def orthoFock(self):
"""Routine to orthogonalize the AO Fock matrix to orthonormal basis"""
self.FO = np.dot(self.X.T,np.dot(self.F,self.X))
python类multi_dot()的实例源码
def unOrthoFock(self):
"""Routine to unorthogonalize the orthonormal Fock matrix to AO basis"""
self.F = np.dot(self.U.T,np.dot(self.FO,self.U))
def orthoDen(self):
"""Routine to orthogonalize the AO Density matrix to orthonormal basis"""
self.PO = np.dot(self.U,np.dot(self.P,self.U.T))
def unOrthoDen(self):
"""Routine to unorthogonalize the orthonormal Density matrix to AO basis"""
self.P = np.dot(self.X,np.dot(self.PO,self.X.T))
def computeDipole(self):
"""Routine to compute the SCF electronic dipole moment"""
self.el_energy = np.einsum('pq,qp',self.Core+self.F,self.P)
for i in range(3):
self.mu[i] = -2*np.trace(np.dot(self.P,self.M[i])) + sum([atom.charge*(atom.origin[i]-self.center_of_charge[i]) for atom in self.atoms])
# to debye
self.mu *= 2.541765
def updateDIIS(self,F,P):
FPS = dot([F,P,self.S])
SPF = self.adj(FPS)
# error must be in orthonormal basis
error = dot([self.X,FPS-SPF,self.X])
self.fockSet.append(self.F)
self.errorSet.append(error)
numFock = len(self.fockSet)
# limit subspace, hardcoded for now
if numFock > 8:
del self.fockSet[0]
del self.errorSet[0]
numFock -= 1
B = np.zeros((numFock + 1,numFock + 1))
B[-1,:] = B[:,-1] = -1.0
B[-1,-1] = 0.0
# B is symmetric
for i in range(numFock):
for j in range(i+1):
B[i,j] = B[j,i] = \
np.real(np.trace(np.dot(self.adj(self.errorSet[i]),
self.errorSet[j])))
residual = np.zeros(numFock + 1)
residual[-1] = -1.0
weights = np.linalg.solve(B,residual)
# weights is 1 x numFock + 1, but first numFock values
# should sum to one if we are doing DIIS correctly
assert np.isclose(sum(weights[:-1]),1.0)
F = np.zeros((self.nbasis,self.nbasis),dtype='complex')
for i, Fock in enumerate(self.fockSet):
F += weights[i] * Fock
return F
def test_basic_function_with_three_arguments(self):
# multi_dot with three arguments uses a fast hand coded algorithm to
# determine the optimal order. Therefore test it separately.
A = np.random.random((6, 2))
B = np.random.random((2, 6))
C = np.random.random((6, 2))
assert_almost_equal(multi_dot([A, B, C]), A.dot(B).dot(C))
assert_almost_equal(multi_dot([A, B, C]), np.dot(A, np.dot(B, C)))
def test_basic_function_with_dynamic_programing_optimization(self):
# multi_dot with four or more arguments uses the dynamic programing
# optimization and therefore deserve a separate
A = np.random.random((6, 2))
B = np.random.random((2, 6))
C = np.random.random((6, 2))
D = np.random.random((2, 1))
assert_almost_equal(multi_dot([A, B, C, D]), A.dot(B).dot(C).dot(D))
def test_vector_as_first_argument(self):
# The first argument can be 1-D
A1d = np.random.random(2) # 1-D
B = np.random.random((2, 6))
C = np.random.random((6, 2))
D = np.random.random((2, 2))
# the result should be 1-D
assert_equal(multi_dot([A1d, B, C, D]).shape, (2,))
def test_vector_as_last_argument(self):
# The last argument can be 1-D
A = np.random.random((6, 2))
B = np.random.random((2, 6))
C = np.random.random((6, 2))
D1d = np.random.random(2) # 1-D
# the result should be 1-D
assert_equal(multi_dot([A, B, C, D1d]).shape, (6,))
def test_vector_as_first_and_last_argument(self):
# The first and last arguments can be 1-D
A1d = np.random.random(2) # 1-D
B = np.random.random((2, 6))
C = np.random.random((6, 2))
D1d = np.random.random(2) # 1-D
# the result should be a scalar
assert_equal(multi_dot([A1d, B, C, D1d]).shape, ())
def test_basic_function_with_three_arguments(self):
# multi_dot with three arguments uses a fast hand coded algorithm to
# determine the optimal order. Therefore test it separately.
A = np.random.random((6, 2))
B = np.random.random((2, 6))
C = np.random.random((6, 2))
assert_almost_equal(multi_dot([A, B, C]), A.dot(B).dot(C))
assert_almost_equal(multi_dot([A, B, C]), np.dot(A, np.dot(B, C)))
def test_basic_function_with_dynamic_programing_optimization(self):
# multi_dot with four or more arguments uses the dynamic programing
# optimization and therefore deserve a separate
A = np.random.random((6, 2))
B = np.random.random((2, 6))
C = np.random.random((6, 2))
D = np.random.random((2, 1))
assert_almost_equal(multi_dot([A, B, C, D]), A.dot(B).dot(C).dot(D))
def test_vector_as_first_argument(self):
# The first argument can be 1-D
A1d = np.random.random(2) # 1-D
B = np.random.random((2, 6))
C = np.random.random((6, 2))
D = np.random.random((2, 2))
# the result should be 1-D
assert_equal(multi_dot([A1d, B, C, D]).shape, (2,))
def test_vector_as_last_argument(self):
# The last argument can be 1-D
A = np.random.random((6, 2))
B = np.random.random((2, 6))
C = np.random.random((6, 2))
D1d = np.random.random(2) # 1-D
# the result should be 1-D
assert_equal(multi_dot([A, B, C, D1d]).shape, (6,))
def test_vector_as_first_and_last_argument(self):
# The first and last arguments can be 1-D
A1d = np.random.random(2) # 1-D
B = np.random.random((2, 6))
C = np.random.random((6, 2))
D1d = np.random.random(2) # 1-D
# the result should be a scalar
assert_equal(multi_dot([A1d, B, C, D1d]).shape, ())
test_linalg.py 文件源码
项目：PyDataLondon29-EmbarrassinglyParallelDAWithAWSLambda
作者: SignalMedia
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def test_basic_function_with_three_arguments(self):
# multi_dot with three arguments uses a fast hand coded algorithm to
# determine the optimal order. Therefore test it separately.
A = np.random.random((6, 2))
B = np.random.random((2, 6))
C = np.random.random((6, 2))
assert_almost_equal(multi_dot([A, B, C]), A.dot(B).dot(C))
assert_almost_equal(multi_dot([A, B, C]), np.dot(A, np.dot(B, C)))
test_linalg.py 文件源码
项目：PyDataLondon29-EmbarrassinglyParallelDAWithAWSLambda
作者: SignalMedia
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def test_basic_function_with_dynamic_programing_optimization(self):
# multi_dot with four or more arguments uses the dynamic programing
# optimization and therefore deserve a separate
A = np.random.random((6, 2))
B = np.random.random((2, 6))
C = np.random.random((6, 2))
D = np.random.random((2, 1))
assert_almost_equal(multi_dot([A, B, C, D]), A.dot(B).dot(C).dot(D))
test_linalg.py 文件源码
项目：PyDataLondon29-EmbarrassinglyParallelDAWithAWSLambda
作者: SignalMedia
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def test_vector_as_first_argument(self):
# The first argument can be 1-D
A1d = np.random.random(2) # 1-D
B = np.random.random((2, 6))
C = np.random.random((6, 2))
D = np.random.random((2, 2))
# the result should be 1-D
assert_equal(multi_dot([A1d, B, C, D]).shape, (2,))
test_linalg.py 文件源码
项目：PyDataLondon29-EmbarrassinglyParallelDAWithAWSLambda
作者: SignalMedia
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def test_vector_as_last_argument(self):
# The last argument can be 1-D
A = np.random.random((6, 2))
B = np.random.random((2, 6))
C = np.random.random((6, 2))
D1d = np.random.random(2) # 1-D
# the result should be 1-D
assert_equal(multi_dot([A, B, C, D1d]).shape, (6,))
test_linalg.py 文件源码
项目：PyDataLondon29-EmbarrassinglyParallelDAWithAWSLambda
作者: SignalMedia
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文件源码
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def test_vector_as_first_and_last_argument(self):
# The first and last arguments can be 1-D
A1d = np.random.random(2) # 1-D
B = np.random.random((2, 6))
C = np.random.random((6, 2))
D1d = np.random.random(2) # 1-D
# the result should be a scalar
assert_equal(multi_dot([A1d, B, C, D1d]).shape, ())
def test_basic_function_with_three_arguments(self):
# multi_dot with three arguments uses a fast hand coded algorithm to
# determine the optimal order. Therefore test it separately.
A = np.random.random((6, 2))
B = np.random.random((2, 6))
C = np.random.random((6, 2))
assert_almost_equal(multi_dot([A, B, C]), A.dot(B).dot(C))
assert_almost_equal(multi_dot([A, B, C]), np.dot(A, np.dot(B, C)))
def test_basic_function_with_dynamic_programing_optimization(self):
# multi_dot with four or more arguments uses the dynamic programing
# optimization and therefore deserve a separate
A = np.random.random((6, 2))
B = np.random.random((2, 6))
C = np.random.random((6, 2))
D = np.random.random((2, 1))
assert_almost_equal(multi_dot([A, B, C, D]), A.dot(B).dot(C).dot(D))
def test_vector_as_first_argument(self):
# The first argument can be 1-D
A1d = np.random.random(2) # 1-D
B = np.random.random((2, 6))
C = np.random.random((6, 2))
D = np.random.random((2, 2))
# the result should be 1-D
assert_equal(multi_dot([A1d, B, C, D]).shape, (2,))
def test_vector_as_last_argument(self):
# The last argument can be 1-D
A = np.random.random((6, 2))
B = np.random.random((2, 6))
C = np.random.random((6, 2))
D1d = np.random.random(2) # 1-D
# the result should be 1-D
assert_equal(multi_dot([A, B, C, D1d]).shape, (6,))
def test_vector_as_first_and_last_argument(self):
# The first and last arguments can be 1-D
A1d = np.random.random(2) # 1-D
B = np.random.random((2, 6))
C = np.random.random((6, 2))
D1d = np.random.random(2) # 1-D
# the result should be a scalar
assert_equal(multi_dot([A1d, B, C, D1d]).shape, ())
def test_basic_function_with_three_arguments(self):
# multi_dot with three arguments uses a fast hand coded algorithm to
# determine the optimal order. Therefore test it separately.
A = np.random.random((6, 2))
B = np.random.random((2, 6))
C = np.random.random((6, 2))
assert_almost_equal(multi_dot([A, B, C]), A.dot(B).dot(C))
assert_almost_equal(multi_dot([A, B, C]), np.dot(A, np.dot(B, C)))
def test_basic_function_with_dynamic_programing_optimization(self):
# multi_dot with four or more arguments uses the dynamic programing
# optimization and therefore deserve a separate
A = np.random.random((6, 2))
B = np.random.random((2, 6))
C = np.random.random((6, 2))
D = np.random.random((2, 1))
assert_almost_equal(multi_dot([A, B, C, D]), A.dot(B).dot(C).dot(D))
def test_vector_as_first_argument(self):
# The first argument can be 1-D
A1d = np.random.random(2) # 1-D
B = np.random.random((2, 6))
C = np.random.random((6, 2))
D = np.random.random((2, 2))
# the result should be 1-D
assert_equal(multi_dot([A1d, B, C, D]).shape, (2,))
def test_vector_as_last_argument(self):
# The last argument can be 1-D
A = np.random.random((6, 2))
B = np.random.random((2, 6))
C = np.random.random((6, 2))
D1d = np.random.random(2) # 1-D
# the result should be 1-D
assert_equal(multi_dot([A, B, C, D1d]).shape, (6,))
