[9cb1415] | 1 | # Note: model title and parameter table are inserted automatically |
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[3c56da87] | 2 | r""" |
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| 3 | This calculates the interparticle structure factor for a hard sphere fluid |
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| 4 | with a narrow attractive well. A perturbative solution of the Percus-Yevick |
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| 5 | closure is used. The strength of the attractive well is described in terms |
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[eb69cce] | 6 | of "stickiness" as defined below. |
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[3c56da87] | 7 | |
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[eb69cce] | 8 | The perturb (perturbation parameter), $\epsilon$, should be held between 0.01 |
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[3c56da87] | 9 | and 0.1. It is best to hold the perturbation parameter fixed and let |
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| 10 | the "stickiness" vary to adjust the interaction strength. The stickiness, |
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[eb69cce] | 11 | $\tau$, is defined in the equation below and is a function of both the |
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| 12 | perturbation parameter and the interaction strength. $\tau$ and $\epsilon$ |
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| 13 | are defined in terms of the hard sphere diameter $(\sigma = 2 R)$, the |
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| 14 | width of the square well, $\Delta$ (same units as $R$\ ), and the depth of |
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| 15 | the well, $U_o$, in units of $kT$. From the definition, it is clear that |
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| 16 | smaller $\tau$ means stronger attraction. |
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[9cb1415] | 17 | |
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[eb69cce] | 18 | .. math:: |
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| 19 | |
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| 20 | \tau &= \frac{1}{12\epsilon} \exp(u_o / kT) \\ |
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[d18f8a8] | 21 | \epsilon &= \Delta / (\sigma + \Delta) |
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[9cb1415] | 22 | |
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| 23 | where the interaction potential is |
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| 24 | |
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[eb69cce] | 25 | .. math:: |
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| 26 | |
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| 27 | U(r) = \begin{cases} |
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| 28 | \infty & r < \sigma \\ |
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| 29 | -U_o & \sigma \leq r \leq \sigma + \Delta \\ |
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| 30 | 0 & r > \sigma + \Delta |
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| 31 | \end{cases} |
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[9cb1415] | 32 | |
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[3c56da87] | 33 | The Percus-Yevick (PY) closure was used for this calculation, and is an |
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| 34 | adequate closure for an attractive interparticle potential. This solution |
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| 35 | has been compared to Monte Carlo simulations for a square well fluid, with |
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| 36 | good agreement. |
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| 37 | |
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[eb69cce] | 38 | The true particle volume fraction, $\phi$, is not equal to $h$, which appears |
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[3c56da87] | 39 | in most of the reference. The two are related in equation (24) of the |
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| 40 | reference. The reference also describes the relationship between this |
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| 41 | perturbation solution and the original sticky hard sphere (or adhesive |
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| 42 | sphere) model by Baxter. |
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| 43 | |
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[eb69cce] | 44 | **NB**: The calculation can go haywire for certain combinations of the input |
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[3c56da87] | 45 | parameters, producing unphysical solutions - in this case errors are |
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[eb69cce] | 46 | reported to the command window and the $S(q)$ is set to -1 (so it will |
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[3c56da87] | 47 | disappear on a log-log plot). Use tight bounds to keep the parameters to |
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| 48 | values that you know are physical (test them) and keep nudging them until |
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[7e224c2] | 49 | the optimization does not hit the constraints. |
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[9cb1415] | 50 | |
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[d529d93] | 51 | In sasview the effective radius may be calculated from the parameters |
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[eb69cce] | 52 | used in the form factor $P(q)$ that this $S(q)$ is combined with. |
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[9cb1415] | 53 | |
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[eb69cce] | 54 | For 2D data the scattering intensity is calculated in the same way |
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| 55 | as 1D, where the $q$ vector is defined as |
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[9cb1415] | 56 | |
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| 57 | .. math:: |
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| 58 | |
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[eb69cce] | 59 | q = \sqrt{q_x^2 + q_y^2} |
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[9cb1415] | 60 | |
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| 61 | |
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[eb69cce] | 62 | References |
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| 63 | ---------- |
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[9cb1415] | 64 | |
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[0507e09] | 65 | .. [#] S V G Menon, C Manohar, and K S Rao, *J. Chem. Phys.*, 95(12) (1991) 9186-9190 |
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| 66 | |
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| 67 | Source |
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| 68 | ------ |
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| 69 | |
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| 70 | `stickyhardsphere.py <https://github.com/SasView/sasmodels/blob/master/sasmodels/models/stickyhardsphere.py>`_ |
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| 71 | |
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| 72 | Authorship and Verification |
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| 73 | ---------------------------- |
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| 74 | |
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| 75 | * **Author:** |
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| 76 | * **Last Modified by:** |
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| 77 | * **Last Reviewed by:** |
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| 78 | * **Source added by :** Steve King **Date:** March 25, 2019 |
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[9cb1415] | 79 | """ |
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| 80 | |
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| 81 | # TODO: refactor so that we pull in the old sansmodels.c_extensions |
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[7e224c2] | 82 | |
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[2d81cfe] | 83 | import numpy as np |
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[7e224c2] | 84 | from numpy import inf |
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[9cb1415] | 85 | |
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| 86 | name = "stickyhardsphere" |
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| 87 | title = "Sticky hard sphere structure factor, with Percus-Yevick closure" |
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| 88 | description = """\ |
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[3e428ec] | 89 | [Sticky hard sphere structure factor, with Percus-Yevick closure] |
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[7e224c2] | 90 | Interparticle structure factor S(Q)for a hard sphere fluid with |
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[3e428ec] | 91 | a narrow attractive well. Fits are prone to deliver non-physical |
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| 92 | parameters, use with care and read the references in the full manual. |
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| 93 | In sasview the effective radius will be calculated from the |
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| 94 | parameters used in P(Q). |
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[9cb1415] | 95 | """ |
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[a5d0d00] | 96 | category = "structure-factor" |
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[8e45182] | 97 | structure_factor = True |
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[9cb1415] | 98 | |
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[13ed84c] | 99 | single = False |
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[3e428ec] | 100 | # ["name", "units", default, [lower, upper], "type","description"], |
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[9cb1415] | 101 | parameters = [ |
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[7e224c2] | 102 | # [ "name", "units", default, [lower, upper], "type", |
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| 103 | # "description" ], |
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[54954e1] | 104 | ["radius_effective", "Ang", 50.0, [0, inf], "volume", |
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[7e224c2] | 105 | "effective radius of hard sphere"], |
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| 106 | ["volfraction", "", 0.2, [0, 0.74], "", |
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| 107 | "volume fraction of hard spheres"], |
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| 108 | ["perturb", "", 0.05, [0.01, 0.1], "", |
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| 109 | "perturbation parameter, epsilon"], |
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| 110 | ["stickiness", "", 0.20, [-inf, inf], "", |
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| 111 | "stickiness, tau"], |
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[9cb1415] | 112 | ] |
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[7e224c2] | 113 | |
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[8f04da4] | 114 | def random(): |
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[b297ba9] | 115 | """Return a random parameter set for the model.""" |
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[8f04da4] | 116 | pars = dict( |
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| 117 | scale=1, background=0, |
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| 118 | radius_effective=10**np.random.uniform(1, 4.7), |
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| 119 | volfraction=np.random.uniform(0.00001, 0.74), |
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| 120 | perturb=10**np.random.uniform(-2, -1), |
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| 121 | stickiness=np.random.uniform(0, 1), |
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| 122 | ) |
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| 123 | return pars |
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| 124 | |
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[9cb1415] | 125 | # No volume normalization despite having a volume parameter |
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| 126 | # This should perhaps be volume normalized? |
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| 127 | form_volume = """ |
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| 128 | return 1.0; |
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| 129 | """ |
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| 130 | |
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| 131 | Iq = """ |
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[3c56da87] | 132 | double onemineps,eta; |
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| 133 | double sig,aa,etam1,etam1sq,qa,qb,qc,radic; |
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| 134 | double lam,lam2,test,mu,alpha,beta; |
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| 135 | double kk,k2,k3,ds,dc,aq1,aq2,aq3,aq,bq1,bq2,bq3,bq,sq; |
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| 136 | |
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| 137 | onemineps = 1.0-perturb; |
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| 138 | eta = volfraction/onemineps/onemineps/onemineps; |
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| 139 | |
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[54954e1] | 140 | sig = 2.0 * radius_effective; |
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[3c56da87] | 141 | aa = sig/onemineps; |
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| 142 | etam1 = 1.0 - eta; |
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| 143 | etam1sq=etam1*etam1; |
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| 144 | //C |
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| 145 | //C SOLVE QUADRATIC FOR LAMBDA |
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| 146 | //C |
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[034e19a] | 147 | qa = eta/6.0; |
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| 148 | qb = stickiness + eta/etam1; |
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[3c56da87] | 149 | qc = (1.0 + eta/2.0)/etam1sq; |
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[034e19a] | 150 | radic = qb*qb - 2.0*qa*qc; |
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[3c56da87] | 151 | if(radic<0) { |
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| 152 | //if(x>0.01 && x<0.015) |
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[3e428ec] | 153 | // Print "Lambda unphysical - both roots imaginary" |
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[3c56da87] | 154 | //endif |
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| 155 | return(-1.0); |
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| 156 | } |
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| 157 | //C KEEP THE SMALLER ROOT, THE LARGER ONE IS UNPHYSICAL |
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[034e19a] | 158 | radic = sqrt(radic); |
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| 159 | lam = (qb-radic)/qa; |
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| 160 | lam2 = (qb+radic)/qa; |
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[3c56da87] | 161 | if(lam2<lam) { |
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| 162 | lam = lam2; |
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| 163 | } |
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| 164 | test = 1.0 + 2.0*eta; |
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| 165 | mu = lam*eta*etam1; |
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| 166 | if(mu>test) { |
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| 167 | //if(x>0.01 && x<0.015) |
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| 168 | // Print "Lambda unphysical mu>test" |
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| 169 | //endif |
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| 170 | return(-1.0); |
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| 171 | } |
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| 172 | alpha = (1.0 + 2.0*eta - mu)/etam1sq; |
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| 173 | beta = (mu - 3.0*eta)/(2.0*etam1sq); |
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| 174 | //C |
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| 175 | //C CALCULATE THE STRUCTURE FACTOR |
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| 176 | //C |
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| 177 | kk = q*aa; |
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| 178 | k2 = kk*kk; |
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| 179 | k3 = kk*k2; |
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| 180 | SINCOS(kk,ds,dc); |
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| 181 | //ds = sin(kk); |
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| 182 | //dc = cos(kk); |
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| 183 | aq1 = ((ds - kk*dc)*alpha)/k3; |
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| 184 | aq2 = (beta*(1.0-dc))/k2; |
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| 185 | aq3 = (lam*ds)/(12.0*kk); |
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| 186 | aq = 1.0 + 12.0*eta*(aq1+aq2-aq3); |
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| 187 | // |
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| 188 | bq1 = alpha*(0.5/kk - ds/k2 + (1.0 - dc)/k3); |
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| 189 | bq2 = beta*(1.0/kk - ds/k2); |
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| 190 | bq3 = (lam/12.0)*((1.0 - dc)/kk); |
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| 191 | bq = 12.0*eta*(bq1+bq2-bq3); |
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| 192 | // |
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| 193 | sq = 1.0/(aq*aq +bq*bq); |
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| 194 | |
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| 195 | return(sq); |
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[9cb1415] | 196 | """ |
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[bfb195e] | 197 | |
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[54954e1] | 198 | demo = dict(radius_effective=200, volfraction=0.2, perturb=0.05, |
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| 199 | stickiness=0.2, radius_effective_pd=0.1, radius_effective_pd_n=40) |
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[7f47777] | 200 | # |
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| 201 | tests = [ |
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[40a87fa] | 202 | [{'scale': 1.0, 'background': 0.0, 'radius_effective': 50.0, |
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| 203 | 'perturb': 0.05, 'stickiness': 0.2, 'volfraction': 0.1, |
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| 204 | 'radius_effective_pd': 0}, |
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| 205 | [0.001, 0.003], [1.09718, 1.087830]], |
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| 206 | ] |
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