Changeset ba51e00 in sasmodels for sasmodels/models

Timestamp:

Sep 8, 2018 10:30:57 AM (6 years ago)

Author:

Torin Cooper-Bennun <torin.cooper-bennun@…>

Branches:

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

Children:

c44b611

Parents:

2773c66 (diff), fbaef04 (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 'beta_approx_new_R_eff' of ​https://github.com/SasView/sasmodels into beta_approx_new_R_eff

Location:

sasmodels/models

Files:

• core_multi_shell.c (modified) (1 diff)
• core_shell_cylinder.c (modified) (2 diffs)
• core_shell_parallelepiped.c (modified) (1 diff)
• elliptical_cylinder.c (modified) (3 diffs)
• hollow_rectangular_prism.c (modified) (1 diff)
• hollow_rectangular_prism.py (modified) (1 diff)
• ellipsoid.py (modified) (1 diff)
• spinodal.py (modified) (3 diffs)

sasmodels/models/core_multi_shell.c

@@ -32 +32 @@
 static double
 effective_radius(int mode, double core_radius, double fp_n, double thickness[])
+// this seems regardless to always give the result for outer radius for n=1 shells; why??
+// printf shows fp_n is always 1, not 0,1,2
 {
-    if (mode == 1) {
+//        printf("fp_n =%g \n",fp_n);
+        if (mode == 1) {
         double r = core_radius;
         int n = (int)(fp_n+0.5);
-        for (int i=0; i < n; i++) {
-            r += thickness[i];
+        if ( n > 0) {
+            for (int i=0; i < n; i++) {
+                r += thickness[i];
+            }
         }
         return r;

sasmodels/models/core_shell_cylinder.c

@@ -24 +24 @@
 {
     const double radius_outer = radius + thickness;
-    const double length_outer = length + thickness;
+    const double length_outer = length + 2.0*thickness;
     return sqrt(radius_outer*radius_outer + 0.25*length_outer*length_outer);
 }
@@ -30 +30 @@
 static double
 effective_radius(int mode, double radius, double thickness, double length)
+//effective_radius_type = ["equivalent sphere","outer radius","half outer length","half min outer dimension",
+//                         "half max outer dimension","half outer diagonal"]
 {
     if (mode == 1) {

sasmodels/models/core_shell_parallelepiped.c

@@ -45 +45 @@
 effective_radius(int mode, double length_a, double length_b, double length_c,
                  double thick_rim_a, double thick_rim_b, double thick_rim_c)
+//effective_radius_type = ["equivalent sphere","half outer length_a", "half outer length_b", "half outer length_c",
+//                         "equivalent circular cross-section","half outer ab diagonal","half outer diagonal"]
+// note the core box is A*B*C with slabs ta, tb & tc on each face but missing the corners, though that fact is ignored here
+// in the equvalent sphere option
 {
     if (mode == 1) {
         return radius_from_volume(length_a, length_b, length_c, thick_rim_a, thick_rim_b, thick_rim_c);
     } else if (mode == 2) {
-        return 0.5 * (length_a + thick_rim_a);
+        return 0.5 * length_a + thick_rim_a;
     } else if (mode == 3) {
-        return 0.5 * (length_b + thick_rim_b);
+        return 0.5 * length_b + thick_rim_b;
     } else if (mode == 4) {
-        return 0.5 * (length_c + thick_rim_c);
+        return 0.5 * length_c + thick_rim_c;
     } else if (mode == 5) {
         return radius_from_crosssection(length_a, length_b, thick_rim_a, thick_rim_b);
     } else if (mode == 6) {
-        return 0.5*sqrt(square(length_a+thick_rim_a) + square(length_b+thick_rim_b));
+        return 0.5*sqrt(square(length_a+ 2.0*thick_rim_a) + square(length_b+ 2.0*thick_rim_b));
     } else {
-        return 0.5*sqrt(square(length_a+thick_rim_a) + square(length_b+thick_rim_b) + square(length_c+thick_rim_c));
+        return 0.5*sqrt(square(length_a+ 2.0*thick_rim_a) + square(length_b+ 2.0*thick_rim_b) + square(length_c+ 2.0*thick_rim_c));
     }
 }

sasmodels/models/elliptical_cylinder.c

@@ -13 +13 @@
 
 static double
-radius_from_min_dimension(double radius_minor, double r_ratio, double length)
+radius_from_min_dimension(double radius_minor, double r_ratio, double hlength)
 {
     const double rad_min = (r_ratio > 1.0 ? radius_minor : r_ratio*radius_minor);
-    return (rad_min < length ? rad_min : length);
+    return (rad_min < hlength ? rad_min : hlength);
 }
 
 static double
-radius_from_max_dimension(double radius_minor, double r_ratio, double length)
+radius_from_max_dimension(double radius_minor, double r_ratio, double hlength)
 {
     const double rad_max = (r_ratio < 1.0 ? radius_minor : r_ratio*radius_minor);
-    return (rad_max > length ? rad_max : length);
+    return (rad_max > hlength ? rad_max : hlength);
 }
 
@@ -35 +35 @@
 static double
 effective_radius(int mode, double radius_minor, double r_ratio, double length)
+//effective_radius_type = ["equivalent sphere","average radius","min radius","max radius",
+//                         "equivalent circular cross-section","half length","half min dimension","half max dimension","half diagonal"]
 {
     if (mode == 1) {
@@ -49 +51 @@
         return 0.5*length;
     } else if (mode == 7) {
-        return radius_from_min_dimension(radius_minor,r_ratio,length);
+        return radius_from_min_dimension(radius_minor,r_ratio,0.5*length);
     } else if (mode == 8) {
-        return radius_from_max_dimension(radius_minor,r_ratio,length);
+        return radius_from_max_dimension(radius_minor,r_ratio,0.5*length);
     } else {
         return radius_from_diagonal(radius_minor,r_ratio,length);

sasmodels/models/hollow_rectangular_prism.c

@@ -15 +15 @@
 static double
 effective_radius(int mode, double length_a, double b2a_ratio, double c2a_ratio, double thickness)
+//effective_radius_type = ["equivalent sphere","half length_a", "half length_b", "half length_c",
+//                         "equivalent outer circular cross-section","half ab diagonal","half diagonal"]
+// NOTE length_a is external dimension!
 {
     if (mode == 1) {

sasmodels/models/hollow_rectangular_prism.py

@@ -126 +126 @@
                "Solvent scattering length density"],
               ["length_a", "Ang", 35, [0, inf], "volume",
-               "Shorter side of the parallelepiped"],
+               "Shortest, external, size of the parallelepiped"],
               ["b2a_ratio", "Ang", 1, [0, inf], "volume",
                "Ratio sides b/a"],

sasmodels/models/ellipsoid.py

@@ -125 +125 @@
 import numpy as np
 from numpy import inf, sin, cos, pi
+
+try:
+    from numpy import cbrt
+except ImportError:
+    def cbrt(x): return x ** (1.0/3.0)
 
 name = "ellipsoid"

sasmodels/models/spinodal.py

@@ -3 +3 @@
 ----------
 
-This model calculates the SAS signal of a phase separating solution
-under spinodal decomposition. The scattering intensity $I(q)$ is calculated as
+This model calculates the SAS signal of a phase separating system 
+undergoing spinodal decomposition. The scattering intensity $I(q)$ is calculated 
+as 
 
 .. math::
     I(q) = I_{max}\frac{(1+\gamma/2)x^2}{\gamma/2+x^{2+\gamma}}+B
 
-where $x=q/q_0$ and $B$ is a flat background. The characteristic structure
-length scales with the correlation peak at $q_0$. The exponent $\gamma$ is
-equal to $d+1$ with d the dimensionality of the off-critical concentration
-mixtures. A transition to $\gamma=2d$ is seen near the percolation threshold
-into the critical concentration regime.
+where $x=q/q_0$, $q_0$ is the peak position, $I_{max}$ is the intensity 
+at $q_0$ (parameterised as the $scale$ parameter), and $B$ is a flat 
+background. The spinodal wavelength is given by $2\pi/q_0$. 
+
+The exponent $\gamma$ is equal to $d+1$ for off-critical concentration 
+mixtures (smooth interfaces) and $2d$ for critical concentration mixtures 
+(entangled interfaces), where $d$ is the dimensionality (ie, 1, 2, 3) of the 
+system. Thus 2 <= $\gamma$ <= 6. A transition from $\gamma=d+1$ to $\gamma=2d$ 
+is expected near the percolation threshold. 
+
+As this function tends to zero as $q$ tends to zero, in practice it may be 
+necessary to combine it with another function describing the low-angle 
+scattering, or to simply omit the low-angle scattering from the fit.
 
 References
@@ -22 +31 @@
 Physica A 123,497 (1984).
 
-Authorship and Verification
-----------------------------
+Revision History
+----------------
 
-* **Author:** Dirk Honecker **Date:** Oct 7, 2016
+* **Author:**  Dirk Honecker **Date:** Oct 7, 2016
+* **Revised:** Steve King    **Date:** Sep 7, 2018
 """
 
@@ -34 +44 @@
 title = "Spinodal decomposition model"
 description = """\
-      I(q) = scale ((1+gamma/2)x^2)/(gamma/2+x^(2+gamma))+background
+      I(q) = Imax ((1+gamma/2)x^2)/(gamma/2+x^(2+gamma)) + background
 
       List of default parameters:
-      scale = scaling
-      gamma = exponent
-      x = q/q_0
+      
+      Imax = correlation peak intensity at q_0
+      background = incoherent background
+      gamma = exponent (see model documentation)
       q_0 = correlation peak position [1/A]
-      background = Incoherent background"""
+      x = q/q_0"""
+      
 category = "shape-independent"