Changeset b0c4271 in sasmodels


Ignore:
Timestamp:
Oct 5, 2016 9:40:41 PM (5 years ago)
Author:
butler
Branches:
master, core_shell_microgels, costrafo411, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests
Children:
63e9cd8
Parents:
bb2d187
Message:

model documentation final format through core_shell_bicelle re: #646

Location:
sasmodels/models
Files:
9 edited

Legend:

Unmodified
Added
Removed
  • sasmodels/models/adsorbed_layer.py

    r52ec91e rb0c4271  
    1 #adsorbed_layer model 
    2 #conversion of Core2ndMomentModel.py 
    3 #converted by Steve King, Mar 2016 
     1r""" 
     2Definition 
     3---------- 
    44 
    5 r""" 
    65This model describes the scattering from a layer of surfactant or polymer 
    76adsorbed on large, smooth, notionally spherical particles under the conditions 
     
    1918the mean of the density distribution (ie, the distance of the centre-of-mass 
    2019of the distribution from the interface), $\sigma = \sqrt{t^2/12}$. 
    21  
    22 Definition 
    23 ---------- 
    2420 
    2521.. math:: 
     
    4440calculation is exact). 
    4541 
     42The code for this model is based originally on a a fortran implementation by 
     43Steve King at ISIS in the SANDRA package c. 1990. 
     44 
    4645References 
    4746---------- 
    4847 
    49 S King, P Griffiths, J Hone, and T Cosgrove, 
    50 *SANS from Adsorbed Polymer Layers*, *Macromol. Symp.*, 190 (2002) 33-42. 
     48.. [#] S King, P Griffiths, J Hone, and T Cosgrove, *SANS from Adsorbed Polymer 
     49   Layers*, *Macromol. Symp.*, 190 (2002) 33-42. 
     50 
     51Authorship and Verification 
     52---------------------------- 
     53 
     54* **Author:** Jae-Hi Cho **Date:** pre 2010 
     55* **Last Modified by:** Paul Kienzle **Date:** April 14, 2016 
     56* **Last Reviewed by:** Steve King **Date:** March 18, 2016 
    5157""" 
    5258 
     
    8086def Iq(q, second_moment, adsorbed_amount, density_shell, radius, 
    8187       volfraction, sld_shell, sld_solvent): 
    82     # pylint: disable = missing-docstring 
    83     #deltarhosqrd =  (sld_shell - sld_solvent) * (sld_shell - sld_solvent) 
    84     #numerator =  6.0 * pi * volfraction * (adsorbed_amount * adsorbed_amount) 
    85     #denominator =  (q * q) * (density_shell * density_shell) * radius 
    86     #eterm =  exp(-1.0 * (q * q) * (second_moment * second_moment)) 
    87     ##scale by 10^-2 for units conversion to cm^-1 
    88     #inten =  1.0e-02 * deltarhosqrd * ((numerator / denominator) * eterm) 
    8988    with errstate(divide='ignore'): 
    9089        aa = ((sld_shell - sld_solvent)/density_shell * adsorbed_amount) / q 
  • sasmodels/models/barbell.py

    r2222134 rb0c4271  
    1 #barbell model 
    2 # Note: model title and parameter table are inserted automatically 
    31r""" 
     2Definition 
     3---------- 
     4 
    45Calculates the scattering from a barbell-shaped cylinder.  Like 
    56:ref:`capped-cylinder`, this is a sphereocylinder with spherical end 
     
    78of the end cap radius lying outside of the cylinder. See the diagram for 
    89the details of the geometry and restrictions on parameter values. 
    9  
    10 Definition 
    11 ---------- 
    1210 
    1311.. figure:: img/barbell_geometry.jpg 
     
    7573 
    7674.. figure:: img/cylinder_angle_projection.jpg 
     75    :width: 600px 
    7776 
    7877    Examples of the angles for oriented pp against the detector plane. 
     
    8180---------- 
    8281 
    83 H Kaya, *J. Appl. Cryst.*, 37 (2004) 37 223-230 
     82.. [#] H Kaya, *J. Appl. Cryst.*, 37 (2004) 37 223-230 
     83.. [#] H Kaya and N R deSouza, *J. Appl. Cryst.*, 37 (2004) 508-509 (addenda 
     84   and errata) 
    8485 
    85 H Kaya and N R deSouza, *J. Appl. Cryst.*, 37 (2004) 508-509 (addenda and errata) 
     86Authorship and Verification 
     87---------------------------- 
     88 
     89* **Author:** NIST IGOR/DANSE **Date:** pre 2010 
     90* **Last Modified by:** Paul Butler **Date:** March 20, 2016 
     91* **Last Reviewed by:** Paul Butler **Date:** March 20, 2016 
    8692""" 
    8793from numpy import inf 
  • sasmodels/models/bcc_paracrystal.py

    r0bef47b rb0c4271  
    1 #bcc paracrystal model 
    2 #note model title and parameter table are automatically inserted 
    3 #note - calculation requires double precision 
    41r""" 
     2Definition 
     3---------- 
     4 
    55Calculates the scattering from a **body-centered cubic lattice** with 
    66paracrystalline distortion. Thermal vibrations are considered to be negligible, 
    77and the size of the paracrystal is infinitely large. Paracrystalline distortion 
    88is assumed to be isotropic and characterized by a Gaussian distribution. 
    9  
    10 Definition 
    11 ---------- 
    129 
    1310The scattering intensity $I(q)$ is calculated as 
     
    2320is the paracrystalline structure factor for a body-centered cubic structure. 
    2421 
    25 Equation (1) of the 1990 reference is used to calculate $Z(q)$, using 
    26 equations (29)-(31) from the 1987 paper for $Z1$, $Z2$, and $Z3$. 
     22Equation (1) of the 1990 reference\ [#CIT1990]_ is used to calculate $Z(q)$, 
     23using equations (29)-(31) from the 1987 paper\ [#CIT1987]_ for $Z1$, $Z2$, and 
     24$Z3$. 
    2725 
    2826The lattice correction (the occupied volume of the lattice) for a 
     
    7977The 2D (Anisotropic model) is based on the reference below where $I(q)$ is 
    8078approximated for 1d scattering. Thus the scattering pattern for 2D may not 
    81 be accurate. Note that we are not responsible for any incorrectness of the 2D 
    82 model computation. 
     79be accurate. 
    8380 
    8481.. figure:: img/bcc_angle_definition.png 
     
    8986---------- 
    9087 
    91 Hideki Matsuoka et. al. *Physical Review B*, 36 (1987) 1754-1765 
    92 (Original Paper) 
     88.. [#CIT1987] Hideki Matsuoka et. al. *Physical Review B*, 36 (1987) 1754-1765 
     89   (Original Paper) 
     90.. [#CIT1990] Hideki Matsuoka et. al. *Physical Review B*, 41 (1990) 3854 -3856 
     91   (Corrections to FCC and BCC lattice structure calculation) 
    9392 
    94 Hideki Matsuoka et. al. *Physical Review B*, 41 (1990) 3854 -3856 
    95 (Corrections to FCC and BCC lattice structure calculation) 
     93Authorship and Verification 
     94---------------------------- 
     95 
     96* **Author:** NIST IGOR/DANSE **Date:** pre 2010 
     97* **Last Modified by:** Paul Butler **Date:** September 29, 2016 
     98* **Last Reviewed by:** Richard Heenan **Date:** March 21, 2016 
    9699""" 
    97100 
     
    109112category = "shape:paracrystal" 
    110113 
     114#note - calculation requires double precision 
    111115single = False 
    112116 
  • sasmodels/models/be_polyelectrolyte.py

    r2c74c11 rb0c4271  
    11r""" 
    2 This model calculates the structure factor of a polyelectrolyte solution with 
    3 the RPA expression derived by Borue and Erukhimovich. 
    4  
    52Definition 
    63---------- 
    7  
    8 The scattering intensity $I(q)$ is calculated as 
     4This model calculates the structure factor of a polyelectrolyte solution with 
     5the RPA expression derived by Borue and Erukhimovich\ [#Borue]_.  The scattering intensity 
     6$I(q)$ is calculated as 
    97 
    108.. math:: 
     
    3634---------- 
    3735 
    38 V Y Borue, I Y Erukhimovich, *Macromolecules*, 21 (1988) 3240 
     36.. [#Borue] V Y Borue, I Y Erukhimovich, *Macromolecules*, 21 (1988) 3240 
     37.. [#] J F Joanny, L Leibler, *Journal de Physique*, 51 (1990) 545 
     38.. [#] A Moussaid, F Schosseler, J P Munch, S Candau, *J. Journal de Physique 
     39   II France*, 3 (1993) 573 
     40.. [#] E Raphael, J F Joanny, *Europhysics Letters*, 11 (1990) 179 
    3941 
    40 J F Joanny, L Leibler, *Journal de Physique*, 51 (1990) 545 
     42Authorship and Verification 
     43---------------------------- 
    4144 
    42 A Moussaid, F Schosseler, J P Munch, S Candau, 
    43 *J. Journal de Physique II France*, 3 (1993) 573 
    44  
    45 E Raphael, J F Joanny, *Europhysics Letters*, 11 (1990) 179 
    46  
     45* **Author:** NIST IGOR/DANSE **Date:** pre 2010 
     46* **Last Modified by:** Paul Kienzle **Date:** July 24, 2016 
     47* **Last Reviewed by:** Piotr rozyczko **Date:** January 27, 2016 
    4748""" 
    4849 
  • sasmodels/models/binary_hard_sphere.py

    r63c6a08 rb0c4271  
    11r""" 
    2  
    32Definition 
    43---------- 
     4 
    55The binary hard sphere model provides the scattering intensity, for binary 
    66mixture of hard spheres including hard sphere interaction between those 
     
    6161---------- 
    6262 
    63 N W Ashcroft and D C Langreth, *Physical Review*, 156 (1967) 685-692 
    64 [Errata found in *Phys. Rev.* 166 (1968) 934] 
     63.. [#] N W Ashcroft and D C Langreth, *Physical Review*, 156 (1967) 685-692 
     64   [Errata found in *Phys. Rev.* 166 (1968) 934] 
     65.. [#] S R Kline, *J Appl. Cryst.*, 39 (2006) 895 
    6566 
    66 S R Kline, *J Appl. Cryst.*, 39 (2006) 895 
     67Authorship and Verification 
     68---------------------------- 
    6769 
    68 **Author:** NIST IGOR/DANSE **on:** pre 2010 
    69  
    70 **Last Modified by:** Paul Butler **on:** March 20, 2016 
    71  
    72 **Last Reviewed by:** Paul Butler **on:** March 20, 2016 
     70* **Author:** NIST IGOR/DANSE **Date:** pre 2010 
     71* **Last Modified by:** Paul Butler **Date:** March 20, 2016 
     72* **Last Reviewed by:** Paul Butler **Date:** March 20, 2016 
    7373""" 
    7474 
  • sasmodels/models/broad_peak.py

    r40a87fa rb0c4271  
    11r""" 
     2Definition 
     3---------- 
     4 
    25This model calculates an empirical functional form for SAS data characterized 
    36by a broad scattering peak. Many SAS spectra are characterized by a broad peak 
     
    912between the scattering inhomogeneities (such as in lamellar, cylindrical, or 
    1013spherical morphologies, or for bicontinuous structures). 
    11  
    12 Definition 
    13 ---------- 
    1414 
    1515The scattering intensity $I(q)$ is calculated as 
     
    3333None. 
    3434 
    35 *2013/09/09 - Description reviewed by King, S and Parker, P.* 
     35Authorship and Verification 
     36---------------------------- 
     37 
     38* **Author:** NIST IGOR/DANSE **Date:** pre 2010 
     39* **Last Modified by:** Paul kienle **Date:** July 24, 2016 
     40* **Last Reviewed by:** Richard Heenan **Date:** March 21, 2016 
    3641""" 
    3742 
  • sasmodels/models/capped_cylinder.py

    r2222134 rb0c4271  
    11r""" 
     2Definitions 
     3----------- 
     4 
    25Calculates the scattering from a cylinder with spherical section end-caps. 
    36Like :ref:`barbell`, this is a sphereocylinder with end caps that have a 
     
    69lens when the length of the cylinder $L=0$. See the diagram for the details 
    710of the geometry and restrictions on parameter values. 
    8  
    9 Definitions 
    10 ----------- 
    1111 
    1212.. figure:: img/capped_cylinder_geometry.jpg 
     
    7676 
    7777.. figure:: img/cylinder_angle_projection.jpg 
     78    :width: 600px 
    7879 
    7980    Examples of the angles for oriented 2D cylinders against the detector plane. 
     
    8283---------- 
    8384 
    84 H Kaya, *J. Appl. Cryst.*, 37 (2004) 223-230 
     85.. [#] H Kaya, *J. Appl. Cryst.*, 37 (2004) 223-230 
     86.. [#] H Kaya and N-R deSouza, *J. Appl. Cryst.*, 37 (2004) 508-509 (addenda  
     87   and errata) 
    8588 
    86 H Kaya and N-R deSouza, *J. Appl. Cryst.*, 37 (2004) 508-509 (addenda and errata) 
     89Authorship and Verification 
     90---------------------------- 
     91 
     92* **Author:** NIST IGOR/DANSE **Date:** pre 2010 
     93* **Last Modified by:** Paul Butler **Date:** September 30, 2016 
     94* **Last Reviewed by:** Richard Heenan **Date:** March 19, 2016 
    8795""" 
    8896from numpy import inf 
  • sasmodels/models/core_multi_shell.py

    r7b68dc5 rb0c4271  
    3333References 
    3434---------- 
    35 See the :ref:`core-shell-sphere` model documentation. 
    3635 
    37 L A Feigin and D I Svergun, 
    38 *Structure Analysis by Small-Angle X-Ray and Neutron Scattering*, 
    39 Plenum Press, New York, 1987. 
     36.. [#] See the :ref:`core-shell-sphere` model documentation. 
     37.. [#] L A Feigin and D I Svergun, *Structure Analysis by Small-Angle X-Ray and Neutron Scattering*, 
     38   Plenum Press, New York, 1987. 
    4039 
    41 **Author:** NIST IGOR/DANSE **on:** pre 2010 
     40Authorship and Verification 
     41---------------------------- 
    4242 
    43 **Last Modified by:** in progress **on:** March 20, 2016 
    44  
    45 **Last Reviewed by:** in progress **on:** March 20, 2016 
     43* **Author:** NIST IGOR/DANSE **Date:** pre 2010 
     44* **Last Modified by:** Paul Kienzle **Date:** September 12, 2016 
     45* **Last Reviewed by:** Under Review **Date:** as of October 5, 2016 
    4646""" 
    4747 
  • sasmodels/models/core_shell_bicelle.py

    r2222134 rb0c4271  
    11r""" 
    2  
    32Definition 
    43---------- 
     
    1312.. figure:: img/core_shell_bicelle_geometry.png 
    1413 
    15     (Graphic from DOI: 10.1039/C0NP00002G, note however that the model here 
    16     calculates for rectangular, not curved, rims.) 
     14    Core shell geometry (Graphic from ref [#Matusmori]_). 
     15    Note however that the model here calculates for rectangular, not curved, rims. 
    1716 
    1817The output of the 1D scattering intensity function for randomly oriented 
     
    2827 
    2928.. figure:: img/cylinder_angle_projection.jpg 
     29    :width: 600px 
    3030 
    3131    Examples of the angles for oriented pp against the detector plane. 
     
    3434---------- 
    3535 
    36 L A Feigin and D I Svergun, 
    37 *Structure Analysis by Small-Angle X-Ray and Neutron Scattering,* 
    38 Plenum Press, New York, (1987) 
     36.. [#Matusmori] `N Matsumori and M Murata <http://dx.doi.org/10.1039/C0NP0000 
     37   2G>`_, *Nat. Prod. Rep.* 27 (2010) 1480-1492 
     38.. [#] L A Feigin and D I Svergun, *Structure Analysis by Small-Angle X-Ray and 
     39   Neutron Scattering,* Plenum Press, New York, (1987) 
     40 
     41Authorship and Verification 
     42---------------------------- 
     43 
     44* **Author:** NIST IGOR/DANSE **Date:** pre 2010 
     45* **Last Modified by:** Paul Butler **Date:** Septmber 30, 2016 
     46* **Last Reviewed by:** Under Review **Date:** October 5, 2016 
    3947 
    4048""" 
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