def my_special_gamma(n):
# return gamma(n/2)
if n % 2 == 0: # n/2 is an integer
return math.factorial(n / 2 - 1)
else:
root_pi = math.sqrt(math.pi)
return root_pi * ss.factorial2(n-2) / math.pow(2.0, (n-1) / 2.0)
def norm_prim_cart(self):
r"""Return the normalization constants of the Cartesian Gaussian primitives.
For a Cartesian primitive with exponent :math:`\alpha_i`, the normalization constant is:
.. math::
N(\alpha_i, \vec{a}) = \sqrt {
\left(\frac{2\alpha_i}{\pi}\right)^\frac{3}{2}
\frac{(4\alpha_i)^{a_x + a_y + a_z}}{(2a_x - 1)!! (2a_y - 1)!! (2a_z - 1)!!}}
Returns
-------
norm_prim_cart : np.ndarray(L, K)
The normalization constants of the Cartesian Gaussian primitives.
`L` is the number of contracted Cartesian Gaussian functions for the given angular
momentum, i.e. :math:`(\ell + 1) * (\ell + 2) / 2`
`K` is the number of exponents (i.e. primitives).
"""
exponents = self.exps[np.newaxis, :]
angmom_components_cart = self.angmom_components_cart[:, :, np.newaxis]
return ((2 * exponents / np.pi)**(3 / 4) * (
(4 * exponents)**(self.angmom / 2)) / np.sqrt(
np.prod(factorial2(2 * angmom_components_cart - 1), axis=1)))
def test_rank_one(n):
"""Test the hafnian of rank one matrices so that it is within
10% of the exact value"""
x = np.random.rand(n)
A = np.outer(x, x)
exact = factorial2(n - 1) * np.prod(x)
approx = hafnian(A, approx=True, num_samples=10000)
assert np.allclose(approx, exact, rtol=2e-1, atol=0)
def ME_to_inverse_half_life(ME, Jinit, lam, Ediff, EM):
"""
inputs:
ME = (Jfinal || O^lam || Jinit)
EM: "E" or "M"
output:
inverse life time (additive quantity)
ln2 / T_1/2
"""
if (abs(ME) < 1.e-10): return 0
hc = physical_constants["Planck constant over 2 pi times c in MeV fm"][0]
if (EM == "E"):
return 5.498e22 * (ediff / hc)**(2 * rank + 1) * (rank + 1) / (
rank * factorial2(2 * lam + 1)**2) * BEM(ME, Jinit)
if (EM == "M"):
return 6.080e20 * (ediff / hc)**(2 * rank + 1) * (rank + 1) / (
rank * factorial2(2 * lam + 1)**2) * BEM(ME, Jinit)
def normalisation(self):
"""Calculates normalisation constant for the primitive gaussian and stores in self.normalisation once called.
Returns
-------
self.normalisation_memo : float
"""
if self.normalisation_memo is None:
l, m, n = self.integral_exponents
out1 = factorial2(2 * l - 1) * factorial2(2 * m -
1) * factorial2(2 * n -
1)
out2 = (pi / (2 * self.exponent))**(3 / 2)
out3 = (4 * self.exponent)**(l + m + n)
self.normalisation_memo = 1 / sqrt((out1 * out2) / out3)
return self.normalisation_memo
def __init__(self, l, coeffs, zetas):
super().__init__()
self.ls = torch.tensor(get_cartesian_angulars(l))
anorms = 1.0 / np.sqrt(factorial2(2 * self.ls - 1).prod(-1))
self.register_buffer('anorms', fp_tensor(anorms))
rnorms = (2 * zetas / np.pi)**(3 / 4) * (4 * zetas)**(l / 2)
self.register_buffer('coeffs', rnorms * coeffs)
self.register_buffer('zetas', zetas)
def __init__(self, epsilon, cutoff, na, q, minSize, maxSize):
self.epsilon = epsilon
self.cutoff = cutoff
self.minSize = minSize
self.maxSize = maxSize
self.na = na
self.q = q
self.coeffs = []
for index in range(0, q + 1):
first_expr = np.power(
-1, index + 1) / (factorial2(2 * q - 2 * index, exact=True) *
factorial2(2 * index, exact=True))
second_expr = factorial2(10 + 2 * q,
exact=True) / (factorial2(8, exact=True) *
(10 + 2 * index))
third_expr = np.power(cutoff, -(10 + 2 * index))
self.coeffs.append(first_expr * second_expr * third_expr)
def normalize(self):
a = np.array(self.a)
N = (2 / np.pi) ** (3 / 4) * 2 ** np.sum(a) * \
self.alpha ** ((2 * np.sum(a) + 3) / 4) / \
np.sqrt(np.prod(factorial2(2 * a - 1)))
self.N = N
self.n_primitives = len(self.alpha)
return
def FACTDOUBLE(number: func_xltypes.XlNumber) -> func_xltypes.XlNumber:
"""Returns the double factorial of a number.
https://support.office.com/en-us/article/
factdouble-function-e67697ac-d214-48eb-b7b7-cce2589ecac8
"""
if number < 0:
raise xlerrors.NumExcelError('Negative values are not allowed')
return factorial2(int(number), exact=True)
def func_temp(ws):
k, kp = ws[0], ws[1]
O1 = binom(n_p, kp) * binom(n, k)
O2 = H(n_p - kp, 0) * H(n - k, 0)
O3 = ((2 * np.sqrt(alphap))**kp) * ((2 * np.sqrt(alpha))**k)
if (k + kp) % 2 != 0:
return 0.
else:
return O1*O2*O3*factorial2(int(k+kp-1))\
/np.sqrt((alpha+alphap)**(k+kp))
def __S(e1, e2, R1, R2, ang1, ang2):
S = (np.pi/(e1+e2))**(3/2)
P = (e1*R1+e2*R2)/(e1+e2)
for i in range(3):
s = 0
for k in range(0, int((ang1[i]+ang2[i])/2)+1):
s += __ck(2*k, ang1[i], ang2[i], P[i]-R1[i], P[i]-R2[i]) * \
special.factorial2(2*k-1, exact=True) / (2*(e1+e2))**k
S *= s
return S
def KaulaF(n, q, p, j):
"""
Series coefficient in the Taylor expansion of the
Kaula inclination function F_{nqp}(I).
See, e.g., Kaula (1962,1966) or Ellis & Murray (2000).
The function returns the jth term of the Taylor
expansion in the variable s = sin(I/2). I.e.
KaulaF(n,q,p,j) = (1/j!) d^j F{nqp}/ ds^j
This implementation is based on the Mathematica
package by Fabio Zugno available at:
https://library.wolfram.com/infocenter/MathSource/4256/
Arguments
---------
n : int
q : int
p : int
j : int
Returns
-------
float
"""
if q == 0 and 2 * p == n:
return (-1)**(j + n) * binom(n, j) * binom(
n + j, j) * factorial2(n - 1) / factorial2(n)
if n - 2 * p - q < 0:
if n - q < 0: return 0
return (-1)**(n - q) * factorial(n + q) * KaulaF(n, -q, n - p,
j) / factorial(n - q)
numerator = (-1)**j * factorial2(2 * n - 2 * p - 1)
numerator *= binom(n / 2 + p + q / 2, j)
numerator *= threeFtwo([-j, -2 * p, -n - q],
[1 + n - 2 * p - q, -(n / 2) - p - q / 2])
if p < 0: return 0.
denom = factorial(n - 2 * p - q) * factorial2(2 * p)
return numerator / denom
def compute_Si(lA, lB, PA, PB, gamma):
"""
Calculate the i-th coordinate contribution to the matrix element S[A,B].
"""
Si = 0.0
for k in range(
int((lA + lB) / 2) + 1
): # note range is up to add INCLUDING floor of (lA+lB)/2, hence +1
Si += compute_ck(2*k, lA, lB, PA, PB) * np.sqrt(np.pi / gamma) * \
(special.factorial2(2*k-1,exact=True) / (2*gamma)**k)
return Si
def pn_leading_order_amplitude(ell, m, x, mass_ratio=1.0):
"""Return the leading-order amplitude of r*h/M in PN theory
These expressions are from Eqs. (330) of Blanchet's Living Review (2014).
Note that `x` is just the orbital angular velocity to the (2/3) power.
"""
from scipy.special import factorial, factorial2
if m < 0:
return (-1)**ell * np.conjugate(
pn_leading_order_amplitude(ell, -m, x, mass_ratio=mass_ratio))
if mass_ratio < 1.0:
mass_ratio = 1.0 / mass_ratio
nu = mass_ratio / (1 + mass_ratio)**2
X1 = mass_ratio / (mass_ratio + 1)
X2 = 1 / (mass_ratio + 1)
def sigma(ell):
return X2**(ell - 1) + (-1)**ell * X1**(ell - 1)
if (ell + m) % 2 == 0:
amplitude = (((-1)**((ell - m + 2) / 2) / (2**(ell + 1) * factorial(
(ell + m) // 2) * factorial(
(ell - m) // 2) * factorial2(2 * ell - 1))) * np.sqrt(
(5 * (ell + 1) *
(ell + 2) * factorial(ell + m) * factorial(ell - m)) /
(ell * (ell - 1) * (2 * ell + 1))) * sigma(ell) *
(1j * m)**ell * x**(ell / 2 - 1))
else:
amplitude = (((-1)**((ell - m - 1) / 2) / (2**(ell - 1) * factorial(
(ell + m - 1) // 2) * factorial(
(ell - m - 1) // 2) * factorial2(2 * ell + 1))) * np.sqrt(
(5 * (ell + 2) *
(2 * ell + 1) * factorial(ell + m) * factorial(ell - m)) /
(ell * (ell - 1) * (ell + 1))) * sigma(ell + 1) * 1j *
(1j * m)**ell * x**((ell - 1) / 2))
return 8 * np.sqrt(np.pi / 5) * nu * x * amplitude
def Nrun(basisset):
# Normalize primitive functions
for i in range(len(basisset)):
for j in range(len(basisset[i][5])):
a = basisset[i][5][j][1]
l = basisset[i][5][j][3]
m = basisset[i][5][j][4]
n = basisset[i][5][j][5]
part1 = (2.0 / math.pi)**(3.0 / 4.0)
part2 = 2.0**(l + m + n) * a**(
(2.0 * l + 2.0 * m + 2.0 * n + 3.0) / (4.0))
part3 = math.sqrt(
scm.factorial2(int(2 * l - 1)) *
scm.factorial2(int(2 * m - 1)) *
scm.factorial2(int(2 * n - 1)))
basisset[i][5][j][0] = part1 * ((part2) / (part3))
"""
# Normalize contractions
for k in range(len(basisset)):
if len(basisset[k][5]) != 1:
l = basisset[k][5][0][3]
m = basisset[k][5][0][4]
n = basisset[k][5][0][5]
L = l+m+n
factor = (np.pi**(3.0/2.0)*scm.factorial2(int(2*l-1))*scm.factorial2(int(2*m-1))*scm.factorial2(int(2*n-1)))/(2.0**L)
sum = 0
for i in range(len(basisset[k][5])):
for j in range(len(basisset[k][5])):
alphai = basisset[k][5][i][1]
alphaj = basisset[k][5][j][1]
ai = basisset[k][5][i][2]*basisset[k][5][i][0]
aj = basisset[k][5][j][2]*basisset[k][5][j][0]
sum += ai*aj/((alphai+alphaj)**(L+3.0/2.0))
Nc = (factor*sum)**(-1.0/2.0)
for i in range(len(basisset[k][5])):
basisset[k][5][i][0] *= Nc
"""
return basisset
def S(self, orb):
'''
Overlap integral
Page 2315
https://journals.jps.jp/doi/pdf/10.1143/JPSJ.21.2313
'''
assert isinstance(orb, pgto)
l1, m1, n1 = self.pow
l2, m2, n2 = orb.pow
a1 = self.exp
a2 = orb.exp
A = self.origin
B = orb.origin
gamma = a1+a2
P = (a1*A+a2*B)/(a1+a2)
AB_sq = dot(A-B, A-B)
PA = sqrt(dot(P-A, P-A))
PB = sqrt(dot(P-B, P-B))
## fj(l,m,a,b)
f = lambda l,m,a,b,j,i : comb(l,i)*comb(m,j-i)*a**i*b**(j-i)
# Sum over 0 <= i <= j for all possible j <=l1+l2
fj = []
for j in range(l1+l2+1):
fj_temp = []
for i in range(j+1):
fj_temp.append(f(l1, l2, PA, PB))
#end for
fj.append(sum(fj_temp))
#end for
## fj complete
# start integral
pre = (pi/gamma)**3./2*exp(-a1*a2*AB_sq/gamma)
int_out = 0
for q in [l1+l2, m1+m2, n1+n2]:
int_in = 1
for i in range(int(ceil(0.5*(q)))):
int_in *= f[2*i]*factorial2(2*i-1)/(2*gamma)**i
#end for
int_out += int_in
#end for
result = pre*int_out
return result
def __init__(self, n_max):
"""Initialize class.
Parameters
----------
n_max : int
Maximum angular momentum.
"""
self.binomials = [[binom(n, i) for i in range(n + 1)] for n in range(n_max + 1)]
facts = [factorial2(m, 2) for m in range(2 * n_max)]
facts.insert(0, 1)
self.facts = np.array(facts)
def low_rank_hafnian(G):
r"""Returns the hafnian of the low rank matrix :math:`\bm{A} = \bm{G} \bm{G}^T` where :math:`\bm{G}` is rectangular of size
:math:`n \times r` with :math:`r \leq n`.
Note that the rank of :math:`\bm{A}` is precisely :math:`r`.
The hafnian is calculated using the algorithm described in Appendix C of
*A faster hafnian formula for complex matrices and its benchmarking on a supercomputer*,
:cite:`bjorklund2018faster`.
Args:
G (array): factorization of the low rank matrix A = G @ G.T.
Returns:
(complex): hafnian of A.
"""
n, r = G.shape
if n % 2 != 0:
return 0
if r == 1:
return factorial2(n - 1) * np.prod(G)
poly = 1
x = symbols("x0:" + str(r))
for k in range(n):
term = 0
for j in range(r):
term += G[k, j] * x[j]
poly = expand(poly * term)
comb = partitions(r, n // 2)
haf_val = 0.0
for c in comb:
monomial = 1
facts = 1
for i, pi in enumerate(c):
monomial *= x[i]**(2 * pi)
facts = facts * factorial2(2 * pi - 1)
haf_val += complex(poly.coeff(monomial) * facts)
return haf_val
def fcint(v1, v2):
aa = 0.0
for k1 in range(v1 + 1):
for k2 in range(v2 + 1):
if (k1 + k2) % 2 == 0:
ik = factorial2(k1 + k2 - 1) / (a1 + a2)**((k1 + k2) / 2)
else:
ik = 0
aa += comb(v1,k1)*comb(v2,k2)*eval_hermite(v1-k1,b1)\
*eval_hermite(v2-k2,b2)*(2*sqrt(a1))**k1*(2*sqrt(a2))**k2*ik
bb = aa * A * exp(-S) / 2**(v1 + v2) / factorial(v1) / factorial(v2) * aa
#bb = A*exp(-S)/2**(v1+v2)
return bb
def F(n, x): #calculate Boys function value by numerical integration
if x < 1e-7:
return 1 / (2 * n + 1)
if n == 20:
res1 = 1 / (2 * n + 1)
#if x < 1e-7:
# return res1
for k in range(1, 11):
res1 += (-x)**k / factorial(k) / (2 * n + 2 * k + 1)
res2 = factorial2(2 * n - 1) / 2**(n + 1) * np.sqrt(
np.pi / x**(2 * n + 1))
res = min(res1, res2)
return res
return (2 * x * F(n + 1, x) + np.exp(-x)) / (2 * n + 1)
def test_evaluate_construct_array_contraction():
"""Test gbasis.evals.eval.Eval.construct_array_contraction."""
test = GeneralizedContractionShell(1, np.array([0.5, 1, 1.5]),
np.array([1.0, 2.0]),
np.array([0.1, 0.01]))
answer = np.array([
_eval_deriv_contractions(
np.array([[2, 3, 4]]),
np.array([0, 0, 0]),
np.array([0.5, 1, 1.5]),
np.array([angmom_comp]),
np.array([0.1, 0.01]),
np.array([1, 2]),
np.array([[
(2 * 0.1 / np.pi)**(3 / 4) * (4 * 0.1)**(1 / 2) /
np.sqrt(np.prod(factorial2(2 * angmom_comp - 1))),
(2 * 0.01 / np.pi)**(3 / 4) * (4 * 0.01)**(1 / 2) /
np.sqrt(np.prod(factorial2(2 * angmom_comp - 1))),
]]),
) for angmom_comp in test.angmom_components_cart
]).reshape(3, 1)
assert np.allclose(
Eval.construct_array_contraction(points=np.array([[2, 3, 4]]),
contractions=test), answer)
with pytest.raises(TypeError):
Eval.construct_array_contraction(points=np.array([[2, 3, 4]]),
contractions=None)
with pytest.raises(TypeError):
Eval.construct_array_contraction(points=np.array([[2, 3, 4]]),
contractions={1: 2})
with pytest.raises(TypeError):
Eval.construct_array_contraction(points=np.array([2, 3, 4]),
contractions=test)
with pytest.raises(TypeError):
Eval.construct_array_contraction(points=np.array([[3, 4]]),
contractions=test)
def gauss_integral(n):
r"""
Solve the integral
\int_0^1 exp(-0.5 * x * x) x^n dx
See
https://en.wikipedia.org/wiki/List_of_integrals_of_Gaussian_functions
Examples
--------
>>> ans = gauss_integral(3)
>>> np.allclose(ans, 2)
True
>>> ans = gauss_integral(4)
>>> np.allclose(ans, 3.75994)
True
"""
factor = np.sqrt(np.pi * 2)
if n % 2 == 0:
return factor * factorial2(n - 1) / 2
elif n % 2 == 1:
return factor * norm.pdf(0) * factorial2(n - 1)
else:
raise ValueError("n must be odd or even.")
def lpKernel(N, freq):
#
# Lowpass filter 1D MAXFLAT kernel generator
#
# N is the filter half-size, must be odd
# freq is the normalised cutoff frequency
#
# Returns the filter kernel of size (2N+1)
#
num = 2 * N + 1
result = np.zeros((num, 1))
for n in range(N + 1):
i = n + N
im = N - n
if (n == 0):
result[i] = freq
else:
p = n % 2
val = (ss.factorial2(N)**2 * np.pi**(p - 1) *
np.sin(n * np.pi * freq)) / (2**p * n * ss.factorial2(i) *
ss.factorial2(im))
result[i] = val
result[im] = val
return result / np.sum(result)
def gaussian_moment(p):
"""
Computes the moments of the standard normal distribution. Used
when training via the method of moments.
Parameters:
-----------
p: int
Returns:
-----------
the pth moment of the standard Gaussian.
"""
if p % 2 == 0:
return factorial2(p - 1)
else:
return 0
def test_gauss_quadrature(self):
degree = 4
alpha = 0.
beta = 0.
ab = jacobi_recurrence(degree + 1,
alpha=alpha,
beta=beta,
probability=True)
x, w = gauss_quadrature(ab, degree + 1)
for ii in range(degree + 1):
if ii % 2 == 0:
assert np.allclose(np.dot(x**ii, w), 1. / (ii + 1.))
else:
assert np.allclose(np.dot(x**ii, w), 0.)
x_np, w_np = np.polynomial.legendre.leggauss(degree + 1)
assert np.allclose(x_np, x)
assert np.allclose(w_np / 2, w)
degree = 4
alpha = 4.
beta = 1.
ab = jacobi_recurrence(degree + 1,
alpha=alpha,
beta=beta,
probability=True)
x, w = gauss_quadrature(ab, degree + 1)
true_moments = [1., -3. / 7., 2. / 7., -4. / 21., 1. / 7.]
for ii in range(degree + 1):
assert np.allclose(np.dot(x**ii, w), true_moments[ii])
degree = 4
rho = 0.
ab = hermite_recurrence(degree + 1, rho, probability=True)
x, w = gauss_quadrature(ab, degree + 1)
from scipy.special import factorial2
assert np.allclose(np.dot(x**degree, w), factorial2(degree - 1))
x_sp, w_sp = sp.roots_hermitenorm(degree + 1)
w_sp /= np.sqrt(2 * np.pi)
assert np.allclose(x_sp, x)
assert np.allclose(w_sp, w)
def gint(m, center1, exponent1, n, center2, exponent2
): #calculate one electron integral of two gaussian primitives
newcenter = (exponent1 * center1 + exponent2 * center2) / (exponent1 +
exponent2)
newexponent = exponent1 + exponent2
tempexponent = exponent1 * exponent2 / (exponent1 + exponent2)
e12 = np.exp(-tempexponent * (center1 - center2)**2)
res = 0
for i in range(m + 1):
for j in range(n + 1):
if (i + j) % 2 == 0:
res += (np.sqrt(np.pi / newexponent) * comb(m, i) *
comb(n, j) * factorial2(i + j - 1) /
(2 * newexponent)**((i + j) / 2) *
(newcenter - center1)**(m - i) *
(newcenter - center2)**(n - j))
res = e12 * res
return res
def gob_cart_normalization(alpha: np.ndarray, n: np.ndarray) -> np.ndarray:
"""Compute normalization of exponent.
Parameters
----------
alpha
Gaussian basis exponents
n
Cartesian subshell angular momenta
Returns
-------
np.ndarray
The normalization constant for the gaussian cartesian basis.
"""
return np.sqrt((4 * alpha)**sum(n) * (2 * alpha / np.pi)**1.5 /
np.prod(factorial2(2 * n - 1)))
def correction_factor(snrval, Nch):
# Calculate the channel-dependent and SNR-dependent correction factor
CONSTFACTOR = math.sqrt(0.5 * math.pi) # Constant
snrval_squared = snrval * snrval
# SNR squared
confluent = hyp1f1(-0.5, float(Nch), -0.5 *
snrval_squared) # confluent hypergeometric function
confluent_squared = confluent * confluent # squared confluent hypergeometric function
Nch_minus_one = Nch - 1 # Number of channel reduced by one
betaval = float(factorial2(2 * Nch - 1)) / float(
(float(factorial(Nch - 1)) * float(2**Nch_minus_one))
) # Factor beta in equation 18, Koay and Basser, JMR (2006), 179, 317-322
factorval = CONSTFACTOR * float(betaval) # One more scaling required
factorval_squared = factorval * factorval # Square the factor
corrfact = 2 * float(
Nch
) + snrval_squared - factorval_squared * confluent_squared # Final correction factor
return corrfact
def muthat_expansion(mu,sig,order):
'''
Calculates the expansion for mu_{\hat{T}} based on mu_D and sigma_D.
The expansion calculates the average of 1/X where X ~ N(mu_D,sigma_D^2):
E[1/X] \approx 1/mu * sum_{k=0}^N (sigma/mu)**2k * (2k-1)!!
Because 1/mu is lumped into Teq after the call to this function, it is
not necessary to multiply the result of the for loop by 1//mu.
Inputs:
- mu, sig: expected value and standard deviation of X
- order: order of the expansion
'''
sigomu = sig/mu
sigomu2 = sigomu**2
approx = 0
for k in range(order):
approx += sigomu2**k * factorial2(2*k-1)
return approx
def G_q2d(n, m):
if n == 0:
num = factorial2(2 * m - 1)
den = 2**(m + 1) * factorial(m - 1)
return num / den
elif n > 0 and m == 1:
t1num = (2 * n**2 - 1) * (n**2 - 1)
t1den = 8 * (4 * n**2 - 1)
term1 = -t1num / t1den
term2 = 1 / 24 * kronecker(n, 1)
return term1 + term2 # this is minus in the paper
else:
# nt1 = numerator term 1, d = denominator...
nt1 = 2 * n * (m + n - 1) - m
nt2 = (n + 1) * (2 * m + 2 * n - 1)
num = nt1 * nt2
dt1 = (m + 2 * n - 2) * (m + 2 * n - 1)
dt2 = (m + 2 * n) * (2 * n + 1)
den = dt1 * dt2
term1 = num / den # there is a leading negative in the paper
return term1 * gamma(n, m)
def _mom(self, k):
return .5*special.factorial2(k-1)*(1+(-1)**k)
