-                      r93b6fcc
+                      r6386cd8
 .. model_functions.rst
-.. NB: This document does not have M Gonzalez's model descriptions in it.
 .. This is a port of the original SasView model_functions.html to ReSTructured text
+.. S King, Apr 2014
+.. with thanks to A Jackson & P Kienzle for advice!
+.. by S King, ISIS, during and after SasView CodeCamp-II in April 2014.
+.. Thanks are due to A Jackson & P Kienzle for advice on RST!
+.. The CoreShellEllipsoidXTModel was ported and documented by R K Heenan, ISIS, Apr 2014
+.. The RectangularPrism models were coded and documented by M A Gonzalez, ILL, Apr 2014
+.. To do:
+.. Remove the 'This is xi' & 'This is zeta' lines before release!
+.. Add example parameters/plots for the CoreShellEllipsoidXTModel
+.. Add example parameters/plots for the RectangularPrism models
+.. Check the content against the NIST Igor Help File
+.. Wordsmith the content for consistency of style, etc
+.. ZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZ
 …
 This is zeta, |zeta|
 SasView Model Functions
 =======================
 …
 Many of our models use the form factor calculations implemented in a c-library provided by the NIST Center for Neutron
 Research and thus some content and figures in this document are originated from or shared with the NIST Igor analysis
 package.
+Research and thus some content and figures in this document are originated from or shared with the NIST SANS Igor-based
+analysis package.
 This software provides form factors for various particle shapes. After giving a mathematical definition of each model,
 …
 Our so-called 1D scattering intensity functions provide *P(q)* for the case where the scatterer is randomly oriented. In
 that case, the scattering intensity only depends on the length of *q* . The intensity measured on the plane of the SANS
+that case, the scattering intensity only depends on the length of *q* . The intensity measured on the plane of the SAS
 detector will have an azimuthal symmetry around *q*\ =0 .
 …
 - ParallelepipedModel_ (including magnetic 2D version)
 - CSParallelepipedModel_
+- RectangularPrismModel_
+- RectangularHollowPrismModel_
+- RectangularHollowPrismInfThinWallsModel_
 .. _Shape-independent:
 …
 .2 Shape-Independent Functions
 -------------------------------
+(In alphabetical order)
 - AbsolutePower_Law_
 …
 - FractalCoreShell_
 - GaussLorentzGel_
+- GelFitModel_
 - Guinier_
 - GuinierPorod_
+- LineModel_
 - Lorentz_
 - MassFractalModel_
 - MassSurfaceFractal_
 - PeakGaussModel
 - PeakLorentzModel
 - Poly_GaussCoil
 - PolyExclVolume
 - PorodModel
 - RPA10Model
 - StarPolymer
+- PeakGaussModel_
+- PeakLorentzModel_
+- Poly_GaussCoil_
+- PolyExclVolume_
+- PorodModel_
+- RPA10Model_
+- StarPolymer_
 - SurfaceFractalModel_
 - TeubnerStrey_
+- TwoLorentzian
+- TwoPowerLaw
+- UnifiedPowerRg
+- LineModel
+- ReflectivityModel
+- ReflectivityIIModel
+- GelFitModel
+- TwoLorentzian_
+- TwoPowerLaw_
+- UnifiedPowerRg_
+- ReflectivityModel_
+- ReflectivityIIModel_
 .. _Structure-factor:
 …
 .. image:: img/image115.JPG
 and its radius of gyration
+and its radius-of-gyration
 .. image:: img/image116.JPG
 …
 and its radius of gyration is
+and its radius-of-gyration is
 .. image:: img/image109.JPG
 …
 be valid.
 If SANS data are in absolute units, and the SLDs are correct, then *scale* should be the total volume fraction of the
+If SAS data are in absolute units, and the SLDs are correct, then *scale* should be the total volume fraction of the
 "outer particle". When *S(q)* is introduced this moves to the *S(q)* volume fraction, and *scale* should then be 1.0,
 or contain some other units conversion factor (for example, if you have SAXS data).
 …
 *semi_axisA* axis is parallel to the *x*-axis of the detector.
 The radius of gyration for this system is *Rg*\ :sup:`2` = (*Ra*\ :sup:`2` *Rb*\ :sup:`2` *Rc*\ :sup:`2`)/5.
+The radius-of-gyration for this system is *Rg*\ :sup:`2` = (*Ra*\ :sup:`2` *Rb*\ :sup:`2` *Rc*\ :sup:`2`)/5.
 The contrast is defined as SLD(ellipsoid) - SLD(solvent). In the parameters, *semi_axisA* = *Ra* (or minor equatorial
 …
 This model provides the form factor, *P(q)*, for a rectangular cylinder (below) where the form factor is normalized by
 the volume of the cylinder.
+the volume of the cylinder. If you need to apply polydispersity, see the RectangularPrismModel_.
 *P(q)* = *scale* \* <*f*\ :sup:`2`> / *V* + *background*
 …
+.. _RectangularPrismModel:
+**2.1.39. RectangularPrismModel**
+This model provides the form factor, *P(q)*, for a rectangular prism.
+Note that this model is almost totally equivalent to the existing ParallelepipedModel_. The only difference is that the
+way the relevant parameters are defined here (*a*, *b/a*, *c/a* instead of *a*, *b*, *c*) allows to use polydispersity
+with this model while keeping the shape of the prism (e.g. setting *b/a* = 1 and *c/a* = 1 and applying polydispersity
+to *a* will generate a distribution of cubes of different sizes).
+*2.1.39.1. Definition*
+The 1D scattering intensity for this model was calculated by Mittelbach and Porod (Mittelbach, 1961), but the
+implementation here is closer to the equations given by Nayuk and Huber (Nayuk, 2012).
+The scattering from a massive parallelepiped with an orientation with respect to the scattering vector given by |theta|
+and |phi| is given by
+.. math::
+  A_P\,(q) =  \frac{\sin \bigl( q \frac{C}{2} \cos\theta \bigr)}{q \frac{C}{2} \cos\theta} \, \times \,
+  \frac{\sin \bigl( q \frac{A}{2} \sin\theta \sin\phi \bigr)}{q \frac{A}{2} \sin\theta \sin\phi} \, \times \,
+  \frac{\sin \bigl( q \frac{B}{2} \sin\theta \cos\phi \bigr)}{q \frac{B}{2} \sin\theta \cos\phi}
+where *A*, *B* and *C* are the sides of the parallelepiped and must fulfill :math:`A \le B \le C`, |theta| is the angle
+between the *z* axis and the longest axis of the parallelepiped *C*, and |phi| is the angle between the scattering
+vector (lying in the *xy* plane) and the *y* axis.
+The normalized form factor in 1D is obtained averaging over all possible orientations
+.. math::
+  P(q) =  \frac{2}{\pi} \times \, \int_0^{\frac{\pi}{2}} \, \int_0^{\frac{\pi}{2}} A_P^2(q) \, \sin\theta \, d\theta \, d\phi
+The 1D scattering intensity is then calculated as
+.. math::
+  I(q) = \mbox{scale} \times V \times (\rho_{\mbox{pipe}} - \rho_{\mbox{solvent}})^2 \times P(q)
+where *V* is the volume of the rectangular prism, :math:`\rho_{\mbox{pipe}}` is the scattering length of the
+parallelepiped, :math:`\rho_{\mbox{solvent}}` is the scattering length of the solvent, and (if the data are in absolute
+units) *scale* represents the volume fraction (which is unitless).
+**The 2D scattering intensity is not computed by this model.**
+The returned value is scaled to units of |cm^-1| and the parameters of the RectangularPrismModel are the following
+==============  ========  =============
+Parameter name  Units     Default value
+==============  ========  =============
+scale           None      1
+short_side      |Ang|     35
+b2a_ratio       None      1
+c2a_ratio       None      1
+sldPipe         |Ang^-2|  6.3e-6
+sldSolv         |Ang^-2|  1.0e-6
+background      |cm^-1|   0
+==============  ========  =============
+*2.1.39.2. Validation of the RectangularPrismModel*
+Validation of the code was conducted by comparing the output of the 1D model to the output of the existing
+parallelepiped model.
+REFERENCES
+P Mittelbach and G Porod, *Acta Physica Austriaca*, 14 (1961) 185-211
+R Nayuk and K Huber, *Z. Phys. Chem.*, 226 (2012) 837-854
+.. _RectangularHollowPrismModel:
+**2.1.40. RectangularHollowPrismModel**
+This model provides the form factor, *P(q)*, for a hollow rectangular parallelepiped with a wall thickness |bigdelta|.
+*2.1.40.1. Definition*
+The 1D scattering intensity for this model is calculated by forming the difference of the amplitudes of two massive
+parallelepipeds differing in their outermost dimensions in each direction by the same length increment 2 |bigdelta|
+(Nayuk, 2012).
+As in the case of the massive parallelepiped, the scattering amplitude is computed for a particular orientation of the
+parallelepiped with respect to the scattering vector and then averaged over all possible orientations, giving
+.. math::
+  P(q) =  \frac{1}{V^2} \frac{2}{\pi} \times \, \int_0^{\frac{\pi}{2}} \, \int_0^{\frac{\pi}{2}} A_{P\Delta}^2(q) \,
+  \sin\theta \, d\theta \, d\phi
+where |theta| is the angle between the *z* axis and the longest axis of the parallelepiped, |phi| is the angle between
+the scattering vector (lying in the *xy* plane) and the *y* axis, and
+.. math::
+  A_{P\Delta}\,(q) =  A \, B \, C \, \times
+                      \frac{\sin \bigl( q \frac{C}{2} \cos\theta \bigr)}{q \frac{C}{2} \cos\theta} \,
+                      \frac{\sin \bigl( q \frac{A}{2} \sin\theta \sin\phi \bigr)}{q \frac{A}{2} \sin\theta \sin\phi} \,
+                      \frac{\sin \bigl( q \frac{B}{2} \sin\theta \cos\phi \bigr)}{q \frac{B}{2} \sin\theta \cos\phi} -
+\, \bigl( \frac{A}{2} - \Delta \bigr) \, \bigl( \frac{B}{2} - \Delta \bigr) \,
+                      \bigl( \frac{C}{2} - \Delta \bigr) \, \times
+                      \frac{\sin \bigl[ q \bigl(\frac{C}{2}-\Delta\bigr) \cos\theta \bigr]}
+                      {q \bigl(\frac{C}{2}-\Delta\bigr) \cos\theta} \,
+                      \frac{\sin \bigl[ q \bigl(\frac{A}{2}-\Delta\bigr) \sin\theta \sin\phi \bigr]}
+                      {q \bigl(\frac{A}{2}-\Delta\bigr) \sin\theta \sin\phi} \,
+                      \frac{\sin \bigl[ q \bigl(\frac{B}{2}-\Delta\bigr) \sin\theta \cos\phi \bigr]}
+                      {q \bigl(\frac{B}{2}-\Delta\bigr) \sin\theta \cos\phi} \,
+where *A*, *B* and *C* are the external sides of the parallelepiped fulfilling :math:`A \le B \le C`, and the volume *V*
+of the parallelepiped is
+.. math::
+  V = A B C \, - \, (A - 2\Delta) (B - 2\Delta) (C - 2\Delta)
+The 1D scattering intensity is then calculated as
+.. math::
+  I(q) = \mbox{scale} \times V \times (\rho_{\mbox{pipe}} - \rho_{\mbox{solvent}})^2 \times P(q)
+where :math:`\rho_{\mbox{pipe}}` is the scattering length of the parallelepiped, :math:`\rho_{\mbox{solvent}}` is the
+scattering length of the solvent, and (if the data are in absolute units) *scale* represents the volume fraction (which
+is unitless).
+**The 2D scattering intensity is not computed by this model.**
+The returned value is scaled to units of |cm^-1| and the parameters of the RectangularHollowPrismModel are the
+following
+==============  ========  =============
+Parameter name  Units     Default value
+==============  ========  =============
+scale           None      1
+short_side      |Ang|     35
+b2a_ratio       None      1
+c2a_ratio       None      1
+thickness       |Ang|     1
+sldPipe         |Ang^-2|  6.3e-6
+sldSolv         |Ang^-2|  1.0e-6
+background      |cm^-1|   0
+==============  ========  =============
+*2.1.40.2. Validation of the RectangularHollowPrismModel*
+Validation of the code was conducted by qualitatively comparing the output of the 1D model to the curves shown in
+(Nayuk, 2012).
+REFERENCES
+R Nayuk and K Huber, *Z. Phys. Chem.*, 226 (2012) 837-854
+.. _RectangularHollowPrismInfThinWallsModel:
+**2.1.41. RectangularHollowPrismInfThinWallsModel**
+This model provides the form factor, *P(q)*, for a hollow rectangular prism with infinitely thin walls.
+*2.1.41.1. Definition*
+The 1D scattering intensity for this model is calculated according to the equations given by Nayuk and Huber
+(Nayuk, 2012).
+Assuming a hollow parallelepiped with infinitely thin walls, edge lengths :math:`A \le B \le C` and presenting an
+orientation with respect to the scattering vector given by |theta| and |phi|, where |theta| is the angle between the
+*z* axis and the longest axis of the parallelepiped *C*, and |phi| is the angle between the scattering vector
+(lying in the *xy* plane) and the *y* axis, the form factor is given by
+.. math::
+  P(q) =  \frac{1}{V^2} \frac{2}{\pi} \times \, \int_0^{\frac{\pi}{2}} \, \int_0^{\frac{\pi}{2}} [A_L(q)+A_T(q)]^2
+  \, \sin\theta \, d\theta \, d\phi
+where
+.. math::
+  V = 2AB + 2AC + 2BC
+.. math::
+  A_L\,(q) =  8 \times \frac{ \sin \bigl( q \frac{A}{2} \sin\phi \sin\theta \bigr)
+                              \sin \bigl( q \frac{B}{2} \cos\phi \sin\theta \bigr)
+                              \cos \bigl( q \frac{C}{2} \cos\theta \bigr) }
+                            {q^2 \, \sin^2\theta \, \sin\phi \cos\phi}
+.. math::
+  A_T\,(q) =  A_F\,(q) \times \frac{2 \, \sin \bigl( q \frac{C}{2} \cos\theta \bigr)}{q \, \cos\theta}
+and
+.. math::
+  A_F\,(q) =  4 \frac{ \cos \bigl( q \frac{A}{2} \sin\phi \sin\theta \bigr)
+                       \sin \bigl( q \frac{B}{2} \cos\phi \sin\theta \bigr) }
+                     {q \, \cos\phi \, \sin\theta} +
+\frac{ \sin \bigl( q \frac{A}{2} \sin\phi \sin\theta \bigr)
+                       \cos \bigl( q \frac{B}{2} \cos\phi \sin\theta \bigr) }
+                     {q \, \sin\phi \, \sin\theta}
+The 1D scattering intensity is then calculated as
+.. math::
+  I(q) = \mbox{scale} \times V \times (\rho_{\mbox{pipe}} - \rho_{\mbox{solvent}})^2 \times P(q)
+where *V* is the volume of the rectangular prism, :math:`\rho_{\mbox{pipe}}` is the scattering length of the
+parallelepiped, :math:`\rho_{\mbox{solvent}}` is the scattering length of the solvent, and (if the data are in absolute
+units) *scale* represents the volume fraction (which is unitless).
+**The 2D scattering intensity is not computed by this model.**
+The returned value is scaled to units of |cm^-1| and the parameters of the RectangularHollowPrismInfThinWallModel
+are the following
+==============  ========  =============
+Parameter name  Units     Default value
+==============  ========  =============
+scale           None      1
+short_side      |Ang|     35
+b2a_ratio       None      1
+c2a_ratio       None      1
+sldPipe         |Ang^-2|  6.3e-6
+sldSolv         |Ang^-2|  1.0e-6
+background      |cm^-1|   0
+==============  ========  =============
+*2.1.41.2. Validation of the RectangularHollowPrismInfThinWallsModel*
+Validation of the code was conducted  by qualitatively comparing the output of the 1D model to the curves shown in
+(Nayuk, 2012).
+REFERENCES
+R Nayuk and K Huber, *Z. Phys. Chem.*, 226 (2012) 837-854
 .2 Shape-independent Functions
 -------------------------------
 The following are models used for shape-independent SANS analysis.
+The following are models used for shape-independent SAS analysis.
 .. _Debye:
 …
 **2.2.1. Debye (Gaussian Coil Model)**
 The Debye model is a form factor for a linear polymer chain. In addition to the radius of gyration, *Rg*, a scale factor
+*scale*, and a constant background term are included in the calculation. **NB: No size polydispersity is included in**
 **this model, use the** Poly_GaussCoil_ **Model instead**
+The Debye model is a form factor for a linear polymer chain obeying Gaussian statistics (ie, it is in the theta state).
+In addition to the radius-of-gyration, *Rg*, a scale factor *scale*, and a constant background term are included in the
+calculation. **NB: No size polydispersity is included in this model, use the** Poly_GaussCoil_ **Model instead**
 .. image:: img/image172.PNG
 …
 **2.2.2. BroadPeakModel**
 This model calculates an empirical functional form for SANS data characterized by a broad scattering peak. Many SANS
+This model calculates an empirical functional form for SAS data characterized by a broad scattering peak. Many SAS
 spectra are characterized by a broad peak even though they are from amorphous soft materials. For example, soft systems
 that show a SANS peak include copolymers, polyelectrolytes, multiphase systems, layered structures, etc.
+that show a SAS peak include copolymers, polyelectrolytes, multiphase systems, layered structures, etc.
 The d-spacing corresponding to the broad peak is a characteristic distance between the scattering inhomogeneities (such
 …
 **2.2.3. CorrLength (Correlation Length Model)**
 Calculates an empirical functional form for SANS data characterized by a low-Q signal and a high-Q signal.
+Calculates an empirical functional form for SAS data characterized by a low-Q signal and a high-Q signal.
 The returned value is scaled to units of |cm^-1|, absolute scale.
 …
 a sum of a low-*q* exponential decay plus a lorentzian at higher *q*-values.
+Also see the GelFitModel_.
 The returned value is scaled to units of |cm^-1|, absolute scale.
 …
 Note that
  the radius of gyration for a sphere of radius *R* is given by *Rg* = *R* sqrt(3/5)
 Â the cross-sectional radius of gyration for a randomly oriented cylinder of radius *R* is given byÂ *Rg* = *R* / sqrt(2)
  the cross-sectional radius of gyration of a randomly oriented lamella of thickness *T* is given by *Rg* = *T* / sqrt(12)
+ the radius-of-gyration for a sphere of radius *R* is given by *Rg* = *R* sqrt(3/5)
+Â the cross-sectional radius-of-gyration for a randomly oriented cylinder of radius *R* is given byÂ *Rg* = *R* / sqrt(2)
+ the cross-sectional radius-of-gyration of a randomly oriented lamella of thickness *T* is given by *Rg* = *T* / sqrt(12)
 For 2D data: The 2D scattering intensity is calculated in the same way as 1D, where the *q* vector is defined as
 …
 **2.2.17. PorodModel**
+A Porod analysis is done by linearizing the data at high q by plotting
+it as log(I) versus log(Q). In the high q region we can fit the
+following model:
+This model fits the Porod function
 .. image:: img/image197.PNG
+C is the scale factor and Â Sv is the specific surface area of the sample
+and ÃâÃï¿œ is the contrast factor.
 The background term is added for data analysis.
+to the data directly without any need for linearisation (*cf*. Log *I(q)* vs Log *q*).
+Here *C* is the scale factor and *Sv* is the specific surface area (ie, surface area / volume) of the sample, and
+|drho| is the contrast factor.
 For 2D data: The 2D scattering intensity is calculated in the same way as 1D, where the *q* vector is defined as
 …
 ==============  ========  =============
+REFERENCE
+None.
 …
 **2.2.18. PeakGaussModel**
+Model describes a Gaussian shaped peak including a flat background,
+This model describes a Gaussian shaped peak on a flat background
 .. image:: img/image198.PNG
+with the peak having height of I0 centered at qpk having standard
+deviation of B.Â  The fwhm is 2.354\*B.Â Â
+Parameters I0, B, qpk, and BGD can all be adjusted during fitting. **NB: These don't match the table!**
+REFERENCE
+None
+with the peak having height of *I0* centered at *q0* and having a standard deviation of *B*.Â  The FWHM (full-width
+half-maximum) is 2.354 B.Â Â
 For 2D data: The 2D scattering intensity is calculated in the same way as 1D, where the *q* vector is defined as
 …
 *Figure. 1D plot using the default values (w/500 data points).*
+REFERENCE
+None.
 …
 **2.2.19. PeakLorentzModel**
+Model describes a Lorentzian shaped peak including a flat background,
+This model describes a Lorentzian shaped peak on a flat background
 .. image:: img/image200.PNG
+with the peak having height of I0 centered at qpk having a hwhm
+(half-width-half-maximum) of B.Â
+The parameters I0, B, qpk, and BGD can all be adjusted during fitting. **NB: These don't match the table!**
+REFERENCE
+None
+with the peak having height of *I0* centered at *q0* and having a HWHM (half-width half-maximum) of B.Â
 For 2D data: The 2D scattering intensity is calculated in the same way as 1D, where the *q* vector is defined as
 …
 *Figure. 1D plot using the default values (w/500 data points).*
+REFERENCE
+None.
 …
 **2.2.20. Poly_GaussCoil (Model)**
+Polydisperse Gaussian Coil: Calculate an empirical functional form for
+scattering from a polydisperse polymer chain ina good solvent. The
+polymer is polydisperse with a Schulz-Zimm polydispersity of the
+molecular weight distribution.Â
+This model calculates an empirical functional form for the scattering from a **polydisperse** polymer chain in the
+theta state assuming a Schulz-Zimm type molecular weight distribution.Â Polydispersity on the radius-of-gyration is also
+provided for.
 The returned value is scaled to units of |cm^-1|, absolute scale.
+*2.2.20.1. Definition*
+The scattering intensity *I(q)* is calculated as
 .. image:: img/image202.PNG
 where the dimensionless chain dimension is:
+where the dimensionless chain dimension is
 .. image:: img/image203.PNG
 and the polydispersion is
+and the polydispersity is
 .. image:: img/image204.PNG
-The scattering intensity *I(q)* is calculated as:
-The polydispersion in rg is provided.
 For 2D data: The 2D scattering intensity is calculated in the same way as 1D, where the *q* vector is defined as
 .. image:: img/image040.GIF
+TEST DATASET
+This example dataset is produced by running the Poly_GaussCoil, using 200 data points, *qmin* = 0.001 |Ang^-1| ,
+qmax = 0.7 |Ang^-1|Â and the default values below.
+This example dataset is produced using 200 data points, using 200 data points,
+*qmin* = 0.001 |Ang^-1|, *qmax* = 0.7 |Ang^-1| and the default values
 ==============  ========  =============
 …
 REFERENCE
+Glatter & Kratky - p404
+O Glatter and O Kratky (editors), *Small Angle X-ray Scattering*, Academic Press, (1982)
+Page 404
 J S Higgins, and H C Benoit, Polymers and Neutron Scattering, Oxford Science Publications (1996)
 …
 **2.2.21. PolymerExclVolume (Model)**
+Calculates the scattering from polymers with excluded volume effects.
+This model describes the scattering from polymer chains subject to excluded volume effects, and has been used as a
+template for describing mass fractals.
 The returned value is scaled to units of |cm^-1|, absolute scale.
+The returned value is P(Q) as written in equation (2), plus the
+incoherent background term. The result is in the units of |cm^-1|,
+absolute scale.
+A model describing polymer chain conformations with excluded volume was
+introduced to describe the conformation of polymer chains, and has been
+used as a template for describing mass fractals. The form factor for
+that model (Benoit, 1957) was originally presented in the following
+integral form:
+.. image:: img/image206.JPGÂ Â Â Â  (1)
+Here n is the excluded volume parameter which is related to the Porod
+exponent m as n = 1/m, a is the polymer chain statistical segment length
+and n is the degree of polymerization. This integral was later put into
+an almost analytical form (Hammouda, 1993) as follows:
+.. image:: img/image207.JPGÂ Â Â  (2)
+Here, g(x,U) is the incomplete gamma function which is a built-in
+function in computer libraries.
+*2.2.21.1 Definition*
+The form factor  was originally presented in the following integral form (Benoit, 1957)
+.. image:: img/image206.JPG
+where |nu| is the excluded volume parameter (which is related to the Porod exponent *m* as |nu| = 1 / *m*), *a* is the
+statistical segment length of the polymer chain, and *n* is the degree of polymerization. This integral was later put
+into an almost analytical form as follows (Hammouda, 1993)
+.. image:: img/image207.JPG
+where |gamma|\ *(x,U)* is the incomplete gamma function
 .. image:: img/image208.JPG
+The variable U is given in terms of the scattering variable Q as:
+and the variable *U* is given in terms of the scattering vector *Q* as
 .. image:: img/image209.JPG
 The radius of gyration squared has been defined as:
+The square of the radius-of-gyration is defined as
 .. image:: img/image210.JPG
+Note that this model describing polymer chains with excluded volume
+applies only in the mass fractal range ( 5/3 <= m <= 3) and does not
+apply to surface fractals ( 3 < m <= 4). It does not reproduce the rigid
+rod limit (m = 1) because it assumes chain flexibility from the outset.Â
+It may cover a portion of the semiflexible chain range ( 1 < m < 5/3).
+The low-Q expansion yields the Guinier form and the high-Q expansion
+yields the Porod form which is given by:
+Note that this model applies only in the mass fractal range (ie, 5/3 <= *m* <= 3) and **does not** apply to surface
+fractals (3 < *m* <= 4). It also does not reproduce the rigid rod limit (*m* = 1) because it assumes chain flexibility
+from the outset.Â It may cover a portion of the semi-flexible chain range (1 < *m* < 5/3).
+A low-*Q* expansion yields the Guinier form and a high-*Q* expansion yields the Porod form which is given by
 .. image:: img/image211.JPG
+Here G(x) = g(x,inf) is the gamma function. The asymptotic limit is
+dominated by the first term:
+Here |biggamma|\ *(x)* = |gamma|\ *(x,inf)* is the gamma function.
+The asymptotic limit is dominated by the first term
 .. image:: img/image212.JPG
+The special case when n = 0.5 (or m = 1/n = 2) corresponds to Gaussian
+chains for which the form factor is given by the familiar Debye
+function.
+The special case when |nu| = 0.5 (or *m* = 1/|nu| = 2) corresponds to Gaussian chains for which the form factor is given
+by the familiar Debye_ function.
 .. image:: img/image213.JPG
-The form factor given by Eq. 2 is the calculated result, and is plotted
-below for the default parameter values.
-REFERENCE
-H Benoit, *Comptes Rendus*, 245 (1957) 2244-2247
-B Hammouda, *SANS from Homogeneous Polymer Mixtures Â A Unified Overview*, *Advances in Polym. Sci.*, 106 (1993) 87-133
 For 2D data: The 2D scattering intensity is calculated in the same way as 1D, where the *q* vector is defined as
 .. image:: img/image040.GIF
+TEST DATASET
+This example dataset is produced, using 200 data points, qmin = 0.001 |Ang^-1| ,Â  qmax = 0.2 |Ang^-1|Â Â and the
+default values below.
+This example dataset is produced using 200 data points, *qmin* = 0.001 |Ang^-1|, *qmax* = 0.2 |Ang^-1| and the default
+values
 ===================  ========  =============
 …
 *Figure. 1D plot using the default values (w/500 data points).*
+REFERENCE
+H Benoit, *Comptes Rendus*, 245 (1957) 2244-2247
+B Hammouda, *SANS from Homogeneous Polymer Mixtures Â A Unified Overview*, *Advances in Polym. Sci.*, 106 (1993) 87-133
 …
 **2.2.22. RPA10Model**
+Calculates the macroscopic scattering intensity (units of cm^-1) for a
+multicomponent homogeneous mixture of polymers using the Random Phase
+Approximation. This general formalism contains 10 specific cases:
+Case 0: C/D Binary mixture of homopolymers
+Case 1: C-D Diblock copolymer
+Case 2: B/C/D Ternary mixture of homopolymers
+Case 3: C/C-D Mixture of a homopolymer B and a diblock copolymer C-D
+Case 4: B-C-D Triblock copolymer
+Case 5: A/B/C/D Quaternary mixture of homopolymers
+Case 6: A/B/C-D Mixture of two homopolymers A/B and a diblock C-D
+Case 7: A/B-C-D Mixture of a homopolymer A and a triblock B-C-D
+Case 8: A-B/C-D Mixture of two diblock copolymers A-B and C-D
+Case 9: A-B-C-D Four-block copolymer
+Note: the case numbers are different from the IGOR/NIST SANS package.
+Only one case can be used at any one time.Â  Plotting a different case
+will overwrite the original parameter waves.
+The returned value is scaled to units of [cm-1].
+Component D is assumed to be the "background" component (all contrasts
+are calculated with respect to component D).
+Scattering contrast for a C/D blend= {SLD (component C) - SLD (component
+D)}2
+Depending on what case is used, the number of fitting parameters varies.
+These represent the segment lengths (ba, bb, etc) and the Chi parameters
+(Kab, Kac, etc). The last one of these is a scaling factor to be held
+constant equal to unity.
+The input parameters are the degree of polymerization, the volume
+fractions for each component the specific volumes and the neutron
+scattering length densities.
+This RPA (mean field) formalism applies only when the multicomponent
+polymer mixture is in the homogeneous mixed-phase region.
+REFERENCE
+A Z Akcasu, R Klein and B Hammouda, *Macromolecules*, 26 (1993) 4136
+Fitting parameters for Case0 Model
+Calculates the macroscopic scattering intensity (units of |cm^-1|) for a multicomponent homogeneous mixture of polymers
+using the Random Phase Approximation. This general formalism contains 10 specific cases
+Case 0: C/D binary mixture of homopolymers
+Case 1: C-D diblock copolymer
+Case 2: B/C/D ternary mixture of homopolymers
+Case 3: C/C-D mixture of a homopolymer B and a diblock copolymer C-D
+Case 4: B-C-D triblock copolymer
+Case 5: A/B/C/D quaternary mixture of homopolymers
+Case 6: A/B/C-D mixture of two homopolymers A/B and a diblock C-D
+Case 7: A/B-C-D mixture of a homopolymer A and a triblock B-C-D
+Case 8: A-B/C-D mixture of two diblock copolymers A-B and C-D
+Case 9: A-B-C-D tetra-block copolymer
+**NB: these case numbers are different from those in the NIST SANS package!**
+Only one case can be used at any one time.
+The returned value is scaled to units of |cm^-1|, absolute scale.
+The RPA (mean field) formalism only applies only when the multicomponent polymer mixture is in the homogeneous
+mixed-phase region.
+**Component D is assumed to be the "background" component (ie, all contrasts are calculated with respect to**
+**component D).** So the scattering contrast for a C/D blend = [SLD(component C) - SLD(component D)]\ :sup:`2`.
+Depending on which case is being used, the number of fitting parameters - the segment lengths (ba, bb, etc) and |chi|
+parameters (Kab, Kac, etc) - vary. The *scale* parameter should be held equal to unity.
+The input parameters are the degrees of polymerization, the volume fractions, the specific volumes, and the neutron
+scattering length densities for each component.
+Fitting parameters for a Case 0 Model
 =======================  ========  =============
 …
 =======================  ========  =============
 Fixed parameters for Case0 Model
+Fixed parameters for a Case 0 Model
 =======================  ========  =============
 …
 *Figure. 1D plot using the default values (w/500 data points).*
+REFERENCE
+A Z Akcasu, R Klein and B Hammouda, *Macromolecules*, 26 (1993) 4136
 …
 **2.2.23. TwoLorentzian (Model)**
+Calculate an empirical functional form for SANS data characterized by a
+two Lorentzian functions.
+This model calculates an empirical functional form for SAS data characterized by two Lorentzian-type functions.
 The returned value is scaled to units of |cm^-1|, absolute scale.
+The scattering intensity *I(q)* is calculated by:Â
+*2.2.23.1. Definition*
+The scattering intensity *I(q)* is calculated as
 .. image:: img/image216.JPGÂ
+A = Lorentzian scale #1
+C = Lorentzian scale #2Â
+where scale is the peak height centered at q0, and B refers to the
+standard deviation of the function.
+The background term is added for data analysis.
+where *A* = Lorentzian scale factor #1, *C* = Lorentzian scale #2, |xi|\ :sub:`1` and |xi|\ :sub:`2` are the
+corresponding correlation lengths, and *n* and *m* are the respective power law exponents (set *n* = *m* = 2 for
+Ornstein-Zernicke behaviour).
 For 2D data: The 2D scattering intensity is calculated in the same way as 1D, where the *q* vector is defined as
 .. image:: img/image040.GIF
-**Default input parameter values**
 ===============================  ========  =============
 …
 REFERENCE
 None
+None.
 …
 **2.2.24. TwoPowerLaw (Model)**
+Calculate an empirical functional form for SANS data characterized by
+two power laws.
+This model calculates an empirical functional form for SAS data characterized by two power laws.
 The returned value is scaled to units of |cm^-1|, absolute scale.
+The scattering intensity *I(q)* is calculated by:
+*2.2.24.1. Definition*
+The scattering intensity *I(q)* is calculated as
 .. image:: img/image218.JPG
+qc is the location of the crossover from one slope to the other. The
+scaling A, sets the overall intensity of the lower Q power law region.
+The scaling of the second power law region is scaled to match the first.
+Be sure to enter the power law exponents as positive values.
+where *qc* is the location of the crossover from one slope to the other. The scaling *coef_A* sets the overall
+intensity of the lower *q* power law region. The scaling of the second power law region is then automatically scaled to
+match the first.
+**NB: Be sure to enter the power law exponents as positive values!**
 For 2D data: The 2D scattering intensity is calculated in the same way as 1D, where the *q* vector is defined as
 .. image:: img/image040.GIF
-**Default input parameter values**
 ==============  ========  =============
 …
 *Figure. 1D plot using the default values (w/500 data points).*
+REFERENCE
+None.
 …
 **2.2.25. UnifiedPowerRg (Beaucage Model)**
+This model deploys the empirical multiple level unified Exponential/Power-law fit method developed by G Beaucage. Four
+functions are included so that 1, 2, 3, or 4 levels can be used. In addition a 0 level has been added which simply
+calculates
+*I(q)* = *scale* / *q* + *background*
 The returned value is scaled to units of |cm^-1|, absolute scale.Â
+Note that the level 0 is an extra function that is the inverse function;
+I (q) = scale/q + background.
+Otherwise, program incorporates the empirical multiple level unified
+Exponential/Power-law fit method developed by G Beaucage. Four
+functions are included so that One, Two, Three, or Four levels can be
+used.
+The empirical expressions are able to reasonably approximate the
+scattering from many different types of particles, including fractal
+clusters, random coils (Debye equation), ellipsoidal particles, etc.Â
+The Beaucage method is able to reasonably approximate the scattering from many different types of particles, including
+fractal clusters, random coils (Debye equation), ellipsoidal particles, etc.Â
+*2.2.25.1 Definition*
 The empirical fit function isÂ
 .. image:: img/image220.JPG
+For each level, the four parameters Gi, Rg,i, Bi and Pi must be chosen.Â
+For example, to approximate the scattering from random coils (Debye
+equation), set Rg,i as the Guinier radius, Pi = 2, and Bi = 2 Gi / Rg,iÂ
+See the listed references for further information on choosing the
+parameters.
+For each level, the four parameters *Gi*, *Rg,i*, *Bi* and *Pi* must be chosen.Â
+For example, to approximate the scattering from random coils (Debye_ equation), set *Rg,i* as the Guinier radius,
+*Pi* = 2, and *Bi* = 2 *Gi* / *Rg,i*Â
+See the references for further information on choosing the parameters.
 For 2D data: The 2D scattering intensity is calculated in the same way as 1D, where the *q* vector is defined as
 .. image:: img/image040.GIF
-**Default input parameter values**
 ==============  ========  =============
 …
 REFERENCE
 G Beaucage (1995).Â  J. Appl. Cryst., vol. 28, p717-728.
 G Beaucage (1996).Â  J. Appl. Cryst., vol. 29, p134-146.
+G Beaucage, *J. Appl. Cryst.*, 28 (1995) 717-728
+G Beaucage, *J. Appl. Cryst.*, 29 (1996) 134-146
 …
 **2.2.26. LineModel**
 This is a linear function that calculates:
+This calculates the simple linear function
 .. image:: img/image222.PNG
+where A and B are the coefficients of the first and second order terms.
+**Note:** For 2D plot, *I(q)* = *I(qx)* / *I(qy)*Â  which is defined differently
+from other shape independent models.
+==============  ========  =============
+Parameter name  Units     Default value
+==============  ========  =============
+A               |cm^-1|   1.0
+B               |Ang|     1.0
+==============  ========  =============
+**NB: For 2D plots,** *I(q)* = *I(qx)*\ *\ *I(qy)*,Â **which is a different definition to other shape independent models.**
+==============  ==============  =============
+Parameter name  Units           Default value
+==============  ==============  =============
+A               |cm^-1|         1.0
+B               |Ang|\ |cm^-1|  1.0
+==============  ==============  =============
+REFERENCE
+None.
+.. _GelFitModel:
+**2.2.27. GelFitModel**
+*This model was implemented by an interested user!*
+Unlike a concentrated polymer solution, the fine-scale polymer distribution in a gel involves at least two
+characteristic length scales, a shorter correlation length (*a1*) to describe the rapid fluctuations in the position
+of the polymer chains that ensure thermodynamic equilibrium, and a longer distance (denoted here as *a2*) needed to
+account for the static accumulations of polymer pinned down by junction points or clusters of such points. The latter
+is derived from a simple Guinier function.
+Also see the GaussLorentzGel_ Model.
+*2.2.27.1. Definition*
+The scattered intensity *I(q)* is calculated as
+.. image:: img/image233.GIF
+where
+.. image:: img/image234.GIF
+Note that the first term reduces to the Ornstein-Zernicke equation when *D* = 2; ie, when the Flory exponent is 0.5
+(theta conditions). In gels with significant hydrogen bonding *D* has been reported to be ~2.6 to 2.8.
+============================  ========  =============
+Parameter name                Units     Default value
+============================  ========  =============
+Background                    |cm^-1|   0.01
+Guinier scale    (= *I(0)G*)  |cm^-1|   1.7
+Lorentzian scale (= *I(0)L*)  |cm^-1|   3.5
+Radius of gyration  (= *Rg*)  |Ang|     104
+Fractal exponent     (= *D*)  None Â     2
+Correlation length  (= *a1*)  |Ang|     16
+============================  ========  =============
+.. image:: img/image235.GIF
+*Figure. 1D plot using the default values (w/300 data points).*
+REFERENCE
+Mitsuhiro Shibayama, Toyoichi Tanaka, Charles C Han, J. Chem. Phys. 1992, 97 (9), 6829-6841
+Simon Mallam, Ferenc Horkay, Anne-Marie Hecht, Adrian R Rennie, Erik Geissler, Macromolecules 1991, 24, 543-548
+.. _StarPolymer:
+**2.2.28. Star Polymer with Gaussian Statistics**
+This model is also known as the Benoit Star model.
+*2.2.28.1. Definition*
+For a star with *f* arms:
+.. image:: img/star1.PNG
+where
+.. image:: img/star2.PNG
+and
+.. image:: img/star3.PNG
+is the square of the ensemble average radius-of-gyration of an arm.
+REFERENCE
+H Benoit, Â  J. Polymer Science.,Â  11, 596-599Â  (1953)
 …
 .. _ReflectivityModel:
+**2.2.27. ReflectivityModel**
+This model calculates the reflectivity and uses the Parrett algorithm.
+Up to nine film layers are supported between Bottom(substrate) and
+Medium(Superstrate where the neutron enters the first top film). Each
+layers are composed of [ Âœ of the interface(from the previous layer or
+substrate) + flat portion + Âœ of the interface(to the next layer or
+medium)]. Only two simple interfacial functions are selectable, error
+function and linear function. The each interfacial thickness is
+equivalent to (- 2.5 sigma to +2.5 sigma for the error function,
+sigma=roughness).
+Note: This model was contributed by an interested user.
+**2.2.29. ReflectivityModel**
+*This model was contributed by an interested user!*
+This model calculates **reflectivity** using the Parrett algorithm.
+Up to nine film layers are supported between Bottom(substrate) and Medium(Superstrate) where the neutron enters the
+first top film. Each of the layers are composed of
+[Âœ of the interface (from the previous layer or substrate) + flat portion + Âœ of the interface (to the next layer or medium)]
+Two simple functions are provided to describe the interfacial density distribution; a linear function and an error
+function. The interfacial thickness is equivalent to (-2.5 |sigma| to +2.5 |sigma| for the error function, where
+|sigma| = roughness).
+Also see ReflectivityIIModel_.
 .. image:: img/image231.BMP
 *Figure. Comparison (using the SLD profile below) with NISTweb calculation (circles)*
+*Figure. Comparison (using the SLD profile below) with the NIST web calculation (circles)*
 http://www.ncnr.nist.gov/resources/reflcalc.html
 .. image:: img/image232.GIF
+*Figure. SLD profile used for the calculation(above).*
+*Figure. SLD profile used for the calculation (above).*
+REFERENCE
+None.
 …
 .. _ReflectivityIIModel:
 **2.2.28. ReflectivityIIModel**
+Â Â Â  Same as the ReflectivityModel except that the it is more
+customizable. More interfacial functions are supplied. The number of
+points (npts_inter) for each interface can be choosen. Â Â Â  The constant
+(A below but 'nu' as a parameter name of the model) for exp, erf, or
+power-law is an input. The SLD at the interface between layers,
 *rinter_i*, is calculated with a function chosen by a user, where the
+functions are:
 ) Erf;
+**2.2.30. ReflectivityIIModel**
+*This model was contributed by an interested user!*
+This **reflectivity** model is a more flexible version of ReflectivityModel_. More interfacial density
+functions are supported, and the number of points (*npts_inter*) for each interface can be chosen.
+The SLD at the interface between layers, |rho|\ *inter_i*, is calculated with a function chosen by a user, where the
+available functions are
+) Erf
 .. image:: img/image051.GIF
 ) Power-Law;
+) Power-Law
 .. image:: img/image050.GIF
 ) Exp;
+) Exp
 .. image:: img/image049.GIF
+Â Â Â  Note: This model was implemented by an interested user.
+.. _GelFitModel:
+**2.2.29. GelFitModel**
+Â Â Â  Unlike a concentrated polymer solution, the fine-scale polymer
+distribution in a gel involves at least two characteristic length
+scales, a shorter correlation length (a1) to describe the rapid
+fluctuations in the position of the polymer chains that ensure
+thermodynamic equilibrium, and a longer distance (denoted here as a2)
+needed to account for the static accumulations of polymer pinned down by
+junction points or clusters of such points. The letter is derived from a
+simple Guinier function.
+The scattered intensity *I(q)* is then calculated as:
+.. image:: img/image233.GIF
+Where:
+.. image:: img/image234.GIF
+Â Â Â  Note the first term reduces to the Ornstein-Zernicke equation when
+D=2; ie, when the Flory exponent is 0.5 (theta conditions). Â  In gels
+with significant hydrogen bonding D has been reported to be ~2.6 to 2.8.
+Â Â Â  Note: This model was implemented by an interested user.
+**Default input parameter values**
+==================  ========  =============
+Parameter name      Units     Default value
+==================  ========  =============
+Background          |cm^-1|   0.01
+Guinier scale       |cm^-1|   1.7
+Lorentzian scale    |cm^-1|   3.5
+Radius of gyration  |Ang|     104
+Fractal exponent    None Â     2
+Correlation length  |Ang|     16
+==================  ========  =============
+.. image:: img/image235.GIF
+*Figure. 1D plot using the default values (w/300 data points,
+qmin=0.001, and qmax=0.3).*
+REFERENCE
+Mitsuhiro Shibayama, Toyoichi Tanaka, Charles C Han, J. Chem. Phys. 1992, 97 (9), 6829-6841
+Simon Mallam, Ferenc Horkay, Anne-Marie Hecht, Adrian R Rennie, Erik Geissler, Macromolecules 1991, 24, 543-548
+.. _StarPolymer:
+**2.2.30. Star Polymer with Gaussian Statistics**
+For a star with *f* arms:
+.. image:: img/star1.PNG
+.. image:: img/star2.PNG
+.. image:: img/star3.PNG
+where is the ensemble average radius of gyration squared of an arm.
+REFERENCE
+H Benoit, Â  J. Polymer Science.,Â  11, 596-599Â  (1953)
+The constant *A* in the expressions above (but the parameter *nu* in the model!) is an input.
+REFERENCE
+None.
 …
 ------------------------------
 The information in this section is originated from NIST SANS IgorPro package.
+The information in this section originated from NIST SANS package.
 .. _HardSphereStructure:

Note: See TracChangeset for help on using the changeset viewer.

SasView

Changeset 6386cd8 in sasview

Legend:

src/sans/models/media/model_functions.rst

Download in other formats: