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Model Functions
Introduction
Shapes:
- Sphere based: > <a href="#SphereModel">SphereModel (Magnetic 2D Model)< a>, BinaryHSModel, FuzzySphereModel, RaspBerryModel, CoreShellModel (Magnetic 2D Model), Core2ndMomentModel, CoreMultiShellModel (Magnetic 2D Model), VesicleModel, MultiShellModel, OnionExpShellModel, SphericalSLDModel, LinearPearlsModel, PearlNecklaceModel
- Cylinder based: > <a href="#CylinderModel">CylinderModel (Magnetic 2D Model)< a>, CoreShellCylinderModel, CoreShellBicelleModel, HollowCylinderModel, FlexibleCylinderModel, FlexCylEllipXModel, StackedDisksModel, EllipticalCylinderModel, BarBellModel, CappedCylinderModel, PringleModel
- Parallelpipeds: > <a href="#ParallelepipedModel">ParallelepipedModel (Magnetic 2D Model)< a>, CSParallelepipedModel
- Ellipsoids: > <a href="#EllipsoidModel">EllipsoidModel< a>, CoreShellEllipsoidModel, TriaxialEllipsoidModel
- Lamellar: > <a href="#LamellarModel">LamellarModel< a>, LamellarFFHGModel, LamellarPSModel, LamellarPSHGModel
- Paracrystals: > <a href="#LamellarPCrystalModel">LamellarPCrystalModel< a>, SCCrystalModel, FCCrystalModel, BCCrystalModel
Shape-Independent: AbsolutePower_Law, BEPolyelectrolyte, BroadPeakModel, CorrLength, DABModel, Debye, FractalModel, FractalCoreShell, GaussLorentzGel, Guinier, GuinierPorod, Lorentz, MassFractalModel, MassSurfaceFractal, PeakGaussModel, PeakLorentzModel, Poly_GaussCoil, PolyExclVolume, PorodModel, RPA10Model, StarPolymer, SurfaceFractalModel, Teubner Strey, TwoLorentzian, TwoPowerLaw, UnifiedPowerRg, LineModel, ReflectivityModel, ReflectivityIIModel, GelFitModel.
Customized Models: testmodel, testmodel_2, sum_p1_p2, sum_Ap1_1_Ap2, polynomial5, sph_bessel_jn.
Structure Factors: HardSphereStructure, SquareWellStructure, HayterMSAStructure, StickyHSStructure.
References
1. ** ** **Introduction **
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.
2. ** ** Shapes (Scattering Intensity Models)
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.
To easily compare to the scattering intensity measured in experiments, we normalize the form factors by the volume of the particle:
with
where P*0 *( **q*)* is the un-normalized form factor, ( **r*)* is the scattering length density at a given point in space and the integration is done over the volume V of the scatterer.
For systems without inter-particle interference, the form factors we provide can be related to the scattering intensity by the particle volume fraction: .
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 detector will have an azimuthal symmetry around *q*=0.
Our so-called 2D scattering intensity functions provide P(q, * *) for an oriented system as a function of a q-vector in the plane of the detector. We define the angle as the angle between the q vector and the horizontal (x) axis of the plane of the detector.
2.1. ** ** Sphere Model (Magnetic 2D Model)
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. For magnetic scattering, please see the 'Polarization/Magnetic Scattering' in Fitting Help. 1.1. ** Definition**
The 1D scattering intensity is calculated in the following way (Guinier, 1955):
where scale is a volume fraction, V is the volume of the scatterer, r is the radius of the sphere, bkg is the background level and sldXXX is the scattering length density (SLD) of the scatterer or the solvent.<p> Note that if your data is in absolute scale, the 'scale' should represent the volume fraction (unitless) if you have a good fit. If not, it should represent the volume fraction * a factor (by which your data might need to be rescaled).
The 2D scattering intensity is the same as above, regardless of the orientation of the q vector.
The returned value is scaled to units of [cm-1] and the parameters of the sphere model are the following:
Parameter name
Units
Default value
scale
None
1
radius
60
sldSph
-2
2.0e-6
sldSolv
-2
1.0e-6
background
cm-1
0
Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006).
2.1. ** Validation of the sphere model**
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 1 shows a comparison of the output of our model and the output of the NIST software.
Figure 1: Comparison of the DANSE scattering intensity for a sphere with the output of the NIST SANS analysis software. The parameters were set to: Scale=1.0, Radius=60 , Contrast=1e-6 -2, and Background=0.01 cm -1.
2013/09/09 and 2014/01/06 - Description reviewed by King, S. and Parker, P.
2.2. ** ** BinaryHSModel
This model (binary hard sphere model) provides the scattering intensity, for binary mixture of spheres including hard sphere interaction between those particles. Using Percus-Yevick closure, the calculation is an exact multi-component solution:
where Sij are the partial structure factors and fi are the scattering amplitudes of the particles. And the subscript 1 is for the smaller particle and 2 is for the larger. The number fraction of the larger particle, ( x = n2/(n1+n2), n = the number density) is internally calculated based on:
.
The 2D scattering intensity is the same as 1D, regardless of the orientation of the q vector which is defined as .
The parameters of the binary hard sphere are the following (in the names, l (or ls) stands for larger spheres while s (or ss) for the smaller spheres):
Parameter name
Units
Default value
background
cm-1
0.001
l_radius
100.0
ss_sld
-2
0.0
ls_sld
-2
3e-6
solvent_sld
-2
6e-6
s_radius
25.0
vol_frac_ls
0.1
vol_frac_ss
0.2
Figure. 1D plot using the default values above (w/200 data point).
Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006).
See the reference for details.
REFERENCE
N. W. Ashcroft and D. C. Langreth, Physical Review, v. 156 (1967) 685-692.
[Errata found in Phys. Rev. 166 (1968) 934.]
2.3. ** ** FuzzySphereModel
****This model is to calculate the scattering from spherical particles with a "fuzzy" interface.
1.1. ** Definition**
The 1D scattering intensity is calculated in the following way (Guinier, 1955):
The returned value is scaled to units of [cm-1 sr-1], absolute scale.
The scattering intensity I(q) is calculated as:
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:
Here A2(q) is the form factor, P(q). The scale is equivalent to the volume fraction of spheres, each of volume, V. Contrast ( ** ) is the difference of scattering length densities of the sphere and the surrounding solvent.
The poly-dispersion in radius and in fuzziness is provided.
(direct from the reference)
The "fuzziness" of the interface is defined by the parameter (sigma)fuzzy. The particle radius R represents the radius of the particle where the scattering length density profile decreased to 1/2 of the core density. The (sigma)fuzzy is the width of the smeared particle surface: i.e., the standard deviation from the average height of the fuzzy interface. The inner regions of the microgel that display a higher density are described by the radial box profile extending to a radius of approximately Rbox ~ R - 2(sigma). the profile approaches zero as Rsans ~ R + 2(sigma).
For 2D data: The 2D scattering intensity is calculated in the same way as 1D, where the q vector is defined as .
REFERENCE
M. Stieger, J. S. Pedersen, P. Lindner, W. Richtering, Langmuir 20 (2004) 7283-7292.
TEST DATASET
This example dataset is produced by running the FuzzySphereModel, using 200 data points, qmin = 0.001 -1, qmax = 0.7 A-1 and the default values:
Parameter name
Units
Default value
scale
None
1.0
radius
60
fuzziness
10
sldSolv
-2
3e-6
sldSph
-2
1e-6
background
cm-1
0.001
Figure. 1D plot using the default values (w/200 data point).
2.4. RaspBerryModel
Calculates the form factor, P(q), for a "Raspberry-like" structure where there are smaller spheres at the surface of a larger sphere, such as the structure of a Pickering emulsion.
1.1. ** Definition**
The structure is:
Ro = the radius of thelarge sphere Rp = the radius of the smaller sphere on the surface delta = the fractional penetration depth surface coverage = fractional coverage of the large sphere surface (0.9 max)
The large and small spheres have their own SLD, as well as the solvent. The surface coverage term is a fractional coverage (maximum of approximately 0.9 for hexagonally packed spheres on a surface). Since not all of the small spheres are necessarily attached to the surface, the excess free (small) spheres scattering is also included in the calculation. The function calculated follows equations (8)-(12) of the reference below, and the equations are not reproduced here.
The returned value is scaled to units of [cm-1]. No interparticle scattering is included in this model.
For 2D data: The 2D scattering intensity is calculated in the same way as 1D, where the q vector is defined as .
REFERENCE Kjersta Larson-Smith, Andrew Jackson, and Danilo C Pozzo, "Small angle scattering model for Pickering emulsions and raspberry particles." Journal of Colloid and Interface Science (2010) vol. 343 (1) pp. 36-41.
TEST DATASET
This example dataset is produced by running the RaspBerryModel, using 2000 data points, qmin = 0.0001 -1, qmax = 0.2 A-1 and the default values, where Ssph/Lsph stands for Smaller/Large sphere andsurfrac_Ssph for the surface fraction of the smaller spheres.
Parameter name
Units
Default value delta_Ssph 0 radius_Lsph 5000 radius_Ssph 100 sld_Lsph -2 -4e-07 sld_Ssph
-2
3.5e-6
sld_solv
-2
6.3e-6
surfrac_Ssph
0.4
volf_Lsph
0.05
volf_Lsph
0.005
background
cm-1
0
Figure. 1D plot using the values of /2000 data points.
2.5. ** ** Core Shell (Sphere) Model (Magnetic 2D Model)
This model provides the form factor, P( q), for a spherical particle with a core-shell structure. The form factor is normalized by the particle volume. For magnetic scattering, please see the 'Polarization/Magnetic Scattering' in Fitting Help. 1.1. ** Definition**
The 1D scattering intensity is calculated in the following way (Guinier, 1955):
where scale is a scale factor, Vs is the volume of the outer shell, Vc is the volume of the core, rs is the radius of the shell, rc is the radius of the core, c is the scattering length density of the core, s is the scattering length density of the shell, solv is the scattering length density of the solvent, and bkg is the background level.
The 2D scattering intensity is the same as P(q) above, regardless of the orientation of the q vector.
For P*S: The outer most radius (= radius + thickness) is used as the effective radius toward S(Q) when P(Q)*S(Q) is applied.
The returned value is scaled to units of [cm-1] and the parameters of the core-shell sphere model are the following:
Here, radius = the radius of the core and thickness = the thickness of the shell.
Parameter name
Units
Default value
scale
None
1.0
(core) radius
60
thickness
10
core_sld
-2
1e-6
shell_sld
-2
2e-6
solvent_sld
-2
3e-6
background
cm-1
0.001
Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006).
REFERENCE
Guinier, A. and G. Fournet, "Small-Angle Scattering of X-Rays", John Wiley and Sons, New York, (1955).
2.1. ** Validation of the core-shell sphere model**
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 1 shows a comparison of the output of our model and the output of the NIST software.
Figure 7: Comparison of the DANSE scattering intensity for a core- shell sphere with the output of the NIST SANS analysis software. The parameters were set to: Scale=1.0, Radius=60 , Contrast=1e-6 -2, and Background=0.001 cm -1.
2.6. ** ** Core2ndMomentModel
This model describes the scattering from a layer of surfactant or polymer adsorbed on spherical particles under the conditions that (i) theparticles (cores) are contrast-matched to the dispersion medium, (ii) S(Q)~1 (ie, the particle volume fraction is dilute), (iii) the particle radius is >> layer thickness (ie, the interface is locally flat), and (iv) scattering from excess unadsorbed adsorbate in the bulk medium is absent or has been corrected for.
Unlike a core-shell model, this model does not assume any form for the density distribution of the adsorbed species normal to the interface (cf, a core-shell model which assumes the density distribution to be a homogeneous step-function). For comparison, if the thickness of a (core-shell like) step function distribution is t, the second moment, sigma = sqrt((t^2)/12). Thesigma is the second moment about the mean of the density distribution (ie, the distance of the centre-of-mass of the distribution from the interface).
1.1. ** Definition**
The I0 is calculated in the following way (King, 2002):
where scale is a scale factor, poly is the sld of the polymer (or surfactant) layer,solv is the sld of the solvent/medium and cores, phi_cores is the volume fraction of the core paraticles, and Gamma and delta arethe adsorbed amount and the bulk density of the polymers respectively. The sigma is the second moment of the thickness distribution.
Note that all parameters except the 'sigma' are correlated for fitting so that fittingthose with more than one parameters will be generally failed. And note that unlike other shape models, no volume normalization was applied to this model.
The returned value is scaled to units of [cm-1] and the parameters are the following:
Parameter name
Units
Default value
scale
None
1.0
density_poly
g/cm2
0.7
radius_core
500
ads_amount
mg/m2
1.9 second_moment 23.0 volf_cores None 0.14 sld_poly
-2
1.5e-6
sld_solv
-2
6.3e-6
background
cm-1
0.0
REFERENCE
S. King, P. Griffiths, J. Hone, and T. Cosgrove, "SANS from Adsorbed Polymer Lyaers", Macromol. Symp. 190, 33-42 (2002).
2.7. ** ** CoreMultiShell(Sphere)Model (Magnetic 2D Model)
This model provides the scattering from spherical core with from 1 up to 4 shell structures. Ithas a core of a specified radius, with four shells. The SLDs of the core and each shell are individually specified. For magnetic scattering, please see the 'Polarization/Magnetic Scattering' in Fitting Help. 1.1. ** Definition**
The returned value is scaled to units of [cm-1sr-1], absolute scale.
This model is a trivial extension of the CoreShell function to a larger number of shells. See the CoreShell function for a diagram and documentation.
Be careful that the SLDs and scale can be highly correlated. Hold as many of these fixed as possible.
The 2D scattering intensity is the same as P(q) of 1D, regardless of the orientation of the q vector.
For P*S: The outer most radius (= radius + 4 thicknesses) is used as the effective radius toward S(Q) if P(Q)*S(Q) is applied.
The returned value is scaled to units of [cm-1] and the parameters of the CoreFourshell sphere model are the following:
Here, rad_core = the radius of the core, thick_shelli = the thickness of the shell i and sld_shelli = the SLD of the shell i.
And the sld_core and the sld_solv are the SLD of the core and the solvent, respectively.
Parameter name
Units
Default value
scale
None
1.0
rad_core
60
sld_core
-2
6.4e-6
sld_shell1
-2
1e-6
sld_shell2
-2
2e-6
sld_shell3
-2
3e-6
sld_shell4
-2
4e-6
sld_solv
-2
6.4e-6
thick_shell1
10
thick_shell2
10
thick_shell3
10
thick_shell4
10
background
cm-1
0.001
Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006).
REFERENCE
See the CoreShell documentation.
TEST DATASET
This example dataset is produced by running the CoreMultiShellModel using 200 data points, qmin = 0.001 -1, qmax = 0.7 -1 and the above default values.
Figure: 1D plot using the default values (w/200 data point).
The scattering length density profile for the default sld values (w/ 4 shells).
Figure: SLD profile against the radius of the sphere for default SLDs.
2.8. ** ** VesicleModel
This model provides the form factor, P( q), for an unilamellar vesicle. The form factor is normalized by the volume of the shell.
The 1D scattering intensity is calculated in the following way (Guinier, 1955):
where scale is a scale factor, Vshell is the volume of the shell, V1 is the volume of the core, V2 is the total volume, R1 is the radius of the core, r2 is the outer radius of the shell, 1 is the scattering length density of the core and the solvent, 2 is the scattering length density of the shell, and bkg is the background level. And J1 = (sin x *- *x*cos *x)/ *x*2. The functional form is identical to a "typical" core-shell structure, except that the scattering is normalized by the volume that is contributing to the scattering, namely the volume of the shell alone. Also, the vesicle is best defined in terms of a core radius (= R1) and a shell thickness, t.
The 2D scattering intensity is the same as P*( *q) above, regardless of the orientation of the q vector which is defined as .
For P*S: The outer most radius (= radius + thickness) is used as the effective radius toward S(Q) when P(Q)*S(Q) is applied.
The returned value is scaled to units of [cm-1] and the parameters of the vesicle model are the following:
In the parameters, the radius represents the core radius (R1) and the thickness (R2 R1) is the shell thickness.
Parameter name
Units
Default value
scale
None
1.0
radius
100
thickness
30
core_sld
-2
6.3e-6
shell_sld
-2
0
background
cm-1
0.0
Figure. 1D plot using the default values (w/200 data point).
Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006).
REFERENCE
Guinier, A. and G. Fournet, "Small-Angle Scattering of X-Rays", John Wiley and Sons, New York, (1955).
2.9. ** ** MultiShellModel
This model provides the form factor, P( q), for a multi-lamellar vesicle with N shells where the core is filled with solvent and the shells are interleaved with layers of solvent. For N = 1, this return to the vesicle model (above).
The 2D scattering intensity is the same as 1D, regardless of the orientation of the q vector which is defined as .
For P*S: The outer most radius (= core_radius + n_pairs * s_thickness + (n_pairs -1) * w_thickness) is used as the effective radius toward S(Q) when P(Q)*S(Q) is applied.
The returned value is scaled to units of [cm-1] and the parameters of the multi-shell model are the following:
In the parameters, the s_thickness is the shell thickness while the w_thickness is the solvent thickness, and the n_pair is the number of shells.
Parameter name
Units
Default value
scale
None
1.0
core_radius
60.0
n_pairs
None
2.0
core_sld
-2
6.3e-6
shell_sld
-2
0.0
background
cm-1
0.0
s_thickness
10
w_thickness
10
Figure. 1D plot using the default values (w/200 data point).
Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006).
REFERENCE
Cabane, B., Small Angle Scattering Methods, Surfactant Solutions: New Methods of Investigation, Ch.2, Surfactant Science Series Vol. 22, Ed. R. Zana, M. Dekker, New York, 1987.
2.10. ** ** OnionExpShellModel
This model provides the form factor, P*( *q), for a multi-shell sphere where the scattering length density (SLD) of the each shell is described by an exponential (linear, or flat-top) function. The form factor is normalized by the volume of the sphere where the SLD is not identical to the SLD of the solvent. We currently provide up to 9 shells with this model.
The 1D scattering intensity is calculated in the following way:
where, for a spherically symmetric particle with a particle density r*( *r) [L.A.Feigin and D.I.Svergun, Structure Analysis by Small- Angle X-Ray and Neutron Scattering, Plenum Press, New York, 1987],
so that
Here we assumed that the SLDs of the core and solvent are constant against r. Now lets consider the SLD of a shell, rshelli, defineded by
An example of a possible SLD profile is shown below where sld_in_shelli ( rin ) and thick_shelli ( Dtshelli ) stand for the SLD of the inner side of the ith shell and the thickness of the ith shell in the equation above, respectively.
For |A|>0,
For A ~ **0 (eg., A = - 0.0001), this function converges to that of the linear SLD profile (ie, *rshelli*( *r*) = *A *****( *r* - *rshelli-1*) / *Dtshelli*) + *B ***), so this case it is equivalent to
For A = 0, the exponential function has no dependence on the radius (so that sld_out_shell# ( rout) is ignored this case) and becomes flat. We set the constant to rin for convenience, and thus the form factor contributed by the shells is
In the equation,
Finally, the form factor can be calculated by
where
The 2D scattering intensity is the same as P*( *q) above, regardless of the orientation of the q vector which is defined as .
For P*S: The outer most radius is used as the effective radius toward S(Q) when P(Q)*S(Q) is applied.
The returned value is scaled to units of [cm-1] and the parameters of this model are the following:
In the parameters, the rad_core represents the core radius (R1) and the thick_shell1 (R2 R1) is the thickness of the shell1, etc.
Note: Only No. of shells = 1 is given below.
Parameter name
Units
Default value
A_shell1
None
1
scale
None
1.0
rad_core
200
thick_shell1
50
sld_core
-2
1.0e-06
sld_in_shell1
-2
1.7e-06
sld_out_shell1
-2
2.0e-06
sld_solv
-2
6.4e-06
background
cm-1
0.0
Figure. 1D plot using the default values (w/400 point).
Figure. SLD profile from the default values.
REFERENCE
L.A.Feigin and D.I.Svergun, Structure Analysis by Small-Angle X-Ray and Neutron Scattering, Plenum Press, New York, 1987
2.11. ** ** SphericalSLDModel
Similarly to the OnionExpShellModel, this model provides the form factor, P*( *q), for a multi-shell sphere, where the interface between the each neighboring shells can be described by one of the functions including error, power-law, and exponential functions. This model is to calculate the scattering intensity by building a continuous custom SLD profile against the radius of the particle. The SLD profile is composed of a flat core, a flat solvent, a number (up to 9 shells) of flat shells, and the interfacial layers between the adjacent flat shells (or core, and solvent) (See below). Unlike OnionExpShellModel (using an analytical integration), the interfacial layers are sub-divided and numerically integrated assuming each sub- layers are described by a line function. The number of the sub-layer can be given by users by setting the integer values of npts_inter# in GUI. The form factor is normalized by the total volume of the sphere.
The 1D scattering intensity is calculated in the following way:
where, for a spherically symmetric particle with a particle density r*( *r) [L.A.Feigin and D.I.Svergun, Structure Analysis by Small- Angle X-Ray and Neutron Scattering, Plenum Press, New York, 1987],
so that
Here we assumed that the SLDs of the core and solvent are constant against r. The SLD at the interface between shells, rinter_i, is calculated with a function chosen by an user, where the functions are:
- Exp;
- Power-Law;
- Erf;
Then the functions are normalized so that it varies between 0 and 1 and they are constrained such that the SLD is continuous at the boundaries of the interface as well as each sub-layers and thus the B and C are determined.
Once the rinter_i is found at the boundary of the sub-layer of the interface, we can find its contribution to the form factor P(q);
where we assume that rho_inter_i (r) can be approximately linear within a sub-layer j.
In the equation,
Finally, the form factor can be calculated by
where
The 2D scattering intensity is the same as P*( *q) above, regardless of the orientation of the q vector which is defined as .
For P*S: The outer most radius is used as the effective radius toward S(Q) when P(Q)*S(Q) is applied.
The returned value is scaled to units of [cm-1] and the parameters of this model are the following:
In the parameters, the rad_core0 represents the core radius (R1).
Note: Only No. of shells = 1 is given below.
Parameter name
Units
Default value
background
cm-1
0.0
npts_inter
35
scale
1
sld_solv
-2
1e-006
func_inter1
Erf
nu_inter
2.5
thick_inter1
50
sld_flat1
-2
4e-006
thick_flat1
100
func_inter0
Erf
nu_inter0
2.5
rad_core0
50
sld_ core0
-2
2.07e-06
thick_ core0
50
Figure. 1D plot using the default values (w/400 point).
Figure. SLD profile from the default values.
REFERENCE
L.A.Feigin and D.I.Svergun, Structure Analysis by Small-Angle X-Ray and Neutron Scattering, Plenum Press, New York, 1987
2.12. LinearPearlsModel
This model provides the form factor for pearls linearly joined by short strings: N pearls (homogeneous spheres), the radius R and the string segment length (or edge separation) l (= A- 2R)). The A is the center to center pearl separation distance. The thickness of each string is assumed to be negligable.
1.1. ** Definition**
The output of the scattering intensity function for the linearpearls model is given by (Dobrynin, 1996):
where the mass mp is (sld(of a pearl) sld(of solvent)) * (volume of the N pearls), V is the total volume.
The 2D scattering intensity is the same as P(q) above, regardless of the orientation of the q vector.
The returned value is scaled to units of [cm-1] and the parameters are the following:
Parameter name
Units
Default value
scale
None
1.0
radius
80.0
edge_separation
350.0
num_pearls
(integer)
3
sld_pearl
-2
1e-6
sld_solv
-2
6.3e-6
background
cm-1
0.0
REFERENCE
A. V. Dobrynin, M. Rubinstein and S. P. Obukhov, Macromol. 29, 2974-2979, 1996.
2.13. ** ** PearlNecklaceModel
This model provides the form factor for a pearl necklace composed of two elements: N pearls (homogeneous spheres) freely jointed by M rods (like strings) (with a total mass Mw = M *mr + N * ms, the radius R and the string segment length (or edge separation) l (= A- 2R)). The A is the center to center pearl separation distance.
1.1. ** Definition**
The output of the scattering intensity function for the pearlnecklace model is given by (Schweins, 2004):
where
,
,
,
,
,
and
.
where the mass mi is (sld(of i) sld(of solvent)) * (volume of the N pearls/rods), V is the total volume of the necklace.
The 2D scattering intensity is the same as P(q) above, regardless of the orientation of the q vector.
The returned value is scaled to units of [cm-1] and the parameters are the following:
Parameter name
Units
Default value
scale
None
1.0
radius
80.0
edge_separation
350.0
num_pearls
(integer)
3
sld_pearl
-2
1e-6
sld_solv
-2
6.3e-6
sld_string
-2
1e-6
thick_string
(=rod diameter)
2.5
background
cm-1
0.0
REFERENCE
R. Schweins and K. Huber, Particle Scattering Factor of Pearl Necklace Chains, Macromol. Symp., 211, 25-42, 2004.
2.14. ** ** Cylinder Model (Magnetic 2D Model)
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. For magnetic scattering, please see the 'Polarization/Magnetic Scattering' in Fitting Help. 1.1. ** Definition**
The output of the 2D scattering intensity function for oriented cylinders is given by (Guinier, 1955):
where 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 ** (contrast) is the scattering length density difference between the scatterer and the solvent. J1 is the first order Bessel function.
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.
Figure 2. Definition of the angles for oriented cylinders.
Figure. Examples of the angles for oriented pp against the detector plane.
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.
The returned value is scaled to units of [cm-1] and the parameters of the cylinder model are the following:
Parameter name
Units
Default value
scale
None
1.0
radius
20.0
length
400.0
contrast
-2
3.0e-6
background
cm-1
0.0
cyl_theta
degree
60
cyl_phi
degree
60
The output of the 1D scattering intensity function for randomly oriented cylinders is then given by:
The cyl_theta and cyl_phi parameter are not used for the 1D output. Our implementation of the scattering kernel and the 1D scattering intensity use the c-library from NIST.
2.1. ** Validation of the cylinder model**
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 3 shows a comparison of the 1D output of our model and the output of the NIST software.
In general, averaging over a distribution of orientations is done by evaluating the following:
where p(, ) is the probability distribution for the orientation and P0(q, ) is the scattering intensity for the fully oriented system. Since we have no other software to compare the implementation of the intensity for fully oriented cylinders, we can compare the result of averaging our 2D output using a uniform distribution p(, ) = 1.0. Figure 4 shows the result of such a cross-check.
Figure 3: Comparison of the DANSE scattering intensity for a cylinder with the output of the NIST SANS analysis software. The parameters were set to: Scale=1.0, Radius=20 , Length=400 , Contrast=3e-6 -2, and Background=0.01 cm -1.
Figure 4: Comparison of the intensity for uniformly distributed cylinders calculated from our 2D model and the intensity from the NIST SANS analysis software. The parameters used were: Scale=1.0, Radius=20 , Length=400 , Contrast=3e-6 -2, and Background=0.0 cm -1.
2.15. ** ** Core-Shell Cylinder Model
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.
1.1. ** Definition**
The output of the 2D scattering intensity function for oriented core- shell cylinders is given by (Kline, 2006):
where is the angle between the axis of the cylinder and the q-vector, Vs is the volume of the outer shell (i.e. the total volume, including the shell), Vc is the volume of the core, L is the length of the core, r is the radius of the core, t is the thickness of the shell, c is the scattering length density of the core, s is the scattering length density of the shell, solv is the scattering length density of the solvent, and bkg is the background level. The outer radius of the shell is given by r+t and the total length of the outer shell is given by L+2t. J1 is the first order Bessel function.
To provide easy access to the orientation of the core-shell cylinder, we define the axis of the cylinder using two angles and . Similarly to the case of the cylinder, those angles are defined on Figure 2 in Cylinder Model.
For P*S: The 2nd virial coefficient of the solid cylinder is calculate based on the (radius+thickness) and 2(length +thickness) values, and used as the effective radius toward S(Q) when P(Q)*S(Q) is applied.
The returned value is scaled to units of [cm-1] and the parameters of the core-shell cylinder model are the following:
Parameter name
Units
Default value
scale
None
1.0
radius
20.0
thickness
10.0
length
400.0
core_sld
-2
1e-6
shell_sld
-2
4e-6
solvent_sld
-2
1e-6
background
cm-1
0.0
axis_theta
degree
90
axis_phi
degree
0.0
The output of the 1D scattering intensity function for randomly oriented cylinders is then given by the equation above.
The axis_theta and axis _phi 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.
2.1. ** Validation of the core-shell cylinder model**
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 8 shows a comparison of the 1D output of our model and the output of the NIST software.
Averaging over a distribution of orientation is done by evaluating the equation above. Since we have no other software to compare the implementation of the intensity for fully oriented core-shell cylinders, we can compare the result of averaging our 2D output using a uniform distribution p(, ) = 1.0. Figure 9 shows the result of such a cross-check.
Figure 8: Comparison of the DANSE scattering intensity for a core- shell cylinder with the output of the NIST SANS analysis software. The parameters were set to: Scale=1.0, Radius=20 , Thickness=10 , Length=400 , Core_sld=1e-6 -2, Shell_sld=4e-6 -2, Solvent_sld=1e-6 -2, and Background=0.01 cm -1.
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 , Thickness=10 , Length=400 , Core_sld=1e-6 -2, Shell_sld=4e-6 -2, Solvent_sld=1e-6 -2, and Background=0.0 cm -1.
Figure. Definition of the angles for oriented core-shell cylinders.
Figure. Examples of the angles for oriented pp against the detector plane.
2013/11/26 - Description reviewed by Heenan, R.
2.16. ** ** Core-Shell (Cylinder) Bicelle Model
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 core-shell cylinder model (seeabove 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.
The returned value is scaled to units of [cm-1] and the parameters of the core-shell cylinder model are the following:
Parameter name
Units
Default value
scale
None
1.0
radius
20.0
rim_thick
10.0 face_thick 10.0 length
400.0
core_sld
-2
1e-6
rim_sld
-2
4e-6 face_sld -2 4e-6 solvent_sld
-2
1e-6
background
cm-1
0.0
axis_theta
degree
90
axis_phi
degree
0.0
The output of the 1D scattering intensity function for randomly oriented cylinders is then given by the equation above.
The axis_theta and axis _phi 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.
Figure. 1D plot using the default values (w/200 data point).
Figure. Definition of the angles for the oriented Core-Shell Cylinder Bicelle Model.
Figure. Examples of the angles for oriented pp against the detector plane.
REFERENCE Feigin, L. A, and D. I. Svergun, "Structure Analysis by Small-Angle X-Ray and Neutron Scattering", Plenum Press, New York, (1987).
2.17. ** ** HollowCylinderModel
This model provides the form factor, P( q), for a monodisperse hollow right angle circular cylinder (tube) where the form factor is normalized by the volume of the tube:
P(q) = scale*<f^2>/Vshell+background where the averaging < > id applied only for the 1D calculation. The inside and outside of the hollow cylinder have the same SLD.
The 1D scattering intensity is calculated in the following way (Guinier, 1955):
where scale is a scale factor, J1 is the 1st order Bessel function, J1 (x)= (sin x *- *x*cos *x)/ *x*2.
To provide easy access to the orientation of the core-shell cylinder, we define the axis of the cylinder using two angles and . Similarly to the case of the cylinder, those angles are defined on Figure 2 in Cylinder Model.
For P*S: The 2nd virial coefficient of the solid cylinder is calculate based on the (radius) and 2(length) values, and used as the effective radius toward S(Q) when P(Q)*S(Q) is applied.
In the parameters, the contrast represents SLD (shell) - SLD (solvent) and the radius = Rhell while core_radius = Rcore.
Parameter name
Units
Default value
scale
None
1.0
radius
30
length
400
core_radius
20
sldCyl
-2
6.3e-6
sldSolv
-2
5e-06
background
cm-1
0.01
Figure. 1D plot using the default values (w/1000 data point).
Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006).
Figure. Definition of the angles for the oriented HollowCylinderModel.
Figure. Examples of the angles for oriented pp against the detector plane.
REFERENCE
Feigin, L. A, and D. I. Svergun, "Structure Analysis by Small-Angle X-Ray and Neutron Scattering", Plenum Press, New York, (1987).
2.18. ** ** FlexibleCylinderModel
This model provides the form factor, P( q), for a flexible cylinder where the form factor is normalized by the volume of the cylinder: Inter-cylinder interactions are NOT included. P(q) = scale*<f^2>/V+background where the averaging < > is applied over all orientation for 1D. The 2D scattering intensity is the same as 1D, regardless of the orientation of the q vector which is defined as .
The chain of contour length, L, (the total length) can be described a chain of some number of locally stiff segments of length lp. The persistence length,lp, is the length along the cylinder over which the flexible cylinder can be considered a rigid rod. The Kuhn length (b = 2*lp) is also used to describe the stiffness of a chain. The returned value is in units of [cm-1], on absolute scale. In the parameters, the sldCyl and sldSolv represent SLD (chain/cylinder) and SLD (solvent) respectively.
Parameter name
Units
Default value
scale
None
1.0
radius
20
length
1000
sldCyl
-2
1e-06
sldSolv
-2
6.3e-06
background
cm-1
0.01
kuhn_length
100
Figure. 1D plot using the default values (w/1000 data point).
Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006):
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. See equations (13,26-27) in the original reference for the details.
REFERENCE
Pedersen, J. S. and P. Schurtenberger (1996). Scattering functions of semiflexible polymers with and without excluded volume effects. Macromolecules 29: 7602-7612.
Correction of the formula can be found in:
Wei-Ren Chen, Paul D. Butler, and Linda J. Magid, "Incorporating Intermicellar Interactions in the Fitting of SANS Data from Cationic Wormlike Micelles" Langmuir, August 2006.
2.19. ** ** FlexCylEllipXModel
**Flexible Cylinder with Elliptical Cross-Section: **Calculates the form factor for a flexible cylinder with an elliptical cross section and a uniform scattering length density. The non-negligible diameter of the cylinder is included by accounting for excluded volume interactions within the walk of a single cylinder. The form factor is normalized by the particle volume such that P(q) = scale*<f^2>/Vol + bkg, where < > is an average over all possible orientations of the flexible cylinder.
1.1. ** Definition**
The function calculated is from the reference given below. From that paper, "Method 3 With Excluded Volume" is used. The model is a parameterization of simulations of a discrete representation of the worm-like chain model of Kratky and Porod applied in the pseudo- continuous limit. See equations (13, 26-27) in the original reference for the details.
NOTE: there are several typos in the original reference that have been corrected by WRC. Details of the corrections are in the reference below.
- Equation (13): the term (1-w(QR)) should swap position with w(QR)
- Equations (23) and (24) are incorrect. WRC has entered these into
Mathematica and solved analytically. The results were converted to code.
- Equation (27) should be q0 = max(a3/sqrt(RgSquare),3) instead of
max(a3*b/sqrt(RgSquare),3)
- The scattering function is negative for a range of parameter values
and q-values that are experimentally accessible. A correction function has been added to give the proper behavior.
The chain of contour length, L, (the total length) can be described a chain of some number of locally stiff segments of length lp. The persistence length, lp, is the length along the cylinder over which the flexible cylinder can be considered a rigid rod. The Kuhn length (b) used in the model is also used to describe the stiffness of a chain, and is simply b = 2*lp.
The cross section of the cylinder is elliptical, with minor radius a. The major radius is larger, so of course, the axis ratio (parameter 4) must be greater than one. Simple constraints should be applied during curve fitting to maintain this inequality.
The returned value is in units of [cm-1], on absolute scale.
The sldCyl = SLD (chain), sldSolv = SLD (solvent). The scale, and the contrast are both multiplicative factors in the model and are perfectly correlated. One or both of these parameters must be held fixed during model fitting.
If the scale is set equal to the particle volume fraction, f, the returned value is the scattered intensity per unit volume, I(q) = f*P(q). However, no inter-particle interference effects are included in this calculation.
For 2D data: The 2D scattering intensity is calculated in the same way as 1D, where the q vector is defined as .
REFERENCE
Pedersen, J. S. and P. Schurtenberger (1996). Scattering functions of semiflexible polymers with and without excluded volume effects. Macromolecules 29: 7602-7612.
Corrections are in:
Wei-Ren Chen, Paul D. Butler, and Linda J. Magid, "Incorporating Intermicellar Interactions in the Fitting of SANS Data from Cationic Wormlike Micelles" Langmuir, August 2006.
TEST DATASET
This example dataset is produced by running the Macro FlexCylEllipXModel, using 200 data points, qmin = 0.001 -1, qmax = 0.7 -1 and the default values below.
Parameter name
Units
Default value
axis_ratio
1.5
background
cm-1
0.0001
Kuhn_length
100
(Contour) length
1e+3
radius
20.0
scale
1.0
sldCyl
-2
1e-6
sldSolv
-2
6.3e-6
Figure. 1D plot using the default values (w/200 data points).
2.20. ** ** **StackedDisksModel **
This model provides the form factor, P( q), for stacked discs (tactoids) with a core/layer structure where the form factor is normalized by the volume of the cylinder. Assuming the next neighbor distance (d-spacing) in a stack of parallel discs obeys a Gaussian distribution, a structure factor S(q) proposed by Kratky and Porod in 1949 is used in this function. Note that the resolution smearing calculation uses 76 Gauss quadrature points to properly smear the model since the function is HIGHLY oscillatory, especially around the q-values that correspond to the repeat distance of the layers.
The 2D scattering intensity is the same as 1D, regardless of the orientation of the q vector which is defined as .
The returned value is in units of [cm-1 sr-1], on absolute scale.
The scattering intensity I(q) is:
where the contrast,
N is the number of discs per unit volume, ais the angle between the axis of the disc and q, and Vt and Vc are the total volume and the core volume of a single disc, respectively.
where d = thickness of the layer (layer_thick), 2h= core thickness (core_thick), and R = radius of the disc (radius).
where n = the total number of the disc stacked (n_stacking), D=the next neighbor center to cent distance (d-spacing), and sD= the Gaussian standard deviation of the d-spacing (sigma_d).
To provide easy access to the orientation of the stackeddisks, we define the axis of the cylinder using two angles and . Similarly to the case of the cylinder, those angles are defined on Figure 2 of CylinderModel.
For P*S: The 2nd virial coefficient of the solid cylinder is calculate based on the (radius) and length = n_stacking*(core_thick +2*layer_thick) values, and used as the effective radius toward S(Q) when P(Q)*S(Q) is applied.
Parameter name
Units
Default value
background
cm-1
0.001
core_sld
-2
4e-006
core_thick
10
layer_sld
-2
0
layer_thick
15
n_stacking
1
radius
3e+003
scale
0.01
sigma_d
0
solvent_sld
-2
5e-006
Figure. 1D plot using the default values (w/1000 data point).
Figure. Examples of the angles for oriented stackeddisks against the detector plane.
Figure. Examples of the angles for oriented pp against the detector plane.
Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006):
REFERENCE
Guinier, A. and Fournet, G., "Small-Angle Scattering of X-Rays", John Wiley and Sons, New York, 1955.
Kratky, O. and Porod, G., J. Colloid Science, 4, 35, 1949.
Higgins, J.S. and Benoit, H.C., "Polymers and Neutron Scattering", Clarendon, Oxford, 1994.
2.21. ** ** Elliptical Cylinder Model
This function calculates the scattering from an oriented elliptical cylinder.
For 2D (orientated system):
The angles theta and phi define the orientation of the axis of the cylinder. The angle psi is defined as the orientation of the major axis of the ellipse with respect to the vector Q. A gaussian poydispersity can be added to any of the orientation angles, and also for the minor radius and the ratio of the ellipse radii.
Figure. a= r_minor and ** **n= r_ratio (i.e., r_major/r_minor).
The function calculated is:
with the functions:
and the angle psi is defined as the orientation of the major axis of the ellipse with respect to the vector Q.
For 1D (no preferred orientation):
The form factor is averaged over all possible orientation before normalized by the particle volume: P(q) = scale*<f^2>/V .
The returned value is scaled to units of [cm-1].
To provide easy access to the orientation of the elliptical, we define the axis of the cylinder using two angles , andY. Similarly to the case of the cylinder, those angles, and , are defined on Figure 2 of CylinderModel. The angle Y is the rotational angle around its own long_c axis against the q plane. For example, Y = 0 when the r_minor axis is parallel to the x-axis of the detector.
All angle parameters are valid and given only for 2D calculation (Oriented system).
Figure. Definition of angels for 2D.
Figure. Examples of the angles for oriented elliptical cylinders
against the detector plane.
For P*S: The 2nd virial coefficient of the solid cylinder is calculate based on the averaged radius (=sqrt(r_minor^2*r_ratio)) and length values, and used as the effective radius toward S(Q) when P(Q)*S(Q) is applied.
Parameter name
Units
Default value
scale
None
1.0
r_minor
20.0
r_ratio
1.5
length
400.0
sldCyl
-2
4e-6
sldSolv
-2
1e-006
background
0
Figure. 1D plot using the default values (w/1000 data point).
Validation of the elliptical cylinder 2D model
Validation of our code was done by comparing the output of the 1D calculation to the angular average of the output of 2 D calculation over all possible angles. The Figure below shows the comparison where the solid dot refers to averaged 2D while the line represents the result of 1D calculation (for 2D averaging, 76, 180, 76 points are taken for the angles of theta, phi, and psi respectively).
Figure. Comparison between 1D and averaged 2D.
In the 2D average, more binning in the angle phi is necessary to get the proper result. The following figure shows the results of the averaging by varying the number of bin over angles.
**Figure. The intensities averaged from 2D over different number **
of points of binning of angles.
REFERENCE
L. A. Feigin and D. I. Svergun Structure Analysis by Small-Angle X-Ray and Neutron Scattering, Plenum, New York, (1987).
2.22. ** ** BarBell(/DumBell)Model
Calculates the scattering from a barbell-shaped cylinder (This model simply becomes the DumBellModel when the length of the cylinder, L, is set to zero). That is, a sphereocylinder with spherical end caps that have a radius larger than that of the cylinder and the center of the end cap radius lies outside of the cylinder All dimensions of the barbell are considered to be monodisperse. See the diagram for the details of the geometry and restrictions on parameter values.
1.1. ** Definition**
The returned value is scaled to units of [cm-1sr-1], absolute scale.
The barbell geometry is defined as:
r is the radius of the cylinder. All other parameters are as defined in the diagram. Since the end cap radius R >= r and by definition for this geometry h > 0, h is then defined by r and R as:
h = sqrt(R^2 - r^2).
The scattering intensity I(q) is calculated as:
where the amplitude A(q) is given as:
The < > brackets denote an average of the structure over all orientations. <A^2(q)> is then the form factor, P(q). The scale factor is equivalent to the volume fraction of cylinders, each of volume, V. Contrast is the difference of scattering length densities of the cylinder and the surrounding solvent.
The volume of the barbell is:
and its radius of gyration:
The necessary conditions of R >= r is not enforced in the model. It is up to you to restrict this during analysis.
REFERENCES
- Kaya, J. Appl. Cryst. (2004) 37, 223-230.
H. Kaya and N-R deSouza, J. Appl. Cryst. (2004) 37, 508-509. (addenda and errata)
TEST DATASET
This example dataset is produced by running the Macro PlotBarbell(), using 200 data points, qmin = 0.001 -1, qmax = 0.7 -1 and the above default values.
Parameter name
Units
Default value
scale
None
1.0
len_bar
400.0
rad_bar
20.0
rad_bell
40.0
sld_barbell
-2
1.0e-006
sld_solv
-2
6.3e-006
background
0
Figure. 1D plot using the default values (w/256 data point).
For 2D data: The 2D scattering intensity is calculated similar to the 2D cylinder model. At the theta = 45 deg and phi =0 deg with default values for other parameters,
Figure. 2D plot (w/(256X265) data points).
Figure. Examples of the angles for oriented pp against the detector plane.
Figure. Definition of the angles for oriented 2D barbells.
2.23. ** ** CappedCylinder(/ConvexLens)Model
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. 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.
1.1. ** Definition**
The returned value is scaled to units of [cm-1sr-1], absolute scale.
The Capped Cylinder geometry is defined as:
r is the radius of the cylinder. All other parameters are as defined in the diagram. Since the end cap radius R >= r and by definition for this geometry h < 0, h is then defined by r and R as:
h = -1*sqrt(R^2 - r^2).
The scattering intensity I(q) is calculated as:
where the amplitude A(q) is given as:
The < > brackets denote an average of the structure over all orientations. <A^2(q)> is then the form factor, P(q). The scale factor is equivalent to the volume fraction of cylinders, each of volume, V. Contrast is the difference of scattering length densities of the cylinder and the surrounding solvent.
The volume of the Capped Cylinder is:
(with h as a positive value here)
and its radius of gyration:
The necessary conditions of R >= r is not enforced in the model. It is up to you to restrict this during analysis.
REFERENCES
- Kaya, J. Appl. Cryst. (2004) 37, 223-230.
H. Kaya and N-R deSouza, J. Appl. Cryst. (2004) 37, 508-509. (addenda and errata)
TEST DATASET
This example dataset is produced by running the Macro CappedCylinder(), using 200 data points, qmin = 0.001 -1, qmax = 0.7 -1 and the above default values.
Parameter name
Units
Default value
scale
None
1.0
len_cyl
400.0
rad_cap
40.0
rad_cyl
20.0
sld_capcyl
-2
1.0e-006
sld_solv
-2
6.3e-006
background
0
Figure. 1D plot using the default values (w/256 data point).
For 2D data: The 2D scattering intensity is calculated similar to the 2D cylinder model. At the theta = 45 deg and phi =0 deg with default values for other parameters,
Figure. 2D plot (w/(256X265) data points).
Figure. Definition of the angles for oriented 2D cylinders.
Figure. Examples of the angles for oriented pp against the detector plane.
2.24. ** ** PringleModel
This model provides the form factor, P( q), for a 'pringle' or 'saddle-shaped' object (a hyperbolic paraboloid).
The returned value is in units of [cm-1], on absolute scale.
The form factor calculated is:
where
The parameters of the model and a plot comparing the pringle model with the equivalent cylinder are shown below.
Parameter name
Units
Default value
background
cm-1
0.0
alpha
0.001
beta
0.02
radius
60
scale
1
sld_pringle
-2
1e-006
sld_solvent
-2
6.3e-006
thickness
10
Figure. 1D plot using the default values (w/150 data point).
REFERENCE
- Alexandru Rautu, Private Communication.
2.25. ** ** **ParallelepipedModel (Magnetic 2D Model) **
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. P(q) = scale*<f^2>/V+background where the volume V= ABC and the averaging < > is applied over all orientation for 1D. For magnetic scattering, please see the 'Polarization/Magnetic Scattering' in Fitting Help.
The side of the solid must be satisfied the condition of A<B
By this definition, assuming
a = A/B<1; b=B/B=1; c=C/B>1, the form factor,
The contrast is defined as
The scattering intensity per unit volume is returned in the unit of [cm-1]; I(q) = fP(q).
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.
To provide easy access to the orientation of the parallelepiped, we define the axis of the cylinder using two angles , andY. Similarly to the case of the cylinder, those angles, and , are defined on Figure 2 of CylinderModel. The angle Y is the rotational angle around its own long_c axis against the q plane. For example, Y = 0 when the short_b axis is parallel to the x-axis of the detector.
Figure. Definition of angles for 2D.
Figure. Examples of the angles for oriented pp against the detector plane.
Parameter name
Units
Default value
background
cm-1
0.0
contrast
-2
5e-006
long_c
400
short_a
-2
35
short_b
75
scale
1
Figure. 1D plot using the default values (w/1000 data point).
Validation of the parallelepiped 2D model
Validation of our code was done by comparing the output of the 1D calculation to the angular average of the output of 2 D calculation over all possible angles. The Figure below shows the comparison where the solid dot refers to averaged 2D while the line represents the result of 1D calculation (for the averaging, 76, 180, 76 points are taken over the angles of theta, phi, and psi respectively).
Figure. Comparison between 1D and averaged 2D.
Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006):
REFERENCE
Mittelbach and Porod, Acta Physica Austriaca 14 (1961) 185-211.
Equations (1), (13-14). (in German)
2.26. ** ** CSParallelepipedModel
Calculates the form factor for a rectangular solid with a core-shell structure. The thickness and the scattering length density of the shell or "rim" can be different on all three (pairs) of faces. The form factor is normalized by the particle volume such that P(q) = scale*<f^2>/Vol + bkg, where < > is an average over all possible orientations of the rectangular solid. An instrument resolution smeared version is also provided.
The function calculated is the form factor of the rectangular solid below. The core of the solid is defined by the dimensions ABC such that A < B < C.
There are rectangular "slabs" of thickness tA that add to the A dimension (on the BC faces). There are similar slabs on the AC (=tB) and AB (=tC) faces. The projection in the AB plane is then:
The volume of the solid is:
meaning that there are "gaps" at the corners of the solid.
The intensity calculated follows the parallelepiped model, with the core-shell intensity being calculated as the square of the sum of the amplitudes of the core and shell, in the same manner as a core-shell sphere.
For the calculation of the form factor to be valid, the sides of the solid MUST be chosen such that A < B < C. If this inequality in not satisfied, the model will not report an error, and the calculation will not be correct.
FITTING NOTES:
If the scale is set equal to the particle volume fraction, f, the returned value is the scattered intensity per unit volume, I(q) = f*P(q). However, no interparticle interference effects are included in this calculation.
There are many parameters in this model. Hold as many fixed as possible with known values, or you will certainly end up at a solution that is unphysical.
Constraints must be applied during fitting to ensure that the inequality A < B < C is not violated. The calculation will not report an error, but the results will not be correct.
The returned value is in units of [cm-1], on absolute scale.
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.
To provide easy access to the orientation of the CSparallelepiped, we define the axis of the cylinder using two angles , andY. Similarly to the case of the cylinder, those angles, and , are defined on Figure 2 of CylinderModel. The angle Y is the rotational angle around its own long_c axis against the q plane. For example, Y = 0 when the short_b axis is parallel to the x-axis of the detector.
Figure. Definition of angles for 2D.
Figure. Examples of the angles for oriented cspp against the detector plane.
TEST DATASET
This example dataset is produced by running the Macro Plot_CSParallelepiped(), using 100 data points, qmin = 0.001 -1, qmax = 0.7 -1 and the below default values.
Parameter name
Units
Default value
background
cm-1
0.06
sld_pcore
-2
1e-006
sld_rimA
-2
2e-006
sld_rimB
-2
4e-006
sld_rimC
-2
2e-006
sld_solv
-2
6e-006
rimA
10
rimB
10
rimC
10
longC
400
shortA
35
midB
75
scale
1
Figure. 1D plot using the default values (w/256 data points).
Figure. 2D plot using the default values (w/(256X265) data points).
Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006):
REFERENCE
see: Mittelbach and Porod, Acta Physica Austriaca 14 (1961) 185-211.
Equations (1), (13-14). (yes, it's in German)
2.27. ** ** Ellipsoid Model
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.
1.1. ** Definition**
The output of the 2D scattering intensity function for oriented ellipsoids is given by (Feigin, 1987):
where is the angle between the axis of the ellipsoid and the q-vector, V is the volume of the ellipsoid, Ra is the radius along the rotation axis of the ellipsoid, Rb is the radius perpendicular to the rotation axis of the ellipsoid and ** (contrast) is the scattering length density difference between the scatterer and the solvent.
To provide easy access to the orientation of the ellipsoid, we define the rotation axis of the ellipsoid using two angles and . Similarly to the case of the cylinder, those angles are defined on Figure 2. For the ellipsoid, is the angle between the rotation axis and the z-axis.
For P*S: The 2nd virial coefficient of the solid ellipsoid is calculate based on the radius_a and radius_b values, and used as the effective radius toward S(Q) when P(Q)*S(Q) is applied.
The returned value is scaled to units of [cm-1] and the parameters of the ellipsoid model are the following:
Parameter name
Units
Default value
scale
None
1.0
radius_a (polar)
20.0
radius_b (equatorial)
400.0
sldEll
-2
4.0e-6
sldSolv
-2
1.0e-6
background
cm-1
0.0
axis_theta
degree
90
axis_phi
degree
0.0
The output of the 1D scattering intensity function for randomly oriented ellipsoids is then given by the equation above.
The axis_theta and axis _phi 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.
Figure. The angles for oriented ellipsoid
2.1. ** Validation of the ellipsoid model**
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.
Averaging over a distribution of orientation is done by evaluating the equation above. Since we have no other software to compare the implementation of the intensity for fully oriented ellipsoids, we can compare the result of averaging our 2D output using a uniform distribution p(, ) = 1.0. Figure 6 shows the result of such a cross-check.
The discrepancy above q=0.3 -1 is due to the way the form factors are calculated in the c-library provided by NIST. A numerical integration has to be performed to obtain P(q) for randomly oriented particles. The NIST software performs that integration with a 76-point Gaussian quadrature rule, which will become imprecise at high q where the amplitude varies quickly as a function of q. The DANSE result shown has been obtained by summing over 501 equidistant points in . Our result was found to be stable over the range of q shown for a number of points higher than 500.
** **
Figure 5: Comparison of the DANSE scattering intensity for an ellipsoid with the output of the NIST SANS analysis software. The parameters were set to: Scale=1.0, Radius_a=20 , Radius_b=400 ,
Contrast=3e-6 -2, and Background=0.01 cm -1.
Figure 6: Comparison of the intensity for uniformly distributed ellipsoids calculated from our 2D model and the intensity from the NIST SANS analysis software. The parameters used were: Scale=1.0, Radius_a=20 , Radius_b=400 , Contrast=3e-6 -2, and Background=0.0 cm -1.
2.28. ** ** **CoreShellEllipsoidModel **
This model provides the form factor, P( q), for a core shell ellipsoid (below) where the form factor is normalized by the volume of the cylinder. P(q) = scale*<f^2>/V+background where the volume V= 4pi/3*rmaj*rmin2 and the averaging < > is applied over all orientation for 1D.
The returned value is in units of [cm-1], on absolute scale.
The form factor calculated is:
To provide easy access to the orientation of the coreshell ellipsoid, we define the axis of the solid ellipsoid using two angles , . Similarly to the case of the cylinder, those angles, and , are defined on Figure 2 of CylinderModel.
The contrast is defined as SLD(core) SLD(shell) or SLD(shell solvent). In the parameters, equat_core = equatorial core radius, polar_core = polar core radius, equat_shell = rmin (or equatorial outer radius), and polar_shell = = rmaj (or polar outer radius).
For P*S: The 2nd virial coefficient of the solid ellipsoid is calculate based on the radius_a (= polar_shell) and radius_b (= equat_shell) values, and used as the effective radius toward S(Q) when P(Q)*S(Q) is applied.
Parameter name
Units
Default value
background
cm-1
0.001
equat_core
200
equat_shell
250
sld_solvent
-2
6e-006
ploar_shell
30
ploar_core
20
scale
1
sld_core
-2
2e-006
sld_shell
-2
1e-006
Figure. 1D plot using the default values (w/1000 data point).
Figure. The angles for oriented coreshellellipsoid .
Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006):
REFERENCE
Kotlarchyk, M.; Chen, S.-H. J. Chem. Phys., 1983, 79, 2461.
Berr, S. J. Phys. Chem., 1987, 91, 4760.
2.29. ** ** TriaxialEllipsoidModel
This model provides the form factor, P( q), for an ellipsoid (below) where all three axes are of different lengths, i.e., Ra =< Rb =< Rc (Note that users should maintains this inequality for the all calculations). P(q) = scale*<f^2>/V+background where the volume V= 4pi/3*Ra*Rb*Rc, and the averaging < > is applied over all orientation for 1D.
The returned value is in units of [cm-1], on absolute scale.
The form factor calculated is:
To provide easy access to the orientation of the triaxial ellipsoid, we define the axis of the cylinder using the angles , andY. Similarly to the case of the cylinder, those angles, and , are defined on Figure 2 of CylinderModel. The angle Y is the rotational angle around its own semi_axisC axis against the q plane. For example, Y = 0 when the semi_axisA axis is parallel to the x-axis of the detector.
The radius of gyration for this system is Rg2 = (Ra2*Rb2*Rc2)/5. The contrast is defined as SLD(ellipsoid) SLD(solvent). In the parameters, semi_axisA = Ra (or minor equatorial radius), semi_axisB = Rb (or major equatorial radius), and semi_axisC = Rc (or polar radius of the ellipsoid).
For P*S: The 2nd virial coefficient of the solid ellipsoid is calculate based on the radius_a (=semi_axisC) and radius_b (=sqrt(semi_axisA* semi_axisB)) values, and used as the effective radius toward S(Q) when P(Q)*S(Q) is applied.
Parameter name
Units
Default value
background
cm-1
0.0
semi_axisA
35
semi_axisB
100
semi_axisC
400
scale
1
sldEll
-2
1.0e-006
sldSolv
-2
6.3e-006
Figure. 1D plot using the default values (w/1000 data point).
Validation of the triaxialellipsoid 2D model
Validation of our code was done by comparing the output of the 1D calculation to the angular average of the output of 2 D calculation over all possible angles. The Figure below shows the comparison where the solid dot refers to averaged 2D while the line represents the result of 1D calculation (for 2D averaging, 76, 180, 76 points are taken for the angles of theta, phi, and psi respectively).
Figure. Comparison between 1D and averaged 2D.
Figure. The angles for oriented ellipsoid.
Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006):
REFERENCE
L. A. Feigin and D. I. Svergun Structure Analysis by Small-Angle X-Ray and Neutron Scattering, Plenum, New York, 1987.
2.30. ** ** LamellarModel
This model provides the scattering intensity, I( q), for a lyotropic lamellar phase where a uniform SLD and random distribution in solution are assumed. The ploydispersion in the bilayer thickness can be applied from the GUI.
The scattering intensity I(q) is:
The form factor is,
where d = bilayer thickness.
The 2D scattering intensity is calculated in the same way as 1D, where the q vector is defined as .
The returned value is in units of [cm-1], on absolute scale. In the parameters, sld_bi = SLD of the bilayer, sld_sol = SLD of the solvent, and bi_thick = the thickness of the bilayer.
Parameter name
Units
Default value
background
cm-1
0.0
sld_bi
-2
1e-006
bi_thick
50
sld_sol
-2
6e-006
scale
1
Figure. 1D plot using the default values (w/1000 data point).
Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006):
REFERENCE
Nallet, Laversanne, and Roux, J. Phys. II France, 3, (1993) 487-502.
also in J. Phys. Chem. B, 105, (2001) 11081-11088.
2.31. ** ** LamellarFFHGModel
This model provides the scattering intensity, I( q), for a lyotropic lamellar phase where a random distribution in solution are assumed. The SLD of the head region is taken to be different from the SLD of the tail region.
The scattering intensity I(q) is:
The form factor is,
where dT = tail length (or t_length), dH = heasd thickness (or h_thickness) , DrH = SLD (headgroup) - SLD(solvent), and DrT = SLD (tail) - SLD(headgroup).
The 2D scattering intensity is calculated in the same way as 1D, where the q vector is defined as .
The returned value is in units of [cm-1], on absolute scale. In the parameters, sld_tail = SLD of the tail group, and sld_head = SLD of the head group.
Parameter name
Units
Default value
background
cm-1
0.0
sld_head
-2
3e-006
scale
1
sld_solvent
-2
6e-006
h_thickness
10
t_length
15
sld_tail
-2
0
Figure. 1D plot using the default values (w/1000 data point).
Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006):
REFERENCE
Nallet, Laversanne, and Roux, J. Phys. II France, 3, (1993) 487-502.
also in J. Phys. Chem. B, 105, (2001) 11081-11088.
2.32. ** ** LamellarPSModel
This model provides the scattering intensity ( form factor * structure factor), I( q), for a lyotropic lamellar phase where a random distribution in solution are assumed.
The scattering intensity I(q) is:
The form factor is
and the structure is
where
Here d= (repeat) spacing, d = bilayer thickness, the contrast Dr = SLD (headgroup) - SLD(solvent), K=smectic bending elasticity, B=compression modulus, and N = number of lamellar plates (n_plates).
Note: When the Caille parameter is greater than approximately 0.8 to 1.0, the assumptions of the model are incorrect. And due to the complication of the model function, users are responsible to make sure that all the assumptions are handled accurately: see the original reference (below) for more details.
The 2D scattering intensity is calculated in the same way as 1D, where the q vector is defined as .
The returned value is in units of [cm-1], on absolute scale.
Parameter name
Units
Default value
background
cm-1
0.0
contrast
-2
5e-006
scale
1
delta
30
n_plates
20
spacing
400
caille
-2
0.1
Figure. 1D plot using the default values (w/6000 data point).
Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006):
REFERENCE
Nallet, Laversanne, and Roux, J. Phys. II France, 3, (1993) 487-502.
also in J. Phys. Chem. B, 105, (2001) 11081-11088.
2.33. ** ** LamellarPSHGModel
This model provides the scattering intensity ( form factor * structure factor), I( q), for a lyotropic lamellar phase where a random distribution in solution are assumed. The SLD of the head region is taken to be different from the SLD of the tail region.
The scattering intensity I(q) is:
The form factor is,
The structure factor is
where
where dT = tail length (or t_length), dH = heasd thickness (or h_thickness) , DrH = SLD (headgroup) - SLD(solvent), and DrT = SLD (tail) - SLD(headgroup). Here d= (repeat) spacing, K=smectic bending elasticity, B=compression modulus, and N = number of lamellar plates (n_plates).
Note: When the Caille parameter is greater than approximately 0.8 to 1.0, the assumptions of the model are incorrect. And due to the complication of the model function, users are responsible to make sure that all the assumptions are handled accurately: see the original reference (below) for more details.
The 2D scattering intensity is calculated in the same way as 1D, where the q vector is defined as .
The returned value is in units of [cm-1], on absolute scale. In the parameters, sld_tail = SLD of the tail group, sld_head = SLD of the head group, and sld_solvent = SLD of the solvent.
Parameter name
Units
Default value
background
cm-1
0.001
sld_head
-2
2e-006
scale
1
sld_solvent
-2
6e-006
deltaH
2
deltaT
10
sld_tail
-2
0
n_plates
30
spacing
40
caille
-2
0.001
Figure. 1D plot using the default values (w/6000 data point).
Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006):
REFERENCE
Nallet, Laversanne, and Roux, J. Phys. II France, 3, (1993) 487-502.
also in J. Phys. Chem. B, 105, (2001) 11081-11088.
2.34. ** ** LamellarPCrystalModel
Lamella ParaCrystal Model: Calculates the scattering from a stack of repeating lamellar structures. The stacks of lamellae (infinite in lateral dimension) are treated as a paracrystal to account for the repeating spacing. The repeat distance is further characterized by a Gaussian polydispersity. This model can be used for large multilamellar vesicles.
The scattering intensity I(q) is calculated as:
The form factor of the bilayer is approximated as the cross section of an infinite, planar bilayer of thickness t.
Here, the scale factor is used instead of the mass per area of the bilayer (G). The scale factor is the volume fraction of the material in the bilayer, not the total excluded volume of the paracrystal. ZN(q) describes the interference effects for aggregates consisting of more than one bilayer. The equations used are (3-5) from the Bergstrom reference below.
Non-integer numbers of stacks are calculated as a linear combination of the lower and higher values:
The 2D scattering intensity is the same as 1D, regardless of the orientation of the q vector which is defined as .
The parameters of the model are the following (Nlayers= no. of layers, pd_spacing= polydispersity of spacing):
Parameter name
Units
Default value
background
cm-1
0
scale
1
Nlayers
20
pd_spacing
0.2
sld_layer
-2
1e-6
sld_solvent
-2
6.34e-6
spacing
250
thickness
33
Figure. 1D plot using the default values above (w/20000 data point).
Our model uses the form factor calculations implemented in a c-library provided by the NIST Center for Neutron Research (Kline, 2006).
See the reference for details.
REFERENCE
M. Bergstrom, J. S. Pedersen, P. Schurtenberger, S. U. Egelhaaf, J. Phys. Chem. B, 103 (1999) 9888-9897.
2.35. ** ** SC(Simple Cubic Para-)CrystalModel
Calculates the scattering from a simple cubic lattice with paracrystalline distortion. Thermal vibrations are considered to be negligible, and the size of the paracrystal is infinitely large. Paracrystalline distortion is assumed to be isotropic and characterized by a Gaussian distribution.
The returned value is scaled to units of [cm-1sr-1], absolute scale.
The scattering intensity I(q) is calculated as:
where scale is the volume fraction of spheres, Vp is the volume of the primary particle, V(lattice) is a volume correction for the crystal structure, P(q) is the form factor of the sphere (normalized) and Z(q) is the paracrystalline structure factor for a simple cubic structure. Equation (16) of the 1987 reference is used to calculate Z(q), using equations (13)-(15) from the 1987 paper for Z1, Z2, and Z3.
The lattice correction (the occupied volume of the lattice) for a simple cubic structure of particles of radius R and nearest neighbor separation D is:
The distortion factor (one standard deviation) of the paracrystal is included in the calculation of Z(q):
where g is a fractional distortion based on the nearest neighbor distance.
The simple cubic lattice is:
For a crystal, diffraction peaks appear at reduced q-values givn by:
where for a simple cubic lattice any h, k, l are allowed and none are forbidden. Thus the peak positions correspond to (just the first 5):
NOTE: The calculation of Z(q) is a double numerical integral that must be carried out with a high density of points to properly capture the sharp peaks of the paracrystalline scattering. So be warned that the calculation is SLOW. Go get some coffee. Fitting of any experimental data must be resolution smeared for any meaningful fit. This makes a triple integral. Very, very slow. Go get lunch.
REFERENCES
Hideki Matsuoka et. al. Physical Review B, 36 (1987) 1754-1765. (Original Paper)
Hideki Matsuoka et. al. Physical Review B, 41 (1990) 3854 -3856. (Corrections to FCC and BCC lattice structure calculation)
Parameter name
Units
Default value
background
cm-1
0
dnn
220
scale
1
sldSolv
-2
6.3e-006
radius
40
sld_Sph
-2
3e-006
d_factor
0.06
TEST DATASET
This example dataset is produced using 200 data points, qmin = 0.01 -1, qmax = 0.1 -1 and the above default values.
Figure. 1D plot in the linear scale using the default values (w/200 data point).
The 2D (Anisotropic model) is based on the reference (above) which I(q) 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.
** **
Figure. 2D plot using the default values (w/200X200 pixels).
2.36. ** ** FC(Face Centered Cubic Para-)CrystalModel
Calculates the scattering from a face-centered cubic lattice with paracrystalline distortion. Thermal vibrations are considered to be negligible, and the size of the paracrystal is infinitely large. Paracrystalline distortion is assumed to be isotropic and characterized by a Gaussian distribution.
The returned value is scaled to units of [cm-1sr-1], absolute scale.
The scattering intensity I(q) is calculated as:
where scale is the volume fraction of spheres, Vp is the volume of the primary particle, V(lattice) is a volume correction for the crystal structure, P(q) is the form factor of the sphere (normalized) and Z(q) is the paracrystalline structure factor for a face-centered cubic structure. Equation (1) of the 1990 reference is used to calculate Z(q), using equations (23)-(25) from the 1987 paper for Z1, Z2, and Z3.
The lattice correction (the occupied volume of the lattice) for a face-centered cubic structure of particles of radius R and nearest neighbor separation D is:
The distortion factor (one standard deviation) of the paracrystal is included in the calculation of Z(q):
where g is a fractional distortion based on the nearest neighbor distance.
The face-centered cubic lattice is:
For a crystal, diffraction peaks appear at reduced q-values givn by:
where for a face-centered cubic lattice h, k, l all odd or all even are allowed and reflections where h, k, l are mixed odd/even are forbidden. Thus the peak positions correspond to (just the first 5):
NOTE: The calculation of Z(q) is a double numerical integral that must be carried out with a high density of points to properly capture the sharp peaks of the paracrystalline scattering. So be warned that the calculation is SLOW. Go get some coffee. Fitting of any experimental data must be resolution smeared for any meaningful fit. This makes a triple integral. Very, very slow. Go get lunch.
REFERENCES
Hideki Matsuoka et. al. Physical Review B, 36 (1987) 1754-1765. (Original Paper)
Hideki Matsuoka et. al. Physical Review B, 41 (1990) 3854 -3856. (Corrections to FCC and BCC lattice structure calculation)
Parameter name
Units
Default value
background
cm-1
0
dnn
220
scale
1
sldSolv
-2
6.3e-006
radius
40
sld_Sph
-2
3e-006
d_factor
0.06
TEST DATASET
This example dataset is produced using 200 data points, qmin = 0.01 -1, qmax = 0.1 -1 and the above default values.
Figure. 1D plot in the linear scale using the default values (w/200 data point).
The 2D (Anisotropic model) is based on the reference (above) in which I(q) 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.
Figure. 2D plot using the default values (w/200X200 pixels).
2.37. ** ** BC(Body Centered Cubic Para-)CrystalModel
Calculates the scattering from a body-centered cubic lattice with paracrystalline distortion. Thermal vibrations are considered to be negligible, and the size of the paracrystal is infinitely large. Paracrystalline distortion is assumed to be isotropic and characterized by a Gaussian distribution.The returned value is scaled to units of [cm-1sr-1], absolute scale.
The scattering intensity I(q) is calculated as:
where scale is the volume fraction of spheres, Vp is the volume of the primary particle, V(lattice) is a volume correction for the crystal structure, P(q) is the form factor of the sphere (normalized) and Z(q) is the paracrystalline structure factor for a body-centered cubic structure. Equation (1) of the 1990 reference is used to calculate Z(q), using equations (29)-(31) from the 1987 paper for Z1, Z2, and Z3.
The lattice correction (the occupied volume of the lattice) for a body-centered cubic structure of particles of radius R and nearest neighbor separation D is:
The distortion factor (one standard deviation) of the paracrystal is included in the calculation of Z(q):
where g is a fractional distortion based on the nearest neighbor distance.
The body-centered cubic lattice is:
For a crystal, diffraction peaks appear at reduced q-values givn by:
where for a body-centered cubic lattice, only reflections where (h+k+l) = even are allowed and reflections where (h+k+l) = odd are forbidden. Thus the peak positions correspond to (just the first 5):
NOTE: The calculation of Z(q) is a double numerical integral that must be carried out with a high density of points to properly capture the sharp peaks of the paracrystalline scattering. So be warned that the calculation is SLOW. Go get some coffee. Fitting of any experimental data must be resolution smeared for any meaningful fit. This makes a triple integral. Very, very slow. Go get lunch.
REFERENCES
Hideki Matsuoka et. al. Physical Review B, 36 (1987) 1754-1765. (Original Paper)
Hideki Matsuoka et. al. Physical Review B, 41 (1990) 3854 -3856. (Corrections to FCC and BCC lattice structure calculation)
Parameter name
Units
Default value
background
cm-1
0
dnn
220
scale
1
sldSolv
-2
6.3e-006
radius
40
sld_Sph
-2
3e-006
d_factor
0.06
TEST DATASET
This example dataset is produced using 200 data points, qmin = 0.001 -1, qmax = 0.1 -1 and the above default values.
Figure. 1D plot in the linear scale using the default values (w/200 data point).
The 2D (Anisotropic model) is based on the reference (1987) in which I(q) 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.
Figure. 2D plot using the default values (w/200X200 pixels).
3. ** ** **Shape-Independent Models **
The following are models used for shape-independent SANS analysis.
3.1. ** ** Debye (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.
For 2D plot, the wave transfer is defined as .
Parameter name
Units
Default value
scale
None
1.0
rg
50.0
background
cm-1
0.0
Figure. 1D plot using the default values (w/200 data point).
Reference: Roe, R.-J., "Methods of X-Ray and Neutron Scattering in Polymer Science", Oxford University Press, New York (2000).
3.2. ** ** BroadPeak Model
Calculate an empirical functional form for SANS data characterized by a broad scattering peak. Many SANS spectra are characterized by a broad peak even though they are from amorphous soft materials. The d-spacing corresponding to the broad peak is a characteristic distance between the scattering inhomogeneities (such as in lamellar, cylindrical, or spherical morphologies or for bicontinuous structures).
The returned value is scaled to units of [cm-1sr-1], absolute scale.
The scattering intensity I(q) is calculated by:
Here the peak position is related to the d-spacing as Q0 = 2pi/d0. Soft systems that show a SANS peak include copolymers, polyelectrolytes, multiphase systems, layered structures, etc.
For 2D plot, the wave transfer is defined as .
Parameter name
Units
Default value
scale_l (= C)
10
scale_p (=A)
1e-05
length_l (=x)
50
q_peak (= Q0)
-1
0.1
exponent_p (=n)
2
exponent_l (=m)
3
Background (=B)
cm-1
0.1
Figure. 1D plot using the default values (w/200 data point).
Reference: None.
2013/09/09 - Description reviewed by King, S. and Parker, P.
3.3. ** ** CorrLength (CorrelationLengthModel)
Calculate an empirical functional form for SANS data characterized by a low-Q signal and a high-Q signal
The returned value is scaled to units of [cm-1sr-1], absolute scale.
The scattering intensity I(q) is calculated by:
The first term describes Porod scattering from clusters (exponent = n) and the second term is a Lorentzian function describing scattering from polymer chains (exponent = m). This second term characterizes the polymer/solvent interactions and therefore the thermodynamics. The two multiplicative factors A and C, the incoherent background B and the two exponents n and m are used as fitting parameters. The final parameter (xi) is a correlation length for the polymer chains. Note that when m = 2, this functional form becomes the familiar Lorentzian function.
For 2D plot, the wave transfer is defined as .
Parameter name
Units
Default value
scale_l (= C)
10
scale_p (=A)
1e-06
length_l (=x)
50
exponent_p (=n)
2
exponent_l (=m)
3
Background (=B)
cm-1
0.1
Figure. 1D plot using the default values (w/500 data points).
REFERENCE
B. Hammouda, D.L. Ho and S.R. Kline, Insight into Clustering in Poly(ethylene oxide) Solutions, Macromolecules 37, 6932-6937 (2004).
2013/09/09 - Description reviewed by King, S. and Parker, P.
3.4. ** ** (Ornstein-Zernicke) Lorentz (Model)
The Ornstein-Zernicke model is defined by:
The parameter L is referred to as the screening length.
For 2D plot, the wave transfer is defined as .
Parameter name
Units
Default value
scale
None
1.0
length
50.0
background
cm-1
0.0
** **
Figure. 1D plot using the default values (w/200 data point).
3.5. ** ** DAB (Debye-Anderson-Brumberger)_Model
Calculates the scattering from a randomly distributed, two-phase system based on the Debye-Anderson-Brumberger (DAB) model for such systems. The two-phase system is characterized by a single length scale, the correlation length, which is a measure of the average spacing between regions of phase 1 and phase 2. The model also assumes smooth interfaces between the phases and hence exhibits Porod behavior (I ~ Q-4) at large Q (Q*correlation length >> 1).
The parameter L is referred to as the correlation length.
For 2D plot, the wave transfer is defined as .
Parameter name
Units
Default value
scale
None
1.0
length
50.0
background
cm-1
0.0
** **
Figure. 1D plot using the default values (w/200 data point).
References:
Debye, Anderson, Brumberger, "Scattering by an Inhomogeneous Solid. II. The Correlation Function and its Application", J. Appl. Phys. 28 (6), 679 (1957).
Debye, Bueche, "Scattering by an Inhomogeneous Solid", J. Appl. Phys. 20, 518 (1949).
2013/09/09 - Description reviewed by King, S. and Parker, P.
3.6. ** ** ** Absolute Power_Law **
This model describes a power law with background.
Note the minus sign in front of the exponent.
Parameter name
Units
Default value
Scale
None
1.0
m
None
4
Background
cm-1
0.0
Figure. 1D plot using the default values (w/200 data point).
3.7. ** ** Teubner Strey (Model)
This function calculates the scattered intensity of a two-component system using the Teubner-Strey model.
For 2D plot, the wave transfer is defined as .
Parameter name
Units
Default value
scale
None
0.1
c1
None
-30.0
c2
None
5000.0
background
cm-1
0.0
Figure. 1D plot using the default values (w/200 data point).
References:
Teubner, M; Strey, R. J. Chem. Phys., 87, 3195 (1987).
Schubert, K-V., Strey, R., Kline, S. R. and E. W. Kaler, J. Chem. Phys., 101, 5343 (1994).
3.8. ** ** ** FractalModel**
Calculates the scattering from fractal-like aggregates built from spherical building blocks following the Texiera reference. The value returned is in cm-1.
The scale parameter is the volume fraction of the building blocks, R0 is the radius of the building block, Df is the fractal dimension, is the correlation length, solvent is the scattering length density of the solvent, and block is the scattering length density of the building blocks.
The polydispersion in radius is provided.
For 2D plot, the wave transfer is defined as .
Parameter name
Units
Default value
scale
None
0.05
radius
5.0
fractal_dim
None
2
corr_length
100.0
block_sld
-2
2e-6
solvent_sld
-2
6e-6
background
cm-1
0.0
Figure. 1D plot using the default values (w/200 data point).
References:
- Teixeira, (1988) J. Appl. Cryst., vol. 21, p781-785
3.9. ** ** MassFractalModel
Calculates the scattering from fractal-like aggregates based on the Mildner reference (below).
The R is the radius of the building block, Dm is the mass fractal dimension, is the correlation (or cutt-off) length, solvent is the scattering length density of the solvent, and particle is the scattering length density of particles.
Note: The mass fractal dimension is valid for 1<mass_dim<6.
Parameter name
Units
Default value
scale
None
1
radius
10.0
mass_dim
None
1.9
co_length
100.0
background
0.0
Figure. 1D plot
References:
D. Mildner, and P. Hall, J. Phys. D.: Appl. Phys., 19, 1535-1545 (1986), Equation(9).
2013/09/09 - Description reviewed by King, S. and Parker, P.
3.10. ** ** ** SurfaceFractalModel**
Calculates the scattering based on the Mildner reference (below).
The R is the radius of the building block, Ds is the surface fractal dimension, is the correlation (or cutt-off) length, solvent is the scattering length density of the solvent, and particle is the scattering length density of particles.
Note: The surface fractal dimension is valid for 1<surface_dim<3. Also it is valid in a limited q range (see the reference for details).
Parameter name
Units
Default value
scale
None
1
radius
10.0
surface_dim
None
2.0
co_length
500.0
background
0.0
Figure. 1D plot
References:
D. Mildner, and P. Hall, J. Phys. D.: Appl. Phys., 19, 1535-1545 (1986), Equation(13).
3.11. ** ** MassSurfaceFractal
A number of natural and commercial processes form high-surface area materials as a result of the vapour-phase aggregation of primary particles. Examples of such materials include soots, aerosols, and fume or pyrogenic silicas. These are all characterised by cluster mass distributions (sometimes also cluster size distributions) and internal surfaces that are fractal in nature. The scattering from such materials displays two distinct breaks in log-log representation, corresponding to the radius-of-gyration of the primary particles, rg, and the radius-of-gyration of the clusters (aggregates), Rg. Between these boundaries the scattering follows a power law related to the mass fractal dimension, Dm, whilst above the high-Q boundary the scattering follows a power law related to the surface fractal dimension of the primary particles, Ds.
The scattered intensity I(Q) is then calculated using a modified Ornstein-Zernicke equation:
The Rg is for the cluster, rg is for the primary, Ds is the surface fractal dimension, Dm is the mass fractal dimension, solvent is the scattering length density of the solvent, and p is the scattering length density of particles.
Note: The surface and mass fractal dimensions are valid for 0<surface_dim<6, 0<mass_dim<6, and (surface_mass+mass_dim)<6.
Parameter name
Units
Default value
scale
None
1
primary_rg
4000.0 cluster_rg 86.7 surface_dim
None
2.3 mass_dim None 1.8 background
0.0
Figure. 1D plot
References:
- Schmidt, J Appl. Cryst., 24, 414-435 (1991), Equation(19).
Hurd, Schaefer, Martin, Phys. Rev. A, 35, 2361-2364 (1987), Equation(2).
3.12. ** ** ** FractalCoreShell(Model)**
Calculates the scattering from a fractal structure with a primary building block of core-shell spheres.
The formfactor P(q) is CoreShellModel with bkg = 0, ,
while the fractal structure factor S(q);
where Df = frac_dim, = cor_length, rc = (core) radius, and scale = volfraction. The fractal structure is as documented in the fractal model. This model could find use for aggregates of coated particles, or aggregates of vesicles.The polydispersity computation of radius and thickness is provided.
The returned value is scaled to units of [cm-1sr-1], absolute scale.
See each of these individual models for full documentation.
For 2D plot, the wave transfer is defined as .
Parameter name
Units
Default value
volfraction
0.05
frac_dim
2
thickness
5.0
raidus
20.0
cor_length
100.0
core_sld
-2
3.5e-6
shell_sld
-2
1e-6
solvent_sld
-2
6.35e-6
background
cm-1
0.0
Figure. 1D plot using the default values (w/500 data points).
References:
See the PolyCore and Fractal documentation. ** **
3.13. ** ** ** GaussLorentzGel(Model)**
Calculates the scattering from a gel structure, typically a physical network. It is modeled as a sum of a low-q exponential decay plus a lorentzian at higher q-values. It is generally applicable to gel structures.
The returned value is scaled to units of [cm-1sr-1], absolute scale.
The scattering intensity I(q) is calculated as (eqn 5 from the reference):
Uppercase Zeta is the static correlations in the gel, which can be attributed to the "frozen-in" crosslinks of some gels. Lowercase zeta is the dynamic correlation length, which can be attributed to the fluctuating polymer chain between crosslinks. IG(0) and IL(0) are the scaling factors for each of these structures. Your physical system may be different, so think about the interpretation of these parameters.
Note that the peaked structure at higher q values (from Figure 2 of the reference below) is not reproduced by the model. Peaks can be introduced into the model by summing this model with the PeakGauss Model function.
For 2D plot, the wave transfer is defined as .
Parameter name
Units
Default value
dyn_colength(=Dynamic correlation length)
20.0
scale_g(=Gauss scale factor)
100
scale_l(=Lorentzian scale factor)
50
stat_colength(=Static correlation Z)
100.0
background
cm-1
0.0
Figure. 1D plot using the default values (w/500 data points).
REFERENCE:
G. Evmenenko, E. Theunissen, K. Mortensen, H. Reynaers, Polymer 42 (2001) 2907-2913.
3.14. ** ** ** BEPolyelectrolyte Model**
Calculates the structure factor of a polyelectrolyte solution with the RPA expression derived by Borue and Erukhimovich. The value returned is in cm-1.
K is a contrast factor of the polymer, Lb is the Bjerrum length, h is the virial parameter, b is the monomer length, Cs is the concentration of monovalent salt, is the ionization degree, Ca is the polymer molar concentration, and background is the incoherent background.
For 2D plot, the wave transfer is defined as .
Parameter name
Units
Default value
K
Barns = 10-24 cm2
10
Lb
7.1
h
-3
12
b
10
Cs
Mol/L
0
alpha
None
0.05
Ca
Mol/L
0.7
background
cm-1
0.0
References:
Borue, V. Y., Erukhimovich, I. Y. Macromolecules 21, 3240 (1988).
Joanny, J.-F., Leibler, L. Journal de Physique 51, 545 (1990).
Moussaid, A., Schosseler, F., Munch, J.-P., Candau, S. J. Journal de Physique II France
3, 573 (1993).
Raphal, E., Joanny, J.-F., Europhysics Letters 11, 179 (1990).
3.15. ** ** Guinier (Model)
A Guinier analysis is done by linearizing the data at low q by plotting it as log(I) versus Q2. The Guinier radius Rg can be obtained by fitting the following model:
For 2D plot, the wave transfer is defined as .
Parameter name
Units
Default value
scale
cm-1
1.0
Rg
0.1
3.16. ** ** GuinierPorod (Model)
Calculates the scattering for a generalized Guinier/power law object. This is an empirical model that can be used to determine the size and dimensionality of scattering objects.
The returned value is P(Q) as written in equation (1), plus the incoherent background term. The result is in the units of [cm-1sr-1], absolute scale.
A Guinier-Porod empirical model can be used to fit SAS data from asymmetric objects such as rods or platelets. It also applies to intermediate shapes between spheres and rod or between rods and platelets. The following functional form is used:
This is based on the generalized Guinier law for such elongated objects [2]. For 3D globular objects (such as spheres), s = 0 and one recovers the standard Guinier formula. For 2D symmetry (such as for rods) s = 1 and for 1D symmetry (such as for lamellae or platelets) s = 2. A dimensionality parameter 3-s is defined, and is 3 for spherical objects, 2 for rods, and 1 for plates.
Enforcing the continuity of the Guinier and Porod functions and their derivatives yields:
and
Note that the radius of gyration for a sphere of radius R is given by Rg = R sqrt(3/5) ,
that for the cross section of an randomly oriented cylinder of radius R is given by Rg = R / sqrt(2).
The cross section of a randomly oriented lamella of thickness T is given by Rg = T / sqrt(12).
The intensity given by Eq. 1 is the calculated result, and is plotted below for the default parameter values.
REFERENCE
[1] Guinier, A.; Fournet, G. "Small-Angle Scattering of X-Rays", John Wiley and Sons, New York, (1955).
[2] Glatter, O.; Kratky, O., Small-Angle X-Ray Scattering, Academic Press (1982). Check out Chapter 4 on Data Treatment, pages 155-156.
For 2D plot, the wave transfer is defined as .
Parameter name
Units
Default value
Scale(=Guinier scale, G)
cm-1
1.0
rg
100
dim(=Dimensional Variable, s)
1
m(=Porod exponent)
3
background
0.1
** **
Figure. 1D plot using the default values (w/500 data points).
3.17. ** ** 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:
C is the scale factor and Sv is the specific surface area of the sample and is the contrast factor.
The background term is added for data analysis.
For 2D plot, the wave transfer is defined as .
Parameter name
Units
Default value
scale
-4
0.1
background
cm-1
0
3.18. ** ** PeakGaussModel
Model describes a Gaussian shaped peak including a flat background,
with the peak having height of I0 centered at qpk having standard deviation of B. The fwhm is 2.354*B.
Parameters I0, B, qpk, and BGD can all be adjusted during fitting.
REFERENCE: None
For 2D plot, the wave transfer is defined as .
Parameter name
Units
Default value
scale
cm-1
100
q0
0.05
B
0.005
background
1
** **
Figure. 1D plot using the default values (w/500 data points).
3.19. ** ** PeakLorentzModel
Model describes a Lorentzian shaped peak including a flat background,
with the peak having height of I0 centered at qpk having a hwhm (half- width-half-maximum) of B.
The parameters I0, B, qpk, and BGD can all be adjusted during fitting.
REFERENCE: None
For 2D plot, the wave transfer is defined as .
Parameter name
Units
Default value
scale
cm-1
100
q0
0.05
B
0.005
background
1
** **
Figure. 1D plot using the default values (w/500 data points).
3.20. 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.
The returned value is scaled to units of [cm-1sr-1], absolute scale.
where the dimensionless chain dimension is:
and the polydispersion is
.
The scattering intensity I(q) is calculated as:
The polydispersion in rg is provided.
For 2D plot, the wave transfer is defined as .
TEST DATASET
This example dataset is produced by running the Poly_GaussCoil, using 200 data points, qmin = 0.001 -1, qmax = 0.7 -1 and the default values below.
Parameter name
Units
Default value
Scale
None
1.0
rg
60.0
poly_m
Mw/Mn
2
background
cm-1
0.001
Figure. 1D plot using the default values (w/200 data point).
Reference:
Glatter & Kratky - pg.404.
J.S. Higgins, and H.C. Benoit, Polymers and Neutron Scattering, Oxford Science
Publications (1996).
3.21. PolymerExclVolume (Model)
Calculates the scattering from polymers with excluded volume effects.
The returned value is scaled to units of [cm-1sr-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-1sr-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:
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:
Here, g(x,U) is the incomplete gamma function which is a built-in function in computer libraries.
The variable U is given in terms of the scattering variable Q as:
The radius of gyration squared has been defined as:
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. 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:
Here G(x) = g(x,inf) is the gamma function. The asymptotic limit is dominated by the first term:
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 form factor given by Eq. 2 is the calculated result, and is plotted below for the default parameter values.
REFERENCE
Benoit, H., Comptes Rendus (1957). 245, 2244-2247.
Hammouda, B., SANS from Homogeneous Polymer Mixtures A Unified Overview, Advances in Polym. Sci. (1993), 106, 87-133.
For 2D plot, the wave transfer is defined as .
TEST DATASET
This example dataset is produced, using 200 data points, qmin = 0.001 -1, qmax = 0.2 -1 and the default values below.
Parameter name
Units
Default value
Scale
None
1.0
rg
60.0
m(=Porod exponent)
3
background
cm-1
0.0
Figure. 1D plot using the default values (w/500 data points).
3.22. ** ** ** 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. 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, 4136 (1993)
Fitting parameters for Case0 Model
Parameter name
Units
Default value
background
cm-1
0.0
scale
1
bc(=Seg. Length bc)
5
bd(=Seg. Length bd)
5
Kcd(Chi Param. Kcd)
-0.0004
Fixed parameters for Case0 Model
Parameter name
Units
Default value
Lc(= Scatter. Length_c)
1e-12
Ld(= Scatter. Length_d)
0
Nc(=Deg.Polym.c)
1000
Nd(=Deg.Polym.d)
1000
Phic(=Vol. fraction of c)
0.25
Phid(=Vol. fraction of d)
0.25
vc(=Spec. vol. of c)
100
vd(=Spec. vol. of d)
100
Figure. 1D plot using the default values (w/500 data points).
3.23. ** ** TwoLorentzian(Model)
Calculate an empirical functional form for SANS data characterized by a two Lorentzian functions.
The returned value is scaled to units of [cm-1sr-1], absolute scale.
The scattering intensity I(q) is calculated by:
A = Lorentzian scale #1
C = Lorentzian scale #2
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.
For 2D plot, the wave transfer is defined as .
Default input parameter values
Parameter name
Units
Default value
scale_1(=A)
10
scale_2(=C)
1
1ength_1 (=Correlation length1)
100
1ength_2(=Correlation length2)
10
exponent_1(=n)
3
exponent_2(=m)
2
Background(=B)
cm-1
0.1
Figure. 1D plot using the default values (w/500 data points).
REFERENCE: None
3.24. ** ** TwoPowerLaw(Model)
Calculate an empirical functional form for SANS data characterized by two power laws.
The returned value is scaled to units of [cm-1sr-1], absolute scale.
The scattering intensity I(q) is calculated by:
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.
For 2D plot, the wave transfer is defined as .
Default input parameter values
Parameter name
Units
Default value
coef_A
1.0
qc
-1
0.04
power_1(=m1)
4
power_2(=m2)
4
background
cm-1
0.0
Figure. 1D plot using the default values (w/500 data points).
3.25. ** ** UnifiedPower(Law and)Rg(Model)
The returned value is scaled to units of [cm-1sr-1], absolute scale.
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. The empirical fit function is
For each level, the four parameters Gi, Rg,i, Bi and Pi must be chosen.
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
See the listed references for further information on choosing the parameters.
For 2D plot, the wave transfer is defined as .
Default input parameter values
Parameter name
Units
Default value
scale
1.0
Rg2
21
power2
2
G2
cm-1sr-1
3
B2
cm-1sr-1
0.0006
Rg1
15.8
power1
4
G1
cm-1sr-1
400
B1
cm-1sr-1
4.5e-006
background
cm-1
0.0
Figure. 1D plot using the default values (w/500 data points).
REFERENCES
- Beaucage (1995). J. Appl. Cryst., vol. 28, p717-728.
- Beaucage (1996). J. Appl. Cryst., vol. 29, p134-146.
3.26. ** ** ** LineModel**
This is a linear function that calculates:
where A and B are the coefficients of the first and second order terms.
Note: For 2D plot, I(q) = I(qx)*I(qy) which is defined differently from other shape independent models.
Parameter name
Units
Default value
A
cm-1
1.0
B
1.0
3.27. ** ** 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 [ of the interface(from the previous layer or substrate) + flat portion + 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.
Figure. Comparison (using the SLD profile below) with NISTweb calculation (circles): http://www.ncnr.nist.gov/resources/reflcalc.html.
Figure. SLD profile used for the calculation(above).
3.28. ** ** ReflectivityIIModel
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. 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;
- Power-Law;
- Exp;
Note: This model was implemented by an interested user.
3.29. ** ** GelFitModel
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:
Where:
Note 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.
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
104
Fractal exponent
2
Correlation length
16
Figure. 1D plot using the default values (w/300 data points, qmin=0.001, and qmax=0.3).
REFERENCES
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.
3.30. ** ** ** Star Polymer with Gaussian Statistics **
For a star with f arms:
where is the ensemble average radius of gyration squared of an arm.
References:
- Benoit, J. Polymer Science., 11, 596-599 (1953)
4. ** ** **Customized Models **
Customized model functions can be redefined or added by users (See SansView tutorial for details).
4.1. **** testmodel
This function, as an example of a user defined function, calculates the intensity = A + Bcos(2q) + Csin(2q).
This function, as an example of a user defined function, calculates the intensity = scale * sin(f)/f, where f = A + Bq + Cq2 + Dq3 + Eq4 + Fq5.
4.3. ** ** **sum_p1_p2 **
This function, as an example of a user defined function, calculates the intensity = scale_factor * (CylinderModel + PolymerExclVolume model). To make your own sum(P1+P2) model, select 'Easy Custom Sum' from the Fitting menu, or modify and compile the file named 'sum_p1_p2.py' from 'Edit Custom Model' in the 'Fitting' menu. It works only for single functional models.
This function, as an example of a user defined function, calculates the intensity = (scale_factor * CylinderModel + (1-scale_factor) * PolymerExclVolume model). To make your own A*p1+(1-A)*p2 model, modify and compile the file named 'sum_Ap1_1_Ap2.py' from 'Edit Custom Model' in the 'Fitting' menu. It works only for single functional models.
4.5. ** ** **polynomial5 **
This function, as an example of a user defined function, calculates the intensity = A + Bq + Cq2 + Dq3 + Eq4 + Fq5. This model can be modified and compiled from 'Edit Custom Model' in the 'Fitting' menu.
This function, as an example of a user defined function, calculates the intensity = C*sph_jn(Ax+B)+D where the sph_jn is spherical Bessel function of the order n. This model can be modified and compiled from 'Edit Custom Model' in the 'Fitting' menu.
5. ** ** Structure Factors
The information in this section is originated from NIST SANS IgorPro package.
5.1. ** ** **HardSphere Structure **
This calculates the interparticle structure factor for monodisperse spherical particles interacting through hard sphere (excluded volume) interactions. The calculation uses the Percus-Yevick closure where the interparticle potential is:
where r is the distance from the center of the sphere of a radius R.
For 2D plot, the wave transfer is defined as .
Parameter name
Units
Default value
effect_radius
50.0
volfraction
0.2
Figure. 1D plot using the default values (in linear scale).
References:
Percus, J. K.; Yevick, J. Phys. Rev. 110, 1. (1958).
5.2. ** ** **SquareWell Structure **
This calculates the interparticle structure factor for a squar well fluid spherical particles The mean spherical approximation (MSA) closure was used for this calculation, and is not the most appropriate closure for an attractive interparticle potential. This solution has been compared to Monte Carlo simulations for a square well fluid, showing this calculation to be limited in applicability to well depths e < 1.5 kT and volume fractions f < 0.08.
Positive well depths correspond to an attractive potential well. Negative well depths correspond to a potential "shoulder", which may or may not be physically reasonable.
The well width (l) is defined as multiples of the particle diameter (2*R)
The interaction potential is:
where r is the distance from the center of the sphere of a radius R.
For 2D plot, the wave transfer is defined as .
Parameter name
Units
Default value
effect_radius
50.0
volfraction
0.04
welldepth
kT
1.5
wellwidth
diameters
1.2
Figure. 1D plot using the default values (in linear scale).
References:
Sharma, R. V.; Sharma, K. C. Physica, 89A, 213. (1977).
5.3. ** ** **HayterMSA Structure **
This calculates the Structure factor (the Fourier transform of the pair correlation function g(r)) for a system of charged, spheroidal objects in a dielectric medium. When combined with an appropriate form factor (such as sphere, core+shell, ellipsoid etc), this allows for inclusion of the interparticle interference effects due to screened coulomb repulsion between charged particles. This routine only works for charged particles. If the charge is set to zero the routine will self destruct. For non-charged particles use a hard sphere potential.
The salt concentration is used to compute the ionic strength of the solution which in turn is used to compute the Debye screening length. At present there is no provision for entering the ionic strength directly nor for use of any multivalent salts. The counterions are also assumed to be monovalent.
For 2D plot, the wave transfer is defined as .
Parameter name
Units
Default value
effect_radius
20.8
charge
19
volfraction
0.2
temperature
K
318
salt conc
M
0
dielectconst
71.1
Figure. 1D plot using the default values (in linear scale).
References:
JP Hansen and JB Hayter, Molecular Physics 46, 651-656 (1982).
JB Hayter and J Penfold, Molecular Physics 42, 109-118 (1981).
5.4. ** ** **StickyHS Structure **
This calculates the interparticle structure factor for a hard sphere fluid with a narrow attractive well. A perturbative solution of the Percus-Yevick closure is used. The strength of the attractive well is described in terms of "stickiness" as defined below. The returned value is a dimensionless structure factor, S(q).
The perturb (perturbation parameter), epsilon, should be held between 0.01 and 0.1. It is best to hold the perturbation parameter fixed and let the "stickiness" vary to adjust the interaction strength. The stickiness, tau, is defined in the equation below and is a function of both the perturbation parameter and the interaction strength. Tau and epsilon are defined in terms of the hard sphere diameter (sigma = 2R), the width of the square well, delta (same units as R), and the depth of the well, uo, in units of kT. From the definition, it is clear that smaller tau mean stronger attraction.
where the interaction potential is
The Percus-Yevick (PY) closure was used for this calculation, and is an adequate closure for an attractive interparticle potential. This solution has been compared to Monte Carlo simulations for a square well fluid, with good agreement.
The true particle volume fraction, f, is not equal to h, which appears in most of the reference. The two are related in equation (24) of the reference. The reference also describes the relationship between this perturbation solution and the original sticky hard sphere (or adhesive sphere) model by Baxter.
NOTES: The calculation can go haywire for certain combinations of the input parameters, producing unphysical solutions - in this case errors are reported to the command window and the S(q) is set to -1 (it will disappear on a log-log plot). Use tight bounds to keep the parameters to values that you know are physical (test them) and keep nudging them until the optimization does not hit the constraints.
For 2D plot, the wave transfer is defined as .
Parameter name
Units
Default value
effect_radius
50
perturb
0.05
volfraction
0.1
stickiness
K
0.2
Figure. 1D plot using the default values (in linear scale).
References:
Menon, S. V. G., Manohar, C. and K. Srinivas Rao J. Chem. Phys., 95(12), 9186-9190 (1991).
References
Feigin, L. A, and D. I. Svergun (1987) "Structure Analysis by Small- Angle X-Ray and Neutron Scattering", Plenum Press, New York.
Guinier, A. and G. Fournet (1955) "Small-Angle Scattering of X-Rays", John Wiley and Sons, New York.
Kline, S. R. (2006) J Appl. Cryst. **39**(6), 895.
Hansen, S., (1990) * J. Appl. Cryst. *23, 344-346.
Henderson, S.J. (1996) *Biophys. J. *70, 1618-1627
Stckel, P., May, R., Strell, I., Cejka, Z., Hoppe, W., Heumann, H., Zillig, W. and Crespi, H. (1980) *Eur. J. Biochem. *112, 411-417.
McAlister, B.C. and Grady, B.P., (1998) J. Appl. Cryst. 31, 594-599.
Porod, G. (1982) in Small Angle X-ray Scattering, editors Glatter, O. and Kratky, O., Academic Press.
*Also, see the references at the end of the each model function descriptions.
