Changeset 31fc4ad in sasmodels for doc/guide

Timestamp:

Oct 22, 2018 12:54:14 PM (6 years ago)

Author:

Paul Kienzle <pkienzle@…>

Branches:

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

Children:

07646b6

Parents:

be43e39

Message:

and notes about shell_volume and Fq to the user guide

File:

• doc/guide/plugin.rst (modified) (7 diffs)

doc/guide/plugin.rst

@@ -291 +291 @@
 
 **Note: The order of the parameters in the definition will be the order of the
-parameters in the user interface and the order of the parameters in Iq(),
-Iqac(), Iqabc() and form_volume(). And** *scale* **and** *background*
-**parameters are implicit to all models, so they do not need to be included
-in the parameter table.**
+parameters in the user interface and the order of the parameters in Fq(), Iq(),
+Iqac(), Iqabc(), form_volume() and shell_volume().
+And** *scale* **and** *background* **parameters are implicit to all models,
+so they do not need to be included in the parameter table.**
 
 - **"name"** is the name of the parameter shown on the FitPage.
@@ -363 +363 @@
     scattered intensity.
 
-  - "volume" parameters are passed to Iq(), Iqac(), Iqabc() and form_volume(),
-    and have polydispersity loops generated automatically.
+  - "volume" parameters are passed to Fq(), Iq(), Iqac(), Iqabc(), form_volume()
+    and shell_volume(), and have polydispersity loops generated automatically.
 
   - "orientation" parameters are not passed, but instead are combined with
@@ -428 +428 @@
         def random():
         ...
-        
-This function provides a model-specific random parameter set which shows model 
-features in the USANS to SANS range.  For example, core-shell sphere sets the 
-outer radius of the sphere logarithmically in `[20, 20,000]`, which sets the Q 
-value for the transition from flat to falling.  It then uses a beta distribution 
-to set the percentage of the shape which is shell, giving a preference for very 
-thin or very thick shells (but never 0% or 100%).  Using `-sets=10` in sascomp 
-should show a reasonable variety of curves over the default sascomp q range.  
-The parameter set is returned as a dictionary of `{parameter: value, ...}`.  
-Any model parameters not included in the dictionary will default according to 
+
+This function provides a model-specific random parameter set which shows model
+features in the USANS to SANS range.  For example, core-shell sphere sets the
+outer radius of the sphere logarithmically in `[20, 20,000]`, which sets the Q
+value for the transition from flat to falling.  It then uses a beta distribution
+to set the percentage of the shape which is shell, giving a preference for very
+thin or very thick shells (but never 0% or 100%).  Using `-sets=10` in sascomp
+should show a reasonable variety of curves over the default sascomp q range.
+The parameter set is returned as a dictionary of `{parameter: value, ...}`.
+Any model parameters not included in the dictionary will default according to
 the code in the `_randomize_one()` function from sasmodels/compare.py.
 
@@ -492 +492 @@
 used.
 
+Hollow shapes, where the volume fraction of particle corresponds to the
+material in the shell rather than the volume enclosed by the shape, must
+also define a *shell_volume(par1, par2, ...)* function.  The parameters
+are the same as for *form_volume*.  The *I(q)* calculation should use
+*shell_volume* squared as its scale factor for the volume normalization.
+The structure factor calculation needs *form_volume* in order to properly
+scale the volume fraction parameter, so both functions are required for
+hollow shapes.
+
+Note: Pure python models do not yet support direct computation of the
+average of $F(q)$ and $F^2(q)$.
+
 Embedded C Models
 .................
@@ -503 +515 @@
 This expands into the equivalent C code::
 
-    #include <math.h>
     double Iq(double q, double par1, double par2, ...);
     double Iq(double q, double par1, double par2, ...)
@@ -512 +523 @@
 *form_volume* defines the volume of the shape. As in python models, it
 includes only the volume parameters.
+
+*form_volume* defines the volume of the shell for hollow shapes. As in
+python models, it includes only the volume parameters.
 
 **source=['fn.c', ...]** includes the listed C source files in the
@@ -548 +562 @@
 The INVALID define can go into *Iq*, or *c_code*, or an external C file
 listed in *source*.
+
+Structure Factors
+.................
+
+Structure factor calculations may need the underlying $<F(q)>$ and $<F^2(q)>$
+rather than $I(q)$.  This is used to compute $\beta = <F(q)>^2/<F^2(q)>$ in
+the decoupling approximation to the structure factor.
+
+Instead of defining the *Iq* function, models can define *Fq* as
+something like::
+
+    double Fq(double q, double *F1, double *F2, double par1, double par2, ...);
+    double Fq(double q, double *F1, double *F2, double par1, double par2, ...)
+    {
+        // Polar integration loop over all orientations.
+        ...
+        *F1 = 1e-2 * total_F1 * contrast * volume;
+        *F2 = 1e-4 * total_F2 * square(contrast * volume);
+        return I(q, par1, par2, ...);
+    }
+
+If the volume fraction scale factor is built into the model (as occurs for
+the vesicle model, for example), then scale *F1* by $\surd V_f$ so that
+$\beta$ is computed correctly.
+
+Structure factor calculations are not yet supported for oriented shapes.
+
+Note: only available as a separate C file listed in *source*, or within
+a *c_code* block within the python model definition file.
 
 Oriented Shapes