Changeset 54954e1 in sasmodels

Timestamp:

Mar 17, 2016 9:58:53 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:

03e8a6e, 3a45c2c

Parents:

15bd6e7

Message:

renam volfrac in adsorbedlayer, sort some docs bugs

Location:

sasmodels/models

Files:

• adsorbed_layer.py (modified) (6 diffs)
• hayter_msa.py (modified) (5 diffs)
• stickyhardsphere.py (modified) (3 diffs)

sasmodels/models/adsorbed_layer.py

@@ -17 +17 @@
      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 paraticles, |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|\ :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.
 
 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).
@@ -46 +46 @@
               ["density_poly", "g/cm3", 0.7, [0.0, inf], "", "Polymer density"],
               ["radius", "Ang", 500.0, [0.0, inf], "", "Particle radius"],
-              ["vol_frac", "None", 0.14, [0.0, inf], "", "Particle vol fraction"],
+              ["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"]]
@@ -52 +52 @@
 # NB: Scale and Background are implicit parameters on every model
 def Iq(q, second_moment, adsorbed_amount, density_poly, radius, 
-        vol_frac, polymer_sld, solvent_sld):
+        volfraction, polymer_sld, solvent_sld):
     # pylint: disable = missing-docstring
     deltarhosqrd =  (polymer_sld - solvent_sld) * (polymer_sld - solvent_sld)
-    numerator =  6.0 * pi * vol_frac * (adsorbed_amount * adsorbed_amount)
+    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))
@@ -73 +73 @@
             density_poly = 0.7,
             radius = 500.0,
-            vol_frac = 0.14,
+            volfraction = 0.14,
             polymer_sld = 1.5e-06,
             solvent_sld = 6.3e-06,
@@ -84 +84 @@
                density_poly = 'density_poly',
                radius = 'radius_core',
-               vol_frac = 'volf_cores',
+               volfraction = 'volf_cores',
                polymer_sld = 'sld_poly',
                solvent_sld = 'sld_solv',
@@ -91 +91 @@
 tests =  [
     [{'scale': 1.0, 'second_moment': 23.0, 'adsorbed_amount': 1.9, 
-     'density_poly': 0.7, 'radius': 500.0, 'vol_frac': 0.14, 
+     'density_poly': 0.7, 'radius': 500.0, 'volfraction': 0.14, 
      'polymer_sld': 1.5e-06, 'solvent_sld': 6.3e-06, 'background': 0.0},
      [0.0106939, 0.469418], [73.741, 9.65391e-53]],

sasmodels/models/hayter_msa.py

@@ -51 +51 @@
 #  dp[2] = volfraction();
 #  dp[3] = temperature();
-#  dp[4] = saltconc();
+#  dp[4] = salt_concentration();
 #  dp[5] = dielectconst();
 
@@ -76 +76 @@
     ["volfraction",   "None",     0.0192, [0, 0.74],   "", "volume fraction of spheres"],
     ["temperature",   "K",  318.16,   [0, inf],    "", "temperature, in Kelvin, for Debye length calculation"],
-    ["saltconc",      "M",    0.0,    [-inf, inf], "", "conc of salt, moles/litre, 1:1 electolyte, for Debye length"],
+    ["salt_concentration",      "M",    0.0,    [-inf, inf], "", "conc of salt, moles/litre, 1:1 electolyte, for Debye length"],
     ["dielectconst",  "None",    71.08,   [-inf, inf], "", "dielectric constant (relative permittivity) of solvent, default water, for Debye length"]
     ]
@@ -96 +96 @@
 oldname = 'HayterMSAStructure'
 #oldpars = dict(effect_radius="radius_effective",effect_radius_pd="radius_effective_pd",effect_radius_pd_n="radius_effective_pd_n")
-oldpars = dict(radius_effective="effect_radius",radius_effective_pd="effect_radius_pd",radius_effective_pd_n="effect_radius_pd_n")
+oldpars = dict(radius_effective="effect_radius",radius_effective_pd="effect_radius_pd",radius_effective_pd_n="effect_radius_pd_n",salt_concentration="saltconc")
 #oldpars = dict( )
 # default parameter set,  use  compare.sh -midQ -linear
 # note the calculation varies in different limiting cases so a wide range of
 # parameters will be required for a thorough test!
-# odd that the default st has saltconc zero
+# odd that the default st has salt_concentration zero
 demo = dict(radius_effective=20.75,
             charge=19.0,
             volfraction=0.0192,
             temperature=318.16,
-            saltconc=0.05,
+            salt_concentration=0.05,
             dielectconst=71.08,
             radius_effective_pd=0.1,
@@ -120 +120 @@
       'volfraction': 0.0192,
       'temperature': 298.0,
-      'saltconc': 0,
+      'salt_concentration': 0,
       'dielectconst': 78.0,
       'radius_effective_pd': 0},
@@ -130 +130 @@
       'volfraction': 0.0192,
       'temperature': 298.0,
-      'saltconc': 0.05,
+      'salt_concentration': 0.05,
       'dielectconst': 78.0,
       'radius_effective_pd': 0.1,

sasmodels/models/stickyhardsphere.py

@@ -88 +88 @@
     #   [ "name", "units", default, [lower, upper], "type",
     #     "description" ],
-    ["effect_radius", "Ang", 50.0, [0, inf], "volume",
+    ["radius_effective", "Ang", 50.0, [0, inf], "volume",
      "effective radius of hard sphere"],
     ["volfraction", "", 0.2, [0, 0.74], "",
@@ -113 +113 @@
     eta = volfraction/onemineps/onemineps/onemineps;
 
-    sig = 2.0 * effect_radius;
+    sig = 2.0 * radius_effective;
     aa = sig/onemineps;
     etam1 = 1.0 - eta;
@@ -179 +179 @@
 
 oldname = 'StickyHSStructure'
-oldpars = dict()
-demo = dict(effect_radius=200, volfraction=0.2, perturb=0.05,
-            stickiness=0.2, effect_radius_pd=0.1, effect_radius_pd_n=40)
+oldpars = dict(radius_effective="effect_radius",radius_effective_pd="effect_radius_pd",radius_effective_pd_n="effect_radius_pd_n")
+demo = dict(radius_effective=200, volfraction=0.2, perturb=0.05,
+            stickiness=0.2, radius_effective_pd=0.1, radius_effective_pd_n=40)
 #
 tests = [
-        [ {'scale': 1.0, 'background' : 0.0, 'effect_radius' : 50.0, 'perturb' : 0.05, 'stickiness' : 0.2, 'volfraction' : 0.1,
-           'effect_radius_pd' : 0}, [0.001, 0.003], [1.09718, 1.087830]]
+        [ {'scale': 1.0, 'background' : 0.0, 'radius_effective' : 50.0, 'perturb' : 0.05, 'stickiness' : 0.2, 'volfraction' : 0.1,
+           'radius_effective_pd' : 0}, [0.001, 0.003], [1.09718, 1.087830]]
         ]