| 1 | |
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| 2 | from sans.models.BaseComponent import BaseComponent |
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| 3 | from sans.models.OnionModel import OnionModel |
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| 4 | import copy |
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| 5 | max_nshells = 10 |
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| 6 | class OnionExpShellModel(BaseComponent): |
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| 7 | """ |
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| 8 | This multi-model is based on CoreMultiShellModel with exponential |
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| 9 | func shells and provides the capability |
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| 10 | of changing the number of shells between 1 and 10. |
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| 11 | """ |
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| 12 | def __init__(self, n_shells=1): |
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| 13 | BaseComponent.__init__(self) |
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| 14 | """ |
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| 15 | :param n_shells: number of shells in the model, |
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| 16 | assumes 1<= n_shells <=10. |
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| 17 | """ |
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| 18 | |
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| 19 | ## Setting model name model description |
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| 20 | self.description="" |
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| 21 | model = OnionModel() |
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| 22 | self.model = model |
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| 23 | self.name = "OnionExpShellModel" |
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| 24 | self.description=model.description |
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| 25 | self.n_shells = n_shells |
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| 26 | ## Define parameters |
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| 27 | self.params = {} |
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| 28 | |
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| 29 | ## Parameter details [units, min, max] |
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| 30 | self.details = {} |
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| 31 | |
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| 32 | ## dispersion |
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| 33 | self._set_dispersion() |
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| 34 | ## Define parameters |
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| 35 | self._set_params() |
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| 36 | |
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| 37 | ## Parameter details [units, min, max] |
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| 38 | self._set_details() |
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| 39 | |
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| 40 | #list of parameter that can be fitted |
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| 41 | self._set_fixed_params() |
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| 42 | self.model.params['n_shells'] = self.n_shells |
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| 43 | ## functional multiplicity info of the model |
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| 44 | # [int(maximum no. of functionality),"str(Titl), |
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| 45 | # [str(name of function0),...], [str(x-asix name of sld),...]] |
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| 46 | self.multiplicity_info = [max_nshells,"No. of Shells:",[],['Radius']] |
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| 47 | |
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| 48 | ## parameters with orientation: can be removed since there is |
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| 49 | # no orientational params |
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| 50 | for item in self.model.orientation_params: |
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| 51 | self.orientation_params.append(item) |
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| 52 | self.getProfile() |
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| 53 | def _clone(self, obj): |
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| 54 | """ |
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| 55 | Internal utility function to copy the internal |
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| 56 | data members to a fresh copy. |
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| 57 | """ |
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| 58 | obj.params = copy.deepcopy(self.params) |
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| 59 | obj.description = copy.deepcopy(self.description) |
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| 60 | obj.details = copy.deepcopy(self.details) |
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| 61 | obj.dispersion = copy.deepcopy(self.dispersion) |
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| 62 | obj.model = self.model.clone() |
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| 63 | |
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| 64 | return obj |
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| 65 | |
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| 66 | |
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| 67 | def _set_dispersion(self): |
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| 68 | """ |
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| 69 | model dispersions |
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| 70 | """ |
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| 71 | ##set dispersion from model |
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| 72 | for name , value in self.model.dispersion.iteritems(): |
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| 73 | |
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| 74 | nshell = 0 |
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| 75 | if name.split('_')[0] == 'thick': |
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| 76 | while nshell<self.n_shells: |
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| 77 | nshell += 1 |
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| 78 | if name.split('_')[1] == 'shell%s' % str(nshell): |
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| 79 | self.dispersion[name]= value |
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| 80 | else: |
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| 81 | continue |
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| 82 | else: |
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| 83 | self.dispersion[name]= value |
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| 84 | |
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| 85 | |
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| 86 | def _set_params(self): |
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| 87 | """ |
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| 88 | Concatenate the parameters of the model to create |
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| 89 | this model parameters |
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| 90 | """ |
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| 91 | # rearrange the parameters for the given # of shells |
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| 92 | for name , value in self.model.params.iteritems(): |
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| 93 | nshell = 0 |
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| 94 | pos = len(name.split('_'))-1 |
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| 95 | if name.split('_')[0] == 'func': |
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| 96 | continue |
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| 97 | elif name.split('_')[pos][0:5] == 'shell': |
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| 98 | while nshell<self.n_shells: |
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| 99 | nshell += 1 |
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| 100 | if name.split('_')[pos] == 'shell%s' % str(nshell): |
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| 101 | self.params[name]= value |
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| 102 | continue |
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| 103 | else: |
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| 104 | self.params[name]= value |
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| 105 | |
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| 106 | self.model.params['n_shells'] = self.n_shells |
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| 107 | |
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| 108 | # set constrained values for the original model params |
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| 109 | self._set_xtra_model_param() |
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| 110 | |
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| 111 | def _set_details(self): |
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| 112 | """ |
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| 113 | Concatenate details of the original model to create |
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| 114 | this model details |
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| 115 | """ |
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| 116 | for name ,detail in self.model.details.iteritems(): |
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| 117 | if name in self.params.iterkeys(): |
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| 118 | self.details[name]= detail |
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| 119 | |
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| 120 | |
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| 121 | def _set_xtra_model_param(self): |
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| 122 | """ |
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| 123 | Set params of original model that are hidden from this model |
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| 124 | """ |
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| 125 | # look for the model parameters that are not in param list |
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| 126 | for key in self.model.params.iterkeys(): |
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| 127 | if key not in self.params.keys(): |
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| 128 | if key.split('_')[0] == 'thick': |
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| 129 | self.model.setParam(key, 0) |
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| 130 | continue |
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| 131 | if key.split('_')[0] == 'A': |
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| 132 | self.model.setParam(key, 0) |
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| 133 | continue |
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| 134 | if key.split('_')[0] == 'func': |
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| 135 | self.model.setParam(key, 2) |
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| 136 | continue |
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| 137 | for nshell in range(self.n_shells,max_nshells): |
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| 138 | if key.split('_')[1] == 'sld_in_shell%s' % str(nshell+1): |
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| 139 | try: |
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| 140 | value = self.model.params['sld_solv'] |
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| 141 | self.model.setParam(key, value) |
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| 142 | except: pass |
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| 143 | def getProfile(self): |
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| 144 | """ |
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| 145 | Get SLD profile |
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| 146 | |
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| 147 | : return: (r, beta) where r is a list of radius of the transition |
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| 148 | points and beta is a list of the corresponding SLD values |
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| 149 | """ |
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| 150 | # max_pts for each shells |
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| 151 | max_pts = 10 |
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| 152 | r = [] |
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| 153 | beta = [] |
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| 154 | # for core at r=0 |
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| 155 | r.append(0) |
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| 156 | beta.append(self.params['sld_core0']) |
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| 157 | # for core at r=rad_core |
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| 158 | r.append(self.params['rad_core0']) |
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| 159 | beta.append(self.params['sld_core0']) |
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| 160 | |
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| 161 | # for shells |
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| 162 | for n in range(1,self.n_shells+1): |
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| 163 | # Left side of each shells |
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| 164 | r0 = r[len(r)-1] |
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| 165 | r.append(r0) |
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| 166 | beta.append(self.params['sld_in_shell%s'% str(n)]) |
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| 167 | |
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| 168 | A = self.params['A_shell%s'% str(n)] |
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| 169 | from math import fabs |
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| 170 | if fabs(A) <1.0e-16: |
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| 171 | # Right side of each shells |
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| 172 | r0 += self.params['thick_shell%s'% str(n)] |
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| 173 | r.append(r0) |
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| 174 | beta.append(self.params['sld_in_shell%s'% str(n)]) |
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| 175 | else: |
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| 176 | from math import exp |
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| 177 | rn = r0 |
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| 178 | for n_sub in range(0,max_pts): |
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| 179 | # Right side of each sub_shells |
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| 180 | rn += self.params['thick_shell%s'% str(n)]/10.0 |
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| 181 | r.append(rn) |
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| 182 | slope = (self.params['sld_out_shell%s'% str(n)] \ |
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| 183 | -self.params['sld_in_shell%s'% str(n)]) \ |
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| 184 | /(exp(self.params['A_shell%s'% str(n)])-1) |
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| 185 | const = (self.params['sld_in_shell%s'% str(n)]-slope) |
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| 186 | beta_n = slope*exp((self.params['A_shell%s'% str(n)]* \ |
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| 187 | (rn-r0)/self.params['thick_shell%s'% str(n)])) + const |
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| 188 | beta.append(beta_n) |
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| 189 | |
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| 190 | # for solvent |
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| 191 | r0 = r[len(r)-1] |
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| 192 | r.append(r0) |
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| 193 | beta.append(self.params['sld_solv']) |
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| 194 | r_solv = 5*r0/4 |
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| 195 | r.append(r_solv) |
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| 196 | beta.append(self.params['sld_solv']) |
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| 197 | |
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| 198 | return r, beta |
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| 199 | |
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| 200 | def setParam(self, name, value): |
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| 201 | """ |
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| 202 | Set the value of a model parameter |
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| 203 | |
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| 204 | : param name: name of the parameter |
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| 205 | : param value: value of the parameter |
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| 206 | """ |
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| 207 | # set param to new model |
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| 208 | self._setParamHelper( name, value) |
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| 209 | |
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| 210 | ## setParam to model |
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| 211 | if name=='sld_solv': |
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| 212 | # the sld_*** model.params not in params must set to value |
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| 213 | # of sld_solv |
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| 214 | for key in self.model.params.iterkeys(): |
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| 215 | if key not in self.params.keys()and key.split('_')[0] == 'sld': |
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| 216 | self.model.setParam(key, value) |
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| 217 | self.model.setParam( name, value) |
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| 218 | |
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| 219 | def _setParamHelper(self, name, value): |
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| 220 | """ |
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| 221 | Helper function to setParam |
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| 222 | """ |
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| 223 | #look for dispersion parameters |
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| 224 | toks = name.split('.') |
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| 225 | if len(toks)==2: |
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| 226 | for item in self.dispersion.keys(): |
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| 227 | if item.lower()==toks[0].lower(): |
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| 228 | for par in self.dispersion[item]: |
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| 229 | if par.lower() == toks[1].lower(): |
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| 230 | self.dispersion[item][par] = value |
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| 231 | return |
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| 232 | # Look for standard parameter |
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| 233 | for item in self.params.keys(): |
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| 234 | if item.lower()==name.lower(): |
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| 235 | self.params[item] = value |
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| 236 | return |
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| 237 | |
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| 238 | raise ValueError, "Model does not contain parameter %s" % name |
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| 239 | |
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| 240 | |
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| 241 | def _set_fixed_params(self): |
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| 242 | """ |
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| 243 | Fill the self.fixed list with the model fixed list |
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| 244 | """ |
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| 245 | for item in self.model.fixed: |
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| 246 | if item.split('.')[0] in self.params.keys(): |
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| 247 | self.fixed.append(item) |
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| 248 | |
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| 249 | self.fixed.sort() |
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| 250 | pass |
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| 251 | |
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| 252 | def run(self, x = 0.0): |
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| 253 | """ |
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| 254 | Evaluate the model |
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| 255 | |
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| 256 | : param x: input q-value (float or [float, float] as [r, theta]) |
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| 257 | : return: (I value) |
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| 258 | """ |
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| 259 | |
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| 260 | return self.model.run(x) |
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| 261 | |
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| 262 | def runXY(self, x = 0.0): |
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| 263 | """ |
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| 264 | Evaluate the model |
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| 265 | |
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| 266 | : param x: input q-value (float or [float, float] as [qx, qy]) |
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| 267 | : return: I value |
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| 268 | """ |
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| 269 | |
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| 270 | return self.model.runXY(x) |
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| 271 | |
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| 272 | ## Now (May27,10) directly uses the model eval function |
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| 273 | ## instead of the for-loop in Base Component. |
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| 274 | def evalDistribution(self, x = []): |
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| 275 | """ |
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| 276 | Evaluate the model in cartesian coordinates |
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| 277 | |
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| 278 | : param x: input q[], or [qx[], qy[]] |
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| 279 | : return: scattering function P(q[]) |
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| 280 | """ |
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| 281 | # set effective radius and scaling factor before run |
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| 282 | return self.model.evalDistribution(x) |
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| 283 | |
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| 284 | def set_dispersion(self, parameter, dispersion): |
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| 285 | """ |
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| 286 | Set the dispersion object for a model parameter |
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| 287 | |
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| 288 | : param parameter: name of the parameter [string] |
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| 289 | :dispersion: dispersion object of type DispersionModel |
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| 290 | """ |
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| 291 | value= None |
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| 292 | try: |
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| 293 | if parameter in self.model.dispersion.keys(): |
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| 294 | value= self.model.set_dispersion(parameter, dispersion) |
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| 295 | self._set_dispersion() |
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| 296 | return value |
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| 297 | except: |
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| 298 | raise |
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