[301e096] | 1 | # Note: model title and parameter table are inserted automatically |
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[5f3c534] | 2 | r""" |
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| 3 | Calculates the interparticle structure factor for monodisperse |
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[529b8b4] | 4 | spherical particles interacting through hard sphere (excluded volume) |
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[5f3c534] | 5 | interactions. This $S(q)$ may also be a reasonable approximation for |
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| 6 | other particle shapes that freely rotate (but see the note below), |
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| 7 | and for moderately polydisperse systems. |
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| 8 | |
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| 9 | .. note:: |
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| 10 | |
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| 11 | This routine is intended for uncharged particles! For charged |
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| 12 | particles try using the :ref:`hayter-msa` $S(q)$ instead. |
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| 13 | |
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| 14 | .. note:: |
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| 15 | |
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| 16 | Earlier versions of SasView did not incorporate the so-called |
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| 17 | $\beta(q)$ ("beta") correction [1] for polydispersity and non-sphericity. |
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| 18 | This is only available in SasView versions 4.2.2 and higher. |
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[301e096] | 19 | |
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[d529d93] | 20 | radius_effective is the effective hard sphere radius. |
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| 21 | volfraction is the volume fraction occupied by the spheres. |
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| 22 | |
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[5f3c534] | 23 | In SasView the effective radius may be calculated from the parameters |
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[d529d93] | 24 | used in the form factor $P(q)$ that this $S(q)$ is combined with. |
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| 25 | |
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[40a87fa] | 26 | For numerical stability the computation uses a Taylor series expansion |
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[5f3c534] | 27 | at very small $qR$, but there may be a very minor glitch at the |
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| 28 | transition point in some circumstances. |
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[d529d93] | 29 | |
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[5f3c534] | 30 | This S(q) uses the Percus-Yevick closure relationship [2] where the |
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| 31 | interparticle potential $U(r)$ is |
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[301e096] | 32 | |
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[eb69cce] | 33 | .. math:: |
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[529b8b4] | 34 | |
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| 35 | U(r) = \begin{cases} |
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| 36 | \infty & r < 2R \\ |
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| 37 | 0 & r \geq 2R |
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| 38 | \end{cases} |
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[301e096] | 39 | |
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[5f3c534] | 40 | where $r$ is the distance from the center of a sphere of a radius $R$. |
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[301e096] | 41 | |
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| 42 | For a 2D plot, the wave transfer is defined as |
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| 43 | |
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| 44 | .. math:: |
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| 45 | |
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[529b8b4] | 46 | q = \sqrt{q_x^2 + q_y^2} |
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[301e096] | 47 | |
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| 48 | |
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[eb69cce] | 49 | References |
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| 50 | ---------- |
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[301e096] | 51 | |
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[5f3c534] | 52 | .. [#] M Kotlarchyk & S-H Chen, *J. Chem. Phys.*, 79 (1983) 2461-2469 |
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| 53 | |
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[0507e09] | 54 | .. [#] J K Percus, J Yevick, *J. Phys. Rev.*, 110, (1958) 1 |
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| 55 | |
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| 56 | Source |
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| 57 | ------ |
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| 58 | |
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| 59 | `hardsphere.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/hardsphere.py>`_ |
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| 60 | |
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| 61 | Authorship and Verification |
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| 62 | ---------------------------- |
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| 63 | |
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| 64 | * **Author:** |
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| 65 | * **Last Modified by:** |
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| 66 | * **Last Reviewed by:** |
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| 67 | * **Source added by :** Steve King **Date:** March 25, 2019 |
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[301e096] | 68 | """ |
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| 69 | |
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[2d81cfe] | 70 | import numpy as np |
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[3c56da87] | 71 | from numpy import inf |
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[301e096] | 72 | |
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[034e19a] | 73 | name = "hardsphere" |
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| 74 | title = "Hard sphere structure factor, with Percus-Yevick closure" |
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[301e096] | 75 | description = """\ |
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[3e428ec] | 76 | [Hard sphere structure factor, with Percus-Yevick closure] |
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[301e096] | 77 | Interparticle S(Q) for random, non-interacting spheres. |
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[5f3c534] | 78 | May be a reasonable approximation for other particle shapes |
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| 79 | that freely rotate, and for moderately polydisperse systems |
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| 80 | . The "beta(q)" correction is available in versions 4.2.2 |
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| 81 | and higher. |
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[d529d93] | 82 | radius_effective is the hard sphere radius |
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[3e428ec] | 83 | volfraction is the volume fraction occupied by the spheres. |
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[301e096] | 84 | """ |
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[a5d0d00] | 85 | category = "structure-factor" |
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[8e45182] | 86 | structure_factor = True |
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[7f1ee79] | 87 | single = False # TODO: check |
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[301e096] | 88 | |
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[3e428ec] | 89 | # ["name", "units", default, [lower, upper], "type","description"], |
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[71b751d] | 90 | parameters = [["radius_effective", "Ang", 50.0, [0, inf], "", |
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[3e428ec] | 91 | "effective radius of hard sphere"], |
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| 92 | ["volfraction", "", 0.2, [0, 0.74], "", |
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| 93 | "volume fraction of hard spheres"], |
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| 94 | ] |
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[301e096] | 95 | |
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[9eb3632] | 96 | Iq = r""" |
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[f0fb9fe] | 97 | double D,A,B,G,X,X2,X4,S,C,FF,HARDSPH; |
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[8f04da4] | 98 | // these are c compiler instructions, can also put normal code inside the "if else" structure |
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[934f906] | 99 | #if FLOAT_SIZE > 4 |
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[2d81cfe] | 100 | // double precision |
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| 101 | // orig had 0.2, don't call the variable cutoff as PAK already has one called that! |
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| 102 | // Must use UPPERCASE name please. |
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| 103 | // 0.05 better, 0.1 OK |
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[934f906] | 104 | #define CUTOFFHS 0.05 |
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| 105 | #else |
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| 106 | // 0.1 bad, 0.2 OK, 0.3 good, 0.4 better, 0.8 no good |
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[8f04da4] | 107 | #define CUTOFFHS 0.4 |
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[934f906] | 108 | #endif |
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[f0fb9fe] | 109 | |
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[d529d93] | 110 | if(fabs(radius_effective) < 1.E-12) { |
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[f0fb9fe] | 111 | HARDSPH=1.0; |
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[9eb3632] | 112 | //printf("HS1 %g: %g\n",q,HARDSPH); |
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[f0fb9fe] | 113 | return(HARDSPH); |
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| 114 | } |
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[2d81cfe] | 115 | // removing use of pow(xxx,2) and rearranging the calcs |
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| 116 | // of A, B & G cut ~40% off execution time ( 0.5 to 0.3 msec) |
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[97e6d3c] | 117 | X = 1.0/( 1.0 -volfraction); |
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| 118 | D= X*X; |
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| 119 | A= (1.+2.*volfraction)*D; |
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| 120 | A *=A; |
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[d529d93] | 121 | X=fabs(q*radius_effective*2.0); |
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[f0fb9fe] | 122 | |
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| 123 | if(X < 5.E-06) { |
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| 124 | HARDSPH=1./A; |
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[9eb3632] | 125 | //printf("HS2 %g: %g\n",q,HARDSPH); |
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[f0fb9fe] | 126 | return(HARDSPH); |
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| 127 | } |
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[97e6d3c] | 128 | X2 =X*X; |
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| 129 | B = (1.0 +0.5*volfraction)*D; |
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| 130 | B *= B; |
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| 131 | B *= -6.*volfraction; |
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[f0fb9fe] | 132 | G=0.5*volfraction*A; |
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| 133 | |
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[934f906] | 134 | if(X < CUTOFFHS) { |
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| 135 | // RKH Feb 2016, use Taylor series expansion for small X |
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[2d81cfe] | 136 | // else no obvious way to rearrange the equations to avoid |
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| 137 | // needing a very high number of significant figures. |
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| 138 | // Series expansion found using Mathematica software. Numerical test |
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| 139 | // in .xls showed terms to X^2 are sufficient |
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[8f04da4] | 140 | // for 5 or 6 significant figures, but I put the X^4 one in anyway |
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[97e6d3c] | 141 | //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; |
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| 142 | // refactoring the polynomial makes it very slightly faster (0.5 not 0.6 msec) |
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| 143 | //FF = 8*A +6*B + 4*G + ( -0.8*A -2.0*B/3.0 -0.5*G +(A/35. +B/40. +G/50.)*X2)*X2; |
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| 144 | |
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| 145 | FF = 8.0*A +6.0*B + 4.0*G + ( -0.8*A -B/1.5 -0.5*G +(A/35. +0.0125*B +0.02*G)*X2)*X2; |
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| 146 | |
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[f0fb9fe] | 147 | // combining the terms makes things worse at smallest Q in single precision |
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| 148 | //FF = (8-0.8*X2)*A +(3.0-X2/3.)*2*B + (4+0.5*X2)*G +(A/35. +B/40. +G/50.)*X4; |
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| 149 | // note that G = -volfraction*A/2, combining this makes no further difference at smallest Q |
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[97e6d3c] | 150 | //FF = (8 +2.*volfraction + ( volfraction/4. -0.8 +(volfraction/100. -1./35.)*X2 )*X2 )*A + (3.0 -X2/3. +X4/40.)*2.*B; |
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[f0fb9fe] | 151 | HARDSPH= 1./(1. + volfraction*FF ); |
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[9eb3632] | 152 | //printf("HS3 %g: %g\n",q,HARDSPH); |
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[f0fb9fe] | 153 | return(HARDSPH); |
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| 154 | } |
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[97e6d3c] | 155 | X4=X2*X2; |
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[f0fb9fe] | 156 | SINCOS(X,S,C); |
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| 157 | |
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[2d81cfe] | 158 | // RKH Feb 2016, use version FISH code as is better than original sasview one |
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| 159 | // at small Q in single precision, and more than twice as fast in double. |
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[97e6d3c] | 160 | //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; |
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| 161 | // refactoring the polynomial here & above makes it slightly faster |
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| 162 | |
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| 163 | FF= (( G*( (4.*X2 -24.)*X*S -(X4 -12.*X2 +24.)*C +24. )/X2 + B*(2.*X*S -(X2-2.)*C -2.) )/X + A*(S-X*C))/X ; |
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[f0fb9fe] | 164 | HARDSPH= 1./(1. + 24.*volfraction*FF/X2 ); |
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| 165 | |
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[97e6d3c] | 166 | // changing /X and /X2 to *MX1 and *MX2, no significantg difference? |
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| 167 | //MX=1.0/X; |
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| 168 | //MX2=MX*MX; |
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| 169 | //FF= (( G*( (4.*X2 -24.)*X*S -(X4 -12.*X2 +24.)*C +24. )*MX2 + B*(2.*X*S -(X2-2.)*C -2.) )*MX + A*(S-X*C)) ; |
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| 170 | //HARDSPH= 1./(1. + 24.*volfraction*FF*MX2*MX ); |
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| 171 | |
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| 172 | // grouping the terms, was about same as sasmodels for single precision issues |
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[f0fb9fe] | 173 | // 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 ); |
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| 174 | // HARDSPH= 1./(1. + 24.*volfraction*FF/X2 ); |
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| 175 | // remove 1/X2 from final line, take more powers of X inside the brackets, stil bad |
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| 176 | // 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; |
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| 177 | // HARDSPH= 1./(1. + 24.*volfraction*FF ); |
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[9eb3632] | 178 | //printf("HS4 %g: %g\n",q,HARDSPH); |
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[f0fb9fe] | 179 | return(HARDSPH); |
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[301e096] | 180 | """ |
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| 181 | |
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[8f04da4] | 182 | def random(): |
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[b297ba9] | 183 | """Return a random parameter set for the model.""" |
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[8f04da4] | 184 | pars = dict( |
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| 185 | scale=1, background=0, |
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| 186 | radius_effective=10**np.random.uniform(1, 4), |
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| 187 | volfraction=10**np.random.uniform(-2, 0), # high volume fraction |
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| 188 | ) |
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| 189 | return pars |
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| 190 | |
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[2d81cfe] | 191 | # Q=0.001 is in the Taylor series, low Q part, so add Q=0.1, |
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| 192 | # assuming double precision sasview is correct |
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[7f47777] | 193 | tests = [ |
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[2d81cfe] | 194 | [{'scale': 1.0, 'background' : 0.0, 'radius_effective' : 50.0, |
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| 195 | 'volfraction' : 0.2, 'radius_effective_pd' : 0}, |
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| 196 | [0.001, 0.1], [0.209128, 0.930587]], |
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| 197 | ] |
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| 198 | # ADDED by: RKH ON: 16Mar2016 using equations from FISH as better than |
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| 199 | # orig sasview, see notes above. Added Taylor expansions at small Q. |
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