Changeset a6ebff8 in sasmodels

Timestamp:

Mar 21, 2016 3:06:36 AM (9 years ago)

Author:

awashington

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:

ca3abe6

Parents:

2684d45 (diff), 3703fde (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' into sesans_units

Files:

• sasmodels/models/img/spherical_sld_1d.jpg (added)
• sasmodels/models/img/spherical_sld_default_profile.jpg (added)
• sasmodels/models/img/spherical_sld_profile.gif (added)
• sasmodels/models/polymer_micelle.py (moved) (moved from sasmodels/models/micelle_spherical_core.py) (3 diffs)
• sasmodels/models/polymer_micelle_kernel.c (moved) (moved from sasmodels/models/micelle_spherical_core.c)
• example/sesans_parameters_css-hs.py (modified) (1 diff)
• sasmodels/models/core_shell_sphere.py (modified) (1 diff)
• sasmodels/sesans.py (modified) (4 diffs)

sasmodels/models/polymer_micelle.py

@@ -27 +27 @@
 from numpy import inf
 
-name = "micelle_spherical_core"
-title = "Micelle Spherical Core model"
+name = "polymer_micelle"
+title = "Polymer micelle model"
 description = """
-    This model provides the form factor, $P(q)$, for a micelle with
-    a spherical core and Gaussian polymer chains attached to the surface.
+    This model provides an approximate form factor, P(q), for a micelle with
+    a spherical core with Gaussian polymer chains attached to the surface.
     """
-category = "shape-independent"
+category = "shape:sphere"
 
 # pylint: disable=bad-whitespace, line-too-long
@@ -51 +51 @@
 # pylint: enable=bad-whitespace, line-too-long
 
-source = ["lib/sph_j1c.c", "micelle_spherical_core.c"]
+source = ["lib/sph_j1c.c", "polymer_micelle_kernel.c"]
 
 demo = dict(scale=1, background=0,
@@ -75 +75 @@
     ]
 # RKH 20Mar2016 - need to check whether the core & corona volumes are per monomer ??? and how aggregation number works!
+# renamed from micelle_spherical_core to polymer_micelle, moved from shape-independent to spheres section.
+# Ought to be able to add polydisp to core? And add ability to x by S(Q) ?

example/sesans_parameters_css-hs.py

@@ -22 +22 @@
 # Initial parameter values (if other than defaults)
 initial_vals = {
-    "sld_core" : 1.0592,
-    "sld_solvent" : 2.88,
-    "radius" : 890,
-    "thickness" : 130
+    "sld_core" : 1.83,
+    "sld_shell" : 1.83,
+    "sld_solvent" : 0,
+    "radius" : 730,
+    "thickness" : 20,
+    "volfraction" : phi,
+    "scale" : (1-phi)
 }
 

sasmodels/models/core_shell_sphere.py

@@ -91 +91 @@
         @param thickness: shell thickness
     """
+    return (1,1)
     whole = 4.0 * pi / 3.0 * pow((radius + thickness), 3)
     core = 4.0 * pi / 3.0 * radius * radius * radius

sasmodels/sesans.py

@@ -29 +29 @@
 
     q_min = dq = 0.1 * 2*pi / Rmax
-    return np.arange(q_min, Converter("1/A")(q_max[0], units=q_max[1]), dq)
+    return np.arange(q_min,
+                     Converter(q_max[1])(q_max[0],
+                                         units="1/A"),
+                     dq)
     
 def make_all_q(data):
@@ -75 +78 @@
 
 def call_hankel(data, q_calc, Iq_calc):
-    return hankel(data.x, data.lam * 1e-9,
-                  data.sample.thickness / 10,
+    return hankel((data.x, data.x_unit),
+                  (data.lam, data.lam_unit),
+                  (data.sample.thickness,
+                   data.sample.thickness_unit),
                   q_calc, Iq_calc)
   
@@ -182 +187 @@
     *I* [cm$^{-1}$] is the value of the SANS model at *q*
     """
+
+    from sas.sascalc.data_util.nxsunit import Converter
+    wavelength = Converter(wavelength[1])(wavelength[0],"A")
+    thickness = Converter(thickness[1])(thickness[0],"A")
+    Iq = Converter("1/cm")(Iq,"1/A") # All models default to inverse centimeters
+    SElength = Converter(SElength[1])(SElength[0],"A")
+
     G = np.zeros_like(SElength, 'd')
 #==============================================================================
@@ -192 +204 @@
 
     # [m^-1] step size in q, needed for integration
-    dq = (q[1]-q[0])*1e10
+    dq = (q[1]-q[0])
 
     # integration step, convert q into [m**-1] and 2 pi circle integration
-    G *= dq*1e10*2*pi
-    G0 *= dq*1e10*2*pi
+    G *= dq*2*pi
+    G0 = np.sum(Iq*q)*dq*2*np.pi
 
     P = exp(thickness*wavelength**2/(4*pi**2)*(G-G0))