Changes in doc/guide/plugin.rst [94bfa42:81751c2] in sasmodels

File:

• doc/guide/plugin.rst (modified) (13 diffs)

doc/guide/plugin.rst

@@ -273 +273 @@
 `Form_Factors`_ for more details.
 
-**model_info = ...** lets you define a model directly, for example, by
-loading and modifying existing models.  This is done implicitly by
-:func:`sasmodels.core.load_model_info`, which can create a mixture model
-from a pair of existing models.  For example::
-
-    from sasmodels.core import load_model_info
-    model_info = load_model_info('sphere+cylinder')
-
-See :class:`sasmodels.modelinfo.ModelInfo` for details about the model
-attributes that are defined.
-
 Model Parameters
 ................
@@ -302 +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.
@@ -374 +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
@@ -503 +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
 .................
@@ -514 +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, ...)
@@ -523 +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
@@ -559 +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
@@ -712 +744 @@
     erf, erfc, tgamma, lgamma:  **do not use**
         Special functions that should be part of the standard, but are missing
-        or inaccurate on some platforms. Use sas_erf, sas_erfc, sas_gamma
-        and sas_lgamma instead (see below).
+        or inaccurate on some platforms. Use sas_erf, sas_erfc and sas_gamma
+        instead (see below). Note: lgamma(x) has not yet been tested.
 
 Some non-standard constants and functions are also provided:
@@ -780 +812 @@
         Gamma function sas_gamma\ $(x) = \Gamma(x)$.
 
-        The standard math function, tgamma(x), is unstable for $x < 1$
+        The standard math function, tgamma(x) is unstable for $x < 1$
         on some platforms.
 
         :code:`source = ["lib/sas_gamma.c", ...]`
         (`sas_gamma.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_gamma.c>`_)
-
-    sas_gammaln(x):
-        log gamma function sas_gammaln\ $(x) = \log \Gamma(|x|)$.
-
-        The standard math function, lgamma(x), is incorrect for single
-        precision on some platforms.
-
-        :code:`source = ["lib/sas_gammainc.c", ...]`
-        (`sas_gammainc.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_gammainc.c>`_)
-
-    sas_gammainc(a, x), sas_gammaincc(a, x):
-        Incomplete gamma function
-        sas_gammainc\ $(a, x) = \int_0^x t^{a-1}e^{-t}\,dt / \Gamma(a)$
-        and complementary incomplete gamma function
-        sas_gammaincc\ $(a, x) = \int_x^\infty t^{a-1}e^{-t}\,dt / \Gamma(a)$
-
-        :code:`source = ["lib/sas_gammainc.c", ...]`
-        (`sas_gammainc.c <https://github.com/SasView/sasmodels/tree/master/sasmodels/models/lib/sas_gammainc.c>`_)
 
     sas_erf(x), sas_erfc(x):
@@ -840 +854 @@
         If $n$ = 0 or 1, it uses sas_J0($x$) or sas_J1($x$), respectively.
 
-        Warning: JN(n,x) can be very inaccurate (0.1%) for x not in [0.1, 100].
-
         The standard math function jn(n, x) is not available on all platforms.
 
@@ -850 +862 @@
         Sine integral Si\ $(x) = \int_0^x \tfrac{\sin t}{t}\,dt$.
 
-        Warning: Si(x) can be very inaccurate (0.1%) for x in [0.1, 100].
-
         This function uses Taylor series for small and large arguments:
 
-        For large arguments use the following Taylor series,
+        For large arguments,
 
         .. math::
@@ -1023 +1033 @@
           "radius": 120., "radius_pd": 0.2, "radius_pd_n":45},
          0.2, 0.228843],
-        [{"radius": 120., "radius_pd": 0.2, "radius_pd_n":45}, "ER", 120.],
-        [{"radius": 120., "radius_pd": 0.2, "radius_pd_n":45}, "VR", 1.],
+        [{"radius": 120., "radius_pd": 0.2, "radius_pd_n":45},
+         0.1, None, None, 120., None, 1.],  # q, F, F^2, R_eff, V, form:shell
+        [{"@S": "hardsphere"}, 0.1, None],
     ]
 
 
-**tests=[[{parameters}, q, result], ...]** is a list of lists.
+**tests=[[{parameters}, q, Iq], ...]** is a list of lists.
 Each list is one test and contains, in order:
 
@@ -1040 +1051 @@
 - input and output values can themselves be lists if you have several
   $q$ values to test for the same model parameters.
-- for testing *ER* and *VR*, give the inputs as "ER" and "VR" respectively;
-  the output for *VR* should be the sphere/shell ratio, not the individual
-  sphere and shell values.
+- for testing effective radius, volume and form:shell volume ratio, use the
+  extended form of the tests results, with *None, None, R_eff, V, V_r*
+  instead of *Iq*.  This calls the kernel *Fq* function instead of *Iq*.
+- for testing F and F^2 (used for beta approximation) do the same as the
+  effective radius test, but include values for the first two elements,
+  $<F(q)>$ and $<F^2(q)>$.
+- for testing interaction between form factor and structure factor, specify
+  the structure factor name in the parameters as *{"@S": "name", ...}* with
+  the remaining list of parameters defined by the *P@S* product model.
 
 .. _Test_Your_New_Model: