def sample_vtk(file,
p1=None,
p2=None,
x_c=0,
N_points=101,
solver=None,
verbose=True):
"""
Samples velocity field in a given VTK file, along a line defined with p1 and p2, or x_c.
:param file: Path to the VTK file
:type file: str
:param p1: Coordinates of the starting point of the sample line. Can be either 2D or 3D [x, y] or [x, y, z]
:type p1: list
:param p2: Coordinates of the ending point of the sample line. Can be either 2D or 3D [x, y] or [x, y, z]
:type p2: list
:param x_c: If p1 and p2 are not provided, this parameter serves the x coordinate of the vertical line.
:type x_c: float
:param N_points: The number of points to sample the velocity in.
:type N_points: int
"""
if verbose:
print 'Sampling a VTK file: {}'.format(file)
solver = solver or postprocess.determineSolver(file)
if type(file) == str:
vtkFile = vtkextract.vtkFile()
vtkFile.solver = solver
vtkFile.readFile(file, verbose=False)
else:
vtkFile = file
centers = vtkFile.getCenters()
vtkFile.getVolumes()
bounds = vtkFile.bounds
p1 = p1 or [x_c, 0, -1]
p2 = p2 or [x_c, 0, np.max(bounds[:, 4:])]
if len(p1) == 2: p1.insert(1, 0) #if 2D data is provided
if len(p2) == 2: p2.insert(1, 0)
line = vtk.vtkLineSource()
line.SetResolution(N_points - 1)
line.SetPoint1(p1)
line.SetPoint2(p2)
probe = vtk.vtkProbeFilter()
probe.SetInputConnection(line.GetOutputPort())
probe.SetSourceConnection(vtkFile.outputPort)
probe.Update()
probe = probe.GetOutput()
vel = probe.GetPointData().GetArray(vtkFile.velArray[solver])
vel = np.array([vel.GetTuple(j) for j in range(probe.GetNumberOfPoints())])
line = np.array(
[probe.GetPoint(j) for j in range(probe.GetNumberOfPoints())])
return line, vel
def sample_vtk(file, p1=None, p2=None, x_c=0, N_points=101, solver=None, verbose=True):
"""
Samples velocity field in a given VTK file, along a line defined with p1 and p2, or x_c.
:param file: Path to the VTK file
:type file: str
:param p1: Coordinates of the starting point of the sample line. Can be either 2D or 3D [x, y] or [x, y, z]
:type p1: list
:param p2: Coordinates of the ending point of the sample line. Can be either 2D or 3D [x, y] or [x, y, z]
:type p2: list
:param x_c: If p1 and p2 are not provided, this parameter serves the x coordinate of the vertical line.
:type x_c: float
:param N_points: The number of points to sample the velocity in.
:type N_points: int
"""
if verbose:
print 'Sampling a VTK file: {}'.format(file)
solver=solver or postprocess.determineSolver(file)
if type(file) == str:
vtkFile = vtkextract.vtkFile()
vtkFile.solver = solver
vtkFile.readFile(file, verbose=False)
else:
vtkFile = file
centers = vtkFile.getCenters()
vtkFile.getVolumes()
bounds = vtkFile.bounds
p1 = p1 or [x_c, 0, -1]
p2 = p2 or [x_c, 0, np.max(bounds[:, 4:])]
if len(p1) == 2: p1.insert(1, 0) #if 2D data is provided
if len(p2) == 2: p2.insert(1, 0)
line = vtk.vtkLineSource()
line.SetResolution(N_points - 1)
line.SetPoint1(p1)
line.SetPoint2(p2)
probe = vtk.vtkProbeFilter()
probe.SetInputConnection(line.GetOutputPort())
probe.SetSourceConnection(vtkFile.outputPort)
probe.Update()
probe = probe.GetOutput()
vel=probe.GetPointData().GetArray(vtkFile.velArray[solver])
vel=np.array([vel.GetTuple(j) for j in range(probe.GetNumberOfPoints())])
line=np.array([probe.GetPoint(j) for j in range(probe.GetNumberOfPoints())])
return line, vel
def determineMesh():
solver = pproc.determineSolver()
if solver == 'Gerris':
lines = open(glob.glob('*.gfs')[0]).readlines()
sx = 1
#FINISHED, BUT I COULD MOVE l = re.split(...) TO THE BEGINNING, TO MAKE IT CLEANER
for l in lines:
if 'GfsSimulation' in l:
NBoxes = int(l.split()[0])
if 'PhysicalParams' in l:
H = float(re.split('[ =,{}]+',l.strip()) [2])
if 'MetricStretch' in l and not '#' in l:
sx = float(re.split('[ =,{}]+',l.strip()) [2])
l = l.split()
if len(l)==2 and l[0] in ['GfsRefine', 'Refine'] and l[1].isdigit():
refine = int(l[1])
if len(l)==3 and l[0] == 'Define' and l[1]== 'REFLEVEL':
refine = int(l[2])
Nx = NBoxes * 2**refine
Ny = 2**refine
L = H*sx*NBoxes
elif solver == 'Truchas':
lines = open(glob.glob('*.inp')[0]).readlines()
for l in lines:
l = filter(None, re.split('[ =,{}\n]+',l))
if 'Ncell' in l:
Nx = int(l[1])
Ny = int(l[2])
if 'Coord' in l:
L = float(l[4]) - float(l[1])
H = float(l[5]) - float(l[2])
elif solver == 'Thetis':
H = 0
L = 0
lines = open(glob.glob('*[0-9]*.don')[0]).readlines()
for l in lines:
l = re.split('[ ]+',l.strip())
if len(l)==3 and l[0] == 'MAILLAGE':
Nx = int(l[1])
Ny = int(l[2])
if 'DIM_MAX' in l:
L = L + float(l[1].replace('D0',''))
H = H + float(l[2].replace('D0',''))
if 'DIM_MIN' in l:
L = L - float(l[1].replace('D0',''))
H = H - float(l[2].replace('D0',''))
return L,H,Nx,Ny
def initialize(a=None, solitonPosition=15):
print 'Initialization of a solitary wave from numerical data'
sys.stdout.flush()
solver = pproc.determineSolver()
a = a or pproc.determineAmplitude()
refDir = os.path.join(referenceDirectoryMain,str(a))
if not os.path.exists(refDir):
print 'No data for given amplitude found. Amplitude provided:',a,', available data:'
for d in sorted(glob.glob(os.path.join(refDir,'../0.*'))):
print d
sys.exit()
surf = np.loadtxt(os.path.join(refDir,'surf'))
surf[:,0] = surf[:,0] + solitonPosition
surf = np.vstack((np.array([-200,0.]),surf,np.array([200,0]))) #if the left side is inside the domain, vofOfManyPolygons has problems
np.savetxt('interface.ini',surf,fmt='%10.6f')
if solver == 'Gerris':
initializeGerris(refDir)
elif solver == 'OpenFOAM':
initializeOpenFOAM(refDir)
elif solver == 'Truchas':
initializeTruchas(refDir)
elif solver == 'Thetis':
initializeThetis(refDir)
def cylinder(path = './', solver=None, cs='cfr'):
if len(cs) > 1:
for cs0 in cs:
cylinder(path, solver, cs0)
return
path = os.path.abspath(path)
solver = solver or postprocess.determineSolver(path)
if solver == 'TruchasEnSight': solver = 'Truchas'
U=1.
R=0.05
if solver == 'Gerris':
gfsFile=glob.glob(os.path.join(path, '*.gfs'))[0]
for l in open(gfsFile).readlines():
if 'SurfaceBc U' in l:
U = -float(l.split()[-1])
if 'SolidMoving' in l:
for i, w in enumerate(l.split()):
if w == 'scale':
R = 0.25 * float(l.split()[i+2])
if 'Define R' in l:
R = float(l.split()[-1])
elif solver == 'Truchas':
inpFile=glob.glob(os.path.join(path, '*.inp'))[0]
for l in open(inpFile).readlines():
l = l.split()
if len(l) ==3 and l[0] == 'R' and l[1] == '=':
R = float(l[2])
elif solver == 'OpenFOAM':
inpFile=glob.glob(os.path.join(path, 'system/snappyHexMeshDict'))[0]
for l in open(inpFile).readlines():
l = (l.replace(';', '')).split()
if len(l) == 2 and l[0] == 'radius':
R = float(l[1])
position = { 'c':0, 'f' : -2*R, 'r' : 2*R }
y0 = { 'c':R, 'f' : 0, 'r' : 0 }
cs_name={ 'c':'center', 'f' : 'front', 'r' : 'rear'}
fig = plt.figure()
fig.subplots_adjust(0.15, 0.15, 0.95, None)
if 'static' in path.lower():
state = 'static'
else:
state = 'moving'
if 'slip' in path:
BC = 'slip'
else:
BC = 'outflow'
plt.title('Cylinder - velocity profiles (' + ', '.join([solver, state, BC, cs_name[cs]]) + ')')
r = np.linspace(y0[cs], 0.5, 100)
ls=['-.', '--', '-', '-', '-']
for i, caseDir in enumerate(sorted(glob.glob(os.path.join(path, '*[1-9]')))[:5]):
vtks = postprocess.globFiles(caseDir, ext='.vtk', exit=0)
if vtks:
print 'Profiles:', caseDir, '*.vtk'
line, u = sample_vtk(vtks[-1], [position[cs], y0[cs]], [position[cs], 0.5])
if 'moving' in path:
u = u+U #we want relative speed
plt.plot(u[:, 0], line[:, 2], label='Resolution '+caseDir[-1], ls=ls[i])
files = glob.glob(os.path.join(caseDir, '*.ensight.CASE'))
if files:
file = files[0]
print 'Profiles:', file
ts = enSightTimeSteps(file)
if len(glob.glob(os.path.join(caseDir, '*.ensight/P.*'))) == ts: #check if computations are finished
line, u = sample_ensight(file, [position[cs], y0[cs]], [position[cs], 0.5])
if 'moving' in path:
u = u+U #we want relative speed
plt.plot(u[:, 0], line[:, 2], label='Resolution '+caseDir[-1], ls=ls[i])
Vx, Vy = cylinderReference(position[cs], r, R)
#plt.plot(U*(1+R**2/r**2), r, label='Reference', lw=2)
plt.plot(Vx, r, label='Reference', c='k', lw=2.0)
legend = { 'c':'upper right', 'f' : 'upper left', 'r' : 'upper left' }
plt.legend(loc=legend[cs])
#plt.ylim([0, line[:, 2].max()])
#plt.ylim([0, 0.15])
if cs == 'c':plt.xlim([1, 2])
plt.ylabel('z $[m]$')
plt.xlabel('Velocity $u_x$ $[\\frac{m}{s}]$')
#name = os.path.split(path)[1] #ex. cylinder-static, cylinder-moving
plt.savefig('-'.join(['cylinder', solver, 'profiles', state, BC, cs]))
plt.savefig('-'.join(['cylinder', solver, 'profiles', state, BC, cs])+'.pdf')
def plotCrossSections(path, time=None, a=None, solver=None, x_c=25, bw=0, suffix='', difference=False):
"""
Plots the velocity profiles along vertical crossections of a solitary wave, for a single time step.
In previous versions multiple timesteps were supported, but is not any more.
:param difference: Take a difference between the reference solution and numerical results
:type difference: bool
"""
solver = solver or postprocess.determineSolver(path)
a = a or postprocess.determineAmplitude(path)
path=os.path.abspath(path)
dirs = glob.glob(path + '/case[1-4]/*postprocessed.dat') + glob.glob(path + '/*-[1-4]/*postprocessed.dat')
dirs = [os.path.split(dir)[0] for dir in dirs]
dirs.sort()
if not (dirs):
print 'Empty directory:', path
return 1
else:
print dirs
#correct time:
dt = postprocess.findDt(path)
time_step = int(round(time/dt))
time = time_step*dt
ref_line, u_ref = get_reference(a, time, x_c)
y_ref = ref_line[:, 1]
ux_ref = u_ref[:, 0]
ux_num_list, sample_line_z_list = [], []
for path in dirs:
vtk_file = postprocess.globFiles(path, ext='.vtk', verbose=False)[time_step]
if difference:
p1 = [x_c, np.min(y_ref)]
p2 = [x_c, np.max(y_ref)]
line, vel = sample_vtk(vtk_file, p1=p1, p2=p2, N_points=len(y_ref))
vel[:, 0] = vel[:, 0] - ux_ref
else:
line, vel = sample_vtk(vtk_file, x_c=x_c)
ux_num_list.append(vel[:, 0]) #x component
sample_line_z_list.append(line[:, 2]) #vertical component
print "Plotting..."
gravity = 'sourceGrav' if 'sourceGrav' in path else ''
results = ['VelCross', "A0{0:g}".format(a*10), solver, gravity, suffix]
results = [p for p in results if p] #remove empty strings
results = '_'.join(results)
xlim = {0.1: [-0.03, 0.45], 0.3: [-0.3, 1.3]}
plt.clf()
fig = plt.figure()
fig.subplots_adjust(0.15, 0.15, 0.95, None)
#plt.title('Propagation of a {2:.1f} soliton, t={0:.2f} s, $\Delta x$={1:.2f}m, {3}'.format(t, x_c-15, a, solver))
ls = ['-.', '--', '-']
for j in range(len(ux_num_list)):
case = dirs[j][-1:]
u = ux_num_list[j]
sample_line_z = sample_line_z_list[j]
if bw:
plt.plot(u, sample_line_z, label='Resolution ' + case, ls=ls[j], color='k')
else:
plt.plot(u, sample_line_z, label='Resolution ' + case, ls=ls[j])
if not difference:
plt.plot(ux_ref, y_ref, label='Reference', color='k', ls='-', lw=2)
plt.legend(loc='best')
plt.ylabel('z $[m]$')
plt.xlabel('Velocity $[\\frac{m}{s}]$')
plt.ylim(-1, np.max(sample_line_z))
plt.xlim(xlim[a])
if bw:
results = results+'_bw'
plt.savefig(results+'.png'.format(time))
plt.savefig(results+'.pdf'.format(time))
def plotCrossSections(path,
time=None,
a=None,
solver=None,
x_c=25,
bw=0,
suffix='',
difference=False):
"""
Plots the velocity profiles along vertical crossections of a solitary wave, for a single time step.
In previous versions multiple timesteps were supported, but is not any more.
:param difference: Take a difference between the reference solution and numerical results
:type difference: bool
"""
solver = solver or postprocess.determineSolver(path)
a = a or postprocess.determineAmplitude(path)
path = os.path.abspath(path)
dirs = glob.glob(path + '/case[1-4]/*postprocessed.dat') + glob.glob(
path + '/*-[1-4]/*postprocessed.dat')
dirs = [os.path.split(dir)[0] for dir in dirs]
dirs.sort()
if not (dirs):
print 'Empty directory:', path
return 1
else:
print dirs
#correct time:
dt = postprocess.findDt(path)
time_step = int(round(time / dt))
time = time_step * dt
ref_line, u_ref = get_reference(a, time, x_c)
y_ref = ref_line[:, 1]
ux_ref = u_ref[:, 0]
ux_num_list, sample_line_z_list = [], []
for path in dirs:
vtk_file = postprocess.globFiles(path, ext='.vtk',
verbose=False)[time_step]
if difference:
p1 = [x_c, np.min(y_ref)]
p2 = [x_c, np.max(y_ref)]
line, vel = sample_vtk(vtk_file, p1=p1, p2=p2, N_points=len(y_ref))
vel[:, 0] = vel[:, 0] - ux_ref
else:
line, vel = sample_vtk(vtk_file, x_c=x_c)
ux_num_list.append(vel[:, 0]) #x component
sample_line_z_list.append(line[:, 2]) #vertical component
print "Plotting..."
gravity = 'sourceGrav' if 'sourceGrav' in path else ''
results = ['VelCross', "A0{0:g}".format(a * 10), solver, gravity, suffix]
results = [p for p in results if p] #remove empty strings
results = '_'.join(results)
xlim = {0.1: [-0.03, 0.45], 0.3: [-0.3, 1.3]}
plt.clf()
fig = plt.figure()
fig.subplots_adjust(0.15, 0.15, 0.95, None)
#plt.title('Propagation of a {2:.1f} soliton, t={0:.2f} s, $\Delta x$={1:.2f}m, {3}'.format(t, x_c-15, a, solver))
ls = ['-.', '--', '-']
for j in range(len(ux_num_list)):
case = dirs[j][-1:]
u = ux_num_list[j]
sample_line_z = sample_line_z_list[j]
if bw:
plt.plot(u,
sample_line_z,
label='Resolution ' + case,
ls=ls[j],
color='k')
else:
plt.plot(u, sample_line_z, label='Resolution ' + case, ls=ls[j])
def cylinder(path='./', solver=None, cs='cfr'):
if len(cs) > 1:
for cs0 in cs:
cylinder(path, solver, cs0)
return
path = os.path.abspath(path)
solver = solver or postprocess.determineSolver(path)
if solver == 'TruchasEnSight': solver = 'Truchas'
U = 1.
R = 0.05
if solver == 'Gerris':
gfsFile = glob.glob(os.path.join(path, '*.gfs'))[0]
for l in open(gfsFile).readlines():
if 'SurfaceBc U' in l:
U = -float(l.split()[-1])
if 'SolidMoving' in l:
for i, w in enumerate(l.split()):
if w == 'scale':
R = 0.25 * float(l.split()[i + 2])
if 'Define R' in l:
R = float(l.split()[-1])
elif solver == 'Truchas':
inpFile = glob.glob(os.path.join(path, '*.inp'))[0]
for l in open(inpFile).readlines():
l = l.split()
if len(l) == 3 and l[0] == 'R' and l[1] == '=':
R = float(l[2])
elif solver == 'OpenFOAM':
inpFile = glob.glob(os.path.join(path, 'system/snappyHexMeshDict'))[0]
for l in open(inpFile).readlines():
l = (l.replace(';', '')).split()
if len(l) == 2 and l[0] == 'radius':
R = float(l[1])
position = {'c': 0, 'f': -2 * R, 'r': 2 * R}
y0 = {'c': R, 'f': 0, 'r': 0}
cs_name = {'c': 'center', 'f': 'front', 'r': 'rear'}
fig = plt.figure()
fig.subplots_adjust(0.15, 0.15, 0.95, None)
if 'static' in path.lower():
state = 'static'
else:
state = 'moving'
if 'slip' in path:
BC = 'slip'
else:
BC = 'outflow'
plt.title('Cylinder - velocity profiles (' +
', '.join([solver, state, BC, cs_name[cs]]) + ')')
r = np.linspace(y0[cs], 0.5, 100)
ls = ['-.', '--', '-', '-', '-']
for i, caseDir in enumerate(
sorted(glob.glob(os.path.join(path, '*[1-9]')))[:5]):
vtks = postprocess.globFiles(caseDir, ext='.vtk', exit=0)
if vtks:
print 'Profiles:', caseDir, '*.vtk'
line, u = sample_vtk(vtks[-1], [position[cs], y0[cs]],
[position[cs], 0.5])
if 'moving' in path:
u = u + U #we want relative speed
plt.plot(u[:, 0],
line[:, 2],
label='Resolution ' + caseDir[-1],
ls=ls[i])
files = glob.glob(os.path.join(caseDir, '*.ensight.CASE'))
if files:
file = files[0]
print 'Profiles:', file
ts = enSightTimeSteps(file)
if len(glob.glob(os.path.join(caseDir, '*.ensight/P.*'))
) == ts: #check if computations are finished
line, u = sample_ensight(file, [position[cs], y0[cs]],
[position[cs], 0.5])
if 'moving' in path:
u = u + U #we want relative speed
plt.plot(u[:, 0],
line[:, 2],
label='Resolution ' + caseDir[-1],
ls=ls[i])
Vx, Vy = cylinderReference(position[cs], r, R)
#plt.plot(U*(1+R**2/r**2), r, label='Reference', lw=2)
plt.plot(Vx, r, label='Reference', c='k', lw=2.0)
legend = {'c': 'upper right', 'f': 'upper left', 'r': 'upper left'}
plt.legend(loc=legend[cs])
#plt.ylim([0, line[:, 2].max()])
#plt.ylim([0, 0.15])
if cs == 'c': plt.xlim([1, 2])
plt.ylabel('z $[m]$')
plt.xlabel('Velocity $u_x$ $[\\frac{m}{s}]$')
#name = os.path.split(path)[1] #ex. cylinder-static, cylinder-moving
plt.savefig('-'.join(['cylinder', solver, 'profiles', state, BC, cs]))
plt.savefig('-'.join(['cylinder', solver, 'profiles', state, BC, cs]) +
'.pdf')
