Changeset 5c028e3 in sasmodels for sasmodels/models


Ignore:
Timestamp:
Mar 27, 2016 4:58:51 PM (8 years ago)
Author:
Paul Kienzle <pkienzle@…>
Branches:
master, core_shell_microgels, costrafo411, magnetic_model, release_v0.94, release_v0.95, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests
Children:
ce896fd
Parents:
d19962c (diff), b274bec (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.
Message:

Merge branch 'master' into polydisp

Location:
sasmodels/models
Files:
1 added
12 edited

Legend:

Unmodified
Added
Removed

  • sasmodels/models/core_multi_shell.py

    r34edbb8 rb274bec  
    2626 
    2727For information about polarised and magnetic scattering, see  
    28 the :ref:`mag_help` documentation. 
     28the :doc:`magnetic help <../sasgui/perspectives/fitting/mag_help>` documentation. 
    2929 
    3030Our model uses the form factor calculations implemented in a c-library provided 

  • sasmodels/models/cylinder.c

    r26141cb re9b1663d  
    33double Iqxy(double qx, double qy, double sld, double solvent_sld, 
    44    double radius, double length, double theta, double phi); 
     5 
     6#define INVALID(v) (v.radius<0 || v.length<0) 
    57 
    68double form_volume(double radius, double length) 
    … …  
    1517    double length) 
    1618{ 
    17     // TODO: return NaN if radius<0 or length<0? 
    1819    // precompute qr and qh to save time in the loop 
    1920    const double qr = q*radius; 
    … …  
    4748    double phi) 
    4849{ 
    49     // TODO: return NaN if radius<0 or length<0? 
    5050    double sn, cn; // slots to hold sincos function output 
    5151 

  • sasmodels/models/gel_fit.c

    r30b4ddf r03cac08  
    1 double form_volume(void); 
    2  
    3 double Iq(double q, 
    4           double guinier_scale, 
    5           double lorentzian_scale, 
    6           double gyration_radius, 
    7           double fractal_exp, 
    8           double cor_length); 
    9  
    10 double Iqxy(double qx, double qy, 
    11           double guinier_scale, 
    12           double lorentzian_scale, 
    13           double gyration_radius, 
    14           double fractal_exp, 
    15           double cor_length); 
    16  
    17 static double _gel_fit_kernel(double q, 
     1static double Iq(double q, 
    182          double guinier_scale, 
    193          double lorentzian_scale, 
    … …  
    248    // Lorentzian Term 
    259    ////////////////////////double a(x[i]*x[i]*zeta*zeta); 
    26     double lorentzian_term = q*q*cor_length*cor_length; 
     10    double lorentzian_term = square(q*cor_length); 
    2711    lorentzian_term = 1.0 + ((fractal_exp + 1.0)/3.0)*lorentzian_term; 
    2812    lorentzian_term = pow(lorentzian_term, (fractal_exp/2.0) ); 
    … …  
    3014    // Exponential Term 
    3115    ////////////////////////double d(x[i]*x[i]*rg*rg); 
    32     double exp_term = q*q*gyration_radius*gyration_radius; 
     16    double exp_term = square(q*gyration_radius); 
    3317    exp_term = exp(-1.0*(exp_term/3.0)); 
    3418 
    … …  
    3721    return result; 
    3822} 
    39 double form_volume(void){ 
    40     // Unused, so free to return garbage. 
    41     return NAN; 
    42 } 
    43  
    44 double Iq(double q, 
    45           double guinier_scale, 
    46           double lorentzian_scale, 
    47           double gyration_radius, 
    48           double fractal_exp, 
    49           double cor_length) 
    50 { 
    51     return _gel_fit_kernel(q, 
    52                           guinier_scale, 
    53                           lorentzian_scale, 
    54                           gyration_radius, 
    55                           fractal_exp, 
    56                           cor_length); 
    57 } 
    58  
    59 // Iqxy is never called since no orientation or magnetic parameters. 
    60 double Iqxy(double qx, double qy, 
    61           double guinier_scale, 
    62           double lorentzian_scale, 
    63           double gyration_radius, 
    64           double fractal_exp, 
    65           double cor_length) 
    66 { 
    67     double q = sqrt(qx*qx + qy*qy); 
    68     return _gel_fit_kernel(q, 
    69                           guinier_scale, 
    70                           lorentzian_scale, 
    71                           gyration_radius, 
    72                           fractal_exp, 
    73                           cor_length); 
    74 } 
    75  

  • sasmodels/models/lib/Si.c

    re7678b2 rba32cdd  
     1// integral of sin(x)/x Taylor series approximated to w/i 0.1% 
    12double Si(double x); 
    23 
    3 // integral of sin(x)/x Taylor series approximated to w/i 0.1% 
    44double Si(double x) 
    55{ 

  • sasmodels/models/lib/polevl.c

    r0b05c24 rba32cdd  
    5151*/ 
    5252 
    53 double polevl( double x, constant double *coef, int N ) { 
     53double polevl( double x, constant double *coef, int N ); 
     54double p1evl( double x, constant double *coef, int N ); 
     55 
     56 
     57double polevl( double x, constant double *coef, int N ) 
     58{ 
    5459 
    5560    int i = 0; 
    … …  
    7075 */ 
    7176 
    72 double p1evl( double x, constant double *coef, int N ) { 
     77double p1evl( double x, constant double *coef, int N ) 
     78{ 
    7379    int i=0; 
    7480    double ans = x+coef[i]; 

  • sasmodels/models/lib/sas_J0.c

    ra776125 rba32cdd  
    4949Copyright 1984, 1987, 1989, 2000 by Stephen L. Moshier 
    5050*/ 
     51 
     52double sas_J0(double x); 
    5153 
    5254/* Note: all coefficients satisfy the relative error criterion 
    … …  
    177179 }; 
    178180 
    179 double sas_J0(double x) { 
     181double sas_J0(double x) 
     182{ 
    180183 
    181184//Cephes single precission 

  • sasmodels/models/lib/sas_J1.c

    r19b9005 rba32cdd  
    3939Copyright 1984, 1987, 1989, 2000 by Stephen L. Moshier 
    4040*/ 
     41double sas_J1(double x); 
     42double sas_J1c(double x); 
    4143 
    4244constant double RPJ1[8] = { 
    … …  
    135137    }; 
    136138 
    137 double sas_J1(double x) { 
     139double sas_J1(double x) 
     140{ 
    138141 
    139142//Cephes double pression function 

  • sasmodels/models/lib/sas_JN.c

    ra776125 rba32cdd  
    4747Copyright 1984, 1987, 2000 by Stephen L. Moshier 
    4848*/ 
    49  
    5049double sas_JN( int n, double x ); 
    5150 
    52 double sas_JN( int n, double x ) { 
     51double sas_JN( int n, double x ) 
     52{ 
    5353 
    5454    const double MACHEP = 1.11022302462515654042E-16; 

  • sasmodels/models/lib/sph_j1c.c

    re6f1410 rba32cdd  
    77* using double precision that are the source. 
    88*/ 
     9double sph_j1c(double q); 
    910 
    1011// The choice of the number of terms in the series and the cutoff value for 
    … …  
    4344#endif 
    4445 
    45 double sph_j1c(double q); 
    4646double sph_j1c(double q) 
    4747{ 

  • sasmodels/models/lib/sphere_form.c

    rad90df9 rba32cdd  
    1 inline double 
    2 sphere_volume(double radius) 
     1double sphere_volume(double radius); 
     2double sphere_form(double q, double radius, double sld, double solvent_sld); 
     3 
     4double sphere_volume(double radius) 
    35{ 
    46    return M_4PI_3*cube(radius); 
    57} 
    68 
    7 inline double 
    8 sphere_form(double q, double radius, double sld, double solvent_sld) 
     9double sphere_form(double q, double radius, double sld, double solvent_sld) 
    910{ 
    1011    const double fq = sphere_volume(radius) * sph_j1c(q*radius); 

  • sasmodels/models/lib/wrc_cyl.c

    re7678b2 rba32cdd  
    22    Functions for WRC implementation of flexible cylinders 
    33*/ 
     4double Sk_WR(double q, double L, double b); 
     5 
     6 
    47static double 
    58AlphaSquare(double x) 
    … …  
    363366} 
    364367 
    365 double Sk_WR(double q, double L, double b); 
    366368double Sk_WR(double q, double L, double b) 
    367369{ 

  • sasmodels/models/rpa.py

    raad336c re9b1663d  
    8686#   ["name", "units", default, [lower, upper], "type","description"], 
    8787parameters = [ 
    88     ["case_num", CASES, 0, [0, 10], "", "Component organization"], 
     88    ["case_num", "", 1, CASES, "", "Component organization"], 
    8989 
    90     ["Na", "", 1000.0, [1, inf], "", "Degree of polymerization"], 
    91     ["Phia", "", 0.25, [0, 1], "", "volume fraction"], 
    92     ["va", "mL/mol", 100.0, [0, inf], "", "specific volume"], 
    93     ["La", "fm", 10.0, [-inf, inf], "", "scattering length"], 
    94     ["ba", "Ang", 5.0, [0, inf], "", "segment length"], 
    95  
    96     ["Nb", "", 1000.0, [1, inf], "", "Degree of polymerization"], 
    97     ["Phib", "", 0.25, [0, 1], "", "volume fraction"], 
    98     ["vb", "mL/mol", 100.0, [0, inf], "", "specific volume"], 
    99     ["Lb", "fm", 10.0, [-inf, inf], "", "scattering length"], 
    100     ["bb", "Ang", 5.0, [0, inf], "", "segment length"], 
    101  
    102     ["Nc", "", 1000.0, [1, inf], "", "Degree of polymerization"], 
    103     ["Phic", "", 0.25, [0, 1], "", "volume fraction"], 
    104     ["vc", "mL/mol", 100.0, [0, inf], "", "specific volume"], 
    105     ["Lc", "fm", 10.0, [-inf, inf], "", "scattering length"], 
    106     ["bc", "Ang", 5.0, [0, inf], "", "segment length"], 
    107  
    108     ["Nd", "", 1000.0, [1, inf], "", "Degree of polymerization"], 
    109     ["Phid", "", 0.25, [0, 1], "", "volume fraction"], 
    110     ["vd", "mL/mol", 100.0, [0, inf], "", "specific volume"], 
    111     ["Ld", "fm", 10.0, [-inf, inf], "", "scattering length"], 
    112     ["bd", "Ang", 5.0, [0, inf], "", "segment length"], 
     90    ["N[4]", "", 1000.0, [1, inf], "", "Degree of polymerization"], 
     91    ["Phi[4]", "", 0.25, [0, 1], "", "volume fraction"], 
     92    ["v[4]", "mL/mol", 100.0, [0, inf], "", "specific volume"], 
     93    ["L[4]", "fm", 10.0, [-inf, inf], "", "scattering length"], 
     94    ["b[4]", "Ang", 5.0, [0, inf], "", "segment length"], 
    11395 
    11496    ["Kab", "", -0.0004, [-inf, inf], "", "Interaction parameter"], 
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