Changeset b4679de in sasview for sansmodels/src


Ignore:
Timestamp:
Aug 4, 2009 3:32:38 PM (15 years ago)
Author:
Jae Cho <jhjcho@…>
Branches:
master, ESS_GUI, ESS_GUI_Docs, ESS_GUI_batch_fitting, ESS_GUI_bumps_abstraction, ESS_GUI_iss1116, ESS_GUI_iss879, ESS_GUI_iss959, ESS_GUI_opencl, ESS_GUI_ordering, ESS_GUI_sync_sascalc, costrafo411, magnetic_scatt, release-4.1.1, release-4.1.2, release-4.2.2, release_4.0.1, ticket-1009, ticket-1094-headless, ticket-1242-2d-resolution, ticket-1243, ticket-1249, ticket885, unittest-saveload
Children:
fbe5d3e
Parents:
8e91f01
Message:

added 2d and model descpt + correction on polydisp. para.

Location:
sansmodels/src/sans/models
Files:
10 edited

Legend:

Unmodified
Added
Removed
  • sansmodels/src/sans/models/LamellarFFHGModel.py

    r34c3020 rb4679de  
    5252        self.name = "LamellarFFHGModel" 
    5353        ## Model description 
    54         self.description =""" 
    55                 NOTE: The total bilayer thickness = 2(h_thickness + t_length) 
    56                 The meaning of the multiplicative scale factor is not well-defined, but should be on the 
    57                 order of the volume fraction of solution occupied by the lamellar crystallites. Please see 
    58                 the original references for clarification.""" 
     54        self.description =""" Parameters: t_length = tail length, h_thickness = head thickness, 
     55                scale = Scale factor, 
     56                background = incoherent Background 
     57                sld_tail = tail scattering length density , 
     58                sld_solvent = solvent scattering length density. 
     59                NOTE: The total bilayer thickness 
     60                = 2(h_thickness+ t_length). 
     61                """ 
    5962        
    6063                ## Parameter details [units, min, max] 
  • sansmodels/src/sans/models/LamellarModel.py

    r34c3020 rb4679de  
    5050        self.name = "LamellarModel" 
    5151        ## Model description 
    52         self.description =""" I(q)= 2*pi*P(q)/(delta *q^(2)) 
    53                 where: 
    54                 P(q)=2*(contrast/q)^(2)*(1-cos(q*delta)*e^(1/2*(q*sigma)^(2))""" 
     52        self.description ="""[Dilute Lamellar Form Factor](from a lyotropic lamellar phase) 
     53                I(q)= 2*pi*P(q)/(delta *q^(2)), where 
     54                P(q)=2*(contrast/q)^(2)*(1-cos(q*delta) 
     55                *e^(1/2*(q*sigma)^(2)). 
     56                delta = bilayer thickness 
     57                sigma = variation in bilayer thickness 
     58                = delta*polydispersity 
     59                contrast = SLD_solvent - SLD_bilayer 
     60                Note: the polydispersity in delta is included.""" 
    5561        
    5662                ## Parameter details [units, min, max] 
     
    6369 
    6470                ## fittable parameters 
    65         self.fixed=['delta.width'] 
     71        self.fixed=[] 
    6672         
    6773        ## parameters with orientation 
  • sansmodels/src/sans/models/VesicleModel.py

    r2c4b289 rb4679de  
    5151        self.name = "VesicleModel" 
    5252        ## Model description 
    53         self.description =""" 
    54                 Model parameters: 
    55                 scale : scale factor 
    56                 core_radius : Core radius of the vesicle 
     53        self.description ="""Model parameters:  core_radius : Core radius of the vesicle 
    5754                thickness: shell thickness 
    5855                core_sld: core scattering length density 
    5956                shell_sld: shell scattering length density 
    60                 background: incoherent background""" 
     57                background: incoherent background 
     58                scale : scale factor""" 
    6159        
    6260                ## Parameter details [units, min, max] 
     
    7068 
    7169                ## fittable parameters 
    72         self.fixed=['core_radius.width'] 
     70        self.fixed=['core_radius.width', 'thickness.width'] 
    7371         
    7472        ## parameters with orientation 
  • sansmodels/src/sans/models/c_extensions/lamellarFF_HG.c

    r34c3020 rb4679de  
    1919double lamellarFF_HG_analytical_1D(LamellarFF_HGParameters *pars, double q) { 
    2020        double dp[7]; 
    21          
     21 
    2222        // Fill paramater array 
    2323        dp[0] = pars->scale; 
     
    2828        dp[5] = pars->sld_solvent; 
    2929        dp[6] = pars->background; 
    30          
     30 
    3131        // Call library function to evaluate model 
    32         return LamellarFF_HG(dp, q);     
     32        return LamellarFF_HG(dp, q); 
    3333} 
    3434 
    3535double lamellarFF_HG_analytical_2D(LamellarFF_HGParameters *pars, double q, double phi){ 
    36         return 1.0; 
     36        return lamellarFF_HG_analytical_1D(pars,q); 
    3737} 
    3838double lamellarFF_HG_analytical_2DXY(LamellarFF_HGParameters *pars, double qx, double qy){ 
    39         return 1.0; 
     39        return lamellarFF_HG_analytical_1D(pars,sqrt(qx*qx+qy*qy)); 
    4040} 
    41 double lamellarFF_HG_analytical_2D_scaled(LamellarFF_HGParameters *pars, double q, double q_x, double q_y){ 
    42         return 1.0; 
    43 } 
    44  
  • sansmodels/src/sans/models/c_extensions/lamellarFF_HG.h

    r34c3020 rb4679de  
    44 * [PYTHONCLASS] = LamellarFFHGModel 
    55 * [DISP_PARAMS] =  t_length, h_thickness 
    6    [DESCRIPTION] = <text>  
    7                                         NOTE: The total bilayer thickness = 2(h_thickness + t_length) 
    8                                         The meaning of the multiplicative scale factor is not well-defined, but should be on the 
    9                                         order of the volume fraction of solution occupied by the lamellar crystallites. Please see 
    10                                         the original references for clarification. 
    11                                    </text> 
     6   [DESCRIPTION] = <text> Parameters: t_length = tail length, h_thickness = head thickness, 
     7                        scale = Scale factor, 
     8                        background = incoherent Background 
     9                        sld_tail = tail scattering length density , 
     10                        sld_solvent = solvent scattering length density. 
     11                        NOTE: The total bilayer thickness 
     12                        = 2(h_thickness+ t_length). 
     13 
     14        </text> 
    1215        [FIXED]= t_length.width, h_thickness.width 
    13         [ORIENTATION_PARAMS]=  
     16        [ORIENTATION_PARAMS]= 
    1417 **/ 
    1518typedef struct { 
     
    2023    //  [DEFAULT]=t_length=15.0 [A] 
    2124    double t_length; 
    22     /// head thickness  
     25    /// head thickness 
    2326    //  [DEFAULT]=h_thickness=10.0 [A] 
    2427    double h_thickness; 
    25         /// tail scrattering density length[1/A²] 
     28        /// tail scrattering length density[1/A²] 
    2629    //  [DEFAULT]=sld_tail=4e-7 [1/A²] 
    2730    double sld_tail; 
    28     /// head group scrattering density length[1/A²] 
     31    /// head group scrattering length density[1/A²] 
    2932    //  [DEFAULT]=sld_head=3e-6 [1/A²] 
    3033    double sld_head; 
    31          /// solvent scrattering density length[1/A²] 
     34         /// solvent scrattering length density[1/A²] 
    3235    //  [DEFAULT]=sld_solvent=6e-6 [1/A²] 
    3336    double sld_solvent; 
     
    3538        //  [DEFAULT]=background=0.0 [1/cm] 
    3639        double background; 
    37     
     40 
    3841} LamellarFF_HGParameters; 
    3942 
     
    4649double lamellarFF_HG_analytical_2D(LamellarFF_HGParameters *pars, double q, double phi); 
    4750double lamellarFF_HG_analytical_2DXY(LamellarFF_HGParameters *pars, double qx, double qy); 
    48 double lamellarFF_HG_analytical_2D_scaled(LamellarFF_HGParameters *pars, double q, double q_x, double q_y); 
    4951 
    5052#endif 
  • sansmodels/src/sans/models/c_extensions/lamellarPS.c

    r27a0771 rb4679de  
    1919double lamellarPS_analytical_1D(LamellarPSParameters *pars, double q) { 
    2020        double dp[8]; 
    21          
     21 
    2222        // Fill paramater array 
    2323        dp[0] = pars->scale; 
     
    3131 
    3232        // Call library function to evaluate model 
    33         return LamellarPS(dp, q);        
     33        return LamellarPS(dp, q); 
    3434} 
    3535/** 
     
    4242        double q; 
    4343        q = sqrt(qx*qx+qy*qy); 
    44     return lamellarPS_analytical_2D_scaled(pars, q, qx/q, qy/q); 
    45 }  
     44    return lamellarPS_analytical_1D(pars, q); 
     45} 
    4646 
    4747 
     
    5454 */ 
    5555double lamellarPS_analytical_2D(LamellarPSParameters *pars, double q, double phi) { 
    56     return lamellarPS_analytical_2D_scaled(pars, q, cos(phi), sin(phi)); 
    57 }  
    58          
     56    return lamellarPS_analytical_1D(pars,q); 
     57} 
     58 
    5959/** 
    6060 * Function to evaluate 2D scattering function 
     
    6565 * @return: function value 
    6666 */ 
    67 double lamellarPS_analytical_2D_scaled(LamellarPSParameters *pars, double q, double q_x, double q_y) { 
    68          
    69         return 1.0; 
    70 } 
    71      
    7267 
     68 
  • sansmodels/src/sans/models/c_extensions/lamellarPS.h

    r27a0771 rb4679de  
    77/** Structure definition for concentrated lamellar form factor parameters 
    88 * [PYTHONCLASS] = LamellarPSModel 
    9  * [DISP_PARAMS] = delta 
    10    [DESCRIPTION] = <text> Calculates the scattered intensity from a lyotropic lamellar phase</text> 
    11    [FIXED]= delta.with 
    12    [ORIENTATION_PARAMS]=  
     9 * [DISP_PARAMS] = spacing 
     10   [DESCRIPTION] = <text>Calculates the scattered intensity from a lyotropic lamellar phase. 
     11           The intensity (form factor and structure factor) 
     12                calculated is for lamellae of uniform scattering 
     13                length density that are randomly distributed in 
     14                solution (a powder average). The lamellae 
     15                thickness is polydisperse. The model can also 
     16                be applied to large, multi-lamellar vesicles. 
     17                No resolution smeared version is included 
     18                in the structure factor of this model. 
     19                *Parameters: spacing = repeat spacing, 
     20                delta = bilayer thickness, 
     21                sigma = variation in bilayer thickness 
     22                contrast = SLD_solvent - SLD_bilayer 
     23                n_plate = # of Lamellar plates 
     24                caille = Caille parameter (<0.8 or <1) 
     25                background = incoherent bgd 
     26                scale = scale factor 
     27</text> 
     28   [FIXED]= spacing.with 
     29   [ORIENTATION_PARAMS]= 
    1330 
    1431 **/ 
     
    3552    //  [DEFAULT]=caille=0.1 
    3653    double caille; 
    37         /// Incoherent Background [1/cm]  
     54        /// Incoherent Background [1/cm] 
    3855        //  [DEFAULT]=background=0.0 [1/cm] 
    3956        double background; 
    40     
     57 
    4158} LamellarPSParameters; 
    4259 
     
    4966double lamellarPS_analytical_2D(LamellarPSParameters *pars, double q, double phi); 
    5067double lamellarPS_analytical_2DXY(LamellarPSParameters *pars, double qx, double qy); 
    51 double lamellarPS_analytical_2D_scaled(LamellarPSParameters *pars, double q, double q_x, double q_y); 
    5268 
    5369#endif 
  • sansmodels/src/sans/models/c_models/flexiblecylinder.cpp

    r2cc633b rb4679de  
    6161        dp[3] = radius(); 
    6262        dp[4] = contrast(); 
    63         dp[5] = background(); 
     63        dp[5] = 0.0; 
    6464 
    6565        // Get the dispersion points for the length 
  • sansmodels/src/sans/models/c_models/lamellarFF_HG.cpp

    r34c3020 rb4679de  
    6262        dp[4] = sld_head(); 
    6363        dp[5] = sld_solvent(); 
    64         dp[6] = background(); 
     64        dp[6] = 0.0; 
    6565 
    6666        // Get the dispersion points for the tail length 
     
    8686                        norm += weights_t_length[i].weight* weights_h_thickness[j].weight; 
    8787                } 
    88                                  
     88 
    8989        } 
    9090        return sum/norm + background(); 
     
    9999 
    100100double LamellarFFHGModel :: operator()(double qx, double qy) { 
    101         LamellarFF_HGParameters dp; 
    102  
    103         // Fill parameter array for IGOR library 
    104         // Add the background after averaging 
    105         dp.scale = scale(); 
    106         dp.t_length = t_length(); 
    107         dp.h_thickness = h_thickness(); 
    108         dp.sld_tail = sld_tail(); 
    109         dp.sld_head = sld_head(); 
    110         dp.sld_solvent = sld_solvent(); 
    111         dp.background = background(); 
    112  
    113  
    114         // Get the dispersion points for the tail length 
    115         vector<WeightPoint> weights_t_length; 
    116         t_length.get_weights(weights_t_length); 
    117  
    118         // Get the dispersion points for the head thickness 
    119         vector<WeightPoint> weights_h_thickness; 
    120         h_thickness.get_weights(weights_h_thickness); 
    121  
    122         // Perform the computation, with all weight points 
    123         double sum = 0.0; 
    124         double norm = 0.0; 
    125  
    126         // Loop over detla  weight points 
    127         for(int i=0; i< (int)weights_t_length.size(); i++) { 
    128                 dp.t_length = weights_t_length[i].value; 
    129  
    130                 for(int j=0; j< (int)weights_h_thickness.size(); j++) { 
    131                         dp.h_thickness = weights_h_thickness[j].value; 
    132  
    133                         sum += weights_t_length[i].weight* weights_h_thickness[j].weight 
    134                                 * lamellarFF_HG_analytical_2DXY(&dp, qx, qy); 
    135                         norm += weights_t_length[i].weight* weights_h_thickness[j].weight; 
    136                 } 
    137                                  
    138         } 
    139         return sum/norm + background(); 
     101        double q = sqrt(qx*qx + qy*qy); 
     102        return (*this).operator()(q); 
    140103} 
    141104 
     
    148111 */ 
    149112double LamellarFFHGModel :: evaluate_rphi(double q, double phi) { 
    150         double qx = q*cos(phi); 
    151         double qy = q*sin(phi); 
    152         return (*this).operator()(qx, qy); 
     113        return (*this).operator()(q); 
    153114} 
  • sansmodels/src/sans/models/c_models/lamellarPS.cpp

    r27a0771 rb4679de  
    3535LamellarPSModel :: LamellarPSModel() { 
    3636        scale      = Parameter(1.0); 
    37         spacing    = Parameter(400.0); 
    38         delta     = Parameter(30.0, true); 
     37        spacing    = Parameter(400.0, true); 
     38        spacing.set_min(0.0); 
     39        delta     = Parameter(30.0); 
    3940        delta.set_min(0.0); 
    40         sigma    = Parameter(0.15, true); 
     41        sigma    = Parameter(0.15); 
     42        sigma.set_min(0.0); 
    4143        contrast   = Parameter(5.3e-6); 
    4244        n_plates     = Parameter(20.0); 
     
    6466        dp[5] = n_plates(); 
    6567        dp[6] = caille(); 
    66         dp[7] = background(); 
    67          
     68        dp[7] = 0.0; 
     69 
    6870 
    6971        // Get the dispersion points for (delta) thickness 
    70         vector<WeightPoint> weights_delta; 
    71         delta.get_weights(weights_delta); 
    72          
     72        vector<WeightPoint> weights_spacing; 
     73        spacing.get_weights(weights_spacing); 
     74 
    7375        // Perform the computation, with all weight points 
    7476        double sum = 0.0; 
    7577        double norm = 0.0; 
    76          
     78 
    7779        // Loop over short_edgeA weight points 
    78         for(int i=0; i< (int)weights_delta.size(); i++) { 
    79                 dp[2] = weights_delta[i].value; 
     80        for(int i=0; i< (int)weights_spacing.size(); i++) { 
     81                dp[1] = weights_spacing[i].value; 
    8082 
    81                 sum += weights_delta[i].weight * LamellarPS(dp, q); 
    82                 norm += weights_delta[i].weight; 
    83                                  
     83                sum += weights_spacing[i].weight * LamellarPS(dp, q); 
     84                norm += weights_spacing[i].weight; 
     85 
    8486        } 
    8587        return sum/norm + background(); 
     
    9294 */ 
    9395double LamellarPSModel :: operator()(double qx, double qy) { 
    94         LamellarPSParameters dp; 
    95         // Fill parameter array 
    96         dp.scale      = scale(); 
    97         dp.spacing   = spacing(); 
    98         dp.delta  = delta(); 
    99         dp.sigma = sigma(); 
    100         dp.contrast   = contrast(); 
    101         dp.n_plates = n_plates(); 
    102         dp.caille = caille(); 
    103         dp.background    = background(); 
    104          
    105  
    106         // Get the dispersion points for the delta 
    107         vector<WeightPoint> weights_delta; 
    108         delta.get_weights(weights_delta); 
    109  
    110         // Perform the computation, with all weight points 
    111         double sum = 0.0; 
    112         double norm = 0.0; 
    113  
    114         // Loop over radius weight points 
    115         for(int i=0; i< (int)weights_delta.size(); i++) { 
    116                 dp.delta = weights_delta[i].value; 
    117  
    118                 sum += weights_delta[i].weight *lamellarPS_analytical_2DXY(&dp, qx, qy);         
    119                 norm += weights_delta[i].weight;         
    120         } 
    121          
    122         return sum/norm + background(); 
     96        double q = sqrt(qx*qx + qy*qy); 
     97        return (*this).operator()(q); 
    12398} 
    124  
    12599 
    126100/** 
     
    132106 */ 
    133107double LamellarPSModel :: evaluate_rphi(double q, double phi) { 
    134         double qx = q*cos(phi); 
    135         double qy = q*sin(phi); 
    136         return (*this).operator()(qx, qy); 
     108        return (*this).operator()(q); 
    137109} 
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