Changeset ead4bd5 in sasmodels

Timestamp:

Mar 18, 2016 5:13:16 AM (9 years ago)

Author:

richardh

Branches:

master, core_shell_microgels, costrafo411, magnetic_model, release_v0.94, release_v0.95, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests

Children:

c079f50

Parents:

eec5fd6 (diff), 5bb9c79 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'master' of ​https://github.com/SasView/sasmodels

Files:

• doc/genmodel.py (modified) (2 diffs)
• example/sesansfit.py (modified) (1 diff)
• sasmodels/sasview_model.py (modified) (2 diffs)
• sasmodels/models/adsorbed_layer.py (modified) (6 diffs)

doc/genmodel.py

@@ -77 +77 @@
 
 
-# Generate image (comment IF for 1D/2D for the moment) and generate only 1D
+# Generate image 
 fig_height = 3.0 # in
 fig_left = 0.6 # in
@@ -109 +109 @@
     fig = plt.figure(figsize=aspect)
     ax1d = fig.add_axes([ax_left, ax_bottom, ax_width, ax_height])
-plot_1d(model, opts, ax1d)
+    plot_1d(model, opts, ax1d)
 
 # Save image in model/img

example/sesansfit.py

@@ -14 +14 @@
     return model
 
-def sesans_fit(file, model_name, initial_vals={}, custom_params={}, param_range=[], acceptance_angle=None):
+def sesans_fit(file, model, initial_vals={}, custom_params={}, param_range=[], acceptance_angle=None):
     """
 

sasmodels/sasview_model.py

@@ -17 +17 @@
 from copy import deepcopy
 import warnings
+import collections
 
 import numpy as np
@@ -57 +58 @@
         ## TODO: reorganize parameter handling
         self.details = dict()
-        self.params = dict()
+        self.params = collections.OrderedDict()
         self.dispersion = dict()
         partype = model.info['partype']
+
         for p in model.info['parameters']:
             self.params[p.name] = p.default

sasmodels/models/adsorbed_layer.py

@@ -6 +6 @@
 
 r"""
-This model describes the scattering from a layer of surfactant or polymer adsorbed on 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.
+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).
@@ -34 +34 @@
 
 description =  """
-    Evaluates the scattering from particles
+    Evaluates the scattering from large particles
     with an adsorbed layer of surfactant or
     polymer, independent of the form of the
@@ -42 +42 @@
 
 #             ["name", "units", default, [lower, upper], "type", "description"],
-parameters =  [["second_moment", "Ang", 23.0, [0.0, inf], "", "Second moment"],
-              ["adsorbed_amount", "mg/m2", 1.9, [0.0, inf], "", "Adsorbed amount"],
-              ["density_poly", "g/cm3", 0.7, [0.0, inf], "", "Polymer density"],
-              ["radius", "Ang", 500.0, [0.0, inf], "", "Particle radius"],
-              ["volfraction", "None", 0.14, [0.0, inf], "", "Particle vol fraction"],
-              ["polymer_sld", "1/Ang^2", 1.5e-06, [-inf, inf], "", "Polymer SLD"],
-              ["solvent_sld", "1/Ang^2", 6.3e-06, [-inf, inf], "", "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"]]
 
 # NB: Scale and Background are implicit parameters on every model
-def Iq(q, second_moment, adsorbed_amount, density_poly, radius, 
-        volfraction, polymer_sld, solvent_sld):
+def Iq(q, second_moment, adsorbed_amount, density_shell, radius, 
+        volfraction, sld_shell, sld_solvent):
     # pylint: disable = missing-docstring
-    deltarhosqrd =  (polymer_sld - solvent_sld) * (polymer_sld - solvent_sld)
-    numerator =  6.0 * pi * volfraction * (adsorbed_amount * adsorbed_amount)
-    denominator =  (q * q) * (density_poly * density_poly) * radius
-    eterm =  exp(-1.0 * (q * q) * (second_moment * second_moment))
-    #scale by 10^10 for units conversion to cm^-1
-    inten =  1.0e+10 * deltarhosqrd * ((numerator / denominator) * eterm)
+#    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
     return inten
 Iq.vectorized =  True  # Iq accepts an array of q values
@@ -71 +75 @@
             second_moment = 23.0,
             adsorbed_amount = 1.9,
-            density_poly = 0.7,
+            density_shell = 0.7,
             radius = 500.0,
             volfraction = 0.14,
-            polymer_sld = 1.5e-06,
-            solvent_sld = 6.3e-06,
+            sld_shell = 1.5,
+            sld_solvent = 6.3,
             background = 0.0)
 
@@ -82 +86 @@
                second_moment = 'second_moment',
                adsorbed_amount = 'ads_amount',
-               density_poly = 'density_poly',
+               density_shell = 'density_poly',
                radius = 'radius_core',
                volfraction = 'volf_cores',
-               polymer_sld = 'sld_poly',
-               solvent_sld = 'sld_solv',
+               sld_shell = 'sld_poly',
+               sld_solvent = 'sld_solv',
                background = 'background')
 
@@ -92 +96 @@
 tests =  [
     [{'scale': 1.0, 'second_moment': 23.0, 'adsorbed_amount': 1.9, 
-     'density_poly': 0.7, 'radius': 500.0, 'volfraction': 0.14, 
-     'polymer_sld': 1.5e-06, 'solvent_sld': 6.3e-06, 'background': 0.0},
+     'density_shell': 0.7, 'radius': 500.0, 'volfraction': 0.14, 
+     'sld_shell': 1.5, 'sld_solvent': 6.3, 'background': 0.0},
      [0.0106939, 0.469418], [73.741, 9.65391e-53]],
     ]
+# ADDED by: SMK  ON: 16Mar2016  convert from sasview, check vs SANDRA, 18Mar2016 RKH some edits & renaming