Changeset a1c91c2 in sasmodels

Timestamp:

Mar 16, 2016 5:40:30 PM (8 years ago)

Author:

smk78

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:

4c05f49

Parents:

bf227cd (diff), 310ddcb (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:

• convert.py (modified) (4 diffs)
• models/mono_gauss_coil.py (modified) (5 diffs)
• models/poly_gauss_coil.py (modified) (5 diffs)

sasmodels/convert.py

@@ -4 +4 @@
 import warnings
 
-STRUCTURE_FACTORS = [
-    'hardsphere',
-    'stickyhardsphere',
-    'squarewell',
-    'HayterMSAsq'
-]
 # List of models which SasView versions don't contain the explicit 'scale' argument.
 # When converting such a model, please update this list.
-MODELS_WITHOUT_SCALE = STRUCTURE_FACTORS + [
+MODELS_WITHOUT_SCALE = [
     'teubner_strey',
     'broad_peak',
@@ -27 +21 @@
 # List of models which SasView versions don't contain the explicit 'background' argument.
 # When converting such a model, please update this list.
-MODELS_WITHOUT_BACKGROUND = STRUCTURE_FACTORS + [
+MODELS_WITHOUT_BACKGROUND = [
     'guinier',
 ]
@@ -128 +122 @@
     # Note: update compare.constrain_pars to match
     name = model_info['id']
-    if name in MODELS_WITHOUT_SCALE:
+    if name in MODELS_WITHOUT_SCALE or model_info['structure_factor']:
         if oldpars.pop('scale', 1.0) != 1.0:
             warnings.warn("parameter scale not used in sasview %s"%name)
-    if name in MODELS_WITHOUT_BACKGROUND:
+    if name in MODELS_WITHOUT_BACKGROUND or model_info['structure_factor']:
         if oldpars.pop('background', 0.0) != 0.0:
             warnings.warn("parameter background not used in sasview %s"%name)
@@ -161 +155 @@
     name = model_info['id']
     # Note: update convert.revert_model to match
-    if name in MODELS_WITHOUT_SCALE:
+    if name in MODELS_WITHOUT_SCALE or model_info['structure_factor']:
         pars['scale'] = 1
-    if name in MODELS_WITHOUT_BACKGROUND:
+    if name in MODELS_WITHOUT_BACKGROUND or model_info['structure_factor']:
         pars['background'] = 0
     # sasview multiplies background by structure factor

sasmodels/models/mono_gauss_coil.py

@@ -8 +8 @@
 This model strictly describes the scattering from *monodisperse* polymer chains in theta solvents or polymer melts, conditions under which the distances between segments follow a Gaussian distribution. Provided the number of segments is large (ie, high molecular weight polymers) the single-chain form factor P(Q) is that described by Debye (1947).
 
-To describe the scattering from *polydisperse* polymer chains, see the poly_gauss_coil model.
+To describe the scattering from *polydisperse* polymer chains, see the To describe the scattering from *monodisperse* polymer chains, see the :ref:`poly_gauss_coil <poly-gauss-coil>` model.
 
 Definition
 ----------
 
-     *I(q)* = *scale* |cdot| *P(q)* + *background*
+     *I(q)* = *scale* |cdot| *I* \ :sub:`0` |cdot| *P(q)* + *background*
          
 where
 
-     *scale* = |phi|\ :sub:`poly` |cdot| *V* |cdot| (|rho|\ :sub:`poly` - |rho|\ :sub:`solv`)\  :sup:`2`
+     *I*\ :sub:`0` = |phi|\ :sub:`poly` |cdot| *V* |cdot| (|rho|\ :sub:`poly` - |rho|\ :sub:`solv`)\  :sup:`2`
 
      *P(q)* = 2 [exp(-Z) + Z - 1] / Z \ :sup:`2`
@@ -28 +28 @@
          
 Here, |phi|\ :sub:`poly` is the volume fraction of polymer, *V* is the volume of a polymer coil, *M* is the molecular weight of the polymer, *N*\ :sub:`A` is Avogadro's Number, |delta| is the bulk density of the polymer, |rho|\ :sub:`poly` is the sld of the polymer, |rho|\ :sub:`solv` is the sld of the solvent, and *R*\ :sub:`g` is the radius of gyration of the polymer coil.
-
-.. figure:: img/mono_gauss_coil_1d.jpg
-
-    1D plot using the default values.
 
 The 2D scattering intensity is calculated in the same way as the 1D, but where the *q* vector is redefined as
@@ -59 +55 @@
 
 #             ["name", "units", default, [lower, upper], "type", "description"],
-parameters =  [["radius_gyration", "Ang", 50.0, [0.0, inf], "", "Radius of gyration"]]
+parameters =  [["i_zero", "1/cm", 1.0, [-inf, inf], "", "Intensity at q=0"],
+               ["radius_gyration", "Ang", 50.0, [0.0, inf], "", "Radius of gyration"]]
 
 # NB: Scale and Background are implicit parameters on every model
@@ -68 +65 @@
        inten = 1.0
     else:
-       inten = 2.0 * (exp(-z) + z - 1.0 ) / (z * z)
+       inten = i_zero * 2.0 * (exp(-z) + z - 1.0 ) / (z * z)
     return inten
 Iq.vectorized =  True  # Iq accepts an array of q values
@@ -78 +75 @@
 
 demo =  dict(scale = 1.0,
+            i_zero = 1.0,
             radius_gyration = 50.0,
             background = 0.0)

sasmodels/models/poly_gauss_coil.py

@@ -5 +5 @@
 
  
-.._ poly_gauss_coil:
 r"""
 This empirical model describes the scattering from *polydisperse* polymer chains in theta solvents or polymer melts, assuming a Schulz-Zimm type molecular weight distribution.
 
-To describe the scattering from *monodisperse* polymer chains, see the mono_gauss_coil model.
+To describe the scattering from *monodisperse* polymer chains, see the :ref:`mono_gauss_coil <mono-gauss-coil>` model.
 
 Definition
 ----------
 
-     *I(q)* = *scale* |cdot| *P(q)* + *background*
+     *I(q)* = *scale* |cdot| *I* \ :sub:`0` |cdot| *P(q)* + *background*
          
 where
 
-     *scale* = |phi|\ :sub:`poly` |cdot| *V* |cdot| (|rho|\ :sub:`poly` - |rho|\ :sub:`solv`)\ :sup:`2`
+     *I*\ :sub:`0` = |phi|\ :sub:`poly` |cdot| *V* |cdot| (|rho|\ :sub:`poly` - |rho|\ :sub:`solv`)\ :sup:`2`
 
      *P(q)* = 2 [(1 + UZ)\ :sup:`-1/U` + Z - 1] / [(1 + U) Z\ :sup:`2`]
@@ -31 +30 @@
          
 Here, |phi|\ :sub:`poly`, is the volume fraction of polymer, *V* is the volume of a polymer coil, *M* is the molecular weight of the polymer, *N*\ :sub:`A` is Avogadro's Number, |delta| is the bulk density of the polymer, |rho|\ :sub:`poly` is the sld of the polymer, |rho|\ :sub:`solv` is the sld of the solvent, and *R*\ :sub:`g` is the radius of gyration of the polymer coil.
-
-.. figure:: img/poly_gauss_coil_1d.jpg
-
-    1D plot using the default values.
 
 The 2D scattering intensity is calculated in the same way as the 1D, but where the *q* vector is redefined as
@@ -65 +60 @@
 
 #             ["name", "units", default, [lower, upper], "type", "description"],
-parameters =  [["radius_gyration", "Ang", 50.0, [0.0, inf], "", "Radius of gyration"],
+parameters =  [["i_zero", "1/cm", 1.0, [-inf, inf], "", "Intensity at q=0"],
+               ["radius_gyration", "Ang", 50.0, [0.0, inf], "", "Radius of gyration"],
                ["polydispersity", "None", 2.0, [1.0, inf], "", "Polymer Mw/Mn"]]
 
@@ -77 +73 @@
         z = ((x * radius_gyration) * (x * radius_gyration)) / (1.0 + 2.0 * u)
         if x == 0:
-           inten = 1.0
+           inten = i_zero * 1.0
         else:
-           inten = 2.0 * (power((1.0 + u * z),minusoneonu) + z - 1.0 ) / ((1.0 + u) * (z * z))
+           inten = i_zero * 2.0 * (power((1.0 + u * z),minusoneonu) + z - 1.0 ) / ((1.0 + u) * (z * z))
         return inten
 Iq.vectorized =  True  # Iq accepts an array of q values
@@ -89 +85 @@
 
 demo =  dict(scale = 1.0,
+            i_zero = 1.0,
             radius_gyration = 50.0,
             polydispersity = 2.0,