[d60b433] | 1 | # Note: model title and parameter table are inserted automatically |
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| 2 | r""" |
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[eb69cce] | 3 | This calculates the structure factor (the Fourier transform of the pair |
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| 4 | correlation function $g(r)$) for a system of charged, spheroidal objects |
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| 5 | in a dielectric medium. When combined with an appropriate form factor |
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| 6 | (such as sphere, core+shell, ellipsoid, etc), this allows for inclusion |
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| 7 | of the interparticle interference effects due to screened coulomb repulsion |
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| 8 | between charged particles. |
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[d60b433] | 9 | |
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[eb69cce] | 10 | **This routine only works for charged particles**. If the charge is set to |
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[d529d93] | 11 | zero the routine may self-destruct! For non-charged particles use a hard |
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[eb69cce] | 12 | sphere potential. |
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[d60b433] | 13 | |
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[eb69cce] | 14 | The salt concentration is used to compute the ionic strength of the solution |
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| 15 | which in turn is used to compute the Debye screening length. At present |
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| 16 | there is no provision for entering the ionic strength directly nor for use |
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[d529d93] | 17 | of any multivalent salts, though it should be possible to simulate the effect |
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[40a87fa] | 18 | of this by increasing the salt concentration. The counterions are also |
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| 19 | assumed to be monovalent. |
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[d529d93] | 20 | |
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| 21 | In sasview the effective radius may be calculated from the parameters |
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| 22 | used in the form factor $P(q)$ that this $S(q)$ is combined with. |
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| 23 | |
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[40a87fa] | 24 | The computation uses a Taylor series expansion at very small rescaled $qR$, to |
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| 25 | avoid some serious rounding error issues, this may result in a minor artefact |
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[d529d93] | 26 | in the transition region under some circumstances. |
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[d60b433] | 27 | |
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[eb69cce] | 28 | For 2D data, the scattering intensity is calculated in the same way as 1D, |
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| 29 | where the $q$ vector is defined as |
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[d60b433] | 30 | |
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| 31 | .. math:: |
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| 32 | |
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[eb69cce] | 33 | q = \sqrt{q_x^2 + q_y^2} |
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[d60b433] | 34 | |
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| 35 | |
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[eb69cce] | 36 | References |
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| 37 | ---------- |
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[d60b433] | 38 | |
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| 39 | J B Hayter and J Penfold, *Molecular Physics*, 42 (1981) 109-118 |
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| 40 | |
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| 41 | J P Hansen and J B Hayter, *Molecular Physics*, 46 (1982) 651-656 |
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| 42 | """ |
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[d529d93] | 43 | from numpy import inf |
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[d60b433] | 44 | |
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[d529d93] | 45 | category = "structure-factor" |
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| 46 | structure_factor = True |
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| 47 | single = False # double precision only! |
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| 48 | |
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| 49 | # dp[0] = 2.0*radius_effective(); |
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[d60b433] | 50 | # dp[1] = fabs(charge()); |
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| 51 | # dp[2] = volfraction(); |
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| 52 | # dp[3] = temperature(); |
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[a807206] | 53 | # dp[4] = concentration_salt(); |
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[d60b433] | 54 | # dp[5] = dielectconst(); |
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| 55 | |
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| 56 | |
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[d529d93] | 57 | |
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[d60b433] | 58 | |
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[348557a] | 59 | name = "hayter_msa" |
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[d529d93] | 60 | title = "Hayter-Penfold rescaled MSA, charged sphere, interparticle S(Q) structure factor" |
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[d60b433] | 61 | description = """\ |
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[d529d93] | 62 | [Hayter-Penfold RMSA charged sphere interparticle S(Q) structure factor] |
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[d60b433] | 63 | Interparticle structure factor S(Q)for a charged hard spheres. |
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[ec2ca99] | 64 | Routine takes absolute value of charge, use HardSphere if charge |
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| 65 | goes to zero. |
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[8f04da4] | 66 | In sasview the effective radius and volume fraction may be calculated |
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[d529d93] | 67 | from the parameters used in P(Q). |
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[d60b433] | 68 | """ |
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[d529d93] | 69 | |
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[ec2ca99] | 70 | |
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| 71 | # pylint: disable=bad-whitespace, line-too-long |
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[b7d432f] | 72 | # [ "name", "units", default, [lower, upper], "type", "description" ], |
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[ec2ca99] | 73 | parameters = [ |
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[d529d93] | 74 | ["radius_effective", "Ang", 20.75, [0, inf], "volume", "effective radius of charged sphere"], |
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| 75 | ["volfraction", "None", 0.0192, [0, 0.74], "", "volume fraction of spheres"], |
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[5702f52] | 76 | ["charge", "e", 19.0, [0, 200], "", "charge on sphere (in electrons)"], |
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[3ad7978] | 77 | ["temperature", "K", 318.16, [0, 450], "", "temperature, in Kelvin, for Debye length calculation"], |
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[5702f52] | 78 | ["concentration_salt", "M", 0.0, [0, inf], "", "conc of salt, moles/litre, 1:1 electolyte, for Debye length"], |
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[d529d93] | 79 | ["dielectconst", "None", 71.08, [-inf, inf], "", "dielectric constant (relative permittivity) of solvent, default water, for Debye length"] |
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[ec2ca99] | 80 | ] |
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| 81 | # pylint: enable=bad-whitespace, line-too-long |
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[d60b433] | 82 | |
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[0bef47b] | 83 | source = ["hayter_msa.c"] |
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[d60b433] | 84 | # No volume normalization despite having a volume parameter |
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| 85 | # This should perhaps be volume normalized? |
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| 86 | form_volume = """ |
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| 87 | return 1.0; |
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| 88 | """ |
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| 89 | # ER defaults to 0.0 |
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| 90 | # VR defaults to 1.0 |
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| 91 | |
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[8f04da4] | 92 | def random(): |
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| 93 | import numpy as np |
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| 94 | # TODO: too many failures for random hayter_msa parameters |
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| 95 | pars = dict( |
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| 96 | scale=1, background=0, |
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| 97 | radius_effective=10**np.random.uniform(1, 4.7), |
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| 98 | volfraction=10**np.random.uniform(-2, 0), # high volume fraction |
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| 99 | charge=min(int(10**np.random.uniform(0, 1.3)+0.5), 200), |
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| 100 | temperature=10**np.random.uniform(0, np.log10(450)), # max T = 450 |
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| 101 | #concentration_salt=10**np.random.uniform(-3, 1), |
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| 102 | dialectconst=10**np.random.uniform(0, 6), |
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| 103 | #charge=10, |
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| 104 | #temperature=318.16, |
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| 105 | concentration_salt=0.0, |
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| 106 | #dielectconst=71.08, |
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| 107 | ) |
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| 108 | return pars |
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| 109 | |
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[ab87a12] | 110 | # default parameter set, use compare.sh -midQ -linear |
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[ec2ca99] | 111 | # note the calculation varies in different limiting cases so a wide range of |
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| 112 | # parameters will be required for a thorough test! |
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[a807206] | 113 | # odd that the default st has concentration_salt zero |
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[d529d93] | 114 | demo = dict(radius_effective=20.75, |
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[ec2ca99] | 115 | charge=19.0, |
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| 116 | volfraction=0.0192, |
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| 117 | temperature=318.16, |
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[a807206] | 118 | concentration_salt=0.05, |
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[ec2ca99] | 119 | dielectconst=71.08, |
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[d529d93] | 120 | radius_effective_pd=0.1, |
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| 121 | radius_effective_pd_n=40) |
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[7f47777] | 122 | # |
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[40a87fa] | 123 | # attempt to use same values as old sasview unit test at Q=.001 was 0.0712928, |
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| 124 | # then add lots new ones assuming values from new model are OK, need some |
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| 125 | # low Q values to test the small Q Taylor expansion |
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[7f47777] | 126 | tests = [ |
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[ec2ca99] | 127 | [{'scale': 1.0, |
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| 128 | 'background': 0.0, |
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[d529d93] | 129 | 'radius_effective': 20.75, |
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[ec2ca99] | 130 | 'charge': 19.0, |
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| 131 | 'volfraction': 0.0192, |
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| 132 | 'temperature': 298.0, |
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[a807206] | 133 | 'concentration_salt': 0, |
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[ec2ca99] | 134 | 'dielectconst': 78.0, |
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[d529d93] | 135 | 'radius_effective_pd': 0}, |
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[40a87fa] | 136 | [0.00001, 0.0010, 0.01, 0.075], [0.0711646, 0.0712928, 0.0847006, 1.07150]], |
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[348557a] | 137 | [{'scale': 1.0, |
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| 138 | 'background': 0.0, |
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[d529d93] | 139 | 'radius_effective': 20.75, |
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[348557a] | 140 | 'charge': 19.0, |
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| 141 | 'volfraction': 0.0192, |
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| 142 | 'temperature': 298.0, |
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[a807206] | 143 | 'concentration_salt': 0.05, |
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[348557a] | 144 | 'dielectconst': 78.0, |
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[d529d93] | 145 | 'radius_effective_pd': 0.1, |
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| 146 | 'radius_effective_pd_n': 40}, |
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[40a87fa] | 147 | [0.00001, 0.0010, 0.01, 0.075], [0.450272, 0.450420, 0.465116, 1.039625]] |
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[ec2ca99] | 148 | ] |
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[d529d93] | 149 | # ADDED by: RKH ON: 16Mar2016 converted from sasview, new Taylor expansion at smallest rescaled Q |
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