def calc_aff_mean_squared(numAtoms, elementList, Q, elementParameters):
"""Function to calculate the mean squared effective electron Form Factor, <f>^2 (eq. FZ-5).
Parameters
----------
numAtoms : int
number of atoms in the molecule
elementList : dictionary("element": multiplicity)
chemical elements of the sample with their multiplicity
element : string
chemical element
multiplicity : int
chemical element multiplicity
Q : numpy array
momentum transfer (nm^-1)
elementParameters : dictionary("element": parameters)
chemical elements of the sample with their parameters
element : string
chemical element
parameters : list
list of the parameters
(Z, a1, b1, a2, b2, a3, b3, a4, b4, c, M, K, L)
Returns
-------
aff_mean_squared : numpy array
squared of the mean form factor: <f>^2
"""
aff_mean_squared = np.zeros(Q.size)
for element, multiplicity in elementList.items():
aff_mean_squared += multiplicity * MainFunctions.calc_aff(
element, Q, elementParameters)
aff_mean_squared /= numAtoms
aff_mean_squared = aff_mean_squared**2
return aff_mean_squared
def calc_iintraFZ(Q, QmaxIntegrate, maxQ, elementList, element, x, y, z,
elementParameters, aff_mean_squared):
"""Function to calculate the intramolecular contribution of i(Q) (eq. 41).
Parameters
----------
Q : numpy array
momentum transfer (nm^-1)
fe_Q : numpy array
effective electric form factor
Ztot : int
total Z number
QmaxIntegrate : float
maximum Q value for the intagrations
maxQ : float
maximum Q value
elementList : dictionary("element": multiplicity)
chemical elements of the sample with their multiplicity
element : string
chemical element
multiplicity : int
chemical element multiplicity
element : string array
array with the elements in the xyz_file
x, y, z : float array
atomic coordinate in the xyz_file (nm)
elementParameters : dictionary("element": parameters)
chemical elements of the sample with their parameters
element : string
chemical element
parameters : list
list of the parameters
(Z, a1, b1, a2, b2, a3, b3, a4, b4, c, M, K, L)
Returns
-------
iintra_Q : numpy array
intramolecular contribution of i(Q)
"""
iintra_Q = np.zeros(Q.size)
sinpq = np.zeros(Q.size)
for ielem in range(len(element)):
for jelem in range(len(element)):
if ielem != jelem:
# print(ielem, jelem)
# print(type(element[ielem]))
# print(element[ielem], elementList[element[ielem]], element[jelem], elementList[element[jelem]])
f_Qi = MainFunctions.calc_aff(element[ielem], Q,
elementParameters)
f_Qj = MainFunctions.calc_aff(element[jelem], Q,
elementParameters)
f_i = np.mean(elementList[element[ielem]] * f_Qi / 3)
f_j = np.mean(elementList[element[jelem]] * f_Qj / 3)
# f_i = np.mean(f_Qi)
# f_j = np.mean(f_Qj)
ff = f_i * f_j
d = Utility.calc_distMol(x[ielem], y[ielem], z[ielem],
x[jelem], y[jelem], z[jelem])
if d != 0.0:
iintra_Q += ff * np.sin(d * Q) / (d * Q)
iintra_Q[Q == 0.0] = ff
iintra_Q[(Q > QmaxIntegrate) & (Q <= maxQ)] = 0.0
iintra_Q /= np.mean(aff_mean_squared)
# iintra_Q /= 3
return iintra_Q