def get_reference_bim(a, t0=0, x_c=0, x0=15, verbose=True):
if type(t0) == list:
return np.array([r for r in imap(getReferenceBIM, repeat(a), t0, repeat(x_c))])
if verbose:
print 'Getting a reference solution for a={} from BIM data'.format(a)
numRefDir = os.path.join(os.environ['HOME'], 'work/soliton/fullPotentialSolution')
if not(os.path.exists(numRefDir)):
sys.exit('Numerical reference directory does not exist: '+numRefDir)
x_c = x_c - solitonVelBIM[a]*t0 - x0
N=200
line = (np.ones(N)*x_c, np.linspace(-1, a, N))
u, ext = postprocess.readGphov(os.path.join(numRefDir, str(a), 'u'))
v, ext = postprocess.readGphov(os.path.join(numRefDir, str(a), 'v'))
grid_x, grid_y = np.mgrid[ext[0]:ext[1]:u.shape[1]*1j, ext[2]:ext[3]:u.shape[0]*1j]
u = u.transpose()
v = v.transpose()
ux_sampled = griddata((grid_x.flatten(), grid_y.flatten()), u.flatten(), line, method='linear', fill_value=0)
uy_sampled = griddata((grid_x.flatten(), grid_y.flatten()), v.flatten(), line, method='linear', fill_value=0)
return np.array(line).transpose(), np.array([ux_sampled, uy_sampled]).transpose()
def initializeThetis(refDir, path='./', solitonPosition=15):
L,H,Nx,Ny = determineMesh()
angle,tx,ty = determineRotation()
dx = L/Nx
dy = H/Ny
#Thetis needs values given for nodes,not cell centers;
#I have to contruct the volumes around 'nodes', to compute volume fractions for them
os.mkdir('objets')
interface = np.loadtxt('interface.ini')
interface = np.vstack((interface[0],interface))
interface = np.vstack((interface,interface[-1]))
interface[0,1] = -20 #to create a closed polygon
interface[-1,1] = -20
interface[:,0],interface[:,1] = rotateMesh(interface[:,0],interface[:,1],-angle)
interface[:,1] = interface[:,1]+ty
N_intf = len(interface)
f = open('objets/interface.mxa','w')
f.write('{0} {0}\n'.format(N_intf))
np.savetxt(f,interface,fmt='%10.4f')
l = np.arange(1,N_intf+1)
lista = np.vstack((l[:-1],l[1:])).transpose()
np.savetxt(f,lista,fmt='%d')
f.write('{0} {1}\n'.format(N_intf,1))
f.close()
Xc,Yc = meshNodes(Nx,Ny,0,L,-1,H-1,tx=tx,ty=ty,angle=angle)
nodes = np.array([Xc.flatten(),Yc.flatten()]).transpose()
for component in ['u','v']:
u,extent = readGphov(os.path.join(refDir,component))
Ny_ref,Nx_ref = u.shape
X_ref,Y_ref = meshNodes(Nx_ref-1,Ny_ref-1,*extent,tx=-solitonPosition)
referencePoints = np.array([X_ref.flatten(),Y_ref.flatten()]).transpose()
interp = griddata(referencePoints, u.flatten(), nodes, fill_value=0)
np.savetxt(component+'.ini',interp,fmt='%10.6f')
def initializeTruchas(refDir, path='./', solitonPosition=15):
L,H,Nx,Ny = determineMesh()
angle,tx,ty = determineRotation()
X,Y = meshNodes(Nx,Ny,0,L,-1,H-1,tx=tx,ty=ty,angle=angle)
f = open('polygons.tmp','w')
for i in range(X.shape[0]-1):
for j in range(X.shape[1]-1):
f.write( "{0:10.6f} {1:10.6f}".format(X[i ,j ],Y[i ,j ]))
f.write(" {0:10.6f} {1:10.6f}".format(X[i+1,j ],Y[i+1,j ]))
f.write(" {0:10.6f} {1:10.6f}".format(X[i+1,j+1],Y[i+1,j+1]))
f.write(" {0:10.6f} {1:10.6f}".format(X[i,j+1 ],Y[i ,j+1]))
f.write("\n")
f.close()
subprocess.call(vofOfManyPolygons + ' interface.ini polygons.tmp vof.ini',shell=True)
# VELOCITY
Xc,Yc = meshCenters(Nx,Ny,0,L,-1,H-1,tx=tx,ty=ty,angle=angle)
cellCenters = np.array([Xc.flatten(),Yc.flatten()]).transpose()
for component in ['u','v']:
u,extent = readGphov(os.path.join(refDir,component))
Ny_ref,Nx_ref = u.shape
X_ref,Y_ref = meshNodes(Nx_ref-1,Ny_ref-1,*extent,tx=-solitonPosition)
referencePoints = np.array([X_ref.flatten(),Y_ref.flatten()]).transpose()
interp = griddata(referencePoints, u.flatten(), cellCenters, fill_value=0)
np.savetxt(component+'.ini',interp,fmt='%10.6f')
def initializeGerris(refDir,solitonPosition=15):
L,H,Nx,Ny = determineMesh()
dx = L/Nx
dy = H/Ny
angle,tx,ty = determineRotation()
f = open('polygons.tmp','w')
X,Y = meshNodes(Nx,Ny,0,L,-1,H-1,tx=tx,ty=ty,angle=angle) #rotated mesh, but also translated to have interface at z=0
eps = 0.000001 #required, so that interpolation points are close, but do not coincide with the actual nodes
for i in range(X.shape[0]-1):
for j in range(X.shape[1]-1):
f.write( "{0:10.6f} {1:10.6f}".format(X[i ,j ],Y[i ,j ]))
f.write(" {0:10.6f} {1:10.6f}".format(X[i+1,j ],Y[i+1,j ]))
f.write(" {0:10.6f} {1:10.6f}".format(X[i+1,j+1],Y[i+1,j+1]))
f.write(" {0:10.6f} {1:10.6f}".format(X[i,j+1 ],Y[i ,j+1]))
f.write("\n")
f.close()
subprocess.call(vofOfManyPolygons + ' interface.ini polygons.tmp t.cgd',shell=True)
Xc,Yc = meshCenters(Nx,Ny,0-eps,L+eps,0-eps,H+eps) #actual mesh, interface is at z=1
vof = open('t.cgd').read()
f = open('t.cgd','w')
f.write('2 y x\n')
f.write('{0} {1}\n'.format(Ny,Nx))
np.savetxt(f,Yc[:,0].reshape(1,-1),fmt='%12.6f') #in Gerris sw-level is at z=1; reshape to have it in 1 line
np.savetxt(f,Xc[0,:].reshape(1,-1),fmt='%12.6f') #dx/2 needed to point at centers of cells
f.write(vof)
f.close()
#VELOCITY
Xc_rot, Yc_rot = meshCenters(Nx,Ny,0,L,-1,H-1,tx=tx,ty=ty,angle=angle) #interface at z=0, for interpolation purposes
cellCenters = np.array([Xc_rot.flatten(),Yc_rot.flatten()]).transpose()
for component in ['u','v']:
u,extent = readGphov(os.path.join(refDir,component))
Ny_ref,Nx_ref = u.shape
X_ref,Y_ref = meshNodes(Nx_ref-1,Ny_ref-1,*extent,tx=-solitonPosition)
referencePoints = np.array([X_ref.flatten(),Y_ref.flatten()]).transpose()
f = open(component+'.cgd','w')
f.write('2 y x\n')
f.write('{0} {1}\n'.format(Ny,Nx))
interp = griddata(referencePoints, u.flatten(), cellCenters, fill_value=0)
np.savetxt(f,Yc[:,0].reshape(1,-1),fmt='%12.6f') #in Gerris sw-level is at z=1; reshape to have it in 1 line
np.savetxt(f,Xc[0,:].reshape(1,-1),fmt='%12.6f') #dx/2 needed to point at centers of cells
np.savetxt(f,interp,fmt='%.4f')
f.close()
def get_reference_bim(a, t0=0, x_c=0, x0=15, verbose=True):
if type(t0) == list:
return np.array(
[r for r in imap(getReferenceBIM, repeat(a), t0, repeat(x_c))])
if verbose:
print 'Getting a reference solution for a={} from BIM data'.format(a)
numRefDir = os.path.join(os.environ['HOME'],
'work/soliton/fullPotentialSolution')
if not (os.path.exists(numRefDir)):
sys.exit('Numerical reference directory does not exist: ' + numRefDir)
x_c = x_c - solitonVelBIM[a] * t0 - x0
N = 200
line = (np.ones(N) * x_c, np.linspace(-1, a, N))
u, ext = postprocess.readGphov(os.path.join(numRefDir, str(a), 'u'))
v, ext = postprocess.readGphov(os.path.join(numRefDir, str(a), 'v'))
grid_x, grid_y = np.mgrid[ext[0]:ext[1]:u.shape[1] * 1j,
ext[2]:ext[3]:u.shape[0] * 1j]
u = u.transpose()
v = v.transpose()
ux_sampled = griddata((grid_x.flatten(), grid_y.flatten()),
u.flatten(),
line,
method='linear',
fill_value=0)
uy_sampled = griddata((grid_x.flatten(), grid_y.flatten()),
v.flatten(),
line,
method='linear',
fill_value=0)
return np.array(line).transpose(), np.array([ux_sampled,
uy_sampled]).transpose()
def initializeOpenFOAM(refDir,path='./',solitonPosition=15):
points = open(os.path.join(path,'constant/polyMesh/points')).readlines()
points = [p.replace('(','').replace(')','') for p in points if p[0] == '(']
points = np.loadtxt(points)
faces = open(os.path.join(path,'constant/polyMesh/faces')).readlines()
#faces = [f[2:].replace(')','') for f in faces if f[:2] == '4(']
faces = [f.replace(')','') for f in faces if f[:2] in ['3(','4(']]
for i in range(len(faces)):
if faces[i][:2] == '3(':
faces[i] = faces[i][:-1] + ' ' + faces[i].split()[-1]+'\n'
faces[i] = faces[i][2:]
faces = np.loadtxt(faces,dtype=np.int)
#reading 'owner' - assigning a cell number to each face
owner = open(os.path.join(path,'constant/polyMesh/owner')).readlines()
owner = [p for p in owner if p[0].isdigit()]
owner = np.loadtxt(owner[1:],dtype=np.int)
#3D->2D
faces = points[faces.flatten()].reshape((-1,12)) #replacing indices with coordinates
cellFilter=np.all(faces[:,2::3]==faces[:,2::3].max(),axis=1) #this is needed, because in OpenFOAM mesh is 3D, therefore 2D version must be obtained
faces = faces.reshape((-1,3))[:,:2].reshape((-1,8)) #third dimension is not needed
faces = faces[cellFilter]
owner = owner[cellFilter]
cells = np.zeros_like(faces)
for iF,iC in enumerate(owner):
cells[iC] = faces[iF]
angle,tx,ty = determineRotation()
x = cells[:,::2]
y = cells[:,1::2]
x = x - tx
y = y - ty
cells[:,::2],cells[:,1::2] = rotateMesh(x,y,angle)
np.savetxt('polygons.tmp',cells,fmt='%12.6f')
subprocess.call(vofOfManyPolygons + ' interface.ini polygons.tmp vof.ini',shell=True)
#formatting alpha1 OpenFOAM initial field file
org = open(os.path.join(path,'0/alpha1')).readlines()
f = open(os.path.join(path,'0/alpha1'),'w')
skip=0
for i,l in enumerate(org):
if not skip:
if 'internalField' in l:
if l.split()[1] == 'nonuniform':
f.write(l)
skip = int(org[i+1]) + 4 #counts for old values, opening and closing brackets and the number of cells and a semicolon
else:
#replacing the 'internalField uniform 0;' line
f.write('internalField nonuniform List<scalar>\n')
f.write(str(len(cells)) + '\n(\n')
f.write(open('vof.ini').read())
f.write(')\n;\n')
else:
f.write(l)
else:
skip = skip-1
f.close()
# VELOCITY AND PRESSURE
interp = {}
cellCenters = np.array([np.average(cells[:,::2],axis=1),np.average(cells[:,1::2],axis=1)]).transpose()
for component in ['u','v','p']:
u,extent = readGphov(os.path.join(refDir,component),rescale=False)
Ny_ref,Nx_ref = u.shape
X_ref,Y_ref = meshNodes(Nx_ref-1,Ny_ref-1,*extent,tx=-solitonPosition)
referencePoints = np.array([X_ref.flatten(),Y_ref.flatten()]).transpose()
interp[component] = griddata(referencePoints, u.flatten(), cellCenters, fill_value=0)
interp['p'] = (interp['p'] - cellCenters[:,1]) * g*1000
interp['u'] = interp['u'] * np.sqrt(g)
interp['v'] = interp['v'] * np.sqrt(g)
org = open(os.path.join(path,'0/U')).readlines()
f = open(os.path.join(path,'0/U'),'w')
skip=0
for i,l in enumerate(org):
if not skip:
if 'internalField' in l:
if l.split()[1] == 'nonuniform':
f.write(l)
skip = int(org[i+1]) + 4 #counts for old values, opening and closing brackets and the number of cells and a semicolon
else:
#replacing the 'internalField uniform 0;' line
f.write('internalField nonuniform List<vector>\n')
f.write(str(len(cells)) + '\n(\n')
np.savetxt(f,np.array([interp['u'],interp['v'],np.zeros(len(cells))]).transpose(),fmt='(%10.6f %10.6f %10.6f)')
f.write(')\n;\n')
else:
f.write(l)
else:
skip = skip-1
f.close()
org = open(os.path.join(path,'0/p_rgh')).readlines()
f = open(os.path.join(path,'0/p_rgh'),'w')
skip=0
for i,l in enumerate(org):
if not skip:
if 'internalField' in l:
if l.split()[1] == 'nonuniform':
f.write(l)
skip = int(org[i+1]) + 4 #counts for old values, opening and closing brackets and the number of cells and a semicolon
else:
#replacing the 'internalField uniform 0;' line
f.write('internalField nonuniform List<scalar>\n')
f.write(str(len(cells)) + '\n(\n')
np.savetxt(f,interp['p'],fmt='%10.6f')
f.write(')\n;\n')
else:
f.write(l)
else:
skip = skip-1
f.close()
