from sans.models.BaseComponent import BaseComponent from sans.models.CoreShellModel import CoreShellModel from scipy.special import gammaln from math import exp, sin, atan from numpy import power from copy import deepcopy class FractalCoreShellModel(BaseComponent): """ Class that evaluates a FractalCoreShellModel List of default parameters: volfraction = 0.05 radius = 20.0 [A] thickness = 5.0 [A] frac_dim = 2.0 cor_length = 100 [A] core_sld = 3.5e-006 [1/A^(2)] shell_sld = 1.0e-006 [1/A^(2)] solvent_sld = 6.35e-006 [1/A^(2)] background = 0.0 [1/cm] """ def __init__(self): BaseComponent.__init__(self) ## Setting model name model description model = CoreShellModel() self.description=model self.model = model self.name = "FractalCoreShell" self.description="""Scattering from a fractal structure with a primary building block of a spherical particle with particle with a core-shell structure. Note: Setting the (core) radius polydispersion with a Schulz distribution is equivalent to the FractalPolyCore function in NIST/Igor Package. List of parameters: volfraction: volume fraction of building block spheres radius: radius of building block thickness: shell thickness frac_dim: fractal dimension cor_length: correlation length of fractal-like aggregates core_sld: SLD of building block shell_sld: SLD of shell solvent_sld: SLD of matrix or solution background: flat background""" ## Define parameters self.params = {} ## Parameter details [units, min, max] self.details = {} # non-fittable parameters self.non_fittable = model.non_fittable ## dispersion self._set_dispersion() ## Define parameters self._set_params() ## Parameter details [units, min, max] self._set_details() ## parameters with orientation: can be removed since there is no orientational params for item in self.model.orientation_params: self.orientation_params.append(item) def _fractalcore(self,x): """ Define model function return S(q): Fractal Structure """ # set local variables Df = self.params['frac_dim'] corr = self.params['cor_length'] r0 = self.params['radius'] #calculate S(q) sq = Df*exp(gammaln(Df-1.0))*sin((Df-1.0)*atan(x*corr)) sq /= power((x*r0),Df) * power((1.0 + 1.0/(x*corr*x*corr)),((Df-1)/2)) sq += 1.0 return sq def _clone(self, obj): """ Internal utility function to copy the internal data members to a fresh copy. """ obj.params = deepcopy(self.params) obj.description = deepcopy(self.description) obj.details = deepcopy(self.details) obj.dispersion = deepcopy(self.dispersion) obj.model = self.model.clone() return obj def _set_dispersion(self): """ model dispersions """ ##set dispersion from model for name , value in self.model.dispersion.iteritems(): self.dispersion[name]= value def _set_params(self): """ Concatenate the parameters of the model to create this model parameters """ # rearrange the parameters for the given # of shells for name , value in self.model.params.iteritems(): if name == 'scale': value = 0.05 elif name == 'radius': value = 20.0 elif name == 'thickness': value = 5.0 elif name == 'core_sld': value = 3.5e-06 elif name == 'shell_sld': value = 1.0e-06 elif name == 'solvent_sld': value = 6.35e-06 elif name == 'background': value = 0.0 self.model.params[name]= value if name == 'scale': name = 'volfraction' self.params[name]= value self.params['frac_dim'] = 2.0 self.params['cor_length'] = 100.0 def _set_details(self): """ Concatenate details of the original model to create this model details """ for name ,detail in self.model.details.iteritems(): if name in self.params.iterkeys(): if name == 'scale': name = 'volfraction' self.details[name]= detail self.details['frac_dim'] = ['', None, None] self.details['cor_length'] = ['[A]', None, None] def setParam(self, name, value): """ Set the value of a model parameter : param name: name of the parameter : param value: value of the parameter """ # set param to new model self._setParamHelper(name, value) if name == 'volfraction': name = 'scale' # model.setParam except the two names below if name != 'frac_dim' and name != 'cor_length': # background is always 0.0 in the coreshellmodel if name == 'background': value = 0.0 self.model.setParam(name, value) def _setParamHelper(self, name, value): """ Helper function to setParam """ #look for dispersion parameters toks = name.split('.') if len(toks)==2: for item in self.dispersion.keys(): if item.lower()==toks[0].lower(): for par in self.dispersion[item]: if par.lower() == toks[1].lower(): self.dispersion[item][par] = value return # Look for standard parameter for item in self.params.keys(): if item.lower()==name.lower(): self.params[item] = value return raise ValueError, "Model does not contain parameter %s" % name def run(self, x = 0.0): """ Evaluate the model : param x: input q-value (float or [float, float] as [r, theta]) : return: (DAB value) """ if x.__class__.__name__ == 'list': # Take absolute value of Q, since this model is really meant to # be defined in 1D for a given length of Q #qx = math.fabs(x[0]*math.cos(x[1])) #qy = math.fabs(x[0]*math.sin(x[1])) return self.params['background']+self._fractalcore(x[0])*self.model.run(x) elif x.__class__.__name__ == 'tuple': raise ValueError, "Tuples are not allowed as input to BaseComponent models" else: return self.params['background']+self._fractalcore(x)*self.model.run(x) return self.params['background']+self._fractalcore(x)*self.model.run(x) def runXY(self, x = 0.0): """ Evaluate the model : param x: input q-value (float or [float, float] as [qx, qy]) : return: DAB value """ if x.__class__.__name__ == 'list': q = math.sqrt(x[0]**2 + x[1]**2) return self.params['background']+self._fractalcore(q)*self.model.runXY(x) elif x.__class__.__name__ == 'tuple': raise ValueError, "Tuples are not allowed as input to BaseComponent models" else: return self.params['background']+self._fractalcore(x)*self.model.runXY(x) def set_dispersion(self, parameter, dispersion): """ Set the dispersion object for a model parameter : param parameter: name of the parameter [string] :dispersion: dispersion object of type DispersionModel """ value= None try: if parameter in self.model.dispersion.keys(): value= self.model.set_dispersion(parameter, dispersion) self._set_dispersion() return value except: raise