Index: sansmodels/src/sans/models/media/model_functions.html
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@@ -7,6 +7,6 @@
 <ul style="margin-top: 0in;" type="disc">
 <li style="line-height: 115%;"><a href="#Introduction"><strong>Introduction</strong></a></li>
-<li style="line-height: 115%;"><a href="#Shapes"><strong>Shapes</strong></a>: <a href="#SphereModel">SphereModel</a>, <a href="#BinaryHSModel">BinaryHSModel</a>, <a href="#FuzzySphereModel">FuzzySphereModel</a>, <a href="#RaspBerryModel">RaspBerryModel</a>, <a href="#CoreShellModel">CoreShellModel</a>,&nbsp;<a href="#Core2ndMomentModel">Core2ndMomentModel</a>, <a href="#CoreMultiShellModel">CoreMultiShellModel</a>, <a href="#VesicleModel">VesicleModel</a>, <a href="#MultiShellModel">MultiShellModel</a>, &nbsp;<a href="#OnionExpShellModel">OnionExpShellModel</a>, <a href="#SphericalSLDModel">SphericalSLDModel</a>, <a href="#LinearPearlsModel">LinearPearlsModel</a>, <a href="#PearlNecklaceModel">PearlNecklaceModel</a> , <a href="#CylinderModel">CylinderModel</a>, <a href="#CoreShellCylinderModel">CoreShellCylinderModel</a>, <a href="#CoreShellBicelleModel">CoreShellBicelleModel</a>,<a href="#HollowCylinderModel">HollowCylinderModel</a>, <a href="#FlexibleCylinderModel">FlexibleCylinderModel</a>, <a href="#FlexibleCylinderModel">FlexCylEllipXModel</a>, <a href="#StackedDisksModel">StackedDisksModel</a>, <a href="#ParallelepipedModel">ParallelepipedModel</a>, <a href="#CSParallelepipedModel">CSParallelepipedModel</a>, <a href="#EllipticalCylinderModel">EllipticalCylinderModel</a>, <a href="#BarBellModel">BarBellModel</a>, <a href="#CappedCylinderModel">CappedCylinderModel</a>, <a href="#EllipsoidModel">EllipsoidModel</a>, <a href="#CoreShellEllipsoidModel">CoreShellEllipsoidModel</a>, <a href="#TriaxialEllipsoidModel">TriaxialEllipsoidModel</a>, <a href="#LamellarModel">LamellarModel</a>, <a href="#LamellarFFHGModel">LamellarFFHGModel</a>, <a href="#LamellarPSModel">LamellarPSModel</a>, <a href="#LamellarPSHGModel">LamellarPSHGModel</a>, <a href="#LamellarPCrystalModel">LamellarPCrystalModel</a>, <a href="#SCCrystalModel">SCCrystalModel</a>, <a href="#FCCrystalModel">FCCrystalModel</a>, <a href="#BCCrystalModel">BCCrystalModel</a>.</li>
-<li style="line-height: 115%;"><a href="#Shape-Independent"><strong>Shape-Independent</strong></a>: <a href="#Absolute%20Power_Law">AbsolutePower_Law</a>, <a href="#BEPolyelectrolyte">BEPolyelectrolyte</a>, <a href="#BroadPeakModel">BroadPeakModel,<span><span style="text-decoration: underline;"><span style="color: blue;">CorrLength</span></span></span><span>,</span></a> <a href="#DABModel">DAB_Model</a>, <a href="#Debye">Debye</a>, <a href="#Number_Density_Fractal">FractalModel</a>, <a href="#FractalCoreShell">FractalCoreShell</a>, <a href="#GaussLorentzGel">GaussLorentzGel</a>, <a href="#Guinier">Guinier</a>, <a href="#GuinierPorod">GuinierPorod</a>, <a href="#Lorentz">Lorentz</a>, <a href="#Mass_Fractal">MassFractalModel</a>, <a href="#MassSurface_Fractal">MassSurfaceFractal</a>, <a href="#Peak%20Gauss%20Model">PeakGaussModel</a>, <a href="#Peak%20Lorentz%20Model">PeakLorentzModel</a>, <a href="#Poly_GaussCoil">Poly_GaussCoil</a>, <a href="#PolymerExclVolume">PolyExclVolume</a>, <a href="#PorodModel">PorodModel</a>, <a href="#RPA10Model">RPA10Model</a>, <a href="#StarPolymer">StarPolymer</a>, <a href="#Surface_Fractal">SurfaceFractalModel</a>, <a href="#TeubnerStreyModel">Teubner Strey</a>, <a href="#TwoLorentzian">TwoLorentzian</a>, <a href="#TwoPowerLaw">TwoPowerLaw</a>, <a href="#UnifiedPowerRg">UnifiedPowerRg</a>, <a href="#LineModel">LineModel</a>, <a href="#ReflectivityModel">ReflectivityModel</a>, <a href="#ReflectivityIIModel">ReflectivityIIModel</a>, <a href="#GelFitModel">GelFitModel</a>.</li>
+<li style="line-height: 115%;"><a href="#Shapes"><strong>Shapes</strong></a>: <a href="#SphereModel">SphereModel (Magnetic 2D Model)</a>, <a href="#BinaryHSModel">BinaryHSModel</a>, <a href="#FuzzySphereModel">FuzzySphereModel</a>, <a href="#RaspBerryModel">RaspBerryModel</a>, <a href="#CoreShellModel">CoreShellModel (Magnetic 2D Model)</a>,&nbsp;<a href="#Core2ndMomentModel">Core2ndMomentModel</a>, <a href="#CoreMultiShellModel">CoreMultiShellModel (Magnetic 2D Model)</a>, <a href="#VesicleModel">VesicleModel</a>, <a href="#MultiShellModel">MultiShellModel</a>, &nbsp;<a href="#OnionExpShellModel">OnionExpShellModel</a>, <a href="#SphericalSLDModel">SphericalSLDModel</a>, <a href="#LinearPearlsModel">LinearPearlsModel</a>, <a href="#PearlNecklaceModel">PearlNecklaceModel</a> , <a href="#CylinderModel">CylinderModel (Magnetic 2D Model)</a>, <a href="#CoreShellCylinderModel">CoreShellCylinderModel</a>, <a href="#CoreShellBicelleModel">CoreShellBicelleModel</a>,<a href="#HollowCylinderModel">HollowCylinderModel</a>, <a href="#FlexibleCylinderModel">FlexibleCylinderModel</a>, <a href="#FlexibleCylinderModel">FlexCylEllipXModel</a>, <a href="#StackedDisksModel">StackedDisksModel</a>, <a href="#ParallelepipedModel">ParallelepipedModel (Magnetic 2D Model)</a>, <a href="#CSParallelepipedModel">CSParallelepipedModel</a>, <a href="#EllipticalCylinderModel">EllipticalCylinderModel</a>, <a href="#BarBellModel">BarBellModel</a>, <a href="#CappedCylinderModel">CappedCylinderModel</a>, <a href="#EllipsoidModel">EllipsoidModel</a>, <a href="#CoreShellEllipsoidModel">CoreShellEllipsoidModel</a>, <a href="#TriaxialEllipsoidModel">TriaxialEllipsoidModel</a>, <a href="#LamellarModel">LamellarModel</a>, <a href="#LamellarFFHGModel">LamellarFFHGModel</a>, <a href="#LamellarPSModel">LamellarPSModel</a>, <a href="#LamellarPSHGModel">LamellarPSHGModel</a>, <a href="#LamellarPCrystalModel">LamellarPCrystalModel</a>, <a href="#SCCrystalModel">SCCrystalModel</a>, <a href="#FCCrystalModel">FCCrystalModel</a>, <a href="#BCCrystalModel">BCCrystalModel</a>.</li>
+<li style="line-height: 115%;"><a href="#Shape-Independent"><strong>Shape-Independent</strong></a>: <a href="#Absolute%20Power_Law">AbsolutePower_Law</a>, <a href="#BEPolyelectrolyte">BEPolyelectrolyte</a>, <a href="#BroadPeakModel">BroadPeakModel,<span><span style="text-decoration: underline;"><span style="color: blue;">CorrLength</span></span></span><span>,</span></a> <a href="#DABModel">DABModel</a>, <a href="#Debye">Debye</a>, <a href="#Number_Density_Fractal">FractalModel</a>, <a href="#FractalCoreShell">FractalCoreShell</a>, <a href="#GaussLorentzGel">GaussLorentzGel</a>, <a href="#Guinier">Guinier</a>, <a href="#GuinierPorod">GuinierPorod</a>, <a href="#Lorentz">Lorentz</a>, <a href="#Mass_Fractal">MassFractalModel</a>, <a href="#MassSurface_Fractal">MassSurfaceFractal</a>, <a href="#Peak%20Gauss%20Model">PeakGaussModel</a>, <a href="#Peak%20Lorentz%20Model">PeakLorentzModel</a>, <a href="#Poly_GaussCoil">Poly_GaussCoil</a>, <a href="#PolymerExclVolume">PolyExclVolume</a>, <a href="#PorodModel">PorodModel</a>, <a href="#RPA10Model">RPA10Model</a>, <a href="#StarPolymer">StarPolymer</a>, <a href="#Surface_Fractal">SurfaceFractalModel</a>, <a href="#TeubnerStreyModel">Teubner Strey</a>, <a href="#TwoLorentzian">TwoLorentzian</a>, <a href="#TwoPowerLaw">TwoPowerLaw</a>, <a href="#UnifiedPowerRg">UnifiedPowerRg</a>, <a href="#LineModel">LineModel</a>, <a href="#ReflectivityModel">ReflectivityModel</a>, <a href="#ReflectivityIIModel">ReflectivityIIModel</a>, <a href="#GelFitModel">GelFitModel</a>.</li>
 <li style="line-height: 115%;"><a href="#Model"><strong>Customized Models</strong></a>: <a href="#testmodel">testmodel</a>, <a href="#testmodel_2">testmodel_2</a>, <a href="#sum_p1_p2">sum_p1_p2</a>, <a href="#sum_Ap1_1_Ap2">sum_Ap1_1_Ap2</a>, <a href="#polynomial5">polynomial5</a>, <a href="#sph_bessel_jn">sph_bessel_jn</a>.</li>
 <li style="line-height: 115%;"><a href="#Structure_Factors"><strong>Structure Factors</strong></a>: <a href="#HardsphereStructure">HardSphereStructure</a>, <a href="#SquareWellStructure">SquareWellStructure</a>, <a href="#HayterMSAStructure">HayterMSAStructure</a>, <a href="#StickyHSStructure">StickyHSStructure</a>.</li>
@@ -17,6 +17,6 @@
 <p>&nbsp;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.</p>
 <p style="margin-left: 0.25in; text-indent: -0.25in;"><strong><span style="font-size: 16pt;">2.</span></strong><strong><span style="font-size: 7pt;">&nbsp;&nbsp;&nbsp; </span></strong><a name="Shapes"></a><strong><span style="font-size: 16pt;">Shapes (Scattering Intensity Models)</span></strong></p>
-<p>This software provides form factors for various particle shapes. After giving a mathematical definition of each model, we draw the list of parameters available to the user. Validation plots for each model are also presented. Instructions on how to use the software is available with the source code, available from SVN:</p>
-<p style="text-indent: 0.25in;"><em>https://sansviewproject.svn.sourceforge.net/svnroot/sansviewproject/</em></p>
+<p>This software provides form factors for various particle shapes. After giving a mathematical definition of each model, we draw the list of parameters available to the user. Validation plots for each model are also presented. Instructions on how to use the software is available with the source code.</p>
+
 <p>To easily compare to the scattering intensity measured in experiments, we normalize the form factors by the volume of the particle:</p>
 <p style="text-align: center;" align="center"><span style="position: relative; top: 12pt;"><img src="img/image001.PNG" alt="" /></span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</p>
@@ -27,6 +27,7 @@
 <p>Our so-called 1D scattering intensity functions provide <em>P(q) </em>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 detector will have an azimuthal symmetry around <em>q</em>=0.</p>
 <p>Our so-called 2D scattering intensity functions provide <em>P(q, </em><em><span style="font-family: 'Arial','sans-serif';">&phi;</span>)</em> for an oriented system as a function of a q-vector in the plane of the detector. We define the angle <span style="font-family: 'Arial','sans-serif';">&phi;</span> as the angle between the q vector and the horizontal (x) axis of the plane of the detector.</p>
-<p style="margin-left: 0.55in; text-indent: -0.3in;"><strong><span style="font-size: 14pt;">2.1.</span></strong><strong><span style="font-size: 7pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></strong><a name="SphereModel"></a><strong><span style="font-size: 14pt;">Sphere Model</span></strong></p>
+<p style="margin-left: 0.55in; text-indent: -0.3in;"><strong><span style="font-size: 14pt;">2.1.</span></strong><strong><span style="font-size: 7pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></strong><a name="SphereModel"></a><strong><span style="font-size: 14pt;">Sphere Model (Magnetic 2D Model)</span></strong></p>
 <p>This model provides the form factor, P(q), for a monodisperse spherical particle with uniform scattering length density. The form factor is normalized by the particle volume as described below.</p>
+For magnetic scattering, please see the '<a href="polar_mag_help.html">Polarization/Magnetic Scattering</a>' in Fitting Help.
 <p style="margin-left: 0.85in; text-indent: -0.35in;"><strong>1.1.</strong><strong><span style="font-size: 7pt;">&nbsp;&nbsp;&nbsp;&nbsp; </span>Definition</strong></p>
 <p>The 1D scattering intensity is calculated in the following way (Guinier, 1955):</p>
@@ -242,5 +243,4 @@
 <p>where the amplitude A(q) is given as the typical sphere scattering convoluted with a Gaussian to get a gradual drop-off in the scattering length density:</p>
 <p style="text-align: center;" align="center"><span style="position: relative; top: 18pt;"><img src="img/image011.PNG" alt="" /></span></p>
-<br>
 <p>Here A2(q) is the form factor, P(q). The &lsquo;scale&rsquo; is equivalent to the volume fraction of spheres, each of volume, V. Contrast (<em><span style="font-family: 'Arial','sans-serif';">&Delta;</span>&rho;</em> ) is the difference of scattering length densities of the sphere and the surrounding solvent.</p>
 <p>The poly-dispersion in radius and in fuzziness is provided.</p>
@@ -453,6 +453,7 @@
 <p style="text-align: center;" align="center">&nbsp;</p>
 <p>&nbsp;</p>
-<p style="margin-left: 0.55in; text-indent: -0.3in;"><strong><span style="font-size: 14pt;">2.5.</span></strong><strong><span style="font-size: 7pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></strong><a name="CoreShellModel"></a><strong><span style="font-size: 14pt;">Core Shell (Sphere) Model</span></strong></p>
+<p style="margin-left: 0.55in; text-indent: -0.3in;"><strong><span style="font-size: 14pt;">2.5.</span></strong><strong><span style="font-size: 7pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></strong><a name="CoreShellModel"></a><strong><span style="font-size: 14pt;">Core Shell (Sphere) Model (Magnetic 2D Model)</span></strong></p>
 <p>This model provides the form factor, P(<em>q</em>), for a spherical particle with a core-shell structure. The form factor is normalized by the particle volume.</p>
+For magnetic scattering, please see the '<a href="polar_mag_help.html">Polarization/Magnetic Scattering</a>' in Fitting Help.
 <p style="margin-left: 0.85in; text-indent: -0.35in;"><strong>1.1.</strong><strong><span style="font-size: 7pt;">&nbsp;&nbsp;&nbsp;&nbsp; </span>Definition</strong></p>
 <p>The 1D scattering intensity is calculated in the following way (Guinier, 1955):</p>
@@ -686,6 +687,7 @@
 <p>&nbsp;</p>
 <p style="text-align: center; page-break-after: avoid;" align="center"><img style="width: 526px; height: 333px;" src="img/secongm_fig1.jpg" alt="core_scondmoment_1D_validation" /></p>
-<p style="margin-left: 0.55in; text-indent: -0.3in;"><strong><span style="font-size: 14pt;">2.7.</span></strong><strong><span style="font-size: 7pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></strong><a name="CoreMultiShellModel"></a><strong><span style="font-size: 14pt;">CoreMultiShell(Sphere)Model</span></strong></p>
+<p style="margin-left: 0.55in; text-indent: -0.3in;"><strong><span style="font-size: 14pt;">2.7.</span></strong><strong><span style="font-size: 7pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></strong><a name="CoreMultiShellModel"></a><strong><span style="font-size: 14pt;">CoreMultiShell(Sphere)Model (Magnetic 2D Model)</span></strong></p>
 <p>This model provides the scattering from spherical core with from 1 up to 4 shell structures. It&nbsp;has a core of a specified radius, with four shells. The SLDs of the core and each shell are individually specified.&nbsp;</p>
+For magnetic scattering, please see the '<a href="polar_mag_help.html">Polarization/Magnetic Scattering</a>' in Fitting Help.
 <p style="margin-left: 0.85in; text-indent: -0.35in;"><strong>1.1.</strong><strong><span style="font-size: 7pt;">&nbsp;&nbsp;&nbsp;&nbsp; </span>Definition</strong></p>
 <p>The returned value is scaled to units of [cm-1sr-1], absolute scale.</p>
@@ -1707,6 +1709,7 @@
 <p><a name="PearlNecklaceModel"></a>R. Schweins and K. Huber, &lsquo;Particle Scattering Factor of Pearl Necklace Chains&rsquo;, Macromol. Symp., 211, 25-42, 2004.</p>
 <p><a name="PearlNecklaceModel"></a>&nbsp;</p>
-<p style="margin-left: 0.55in; text-indent: -0.3in;"><a name="PearlNecklaceModel"></a><strong><span style="font-size: 14pt;">2.14.</span></strong><strong><span style="font-size: 7pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></strong><a name="CylinderModel"></a><strong><span style="font-size: 14pt;">Cylinder Model</span></strong></p>
+<p style="margin-left: 0.55in; text-indent: -0.3in;"><a name="PearlNecklaceModel"></a><strong><span style="font-size: 14pt;">2.14.</span></strong><strong><span style="font-size: 7pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></strong><a name="CylinderModel"></a><strong><span style="font-size: 14pt;">Cylinder Model (Magnetic 2D Model)</span></strong></p>
 <p>This model provides the form factor for a right circular cylinder with uniform scattering length density. The form factor is normalized by the particle volume.</p>
+For magnetic scattering, please see the '<a href="polar_mag_help.html">Polarization/Magnetic Scattering</a>' in Fitting Help.
 <p style="margin-left: 0.85in; text-indent: -0.35in;"><strong>1.1.</strong><strong><span style="font-size: 7pt;">&nbsp;&nbsp;&nbsp;&nbsp; </span>Definition</strong></p>
 <p>The output of the 2D scattering intensity function for oriented cylinders is given by (Guinier, 1955):</p>
@@ -1715,8 +1718,11 @@
 <p>where <span style="font-family: 'Arial','sans-serif';">&alpha;</span> is the angle between the axis of the cylinder and the q-vector, V is the volume of the cylinder, L is the length of the cylinder, r is the radius of the cylinder, and <em><span style="font-family: 'Arial','sans-serif';">&Delta;</span>&rho;</em> (contrast) is the scattering length density difference between the scatterer and the solvent. J1 is the first order Bessel function.</p>
 <p>To provide easy access to the orientation of the cylinder, we define the axis of the cylinder using two angles theta and phi. Those angles are defined on Figure 2.</p>
-<p style="text-align: center; page-break-after: avoid;" align="center"><img src="img/image061.jpg" alt="cylinderangles.gif" width="478" height="258" /></p>
-<p style="text-align: center;" align="center"><a name="_Ref173213915"></a><a name="_Ref173306040"></a>Figure 2a. Definition of the angles for oriented cylinders.</p>
-<p style="text-align: center;" align="center"><img src="img/image062.jpg" alt="cylinderangles2.gif" width="464" height="313" /></p>
-<p style="text-align: center;" align="center">Figure 2b. Examples of the angles for oriented cylinders against the detector plane.</p>
+<p style="text-align: center; page-break-after: avoid;" align="center"><img src="img/image061.jpg" /></p>
+<p style="text-align: center;" align="center"><a name="_Ref173213915"></a><a name="_Ref173306040"></a>Figure 2. Definition of the angles for oriented cylinders.</p>
+
+<p style="text-align: center;" align="center"><img src="img/image062.jpg" alt="" width="379" height="256" /></p>
+<p style="text-align: center;" align="center">Figure. Examples of the angles for oriented pp against the detector plane.</p>
+
+
 <p>For P*S: The 2nd virial coefficient of the cylinder is calculate based on the radius and length values, and used as the effective radius toward S(Q) when P(Q)*S(Q) is applied.</p>
 <p>The returned value is scaled to units of [cm-1] and the parameters of the cylinder model are the following:</p>
@@ -1981,4 +1987,10 @@
 <p style="text-align: center; page-break-after: avoid;" align="center">&nbsp;</p>
 <p><a name="_Ref173307204"></a>Figure 9: Comparison of the intensity for uniformly distributed core-shell cylinders calculated from our 2D model and the intensity from the NIST SANS analysis software. The parameters used were: Scale=1.0, Radius=20 &Aring;, Thickness=10 &Aring;, Length=400 &Aring;, Core_sld=1e-6 &Aring; -2, Shell_sld=4e-6 &Aring; -2, Solvent_sld=1e-6 &Aring; -2, and Background=0.0 cm -1.</p>
+
+<p style="text-align: center; page-break-after: avoid;" align="center"><img src="img/image061.jpg" /></p>
+<p style="text-align: center;" align="center"><a name="_Ref173213915"></a><a name="_Ref173306040"></a>Figure. Definition of the angles for oriented core-shell cylinders.</p>
+<p style="text-align: center;" align="center"><img src="img/image062.jpg" alt="" width="379" height="256" /></p>
+<p style="text-align: center;" align="center">Figure. Examples of the angles for oriented pp against the detector plane.</p>
+
 <p style="margin-left: 0.55in; text-indent: -0.3in;"><strong><span style="font-size: 14pt;">2.16.</span></strong><strong><span style="font-size: 7pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></strong><a name="CoreShellBicelleModel"></a><strong><span style="font-size: 14pt;">Core-Shell (Cylinder) Bicelle Model</span></strong></p>
 <p>This model provides the form factor for a circular cylinder with a core-shell scattering length density profile. The form factor is normalized by the particle volume. This model is a more general case of <a href="#CoreShellCylinderModel">core-shell cylinder model </a> (see&nbsp;above and reference below) in that the parameters of the shell are separated into a face-shell and a rim-shell so that users can set different values of the thicknesses and slds.&nbsp;</p>
@@ -2127,4 +2139,13 @@
 <p style="text-align: center;" align="center"><img id="cscylbicelle" style="width: 512px; height: 377px;" src="img/cscylbicelle_pic.jpg" alt="" /></p>
 <p style="text-align: center;" align="center"><strong>Figure. 1D plot using the default values (w/200 data point).</strong></p>
+
+
+<p style="text-align: center; page-break-after: avoid;" align="center"><img src="img/image061.jpg" /></p>
+<p style="text-align: center;" align="center"><a name="_Ref173213915"></a><a name="_Ref173306040"></a>Figure. Definition of the angles for the 
+oriented Core-Shell Cylinder Bicelle Model.</p>
+<p style="text-align: center;" align="center"><img src="img/image062.jpg" alt="" width="379" height="256" /></p>
+<p style="text-align: center;" align="center">Figure. Examples of the angles for oriented pp against the detector plane.</p>
+
+
 <p>&nbsp;REFERENCE<br /> Feigin, L. A, and D. I. Svergun, "Structure Analysis by Small-Angle X-Ray and Neutron Scattering", Plenum Press, New York, (1987).</p>
 <p style="margin-left: 0.55in; text-indent: -0.3in;"><strong><span style="font-size: 14pt;">2.17.</span></strong><strong><span style="font-size: 7pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></strong><a name="HollowCylinderModel"></a><strong><span style="font-size: 14pt;">HollowCylinderModel</span></strong></p>
@@ -2237,4 +2258,11 @@
 <p style="text-align: center;" align="center"><strong>Figure. 1D plot using the default values (w/1000 data point).</strong></p>
 <p>Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006).</p>
+
+<p style="text-align: center; page-break-after: avoid;" align="center"><img src="img/image061.jpg" /></p>
+<p style="text-align: center;" align="center"><a name="_Ref173213915"></a><a name="_Ref173306040"></a>Figure. Definition of the angles for the 
+oriented HollowCylinderModel.</p>
+<p style="text-align: center;" align="center"><img src="img/image062.jpg" alt="" width="379" height="256" /></p>
+<p style="text-align: center;" align="center">Figure. Examples of the angles for oriented pp against the detector plane.</p>
+
 <p>REFERENCE</p>
 <p>Feigin, L. A, and D. I. Svergun, "Structure Analysis by Small-Angle X-Ray and Neutron Scattering", Plenum Press, New York, (1987).</p>
@@ -2341,4 +2369,5 @@
 <p style="text-align: center;" align="center"><img id="Picture 228" src="img/image076.jpg" alt="" width="465" height="345" /></p>
 <p style="text-align: center;" align="center"><strong>Figure. 1D plot using the default values (w/1000 data point).</strong></p>
+
 <p>Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006):</p>
 <p>From the reference, "Method 3 With Excluded Volume" is used. The model is a parametrization of simulations of a discrete representation of the worm-like chain model of Kratky and Porod applied in the pseudocontinuous limit.&nbsp; See equations (13,26-27) in the original reference for the details.</p>
@@ -2616,6 +2645,11 @@
 <p style="text-align: center;" align="center"><img src="img/image085.jpg" alt="" width="451" height="334" /></p>
 <p style="text-align: center;" align="center"><strong>Figure. 1D plot using the default values (w/1000 data point).</strong></p>
-<p style="text-align: center;" align="center"><img id="Picture 101" src="img/image086.jpg" alt="" width="377" height="215" /></p>
+<p style="text-align: center;" align="center"><img id="Picture 101" src="img/image086.jpg"  /></p>
 <p style="text-align: center;" align="center">Figure. Examples of the angles for oriented stackeddisks against the detector plane.</p>
+
+<p style="text-align: center;" align="center"><img src="img/image062.jpg" alt="" width="379" height="256" /></p>
+<p style="text-align: center;" align="center">Figure. Examples of the angles for oriented pp against the detector plane.</p>
+
+
 <p>Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006):</p>
 <p>REFERENCE</p>
@@ -2623,6 +2657,7 @@
 <p>Kratky, O. and Porod, G., J. Colloid Science, 4, 35, 1949.</p>
 <p>Higgins, J.S. and Benoit, H.C., "Polymers and Neutron Scattering", Clarendon, Oxford, 1994.</p>
-<p style="margin-left: 0.55in; text-indent: -0.3in;"><strong><span style="font-size: 14pt;">2.21.</span></strong><strong><span style="font-size: 7pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></strong><a name="ParallelepipedModel"></a><strong><span style="font-size: 14pt;">ParallelepipedModel</span></strong></p>
+<p style="margin-left: 0.55in; text-indent: -0.3in;"><strong><span style="font-size: 14pt;">2.21.</span></strong><strong><span style="font-size: 7pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></strong><a name="ParallelepipedModel"></a><strong><span style="font-size: 14pt;">ParallelepipedModel (Magnetic 2D Model) </span></strong></p>
 <p>This model provides the form factor, P(<em>q</em>), for a rectangular cylinder (below) where the form factor is normalized by the volume of the cylinder. P(q) = scale*&lt;f^2&gt;/V+background where the volume V= ABC and the averaging &lt; &gt;&nbsp; is applied over all orientation for 1D. &nbsp;</p>
+For magnetic scattering, please see the '<a href="polar_mag_help.html">Polarization/Magnetic Scattering</a>' in Fitting Help.
 <p><span style="font-size: 14pt;">&nbsp;</span></p>
 <p style="text-align: center;" align="center"><img src="img/image087.jpg" alt="" width="326" height="247" /></p>
@@ -2636,5 +2671,5 @@
 <p>For P*S: The 2nd virial coefficient of the solid cylinder is calculate based on the averaged effective radius (= sqrt(short_a*short_b/pi)) and length( = long_c) values, and used as the effective radius toward S(Q) when P(Q)*S(Q) is applied.</p>
 <p>To provide easy access to the orientation of the parallelepiped, we define the axis of the cylinder using two angles &theta; , <span style="font-family: 'Arial','sans-serif';">&phi; </span>and<span style="font-family: Symbol;">Y</span>. Similarly to the case of the cylinder, those angles, &theta; &nbsp;and <span style="font-family: 'Arial','sans-serif';">&phi;,</span> are defined on Figure 2 of CylinderModel. The angle <span style="font-family: Symbol;">Y </span>is the rotational angle around its own long_c axis against the q plane. For example, <span style="font-family: Symbol;">Y </span>= 0 when the short_b axis is parallel to the x-axis of the detector.</p>
-<p style="text-align: center;" align="center"><img src="img/image090.jpg" alt="" width="352" height="264" /></p>
+<p style="text-align: center;" align="center"><img src="img/image090.jpg"/></p>
 <p style="text-align: center;" align="center"><strong>Figure. Definition of angles for 2D</strong>.</p>
 <p style="text-align: center;" align="center"><img src="img/image091.jpg" alt="" width="379" height="256" /></p>
@@ -2749,5 +2784,5 @@
 <p>For P*S: The 2nd virial coefficient of this CSPP is calculate based on the averaged effective radius (= sqrt((short_a+2*rim_a)*(short_b+2*rim_b)/pi)) and length( = long_c+2*rim_c) values, and used as the effective radius toward S(Q) when P(Q)*S(Q) is applied.</p>
 <p>To provide easy access to the orientation of the CSparallelepiped, we define the axis of the cylinder using two angles &theta; , <span style="font-family: 'Arial','sans-serif';">&phi; </span>and<span style="font-family: Symbol;">Y</span>. Similarly to the case of the cylinder, those angles, &theta; &nbsp;and <span style="font-family: 'Arial','sans-serif';">&phi;,</span> are defined on Figure 2 of CylinderModel. The angle <span style="font-family: Symbol;">Y </span>is the rotational angle around its own long_c axis against the q plane. For example, <span style="font-family: Symbol;">Y </span>= 0 when the short_b axis is parallel to the x-axis of the detector.</p>
-<p style="text-align: center;" align="center"><img id="Picture 102" src="img/image090.jpg" alt="" width="352" height="264" /></p>
+<p style="text-align: center;" align="center"><img id="Picture 102" src="img/image090.jpg" /></p>
 <p style="text-align: center;" align="center"><strong>Figure. Definition of angles for 2D</strong>.</p>
 <p style="text-align: center;" align="center"><img id="Picture 103" src="img/image091.jpg" alt="" width="379" height="256" /></p>
@@ -2918,4 +2953,5 @@
 <p style="text-align: center;" align="center"><img id="Picture 34" src="img/image097.jpg" alt="" width="451" height="339" /></p>
 <p style="text-align: center;" align="center"><strong>Figure. 2D plot using the default values (w/(256X265) data points).</strong></p>
+
 <p>Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006):</p>
 <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; REFERENCE</p>
@@ -2940,7 +2976,7 @@
 <p>To provide easy access to the orientation of the elliptical, we define the axis of the cylinder using two angles &theta; , <span style="font-family: 'Arial','sans-serif';">&phi; </span>and<span style="font-family: Symbol;">Y</span>. Similarly to the case of the cylinder, those angles, &theta; &nbsp;and <span style="font-family: 'Arial','sans-serif';">&phi;,</span> are defined on Figure 2 of CylinderModel. The angle <span style="font-family: Symbol;">Y </span>is the rotational angle around its own long_c axis against the q plane. For example, <span style="font-family: Symbol;">Y </span>= 0 when the r_minor axis is parallel to the x-axis of the detector.</p>
 <p>All angle parameters are valid and given only for 2D calculation (Oriented system).</p>
-<p style="text-align: center;" align="center"><img id="Picture 105" src="img/image101.jpg" alt="" width="370" height="277" /></p>
+<p style="text-align: center;" align="center"><img id="Picture 105" src="img/image101.jpg" /></p>
 <p style="text-align: center;" align="center"><strong>Figure. Definition of angels for 2D</strong>.</p>
-<p style="text-align: center;" align="center"><img id="Picture 114" src="img/image091.jpg" alt="" width="379" height="256" /></p>
+<p style="text-align: center;" align="center"><img id="Picture 114" src="img/image062.jpg" alt="" width="379" height="256" /></p>
 <p style="text-align: center;" align="center"><span style="font-size: 12pt;">Figure. Examples of the angles for oriented elliptical cylinders </span></p>
 <p style="text-align: center;" align="center"><span style="font-size: 12pt;">against the detector plane.</span></p>
@@ -3173,4 +3209,13 @@
 <p style="text-align: center;" align="center"><img id="Picture 66" src="img/image111.jpg" alt="" width="425" height="346" /></p>
 <p style="text-align: center;" align="center"><strong>Figure. 2D plot (w/(256X265) data points).</strong></p>
+
+<p style="text-align: center; page-break-after: avoid;" align="center"><img src="img/image061.jpg" /></p>
+<p style="text-align: center;" align="center"><img src="img/image062.jpg" alt="" width="379" height="256" /></p>
+<p style="text-align: center;" align="center">Figure. Examples of the angles for oriented pp against the detector plane.</p>
+
+
+<p style="text-align: center;" align="center"><a name="_Ref173213915"></a><a name="_Ref173306040"></a>Figure. Definition of the angles for oriented 2D barbells.</p>
+
+
 <p style="margin-left: 0.55in; text-indent: -0.3in;"><strong><span style="font-size: 14pt;">2.25.</span></strong><strong><span style="font-size: 7pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></strong><a name="CappedCylinderModel"></a><strong><span style="font-size: 14pt;">CappedCylinder(/ConvexLens)Model</span></strong></p>
 <p>Calculates the scattering from a cylinder with spherical section end-caps(This model simply becomes the ConvexLensModel when the length of the cylinder L = 0. &nbsp;That is, a sphereocylinder with end caps that have a radius larger than that of the cylinder and the center of the end cap radius lies within the cylinder. See the diagram for the details of the geometry and restrictions on parameter values.</p>
@@ -3295,4 +3340,11 @@
 <p style="text-align: center;" align="center"><img id="Picture 71" src="img/image118.jpg" alt="" width="402" height="334" /></p>
 <p style="text-align: center;" align="center"><strong>Figure. 2D plot (w/(256X265) data points).</strong></p>
+<p style="text-align: center; page-break-after: avoid;" align="center"><img src="img/image061.jpg" /></p>
+<p style="text-align: center;" align="center"><a name="_Ref173213915"></a><a name="_Ref173306040"></a>Figure. Definition of the angles for oriented 2D cylinders.</p>
+<p style="text-align: center;" align="center"><img src="img/image062.jpg" alt="" width="379" height="256" /></p>
+<p style="text-align: center;" align="center">Figure. Examples of the angles for oriented pp against the detector plane.</p>
+
+
+
 <p style="margin-left: 0.55in; text-indent: -0.3in;"><strong><span style="font-size: 14pt;">2.26.</span></strong><strong><span style="font-size: 7pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></strong><a name="EllipsoidModel"></a><strong><span style="font-size: 14pt;">Ellipsoid Model</span></strong></p>
 <p>This model provides the form factor for an ellipsoid (ellipsoid of revolution) with uniform scattering length density. The form factor is normalized by the particle volume.</p>
@@ -3414,7 +3466,7 @@
 <p>The output of the 1D scattering intensity function for randomly oriented ellipsoids is then given by the equation above.</p>
 <p>The <em>axis_theta</em> and axis<em>_phi</em> parameters are not used for the 1D output. Our implementation of the scattering kernel and the 1D scattering intensity use the c-library from NIST.</p>
-<p style="text-align: center;" align="center"><img src="img/image122.jpg" alt="" width="396" height="297" /></p>
-<p style="text-align: center;" align="center"><span style="font-size: 12pt;">Figure. Examples of the angles for oriented ellipsoid </span></p>
-<p style="text-align: center;" align="center"><span style="font-size: 12pt;">against the detector plane</span>.</p>
+<p style="text-align: center;" align="center"><img src="img/image122.jpg" alt="" width="379" height="256"/></p>
+<p style="text-align: center;" align="center"><span style="font-size: 12pt;">Figure. The angles for oriented ellipsoid </span></p>
+
 <p style="margin-left: 0.85in; text-indent: -0.35in;"><strong>2.1.</strong><strong><span style="font-size: 7pt;">&nbsp;&nbsp;&nbsp;&nbsp; </span>Validation of the ellipsoid model</strong></p>
 <p>Validation of our code was done by comparing the output of the 1D model to the output of the software provided by the NIST (Kline, 2006). Figure 5 shows a comparison of the 1D output of our model and the output of the NIST software.</p>
@@ -3558,6 +3610,6 @@
 <p style="text-align: center;" align="center"><strong>Figure. 1D plot using the default values (w/1000 data point).</strong></p>
 <p style="text-align: center;" align="center"><strong>&nbsp;</strong></p>
-<p style="text-align: center;" align="center"><img src="img/image122.jpg" alt="" width="396" height="297" /></p>
-<p style="text-align: center;" align="center">Figure. Examples of the angles for oriented coreshellellipsoid against the detector plane where a =polar axis.</p>
+<p style="text-align: center;" align="center"><img src="img/image122.jpg" alt="" width="379" height="256"/></p>
+<p style="text-align: center;" align="center">Figure. The angles for oriented coreshellellipsoid .</p>
 <p>Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006):</p>
 <p>REFERENCE</p>
@@ -3674,6 +3726,6 @@
 <p style="text-align: center;" align="center"><img src="img/image131.gif" alt="" width="438" height="272" /></p>
 <p style="text-align: center;" align="center"><strong>Figure. Comparison between 1D and averaged 2D.</strong></p>
-<p style="text-align: center;" align="center"><img src="img/image132.jpg" alt="" width="396" height="297" /></p>
-<p style="text-align: center;" align="center">Figure. Examples of the angles for oriented ellipsoid against the detector plane.</p>
+<p style="text-align: center;" align="center"><img src="img/image132.jpg" alt="" width="379" height="256" /></p>
+<p style="text-align: center;" align="center">Figure. The angles for oriented ellipsoid.</p>
 <p>Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006):</p>
 <p>REFERENCE</p>
@@ -4368,5 +4420,5 @@
 <p style="text-align: center;" align="center"><strong>Figure. 1D plot in the linear scale using the default values (w/200 data point).</strong></p>
 <p>&nbsp;The 2D (Anisotropic model) is based on the reference (above) which I(q) &nbsp;is approximated for 1d scattering. Thus the scattering pattern for 2D may not be accurate. Note that we are not responsible for any incorrectness of the 2D model computation.</p>
-<p style="text-align: center;" align="center"><img id="Object 23" src="img/image156.gif" alt="" width="304" height="321" /></p>
+<p style="text-align: center;" align="center"><img id="Object 23" src="img/image156.jpg" /></p>
 <p style="text-align: center;" align="center">&nbsp;</p>
 <p>&nbsp;</p>
@@ -4493,5 +4545,5 @@
 <p style="text-align: center;" align="center"><strong>Figure. 1D plot in the linear scale using the default values (w/200 data point).</strong></p>
 <p>&nbsp;The 2D (Anisotropic model) is based on the reference (above) in which I(q)&nbsp; is approximated for 1d scattering. Thus the scattering pattern for 2D may not be accurate. Note that we are not responsible for any incorrectness of the 2D model computation.</p>
-<p style="text-align: center;" align="center"><img src="img/image165.gif" alt="" width="304" height="321" /></p>
+<p style="text-align: center;" align="center"><img src="img/image165.gif" /></p>
 <p style="text-align: center;" align="center">&nbsp;</p>
 <p>&nbsp;</p>
@@ -4617,5 +4669,5 @@
 <p style="text-align: center;" align="center"><strong>Figure. 1D plot in the linear scale using the default values (w/200 data point).</strong></p>
 <p>&nbsp;The 2D (Anisotropic model) is based on the reference (1987) in which I(q) &nbsp;is approximated for 1d scattering. Thus the scattering pattern for 2D may not be accurate. Note that we are not responsible for any incorrectness of the 2D model computation.</p>
-<p style="text-align: center;" align="center"><img id="Object 31" src="img/image165.gif" alt="" width="304" height="321" /></p>
+<p style="text-align: center;" align="center"><img id="Object 31" src="img/image165.gif" /></p>
 <p style="text-align: center;" align="center">&nbsp;</p>
 <p>&nbsp;</p>
