no sense
pts=vtktools.arr([ [-5.3500, 36.1333, -2.00], [-4.4500, 36.7000, 0.00], [-3.9167, 35.2500, 0.00], [-2.4500, 36.8333, 0.00], [-0.5833, 38.3333, 0.00], [2.6333, 39.5833, 0.00], [3.1000, 42.4833, 0.00], [5.3500, 43.3000, 0.00], [6.9167, 36.8833, 0.00], [8.0167, 43.8667, 0.00], [8.3000, 39.1500, 0.00], [8.9000, 44.4000, 0.00], [9.1667, 39.2000, 0.00], [9.8500, 44.0667, 0.00], [10.1167, 33.8833, 0.00], [10.3000, 43.5333, 0.00], [10.7667, 34.7333, 0.00], [11.1167, 33.5000, 0.00], [11.7833, 42.1000, 0.00], [12.0000, 36.7833, 0.00], [12.3333, 45.4167, 0.00], [12.5000, 35.5000, 0.00], [12.5833, 37.6333, 0.00], [12.8167, 36.1667, 0.00], [13.2000, 32.9000, 0.00], [13.3333, 38.1333, 0.00], [13.5000, 43.6167, 0.00], [13.5000, 37.2500, 0.00], [13.7500, 45.6500, 0.00], [13.9333, 40.7333, 0.00], [14.2667, 40.8667, 0.00], [14.4000, 42.5167, 0.00], [14.5167, 35.9000, 0.00], [14.5333, 45.3000, 0.00], [14.9667, 38.4833, 0.00], #[15.1000, 38.5000, 0.00], [15.1500, 36.6833, 0.00], [15.2500, 38.2167, 0.00], [15.6500, 38.1167, 0.00], [15.7667, 43.0333, 0.00], [16.1833, 41.8833, 0.00], [16.4333, 43.5000, 0.00], [17.2167, 40.4667, 0.00], [17.9333, 40.6333, 0.00], [18.5000, 40.1500, 0.00], [19.1000, 42.0667, 0.00], [20.7000, 38.8333, 0.00], [21.3167, 37.6333, 0.00], [22.1333, 37.0167, 0.00], [23.0333, 40.6167, 0.00], [23.8000, 32.1833, 0.00], [24.0500, 35.5000, 0.00], [24.9167, 37.4333, 0.00], [25.1333, 35.3333, 0.00], [25.3833, 40.8500, 0.00], [25.7000, 31.7667, 0.00], [26.1500, 38.3833, 0.00], [26.8833, 37.0833, 0.00], [28.2333, 36.4333, 0.00], [29.8667, 31.2000, 0.00], [32.3167, 31.2667, 0.00], [33.3167, 35.3333, 0.00], [33.9500, 35.1167, 0.00]])
filename = '/tamay2/mensa/fluidity/'+exp+'/particles.detectors'
filename2 = '/tamay2/mensa/fluidity/'+exp+'/ring_10.pvtu'
data = vtktools.vtu(filename2)
coords = data.GetLocations()
depths = sorted(list(set(coords[:,2])))
Xlist = np.linspace(-180000,180000,50)# x co-ordinates of the desired array shape
Ylist = np.arange(0,1)*0.0
Zlist = np.linspace(0,-900,20)# y co-ordinates of the desired array shape
[X,Y,Z] = myfun.meshgrid2(Xlist,Ylist,Zlist)
Y = np.reshape(Y,(np.size(Y),))
X = np.reshape(X,(np.size(X),))
Z = np.reshape(Z,(np.size(Z),))
pts = vtktools.arr(zip(X,Y,Z))
R = data.ProbeData(pts, 'Density_CG')
rho = np.reshape(R,[len(Zlist),len(Ylist),len(Xlist)])
try: os.stat('./plot/'+exp)
except OSError: os.mkdir('./plot/'+exp)
print 'reading detectors'
det = fluidity_tools.stat_parser(filename)
keys = det.keys() # particles
print 'done.'
pt = int(os.popen('grep position '+filename+'| wc -l').read()) # read the number of particles grepping all the positions in the file
tt = 45000
def MLD(filelist, unique_string):
x0 = 166.6
y0 = 50.
tke0 = 1.0e-5
times = []
depths = []
Dm = []
nums = []
# check for no files
if (len(filelist) == 0):
print "No files!"
sys.exit(1)
for file in filelist:
try:
os.stat(file)
except:
print "No such file: %s" % file
sys.exit(1)
num = int(file.split(".vtu")[0].split('_')[-1])
if (num < 1):
continue
nums.append(num)
nums.sort()
last_mld = 0.
for num in nums:
file = "gls-MixedLayer-"+unique_string+"_"+str(num)+".vtu"
u=vtktools.vtu(file)
time = u.GetScalarField('Time')
tt = time[0]
kk = u.GetScalarField('GLSTurbulentKineticEnergy')
pos = u.GetLocations()
xyzkk = []
for i in range(0,len(kk)):
if( abs(pos[i,0] - x0) < 0.1 and abs(pos[i,1] - y0) < 0.1):
xyzkk.append((pos[i,0],pos[i,1],-pos[i,2],(kk[i])))
xyzkkarr = vtktools.arr(xyzkk)
III = argsort(xyzkkarr[:,2])
xyzkkarrsort = xyzkkarr[III,:]
# march down the column, grabbing the last value above tk0 and the first
# one less than tke0. Interpolate between to get the MLD
kea = 1000
keb = 0
zza = 0
zzb = 0
for values in xyzkkarrsort:
if (values[3] > tke0):
kea = values[3]
zza = -values[2]
if (values[3] < tke0):
keb = values[3]
zzb = -values[2]
break
# We're using quite low resolution, so a better estimate of the MLD is
# somewhere between the 2 layers
mld = zza
if (last_mld == mld):
continue
times.append(tt)
depths.append(-1.0*mld)
last_mld = mld
Dm.append(1.05*0.01*(1.0/sqrt(0.01))*sqrt(tt))
return times, depths, Dm
def MLD(filelist, unique_string):
x0 = 166.6
y0 = 50.
tke0 = 1.0e-5
times = []
depths = []
Dm = []
nums = []
# check for no files
if (len(filelist) == 0):
print "No files!"
sys.exit(1)
for file in filelist:
try:
os.stat(file)
except:
print "No such file: %s" % file
sys.exit(1)
num = int(file.split(".vtu")[0].split('_')[-1])
if (num < 1):
continue
nums.append(num)
nums.sort()
last_mld = 0.
for num in nums:
file = "gls-MixedLayer-" + unique_string + "_" + str(num) + ".vtu"
u = vtktools.vtu(file)
time = u.GetScalarField('Time')
tt = time[0]
kk = u.GetScalarField('GLSTurbulentKineticEnergy')
pos = u.GetLocations()
xyzkk = []
for i in range(0, len(kk)):
if (abs(pos[i, 0] - x0) < 0.1 and abs(pos[i, 1] - y0) < 0.1):
xyzkk.append((pos[i, 0], pos[i, 1], -pos[i, 2], (kk[i])))
xyzkkarr = vtktools.arr(xyzkk)
III = argsort(xyzkkarr[:, 2])
xyzkkarrsort = xyzkkarr[III, :]
# march down the column, grabbing the last value above tk0 and the first
# one less than tke0. Interpolate between to get the MLD
kea = 1000
keb = 0
zza = 0
zzb = 0
for values in xyzkkarrsort:
if (values[3] > tke0):
kea = values[3]
zza = -values[2]
if (values[3] < tke0):
keb = values[3]
zzb = -values[2]
break
# We're using quite low resolution, so a better estimate of the MLD is
# somewhere between the 2 layers
mld = zza
if (last_mld == mld):
continue
times.append(tt)
depths.append(-1.0 * mld)
last_mld = mld
Dm.append(1.05 * 0.01 * (1.0 / sqrt(0.01)) * sqrt(tt))
return times, depths, Dm
# dimensions archives xstep = 5000 ystep = 1 zstep = -20 Xlist = np.arange(loni,lonf+xstep,xstep)# x co-ordinates of the desired array shape Ylist = np.arange(lati,latf+ystep,ystep)# y co-ordinates of the desired array shape Zlist = np.arange(depthi,depthf+zstep,zstep)# y co-ordinates of the desired array shape [X,Y,Z] = myfun.meshgrid2(Xlist,Ylist,Zlist) Y = np.reshape(Y,(np.size(Y),)) X = np.reshape(X,(np.size(X),)) Z = np.reshape(Z,(np.size(Z),)) pts = zip(X,Y,Z) pts = vtktools.arr(pts) # define flux flux = [] flux_t = np.linspace(0,24,50) for t in flux_t: tt = t%24/6.0 if tt >=0 and tt < 1: flux.append(-250 + 1000.0*tt) elif tt >= 1 and tt < 2: flux.append(1750 - 1000.0*tt) else: flux.append(-250.0)
#fsle param
di = 0.5 # base separation distance [m]. Taken as the distance between the particles in the triplet.
# read ML depth from file
Tref = [0.2,0.3]
mld = []
for i in range(len(Tref)):
Data = pyvtk.VtkData('/nethome/jmensa/scripts_fluidity/2D/ML/output/'+exp+'/ML_'+myfun.digit(Tref[i],3)+'_'+exp+'_'+day+'.vtk')
mld.append(np.reshape(Data.point_data.data[0].scalars,[len(Ylist),len(Xlist)]))
# read T from archive
data = vtktools.vtu('/tamay/mensa/fluidity/'+exp+'/mli_'+day+'.pvtu')
Ts = np.reshape(data.ProbeData(vtktools.arr(zip(X,Y,Z)), 'Temperature'),[len(Zlist),len(Ylist),len(Xlist)])
# for future plotting
Yf, Zf = np.meshgrid(Ylist,Zlist)
Y, Z = np.meshgrid(y,z)
for r in np.linspace(2,5,3):
#print 'plotting for dr:',r*di
fsle = np.zeros(pt/4)
fslec = np.zeros((pt/4,3))
df = r*di # separation distance
#
# loop triplets in time
#
for t in range(tt):
for d in range(0,pt,4):
u = vtktools.vtu(file)
time = u.GetScalarField('Time')
tt = time[0]
kk = u.GetScalarField('GLSTurbulentKineticEnergy')
pos = u.GetLocations()
if (tt < 100):
continue
xyzkk = []
for i in range(0, len(kk)):
if (abs(pos[i, 0] - x0) < 0.1):
xyzkk.append((pos[i, 0], -pos[i, 1], pos[i, 2], (kk[i])))
xyzkkarr = vtktools.arr(xyzkk)
III = argsort(xyzkkarr[:, 1])
xyzkkarrsort = xyzkkarr[III, :]
# march down the column, grabbing the last value above tk0 and the first
# one less than tke0. Interpolate between to get the MLD
kea = 1000
keb = 0
zza = 0
zzb = 0
for values in xyzkkarrsort:
if (values[3] > tke0):
kea = values[3]
zza = -values[1]
if (values[3] < tke0):
keb = values[3]
zzb = -values[1]
timeee = u.GetScalarField('Time')
Time = timeee[0]
temp = u.GetScalarField("Temperature")
vert_diff = u.GetScalarField("GLSVerticalDiffusivity")
vert_visc = u.GetScalarField("GLSVerticalViscosity")
uvw = u.GetVectorField("Velocity")
kk = u.GetScalarField('GLSTurbulentKineticEnergy')
pos = u.GetLocations()
xyzkk = []
for i in range(0,len(kk)):
if( abs(pos[i,0] - x0) < 0.1 ):
xyzkk.append((pos[i,0],-pos[i,1],pos[i,2],kk[i],temp[i],uvw[i,0],vert_diff[i],vert_visc[i]))
xyzkkarr = vtktools.arr(xyzkk)
III = argsort(xyzkkarr[:,1])
xyzkkarrsort = xyzkkarr[III,:]
zzz = -xyzkkarrsort[:,1]
kkk = xyzkkarrsort[:,3]
ttt = xyzkkarrsort[:,4]
uuu = xyzkkarrsort[:,5]
diff = xyzkkarrsort[:,6]
visc = xyzkkarrsort[:,7]
fig = figure()
pts = vtktools.arr([
#[-5.3500, 36.1333, -2.00],
#[-4.4500, 36.7000, 0.00],
#[-3.9167, 35.2500, 0.00],
#[-2.4500, 36.8333, 0.00],
#[-0.5833, 38.3333, 0.00],
[2.6333, 39.5833, 0.00],
#[3.1000, 42.4833, 0.00],
#[5.3500, 43.3000, 0.00],
#[6.9167, 36.8833, 0.00],
[8.0167, 43.8667, 0.00],
[8.3000, 39.1500, 0.00],
[8.9000, 44.4000, 0.00],
[9.1667, 39.2000, 0.00],
#[9.8500, 44.0667, 0.00],
#[10.1167, 33.8833, 0.00],
[10.3000, 43.5333, 0.00],
#[10.7667, 34.7333, 0.00],
#[11.1167, 33.5000, 0.00],
#[11.7833, 42.1000, 0.00],
[12.0000, 36.7833, 0.00],
#[12.3333, 45.4167, 0.00],
[12.5000, 35.5000, 0.00],
[12.5833, 37.6333, 0.00],
[12.8167, 36.1667, 0.00],
[13.2000, 32.9000, 0.00],
#[13.3333, 38.1333, 0.00],
#[13.5000, 43.6167, 0.00],
[13.5000, 37.2500, 0.00],
[13.7500, 45.6500, 0.00],
[13.9333, 40.7333, 0.00],
#[14.2667, 40.8667, 0.00],
[14.4000, 42.5167, 0.00],
[14.5167, 35.9000, 0.00],
#[14.5333, 45.3000, 0.00],
[14.9667, 38.4833, 0.00],
#[15.1000, 38.5000, 0.00],
[15.1500, 36.6833, 0.00],
#[15.2500, 38.2167, 0.00],
#[15.6500, 38.1167, 0.00],
[15.7667, 43.0333, 0.00],
[16.1833, 41.8833, 0.00],
#[16.4333, 43.5000, 0.00],
#[17.2167, 40.4667, 0.00],
#[17.9333, 40.6333, 0.00],
#[18.5000, 40.1500, 0.00],
[19.1000, 42.0667, 0.00],
#[20.7000, 38.8333, 0.00],
[21.3167, 37.6333, 0.00],
#[22.1333, 37.0167, 0.00],
#[23.0333, 40.6167, 0.00],
[23.8000, 32.1833, 0.00],
#[24.0500, 35.5000, 0.00],
[24.9167, 37.4333, 0.00],
#[25.1333, 35.3333, 0.00],
[25.3833, 40.8500, 0.00],
[25.7000, 31.7667, 0.00],
[26.1500, 38.3833, 0.00],
[26.8833, 37.0833, 0.00],
[28.2333, 36.4333, 0.00],
[29.8667, 31.2000, 0.00],
[32.3167, 31.2667, 0.00],
#[33.3167, 35.3333, 0.00],
#[33.9500, 35.1167, 0.00]
])
