Changeset 5a22548 in sasmodels

Timestamp:

Oct 10, 2016 11:13:49 AM (8 years ago)

Author:

richardh

Branches:

master, core_shell_microgels, costrafo411, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests

Children:

20a70bc

Parents:

e77872e (diff), 2f2c70c (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

Location:

sasmodels

Files:

• sasview_model.py (modified) (5 diffs)
• models/multilayer_vesicle.py (modified) (4 diffs)
• models/vesicle.py (modified) (1 diff)

sasmodels/sasview_model.py

@@ -127 +127 @@
         model = _make_model_from_info(model_info)
 
-    # If we are trying to load a model that already exists,
-    # append a version number to its name.
-    # Note that models appear to be periodically reloaded 
-    # by SasView and keeping track of whether we are reloading 
-    # a model or loading it for the first time is tricky.
-    # For now, just allow one custom model of a given name.
-    if model.name in MODELS:
-        model.name = "%s_v2" % model.name
+    # If a model name already exists and we are loading a different model,
+    # use the model file name as the model name.
+    if model.name in MODELS and not model.filename == MODELS[model.name].filename:
+        _previous_name = model.name
+        model.name = model.id
+        
+        # If the new model name is still in the model list (for instance,
+        # if we put a cylinder.py in our plug-in directory), then append
+        # an identifier.
+        if model.name in MODELS and not model.filename == MODELS[model.name].filename:
+            model.name = model.id + '_user'
+        logging.info("Model %s already exists: using %s [%s]", _previous_name, model.name, model.filename)
 
     MODELS[model.name] = model
@@ -163 +167 @@
     attrs = _generate_model_attributes(model_info)
     attrs['__init__'] = __init__
+    attrs['filename'] = model_info.filename
     ConstructedModel = type(model_info.name, (SasviewModel,), attrs) # type: SasviewModelType
     return ConstructedModel
@@ -320 +325 @@
         else:
             hidden = set()
+        if self._model_info.structure_factor:
+            hidden.add('scale')
+            hidden.add('background')
+            self._model_info.parameters.defaults['background'] = 0.
 
         self._persistency_dict = {}
@@ -668 +677 @@
                 return [self.multiplicity], [1.0]
             else:
-                return [np.NaN], [1.0]
+                # For hidden parameters use the default value.
+                value = self._model_info.parameters.defaults.get(par.name, np.NaN)
+                return [value], [1.0]
         elif par.polydisperse:
             dis = self.dispersion[par.name]
@@ -689 +700 @@
     cylinder = Cylinder()
     return cylinder.evalDistribution([0.1, 0.1])
+
+def test_structure_factor():
+    # type: () -> float
+    """
+    Test that a sasview model (cylinder) can be run.
+    """
+    Model = _make_standard_model('hardsphere')
+    model = Model()
+    value = model.evalDistribution([0.1, 0.1])
+    if np.isnan(value):
+        raise ValueError("hardsphere returns null")
 
 def test_rpa():

sasmodels/models/multilayer_vesicle.py

@@ -5 +5 @@
 This model is a trivial extension of the core_shell_sphere function to include
 *N* shells where the core is filled with solvent and the shells are interleaved
-with layers of solvent. For *N = 1*, this returns the same as the vesicle model.
-The shell thicknessess and SLD are constant across all shells as expected for
+with layers of solvent. For *N = 1*, this returns the same as the vesicle model,
+except for the normalisation, which here is to outermost volume.
+The shell thicknessess and SLD are constant for all shells as expected for
 a multilayer vesicle.
 
@@ -24 +25 @@
 .. note:
     The outer most radius
-    $radius + n_pairs * thicn_shell + (n_pairs - 1) * thick_solvent$
-    is used as the effective radius for *S(Q)* when $P(Q) * S(Q)$ is applied.
+    $radius + n_pairs * thick_shell + (n_pairs - 1) * thick_solvent$
+    is used for both the volume fraction normalization and for the 
+    effective radius for *S(Q)* when $P(Q) * S(Q)$ is applied.
 
 For information about polarised and magnetic scattering, see
@@ -62 +64 @@
     sld_solvent: solvent scattering length density
     sld: shell scattering length density
-    n_pairs:number of pairs of water/shell
+    n_pairs:number of "shell plus solvent" layer pairs
     background: incoherent background
         """
@@ -71 +73 @@
 parameters = [
     ["volfraction", "",  0.05, [0.0, 1],  "", "volume fraction of vesicles"],
-    ["radius", "Ang", 60.0, [0.0, inf],  "", "Core radius of the multishell"],
-    ["thick_shell", "Ang",        10.0, [0.0, inf],  "", "Shell thickness"],
-    ["thick_solvent", "Ang",        10.0, [0.0, inf],  "", "Water thickness"],
-    ["sld_solvent",    "1e-6/Ang^2",  6.4, [-inf, inf], "sld", "Core scattering length density"],
+    ["radius", "Ang", 60.0, [0.0, inf],  "", "radius of solvent filled core"],
+    ["thick_shell", "Ang",        10.0, [0.0, inf],  "", "thickness of one shell"],
+    ["thick_solvent", "Ang",        10.0, [0.0, inf],  "", "solvent thickness between shells"],
+    ["sld_solvent",    "1e-6/Ang^2",  6.4, [-inf, inf], "sld", "solvent scattering length density"],
     ["sld",   "1e-6/Ang^2",  0.4, [-inf, inf], "sld", "Shell scattering length density"],
-    ["n_pairs",     "",            2.0, [1.0, inf],  "", "Number of pairs of water and shell"],
+    ["n_pairs",     "",            2.0, [1.0, inf],  "", "Number of shell plus solvent layer pairs"],
     ]
 # pylint: enable=bad-whitespace, line-too-long

sasmodels/models/vesicle.py

@@ -75 +75 @@
         thickness: the shell thickness
         sld: the shell SLD
-        sld_slovent: the solvent (and core) SLD
+        sld_solvent: the solvent (and core) SLD
         background: incoherent background
         volfraction: shell volume fraction