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
elementList = Utility.molToelemList(variables.molecule) elementParameters = Utility.read_parameters(elementList, variables.element_params_path) 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(