Changes in / [7d4428c:66d119f] in sasmodels


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15 deleted
7 edited

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  • .gitignore

    r4a82d4d r66ebdd6  
    11/build/ 
    22/dist/ 
    3 /logs/ 
    43/*.csv 
    54*.pyc 
    … …  
    1716/.project 
    1817/.pydevproject 
    19 /.idea 
    20 /sasmodels.egg-info/ 

  • doc/rst_prolog

    r0a4628d r19dcb933  
    6060.. |g/cm^3| replace:: g\ |cdot|\ cm\ :sup:`-3` 
    6161.. |fm^2| replace:: fm\ :sup:`2` 
    62 .. |Ang*cm^-1| replace:: |Ang|\ |cdot|\ cm\ :sup:`-1` 

  • multi_compare.sh

    r0a4628d r5753e4e  
    1 #!/bin/bash 
     1#!/bin/sh 
    22 
    33sasview=( ../sasview/build/lib.* ) 

  • sasmodels/convert.py

    r34d6cab r3964f92  
    1010    'broad_peak', 
    1111    'two_lorentzian', 
    12     "two_power_law", 
    1312    'gel_fit', 
    1413    'gauss_lorentz_gel', 
    … …  
    152151        pars['string_thickness_pd_n'] = 0 
    153152        pars['number_of_pearls_pd_n'] = 0 
    154     elif name == 'line': 
    155         pars['scale'] = 1 
    156         pars['background'] = 0 
    157153    elif name == 'rpa': 
    158154        pars['case_num'] = int(pars['case_num']) 

  • sasmodels/generate.py

    r0a4628d reafc9fa  
    233233    "degrees": "degree", 
    234234    "1/cm": "|cm^-1|", 
    235     "Ang/cm": "|Ang*cm^-1|", 
    236235    "": "None", 
    237236    } 

  • sasmodels/models/hardsphere.py

    r093f754 r13ed84c  
    3535from numpy import inf 
    3636 
    37 name = "hardsphere_fish" 
    38 title = "Hard sphere structure factor from FISH, with Percus-Yevick closure" 
     37name = "hardsphere" 
     38title = "Hard sphere structure factor, with Percus-Yevick closure" 
    3939description = """\ 
    4040    [Hard sphere structure factor, with Percus-Yevick closure] 
    … …  
    5555               "volume fraction of hard spheres"], 
    5656             ] 
     57single = False 
    5758 
    5859# No volume normalization despite having a volume parameter 
    … …  
    6364 
    6465Iq = """ 
    65       double D,A,B,G,X,X2,X4,S,C,FF,HARDSPH; 
     66    double denom,dnum,alpha,beta,gamm,a,asq,ath,afor,rca,rsa; 
     67    double calp,cbeta,cgam,prefac,c,vstruc; 
     68    double struc; 
    6669 
    67       if(fabs(effect_radius) < 1.E-12) { 
    68                HARDSPH=1.0; 
    69                return(HARDSPH); 
    70       } 
    71       D=pow((1.-volfraction),2); 
    72       A=pow((1.+2.*volfraction)/D, 2); 
    73       X=fabs(q*effect_radius*2.0); 
     70    //  compute constants 
     71    denom = pow((1.0-volfraction),4); 
     72    dnum = pow((1.0 + 2.0*volfraction),2); 
     73    alpha = dnum/denom; 
     74    beta = -6.0*volfraction*pow((1.0 + volfraction/2.0),2)/denom; 
     75    gamm = 0.50*volfraction*dnum/denom; 
     76    // 
     77    //  calculate the structure factor 
     78    // 
     79    a = 2.0*q*effect_radius; 
     80    asq = a*a; 
     81    ath = asq*a; 
     82    afor = ath*a; 
     83    SINCOS(a,rsa,rca); 
     84    //rca = cos(a); 
     85    //rsa = sin(a); 
     86    calp = alpha*(rsa/asq - rca/a); 
     87    cbeta = beta*(2.0*rsa/asq - (asq - 2.0)*rca/ath - 2.0/ath); 
     88    cgam = gamm*(-rca/a + (4.0/a)*((3.0*asq - 6.0)*rca/afor + (asq - 6.0)*rsa/ath + 6.0/afor)); 
     89    prefac = -24.0*volfraction/a; 
     90    c = prefac*(calp + cbeta + cgam); 
     91    vstruc = 1.0/(1.0-c); 
     92    struc = vstruc; 
    7493 
    75       if(X < 5.E-06) { 
    76                  HARDSPH=1./A; 
    77                  return(HARDSPH); 
    78       } 
    79       X2=pow(X,2); 
    80       X4=pow(X2,2); 
    81       B=-6.*volfraction* pow((1.+0.5*volfraction)/D ,2); 
    82       G=0.5*volfraction*A; 
    83  
    84       if(X < 0.2) { 
    85       // use Taylor series expansion for small X, IT IS VERY PICKY ABOUT THE X CUT OFF VALUE, ought to be lower in double.  
    86       // No obvious way to rearrange the equations to avoid needing a very high number of significant figures.  
    87       // Series expansion found using Mathematica software. Numerical test in .xls showed terms to X^2 are sufficient  
    88       // for 5 or 6 significant figures but I put the X^4 one in anyway  
    89             FF = 8*A +6*B + 4*G - (0.8*A +2.0*B/3.0 +0.5*G)*X2 +(A/35. +B/40. +G/50.)*X4; 
    90             // combining the terms makes things worse at smallest Q in single precision 
    91             //FF = (8-0.8*X2)*A +(3.0-X2/3.)*2*B + (4+0.5*X2)*G +(A/35. +B/40. +G/50.)*X4; 
    92             // note that G = -volfraction*A/2, combining this makes no further difference at smallest Q 
    93             //FF = (8 +2.*volfraction + ( volfraction/4. -0.8 +(volfraction/100. -1./35.)*X2 )*X2 )*A  + (3.0 -X2/3. +X4/40)*2*B; 
    94             HARDSPH= 1./(1. + volfraction*FF ); 
    95             return(HARDSPH); 
    96       } 
    97       SINCOS(X,S,C); 
    98  
    99 // RKH Feb 2016, use version from FISH code as it is better than original sasview one at small Q in single precision 
    100       FF=A*(S-X*C)/X + B*(2.*X*S -(X2-2.)*C -2.)/X2 + G*( (4.*X2*X -24.*X)*S -(X4 -12.*X2 +24.)*C +24. )/X4; 
    101       HARDSPH= 1./(1. + 24.*volfraction*FF/X2 ); 
    102  
    103 // rearrange the terms, is now about same as sasmodels 
    104 //     FF=A*(S/X-C) + B*(2.*S/X - C +2.0*(C-1.0)/X2) + G*( (4./X -24./X3)*S -(1.0 -12./X2 +24./X4)*C +24./X4 ); 
    105 //     HARDSPH= 1./(1. + 24.*volfraction*FF/X2 ); 
    106 // remove 1/X2 from final line, take more powers of X inside the brackets, stil bad 
    107 //      FF=A*(S/X3-C/X2) + B*(2.*S/X3 - C/X2 +2.0*(C-1.0)/X4) + G*( (4./X -24./X3)*S -(1.0 -12./X2 +24./X4)*C +24./X4 )/X2; 
    108 //      HARDSPH= 1./(1. + 24.*volfraction*FF ); 
    109       return(HARDSPH); 
     94    return(struc); 
    11095   """ 
    11196 
    … …  
    121106oldname = 'HardsphereStructure' 
    122107oldpars = dict() 
    123 # Q=0.001 is in the Taylor series, low Q part, so add Q=0.1, assuming double precision sasview is correct 
     108 
    124109tests = [ 
    125110        [ {'scale': 1.0, 'background' : 0.0, 'effect_radius' : 50.0, 'volfraction' : 0.2, 
    126            'effect_radius_pd' : 0}, [0.001,0.1], [0.209128,0.930587]] 
     111           'effect_radius_pd' : 0}, [0.001], [0.209128]] 
    127112        ] 
    128113 

  • setup.py

    r3eb3312 r040575f  
    1111    version = "1.0.0a", 
    1212    description = "sasmodels package", 
    13     long_description=open('README.md').read(), 
     13    long_description=open('README.rst').read(), 
    1414    author = "SasView Collaboration", 
    1515    author_email = "management@sasview.org", 
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