Changeset 168052c in sasmodels for sasmodels/models/flexible_cylinder.py


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Timestamp:
Jan 29, 2016 6:02:35 AM (8 years ago)
Author:
piotr
Branches:
master, core_shell_microgels, costrafo411, magnetic_model, release_v0.94, release_v0.95, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests
Children:
ed82794
Parents:
bf6631a
Message:

pylint prettification

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1 edited

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  • sasmodels/models/flexible_cylinder.py

    rf94d8a2 r168052c  
    11r""" 
    2 This model provides the form factor, $P(q)$, for a flexible cylinder where the form factor 
    3 is normalized by the volume of the cylinder. 
     2This model provides the form factor, $P(q)$, for a flexible cylinder 
     3where the form factor is normalized by the volume of the cylinder. 
    44**Inter-cylinder interactions are NOT provided for.** 
    55 
    … …  
    88    P(q) = \text{scale} \left<F^2\right>/V + \text{background} 
    99 
    10 where the averaging $\left<\ldots\right>$ is applied only for the 1D calculation 
     10where the averaging $\left<\ldots\right>$ is applied only for the 1D 
     11calculation 
    1112 
    12 The 2D scattering intensity is the same as 1D, regardless of the orientation of the q vector which is defined as 
     13The 2D scattering intensity is the same as 1D, regardless of the orientation of 
     14the q vector which is defined as 
    1315 
    1416.. math:: 
    … …  
    2224 
    2325 
    24 The chain of contour length, $L$, (the total length) can be described as a chain of some number of 
    25 locally stiff segments of length $l_p$, the persistence length (the length along the cylinder over 
    26 which the flexible cylinder can be considered a rigid rod). 
     26The chain of contour length, $L$, (the total length) can be described as a 
     27chain of some number of locally stiff segments of length $l_p$, the persistence 
     28length (the length along the cylinder over which the flexible cylinder can be 
     29considered a rigid rod). 
    2730The Kuhn length $(b = 2*l_p)$ is also used to describe the stiffness of a chain. 
    2831 
    2932The returned value is in units of $cm^-1$, on absolute scale. 
    3033 
    31 In the parameters, the sldCyl and sldSolv represent the SLD of the chain/cylinder and solvent respectively. 
     34In the parameters, the sldCyl and sldSolv represent the SLD of the chain/cylinder 
     35and solvent respectively. 
    3236 
    3337 
    … …  
    3741 
    3842 
    39 Our model uses the form factor calculations implemented in a c-library provided by the NIST Center 
    40 for Neutron Research (Kline, 2006). 
     43Our model uses the form factor calculations implemented in a c-library provided 
     44by the NIST Center for Neutron Research (Kline, 2006). 
    4145 
    4246 
    … …  
    4549    'Method 3 With Excluded Volume' is used. 
    4650    The model is a parametrization of simulations of a discrete representation 
    47     of the worm-like chain model of Kratky and Porod applied in the pseudocontinuous limit. 
     51    of the worm-like chain model of Kratky and Porod applied in the 
     52    pseudocontinuous limit. 
    4853    See equations (13,26-27) in the original reference for the details. 
    4954 
    … …  
    5156---------- 
    5257 
    53 J S Pedersen and P Schurtenberger. *Scattering functions of semiflexible polymers with and 
    54 without excluded volume effects.* Macromolecules, 29 (1996) 7602-7612 
     58J S Pedersen and P Schurtenberger. *Scattering functions of semiflexible 
     59polymers with and without excluded volume effects.* Macromolecules, 
     6029 (1996) 7602-7612 
    5561 
    5662Correction of the formula can be found in 
    5763 
    58 W R Chen, P D Butler and L J Magid, *Incorporating Intermicellar Interactions in the Fitting of 
    59 SANS Data from Cationic Wormlike Micelles.* Langmuir, 22(15) 2006 6539-6548 
     64W R Chen, P D Butler and L J Magid, *Incorporating Intermicellar Interactions 
     65in the Fitting of SANS Data from Cationic Wormlike Micelles.* Langmuir, 
     6622(15) 2006 6539-6548 
    6067""" 
    6168from numpy import inf 
    6269 
    6370name = "flexible_cylinder" 
    64 title = "Flexible cylinder where the form factor is normalized by the volume of the cylinder." 
    65 description = """Note : scale and contrast=sld-solvent_sld are both multiplicative factors in the 
    66                 model and are perfectly correlated. One or 
    67                 both of these parameters must be held fixed 
     71title = "Flexible cylinder where the form factor is normalized by the volume" \ 
     72        "of the cylinder." 
     73description = """Note : scale and contrast=sld-solvent_sld are both 
     74                multiplicative factors in the model and are perfectly 
     75                correlated. One or both of these parameters must be held fixed 
    6876                during model fitting. 
    6977              """ 
    … …  
    7179category = "shape:cylinder" 
    7280 
     81# pylint: disable=bad-whitespace, line-too-long 
    7382#             ["name", "units", default, [lower, upper], "type", "description"], 
    7483parameters = [ 
    75               ["length",      "Ang",       1000.0, [0, inf],    "volume", "Length of the flexible cylinder"], 
    76               ["kuhn_length", "Ang",        100.0, [0, inf],    "volume", "Kuhn length of the flexible cylinder"], 
    77               ["radius",      "Ang",         20.0, [0, inf],    "volume", "Radius of the flexible cylinder"], 
    78               ["sld",         "1e-6/Ang^2",   1.0, [-inf, inf], "",       "Cylinder scattering length density"], 
    79               ["solvent_sld", "1e-6/Ang^2",   6.3, [-inf, inf], "",       "Solvent scattering length density"], 
    80              ] 
    81  
     84    ["length",      "Ang",       1000.0, [0, inf],    "volume", "Length of the flexible cylinder"], 
     85    ["kuhn_length", "Ang",        100.0, [0, inf],    "volume", "Kuhn length of the flexible cylinder"], 
     86    ["radius",      "Ang",         20.0, [0, inf],    "volume", "Radius of the flexible cylinder"], 
     87    ["sld",         "1e-6/Ang^2",   1.0, [-inf, inf], "",       "Cylinder scattering length density"], 
     88    ["solvent_sld", "1e-6/Ang^2",   6.3, [-inf, inf], "",       "Solvent scattering length density"], 
     89    ] 
     90# pylint: enable=bad-whitespace, line-too-long 
    8291source = ["lib/J1.c", "lib/wrc_cyl.c", "flexible_cylinder.c"] 
    8392 
    … …  
    94103 
    95104tests = [ 
    96          # Accuracy tests based on content in test/utest_other_models.py 
    97          # Currently fails in OCL 
    98          # [{'length':     1000.0, 
    99          #  'kuhn_length': 100.0, 
    100          #  'radius':       20.0, 
    101          #  'sld':           1.0, 
    102          #  'solvent_sld':   6.3, 
    103          #  'background':    0.0001, 
    104          #  }, 0.001, 3509.2187], 
     105    # Accuracy tests based on content in test/utest_other_models.py 
     106    # Currently fails in OCL 
     107    # [{'length':     1000.0, 
     108    #  'kuhn_length': 100.0, 
     109    #  'radius':       20.0, 
     110    #  'sld':           1.0, 
     111    #  'solvent_sld':   6.3, 
     112    #  'background':    0.0001, 
     113    #  }, 0.001, 3509.2187], 
    105114 
    106          # Additional tests with larger range of parameters 
    107          [{'length':     1000.0, 
    108            'kuhn_length': 100.0, 
    109            'radius':       20.0, 
    110            'sld':           1.0, 
    111            'solvent_sld':   6.3, 
    112            'background':    0.0001, 
    113            }, 1.0, 0.000595345], 
    114         [{'length':        10.0, 
    115            'kuhn_length': 800.0, 
    116            'radius':        2.0, 
    117            'sld':           6.0, 
    118            'solvent_sld':  12.3, 
    119            'background':    0.001, 
    120            }, 0.1, 1.55228], 
    121        [{'length':        100.0, 
    122            'kuhn_length': 800.0, 
    123            'radius':       50.0, 
    124            'sld':           0.1, 
    125            'solvent_sld':   5.1, 
    126            'background':    0.0, 
    127            }, 1.0, 0.000938456] 
    128          ] 
     115    # Additional tests with larger range of parameters 
     116    [{'length':    1000.0, 
     117      'kuhn_length': 100.0, 
     118      'radius':       20.0, 
     119      'sld':           1.0, 
     120      'solvent_sld':   6.3, 
     121      'background':    0.0001, 
     122     }, 1.0, 0.000595345], 
     123    [{'length':        10.0, 
     124      'kuhn_length': 800.0, 
     125      'radius':        2.0, 
     126      'sld':           6.0, 
     127      'solvent_sld':  12.3, 
     128      'background':    0.001, 
     129     }, 0.1, 1.55228], 
     130    [{'length':        100.0, 
     131      'kuhn_length': 800.0, 
     132      'radius':       50.0, 
     133      'sld':           0.1, 
     134      'solvent_sld':   5.1, 
     135      'background':    0.0, 
     136     }, 1.0, 0.000938456] 
     137    ] 
    129138 
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