Changeset d8b4c5a in sasmodels


Ignore:
Timestamp:
Sep 26, 2018 5:45:11 PM (3 months ago)
Author:
butler
Branches:
master, beta_approx, cuda-test, py3, ticket-1015-gpu-mem-error, ticket-1015-quick-fix, ticket-1157, ticket-608-user-defined-weights, ticket_1156
Children:
9235fc3
Parents:
2effdf6
Message:

Fix typo, clarify validation text and add tests

Addresses PR comments: removed redundant information in Iq function: doc
string replaced as suggested with text pointing to table and remove
default values on each parameter in the function call.
Also added verbiage to validation section to hopefully clarify what was
happening and what was done, fixed typo, and added back unit tests with
salt along with comment that these are "self-validated" and need proper
tests at some point in the future

File:
1 edited

Legend:

Unmodified
Added
Removed
  • sasmodels/models/be_polyelectrolyte.py

    r2effdf6 rd8b4c5a  
    6161history of this code goes back to a 1998 implementation. It was recently noted 
    6262that in that implementation, while both the polymer concentration and salt 
    63 concentration were converted to units of 1/|Ang|, only the converted polymer 
    64 concentration was used in the calculation while the unconverted salt 
    65 concentration was used.  This was carried through to sasmodles today (except 
    66 that the conversion equation for the salt concentration was dropped somewhere 
    67 along the line). Simple dimensional analysis of the calculation shows that the 
     63concentration were converted from experimental units of mol/L to more 
     64dimensionally useful units of 1/|Ang|^3, only the converted version of the 
     65polymer concentration was actually being used in the calculation while the 
     66unconverted salt concentration (still in units of mol/L) was being used.  This 
     67was carried through to sasmodels today (except that the line of code converting 
     68the salt concentration to the new units was dropped somewhere along the line). 
     69Simple dimensional analysis of the calculation shows that it is in fact the 
    6870converted salt concentration must be used and the original code suggests that 
    6971was the intention.  We therefore believe this is now correct.  Once better 
     
    119121 
    120122def Iq(q, 
    121        contrast_factor=10.0, 
    122        bjerrum_length=7.1, 
    123        virial_param=12.0, 
    124        monomer_length=10.0, 
    125        salt_concentration=0.0, 
    126        ionization_degree=0.05, 
    127        polymer_concentration=0.7): 
     123       contrast_factor, 
     124       bjerrum_length, 
     125       virial_param, 
     126       monomer_length, 
     127       salt_concentration, 
     128       ionization_degree, 
     129       polymer_concentration): 
    128130    """ 
    129     :param q:                     Input q-value 
    130     :param contrast_factor:       Contrast factor of the polymer 
    131     :param bjerrum_length:        Bjerrum length 
    132     :param virial_param:          Virial parameter 
    133     :param monomer_length:        Monomer length 
    134     :param salt_concentration:    Concentration of monovalent salt 
    135     :param ionization_degree:     Degree of ionization 
    136     :param polymer_concentration: Polymer molar concentration 
    137     :return:                      1-D intensity 
     131    :params: see parameter table 
     132    :return: 1-D form factor for polyelectrolytes in low salt 
     133     
     134    parameter names, units, default values, and behavior (volume, sld etc) are 
     135    defined in the parameter table.  The concentrations are converted from 
     136    experimental mol/L to dimensionaly useful 1/A3 in first two lines 
    138137    """ 
    139138 
     
    192191 
    193192    # Accuracy tests based on content in test/utest_other_models.py 
     193    # Note that these should some day be validated beyond this self validation 
     194    # (circular reasoning). -- i.e. the "good value," at least for those with 
     195    # non zero salt concentrations, were obtained by running the current 
     196    # model in SasView and copying the appropriate result here. 
     197    #    PDB -- Sep 26, 2018 
    194198    [{'contrast_factor':       10.0, 
    195199      'bjerrum_length':         7.1, 
     
    202206     }, 0.001, 0.0948379], 
    203207 
    204     #Comment out rest of tests as they use non zero salt concentrations. With 
    205     #the new code the results will change. We can just take the answer the code 
    206     #gives and call it correct but not sure that is appropriate.  May however 
    207     #be the best we can do? How were these generated in the first place? 
    208     #In the meantime comment them out.  
    209     #Additional tests with larger range of parameters 
    210 #    [{'contrast_factor':       10.0, 
    211 #      'bjerrum_length':       100.0, 
    212 #      'virial_param':           3.0, 
    213 #      'monomer_length':         1.0, 
    214 #      'salt_concentration':    10.0, 
    215 #      'ionization_degree':      2.0, 
    216 #      'polymer_concentration': 10.0, 
    217 #      'background':             0.0, 
    218 #     }, 0.1, -3.75693800588], 
    219  
    220 #    [{'contrast_factor':       10.0, 
    221 #      'bjerrum_length':       100.0, 
    222 #      'virial_param':           3.0, 
    223 #      'monomer_length':         1.0, 
    224 #      'salt_concentration':    10.0, 
    225 #      'ionization_degree':      2.0, 
    226 #      'polymer_concentration': 10.0, 
    227 #      'background':           100.0 
    228 #     }, 5.0, 100.029142149], 
    229 # 
    230 #    [{'contrast_factor':     100.0, 
    231 #      'bjerrum_length':       10.0, 
    232 #      'virial_param':        180.0, 
    233 #      'monomer_length':        1.0, 
    234 #      'salt_concentration':    0.1, 
    235 #      'ionization_degree':     0.5, 
    236 #      'polymer_concentration': 0.1, 
    237 #      'background':             0.0, 
    238 #     }, 200., 1.80664667511e-06], 
     208    [{'contrast_factor':       10.0, 
     209      'bjerrum_length':       100.0, 
     210      'virial_param':           3.0, 
     211      'monomer_length':         5.0, 
     212      'salt_concentration':     1.0, 
     213      'ionization_degree':      0.1, 
     214      'polymer_concentration':  1.0, 
     215      'background':             0.0, 
     216     }, 0.1, 0.253469484], 
     217 
     218    [{'contrast_factor':       10.0, 
     219      'bjerrum_length':       100.0, 
     220      'virial_param':           3.0, 
     221      'monomer_length':         5.0, 
     222      'salt_concentration':     1.0, 
     223      'ionization_degree':      0.1, 
     224      'polymer_concentration':  1.0, 
     225      'background':             1.0, 
     226     }, 0.05, 1.738358122], 
     227 
     228    [{'contrast_factor':     100.0, 
     229      'bjerrum_length':       10.0, 
     230      'virial_param':         12.0, 
     231      'monomer_length':       10.0, 
     232      'salt_concentration':    0.1, 
     233      'ionization_degree':     0.5, 
     234      'polymer_concentration': 0.1, 
     235      'background':           0.01, 
     236     }, 0.5, 0.012881893], 
    239237    ] 
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