def compare_one_electron_part_gradients(self, D):
"""
compare analytical and numerical gradients for the contraction
dH d (m|h^(1)|n)
--(D) = sum ------------- D
dx m,n d x mn
"""
polham_grad = PolarizationHamiltonianGradients(*self.args, **self.kwds)
molecule, basis, ribasis, polarizable_atoms = self.args[0:4]
# analytical gradient on QM atoms and point charges
grad = polham_grad.one_electron_part_GRAD(D)
grad_QM, grad_POL, grad_CHG = polham_grad.split_gradient(grad)
# step size for finite differences
step = 0.0001
# numerical gradient on QM atoms
grad_QM_NUM = [None for k in range(0, 3*molecule.natom())]
for i in range(0, molecule.natom()):
for xyz in [0,1,2]:
def shift_coords(step):
molecule_ = molecule.clone()
coords = molecule_.geometry().np
coords[i,xyz] += step
molecule_.set_geometry(psi4.core.Matrix.from_array(coords))
# The centers of the basis functions are taken from the basis object.
wfn = psi4.core.Wavefunction.build(molecule_, basis.name() )
basis_ = wfn.basisset()
args_ = list(self.args[:])
args_[0:3] = (molecule_, basis_, basis_)
polham = PolarizationHamiltonian(*args_, **self.kwds)
return polham
# f(x+dx)
H_plus = shift_coords(step).one_electron_part()
HD_plus = np.einsum('mn,mn', H_plus, D)
# f(x-dx)
H_minus = shift_coords(-step).one_electron_part()
HD_minus = np.einsum('mn,mn', H_minus, D)
# df/dx = (f(x+dx) - f(x-dx))/(2 dx)
grad_QM_NUM[3*i+xyz] = (HD_plus - HD_minus)/(2*step)
grad_QM = np.array(grad_QM)
grad_QM_NUM = np.array(grad_QM_NUM)
err_QM = la.norm(grad_QM - grad_QM_NUM)
print("+++ Gradient of core Hamiltonian-like contraction sum_{m,n} d(m|h^(1)|n)/dx D_{m,n} on QM atoms +++")
print(" Analytical:")
print(grad_QM)
print(" Numerical:")
print(grad_QM_NUM)
print(f" Error: {err_QM}")
# numerical gradient on polarizable sites
npol = polarizable_atoms.natom()
grad_POL_NUM = np.zeros(3*npol)
for i in range(0, npol):
for xyz in [0,1,2]:
def shift_coords(step):
polarizable_atoms_ = polarizable_atoms.clone()
coords = polarizable_atoms_.geometry().np
coords[i,xyz] += step
polarizable_atoms_.set_geometry(psi4.core.Matrix.from_array(coords))
args_ = list(self.args[:])
args_[3] = polarizable_atoms_
polham = PolarizationHamiltonian(*args_, **self.kwds)
return polham
# f(x+dx)
H_plus = shift_coords(step).one_electron_part()
HD_plus = np.einsum('mn,mn', H_plus, D)
# f(x-dx)
H_minus = shift_coords(-step).one_electron_part()
HD_minus = np.einsum('mn,mn', H_minus, D)
# df/dx = (f(x+dx) - f(x-dx))/(2 dx)
grad_POL_NUM[3*i+xyz] = (HD_plus - HD_minus)/(2*step)
grad_POL = np.array(grad_POL)
err_POL = la.norm(grad_POL - grad_POL_NUM)
print("+++ Gradient of core Hamiltonian-like contraction sum_{m,n} d(m|h^(1)|n)/dx D_{m,n} on polarizable sites +++")
print(" Analytical:")
print(grad_POL)
print(" Numerical:")
print(grad_POL_NUM)
print(f" Error: {err_POL}")
# numerical gradient on point charges
point_charges = self.args[4]
grad_CHG_NUM = [None for k in range(0, 3*point_charges.natom())]
for i in range(0, point_charges.natom()):
for xyz in [0,1,2]:
def shift_coords(step):
point_charges_ = point_charges.clone()
coords = point_charges_.geometry().np
coords[i,xyz] += step
point_charges_.set_geometry(psi4.core.Matrix.from_array(coords))
args_ = list(self.args[:])
args_[4] = point_charges_
polham = PolarizationHamiltonian(*args_, **self.kwds)
return polham
# f(x+dx)
H_plus = shift_coords(step).one_electron_part()
HD_plus = np.einsum('mn,mn', H_plus, D)
# f(x-dx)
H_minus = shift_coords(-step).one_electron_part()
HD_minus = np.einsum('mn,mn', H_minus, D)
# df/dx = (f(x+dx) - f(x-dx))/(2 dx)
grad_CHG_NUM[3*i+xyz] = (HD_plus - HD_minus)/(2*step)
grad_CHG = np.array(grad_CHG)
grad_CHG_NUM = np.array(grad_CHG_NUM)
err_CHG = la.norm(grad_CHG - grad_CHG_NUM)
print("+++ Gradient of core Hamiltonian-like contraction sum_{m,n} d(m|h^(1)|n)/dx D_{m,n} on point charges +++")
print(" Analytical:")
print(grad_CHG)
print(" Numerical:")
print(grad_CHG_NUM)
print(f" Error: {err_CHG}")
assert err_QM < 1.0e-5
assert err_POL < 1.0e-5
assert err_CHG < 1.0e-5
# all tests passed
return True
def compare_exchange_K_gradients(self, D1, D2):
"""
compare analytical and numerical gradients for the contraction
dK (1) d (pr|h^(2)|qs) (2)
--(D1,D2) = sum D --------------- D
dx p,q,r,s p,q d x r,s
"""
polham_grad = PolarizationHamiltonianGradients(*self.args, **self.kwds)
molecule, basis, ribasis, polarizable_atoms = self.args[0:4]
# analytical gradient on QM atoms and point charges
grad = polham_grad.exchange_K_GRAD(D1, D2)
grad_QM, grad_POL, grad_CHG = polham_grad.split_gradient(grad)
assert la.norm(grad_CHG) == 0.0
# step size for finite differences
step = 0.001
# numerical gradient on QM atoms
grad_QM_NUM = [None for k in range(0, 3*molecule.natom())]
for i in range(0, molecule.natom()):
for xyz in [0,1,2]:
def shift_coords(step):
molecule_ = molecule.clone()
coords = molecule_.geometry().np
coords[i,xyz] += step
molecule_.set_geometry(psi4.core.Matrix.from_array(coords))
# The centers of the basis functions are taken from the basis object.
wfn = psi4.core.Wavefunction.build(molecule_, basis.name() )
basis_ = wfn.basisset()
args_ = list(self.args[:])
args_[0:3] = (molecule_, basis_, basis_)
polham = PolarizationHamiltonian(*args_, **self.kwds)
return polham
# f(x+dx)
K_plus = shift_coords(step).exchange_K(D2)
DKD_plus = np.einsum('mn,mn', D1, K_plus)
# f(x-dx)
K_minus = shift_coords(-step).exchange_K(D2)
DKD_minus = np.einsum('mn,mn', D1, K_minus)
# df/dx = (f(x+dx) - f(x-dx))/(2 dx)
grad_QM_NUM[3*i+xyz] = (DKD_plus - DKD_minus)/(2*step)
grad_QM = np.array(grad_QM)
grad_QM_NUM = np.array(grad_QM_NUM)
err_QM = la.norm(grad_QM - grad_QM_NUM)
print("+++ Gradient of K-like contraction sum_{p,q,r,s} D1_{p,q} d(pr|h^(2)|qs)/dx D2_{r,s} on QM atoms +++")
print(" Analytical:")
print(grad_QM)
print(" Numerical:")
print(grad_QM_NUM)
print(f" Error: {err_QM}")
# numerical gradient on polarizable sites
npol = polarizable_atoms.natom()
grad_POL_NUM = np.zeros(3*npol)
for i in range(0, npol):
for xyz in [0,1,2]:
def shift_coords(step):
polarizable_atoms_ = polarizable_atoms.clone()
coords = polarizable_atoms_.geometry().np
coords[i,xyz] += step
polarizable_atoms_.set_geometry(psi4.core.Matrix.from_array(coords))
args_ = list(self.args[:])
args_[3] = polarizable_atoms_
polham = PolarizationHamiltonian(*args_, **self.kwds)
return polham
# f(x+dx)
K_plus = shift_coords(step).exchange_K(D2)
DKD_plus = np.einsum('mn,mn', D1, K_plus)
# f(x-dx)
K_minus = shift_coords(-step).exchange_K(D2)
DKD_minus = np.einsum('mn,mn', D1, K_minus)
# df/dx = (f(x+dx) - f(x-dx))/(2 dx)
grad_POL_NUM[3*i+xyz] = (DKD_plus - DKD_minus)/(2*step)
grad_POL = np.array(grad_POL)
err_POL = la.norm(grad_POL - grad_POL_NUM)
print("+++ Gradient of K-like contraction sum_{p,q,r,s} D1_{p,q} d(pr|h^(2)|qs)/dx D1_{r,s} on polarizable sites +++")
print(" Analytical:")
print(grad_POL)
print(" Numerical:")
print(grad_POL_NUM)
print(f" Error: {err_POL}")
assert err_QM < 1.0e-5
assert err_POL < 1.0e-5
# all tests passed
return True
def compare_gradients(self, function_name):
"""
compare analytical and numerical gradients for the quantity computed by the member
function `function_name`.
The function computes the gradients
* on QM atoms
* polarizable sites and
* point charges
first analytically and then by a two-point finite difference formula.
Example
-------
>>> ...
>>> G = GradientComparison(molecule, basis, ribasis, polarizable_atoms, point_charges)
>>> G.compare_gradients('zero_electron_part')
"""
polham_grad = PolarizationHamiltonianGradients(*self.args, **self.kwds)
molecule = self.args[0]
# analytical gradients
func_GRAD = getattr(polham_grad, function_name + "_GRAD")
grad = func_GRAD()
grad_QM, grad_POL, grad_CHG = polham_grad.split_gradient(grad)
# Step size for finite differences
step = 0.001
# numerical gradient on QM atoms
grad_QM_NUM = [None for k in range(0, 3*molecule.natom())]
for i in range(0, molecule.natom()):
for xyz in [0,1,2]:
def shift_coords(step):
molecule_ = molecule.clone()
coords = molecule_.geometry().np
coords[i,xyz] += step
molecule_.set_geometry(psi4.core.Matrix.from_array(coords))
args_ = list(self.args[:])
args_[0] = molecule_
polham = PolarizationHamiltonian(*args_, **self.kwds)
return polham
# f(x+dx)
# call member function by its name
h_plus = getattr(shift_coords(step), function_name)()
# f(x-dx)
h_minus = getattr(shift_coords(-step), function_name)()
# df/dx = (f(x+dx) - f(x-dx))/(2 dx)
grad_QM_NUM[3*i+xyz] = (h_plus - h_minus)/(2*step)
grad_QM = np.array(grad_QM)
grad_QM_NUM = np.array(grad_QM_NUM)
err_QM = la.norm(grad_QM - grad_QM_NUM)
print(f"+++ Gradient of {function_name} on QM atoms +++")
print(" Analytical:")
print(grad_QM)
print(" Numerical:")
print(grad_QM_NUM)
print(f" Error: {err_QM}")
# numerical gradient on polarizable sites
polarizable_atoms = self.args[3]
grad_POL_NUM = [None for k in range(0, 3*polarizable_atoms.natom())]
for i in range(0, polarizable_atoms.natom()):
for xyz in [0,1,2]:
def shift_coords(step):
polarizable_atoms_ = polarizable_atoms.clone()
coords = polarizable_atoms_.geometry().np
coords[i,xyz] += step
polarizable_atoms_.set_geometry(psi4.core.Matrix.from_array(coords))
args_ = list(self.args[:])
args_[3] = polarizable_atoms_
polham = PolarizationHamiltonian(*args_, **self.kwds)
return polham
# f(x+dx)
# call member function by its name
h_plus = getattr(shift_coords(step), function_name)()
# f(x-dx)
h_minus = getattr(shift_coords(-step), function_name)()
# df/dx = (f(x+dx) - f(x-dx))/(2 dx)
grad_POL_NUM[3*i+xyz] = (h_plus - h_minus)/(2*step)
grad_POL = np.array(grad_POL)
grad_POL_NUM = np.array(grad_POL_NUM)
err_POL = la.norm(grad_POL - grad_POL_NUM)
print(f"+++ Gradient of {function_name} on polarizable sites +++")
print(" Analytical:")
print(grad_POL)
print(" Numerical:")
print(grad_POL_NUM)
print(f" Error: {err_POL}")
# numerical gradient on point charges
point_charges = self.args[4]
grad_CHG_NUM = [None for k in range(0, 3*point_charges.natom())]
for i in range(0, point_charges.natom()):
for xyz in [0,1,2]:
def shift_coords(step):
point_charges_ = point_charges.clone()
coords = point_charges_.geometry().np
coords[i,xyz] += step
point_charges_.set_geometry(psi4.core.Matrix.from_array(coords))
args_ = list(self.args[:])
args_[4] = point_charges_
polham = PolarizationHamiltonian(*args_, **self.kwds)
return polham
# f(x+dx)
# call member function by its name
h_plus = getattr(shift_coords(step), function_name)()
# f(x-dx)
h_minus = getattr(shift_coords(-step), function_name)()
# df/dx = (f(x+dx) - f(x-dx))/(2 dx)
grad_CHG_NUM[3*i+xyz] = (h_plus - h_minus)/(2*step)
grad_CHG = np.array(grad_CHG)
grad_CHG_NUM = np.array(grad_CHG_NUM)
err_CHG = la.norm(grad_CHG - grad_CHG_NUM)
print(f"+++ Gradient of {function_name} on point charges +++")
print(" Analytical:")
print(grad_CHG)
print(" Numerical:")
print(grad_CHG_NUM)
print(f" Error: {err_CHG}")
assert err_QM < 1.0e-5
assert err_POL < 1.0e-5
assert err_CHG < 1.0e-5
# all tests passed
return True
def compare_contracted_gradients_diagA(self, V):
"""
compare analytical and numerical gradients for the contraction
d diag(A) d A_{3*k+a,3*k+b}
--------- (V) = sum sum ----------------- V
d x k a,b d x k,a,b
"""
polham_grad = PolarizationHamiltonianGradients(*self.args, **self.kwds)
molecule, basis, ribasis, polarizable_atoms = self.args[0:4]
# analytical gradient on QM atoms and point charges
grad = polham_grad._gradDiagA(V)
grad_QM, grad_POL, grad_CHG = polham_grad.split_gradient(grad)
assert la.norm(grad_QM ) == 0.0
assert la.norm(grad_CHG) == 0.0
# step size for finite differences
step = 0.001
# numerical gradient on polarizable sites
npol = polarizable_atoms.natom()
grad_POL_NUM = np.zeros(3*npol)
for i in range(0, npol):
for xyz in [0,1,2]:
def shift_coords(step):
polarizable_atoms_ = polarizable_atoms.clone()
coords = polarizable_atoms_.geometry().np
coords[i,xyz] += step
polarizable_atoms_.set_geometry(psi4.core.Matrix.from_array(coords))
args_ = list(self.args[:])
args_[3] = polarizable_atoms_
polham = PolarizationHamiltonian(*args_, **self.kwds)
return polham
def contract_diagonal(A, V):
AV = 0.0
npol = polham_grad.npol
for k in range(0, npol):
for a in [0,1,2]:
for b in [0,1,2]:
AV += A[3*k+a,3*k+b] * V[k,a,b]
return AV
# f(x+dx)
A_plus = shift_coords(step).A
AV_plus = contract_diagonal(A_plus, V)
# f(x-dx)
A_minus = shift_coords(-step).A
AV_minus = contract_diagonal(A_minus, V)
# df/dx = (f(x+dx) - f(x-dx))/(2 dx)
grad_POL_NUM[3*i+xyz] = (AV_plus - AV_minus)/(2*step)
grad_POL = np.array(grad_POL)
err_POL = la.norm(grad_POL - grad_POL_NUM)
print("+++ Gradient of contraction sum_{k,a,b} diag(A)_{k,a,b} V_{k,a,b} on polarizable sites +++")
print(" Analytical:")
print(grad_POL)
print(" Numerical:")
print(grad_POL_NUM)
print(f" Error: {err_POL}")
assert err_POL < 1.0e-4
# all tests passed
return True
def compare_contracted_gradients_overlap(self, R):
"""
compare analytical and numerical gradients for the contraction of the
overlap matrix with some density matrix R
dS
-- (R) = sum d/dx (S ) R
dx m,n m,n m,n
"""
polham_grad = PolarizationHamiltonianGradients(*self.args, **self.kwds)
molecule, basis, ribasis, polarizable_atoms = self.args[0:4]
# analytical gradient on QM atoms and point charges
grad = polham_grad._gradS(R)
grad_QM, grad_POL, grad_CHG = polham_grad.split_gradient(grad)
assert la.norm(grad_CHG) == 0.0
assert la.norm(grad_POL) == 0.0
# step size for finite differences
step = 0.001
# numerical gradient on QM atoms
grad_QM_NUM = [None for k in range(0, 3*molecule.natom())]
for i in range(0, molecule.natom()):
for xyz in [0,1,2]:
def shift_coords(step):
molecule_ = molecule.clone()
coords = molecule_.geometry().np
coords[i,xyz] += step
molecule_.set_geometry(psi4.core.Matrix.from_array(coords))
# The centers of the basis functions are taken from the basis object.
wfn = psi4.core.Wavefunction.build(molecule_, basis.name() )
basis_ = wfn.basisset()
# compute the overlap matrix
mints_ri = psi4.core.MintsHelper(basis_)
S = mints_ri.ao_overlap()
return S
# f(x+dx)
S_plus = shift_coords(step)
SR_plus = np.einsum('mn,mn', S_plus, R)
# f(x-dx)
S_minus = shift_coords(-step)
SR_minus = np.einsum('mn,mn', S_minus, R)
# df/dx = (f(x+dx) - f(x-dx))/(2 dx)
grad_QM_NUM[3*i+xyz] = (SR_plus - SR_minus)/(2*step)
grad_QM = np.array(grad_QM)
grad_QM_NUM = np.array(grad_QM_NUM)
err_QM = la.norm(grad_QM - grad_QM_NUM)
print("+++ Gradient of contraction sum_{m,n} S_{m,n} R_{m,n} on QM atoms +++")
print(" Analytical:")
print(grad_QM)
print(" Numerical:")
print(grad_QM_NUM)
print(f" Error: {err_QM}")
assert err_QM < 1.0e-5
# all tests passed
return True
def compare_contracted_gradients_I(self, Y):
"""
compare analytical and numerical gradients for the contraction
dI (elec)
-- (Y) = sum d/dx (I ) Y
dx k,a,b,m,n k;a,b;m,n k;a,b;m,n
"""
polham_grad = PolarizationHamiltonianGradients(*self.args, **self.kwds)
molecule, basis, ribasis, polarizable_atoms = self.args[0:4]
# analytical gradient on QM atoms and point charges
grad = polham_grad._gradI1e(Y)
grad_QM, grad_POL, grad_CHG = polham_grad.split_gradient(grad)
assert la.norm(grad_CHG) == 0.0
# step size for finite differences
step = 0.001
# numerical gradient on QM atoms
grad_QM_NUM = [None for k in range(0, 3*molecule.natom())]
for i in range(0, molecule.natom()):
for xyz in [0,1,2]:
def shift_coords(step):
molecule_ = molecule.clone()
coords = molecule_.geometry().np
coords[i,xyz] += step
molecule_.set_geometry(psi4.core.Matrix.from_array(coords))
# The centers of the basis functions are taken from the basis object.
wfn = psi4.core.Wavefunction.build(molecule_, basis.name() )
basis_ = wfn.basisset()
args_ = list(self.args[:])
args_[0:3] = (molecule_, basis_, basis_)
polham = PolarizationHamiltonian(*args_, **self.kwds)
return polham
# f(x+dx)
I_plus = shift_coords(step)._polarization_integrals_I()
IY_plus = np.einsum('kabmn,kabmn', I_plus, Y)
# f(x-dx)
I_minus = shift_coords(-step)._polarization_integrals_I()
IY_minus = np.einsum('kabmn,kabmn', I_minus, Y)
# df/dx = (f(x+dx) - f(x-dx))/(2 dx)
grad_QM_NUM[3*i+xyz] = (IY_plus - IY_minus)/(2*step)
grad_QM = np.array(grad_QM)
grad_QM_NUM = np.array(grad_QM_NUM)
err_QM = la.norm(grad_QM - grad_QM_NUM)
print("+++ Gradient of contraction sum_{k,a,b,m,n} I^(elec)_{k,a,b,m,n} Y_{k,a,b,m,n} on QM atoms +++")
print(" Analytical:")
print(grad_QM)
print(" Numerical:")
print(grad_QM_NUM)
print(f" Error: {err_QM}")
# numerical gradient on polarizable sites
npol = polarizable_atoms.natom()
grad_POL_NUM = np.zeros(3*npol)
for i in range(0, npol):
for xyz in [0,1,2]:
def shift_coords(step):
polarizable_atoms_ = polarizable_atoms.clone()
coords = polarizable_atoms_.geometry().np
coords[i,xyz] += step
polarizable_atoms_.set_geometry(psi4.core.Matrix.from_array(coords))
args_ = list(self.args[:])
args_[3] = polarizable_atoms_
polham = PolarizationHamiltonian(*args_, **self.kwds)
return polham
# f(x+dx)
I_plus = shift_coords(step)._polarization_integrals_I()
IY_plus = np.einsum('kabmn,kabmn', I_plus, Y)
# f(x-dx)
I_minus = shift_coords(-step)._polarization_integrals_I()
IY_minus = np.einsum('kabmn,kabmn', I_minus, Y)
# df/dx = (f(x+dx) - f(x-dx))/(2 dx)
grad_POL_NUM[3*i+xyz] = (IY_plus - IY_minus)/(2*step)
grad_POL = np.array(grad_POL)
err_POL = la.norm(grad_POL - grad_POL_NUM)
print("+++ Gradient of contraction sum_{k,a,b,m,n} I^(elec)_{k,a,b,m,n} Y_{k,a,b,m,n} on polarizable sites +++")
print(" Analytical:")
print(grad_POL)
print(" Numerical:")
print(grad_POL_NUM)
print(f" Error: {err_POL}")
assert err_QM < 1.0e-5
assert err_POL < 1.0e-5
# all tests passed
return True