-                      rec45c4f
+                      r62cf915
 #converted by Steve King, Mar 2016
+r"""
+This model describes the scattering from a layer of surfactant or polymer
+adsorbed on large, smooth, notionally spherical particles under the conditions
+that (i) the particles (cores) are contrast-matched to the dispersion medium,
+(ii) $S(Q) \sim 1$ (ie, the particle volume fraction is dilute), (iii) the
+particle radius is >> layer thickness (ie, the interface is locally flat),
+and (iv) scattering from excess unadsorbed adsorbate in the bulk medium is
+absent or has been corrected for.
+r"""
+This model describes the scattering from a layer of surfactant or polymer adsorbed on large, smooth, notionally spherical particles under the conditions that (i) the particles (cores) are contrast-matched to the dispersion medium, (ii) *S(Q)* ~ 1 (ie, the particle volume fraction is dilute), (iii) the particle radius is >> layer thickness (ie, the interface is locally flat), and (iv) scattering from excess unadsorbed adsorbate in the bulk medium is absent or has been corrected for.
+Unlike many other core-shell models, this model does not assume any form for the density distribution of the adsorbed species normal to the interface (cf, a core-shell model normally assumes the density distribution to be a homogeneous step-function). For comparison, if the thickness of a (traditional core-shell like) step function distribution is *t*, the second moment about the mean of the density distribution (ie, the distance of the centre-of-mass of the distribution from the interface), |sigma| =  sqrt((*t* :sup:`2` )/12).
+Unlike many other core-shell models, this model does not assume any form
+for the density distribution of the adsorbed species normal to the interface
+(cf, a core-shell model normally assumes the density distribution to be a
+homogeneous step-function). For comparison, if the thickness of a (traditional
+core-shell like) step function distribution is $t$, the second moment about
+the mean of the density distribution (ie, the distance of the centre-of-mass
+of the distribution from the interface), $\sigma = \sqrt{t^2/12}$.
 Definition
 …
 .. math::
+     I(q) = \text{scale} \cdot(\rho_\text{poly}-\rho_\text{solvent})^2    \left[\frac{6\pi\phi_\text{core}}{Q^2}\frac{\Gamma^2}{\delta_\text{poly}^2R_\text{core}} \exp(-Q^2\sigma^2)\right] + \text{background}
+     I(q) = \text{scale} \cdot (\rho_\text{poly}-\rho_\text{solvent})^2
+         \left[
+             \frac{6\pi\phi_\text{core}}{Q^2}
+             \frac{\Gamma^2}{\delta_\text{poly}^2R_\text{core}}
+             \exp(-Q^2\sigma^2)
+         \right] + \text{background}
+where *scale* is a scale factor, |rho|\ :sub:`poly` is the sld of the polymer (or surfactant) layer, |rho|\ :sub:`solv` is the sld of the solvent/medium and cores, |phi|\ :sub:`core` is the volume fraction of the core particles, |delta|\ :sub:`poly` is the bulk density of the polymer, |biggamma| is the adsorbed amount, and |sigma| is the second moment of the thickness distribution.
+where *scale* is a scale factor, $\rho_\text{poly}$ is the sld of the
+polymer (or surfactant) layer, $\rho_\text{solv}$ is the sld of the
+solvent/medium and cores, $\phi_\text{core}$ is the volume fraction of
+the core particles, $\delta_\text{poly}$ is the bulk density of the
+polymer, $\Gamma$ is the adsorbed amount, and $\sigma$ is the second
+moment of the thickness distribution.
+Note that all parameters except the |sigma| are correlated so fitting more than one of these parameters will generally fail. Also note that unlike other shape models, no volume normalization is applied to this model (the calculation is exact).
+Note that all parameters except $\sigma$ are correlated so fitting more
+than one of these parameters will generally fail. Also note that unlike
+other shape models, no volume normalization is applied to this model (the
+calculation is exact).
 References
 ----------
 S King, P Griffiths, J Hone, and T Cosgrove, *SANS from Adsorbed Polymer Layers*,
 *Macromol. Symp.*, 190 (2002) 33-42.
+S King, P Griffiths, J Hone, and T Cosgrove,
+*SANS from Adsorbed Polymer Layers*, *Macromol. Symp.*, 190 (2002) 33-42.
 """
 from numpy import inf, sqrt, pi, exp
 name =  "adsorbed_layer"
 title =  "Scattering from an adsorbed layer on particles"
+name = "adsorbed_layer"
+title = "Scattering from an adsorbed layer on particles"
 description =  """
+description = """
     Evaluates the scattering from large particles
     with an adsorbed layer of surfactant or
 …
     density distribution.
     """
 category =  "shape:sphere"
+category = "shape:sphere"
+# pylint: disable=bad-whitespace, line-too-long
 #             ["name", "units", default, [lower, upper], "type", "description"],
+parameters =  [["second_moment", "Ang", 23.0, [0.0, inf], "", "Second moment of polymer distribution"],
+              ["adsorbed_amount", "mg/m2", 1.9, [0.0, inf], "", "Adsorbed amount of polymer"],
+              ["density_shell", "g/cm3", 0.7, [0.0, inf], "", "Bulk density of polymer in the shell"],
+              ["radius", "Ang", 500.0, [0.0, inf], "", "Core particle radius"],
+              ["volfraction", "None", 0.14, [0.0, inf], "", "Core particle volume fraction"],
+              ["sld_shell", "1e-6/Ang^2", 1.5, [-inf, inf], "sld", "Polymer shell SLD"],
+              ["sld_solvent", "1e-6/Ang^2", 6.3, [-inf, inf], "sld", "Solvent SLD"]]
+parameters = [
+    ["second_moment", "Ang", 23.0, [0.0, inf], "", "Second moment of polymer distribution"],
+    ["adsorbed_amount", "mg/m2", 1.9, [0.0, inf], "", "Adsorbed amount of polymer"],
+    ["density_shell", "g/cm3", 0.7, [0.0, inf], "", "Bulk density of polymer in the shell"],
+    ["radius", "Ang", 500.0, [0.0, inf], "", "Core particle radius"],
+    ["volfraction", "None", 0.14, [0.0, inf], "", "Core particle volume fraction"],
+    ["sld_shell", "1e-6/Ang^2", 1.5, [-inf, inf], "sld", "Polymer shell SLD"],
+    ["sld_solvent", "1e-6/Ang^2", 6.3, [-inf, inf], "sld", "Solvent SLD"],
+]
+# pylint: disable=bad-whitespace, line-too-long
 # NB: Scale and Background are implicit parameters on every model
 def Iq(q, second_moment, adsorbed_amount, density_shell, radius,
         volfraction, sld_shell, sld_solvent):
+def Iq(q, second_moment, adsorbed_amount, density_shell, radius,
+       volfraction, sld_shell, sld_solvent):
     # pylint: disable = missing-docstring
 #    deltarhosqrd =  (sld_shell - sld_solvent) * (sld_shell - sld_solvent)
 #    numerator =  6.0 * pi * volfraction * (adsorbed_amount * adsorbed_amount)
 #    denominator =  (q * q) * (density_shell * density_shell) * radius
 #    eterm =  exp(-1.0 * (q * q) * (second_moment * second_moment))
 #    #scale by 10^-2 for units conversion to cm^-1
 #    inten =  1.0e-02 * deltarhosqrd * ((numerator / denominator) * eterm)
     aa =  (sld_shell - sld_solvent) * adsorbed_amount / q / density_shell
+    #deltarhosqrd =  (sld_shell - sld_solvent) * (sld_shell - sld_solvent)
+    #numerator =  6.0 * pi * volfraction * (adsorbed_amount * adsorbed_amount)
+    #denominator =  (q * q) * (density_shell * density_shell) * radius
+    #eterm =  exp(-1.0 * (q * q) * (second_moment * second_moment))
+    ##scale by 10^-2 for units conversion to cm^-1
+    #inten =  1.0e-02 * deltarhosqrd * ((numerator / denominator) * eterm)
+    aa = (sld_shell - sld_solvent) * adsorbed_amount / q / density_shell
     bb = q * second_moment
     #scale by 10^-2 for units conversion to cm^-1
     inten =  6.0e-02 * pi * volfraction * aa * aa * exp(-bb * bb) / radius
+    inten = 6.0e-02 * pi * volfraction * aa * aa * exp(-bb * bb) / radius
     return inten
 Iq.vectorized =  True  # Iq accepts an array of q values
 …
     # pylint: disable = missing-docstring
     return Iq(sqrt(qx ** 2 + qy ** 2), *args)
 Iqxy.vectorized =  True # Iqxy accepts an array of qx, qy values
+Iqxy.vectorized = True # Iqxy accepts an array of qx, qy values
+demo =  dict(scale = 1.0,
+            second_moment = 23.0,
+            adsorbed_amount = 1.9,
+            density_shell = 0.7,
+            radius = 500.0,
+            volfraction = 0.14,
+            sld_shell = 1.5,
+            sld_solvent = 6.3,
+            background = 0.0)
+# unit test values taken from SasView 3.1.2
+tests =  [
+    [{'scale': 1.0, 'second_moment': 23.0, 'adsorbed_amount': 1.9,
+      'density_shell': 0.7, 'radius': 500.0, 'volfraction': 0.14,
+      'sld_shell': 1.5, 'sld_solvent': 6.3, 'background': 0.0},
+     [0.0106939, 0.1], [73.741, 4.51684e-3]],
+]
+# these unit test values taken from SasView 3.1.2
+tests =  [
+    [{'scale': 1.0, 'second_moment': 23.0, 'adsorbed_amount': 1.9,
+     'density_shell': 0.7, 'radius': 500.0, 'volfraction': 0.14,
+     'sld_shell': 1.5, 'sld_solvent': 6.3, 'background': 0.0},
+     [0.0106939, 0.1], [73.741, 4.51684e-3]],
+    ]
+# ADDED by: SMK  ON: 16Mar2016  convert from sasview, check vs SANDRA, 18Mar2016 RKH some edits & renaming
+# 2016-03-16 SMK converted from sasview, checked vs SANDRA
+# 2016-03-18 RKH some edits & renaming
+# 2016-04-14 PAK reformatting

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Changeset 62cf915 in sasmodels

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sasmodels/models/adsorbed_layer.py

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