path = Utility.path_xyz_file(variables.molecule)
numAtoms, element, x, y, z = Utility.read_xyz_file(path)
Q, I_Q = Utility.read_file(variables.data_file)
Qbkg, Ibkg_Q = Utility.read_file(variables.bkg_file)
# -------------------Preliminary calculation-------------------------------
fe_Q, Ztot = MainFunctions.calc_eeff(elementList, Q, elementParameters)
Iincoh_Q = MainFunctions.calc_Iincoh(elementList, Q, elementParameters)
J_Q = MainFunctions.calc_JQ(Iincoh_Q, Ztot, fe_Q)
Sinf = MainFunctions.calc_Sinf(elementList, fe_Q, Q, Ztot,
elementParameters)
dampingFunction = UtilityAnalysis.calc_dampingFunction(
Q, variables.dampingFactor, variables.QmaxIntegrate,
variables.typeFunction)
# ------------------Intra-molecular components-----------------------------
iintra_Q = Optimization.calc_iintra(Q, fe_Q, Ztot, variables.QmaxIntegrate,
variables.maxQ, elementList, element,
x, y, z, elementParameters)
iintradamp_Q = UtilityAnalysis.calc_iintradamp(iintra_Q, dampingFunction)
Qiintradamp_Q = Q * iintradamp_Q
rintra, Fintra_r = MainFunctions.calc_Fr(
Q[Q <= variables.QmaxIntegrate],
Qiintradamp_Q[Q <= variables.QmaxIntegrate])
# _, Fintra_r = UtilityAnalysis.rebinning(rintra, Fintra_r, np.amin(Fintra_r),
# np.amax(Fintra_r), 8192)
def SQ(self):
"""Function to calculate and plot the structure factor S(Q)"""
self.elementList = Utility.molToElemList(self.molecule)
# self.elementList = Utility.molToElemList("Ar")
self.elementParameters = Utility.read_parameters(
self.elementList, "./elementParameters.txt")
# print(elementList)
# print(elementParameters)
self.Q, self.I_Q, self.Qbkg, self.Ibkg_Q = UtilityAnalysis.check_data_length(
self.Q, self.I_Q, self.Qbkg, self.Ibkg_Q, self.ui.minQ.value(),
self.ui.maxQ.value())
two_theta = UtilityAnalysis.Qto2theta(self.Q)
absCorrFactor = Geometry.calcAbsCorrection(
self.ui.absLength.value(), two_theta, self.ui.dacThickness.value(),
self.ui.dacAngle.value())
self.I_Q = self.I_Q / absCorrFactor
self.Ibkg_Q = self.Ibkg_Q / absCorrFactor
self.fe_Q, self.Ztot = MainFunctions.calc_eeff(self.elementList,
self.Q,
self.elementParameters)
self.Iincoh_Q = MainFunctions.calc_Iincoh(self.elementList, self.Q,
self.elementParameters)
self.J_Q = MainFunctions.calc_JQ(self.Iincoh_Q, self.Ztot, self.fe_Q)
self.Sinf = MainFunctions.calc_Sinf(self.elementList, self.fe_Q,
self.Q, self.Ztot,
self.elementParameters)
self.dampingFunct = UtilityAnalysis.calc_dampingFunction(
self.Q,
self.ui.dampingFactor.value(), self.ui.QmaxIntegrate.value(),
self.ui.dampingFunction.currentText())
Isample_Q = MainFunctions.calc_IsampleQ(
self.I_Q, self.ui.scaleFactorValue.value(), self.Ibkg_Q)
alpha = MainFunctions.calc_alpha(
self.J_Q[self.Q <= self.ui.QmaxIntegrate.value()], self.Sinf,
self.Q[self.Q <= self.ui.QmaxIntegrate.value()],
Isample_Q[self.Q <= self.ui.QmaxIntegrate.value()],
self.fe_Q[self.Q <= self.ui.QmaxIntegrate.value()], self.Ztot,
self.ui.densityValue.value())
Icoh_Q = MainFunctions.calc_Icoh(alpha, Isample_Q, self.Iincoh_Q)
S_Q = MainFunctions.calc_SQ(Icoh_Q, self.Ztot, self.fe_Q, self.Sinf,
self.Q, self.ui.minQ.value(),
self.ui.QmaxIntegrate.value(),
self.ui.maxQ.value())
Ssmooth_Q = UtilityAnalysis.calc_SQsmoothing(
self.Q, S_Q, self.Sinf, self.ui.smoothingFactor.value(),
self.ui.minQ.value(), self.ui.QmaxIntegrate.value(),
self.ui.maxQ.value())
self.SsmoothDamp_Q = UtilityAnalysis.calc_SQdamp(
Ssmooth_Q, self.Sinf, self.dampingFunct)
# self.ui.factorPlot.canvas.ax.plot(self.Q, self.SsmoothDamp_Q, "b", label=r"$S(Q)$")
# self.ui.factorPlot.canvas.ax.legend()
# self.ui.factorPlot.canvas.draw()
return self.SsmoothDamp_Q
inputVariables["numPoints"])
Qbkg, Ibkg_Q = UtilityAnalysis.data_interpolation(
Qbkg, Ibkg_Q, inputVariables["minQ"], inputVariables["maxQ"],
inputVariables["numPoints"])
# plt.plot(Q, I_Q)
# plt.plot(Qbkg, Ibkg_Q)
# plt.show
fe_Q, Ztot = MainFunctions.calc_eeff(elementList, Q, elementParameters)
Iincoh_Q = MainFunctions.calc_Iincoh(elementList, Q, elementParameters)
J_Q = MainFunctions.calc_JQ(Iincoh_Q, Ztot, fe_Q)
Sinf = MainFunctions.calc_Sinf(elementList, fe_Q, Q, Ztot,
elementParameters)
dampingFunction = UtilityAnalysis.calc_dampingFunction(
Q, inputVariables["dampingFactor"], inputVariables["QmaxIntegrate"],
inputVariables["typeFunction"])
#-------------------Intra-molecular components-----------------------------
iintra_Q = Optimization.calc_iintra(
Q, fe_Q, Ztot, inputVariables["QmaxIntegrate"], inputVariables["maxQ"],
elementList, elementPosition["element"], elementPosition["x"],
elementPosition["y"], elementPosition["z"], elementParameters)
iintradamp_Q = UtilityAnalysis.calc_iintradamp(iintra_Q, dampingFunction)
Qiintradamp_Q = Q * iintradamp_Q
rintra, Fintra_r = MainFunctions.calc_Fr(
Q[Q <= inputVariables["QmaxIntegrate"]],
Qiintradamp_Q[Q <= inputVariables["QmaxIntegrate"]])
# ---------------------Geometrical correction------------------------------