Changeset d999185 in sasmodels

Timestamp:

Mar 21, 2016 2:36:08 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:

3f167d9

Parents:

42f71da (diff), 616df8f (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

Location:

sasmodels/models

Files:

• core_shell_ellipsoid.py (modified) (1 diff)
• core_shell_ellipsoid_xt.py (modified) (1 diff)
• flexible_cylinder_elliptical.py (modified) (1 diff)
• img/pringle-vs-cylinder.png (added)
• micelle_spherical_core.py (modified) (5 diffs)
• onion.py (moved) (moved from sasmodels/models/_onion.py) (1 diff)
• pringle.py (modified) (1 diff)
• raspberry.c (modified) (1 diff)
• spherical_sld.py (added)

sasmodels/models/core_shell_ellipsoid.py

@@ -117 +117 @@
 source = ["lib/sph_j1c.c", "lib/gfn.c", "lib/gauss76.c", "core_shell_ellipsoid.c"]
 
+def ER(equat_shell, polar_shell):
+    """
+        Returns the effective radius used in the S*P calculation
+    """
+    import numpy as np
+    from .ellipsoid import ER as ellipsoid_ER
+    return ellipsoid_ER(rpolar, equat_shell)
+
+
 demo = dict(scale=1, background=0.001,
             equat_core=200.0,

sasmodels/models/core_shell_ellipsoid_xt.py

@@ -103 +103 @@
           "core_shell_ellipsoid_xt.c"]
 
+def ER(equat_core, x_core, t_shell, x_polar_shell):
+    """
+        Returns the effective radius used in the S*P calculation
+    """
+    import numpy as np
+    from .ellipsoid import ER as ellipsoid_ER
+    return ellipsoid_ER(equat_core*x_core + t_shell*x_polar_shell, equat_shell + t_shell)
+
+
 demo = dict(scale=0.05, background=0.001,
             equat_core=20.0,

sasmodels/models/flexible_cylinder_elliptical.py

@@ -85 +85 @@
 from numpy import inf
 
-name = "flexible_cylinder_ex"
+name = "flexible_cylinder_elliptical"
 title = "Flexible cylinder wth an elliptical cross section and a uniform " \
         "scattering length density."

sasmodels/models/micelle_spherical_core.py

@@ -2 +2 @@
 
 This model provides the form factor, $P(q)$, for a micelle with a spherical
-core and Gaussian polymer chains attached to the surface.
+core and Gaussian polymer chains attached to the surface, thus may be applied
+to block copolymer micelles. To work well the Gaussian chains must be much smaller
+than the core, which is often not the case.  Please study the reference carefully.
 
 Definition
@@ -16 +18 @@
 
 
-Reference
----------
+References
+----------
 
 J Pedersen, *J. Appl. Cryst.*, 33 (2000) 637-640
@@ -37 +39 @@
 parameters = [
     ["ndensity",      "1e15/cm^3",  8.94, [0.0, inf], "", "Number density of micelles"],
-    ["v_core",        "Ang^3",  62624.0,  [0.0, inf], "", "Core volume"],
+    ["v_core",        "Ang^3",  62624.0,  [0.0, inf], "", "Core volume "],
     ["v_corona",      "Ang^3",  61940.0,  [0.0, inf], "", "Corona volume"],
-    ["solvent_sld",   "1e-6/Ang^2", 6.4,  [0.0, inf], "", "Solvent scattering length density"],
-    ["core_sld",      "1e-6/Ang^2", 0.34, [0.0, inf], "", "Core scattering length density"],
-    ["corona_sld",    "1e-6/Ang^2", 0.8,  [0.0, inf], "", "Corona scattering length density"],
-    ["radius_core",   "Ang",       45.0,  [0.0, inf], "", "Radius of core"],
+    ["sld_solvent",   "1e-6/Ang^2", 6.4,  [0.0, inf], "", "Solvent scattering length density"],
+    ["sld_core",      "1e-6/Ang^2", 0.34, [0.0, inf], "", "Core scattering length density"],
+    ["sld_corona",    "1e-6/Ang^2", 0.8,  [0.0, inf], "", "Corona scattering length density"],
+    ["radius_core",   "Ang",       45.0,  [0.0, inf], "", "Radius of core ( must be >> radius_gyr )"],
     ["radius_gyr",    "Ang",       20.0,  [0.0, inf], "", "Radius of gyration of chains in corona"],
     ["d_penetration", "",           1.0,  [-inf, inf], "", "Factor to mimic non-penetration of Gaussian chains"],
@@ -55 +57 @@
             v_core=62624.0,
             v_corona=61940.0,
-            solvent_sld=6.4,
-            core_sld=0.34,
-            corona_sld=0.8,
+            sld_solvent=6.4,
+            sld_core=0.34,
+            sld_corona=0.8,
             radius_core=45.0,
             radius_gyr=20.0,
@@ -65 +67 @@
 
 oldname = 'MicelleSphCoreModel'
-oldpars = dict(solvent_sld='rho_solv',
-               core_sld='rho_core',
-               corona_sld='rho_corona')
+oldpars = dict(sld_solvent='rho_solv',
+               sld_core='rho_core',
+               sld_corona='rho_corona')
 
 tests = [
     [{}, 0.01, 15.3532],
     ]
+# RKH 20Mar2016 - need to check whether the core & corona volumes are per monomer ??? and how aggregation number works!

sasmodels/models/onion.py

@@ -310 +310 @@
               ]
 
-source = ["lib/sph_j1c.c", "onion.c"]
+#source = ["lib/sph_j1c.c", "onion.c"]
+
+def Iq(q, *args, **kw):
+    return q
+
+def Iqxy(qx, *args, **kw):
+    return qx
 
 

sasmodels/models/pringle.py

@@ -43 +43 @@
 ---------
 
-S Alexandru Rautu, Private Communication.
+Stefan Alexandru Rautu, Private Communication. 2012.
+As of 2016: stefanar@ncbs.res.in
 
 """

sasmodels/models/raspberry.c

@@ -27 +27 @@
 
 
-    double vfL, rL, sldL, vfS, rS, sldS, deltaS, delrhoL, delrhoS, sldSolv, aSs;
+    double vfL, rL, sldL, vfS, rS, sldS, deltaS, delrhoL, delrhoS, sldSolv;
     double VL, VS, Np, f2, fSs;
     double psiL,psiS;
-    double sfLS,sfSS,Np2,fSs2;
+    double sfLS,sfSS;
     double slT;