Changeset e65a3e7 in sasmodels for sasmodels

Timestamp:

Mar 19, 2016 3:37:29 PM (8 years ago)

Author:

richardh

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:

aa24114

Parents:

81d3a0c

Message:

tidy docs and renam solvent_sld

Location:

sasmodels/models

Files:

• capped_cylinder.py (modified) (6 diffs)
• elliptical_cylinder.py (modified) (6 diffs)
• flexible_cylinder.py (modified) (9 diffs)

sasmodels/models/capped_cylinder.py

@@ -3 +3 @@
 Like :ref:`barbell`, this is a sphereocylinder with end caps that have a
 radius larger than that of the cylinder, but with the center of the end cap
-radius lying within the cylinder. This model simply becomes the a convex
+radius lying within the cylinder. This model simply becomes a convex
 lens when the length of the cylinder $L=0$. See the diagram for the details
 of the geometry and restrictions on parameter values.
@@ -95 +95 @@
     end cap radius lies within the cylinder.
     Note: As the length of cylinder -->0,
-    it becomes a ConvexLens.
+    it becomes a Convex Lens.
     It must be that radius <(=) cap_radius.
     [Parameters];
@@ -104 +104 @@
     cap_radius: radius of the semi-spherical cap,
     sld: SLD of the capped cylinder,
-    solvent_sld: SLD of the solvent.
+    sld_solvent: SLD of the solvent.
 """
 category = "shape:cylinder"
@@ -110 +110 @@
 #             ["name", "units", default, [lower, upper], "type", "description"],
 parameters = [["sld",         "1e-6/Ang^2", 4, [-inf, inf], "",       "Cylinder scattering length density"],
-              ["solvent_sld", "1e-6/Ang^2", 1, [-inf, inf], "",       "Solvent scattering length density"],
+              ["sld_solvent", "1e-6/Ang^2", 1, [-inf, inf], "",       "Solvent scattering length density"],
               ["radius",      "Ang",       20, [0, inf],    "volume", "Cylinder radius"],
 
@@ -132 +132 @@
 
 demo = dict(scale=1, background=0,
-            sld=6, solvent_sld=1,
+            sld=6, sld_solvent=1,
             radius=260, cap_radius=290, length=290,
             theta=30, phi=15,
@@ -142 +142 @@
 oldname = 'CappedCylinderModel'
 oldpars = dict(sld='sld_capcyl',
-               solvent_sld='sld_solv',
+               sld_solvent='sld_solv',
                length='len_cyl',
                radius='rad_cyl',

sasmodels/models/elliptical_cylinder.py

@@ -12 +12 @@
 .. figure:: img/elliptical_cylinder_geometry.png
 
-    *a* = *r_minor* and |nu|\ :sub:`n` = $r_ratio$ (i.e., $r_major / r_minor$).
+   Elliptical cylinder geometry $a$ = $r_{minor}$ and \nu = $r_{ratio}$ = $r_{major} / r_{minor}$
 
 The function calculated is
@@ -26 +26 @@
     F(\mathbf{q},\alpha,\psi)=2\frac{J_1(a)\sin(b)}{ab}
     \\
-    a = \mathbf{q}\sin(\alpha)\left[ r^2_{major}\sin^2(\psi)+r^2_{minor}\cos(\psi) \right]^{1/2}
+    where  a = \mathbf{q}\sin(\alpha)\left[ r^2_{major}\sin^2(\psi)+r^2_{minor}\cos(\psi) \right]^{1/2}
     \\
     b=\mathbf{q}\frac{L}{2}\cos(\alpha)
@@ -74 +74 @@
     The intensities averaged from 2D over different numbers of bins and angles.
 
-Reference
----------
+References
+----------
 
 L A Feigin and D I Svergun, *Structure Analysis by Small-Angle X-Ray and Neutron Scattering*, Plenum,
@@ -98 +98 @@
               ["length",      "Ang",        400.0, [1, inf],    "volume",      "Length of the cylinder"],
               ["sld",         "1e-6/Ang^2", 4.0,   [-inf, inf], "",            "Cylinder scattering length density"],
-              ["solvent_sld", "1e-6/Ang^2", 1.0,   [-inf, inf], "",            "Solvent scattering length density"],
+              ["sld_solvent", "1e-6/Ang^2", 1.0,   [-inf, inf], "",            "Solvent scattering length density"],
               ["theta",       "degrees",    90.0,  [-360, 360], "orientation", "In plane angle"],
               ["phi",         "degrees",    0,     [-360, 360], "orientation", "Out of plane angle"],
@@ -108 +108 @@
 
 demo = dict(scale=1, background=0, r_minor=100, r_ratio=1.5, length=400.0,
-            sld=4.0, solvent_sld=1.0, theta=10.0, phi=20, psi=30, theta_pd=10, phi_pd=2, psi_pd=3)
+            sld=4.0, sld_solvent=1.0, theta=10.0, phi=20, psi=30, theta_pd=10, phi_pd=2, psi_pd=3)
 
 oldname = 'EllipticalCylinderModel'
-oldpars = dict(theta='cyl_theta', phi='cyl_phi', psi='cyl_psi', sld='sldCyl', solvent_sld='sldSolv')
+oldpars = dict(theta='cyl_theta', phi='cyl_phi', psi='cyl_psi', sld='sldCyl', sld_solvent='sldSolv')
 
 def ER(r_minor, r_ratio, length):
@@ -132 +132 @@
            'sld': 4.0,
            'length':400.0,
-           'solvent_sld':1.0,
+           'sld_solvent':1.0,
            'background':0.0
           }, 0.001, 675.504402]]

sasmodels/models/flexible_cylinder.py

@@ -30 +30 @@
 The Kuhn length $(b = 2*l_p)$ is also used to describe the stiffness of a chain.
 
-The returned value is in units of $cm^-1$, on absolute scale.
+The returned value is in units of $cm^{-1}$, on absolute scale.
 
 In the parameters, the sldCyl and sldSolv represent the SLD of the chain/cylinder
@@ -65 +65 @@
 title = "Flexible cylinder where the form factor is normalized by the volume" \
         "of the cylinder."
-description = """Note : scale and contrast=sld-solvent_sld are both
+description = """Note : scale and contrast = (sld - sld_solvent) are both
                 multiplicative factors in the model and are perfectly
                 correlated. One or both of these parameters must be held fixed
@@ -72 +72 @@
 
 category = "shape:cylinder"
-single = False
+single = False  # double precision only!
 
 # pylint: disable=bad-whitespace, line-too-long
@@ -81 +81 @@
     ["radius",      "Ang",         20.0, [0, inf],    "volume", "Radius of the flexible cylinder"],
     ["sld",         "1e-6/Ang^2",   1.0, [-inf, inf], "",       "Cylinder scattering length density"],
-    ["solvent_sld", "1e-6/Ang^2",   6.3, [-inf, inf], "",       "Solvent scattering length density"],
+    ["sld_solvent", "1e-6/Ang^2",   6.3, [-inf, inf], "",       "Solvent scattering length density"],
     ]
 # pylint: enable=bad-whitespace, line-too-long
@@ -91 +91 @@
             radius=20.0,
             sld=1.0,
-            solvent_sld=6.3)
+            sld_solvent=6.3)
 
 oldname = 'FlexibleCylinderModel'
-oldpars = dict(sld='sldCyl', solvent_sld='sldSolv')
+oldpars = dict(sld='sldCyl', sld_solvent='sldSolv')
 
 
@@ -104 +104 @@
     #  'radius':       20.0,
     #  'sld':           1.0,
-    #  'solvent_sld':   6.3,
+    #  'sld_solvent':   6.3,
     #  'background':    0.0001,
     #  }, 0.001, 3509.2187],
@@ -113 +113 @@
       'radius':       20.0,
       'sld':           1.0,
-      'solvent_sld':   6.3,
+      'sld_solvent':   6.3,
       'background':    0.0001,
      }, 1.0, 0.000595345],
@@ -120 +120 @@
       'radius':        2.0,
       'sld':           6.0,
-      'solvent_sld':  12.3,
+      'sld_solvent':  12.3,
       'background':    0.001,
      }, 0.1, 1.55228],
@@ -127 +127 @@
       'radius':       50.0,
       'sld':           0.1,
-      'solvent_sld':   5.1,
+      'sld_solvent':   5.1,
       'background':    0.0,
      }, 1.0, 0.000938456]