This commit is contained in:
Lars Ruthotto
2013-07-12 10:20:28 -07:00
16 changed files with 1462 additions and 248 deletions
+87
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@@ -0,0 +1,87 @@
from numpy import *
import numpy as np
def diff(A, d):
if(d == 1):
return A[1:, :, :] - A[:-1, :, :]
elif(d == 2):
return A[:, 1:, :] - A[:, :-1, :]
else:
return A[:, :, 1:] - A[:, :, :-1]
#else:
# print('d must be 1,2 or 3')
def diffp(A, d1, d2):
if(d1 == 1 and d2 == 2):
return A[1:, 1:, :] - A[:-1, :-1, :]
elif(d1 == 1 and d2 == 3):
return A[1:, :, 1:] - A[:-1, :, :-1]
else:
return A[:, 1:, 1:] - A[:, :-1, :-1]
def diffm(A, d1, d2):
if(d1 == 3 and d2 == 2):
return A[:, :-1, 1:] - A[:, 1:, :-1]
elif(d1 == 1 and d2 == 3):
return A[1:, :, :-1] - A[:-1, :, 1:]
elif(d1 == 2 and d2 == 1):
return A[:-1, 1:, :] - A[1:, :-1, :]
else:
print('d must be 1, 2 or 3')
def ave(A, d):
if(d == 1):
return 0.5*(A[1:, :, :] + A[:-1, :, :])
elif(d == 2):
return 0.5*(A[:, 1:, :] + A[:, :-1, :])
elif(d == 3):
return 0.5*(A[:, :, 1:] + A[:, :, :-1])
else:
print('d must be 1,2 or 3')
def mkmat(x):
return reshape(matrix(x), (size(x), 1), 'F')
def hstack3(a, b, c):
a = mkvc(a)
b = mkvc(b)
c = mkvc(c)
a = mkmat(a)
b = mkmat(b)
c = mkmat(c)
return hstack((hstack((a, b)), c))
def ind2sub(shape, ind):
"""From the given shape, returns the subscrips of the given index"""
revshp = []
revshp.extend(shape)
mult = [1]
for i in range(0, len(revshp)-1):
mult.extend([mult[i]*revshp[i]])
mult = array(mult).reshape(len(mult))
sub = []
for i in range(0, len(shape)):
sub.extend([math.floor(ind / mult[i])])
ind = ind - (math.floor(ind/mult[i]) * mult[i])
return sub
def sub2ind(shape, subs):
"""From the given shape, returns the index of the given subscript"""
revshp = list(shape)
mult = [1]
for i in range(0, len(revshp)-1):
mult.extend([mult[i]*revshp[i]])
mult = array(mult).reshape(len(mult), 1)
idx = dot((subs), (mult))
return idx
-144
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@@ -1,144 +0,0 @@
import numpy as np
from utils import ndgrid
class TensorGrid(object):
"""
Define nodal, cell-centered and staggered tensor grids for 1, 2 and 3
dimensions.
This class is inherited by TensorMesh
"""
def __init__(self):
pass
def vectorNx():
doc = "Nodal grid vector (1D) in the x direction."
fget = lambda self: np.r_[0., self.hx.cumsum()] + self.x0[0]
return locals()
vectorNx = property(**vectorNx())
def vectorNy():
doc = "Nodal grid vector (1D) in the y direction."
fget = lambda self: None if self.dim < 2 else np.r_[0., self.hy.cumsum()] + self.x0[1]
return locals()
vectorNy = property(**vectorNy())
def vectorNz():
doc = "Nodal grid vector (1D) in the z direction."
fget = lambda self: None if self.dim < 3 else np.r_[0., self.hz.cumsum()] + self.x0[2]
return locals()
vectorNz = property(**vectorNz())
def vectorCCx():
doc = "Cell-centered grid vector (1D) in the x direction."
fget = lambda self: np.r_[0, self.hx[:-1].cumsum()] + self.hx*0.5 + self.x0[0]
return locals()
vectorCCx = property(**vectorCCx())
def vectorCCy():
doc = "Cell-centered grid vector (1D) in the y direction."
fget = lambda self: None if self.dim < 2 else np.r_[0, self.hy[:-1].cumsum()] + self.hy*0.5 + self.x0[1]
return locals()
vectorCCy = property(**vectorCCy())
def vectorCCz():
doc = "Cell-centered grid vector (1D) in the z direction."
fget = lambda self: None if self.dim < 3 else np.r_[0, self.hz[:-1].cumsum()] + self.hz*0.5 + self.x0[2]
return locals()
vectorCCz = property(**vectorCCz())
def gridCC():
doc = "Cell-centered grid."
def fget(self):
if self._gridCC is None:
self._gridCC = ndgrid([x for x in [self.vectorCCx, self.vectorCCy, self.vectorCCz] if not x is None])
return self._gridCC
return locals()
_gridCC = None # Store grid by default
gridCC = property(**gridCC())
def gridN():
doc = "Nodal grid."
def fget(self):
if self._gridN is None:
self._gridN = ndgrid([x for x in [self.vectorNx, self.vectorNy, self.vectorNz] if not x is None])
return self._gridN
return locals()
_gridN = None # Store grid by default
gridN = property(**gridN())
def gridFx():
doc = "Face staggered grid in the x direction."
def fget(self):
if self._gridFx is None:
self._gridFx = ndgrid([x for x in [self.vectorNx, self.vectorCCy, self.vectorCCz] if not x is None])
return self._gridFx
return locals()
_gridFx = None # Store grid by default
gridFx = property(**gridFx())
def gridFy():
doc = "Face staggered grid in the y direction."
def fget(self):
if self._gridFy is None:
self._gridFy = ndgrid([x for x in [self.vectorCCx, self.vectorNy, self.vectorCCz] if not x is None])
return self._gridFy
return locals()
_gridFy = None # Store grid by default
gridFy = property(**gridFy())
def gridFz():
doc = "Face staggered grid in the z direction."
def fget(self):
if self._gridFz is None:
self._gridFz = ndgrid([x for x in [self.vectorCCx, self.vectorCCy, self.vectorNz] if not x is None])
return self._gridFz
return locals()
_gridFz = None # Store grid by default
gridFz = property(**gridFz())
def gridEx():
doc = "Edge staggered grid in the x direction."
def fget(self):
if self._gridEx is None:
self._gridEx = ndgrid([x for x in [self.vectorCCx, self.vectorNy, self.vectorNz] if not x is None])
return self._gridEx
return locals()
_gridEx = None # Store grid by default
gridEx = property(**gridEx())
def gridEy():
doc = "Edge staggered grid in the y direction."
def fget(self):
if self._gridEy is None:
self._gridEy = ndgrid([x for x in [self.vectorNx, self.vectorCCy, self.vectorNz] if not x is None])
return self._gridEy
return locals()
_gridEy = None # Store grid by default
gridEy = property(**gridEy())
def gridEz():
doc = "Edge staggered grid in the z direction."
def fget(self):
if self._gridEz is None:
self._gridEz = ndgrid([x for x in [self.vectorNx, self.vectorNy, self.vectorCCz] if not x is None])
return self._gridEz
return locals()
_gridEz = None # Store grid by default
gridEz = property(**gridEz())
def getBoundaryIndex(self, gridType):
"""Needed for faces edges and cells"""
pass
def getCellNumbering(self):
pass
+132
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@@ -2,6 +2,7 @@ import numpy as np
from BaseMesh import BaseMesh
from TensorGrid import TensorGrid
from TensorView import TensorView
from utils import ndgrid
class TensorMesh(BaseMesh, TensorGrid, TensorView):
@@ -55,6 +56,137 @@ class TensorMesh(BaseMesh, TensorGrid, TensorView):
return locals()
hz = property(**hz())
def vectorNx():
doc = "Nodal grid vector (1D) in the x direction."
fget = lambda self: np.r_[0., self.hx.cumsum()] + self.x0[0]
return locals()
vectorNx = property(**vectorNx())
def vectorNy():
doc = "Nodal grid vector (1D) in the y direction."
fget = lambda self: None if self.dim < 2 else np.r_[0., self.hy.cumsum()] + self.x0[1]
return locals()
vectorNy = property(**vectorNy())
def vectorNz():
doc = "Nodal grid vector (1D) in the z direction."
fget = lambda self: None if self.dim < 3 else np.r_[0., self.hz.cumsum()] + self.x0[2]
return locals()
vectorNz = property(**vectorNz())
def vectorCCx():
doc = "Cell-centered grid vector (1D) in the x direction."
fget = lambda self: np.r_[0, self.hx[:-1].cumsum()] + self.hx*0.5 + self.x0[0]
return locals()
vectorCCx = property(**vectorCCx())
def vectorCCy():
doc = "Cell-centered grid vector (1D) in the y direction."
fget = lambda self: None if self.dim < 2 else np.r_[0, self.hy[:-1].cumsum()] + self.hy*0.5 + self.x0[1]
return locals()
vectorCCy = property(**vectorCCy())
def vectorCCz():
doc = "Cell-centered grid vector (1D) in the z direction."
fget = lambda self: None if self.dim < 3 else np.r_[0, self.hz[:-1].cumsum()] + self.hz*0.5 + self.x0[2]
return locals()
vectorCCz = property(**vectorCCz())
def gridCC():
doc = "Cell-centered grid."
def fget(self):
if self._gridCC is None:
self._gridCC = ndgrid([x for x in [self.vectorCCx, self.vectorCCy, self.vectorCCz] if not x is None])
return self._gridCC
return locals()
_gridCC = None # Store grid by default
gridCC = property(**gridCC())
def gridN():
doc = "Nodal grid."
def fget(self):
if self._gridN is None:
self._gridN = ndgrid([x for x in [self.vectorNx, self.vectorNy, self.vectorNz] if not x is None])
return self._gridN
return locals()
_gridN = None # Store grid by default
gridN = property(**gridN())
def gridFx():
doc = "Face staggered grid in the x direction."
def fget(self):
if self._gridFx is None:
self._gridFx = ndgrid([x for x in [self.vectorNx, self.vectorCCy, self.vectorCCz] if not x is None])
return self._gridFx
return locals()
_gridFx = None # Store grid by default
gridFx = property(**gridFx())
def gridFy():
doc = "Face staggered grid in the y direction."
def fget(self):
if self._gridFy is None:
self._gridFy = ndgrid([x for x in [self.vectorCCx, self.vectorNy, self.vectorCCz] if not x is None])
return self._gridFy
return locals()
_gridFy = None # Store grid by default
gridFy = property(**gridFy())
def gridFz():
doc = "Face staggered grid in the z direction."
def fget(self):
if self._gridFz is None:
self._gridFz = ndgrid([x for x in [self.vectorCCx, self.vectorCCy, self.vectorNz] if not x is None])
return self._gridFz
return locals()
_gridFz = None # Store grid by default
gridFz = property(**gridFz())
def gridEx():
doc = "Edge staggered grid in the x direction."
def fget(self):
if self._gridEx is None:
self._gridEx = ndgrid([x for x in [self.vectorCCx, self.vectorNy, self.vectorNz] if not x is None])
return self._gridEx
return locals()
_gridEx = None # Store grid by default
gridEx = property(**gridEx())
def gridEy():
doc = "Edge staggered grid in the y direction."
def fget(self):
if self._gridEy is None:
self._gridEy = ndgrid([x for x in [self.vectorNx, self.vectorCCy, self.vectorNz] if not x is None])
return self._gridEy
return locals()
_gridEy = None # Store grid by default
gridEy = property(**gridEy())
def gridEz():
doc = "Edge staggered grid in the z direction."
def fget(self):
if self._gridEz is None:
self._gridEz = ndgrid([x for x in [self.vectorNx, self.vectorNy, self.vectorCCz] if not x is None])
return self._gridEz
return locals()
_gridEz = None # Store grid by default
gridEz = property(**gridEz())
def getBoundaryIndex(self, gridType):
"""Needed for faces edges and cells"""
pass
def getCellNumbering(self):
pass
if __name__ == '__main__':
print('Welcome to tensor mesh!')
+75
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@@ -0,0 +1,75 @@
import numpy as np
from scipy import sparse
from utils import mkvc
from sputils import ddx, sdiag, speye, kron3
def getvol(h):
# Cell sizes in each direction
h1 = h[0]
h2 = h[1]
h3 = h[2]
# Compute cell volumes
v12 = h1.T*h2
V = mkvc(v12.reshape(-1,1)*h3)
return V
def getarea(h):
# Cell sizes in each direction
h1 = h[0]
h2 = h[1]
h3 = h[2]
# The number of cell centers in each direction
n1 = np.size(h1)
n2 = np.size(h2)
n3 = np.size(h3)
# Compute areas of cell faces
area1 = np.ones((n1+1,1))*mkvc(h2.T*h3)
area2 = h1.T*mkvc(np.ones((n2+1,1))*h3)
area3 = h1.T*mkvc(h2.T*np.ones(n3+1))
area = np.hstack((np.hstack((mkvc(area1), mkvc(area2))), mkvc(area3)))
return area
def getDivMatrix(h):
"""Consturct the 3D divergence operator on Faces."""
# Cell sizes in each direction
h1 = h[0]
h2 = h[1]
h3 = h[2]
# The number of cell centers in each direction
n1 = np.size(h1)
n2 = np.size(h2)
n3 = np.size(h3)
# Compute areas of cell faces
#area1 = np.ones((n1+1,1))*mkvc(h2.T*h3)
#area2 = h1.T*mkvc(np.ones((n2+1,1))*h3)
#area3 = h1.T*mkvc(h2.T*np.ones(n3+1))
#area = np.hstack((np.hstack((mkvc(area1), mkvc(area2))), mkvc(area3)))
area = getarea(h)
S = sdiag(area)
# Compute cell volumes
#v12 = h1.T*h2
#V = mkvc(v12.reshape(-1,1)*h3)
V = getvol(h)
# Compute divergence operator on faces
d1 = ddx(n1)
d2 = ddx(n2)
d3 = ddx(n3)
D1 = kron3(speye(n3), speye(n2), d1)
D2 = kron3(speye(n3), d2, speye(n1))
D3 = kron3(d3, speye(n2), speye(n1))
D = sparse.hstack((sparse.hstack((D1, D2)), D3))
return sdiag(1/V)*D*S
+18
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@@ -0,0 +1,18 @@
import numpy as np
from scipy import sparse
def ddx(n):
"""Define 1D derivatives"""
return sparse.spdiags((np.ones((n+1,1))*[-1,1]).T, [0,1], n, n+1)
def sdiag(h):
"""Sparse diagonal matrix"""
return sparse.spdiags(h, 0, np.size(h), np.size(h))
def speye(n):
"""Sparse identity"""
return sparse.identity(n)
def kron3(A, B, C):
"""Two kron prods"""
return sparse.kron(sparse.kron(A, B), C)
+45
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@@ -0,0 +1,45 @@
import numpy as np
import sys
sys.path.append('../')
from TensorMesh import TensorMesh
from getDIV import getDivMatrix, getarea, getvol
# Define the mesh
err=0.
for i in range(4):
icount=i+1;
nc = 2*icount;
h1 = np.pi/nc*np.ones((1,nc))
h2 = np.pi/nc*np.ones((1,nc))
h3 = np.pi/nc*np.ones((1,nc))
h = [h1, h2, h3]
x0 = -np.pi/2*np.ones((3, 1))
M = TensorMesh(h, x0)
#n = M.plotGrid()
# Generate DIV matrix
DIV = getDivMatrix(h)
#Test function
fun = lambda x: np.sin(x)
Fx = fun(M.gridFx[:,0])
Fy = fun(M.gridFy[:,1])
Fz = fun(M.gridFz[:,2])
F = np.concatenate((Fx,Fy,Fz))
divF = DIV*F
sol = lambda x, y, z: (np.cos(x)+np.cos(y)+np.cos(z))
divF_anal = sol(M.gridCC[:,0], M.gridCC[:,1], M.gridCC[:,2])
area = getarea(h)
vol = getvol(h)
err = np.linalg.norm((divF-divF_anal)*np.sqrt(vol), 2)
if icount == 1:
err1 = err
print 'h | 2 norm | error ratio'
print '---------------------------------------'
print '%6.4f | %8.2e |'% (h1[0,0], err)
else:
print '%6.4f | %8.2e | %6.4f' % (h1[0,0], err, err1/err)
+56 -104
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@@ -1,49 +1,6 @@
from numpy import *
import numpy as np
def diff(A, d):
if(d == 1):
return A[1:, :, :] - A[:-1, :, :]
elif(d == 2):
return A[:, 1:, :] - A[:, :-1, :]
else:
return A[:, :, 1:] - A[:, :, :-1]
#else:
# print('d must be 1,2 or 3')
def diffp(A, d1, d2):
if(d1 == 1 and d2 == 2):
return A[1:, 1:, :] - A[:-1, :-1, :]
elif(d1 == 1 and d2 == 3):
return A[1:, :, 1:] - A[:-1, :, :-1]
else:
return A[:, 1:, 1:] - A[:, :-1, :-1]
def diffm(A, d1, d2):
if(d1 == 3 and d2 == 2):
return A[:, :-1, 1:] - A[:, 1:, :-1]
elif(d1 == 1 and d2 == 3):
return A[1:, :, :-1] - A[:-1, :, 1:]
elif(d1 == 2 and d2 == 1):
return A[:-1, 1:, :] - A[1:, :-1, :]
else:
print('d must be 1, 2 or 3')
def ave(A, d):
if(d == 1):
return 0.5*(A[1:, :, :] + A[:-1, :, :])
elif(d == 2):
return 0.5*(A[:, 1:, :] + A[:, :-1, :])
elif(d == 3):
return 0.5*(A[:, :, 1:] + A[:, :, :-1])
else:
print('d must be 1,2 or 3')
def reshapeF(x, size):
return np.reshape(x, size, order='F')
@@ -53,7 +10,7 @@ def mkvc(x, numDims=1):
e.g.:
a = np.array(1,2,3)
a = np.array([1, 2, 3])
mkvc(a, 1).shape
> (3, )
@@ -75,8 +32,45 @@ def mkvc(x, numDims=1):
return x.flatten(order='F')[:, np.newaxis, np.newaxis]
def ndgrid(*args):
"""Form tensorial grid for 1, 2 and 3 dimensions. Return X1,X2,X3 arrays depending on the dimension"""
def ndgrid(*args, **kwargs):
"""
Form tensorial grid for 1, 2, or 3 dimensions.
Returns as column vectors by default.
To return as matrix input:
ndgrid(..., vector=False)
The inputs can be a list or separate arguments.
e.g.
a = np.array([1, 2, 3])
b = np.array([1, 2])
XY = ndgrid(a, b)
> [[1 1]
[2 1]
[3 1]
[1 2]
[2 2]
[3 2]]
X, Y = ndgrid(a, b, vector=False)
> X = [[1 1]
[2 2]
[3 3]]
> Y = [[1 2]
[1 2]
[1 2]]
"""
# Read the keyword arguments, and only accept a vector=True/False
vector = kwargs.pop('vector', True)
assert type(vector) == bool, "'vector' keyword must be a bool"
assert len(kwargs) == 0, "Only 'vector' keyword accepted"
# you can either pass a list [x1, x2, x3] or each seperately
if type(args[0]) == list:
@@ -84,64 +78,22 @@ def ndgrid(*args):
else:
xin = args
# Each vector needs to be a numpy array
assert np.all([type(x) == np.ndarray for x in xin]), "All vectors must be numpy arrays."
if len(xin) == 1:
return xin
return xin[0]
elif len(xin) == 2:
X2, X1 = [mkvc(x) for x in np.broadcast_arrays(mkvc(xin[1], 1), mkvc(xin[0], 2))]
return np.c_[X1, X2]
XY = np.broadcast_arrays(mkvc(xin[1], 1), mkvc(xin[0], 2))
if vector:
X2, X1 = [mkvc(x) for x in XY]
return np.c_[X1, X2]
else:
return XY[1], XY[0]
elif len(xin) == 3:
X3, X2, X1 = [mkvc(x) for x in np.broadcast_arrays(mkvc(xin[2], 1), mkvc(xin[1], 2), mkvc(xin[0], 3))]
return np.c_[X1, X2, X3]
def ind2sub(shape, ind):
# From the given shape, returns the subscrips of the given index
revshp = []
revshp.extend(shape)
mult = [1]
for i in range(0, len(revshp)-1):
mult.extend([mult[i]*revshp[i]])
mult = array(mult).reshape(len(mult))
sub = []
for i in range(0, len(shape)):
sub.extend([math.floor(ind / mult[i])])
ind = ind - (math.floor(ind/mult[i]) * mult[i])
return sub
def sub2ind(shape, subs):
# From the given shape, returns the index of the given subscript
revshp = list(shape)
mult = [1]
for i in range(0, len(revshp)-1):
mult.extend([mult[i]*revshp[i]])
mult = array(mult).reshape(len(mult), 1)
idx = dot((subs), (mult))
return idx
def mkmat(x):
return reshape(matrix(x), (size(x), 1), 'F')
def hstack3(a, b, c):
a = mkvc(a)
b = mkvc(b)
c = mkvc(c)
a = mkmat(a)
b = mkmat(b)
c = mkmat(c)
return hstack((hstack((a, b)), c))
if __name__ == '__main__':
X, Y, Z = mgrid[0:4, 0:5, 0:6]
print Z
t = ave(X, 1)
print t
XYZ = np.broadcast_arrays(mkvc(xin[2], 1), mkvc(xin[1], 2), mkvc(xin[0], 3))
if vector:
X3, X2, X1 = [mkvc(x) for x in XYZ]
return np.c_[X1, X2, X3]
else:
return XYZ[2], XYZ[1], XYZ[0]