Changes in sasmodels/models/elliptical_cylinder.py [fcb33e4:9802ab3] in sasmodels

File:

• sasmodels/models/elliptical_cylinder.py (modified) (5 diffs)

sasmodels/models/elliptical_cylinder.py

@@ -57 +57 @@
 define the axis of the cylinder using two angles $\theta$, $\phi$ and $\Psi$
 (see :ref:`cylinder orientation <cylinder-angle-definition>`). The angle
-$\Psi$ is the rotational angle around its own long_c axis against the $q$ plane.
-For example, $\Psi = 0$ when the $r_\text{minor}$ axis is parallel to the
-$x$ axis of the detector.
+$\Psi$ is the rotational angle around its own long_c axis. 
 
 All angle parameters are valid and given only for 2D calculation; ie, an
 oriented system.
 
-.. figure:: img/elliptical_cylinder_angle_definition.jpg
+.. figure:: img/elliptical_cylinder_angle_definition.png
 
-    Definition of angles for 2D
+    Definition of angles for oriented elliptical cylinder, where axis_ratio is drawn >1,
+    and angle $\Psi$ is now a rotation around the axis of the cylinder.
 
-.. figure:: img/cylinder_angle_projection.jpg
+.. figure:: img/elliptical_cylinder_angle_projection.png
 
     Examples of the angles for oriented elliptical cylinders against the
-    detector plane.
+    detector plane, with $\Psi$ = 0.
+
+The $\theta$ and $\phi$ parameters to orient the cylinder only appear in the model when fitting 2d data. 
+On introducing "Orientational Distribution" in the angles, "distribution of theta" and "distribution of phi" parameters will
+appear. These are actually rotations about the axes $\delta_1$ and $\delta_2$ of the cylinder, the $b$ and $a$ axes of the 
+cylinder cross section. (When $\theta = \phi = 0$ these are parallel to the $Y$ and $X$ axes of the instrument.) 
+The third orientation distribution, in $\psi$, is about the $c$ axis of the particle. Some experimentation may be required to 
+understand the 2d patterns fully. (Earlier implementations had numerical integration issues in some circumstances when orientation 
+distributions passed through 90 degrees, such situations, with very broad distributions, should still be approached with care.) 
 
 NB: The 2nd virial coefficient of the cylinder is calculated based on the
@@ -108 +115 @@
 """
 
-from numpy import pi, inf, sqrt
+from numpy import pi, inf, sqrt, sin, cos
 
 name = "elliptical_cylinder"
@@ -125 +132 @@
               ["sld",         "1e-6/Ang^2", 4.0,   [-inf, inf], "sld",         "Cylinder scattering length density"],
               ["sld_solvent", "1e-6/Ang^2", 1.0,   [-inf, inf], "sld",         "Solvent scattering length density"],
-              ["theta",       "degrees",    90.0,  [-360, 360], "orientation", "In plane angle"],
-              ["phi",         "degrees",    0,     [-360, 360], "orientation", "Out of plane angle"],
-              ["psi",         "degrees",    0,     [-360, 360], "orientation", "Major axis angle relative to Q"]]
+              ["theta",       "degrees",    90.0,  [-360, 360], "orientation", "cylinder axis to beam angle"],
+              ["phi",         "degrees",    0,     [-360, 360], "orientation", "rotation about beam"],
+              ["psi",         "degrees",    0,     [-360, 360], "orientation", "rotation about cylinder axis"]]
 
 # pylint: enable=bad-whitespace, line-too-long
@@ -149 +156 @@
                            + (length + radius) * (length + pi * radius))
     return 0.5 * (ddd) ** (1. / 3.)
+q = 0.1
+# april 6 2017, rkh added a 2d unit test, NOT READY YET pull #890 branch assume correct!
+qx = q*cos(pi/6.0)
+qy = q*sin(pi/6.0)
 
 tests = [
@@ -158 +169 @@
       'sld_solvent':1.0, 'background':0.0},
      0.001, 675.504402],
+#    [{'theta':80., 'phi':10.}, (qx, qy), 7.88866563001 ],
 ]