Changeset 96b59384 in sasview for sansmodels


Ignore:
Timestamp:
Aug 4, 2009 6:02:28 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:
8dc0b746
Parents:
b341b16
Message:

added 2D and model descpt.

Location:
sansmodels/src
Files:
9 edited

Legend:

Unmodified
Added
Removed

  • sansmodels/src/libigor/libCylinder.c

    r8e91f01 r96b59384  
    972972 
    973973        Euler = 0.5772156649;           // Euler's constant 
    974         dQDefault = 0.0025;             //[=] 1/A, q-resolution, default value 
     974        dQDefault = 0; //0.0025;                //[=] 1/A, q-resolution, default value 
    975975        dQ = dQDefault; 
    976976 

  • sansmodels/src/sans/models/c_extensions/lamellarPS.h

    rb4679de r96b59384  
    88 * [PYTHONCLASS] = LamellarPSModel 
    99 * [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 
     10   [DESCRIPTION] = <text>[Concentrated Lamellar Form Factor] Calculates the scattered 
     11           intensity from a lyotropic lamellar phase. 
     12           The intensity (form factor and structure 
     13           factor)calculated is for lamellae of 
     14           uniform scattering length density that 
     15           are randomly distributed in solution 
     16           (a powder average). The lamellae thickness 
     17                is polydisperse. The model can also 
    1618                be applied to large, multi-lamellar vesicles. 
    1719                No resolution smeared version is included 
    … …  
    2628                scale = scale factor 
    2729</text> 
    28    [FIXED]= spacing.with 
     30   [FIXED]= spacing.width 
    2931   [ORIENTATION_PARAMS]= 
    3032 

  • sansmodels/src/sans/models/c_extensions/lamellarPS_HG.c

    r27a0771 r96b59384  
    1919double lamellarPS_HG_analytical_1D(LamellarPSHGParameters *pars, double q) { 
    2020        double dp[10]; 
    21          
     21 
    2222        // Fill paramater array 
    2323        dp[0] = pars->scale; 
    … …  
    3333 
    3434        // Call library function to evaluate model 
    35         return LamellarPS_HG(dp, q);     
     35        return LamellarPS_HG(dp, q); 
    3636} 
    3737/** 
    … …  
    4242 */ 
    4343double lamellarPS_HG_analytical_2DXY(LamellarPSHGParameters *pars, double qx, double qy) { 
    44         double q; 
    45         q = sqrt(qx*qx+qy*qy); 
    46     return lamellarPS_HG_analytical_2D_scaled(pars, q, qx/q, qy/q); 
    47 }  
     44    return lamellarPS_HG_analytical_1D(pars, sqrt(qx*qx+qy*qy)); 
     45} 
    4846 
    4947 
    … …  
    5654 */ 
    5755double lamellarPS_HG_analytical_2D(LamellarPSHGParameters *pars, double q, double phi) { 
    58     return lamellarPS_HG_analytical_2D_scaled(pars, q, cos(phi), sin(phi)); 
    59 }  
    60          
    61 /** 
    62  * Function to evaluate 2D scattering function 
    63  * @param pars: parameters of the lamellar 
    64  * @param q: q-value 
    65  * @param q_x: q_x / q 
    66  * @param q_y: q_y / q 
    67  * @return: function value 
    68  */ 
    69 double lamellarPS_HG_analytical_2D_scaled(LamellarPSHGParameters *pars, double q, double q_x, double q_y) { 
    70         return 1.0; 
     56    return lamellarPS_HG_analytical_1D(pars, q); 
    7157} 
    72      
    7358 

  • sansmodels/src/sans/models/c_extensions/lamellarPS_HG.h

    r27a0771 r96b59384  
    77/** Structure definition for concentrated lamellar form factor parameters 
    88 * [PYTHONCLASS] = LamellarPSHGModel 
    9  * [DISP_PARAMS] = deltaT,deltaH 
    10    [DESCRIPTION] = <text> Calculates the scattered intensity from a concentrated lamellar phase</text> 
    11    [FIXED]= deltaT.with;deltaH.with 
    12    [ORIENTATION_PARAMS]=  
     9 * [DISP_PARAMS] = deltaT,deltaH,spacing 
     10   [DESCRIPTION] = <text>[Concentrated Lamellar (head+tail) Form Factor]: Calculates the 
     11           intensity from a lyotropic lamellar phase. 
     12           The intensity (form factor and structure factor) 
     13                calculated is for lamellae of two-layer scattering 
     14                length density that are randomly distributed in 
     15                solution (a powder average). The scattering 
     16                length density of the tail region, headgroup 
     17                region, and solvent are taken to be different. 
     18                The model can also be applied to large, 
     19                multi-lamellar vesicles. 
     20                No resolution smeared version is included 
     21                in the structure factor of this model. 
     22                *Parameters: spacing = repeat spacing, 
     23                deltaT = tail length, 
     24                deltaH = headgroup thickness, 
     25                n_plates = # of Lamellar plates 
     26                caille = Caille parameter (<0.8 or <1) 
     27                background = incoherent bgd 
     28                scale = scale factor ... 
     29</text> 
     30   [FIXED]= deltaT.width;deltaH.width;spacing.width 
     31   [ORIENTATION_PARAMS]= 
    1332 
    1433 **/ 
    … …  
    2746    double deltaH; 
    2847    /// scattering density length of tails [1/A²] 
    29     //  [DEFAULT]=sld_tail=4e-7 [1/A²] 
     48    //  [DEFAULT]=sld_tail=0.4e-6 [1/A²] 
    3049    double sld_tail; 
    3150        /// scattering density length of head [1/A²] 
    … …  
    4160    //  [DEFAULT]=caille=0.001 
    4261    double caille; 
    43         /// Incoherent Background [1/cm]  
     62        /// Incoherent Background [1/cm] 
    4463        //  [DEFAULT]=background=0.001 [1/cm] 
    4564        double background; 
    46     
     65 
    4766} LamellarPSHGParameters; 
    4867 
    … …  
    5574double lamellarPS_HG_analytical_2D(LamellarPSHGParameters *pars, double q, double phi); 
    5675double lamellarPS_HG_analytical_2DXY(LamellarPSHGParameters *pars, double qx, double qy); 
    57 double lamellarPS_HG_analytical_2D_scaled(LamellarPSHGParameters *pars, double q, double q_x, double q_y); 
    5876 
    5977#endif 

  • sansmodels/src/sans/models/c_extensions/oblate.c

    r27a0771 r96b59384  
    11/** 
    2  * Scattering model for a oblate 
     2 * Scattering model for a oblate core shell 
    33 * @author: Gervaise B Alina/ UTK 
    44 */ 
    … …  
    1818 */ 
    1919double oblate_analytical_1D(OblateParameters *pars, double q) { 
    20         double dp[10]; 
    21          
     20        double dp[8]; 
     21 
    2222        // Fill paramater array 
    2323        dp[0] = pars->scale; 
    … …  
    2929        dp[6] = pars->sld_solvent; 
    3030        dp[7] = pars->background; 
    31         dp[8] = pars->axis_theta; 
    32         dp[9] = pars->axis_phi; 
    33          
     31 
    3432        // Call library function to evaluate model 
    35         return OblateForm(dp, q);        
     33        return OblateForm(dp, q); 
    3634} 
    3735 
    … …  
    4543        double q; 
    4644        q = sqrt(qx*qx+qy*qy); 
    47     return oblate_analytical_2D_scaled(pars, q, qx/q, qy/q); 
    48 }  
     45    return oblate_analytical_1D(pars, q); 
     46} 
    4947 
    5048 
    … …  
    5755 */ 
    5856double oblate_analytical_2D(OblateParameters *pars, double q, double phi) { 
    59     return oblate_analytical_2D_scaled(pars, q, cos(phi), sin(phi)); 
    60 }  
    61          
     57    return oblate_analytical_1D(pars, q); 
     58} 
     59 
    6260/** 
    6361 * Function to evaluate 2D scattering function 
    … …  
    6866 * @return: function value 
    6967 */ 
     68/* 
    7069double oblate_analytical_2D_scaled(OblateParameters *pars, double q, double q_x, double q_y) { 
    71          
     70 
    7271        return 1.0; 
    7372} 
    74      
     73*/ 

  • sansmodels/src/sans/models/c_extensions/oblate.h

    r27a0771 r96b59384  
    33/** Structure definition for oblate parameters 
    44 * [PYTHONCLASS] = OblateModel 
    5  * [DISP_PARAMS] = major_core, minor_core, major_shell,minor_shell, axis_theta, axis_phi 
    6    [DESCRIPTION] = <text> Calculates the form factor for an oblate ellipsoid particle with a core/shell structure. 
    7                         Note:It is the users' responsibility to ensure that shell radii are larger than core radii, and 
    8                                         that major radii are larger than minor radii.</text> 
     5 * [DISP_PARAMS] = major_core, minor_core, major_shell,minor_shell 
     6   [DESCRIPTION] = <text>[OblateCoreShellModel] Calculates the form factor for an oblate 
     7                        ellipsoid particle with a core_shell structure. 
     8                        The form factor is averaged over all possible 
     9                        orientations of the ellipsoid such that P(q) 
     10                        = scale*<f^2>/Vol + bkg, where f is the 
     11                        single particle scattering amplitude. 
     12                        [Parameters]: 
     13                        major_core = radius of major_core, 
     14                        minor_core = radius of minor_core, 
     15                        major_shell = radius of major_shell, 
     16                        minor_shell = radius of minor_shell, 
     17                        contrast = SLD_core - SLD_shell 
     18                        sld_solvent = SLD_solvent 
     19                        background = Incoherent bkg 
     20                        scale =scale 
     21                        Note:It is the users' responsibility to ensure 
     22                        that shell radii are larger than core radii. 
     23                        </text> 
    924 
    10    [FIXED] = <text>axis_phi.width; axis_theta.width; major_core.width;minor_core.width; major_shell; minor_shell</text> 
    11    [ORIENTATION_PARAMS] = <text>axis_phi; axis_theta; axis_phi.width; axis_theta.width</text> 
     25   [FIXED] = <text>major_core.width;minor_core.width; major_shell.width; minor_shell.width</text> 
     26   [ORIENTATION_PARAMS] = 
    1227 
    1328 **/ 
    … …  
    3752        //  [DEFAULT]=background=0.001 [1/cm] 
    3853        double background; 
     54        /*//Disable for now 
    3955    /// Orientation of the oblate axis w/respect incoming beam [rad] 
    4056    //  [DEFAULT]=axis_theta=1.0 [rad] 
    … …  
    4359    //  [DEFAULT]=axis_phi=1.0 [rad] 
    4460    double axis_phi; 
    45  
     61        */ 
    4662} OblateParameters; 
    4763 
    … …  
    5470double oblate_analytical_2D(OblateParameters *pars, double q, double phi); 
    5571double oblate_analytical_2DXY(OblateParameters *pars, double qx, double qy); 
    56 double oblate_analytical_2D_scaled(OblateParameters *pars, double q, double q_x, double q_y); 
     72//double oblate_analytical_2D_scaled(OblateParameters *pars, double q, double q_x, double q_y); 
    5773 
    5874#endif 

  • sansmodels/src/sans/models/c_models/CLamellarPSHGModel.cpp

    r27a0771 r96b59384  
    102102        self->model->deltaH.dispersion->accept_as_source(visitor, self->model->deltaH.dispersion, disp_dict); 
    103103        PyDict_SetItemString(self->dispersion, "deltaH", disp_dict); 
     104        disp_dict = PyDict_New(); 
     105        self->model->spacing.dispersion->accept_as_source(visitor, self->model->spacing.dispersion, disp_dict); 
     106        PyDict_SetItemString(self->dispersion, "spacing", disp_dict); 
    104107 
    105108 
    … …  
    171174    disp_dict = PyDict_GetItemString(self->dispersion, "deltaH"); 
    172175    self->model->deltaH.dispersion->accept_as_destination(visitor, self->model->deltaH.dispersion, disp_dict); 
     176    disp_dict = PyDict_GetItemString(self->dispersion, "spacing"); 
     177    self->model->spacing.dispersion->accept_as_destination(visitor, self->model->spacing.dispersion, disp_dict); 
    173178 
    174179         
    … …  
    239244    disp_dict = PyDict_GetItemString(self->dispersion, "deltaH"); 
    240245    self->model->deltaH.dispersion->accept_as_destination(visitor, self->model->deltaH.dispersion, disp_dict); 
     246    disp_dict = PyDict_GetItemString(self->dispersion, "spacing"); 
     247    self->model->spacing.dispersion->accept_as_destination(visitor, self->model->spacing.dispersion, disp_dict); 
    241248 
    242249         
    … …  
    298305    } else    if (!strcmp(par_name, "deltaH")) { 
    299306        self->model->deltaH.dispersion = dispersion; 
     307    } else    if (!strcmp(par_name, "spacing")) { 
     308        self->model->spacing.dispersion = dispersion; 
    300309    } else { 
    301310            PyErr_SetString(CLamellarPSHGModelError, 

  • sansmodels/src/sans/models/c_models/lamellarPS_HG.cpp

    r27a0771 r96b59384  
    3535LamellarPSHGModel :: LamellarPSHGModel() { 
    3636        scale      = Parameter(1.0); 
    37         spacing    = Parameter(40.0); 
     37        spacing    = Parameter(40.0, true); 
     38        spacing.set_min(0.0); 
    3839        deltaT     = Parameter(10.0, true); 
    3940        deltaT.set_min(0.0); 
    … …  
    6970        dp[7] = n_plates(); 
    7071        dp[8] = caille(); 
    71         dp[9] = background(); 
    72          
     72        dp[9] = 0.0; 
     73 
    7374 
    7475        // Get the dispersion points for (deltaT) thickness of the tail 
    7576        vector<WeightPoint> weights_deltaT; 
    7677        deltaT.get_weights(weights_deltaT); 
    77          
     78 
    7879        // Get the dispersion points for (deltaH) thickness of the head 
    7980        vector<WeightPoint> weights_deltaH; 
    8081        deltaH.get_weights(weights_deltaH); 
    8182 
     83        // Get the dispersion points for spacing 
     84        vector<WeightPoint> weights_spacing; 
     85        spacing.get_weights(weights_spacing); 
     86 
    8287        // Perform the computation, with all weight points 
    8388        double sum = 0.0; 
    8489        double norm = 0.0; 
    85          
     90 
    8691        // Loop over deltaT  weight points 
    8792        for(int i=0; i< (int)weights_deltaT.size(); i++) { 
    … …  
    9196                for(int j=0; j< (int)weights_deltaH.size(); j++) { 
    9297                        dp[3] = weights_deltaH[j].value; 
     98                        // Loop over spacing weight points 
     99                        for(int k=0; k< (int)weights_spacing.size(); k++) { 
     100                                dp[1] = weights_spacing[k].value; 
    93101 
    94                         sum += weights_deltaT[i].weight * weights_deltaH[j].weight *LamellarPS_HG(dp, q); 
    95                         norm += weights_deltaT[i].weight * weights_deltaH[j].weight; 
     102                                sum += weights_deltaT[i].weight * weights_deltaH[j].weight *weights_spacing[k].weight 
     103                                                                *LamellarPS_HG(dp, q); 
     104                                norm += weights_deltaT[i].weight * weights_deltaH[j].weight * weights_spacing[k].weight; 
     105                        } 
    96106                } 
    97                                  
    98107        } 
    99108        return sum/norm + background(); 
    … …  
    105114 * @return: function value 
    106115 */ 
     116double LamellarPSHGModel :: operator()(double qx, double qy) { 
     117        double q = sqrt(qx*qx + qy*qy); 
     118        return (*this).operator()(q); 
     119} 
     120 
     121/** 
     122 * Function to evaluate 2D scattering function 
     123 * @param pars: parameters of the lamellarPS_HG 
     124 * @param q: q-value 
     125 * @param phi: angle phi 
     126 * @return: function value 
     127 */ 
     128double LamellarPSHGModel :: evaluate_rphi(double q, double phi) { 
     129        return (*this).operator()(q); 
     130} 
     131 
     132/* 
    107133double LamellarPSHGModel :: operator()(double qx, double qy) { 
    108134        LamellarPSHGParameters dp; 
    … …  
    118144        dp.caille = caille(); 
    119145        dp.background    = background(); 
    120          
     146 
    121147        // Get the dispersion points for the deltaT 
    122148        vector<WeightPoint> weights_deltaT; 
    … …  
    134160        for(int i=0; i< (int)weights_deltaT.size(); i++) { 
    135161                dp.deltaT = weights_deltaT[i].value; 
    136                  
     162 
    137163                // Loop over deltaH weight points 
    138164                for(int j=0; j< (int)weights_deltaH.size(); j++) { 
    139165                        dp.deltaH = weights_deltaH[j].value; 
    140166 
    141                         sum += weights_deltaT[i].weight *weights_deltaH[j].weight *lamellarPS_HG_analytical_2DXY(&dp, qx, qy);   
    142                         norm += weights_deltaT[i].weight * weights_deltaH[j].weight;     
     167                        sum += weights_deltaT[i].weight *weights_deltaH[j].weight *lamellarPS_HG_analytical_2DXY(&dp, qx, qy); 
     168                        norm += weights_deltaT[i].weight * weights_deltaH[j].weight; 
    143169                } 
    144170        } 
    145171        return sum/norm + background(); 
    146172} 
     173*/ 
    147174 
    148175 
    149 /** 
    150  * Function to evaluate 2D scattering function 
    151  * @param pars: parameters of the lamellar 
    152  * @param q: q-value 
    153  * @param phi: angle phi 
    154  * @return: function value 
    155  */ 
    156 double LamellarPSHGModel :: evaluate_rphi(double q, double phi) { 
    157         double qx = q*cos(phi); 
    158         double qy = q*sin(phi); 
    159         return (*this).operator()(qx, qy); 
    160 } 

  • sansmodels/src/sans/models/c_models/oblate.cpp

    r27a0771 r96b59384  
    4545        sld_solvent = Parameter(6.3e-6); 
    4646        background = Parameter(0.0); 
    47         axis_theta  = Parameter(0.0, true); 
    48         axis_phi    = Parameter(0.0, true); 
    4947} 
    5048 
    … …  
    6765        dp[5] = contrast(); 
    6866        dp[6] = sld_solvent(); 
    69         dp[7] = background(); 
    70          
     67        dp[7] = 0.0; 
     68 
    7169        // Get the dispersion points for the major core 
    7270        vector<WeightPoint> weights_major_core; 
    … …  
    106104                                        dp[4] = weights_minor_shell[l].value; 
    107105 
    108                                         sum += weights_major_core[i].weight* weights_minor_core[j].weight * weights_major_shell[k].weight  
     106                                        sum += weights_major_core[i].weight* weights_minor_core[j].weight * weights_major_shell[k].weight 
    109107                                                * weights_minor_shell[l].weight * OblateForm(dp, q); 
    110                                         norm += weights_major_core[i].weight* weights_minor_core[j].weight * weights_major_shell[k].weight  
     108                                        norm += weights_major_core[i].weight* weights_minor_core[j].weight * weights_major_shell[k].weight 
    111109                                                        * weights_minor_shell[l].weight; 
    112110                                } 
    … …  
    123121 * @return: function value 
    124122 */ 
     123 
    125124double OblateModel :: operator()(double qx, double qy) { 
     125        double q = sqrt(qx*qx + qy*qy); 
     126 
     127        return (*this).operator()(q); 
     128} 
     129 
     130 
     131/** 
     132 * Function to evaluate 2D scattering function 
     133 * @param pars: parameters of the oblate 
     134 * @param q: q-value 
     135 * @param phi: angle phi 
     136 * @return: function value 
     137 */ 
     138double OblateModel :: evaluate_rphi(double q, double phi) { 
     139        return (*this).operator()(q); 
     140} 
     141 
     142/* disable below for now 
     143double OblateShellModel :: operator()(double qx, double qy) { 
    126144        OblateParameters dp; 
    127145        // Fill parameter array 
    … …  
    215233        return sum/norm + background(); 
    216234} 
    217  
    218 /** 
    219  * Function to evaluate 2D scattering function 
    220  * @param pars: parameters of the oblate 
    221  * @param q: q-value 
    222  * @param phi: angle phi 
    223  * @return: function value 
    224  */ 
    225 double OblateModel :: evaluate_rphi(double q, double phi) { 
    226         double qx = q*cos(phi); 
    227         double qy = q*sin(phi); 
    228         return (*this).operator()(qx, qy); 
    229 } 
     235*/// 
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