# Changeset 9624545 in sasmodels

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Timestamp:
Mar 31, 2019 6:08:06 AM (3 months ago)
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master
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4d00de6
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1dd78a2b
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Overhaul of fitting_sq.rst for readability & clarification

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• ## doc/guide/fitting_sq.rst

 r1423ddb This help document is under development .. figure:: p_and_s_buttons.png **Product models**, or $P@S$ models for short, multiply the form factor $P(Q)$ by the structure factor $S(Q)$, modulated by the **effective radius** of the form factor. of the form factor. For the theory behind this, see :ref:PStheory later. **If writing your own** $P@S$ **models, DO NOT give your model parameters** **these names!** Parameters ^^^^^^^^^^ Many parameters are common amongst $P@S$ models, but take on specific meanings: * *scale*: Overall model scale factor. To compute number density $n$ the volume fraction $V_f$ (parameterised as **volfraction**) is needed.  In most $P(Q)$ models $V_f$ is not defined and **scale** is used instead. Some $P(Q)$ models, such as the *vesicle*, do define **volfraction** and so can leave **scale** at 1.0. Structure factor models $S(Q)$ contain **volfraction**. In $P@S$ models this is *also* used as the volume fraction for the form factor model $P(Q)$, *replacing* any **volfraction** parameter in $P(Q)$. This means that $P@S$ models can also leave **scale** at 1.0. If the volume fraction required for $S(Q)$ is *not* the volume fraction needed to compute the $n$ for $P(Q)$, then leave **volfraction** as the $V_f$ for $S(Q)$ and use **scale** to define the $V_f$ for $P(Q)$ as $V_f$ = **scale**  $\cdot$  **volfraction**.  This situation may occur in a mixed phase system where the effective volume fraction needed to compute the structure is much higher than the true volume fraction. * *volfraction*: The volume fraction of material, $V_f$. For hollow shapes, **volfraction** still represents the volume fraction of material but the $S(Q)$ calculation needs the volume fraction *enclosed by* *the shape.*  To remedy this the user-specified **volfraction** is scaled by the ratio form:shell computed from the average form volume and average shell volume returned from the $P(Q)$ calculation when calculating $S(Q)$. The original **volfraction** is divided by the shell volume to compute the number density $n$ used in the $P@S$ model to get the absolute scaling on the final $I(Q)$. * *radius_effective*: The radial distance determining the range of the $S(Q)$ interaction. This may be estimated from the "size" parameters $\mathbf \xi$ describing the form of the shape.  For example, in a system containing freely-rotating cylinders, the volume of space each cylinder requires to tumble will be much larger than the volume of the cylinder itself. Thus the *effective* radius of a cylinder will be larger than either its actual radius or half- length. In use, it may be sensible to tie or constrain **radius_effective** to one or other of the "size" parameters describing the form of the shape. **radius_effective** may also be specified directly, independent of the estimate from $P(Q)$. If **radius_effective** is calculated by $P(Q)$, it will be the weighted average of the effective radii computed for the polydisperse shape parameters, and that average is used to compute $S(Q)$. When specified directly, the value of **radius_effective** may be polydisperse, and $S(Q)$ will be averaged over a range of effective radii. Whether this makes any physical sense will depend on the system. .. note:: The following additional parameters are only available in SasView 5.0 and later. * *radius_effective_mode*: Defines how the effective radius (parameter **radius_effective**) should be computed from the parameters of the shape. When **radius_effective_mode = 0** then unconstrained **radius_effective** parameter in the $S(Q)$ model is used. *This is the default in SasView* *versions 4.x and earlier*. Otherwise, in SasView 5.x and later, **radius_effective_mode = k** represents an index in a list of alternative **radius_effective** calculations which will appear in a drop-down box. For example, the *ellipsoid* model defines the following **radius_effective_modes**:: 1 => average curvature 2 => equivalent volume sphere 3 => min radius 4 => max radius Note: **radius_effective_mode** will only appear in the parameter table if the model defines the list of modes, otherwise it will be set permanently to 0 for the user-defined effective radius. **WARNING! If** $P(Q)$ **is multiplied by** $S(Q)$ **in the FitPage,** **instead of being generated in the Sum|Multi dialog, the** **radius_effective used is constrained (equivalent to** **radius_effective_mode = 1)**. * *structure_factor_mode*: The type of structure factor calculation to use. If the $P@S$ model supports the $\beta(Q)$ *decoupling correction* [1] then **structure_factor_mode** will appear in the parameter table after the $S(Q)$ parameters. If **structure_factor_mode = 0** then the *local monodisperse approximation* will be used, i.e.: .. math:: I(Q) = \text{scale} \frac{V_f}{V} P(Q) S(Q) + \text{background} where $P(Q) = \langle F(Q)^2 \rangle$. *This is the default in SasView* *versions 4.x and earlier*. If **structure_factor_mode = 1** then the $\beta(Q)$ correction will be used, i.e.: .. math:: I(Q) = \text{scale} \frac{V_f}{V} P(Q) [ 1 + \beta(Q) (S(Q) - 1) ] + \text{background} The $\beta(Q)$ decoupling approximation has the effect of damping the oscillations in the normal (local monodisperse) $S(Q)$. When $\beta(Q) = 1$ the local monodisperse approximation is recovered. *This mode is only* *available in SasView 5.x and later*. More mode options may appear in future as more complicated operations are added. .. _PStheory: Theory ^^^^^^ Scattering at vector $\mathbf Q$ for an individual particle with \big/ V(\mathbf\xi) with particle volume $V(\mathbf \xi)$ and with the particle volume $V(\mathbf \xi)$ and .. math:: F(\mathbf Q, \mathbf\xi) = \int_{\mathbb R^3} \rho_c(\mathbf r, \mathbf\xi) e^{i \mathbf Q \cdot \mathbf r} \,\mathrm d \mathbf r e^{i \mathbf Q \cdot \mathbf r} \,\mathrm d \mathbf r = F The 1-D scattering pattern for monodisperse particles uses the orientation .. math:: n = V_f/V(\mathbf\xi) is the number density of scatterers estimated from the volume fraction is the number density of scatterers estimated from the volume fraction $V_f$ of particles in solution. In this formalism, each incoming wave interacts with exactly one particle before being scattered into the .. math:: I(Q) = n \langle F F^* \rangle S(Q) For particles without spherical symmetry, the decoupling approximation (DA) For particles without spherical symmetry, the decoupling approximation is more accurate, with .. math:: I(Q) = P(Q)[1 + \beta\,(S(Q) - 1)] with form factor $P(Q) = n \langle F F^* \rangle$ and with the form factor $P(Q) = n \langle F F^* \rangle$ and $\beta = \langle F \rangle \langle F \rangle^* \big/ \langle F F^* \rangle$. These approximations can be extended to heterogeneous systems using averages over size, $\langle \cdot \rangle_\mathbf\xi = \int_\Xi P_\mathbf\xi \langle\cdot\rangle\,\mathrm d\mathbf\xi \big/ \int_\Xi P_\mathbf\xi \,\mathrm d\mathbf\xi$ and setting $n = V_f\big/\langle V \rangle_\mathbf\xi$. Further improvements can be made using the local monodisperse approximation (LMA) or using partial structure factors, as described in \cite{bresler_sasfit:_2015}. Many parameters are common amongst $P@S$ models, and take on specific meanings: * *scale*: Overall model scale factor. To compute number density $n$ the volume fraction $V_f$ is needed.  In most $P(Q)$ models $V_f$ is not defined and **scale** is used instead. Some $P(Q)$ models, such as *vesicle*, do define **volfraction** and so can leave **scale** at 1.0. The structure factor model $S(Q)$ has **volfraction**.  This is also used as the volume fraction for the form factor model $P(Q)$, replacing the **volfraction** parameter if it exists in $P$. This means that $P@S$ models can leave **scale** at 1.0. If the volume fraction required for $S(Q)$ is *not* the volume fraction needed to compute the number density for $P(Q)$, then leave **volfraction** as the volume fraction for $S(Q)$ and use **scale** to define the volume fraction for $P(Q)$ as $V_f$ = **scale**  $\cdot$  **volfraction**.  This situation may occur in a mixed phase system where the effective volume fraction needed to compute the structure is much higher than the true volume fraction. * *volfraction*: The volume fraction of material. For hollow shapes, **volfraction** still represents the volume fraction of material but the $S(Q)$ calculation needs the volume fraction *enclosed by* *the shape.*  Thus the user-specified **volfraction** is scaled by the ratio form:shell computed from the average form volume and average shell volume returned from the $P(Q)$ calculation when calculating $S(Q)$.  The original **volfraction** is divided by the shell volume to compute the number density $n$ used in $P@S$ to get the absolute scaling on the final $I(Q)$. * *radius_effective*: The radial distance determining the range of the $S(Q)$ interaction. This may be estimated from the "size" parameters $\mathbf \xi$ describing the form of the shape.  For example, in a system containing freely-rotating cylinders, the volume of space each cylinder requires to tumble will be much larger than the volume of the cylinder itself.  Thus the effective radius will be larger than either the radius or the half-length of the cylinder.  It may be sensible to tie or constrain **radius_effective** to one or other of these "size" parameters. **radius_effective** may also be specified directly, independent of the estimate from $P(Q)$. If it is calculated by $P(Q)$, **radius_effective** will be the weighted average of the effective radii computed for the polydisperse shape parameters, and that average used to compute $S(Q)$.  When specified directly, the value of **radius_effective** may be polydisperse, and $S(Q)$ will be averaged over a range of effective radii.  Whether this makes any physical sense will depend on the system. * *radius_effective_mode*: Selects the **radius_effective** value to use. When **radius_effective_mode = 0** then the **radius_effective** parameter in the $P@S$ model is used.  Otherwise **radius_effective_mode = k** is the index into the list of **radius_effective_modes** defined by the model indicating how the effective radius should be computed from the parameters of the shape. For example, the *ellipsoid* model defines the following:: 1 => average curvature 2 => equivalent volume sphere 3 => min radius 4 => max radius **radius_effective_mode** will only appear in the parameter table if the model defines the list of modes, otherwise it will be set permanently to 0 for user defined effective radius. * *structure_factor_mode*: The type of structure factor calculation to use. If the $P@S$ model supports the $\beta(Q)$ *decoupling correction* [1] then **structure_factor_mode** will appear in the parameter table after the $S(Q)$ parameters. If **structure_factor_mode = 0** then the *local monodisperse approximation* will be used, i.e.: .. math:: I(Q) = \text{scale} \frac{V_f}{V} P(Q) S(Q) + \text{background} where $P(Q) = \langle F(Q)^2 \rangle$. If **structure_factor_mode = 1** then the $\beta(Q)$ correction will be used, i.e.: .. math:: I(Q) = \text{scale} \frac{V_f}{V} P(Q) [ 1 + \beta(Q) (S(Q) - 1) ] + \text{background} The $\beta(Q)$ decoupling approximation has the effect of damping the oscillations in the normal (local monodisperse) $S(Q)$. When $\beta(Q) = 1$ the local monodisperse approximation is recovered. More mode options may appear in future as more complicated operations are added. approximation (LMA) or using partial structure factors [2]. References .. [#] Kotlarchyk, M.; Chen, S.-H. *J. Chem. Phys.*, 1983, 79, 2461 .. [#] Bressler I., Kohlbrecher J., Thunemann A.F. *J. Appl. Crystallogr.* 48 (2015) 1587-1598 .. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ *Document History* | 2019-03-30 Paul Kienzle & Steve King | 2019-03-31 Paul Kienzle, Steve King & Richard Heenan
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