Changes in / [797a8e3:f80f334] in sasmodels
- Location:
- sasmodels/models
- Files:
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- 4 edited
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be_polyelectrolyte.py (modified) (1 diff)
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core_multi_shell.py (modified) (4 diffs)
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core_shell_cylinder.py (modified) (3 diffs)
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core_shell_parallelepiped.py (modified) (5 diffs)
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sasmodels/models/be_polyelectrolyte.py
rbf9de53 r5df888c 67 67 * **Author:** NIST IGOR/DANSE **Date:** pre 2010 68 68 * **Last Modified by:** Paul Kienzle **Date:** July 24, 2016 69 * **Last Reviewed by:** Paul Butler and Richard Heenan **Date:** 70 October 07, 2016 69 * **Last Reviewed by:** Piotr rozyczko **Date:** January 27, 2016 71 70 """ 72 71 -
sasmodels/models/core_multi_shell.py
r2d73a53 rb0c4271 13 13 14 14 The 2D scattering intensity is the same as $P(q)$ above, regardless of the 15 orientation of the $ \vecq$ vector which is defined as15 orientation of the $q$ vector which is defined as 16 16 17 17 .. math:: … … 29 29 30 30 Our model uses the form factor calculations implemented in a c-library provided 31 by the NIST Center for Neutron Research (Kline, 2006) [#kline]_.31 by the NIST Center for Neutron Research (Kline, 2006). 32 32 33 33 References … … 35 35 36 36 .. [#] See the :ref:`core-shell-sphere` model documentation. 37 .. [#kline] S R Kline, *J Appl. Cryst.*, 39 (2006) 895 38 .. [#] L A Feigin and D I Svergun, *Structure Analysis by Small-Angle X-Ray and 39 Neutron Scattering*, Plenum Press, New York, 1987. 37 .. [#] L A Feigin and D I Svergun, *Structure Analysis by Small-Angle X-Ray and Neutron Scattering*, 38 Plenum Press, New York, 1987. 40 39 41 40 Authorship and Verification … … 44 43 * **Author:** NIST IGOR/DANSE **Date:** pre 2010 45 44 * **Last Modified by:** Paul Kienzle **Date:** September 12, 2016 46 * **Last Reviewed by:** Paul Kienzle **Date:** September 12, 201645 * **Last Reviewed by:** Under Review **Date:** as of October 5, 2016 47 46 """ 48 47 -
sasmodels/models/core_shell_cylinder.py
r755ecc2 r40a87fa 1 # core shell cylinder model 2 # Note: model title and parameter table are inserted automatically 1 3 r""" 4 The form factor is normalized by the particle volume. 5 2 6 Definition 3 7 ---------- 4 8 5 9 The output of the 2D scattering intensity function for oriented core-shell 6 cylinders is given by (Kline, 2006 [#kline]_). The form factor is normalized 7 by the particle volume. 10 cylinders is given by (Kline, 2006) 8 11 9 12 .. math:: … … 58 61 The $\theta$ and $\phi$ parameters are not used for the 1D output. 59 62 63 Validation 64 ---------- 65 66 Validation of our code was done by comparing the output of the 1D model to 67 the output of the software provided by the NIST (Kline, 2006). 68 69 Averaging over a distribution of orientation is done by evaluating the 70 equation above. Since we have no other software to compare the 71 implementation of the intensity for fully oriented cylinders, we 72 compared the result of averaging our 2D output using a uniform 73 distribution $p(\theta,\phi) = 1.0$. 74 60 75 Reference 61 76 --------- 77 see, for example, Ian Livsey J. Chem. Soc., Faraday Trans. 2, 1987,83, 1445-1452 62 78 63 .. [#] see, for example, Ian Livsey J. Chem. Soc., Faraday Trans. 2, 1987,83, 64 1445-1452 65 .. [#kline] S R Kline, *J Appl. Cryst.*, 39 (2006) 895 66 67 Authorship and Verification 68 ---------------------------- 69 70 * **Author:** NIST IGOR/DANSE **Date:** pre 2010 71 * **Last Modified by:** Paul Kienzle **Date:** Aug 8, 2016 72 * **Last Reviewed by:** Richard Heenan **Date:** March 18, 2016 79 2016/03/18 - Description reviewed by RKH 73 80 """ 74 81 … … 151 158 theta_pd=15, theta_pd_n=45, 152 159 phi_pd=15, phi_pd_n=1) 153 160 # ADDED by: RKH ON: 18Mar2016 renamed sld's etc -
sasmodels/models/core_shell_parallelepiped.py
r5810f00 r14838a3 1 # core_shell_parallelepiped model 2 # Note: model title and parameter table are inserted automatically 1 3 r""" 2 Definition3 ----------4 5 4 Calculates the form factor for a rectangular solid with a core-shell structure. 6 5 **The thickness and the scattering length density of the shell or "rim" … … 16 15 of the rectangular solid. 17 16 17 An instrument resolution smeared version of the model is also provided. 18 19 20 Definition 21 ---------- 18 22 19 23 The function calculated is the form factor of the rectangular solid below. … … 37 41 **meaning that there are "gaps" at the corners of the solid.** 38 42 39 The intensity calculated follows the :ref:`parallelepiped` model, with the 40 core-shell intensity being calculated as the square of the sumof the41 amplitudes of thecore and shell, in the same manner as a core-shell model.43 The intensity calculated follows the :ref:`parallelepiped` model, with the core-shell 44 intensity being calculated as the square of the sum of the amplitudes of the 45 core and shell, in the same manner as a core-shell model. 42 46 43 .. math:: 44 45 F_{a}(Q,\alpha,\beta)= 46 \Bigg(\frac{sin(Q(L_A+2t_A)/2sin\alpha sin\beta)}{Q(L_A+2t_A)/2sin\alpha 47 sin\beta)} 48 - \frac{sin(QL_A/2sin\alpha sin\beta)}{QL_A/2sin\alpha sin\beta)} \Bigg) 49 + \frac{sin(QL_B/2sin\alpha sin\beta)}{QL_B/2sin\alpha sin\beta)} 50 + \frac{sin(QL_C/2sin\alpha sin\beta)}{QL_C/2sin\alpha sin\beta)} 51 52 .. note:: 53 54 For the calculation of the form factor to be valid, the sides of the solid 55 MUST be chosen such that** $A < B < C$. 56 If this inequality is not satisfied, the model will not report an error, 57 but the calculation will not be correct and thus the result wrong. 47 **For the calculation of the form factor to be valid, the sides of the solid 48 MUST be chosen such that** $A < B < C$. 49 **If this inequality is not satisfied, the model will not report an error, 50 and the calculation will not be correct.** 58 51 59 52 FITTING NOTES 60 53 If the scale is set equal to the particle volume fraction, |phi|, the returned 61 54 value is the scattered intensity per unit volume, $I(q) = \phi P(q)$. 62 However, **no interparticle interference effects are included in this 63 calculation.** 55 However, **no interparticle interference effects are included in this calculation.** 64 56 65 57 There are many parameters in this model. Hold as many fixed as possible with … … 76 68 and length $(C+2t_C)$ values, and used as the effective radius 77 69 for $S(Q)$ when $P(Q) * S(Q)$ is applied. 70 71 .. Comment by Miguel Gonzalez: 72 The later seems to contradict the previous statement that interparticle interference 73 effects are not included. 78 74 79 75 To provide easy access to the orientation of the parallelepiped, we define the … … 102 98 ---------- 103 99 104 .. [#] P Mittelbach and G Porod, *Acta Physica Austriaca*, 14 (1961) 185-211 105 Equations (1), (13-14). (in German) 106 .. [#] D Singh (2009). *Small angle scattering studies of self assembly in 107 lipid mixtures*, John's Hopkins University Thesis (2009) 223-225. `Available 108 from Proquest <http://search.proquest.com/docview/304915826?accountid 109 =26379>`_ 100 P Mittelbach and G Porod, *Acta Physica Austriaca*, 14 (1961) 185-211 101 Equations (1), (13-14). (in German) 110 102 111 Authorship and Verification112 ----------------------------113 114 * **Author:** NIST IGOR/DANSE **Date:** pre 2010115 * **Last Modified by:** Paul Butler **Date:** September 30, 2016116 * **Last Reviewed by:** Miguel Gonzales **Date:** March 21, 2016117 103 """ 118 104
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