def Creating_z(Plane,Slope,Sediment,Start_time,End_time,Time_step):
vtuObject = vtktools.vtu(Plane)
vtuObject.GetFieldNames()
gradient = vtuObject.GetScalarField('u')
ugrid = vtk.vtkUnstructuredGrid()
gridreader=vtk.vtkXMLUnstructuredGridReader()
gridreader.SetFileName(Plane)
gridreader.Update()
ugrid = gridreader.GetOutput()
points = ugrid.GetPoints()
nPoints = ugrid.GetNumberOfPoints()
for p in range(0,nPoints):
x = (points.GetPoint(p)[:2] + (gradient[p],))
points.SetPoint(p,x)
ugrid.Update()
###################################################################################################################
t = Start_time
dt = Time_step
et = End_time
while t <= et:
Import = Sediment + str(t) +'000000.vtu'
NewSave = Sediment + str(t) + '_sed_slope.pvd'
vtuObjectSed = vtktools.vtu(Import)
vtuObjectSed.GetFieldNames()
gradientSed = vtuObjectSed.GetScalarField('u')
sedgrid = vtk.vtkUnstructuredGrid()
sedgridreader=vtk.vtkXMLUnstructuredGridReader()
sedgridreader.SetFileName(Import)
sedgridreader.Update()
sedgrid = sedgridreader.GetOutput()
s = sedgrid.GetPoints()
for p in range(0,nPoints):
x = ((s.GetPoint(p)[0],) + (s.GetPoint(p)[1],) + ((gradientSed[p]+gradient[p]),))
s.SetPoint(p,x)
writer = vtk.vtkUnstructuredGridWriter()
writer.SetFileName(NewSave)
writer.SetInput(sedgrid)
writer.Update()
writer.Write()
t += dt
writer = vtk.vtkUnstructuredGridWriter()
writer.SetFileName(Slope)
writer.SetInput(ugrid)
writer.Update()
writer.Write()
def probe_visc():
# Files and probing resolution:
vtufile = "Benchmark_Case_1a_1.pvtu"
npoints = 500
# First probe viscosity at y = 550e3
# Setup Coordinates:
colx = numpy.array([numpy.linspace(0,500e3,npoints)]).reshape(npoints,1)
colz = numpy.zeros((npoints,1))
coly = numpy.ones((npoints,1))*550e3
coordinates = numpy.concatenate((colx,coly,colz),1)
# Open file and probe for Viscosity:
vtu = vtktools.vtu(vtufile)
viscosity_y_550 = vtktools.vtu.ProbeData(vtu,coordinates,'Mantle::Viscosity')[:,0,0]
# Next probe viscosity at x = 500e3
# Setup Coordinates:
coly = numpy.array([numpy.linspace(0,660e3,npoints)]).reshape(npoints,1)
colz = numpy.zeros((npoints,1))
colx = numpy.ones((npoints,1))
coordinates = numpy.concatenate((colx,coly,colz),1)
# Open file and probe for Viscosity:
vtu = vtktools.vtu(vtufile)
viscosity_x_500 = vtktools.vtu.ProbeData(vtu,coordinates,'Mantle::Viscosity')[:,0,0]
return min(viscosity_y_550), max(viscosity_y_550), min(viscosity_x_500), max(viscosity_x_500)
def probe_visc():
# Files and probing resolution:
vtufile = "Benchmark_Case_1a_1.pvtu"
npoints = 500
# First probe viscosity at y = 550e3
# Setup Coordinates:
colx = numpy.array([numpy.linspace(0, 500e3, npoints)]).reshape(npoints, 1)
colz = numpy.zeros((npoints, 1))
coly = numpy.ones((npoints, 1)) * 550e3
coordinates = numpy.concatenate((colx, coly, colz), 1)
# Open file and probe for Viscosity:
vtu = vtktools.vtu(vtufile)
viscosity_y_550 = vtktools.vtu.ProbeData(vtu, coordinates,
'Mantle::Viscosity')[:, 0, 0]
# Next probe viscosity at x = 500e3
# Setup Coordinates:
coly = numpy.array([numpy.linspace(0, 660e3, npoints)]).reshape(npoints, 1)
colz = numpy.zeros((npoints, 1))
colx = numpy.ones((npoints, 1))
coordinates = numpy.concatenate((colx, coly, colz), 1)
# Open file and probe for Viscosity:
vtu = vtktools.vtu(vtufile)
viscosity_x_500 = vtktools.vtu.ProbeData(vtu, coordinates,
'Mantle::Viscosity')[:, 0, 0]
return min(viscosity_y_550), max(viscosity_y_550), min(
viscosity_x_500), max(viscosity_x_500)
def l2(file, numericalfield, analyticalfield):
ug = vtktools.vtu(file)
ug.GetFieldNames()
uv = ug.GetScalarField(numericalfield)
ex = ug.GetScalarField(analyticalfield)
pos = ug.GetLocations()
x = pos[:,0]; y=pos[:,1]; z=pos[:,2]
NE = ug.ugrid.GetNumberOfCells()
ML = zeros(size(x), float)
for ele in range(NE):
ndglno = ug.GetCellPoints(ele)
if(size(ndglno)==4):
t = tetvol(x[ndglno],y[ndglno],z[ndglno])
elif(size(ndglno)==3):
t = triarea(x[ndglno],y[ndglno])
for nod in ndglno:
ML[nod] = ML[nod]+t/size(ndglno)
err_x = ex- uv
norm_x = 0.0
diff = zeros(size(x), float)
for nod in range(size(x)):
norm_x = norm_x + ML[nod]*(err_x[nod])**2
norm_x = sqrt(abs(norm_x))
return (norm_x)
def get_velocity_field(fileNumber):
"""
Used to get the Velocity Field as a numpy array corresponding to a vtu file
from the Fluids dataset. Note this normalises the returned array.
:param fileNumber: int or string
Used to identify which vtu file to return
Values are between 0 and 988
:return: numpy array
Velocity Fields are returned as numpy array
"""
folderPath = defaultFilePath + '/small3DLSBU'
filePath = folderPath + '/LSBU_' + str(fileNumber) + '.vtu'
sys.path.append('fluidity-master')
ug = vtktools.vtu(filePath)
ug.GetFieldNames()
p = ug.GetVectorField('Velocity')
p = np.array(p)
# Normalise p
p = normalise(p, x_min, x_max)
# Convert p into 1 x N array
p = np.array(p)
p = p.transpose()
#p = np.array([p[:]])
return p
def get_prediction_velocity(fileNumber):
"""
Used to get the Tracers as a numpy array corresponding to a vtu file from the Fluids dataset
:param fileNumber: int or string
Used to identify which vtu file to return
Values are between 0 and 988
:return: numpy array
Tracers are returned as numpy array
"""
networkName = 'vDA' # Change this to prediction folder name
folderPath = defaultFilePath + '/' + networkName
filePath = folderPath + '/' + networkName + '_' + str(fileNumber) + '.vtu'
sys.path.append('fluidity-master')
ug = vtktools.vtu(filePath)
ug.GetFieldNames()
p = ug.GetVectorField('Latent-GAN')
p = np.array(p)
# Normalise p
p = normalise(p, x_min, x_max)
# Convert p into 3 x N array
#p = np.array([p[:]])
p = p.transpose()
return p
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 create_velocity_field_VTU_GAN(fileNumber, prediction, networkName):
"""
Duplicates preexisting VTU file and attaches a prediction field alongside it.
Files are named based on the input timestep t.
Files contain prediction for t+1 and ground truth for t+1.
:param fileNumber: int or string
Used to identify which vtu file to return
Values are between 0 and 988
:param prediction: numpy array
Predicted tracers
:param networkName: string
Name of the network e.g. "AE", "GAN" or "AEGAN" etc.
All created tracers will be saved to the default file directory in a
folder with the network name.
"""
folderPath = defaultFilePath + '/small3DLSBU'
filePath = folderPath + '/LSBU_' + str(fileNumber + 1) + '.vtu'
sys.path.append('fluidity-master')
ug = vtktools.vtu(filePath)
ug.AddVectorField('Latent-GAN', prediction)
saveFolderPath = defaultFilePath + '/' + networkName
saveFolderPath = 'E:/MSc Individual Project/Fluids Dataset'
saveFilePath = saveFolderPath + '/' + networkName + '_' + str(
fileNumber) + '.vtu'
ug.Write(saveFilePath)
def get_water_depths(filelist, xarray, delta):
results = []
for f in filelist:
try:
os.stat(f)
except:
print "No such file: %s" % f
sys.exit(1)
y = numpy.arange(delta/2.0,2.0+delta/2.0,delta)[:,numpy.newaxis]
num = int(f.split(".vtu")[0].split('_')[-1])
vtu = vtktools.vtu(f)
for name in vtu.GetFieldNames():
if name.endswith("Time"):
time = max(vtu.GetScalarRange(name))
break
waterdepths = []
waterdepths.append(num)
waterdepths.append(time)
for x in range(len(xarray)):
coordinates = numpy.concatenate((numpy.ones((len(y),1))*xarray[x], y, numpy.zeros((len(y),1))),1)
waterdepths.append(sum(vtu.ProbeData(coordinates, "Water::MaterialVolumeFraction"))[0]*delta)
results.append(waterdepths)
results.sort(key=operator.itemgetter(1))
results = numpy.array(results)
return results
def GetXandt(filelist):
time = []
X_ns = []
X_fs = []
for files in filelist:
data = vtktools.vtu(files)
time.append(data.GetScalarField("Time")[0])
# Get X
data.ugrid.GetPointData().SetActiveScalars('Temperature')
data = data.ugrid
contour = vtk.vtkContourFilter()
if vtk.vtkVersion.GetVTKMajorVersion() <= 5:
contour.SetInput(data)
else:
contour.SetInputData(data)
contour.SetValue(0, 0.0)
contour.Update()
polydata = contour.GetOutput()
bounding_box = polydata.GetBounds()
X_ns.append(bounding_box[1])
X_fs.append(bounding_box[0])
return time, X_ns, X_fs
def create_X_from_fps(fps, settings, field_type="scalar"):
"""Creates a numpy array of values of scalar field_name
Input list must be sorted"""
M = len(fps) #number timesteps
for idx, fp in enumerate(fps):
# create array of tracer
ug = vtktools.vtu(fp)
if not settings.THREE_DIM:
matrix = FluidityUtils.get_1D_grid(ug, settings.FIELD_NAME,
field_type)
elif settings.THREE_DIM == True:
matrix = FluidityUtils().get_3D_grid(ug, settings)
else:
raise ValueError(
"<config>.THREE_DIM must be True or eval to False")
mat_size = matrix.shape
if idx == 0:
#fix length of vectors and initialize the output array:
n = matrix.shape
size = (M, ) + n
output = np.zeros(size)
else:
#enforce all vectors are of the same length
assert mat_size == n, "All input .vtu files must be of the same size."
output[idx] = matrix
#return (M x nx x ny x nz) or (M x n)
if settings.SAVE:
np.save(settings.X_FP, output, allow_pickle=True)
return output
def get_water_depths(filelist, xarray, delta):
results = []
for f in filelist:
try:
os.stat(f)
except:
print "No such file: %s" % f
sys.exit(1)
y = numpy.arange(delta / 2.0, 2.0 + delta / 2.0, delta)[:,
numpy.newaxis]
num = int(f.split(".vtu")[0].split('_')[-1])
vtu = vtktools.vtu(f)
for name in vtu.GetFieldNames():
if name.endswith("Time"):
time = max(vtu.GetScalarRange(name))
break
waterdepths = []
waterdepths.append(num)
waterdepths.append(time)
for x in range(len(xarray)):
coordinates = numpy.concatenate((numpy.ones(
(len(y), 1)) * xarray[x], y, numpy.zeros((len(y), 1))), 1)
waterdepths.append(
sum(vtu.ProbeData(coordinates,
"Water::MaterialVolumeFraction"))[0] * delta)
results.append(waterdepths)
results.sort(key=operator.itemgetter(1))
results = numpy.array(results)
return results
def meanvelo(file, x, y):
print("\nRunning velocity profile script on files at times...\n")
##### create array of points. Correct for origin not at step.
pts = []
for i in range(len(x)):
for j in range(len(y)):
pts.append([x[i] + 5.0, y[j], 0.0])
pts = numpy.array(pts)
profiles = numpy.zeros([x.size, y.size], float)
datafile = vtktools.vtu(file)
##### Get x-velocity
uvw = datafile.ProbeData(pts, "AverageVelocity")
u = uvw[:, 0]
u = u.reshape([x.size, y.size])
for i in range(len(x)):
umax = max(u[i, :])
u[i, :] = u[i, :] / umax
profiles[:, :] = u
print("\n...Finished writing data files.\n")
return profiles
def create_tracer_VTU_AE(fileNumber, prediction, networkName):
"""
Duplicates preexisting VTU file and attaches a reconstruction field alongside it.
:param fileNumber: int or string
Used to identify which vtu file to return
Values are between 0 and 988
:param prediction: numpy array
Predicted tracers
:param networkName: string
Name of the network e.g. "AE", "GAN" or "AEGAN" etc.
All created tracers will be saved to the default file directory in a
folder with the network name.
"""
folderPath = defaultFilePath + '/small3DLSBU'
filePath = folderPath + '/LSBU_' + str(fileNumber) + '.vtu'
sys.path.append('fluidity-master')
ug = vtktools.vtu(filePath)
ug.AddScalarField('Latent-AE', prediction)
saveFolderPath = defaultFilePath + '/' + networkName
saveFolderPath = 'E:/MSc Individual Project/Fluids Dataset/tLatentGANExtrap'
saveFilePath = saveFolderPath + '/' + networkName + '_' + str(
fileNumber) + '.vtu'
ug.Write(saveFilePath)
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 meanvelo(file,x,y):
print "\nRunning velocity profile script on files at times...\n"
##### create array of points. Correct for origin not at step.
pts=[]
for i in range(len(x)):
for j in range(len(y)):
pts.append([x[i]+5.0, y[j], 0.0])
pts=numpy.array(pts)
profiles=numpy.zeros([x.size, y.size], float)
datafile = vtktools.vtu(file)
##### Get x-velocity
uvw = datafile.ProbeData(pts, "AverageVelocity")
u = uvw[:,0]
u=u.reshape([x.size,y.size])
for i in range(len(x)):
umax = max(u[i,:])
u[i,:] = u[i,:]/umax
profiles[:,:] = u
print "\n...Finished writing data files.\n"
return profiles
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 GetXandt(filelist):
time = []
X_ns = []
X_fs = []
for files in filelist:
data = vtktools.vtu(files)
time.append(data.GetScalarField("Time")[0])
# Get X
data.ugrid.GetPointData().SetActiveScalars('Temperature')
data = data.ugrid
contour = vtk.vtkContourFilter()
if vtk.vtkVersion.GetVTKMajorVersion() <= 5:
contour.SetInput(data)
else:
contour.SetInputData(data)
contour.SetValue(0, 0.0)
contour.Update()
polydata = contour.GetOutput()
bounding_box = polydata.GetBounds()
X_ns.append(bounding_box[1])
X_fs.append(bounding_box[0])
return time, X_ns, X_fs
def l2(file, numericalfield, analyticalfield):
ug = vtktools.vtu(file)
ug.GetFieldNames()
uv = ug.GetScalarField(numericalfield)
ex = ug.GetScalarField(analyticalfield)
pos = ug.GetLocations()
x = pos[:, 0]
y = pos[:, 1]
z = pos[:, 2]
NE = ug.ugrid.GetNumberOfCells()
ML = zeros(size(x), float)
for ele in range(NE):
ndglno = ug.GetCellPoints(ele)
if (size(ndglno) == 4):
t = tetvol(x[ndglno], y[ndglno], z[ndglno])
elif (size(ndglno) == 3):
t = triarea(x[ndglno], y[ndglno])
for nod in ndglno:
ML[nod] = ML[nod] + t / size(ndglno)
err_x = ex - uv
norm_x = 0.0
diff = zeros(size(x), float)
for nod in range(size(x)):
norm_x = norm_x + ML[nod] * (err_x[nod])**2
norm_x = sqrt(abs(norm_x))
return (norm_x)
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 reattachment_length(filelist):
print "Calculating reattachment point locations using change of x-velocity sign\n"
nums = []
results = []
files = []
##### 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)
files.append(file)
sort_nicely(files)
for file in files:
##### Read in data from vtu
datafile = vtktools.vtu(file)
##### Get time for plot:
t = min(datafile.GetScalarField("Time"))
print file, ', elapsed time = ', t
##### points near bottom surface, 0 < x < 20
pts = []
no_pts = 82
offset = 0.1
x = 5.0
for i in range(1, no_pts):
pts.append((x, offset, 0.0))
x += 0.25
pts = numpy.array(pts)
##### Get x-velocity on bottom boundary
uvw = datafile.ProbeData(pts, "Velocity")
u = []
u = uvw[:, 0]
points = []
for i in range(len(u) - 1):
##### Hack to ignore division by zero entries in u.
##### All u should be nonzero away from boundary!
if ((u[i] / u[i + 1]) < 0. and not numpy.isinf(u[i] / u[i + 1])):
##### interpolate between nodes. Correct for origin not at step.
p = pts[i][0] + (pts[i + 1][0] - pts[i][0]) * (0.0 - u[i]) / (
u[i + 1] - u[i]) - 5.0
##### Ignore spurious corner points
if (p > 1.0):
points.append(p)
##### Append actual reattachment point and time:
results.append([points[0], t])
return results
def reattachment_length(filelist):
print "Calculating reattachment point locations using change of x-velocity sign\n"
nums=[]; results=[]; files = []
##### 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)
files.append(file)
sort_nicely(files)
for file in files:
##### Read in data from vtu
datafile = vtktools.vtu(file)
##### Get time for plot:
t = min(datafile.GetScalarField("Time"))
print file, ', elapsed time = ', t
##### points near bottom surface, 0 < x < 20
pts=[]; no_pts = 82; offset = 0.01
x = 5.0
for i in range(1, no_pts):
pts.append((x, offset, 0.0))
x += 0.25
pts = numpy.array(pts)
##### Get x-velocity on bottom boundary
uvw = datafile.ProbeData(pts, "AverageVelocity")
u = []
u = uvw[:,0]
points = 0.0
for i in range(len(u)-1):
##### Hack to ignore division by zero entries in u.
##### All u should be nonzero away from boundary!
if((u[i] / u[i+1]) < 0. and u[i+1] > 0. and not numpy.isinf(u[i] / u[i+1])):
##### interpolate between nodes. Correct for origin not at step.
p = pts[i][0] + (pts[i+1][0]-pts[i][0]) * (0.0-u[i]) / (u[i+1]-u[i]) -5.0
print 'p ', p
##### Ignore spurious corner points
if(p>2):
points = p
##### We have our first point on this plane so...
break
print "reattachment point found at: ", points
##### Append actual reattachment point and time:
results.append([points,t])
return results
def meanvelo(filelist, xarray, yarray, zarray):
print "\nRunning velocity profile script on files at times...\n"
##### check for no files
if (len(filelist) < 0):
print "No files!"
sys.exit(1)
##### create array of points
pts = []
for i in range(len(xarray)):
for j in range(len(yarray)):
for k in range(len(zarray)):
pts.append([xarray[i], yarray[j], zarray[k]])
pts = numpy.array(pts)
##### Create output array of correct shape
files = 3
filecount = 0
profiles = numpy.zeros([files, xarray.size, zarray.size], float)
for file in filelist:
try:
os.stat(file)
except:
f_log.write("No such file: %s" % files)
sys.exit(1)
##### Only process these 3 datafiles:
vtu_no = float(file.split('_')[-1].split('.')[0])
if (vtu_no == 6 or vtu_no == 11 or vtu_no == 33):
datafile = vtktools.vtu(file)
t = min(datafile.GetScalarField("Time"))
print file, ', elapsed time = ', t
##### Get x-velocity
uvw = datafile.ProbeData(pts, "Velocity")
umax = max(abs(datafile.GetVectorField("Velocity")[:, 0]))
u = uvw[:, 0] / umax
u = u.reshape([xarray.size, yarray.size, zarray.size])
##### Spanwise averaging
usum = numpy.zeros([xarray.size, zarray.size], float)
usum = numpy.array(usum)
for i in range(len(yarray)):
uav = u[:, i, :]
uav = numpy.array(uav)
usum += uav
usum = usum / len(yarray)
profiles[filecount, :, :] = usum
##### reset time to something big to prevent infinite loop
t = 100.
filecount += 1
print "\n...Finished extracting data.\n"
return profiles
def meanvelo(filelist,xarray,yarray,zarray):
print "\nRunning velocity profile script on files at times...\n"
##### check for no files
if (len(filelist) < 0):
print "No files!"
sys.exit(1)
##### create array of points
pts=[]
for i in range(len(xarray)):
for j in range(len(yarray)):
for k in range(len(zarray)):
pts.append([xarray[i], yarray[j], zarray[k]])
pts=numpy.array(pts)
##### Create output array of correct shape
files = 3; filecount = 0
profiles = numpy.zeros([files, xarray.size, zarray.size], float)
for file in filelist:
try:
os.stat(file)
except:
f_log.write("No such file: %s" % files)
sys.exit(1)
##### Only process these 3 datafiles:
vtu_no = float(file.split('_')[-1].split('.')[0])
if (vtu_no == 6 or vtu_no == 11 or vtu_no == 33):
datafile = vtktools.vtu(file)
t = min(datafile.GetScalarField("Time"))
print file, ', elapsed time = ', t
##### Get x-velocity
uvw = datafile.ProbeData(pts, "Velocity")
umax = max(abs(datafile.GetVectorField("Velocity")[:,0]))
u = uvw[:,0]/umax
u = u.reshape([xarray.size,yarray.size,zarray.size])
##### Spanwise averaging
usum = numpy.zeros([xarray.size,zarray.size],float)
usum = numpy.array(usum)
for i in range(len(yarray)):
uav = u[:,i,:]
uav = numpy.array(uav)
usum += uav
usum = usum / len(yarray)
profiles[filecount,:,:] = usum
##### reset time to something big to prevent infinite loop
t = 100.
filecount += 1
print "\n...Finished extracting data.\n"
return profiles
def values_per_node(file):
u=vtktools.vtu(file)
zoo = u.GetScalarField('Zooplankton')
phyto = u.GetScalarField('Phytoplankton')
nut = u.GetScalarField('Nutrient')
det = u.GetScalarField('Detritus')
return phyto, zoo, nut, det
def values_per_node(file):
u = vtktools.vtu(file)
zoo = u.GetScalarField('Zooplankton')
phyto = u.GetScalarField('Phytoplankton')
nut = u.GetScalarField('Nutrient')
det = u.GetScalarField('Detritus')
return phyto, zoo, nut, det
def inf(file, numericalfield, analyticalfield):
ug = vtktools.vtu(file)
ug.GetFieldNames()
uv = ug.GetScalarField(numericalfield)
ex = ug.GetScalarField(analyticalfield)
err_x = ex - uv
norm_x = max(abs(err_x))
return (norm_x)
def save_vtu_file(arr, name, filename, sample_fp=None):
"""Saves an unstructured VTU file - NOTE TODO - should be using deep copy method in vtktools.py -> VtuDiff()"""
if sample_fp == None:
sample_fp = vda.get_sorted_fps_U(self.settings.DATA_FP)[0]
ug = vtktools.vtu(
sample_fp) #use sample fp to initialize positions on grid
ug.AddScalarField('name', arr)
ug.Write(filename)
def inf(file, numericalfield, analyticalfield):
ug = vtktools.vtu(file)
ug.GetFieldNames()
uv = ug.GetScalarField(numericalfield)
ex = ug.GetScalarField(analyticalfield)
err_x = ex - uv
norm_x = max(abs(err_x))
return (norm_x)
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 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 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 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 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 get_cloud_front(path_prefix, n_files, resolution, threshold):
# Size of the domain
lx = 0.025
ly = 4.5
# Arrays to store the results
# Note: n_files is the number of VTU files to be read.
upper_positions = numpy.zeros(n_files)
lower_positions = numpy.zeros(n_files)
times = numpy.zeros(n_files)
path = path_prefix # + "/output/"
# For each vtu file...
for i in range(0, n_files, 20):
# Open the VTU files one by one
try:
file = vtktools.vtu(path +
'/mphase_rogue_shock_tube_dense_bed_nylon_' +
str(i) + '.pvtu')
except:
print("WARNING: Could not open VTU file!")
front_position[i] = 0
times[i] = 0
continue
file.GetFieldNames()
time = max(file.GetScalarField('Gas::Time'))
print("At time t = %f s" % time)
# Generate a set of probe positions
probes = numpy.linspace(1.35, 1.7, (ly / resolution))
# Loop over each of the probes in the y direction, from the top down
for j in range(len(probes) - 1, -1, -1):
vfrac = vtktools.vtu.ProbeData(file,
numpy.array([[0.0, probes[j], 0]]),
'Particles::PhaseVolumeFraction')
if (vfrac >= 0.3):
upper_positions[i] = probes[j]
break
for j in range(0, len(probes)):
vfrac = vtktools.vtu.ProbeData(file,
numpy.array([[0.0, probes[j], 0]]),
'Particles::PhaseVolumeFraction')
if (vfrac >= 0.01):
lower_positions[i] = probes[j]
break
times[i] = time - 0.0008
return times, upper_positions, lower_positions
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 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 flux(file,x,y):
u=vtktools.vtu(file)
flux = u.GetScalarField('HeatFlux')
pos = u.GetLocations()
f = finfo(float)
for i in range(0,len(flux)):
if( abs(pos[i,0] - x) < f.eps and abs(pos[i,1] - y) < f.eps and (pos[i,2] - 0.0) < f.eps ):
return flux[i]
return -666
def get_interface_depth(file):
vtu = vtktools.vtu(file)
data = vtu.ugrid
data.GetPointData().SetActiveScalars("Dense::MaterialVolumeFraction")
contour = vtk.vtkContourFilter()
contour.SetInput(data)
contour.SetValue(0, 0.5)
contour.Update()
polydata = contour.GetOutput()
bounding_box = polydata.GetBounds()
interface_depth = bounding_box[2]
return interface_depth
def get_interface_depth(file):
vtu=vtktools.vtu(file)
data = vtu.ugrid
data.GetPointData().SetActiveScalars("Dense::MaterialVolumeFraction")
contour = vtk.vtkContourFilter ()
contour.SetInput(data)
contour.SetValue(0, 0.5)
contour.Update()
polydata = contour.GetOutput()
bounding_box = polydata.GetBounds()
interface_depth = bounding_box[2]
return interface_depth
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 testVtuDim(self):
import vtktools
vtu = vtktools.vtu()
self.assertEquals(VtuDim(vtu), 0)
points = vtk.vtkPoints()
points.SetDataTypeToDouble()
points.InsertNextPoint(0.0, 0.0, 0.0)
points.InsertNextPoint(0.0, 0.0, 1.0)
vtu.ugrid.SetPoints(points)
self.assertEquals(VtuDim(vtu), 1)
return
def testVtuDim(self): import vtktools vtu = vtktools.vtu() self.assertEquals(VtuDim(vtu), 0) points = vtk.vtkPoints() points.SetDataTypeToDouble() points.InsertNextPoint(0.0, 0.0, 0.0) points.InsertNextPoint(0.0, 0.0, 1.0) vtu.ugrid.SetPoints(points) self.assertEquals(VtuDim(vtu), 1) return
def flux(file, x, y):
u = vtktools.vtu(file)
flux = u.GetScalarField('HeatFlux')
pos = u.GetLocations()
f = finfo(float)
for i in range(0, len(flux)):
if (abs(pos[i, 0] - x) < f.eps and abs(pos[i, 1] - y) < f.eps
and (pos[i, 2] - 0.0) < f.eps):
return flux[i]
return -666
def __call__(self, options):
stem = '{}/{}'.format(options.case_name, options.simulation_name)
# get the last dump file
n = 0
while os.path.isfile(get_filename(options, n + 1)):
n += 1
# load results and plot
vtu_obj = vtktools.vtu(get_filename(options, n))
x = vtu_obj.GetLocations()[:,0]
f = vtu_obj.GetScalarField('Tracer')
x, f = monotonic(x, f)
plt.plot(x, f, label=options.simulation_name)
self.print_end(options.simulation_name, options)
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_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 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 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 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_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 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 get_cloud_front(path_prefix, n_files, resolution, threshold):
# Size of the domain
lx = 0.025
ly = 4.5
# Arrays to store the results
# Note: n_files is the number of VTU files to be read.
upper_positions = numpy.zeros(n_files)
lower_positions = numpy.zeros(n_files)
times = numpy.zeros(n_files)
path = path_prefix# + "/output/"
# For each vtu file...
for i in range(0, n_files, 20):
# Open the VTU files one by one
try:
file = vtktools.vtu(path + '/mphase_rogue_shock_tube_dense_bed_nylon_' + str(i) + '.pvtu')
except:
print "WARNING: Could not open VTU file!"
front_position[i] = 0
times[i] = 0
continue
file.GetFieldNames()
time = max(file.GetScalarField('Gas::Time'))
print "At time t = %f s" % time
# Generate a set of probe positions
probes = numpy.linspace(1.35, 1.7, (ly/resolution))
# Loop over each of the probes in the y direction, from the top down
for j in range(len(probes)-1, -1, -1):
vfrac = vtktools.vtu.ProbeData(file, numpy.array([[0.0, probes[j], 0]]), 'Particles::PhaseVolumeFraction')
if(vfrac >= 0.3):
upper_positions[i] = probes[j]
break
for j in range(0, len(probes)):
vfrac = vtktools.vtu.ProbeData(file, numpy.array([[0.0, probes[j], 0]]), 'Particles::PhaseVolumeFraction')
if(vfrac >= 0.01):
lower_positions[i] = probes[j]
break
times[i] = time - 0.0008
return times, upper_positions, lower_positions
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 testVtuBoundingBox(self): import vtktools vtu = vtktools.vtu() points = vtk.vtkPoints() points.SetDataTypeToDouble() points.InsertNextPoint(-1.0, 2.0, -3.0) points.InsertNextPoint(1.0, -2.0, 3.0) vtu.ugrid.SetPoints(points) lbound, ubound = VtuBoundingBox(vtu).GetBounds() self.assertAlmostEquals(lbound[0], -1.0) self.assertAlmostEquals(lbound[1], -2.0) self.assertAlmostEquals(lbound[2], -3.0) self.assertAlmostEquals(ubound[0], 1.0) self.assertAlmostEquals(ubound[1], 2.0) self.assertAlmostEquals(ubound[2], 3.0) return
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
