Files
simpeg/SimPEG/Mesh/InnerProducts.py
T
2014-04-25 17:21:31 -07:00

556 lines
21 KiB
Python

from scipy import sparse as sp
from SimPEG.Utils import *
import numpy as np
class InnerProducts(object):
"""
This is a base for the SimPEG.Mesh classes. This mixIn creates the all the inner product matrices that you need!
"""
def __init__(self):
raise Exception('InnerProducts is a base class providing inner product matrices for meshes and cannot run on its own. Inherit to your favorite Mesh class.')
def getFaceInnerProduct(self, prop=None, returnP=False,
invProp=False, invMat=False, doFast=True):
"""
:param numpy.array prop: material property (tensor properties are possible) at each cell center (nC, (1, 3, or 6))
:param bool returnP: returns the projection matrices
:param bool invProp: inverts the material property
:param bool invMat: inverts the matrix
:param bool doFast: do a faster implementation if available.
:rtype: scipy.csr_matrix
:return: M, the inner product matrix (nF, nF)
"""
fast = None
if returnP is False and hasattr(self, '_fastFaceInnerProduct') and doFast:
fast = self._fastFaceInnerProduct(prop=prop, invProp=invProp, invMat=invMat)
if fast is not None:
return fast
if invProp:
prop = invPropertyTensor(self, prop)
Mu = makePropertyTensor(self, prop)
d = self.dim
# We will multiply by sqrt on each side to keep symmetry
V = sp.kron(sp.identity(d), sdiag(np.sqrt((2**(-d))*self.vol)))
if d == 1:
fP = _getFacePx(self)
P000 = V*fP('fXm')
P100 = V*fP('fXp')
elif d == 2:
fP = _getFacePxx(self)
P000 = V*fP('fXm', 'fYm')
P100 = V*fP('fXp', 'fYm')
P010 = V*fP('fXm', 'fYp')
P110 = V*fP('fXp', 'fYp')
elif d == 3:
fP = _getFacePxxx(self)
P000 = V*fP('fXm', 'fYm', 'fZm')
P100 = V*fP('fXp', 'fYm', 'fZm')
P010 = V*fP('fXm', 'fYp', 'fZm')
P110 = V*fP('fXp', 'fYp', 'fZm')
P001 = V*fP('fXm', 'fYm', 'fZp')
P101 = V*fP('fXp', 'fYm', 'fZp')
P011 = V*fP('fXm', 'fYp', 'fZp')
P111 = V*fP('fXp', 'fYp', 'fZp')
A = P000.T*Mu*P000 + P100.T*Mu*P100
P = [P000, P100]
if d > 1:
A = A + P010.T*Mu*P010 + P110.T*Mu*P110
P += [P010, P110]
if d > 2:
A = A + P001.T*Mu*P001 + P101.T*Mu*P101 + P011.T*Mu*P011 + P111.T*Mu*P111
P += [P001, P101, P011, P111]
if invMat and tensorType(self, prop) < 3:
A = sdInv(A)
elif invMat and tensorType(self, prop) == 3:
raise Exception('Solver needed to invert A.')
if returnP:
return A, P
else:
return A
def getFaceInnerProductDeriv(self, prop=None, v=None, P=None, doFast=True):
"""
:param numpy.array prop: material property (tensor properties are possible) at each cell center (nC, (1, 3, or 6))
:param numpy.array v: vector to multiply (required in the general implementation)
:param list P: list of projection matrices
:param bool doFast: do a faster implementation if available.
:rtype: scipy.csr_matrix
:return: dMdm, the derivative of the inner product matrix (nF, nC*nA)
"""
fast = None
if hasattr(self, '_fastFaceInnerProductDeriv') and doFast:
fast = self._fastFaceInnerProductDeriv(prop=prop, v=v)
if fast is not None:
return fast
if P is None:
M, P = self.getFaceInnerProduct(prop=prop, returnP=True)
return self._getInnerProductDeriv(prop, v, P, self.nF)
def getEdgeInnerProduct(self, prop=None, returnP=False,
invProp=False, invMat=False, doFast=True):
"""
:param numpy.array prop: material property (tensor properties are possible) at each cell center (nC, (1, 3, or 6))
:param bool returnP: returns the projection matrices
:param bool invProp: inverts the material property
:param bool invMat: inverts the matrix
:param bool doFast: do a faster implementation if available.
:rtype: scipy.csr_matrix
:return: M, the inner product matrix (nE, nE)
"""
fast = None
if returnP is False and hasattr(self, '_fastEdgeInnerProduct') and doFast:
fast = self._fastEdgeInnerProduct(prop=prop, invProp=invProp, invMat=invMat)
if fast is not None:
return fast
if invProp:
prop = invPropertyTensor(self, prop)
Mu = makePropertyTensor(self, prop)
d = self.dim
# We will multiply by sqrt on each side to keep symmetry
V = sp.kron(sp.identity(d), sdiag(np.sqrt((2**(-d))*self.vol)))
if d == 1:
raise NotImplementedError('getEdgeInnerProduct not implemented for 1D')
elif d == 2:
eP = _getEdgePxx(self)
P000 = V*eP('eX0', 'eY0')
P100 = V*eP('eX0', 'eY1')
P010 = V*eP('eX1', 'eY0')
P110 = V*eP('eX1', 'eY1')
elif d == 3:
eP = _getEdgePxxx(self)
P000 = V*eP('eX0', 'eY0', 'eZ0')
P100 = V*eP('eX0', 'eY1', 'eZ1')
P010 = V*eP('eX1', 'eY0', 'eZ2')
P110 = V*eP('eX1', 'eY1', 'eZ3')
P001 = V*eP('eX2', 'eY2', 'eZ0')
P101 = V*eP('eX2', 'eY3', 'eZ1')
P011 = V*eP('eX3', 'eY2', 'eZ2')
P111 = V*eP('eX3', 'eY3', 'eZ3')
Mu = makePropertyTensor(self, prop)
A = P000.T*Mu*P000 + P100.T*Mu*P100 + P010.T*Mu*P010 + P110.T*Mu*P110
P = [P000, P100, P010, P110]
if d == 3:
A = A + P001.T*Mu*P001 + P101.T*Mu*P101 + P011.T*Mu*P011 + P111.T*Mu*P111
P += [P001, P101, P011, P111]
if invMat and tensorType(self, prop) < 3:
A = sdInv(A)
elif invMat and tensorType(self, prop) == 3:
raise Exception('Solver needed to invert A.')
if returnP:
return A, P
else:
return A
def getEdgeInnerProductDeriv(self, prop=None, v=None, P=None, doFast=True):
"""
:param numpy.array prop: material property (tensor properties are possible) at each cell center (nC, (1, 3, or 6))
:param numpy.array v: vector to multiply (required in the general implementation)
:param list P: list of projection matrices
:param bool doFast: do a faster implementation if available.
:rtype: scipy.csr_matrix
:return: dMdm, the derivative of the inner product matrix (nE, nC*nA)
"""
fast = None
if hasattr(self, '_fastEdgeInnerProductDeriv') and doFast:
fast = self._fastEdgeInnerProductDeriv(prop=prop, v=v)
if fast is not None:
return fast
if P is None:
M, P = self.getEdgeInnerProduct(prop=prop, returnP=True)
return self._getInnerProductDeriv(prop, v, P, self.nE)
def _getInnerProductDeriv(self, prop, v, P, n):
"""
:param numpy.array prop: material property (tensor properties are possible) at each cell center (nC, (1, 3, or 6))
:param numpy.array v: vector to multiply (required in the general implementation)
:param list P: list of projection matrices
:param int n: nF or nE
:rtype: scipy.csr_matrix
:return: dMdm, the derivative of the inner product matrix (n, nC*nA)
"""
if prop is None:
return None
if v is None:
raise Exception('v must be supplied for this implementation.')
d = self.dim
Z = spzeros(self.nC, self.nC)
if isScalar(prop):
dMdm = spzeros(n, 1)
for i, p in enumerate(P):
dMdm = dMdm + sp.csr_matrix((p.T * (p * v), (range(n), np.zeros(n))), shape=(n,1))
if d == 1:
if prop.size == self.nC:
dMdm = spzeros(n, self.nC)
for i, p in enumerate(P):
dMdm = dMdm + p.T * sdiag( p * v )
elif d == 2:
if prop.size == self.nC:
dMdm = spzeros(n, self.nC)
for i, p in enumerate(P):
Y = p * v
y1 = Y[:self.nC]
y2 = Y[self.nC:]
dMdm = dMdm + p.T * sp.vstack((sdiag( y1 ), sdiag( y2 )))
elif prop.size == self.nC*2:
dMdms = [spzeros(n, self.nC) for _ in range(2)]
for i, p in enumerate(P):
Y = p * v
y1 = Y[:self.nC]
y2 = Y[self.nC:]
dMdms[0] = dMdms[0] + p.T * sp.vstack(( sdiag( y1 ), Z))
dMdms[1] = dMdms[1] + p.T * sp.vstack(( Z, sdiag( y2 )))
dMdm = sp.hstack(dMdms)
elif prop.size == self.nC*3:
dMdms = [spzeros(n, self.nC) for _ in range(3)]
for i, p in enumerate(P):
Y = p * v
y1 = Y[:self.nC]
y2 = Y[self.nC:]
dMdms[0] = dMdms[0] + p.T * sp.vstack(( sdiag( y1 ), Z))
dMdms[1] = dMdms[1] + p.T * sp.vstack(( Z, sdiag( y2 )))
dMdms[2] = dMdms[2] + p.T * sp.vstack(( sdiag( y2 ), sdiag( y1 )))
dMdm = sp.hstack(dMdms)
elif d == 3:
if prop.size == self.nC:
dMdm = spzeros(n, self.nC)
for i, p in enumerate(P):
Y = p * v
y1 = Y[:self.nC]
y2 = Y[self.nC:self.nC*2]
y3 = Y[self.nC*2:]
dMdm = dMdm + p.T * sp.vstack((sdiag( y1 ), sdiag( y2 ), sdiag( y3 )))
elif prop.size == self.nC*3:
dMdms = [spzeros(n, self.nC) for _ in range(3)]
for i, p in enumerate(P):
Y = p * v
y1 = Y[:self.nC]
y2 = Y[self.nC:self.nC*2]
y3 = Y[self.nC*2:]
dMdms[0] = dMdms[0] + p.T * sp.vstack(( sdiag( y1 ), Z, Z))
dMdms[1] = dMdms[1] + p.T * sp.vstack(( Z, sdiag( y2 ), Z))
dMdms[2] = dMdms[2] + p.T * sp.vstack(( Z, Z, sdiag( y3 )))
dMdm = sp.hstack(dMdms)
elif prop.size == self.nC*6:
dMdms = [spzeros(n, self.nC) for _ in range(6)]
for i, p in enumerate(P):
Y = p * v
y1 = Y[:self.nC]
y2 = Y[self.nC:self.nC*2]
y3 = Y[self.nC*2:]
dMdms[0] = dMdms[0] + p.T * sp.vstack(( sdiag( y1 ), Z, Z))
dMdms[1] = dMdms[1] + p.T * sp.vstack(( Z, sdiag( y2 ), Z))
dMdms[2] = dMdms[2] + p.T * sp.vstack(( Z, Z, sdiag( y3 )))
dMdms[3] = dMdms[3] + p.T * sp.vstack(( sdiag( y2 ), sdiag( y1 ), Z))
dMdms[4] = dMdms[4] + p.T * sp.vstack(( sdiag( y3 ), Z, sdiag( y1 )))
dMdms[5] = dMdms[5] + p.T * sp.vstack(( Z, sdiag( y3 ), sdiag( y2 )))
dMdm = sp.hstack(dMdms)
return dMdm
# ------------------------ Geometries ------------------------------
#
#
# node(i,j,k+1) ------ edge2(i,j,k+1) ----- node(i,j+1,k+1)
# / /
# / / |
# edge3(i,j,k) face1(i,j,k) edge3(i,j+1,k)
# / / |
# / / |
# node(i,j,k) ------ edge2(i,j,k) ----- node(i,j+1,k)
# | | |
# | | node(i+1,j+1,k+1)
# | | /
# edge1(i,j,k) face3(i,j,k) edge1(i,j+1,k)
# | | /
# | | /
# | |/
# node(i+1,j,k) ------ edge2(i+1,j,k) ----- node(i+1,j+1,k)
def _getFacePx(M):
assert M._meshType == 'TENSOR', 'Only supported for a tensor mesh'
return _getFacePx_Rectangular(M)
def _getFacePxx(M):
if M._meshType == 'TREE':
return M._getFacePxx
return _getFacePxx_Rectangular(M)
def _getFacePxxx(M):
if M._meshType == 'TREE':
return M._getFacePxxx
return _getFacePxxx_Rectangular(M)
def _getEdgePxx(M):
if M._meshType == 'TREE':
return M._getEdgePxx
return _getEdgePxx_Rectangular(M)
def _getEdgePxxx(M):
if M._meshType == 'TREE':
return M._getEdgePxxx
return _getEdgePxxx_Rectangular(M)
def _getFacePx_Rectangular(M):
"""Returns a function for creating projection matrices
"""
ii = np.int64(range(M.nCx))
def Px(xFace):
"""
xFace is 'fXp' or 'fXm'
"""
posFx = 0 if xFace == 'fXm' else 1
IND = ii + posFx
PX = sp.csr_matrix((np.ones(M.nC), (range(M.nC), IND)), shape=(M.nC, M.nF))
return PX
return Px
def _getFacePxx_Rectangular(M):
"""returns a function for creating projection matrices
Mats takes you from faces a subset of all faces on only the
faces that you ask for.
These are centered around a single nodes.
For example, if this was your entire mesh:
f3(Yp)
2_______________3
| |
| |
| |
f0(Xm) | x | f1(Xp)
| |
| |
|_______________|
0 1
f2(Ym)
Pxx('fXm','fYm') = | 1, 0, 0, 0 |
| 0, 0, 1, 0 |
Pxx('fXp','fYm') = | 0, 1, 0, 0 |
| 0, 0, 1, 0 |
"""
i, j = np.int64(range(M.nCx)), np.int64(range(M.nCy))
iijj = ndgrid(i, j)
ii, jj = iijj[:, 0], iijj[:, 1]
if M._meshType == 'LRM':
fN1 = M.r(M.normals, 'F', 'Fx', 'M')
fN2 = M.r(M.normals, 'F', 'Fy', 'M')
def Pxx(xFace, yFace):
"""
xFace is 'fXp' or 'fXm'
yFace is 'fYp' or 'fYm'
"""
# no | node | f1 | f2
# 00 | i ,j | i , j | i, j
# 10 | i+1,j | i+1, j | i, j
# 01 | i ,j+1 | i , j | i, j+1
# 11 | i+1,j+1 | i+1, j | i, j+1
posFx = 0 if xFace == 'fXm' else 1
posFy = 0 if yFace == 'fYm' else 1
ind1 = sub2ind(M.vnFx, np.c_[ii + posFx, jj])
ind2 = sub2ind(M.vnFy, np.c_[ii, jj + posFy]) + M.nFx
IND = np.r_[ind1, ind2].flatten()
PXX = sp.csr_matrix((np.ones(2*M.nC), (range(2*M.nC), IND)), shape=(2*M.nC, M.nF))
if M._meshType == 'LRM':
I2x2 = inv2X2BlockDiagonal(getSubArray(fN1[0], [i + posFx, j]), getSubArray(fN1[1], [i + posFx, j]),
getSubArray(fN2[0], [i, j + posFy]), getSubArray(fN2[1], [i, j + posFy]))
PXX = I2x2 * PXX
return PXX
return Pxx
def _getFacePxxx_Rectangular(M):
"""returns a function for creating projection matrices
Mats takes you from faces a subset of all faces on only the
faces that you ask for.
These are centered around a single nodes.
"""
i, j, k = np.int64(range(M.nCx)), np.int64(range(M.nCy)), np.int64(range(M.nCz))
iijjkk = ndgrid(i, j, k)
ii, jj, kk = iijjkk[:, 0], iijjkk[:, 1], iijjkk[:, 2]
if M._meshType == 'LRM':
fN1 = M.r(M.normals, 'F', 'Fx', 'M')
fN2 = M.r(M.normals, 'F', 'Fy', 'M')
fN3 = M.r(M.normals, 'F', 'Fz', 'M')
def Pxxx(xFace, yFace, zFace):
"""
xFace is 'fXp' or 'fXm'
yFace is 'fYp' or 'fYm'
zFace is 'fZp' or 'fZm'
"""
# no | node | f1 | f2 | f3
# 000 | i ,j ,k | i , j, k | i, j , k | i, j, k
# 100 | i+1,j ,k | i+1, j, k | i, j , k | i, j, k
# 010 | i ,j+1,k | i , j, k | i, j+1, k | i, j, k
# 110 | i+1,j+1,k | i+1, j, k | i, j+1, k | i, j, k
# 001 | i ,j ,k+1 | i , j, k | i, j , k | i, j, k+1
# 101 | i+1,j ,k+1 | i+1, j, k | i, j , k | i, j, k+1
# 011 | i ,j+1,k+1 | i , j, k | i, j+1, k | i, j, k+1
# 111 | i+1,j+1,k+1 | i+1, j, k | i, j+1, k | i, j, k+1
posX = 0 if xFace == 'fXm' else 1
posY = 0 if yFace == 'fYm' else 1
posZ = 0 if zFace == 'fZm' else 1
ind1 = sub2ind(M.vnFx, np.c_[ii + posX, jj, kk])
ind2 = sub2ind(M.vnFy, np.c_[ii, jj + posY, kk]) + M.nFx
ind3 = sub2ind(M.vnFz, np.c_[ii, jj, kk + posZ]) + M.nFx + M.nFy
IND = np.r_[ind1, ind2, ind3].flatten()
PXXX = sp.coo_matrix((np.ones(3*M.nC), (range(3*M.nC), IND)), shape=(3*M.nC, M.nF)).tocsr()
if M._meshType == 'LRM':
I3x3 = inv3X3BlockDiagonal(getSubArray(fN1[0], [i + posX, j, k]), getSubArray(fN1[1], [i + posX, j, k]), getSubArray(fN1[2], [i + posX, j, k]),
getSubArray(fN2[0], [i, j + posY, k]), getSubArray(fN2[1], [i, j + posY, k]), getSubArray(fN2[2], [i, j + posY, k]),
getSubArray(fN3[0], [i, j, k + posZ]), getSubArray(fN3[1], [i, j, k + posZ]), getSubArray(fN3[2], [i, j, k + posZ]))
PXXX = I3x3 * PXXX
return PXXX
return Pxxx
def _getEdgePxx_Rectangular(M):
i, j = np.int64(range(M.nCx)), np.int64(range(M.nCy))
iijj = ndgrid(i, j)
ii, jj = iijj[:, 0], iijj[:, 1]
if M._meshType == 'LRM':
eT1 = M.r(M.tangents, 'E', 'Ex', 'M')
eT2 = M.r(M.tangents, 'E', 'Ey', 'M')
def Pxx(xEdge, yEdge):
# no | node | e1 | e2
# 00 | i ,j | i ,j | i ,j
# 10 | i+1,j | i ,j | i+1,j
# 01 | i ,j+1 | i ,j+1 | i ,j
# 11 | i+1,j+1 | i ,j+1 | i+1,j
posX = 0 if xEdge == 'eX0' else 1
posY = 0 if yEdge == 'eY0' else 1
ind1 = sub2ind(M.vnEx, np.c_[ii, jj + posX])
ind2 = sub2ind(M.vnEy, np.c_[ii + posY, jj]) + M.nEx
IND = np.r_[ind1, ind2].flatten()
PXX = sp.coo_matrix((np.ones(2*M.nC), (range(2*M.nC), IND)), shape=(2*M.nC, M.nE)).tocsr()
if M._meshType == 'LRM':
I2x2 = inv2X2BlockDiagonal(getSubArray(eT1[0], [i, j + posX]), getSubArray(eT1[1], [i, j + posX]),
getSubArray(eT2[0], [i + posY, j]), getSubArray(eT2[1], [i + posY, j]))
PXX = I2x2 * PXX
return PXX
return Pxx
def _getEdgePxxx_Rectangular(M):
i, j, k = np.int64(range(M.nCx)), np.int64(range(M.nCy)), np.int64(range(M.nCz))
iijjkk = ndgrid(i, j, k)
ii, jj, kk = iijjkk[:, 0], iijjkk[:, 1], iijjkk[:, 2]
if M._meshType == 'LRM':
eT1 = M.r(M.tangents, 'E', 'Ex', 'M')
eT2 = M.r(M.tangents, 'E', 'Ey', 'M')
eT3 = M.r(M.tangents, 'E', 'Ez', 'M')
def Pxxx(xEdge, yEdge, zEdge):
# no | node | e1 | e2 | e3
# 000 | i ,j ,k | i ,j ,k | i ,j ,k | i ,j ,k
# 100 | i+1,j ,k | i ,j ,k | i+1,j ,k | i+1,j ,k
# 010 | i ,j+1,k | i ,j+1,k | i ,j ,k | i ,j+1,k
# 110 | i+1,j+1,k | i ,j+1,k | i+1,j ,k | i+1,j+1,k
# 001 | i ,j ,k+1 | i ,j ,k+1 | i ,j ,k+1 | i ,j ,k
# 101 | i+1,j ,k+1 | i ,j ,k+1 | i+1,j ,k+1 | i+1,j ,k
# 011 | i ,j+1,k+1 | i ,j+1,k+1 | i ,j ,k+1 | i ,j+1,k
# 111 | i+1,j+1,k+1 | i ,j+1,k+1 | i+1,j ,k+1 | i+1,j+1,k
posX = [0,0] if xEdge == 'eX0' else [1, 0] if xEdge == 'eX1' else [0,1] if xEdge == 'eX2' else [1,1]
posY = [0,0] if yEdge == 'eY0' else [1, 0] if yEdge == 'eY1' else [0,1] if yEdge == 'eY2' else [1,1]
posZ = [0,0] if zEdge == 'eZ0' else [1, 0] if zEdge == 'eZ1' else [0,1] if zEdge == 'eZ2' else [1,1]
ind1 = sub2ind(M.vnEx, np.c_[ii, jj + posX[0], kk + posX[1]])
ind2 = sub2ind(M.vnEy, np.c_[ii + posY[0], jj, kk + posY[1]]) + M.nEx
ind3 = sub2ind(M.vnEz, np.c_[ii + posZ[0], jj + posZ[1], kk]) + M.nEx + M.nEy
IND = np.r_[ind1, ind2, ind3].flatten()
PXXX = sp.coo_matrix((np.ones(3*M.nC), (range(3*M.nC), IND)), shape=(3*M.nC, M.nE)).tocsr()
if M._meshType == 'LRM':
I3x3 = inv3X3BlockDiagonal(getSubArray(eT1[0], [i, j + posX[0], k + posX[1]]), getSubArray(eT1[1], [i, j + posX[0], k + posX[1]]), getSubArray(eT1[2], [i, j + posX[0], k + posX[1]]),
getSubArray(eT2[0], [i + posY[0], j, k + posY[1]]), getSubArray(eT2[1], [i + posY[0], j, k + posY[1]]), getSubArray(eT2[2], [i + posY[0], j, k + posY[1]]),
getSubArray(eT3[0], [i + posZ[0], j + posZ[1], k]), getSubArray(eT3[1], [i + posZ[0], j + posZ[1], k]), getSubArray(eT3[2], [i + posZ[0], j + posZ[1], k]))
PXXX = I3x3 * PXXX
return PXXX
return Pxxx
if __name__ == '__main__':
from TensorMesh import TensorMesh
h = [np.array([1, 2, 3, 4]), np.array([1, 2, 1, 4, 2]), np.array([1, 1, 4, 1])]
M = TensorMesh(h)
mu = np.ones((M.nC, 6))
A, P = M.getFaceInnerProduct(mu, returnP=True)
B, P = M.getEdgeInnerProduct(mu, returnP=True)