Changeset 885ee37 in sasmodels

Timestamp:

Apr 4, 2016 11:09:26 AM (9 years ago)

Author:

Paul Kienzle <pkienzle@…>

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:

5b0335b

Parents:

aaf75b6 (diff), 7a1143b (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 'polydisp' of github.com:sasview/sasmodels into polydisp

Conflicts:

sasmodels/direct_model.py

Location:

sasmodels

Files:

• direct_model.py (modified) (2 diffs)
• models/adsorbed_layer.py (modified) (1 diff)
• models/core_shell_ellipsoid.py (modified) (2 diffs)
• models/core_shell_ellipsoid_xt.py (modified) (1 diff)
• models/core_shell_sphere.py (modified) (1 diff)
• models/onion.py (modified) (2 diffs)
• models/sphere.py (modified) (1 diff)
• models/squarewell.py (modified) (1 diff)
• product.py (modified) (1 diff)
• resolution.py (modified) (5 diffs)

sasmodels/direct_model.py

@@ -25 +25 @@
 import numpy as np
 
+from .core import make_kernel
 from .core import call_kernel, call_ER_VR
 from . import sesans
@@ -170 +171 @@
     def _calc_theory(self, pars, cutoff=0.0):
         if self._kernel is None:
-            self._kernel = self._model.make_kernel(self._kernel_inputs)
-            self._kernel_mono = (self._model.make_kernel(self._kernel_mono_inputs)
+            self._kernel = make_kernel(self._model, self._kernel_inputs)  # pylint: disable=attribute-dedata_type
+            self._kernel_mono = (make_kernel(self._model, self._kernel_mono_inputs)
                                  if self._kernel_mono_inputs else None)
 

sasmodels/models/adsorbed_layer.py

@@ -98 +98 @@
      '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]],
+     [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

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):
+def ER(equat_core, polar_core, equat_shell, polar_shell):
     """
         Returns the effective radius used in the S*P calculation
@@ -123 +123 @@
     import numpy as np
     from .ellipsoid import ER as ellipsoid_ER
-    return ellipsoid_ER(rpolar, equat_shell)
+    return ellipsoid_ER(polar_shell, equat_shell)
 
 

sasmodels/models/core_shell_ellipsoid_xt.py

@@ -107 +107 @@
         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)
+    polar_outer = equat_core*x_core + t_shell*x_polar_shell
+    equat_outer = equat_core + t_shell
+    return ellipsoid_ER(polar_outer, equat_outer)
 
 

sasmodels/models/core_shell_sphere.py

@@ -99 +99 @@
 
 tests = [[{'radius': 20.0, 'thickness': 10.0}, 'ER', 30.0],
-         [{'radius': 20.0, 'thickness': 10.0}, 'VR', 0.703703704],
+         # TODO: VR test suppressed until we sort out new product model
+         # and determine what to do with volume ratio.
+         #[{'radius': 20.0, 'thickness': 10.0}, 'VR', 0.703703704],
 
          # The SasView test result was 0.00169, with a background of 0.001

sasmodels/models/onion.py

@@ -290 +290 @@
 category = "shape:sphere"
 
+# TODO: n is a volume parameter that is not polydisperse
 
 #             ["name", "units", default, [lower, upper], "type","description"],
@@ -364 +365 @@
 
 def ER(core_radius, n, thickness):
-    return np.sum(thickness[:n], axis=0) + core_radius
+    return np.sum(thickness[:n[0]], axis=0) + core_radius
 
 def VR(core_radius, n, thickness):
-    return 1.0
+    return 1.0, 1.0
 
 demo = {

sasmodels/models/sphere.py

@@ -86 +86 @@
 def ER(radius):
     """
-        Return equivalent radius (ER)
+    Return equivalent radius (ER)
     """
     return radius

sasmodels/models/squarewell.py

@@ -55 +55 @@
 category = "structure-factor"
 structure_factor = True
+single = False
 
 #single = False

sasmodels/product.py

@@ -20 +20 @@
 VOLFRACTION=3
 
+# TODO: core_shell_sphere model has suppressed the volume ratio calculation
+# revert it after making VR and ER available at run time as constraints.
 def make_product_info(p_info, s_info):
     """

sasmodels/resolution.py

@@ -805 +805 @@
         pars = {
             'scale':0.05,
-            'rpolar':500, 'requatorial':15000,
-            'sld':6, 'solvent_sld': 1,
+            'r_polar':500, 'r_equatorial':15000,
+            'sld':6, 'sld_solvent': 1,
             }
         form = load_model('ellipsoid', dtype='double')
@@ -837 +837 @@
 TEST_PARS_PINHOLE_SPHERE = {
     'scale': 1.0, 'background': 0.01,
-    'radius': 60.0, 'sld': 1, 'solvent_sld': 6.3,
+    'radius': 60.0, 'sld': 1, 'sld_solvent': 6.3,
     }
 # Q, dQ, I(Q) calculated by NIST Igor SANS package
@@ -946 +946 @@
 TEST_PARS_SLIT_SPHERE = {
     'scale': 0.01, 'background': 0.01,
-    'radius': 60000, 'sld': 1, 'solvent_sld': 4,
+    'radius': 60000, 'sld': 1, 'sld_solvent': 4,
     }
 # Q dQ I(Q) I_smeared(Q)
@@ -1047 +1047 @@
 
     if name == 'cylinder':
-        pars = {'length':210, 'radius':500}
+        pars = {'length':210, 'radius':500, 'background': 0}
     elif name == 'teubner_strey':
         pars = {'a2':0.003, 'c1':-1e4, 'c2':1e10, 'background':0.312643}
@@ -1054 +1054 @@
     elif name == 'ellipsoid':
         pars = {
-            'scale':0.05,
-            'rpolar':500, 'requatorial':15000,
-            'sld':6, 'solvent_sld': 1,
+            'scale':0.05, 'background': 0,
+            'r_polar':500, 'r_equatorial':15000,
+            'sld':6, 'sld_solvent': 1,
             }
     else: