Changeset dcdf29d in sasmodels
- Timestamp:
- Feb 2, 2016 7:51:27 AM (9 years ago)
- 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:
- 7f47777, 8007311
- Parents:
- 577912b
- Location:
- sasmodels/models
- Files:
-
- 4 edited
-
barbell.py (modified) (1 diff)
-
bcc.py (modified) (1 diff)
-
broad_peak.py (modified) (2 diffs)
-
capped_cylinder.py (modified) (3 diffs)
Legend:
- Unmodified
- Added
- Removed
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sasmodels/models/barbell.py
reb69cce rdcdf29d 100 100 title = "Cylinder with spherical end caps" 101 101 description = """ 102 Calculates the scattering from a barbell-shaped cylinder. 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 103 radius lies outside of the cylinder. 104 Note: As the length of cylinder(bar) -->0,it becomes a dumbbell. And when rad_bar = rad_bell, it is a spherocylinder. 105 It must be that rad_bar <(=) rad_bell. 102 Calculates the scattering from a barbell-shaped cylinder. 103 That is a sphereocylinder with spherical end caps that have a radius larger 104 than that of the cylinder and the center of the end cap radius lies outside 105 of the cylinder. 106 Note: As the length of cylinder(bar) -->0,it becomes a dumbbell. And when 107 rad_bar = rad_bell, it is a spherocylinder. 108 It must be that rad_bar <(=) rad_bell. 106 109 """ 107 110 category = "shape:cylinder" 108 111 # pylint: disable=bad-whitespace, line-too-long 109 112 # ["name", "units", default, [lower, upper], "type","description"], 110 parameters = [["sld", "4e-6/Ang^2", 4, [-inf, inf], "","Barbell scattering length density"],111 ["solvent_sld", "1e-6/Ang^2", 1, [-inf, inf], "","Solvent scattering length density"],112 ["bell_radius", "Ang", 40, [0, inf], "volume","Spherical bell radius"],113 ["radius", "Ang", 20, [0, inf], "volume","Cylindrical bar radius"],114 ["length", "Ang", 400, [0, inf], "volume","Cylinder bar length"],115 ["theta", "degrees",60, [-inf, inf], "orientation", "In plane angle"],116 ["phi", "degrees",60, [-inf, inf], "orientation", "Out of plane angle"],113 parameters = [["sld", "4e-6/Ang^2", 4, [-inf, inf], "", "Barbell scattering length density"], 114 ["solvent_sld", "1e-6/Ang^2", 1, [-inf, inf], "", "Solvent scattering length density"], 115 ["bell_radius", "Ang", 40, [0, inf], "volume", "Spherical bell radius"], 116 ["radius", "Ang", 20, [0, inf], "volume", "Cylindrical bar radius"], 117 ["length", "Ang", 400, [0, inf], "volume", "Cylinder bar length"], 118 ["theta", "degrees", 60, [-inf, inf], "orientation", "In plane angle"], 119 ["phi", "degrees", 60, [-inf, inf], "orientation", "Out of plane angle"], 117 120 ] 121 # pylint: enable=bad-whitespace, line-too-long 118 122 119 123 source = ["lib/J1.c", "lib/gauss76.c", "barbell.c"] -
sasmodels/models/bcc.py
reb69cce rdcdf29d 109 109 title = "Body-centred cubic lattic with paracrystalline distortion" 110 110 description = """ 111 Calculates the scattering from a **body-centered cubic lattice** with paracrystalline distortion. Thermal vibrations 112 are considered to be negligible, and the size of the paracrystal is infinitely large. Paracrystalline distortion is 113 assumed to be isotropic and characterized by a Gaussian distribution. 111 Calculates the scattering from a **body-centered cubic lattice** with 112 paracrystalline distortion. Thermal vibrations are considered to be 113 negligible, and the size of the paracrystal is infinitely large. 114 Paracrystalline distortion is assumed to be isotropic and characterized 115 by a Gaussian distribution. 114 116 """ 115 117 category = "shape:paracrystal" 116 118 # pylint: disable=bad-whitespace, line-too-long 117 119 # ["name", "units", default, [lower, upper], "type","description" ], 118 parameters = [["dnn", "Ang", 220, [-inf, inf], "","Nearest neighbour distance"],119 ["d_factor", "", 0.06, [-inf, inf], "","Paracrystal distortion factor"],120 ["radius", "Ang", 40, [0, inf], "volume","Particle radius"],121 ["sld", "1e-6/Ang^2", 4, [-inf, inf], "","Particle scattering length density"],122 ["solvent_sld", "1e-6/Ang^2", 1, [-inf, inf], "","Solvent scattering length density"],123 ["theta", "degrees", 60,[-inf, inf], "orientation", "In plane angle"],124 ["phi", "degrees", 60,[-inf, inf], "orientation", "Out of plane angle"],125 ["psi", "degrees", 60,[-inf, inf], "orientation", "Out of plane angle"]120 parameters = [["dnn", "Ang", 220, [-inf, inf], "", "Nearest neighbour distance"], 121 ["d_factor", "", 0.06, [-inf, inf], "", "Paracrystal distortion factor"], 122 ["radius", "Ang", 40, [0, inf], "volume", "Particle radius"], 123 ["sld", "1e-6/Ang^2", 4, [-inf, inf], "", "Particle scattering length density"], 124 ["solvent_sld", "1e-6/Ang^2", 1, [-inf, inf], "", "Solvent scattering length density"], 125 ["theta", "degrees", 60, [-inf, inf], "orientation", "In plane angle"], 126 ["phi", "degrees", 60, [-inf, inf], "orientation", "Out of plane angle"], 127 ["psi", "degrees", 60, [-inf, inf], "orientation", "Out of plane angle"] 126 128 ] 129 # pylint: enable=bad-whitespace, line-too-long 127 130 128 131 source = ["lib/J1.c", "lib/gauss150.c", "bcc.c"] -
sasmodels/models/broad_peak.py
reb69cce rdcdf29d 60 60 category = "shape-independent" 61 61 62 # pylint: disable=bad-whitespace, line-too-long 62 63 # ["name", "units", default, [lower, upper], "type", "description"], 63 parameters = [["porod_scale", "",1.0e-05, [-inf, inf], "", "Power law scale factor"],64 ["porod_exp", "",3.0, [-inf, inf], "", "Exponent of power law"],65 ["lorentz_scale", "",10.0, [-inf, inf], "", "Scale factor for broad Lorentzian peak"],66 ["lorentz_length", "Ang", 50.0, [-inf, inf], "", "Lorentzian screening length"],67 ["peak_pos", "1/Ang", 0.1, [-inf, inf], "", "Peak postion in q"],68 ["lorentz_exp", "", 2.0, [-inf, inf], "", "exponent of Lorentz function"],64 parameters = [["porod_scale", "", 1.0e-05, [-inf, inf], "", "Power law scale factor"], 65 ["porod_exp", "", 3.0, [-inf, inf], "", "Exponent of power law"], 66 ["lorentz_scale", "", 10.0, [-inf, inf], "", "Scale factor for broad Lorentzian peak"], 67 ["lorentz_length", "Ang", 50.0, [-inf, inf], "", "Lorentzian screening length"], 68 ["peak_pos", "1/Ang", 0.1, [-inf, inf], "", "Peak position in q"], 69 ["lorentz_exp", "", 2.0, [-inf, inf], "", "Exponent of Lorentz function"], 69 70 ] 71 # pylint: enable=bad-whitespace, line-too-long 70 72 71 def Iq(q, porod_scale, porod_exp, lorentz_scale, lorentz_length, peak_pos, lorentz_exp): 73 def Iq(q, 74 porod_scale=1.0e-5, 75 porod_exp=3.0, 76 lorentz_scale=10.0, 77 lorentz_length=50.0, 78 peak_pos=0.1, 79 lorentz_exp=2.0): 80 """ 81 :param q: Input q-value 82 :param porod_scale: Power law scale factor 83 :param porod_exp: Exponent of power law 84 :param lorentz_scale: Scale factor for broad Lorentzian peak 85 :param lorentz_length: Lorentzian screening length 86 :param peak_pos: Peak position in q 87 :param lorentz_exp: Exponent of Lorentz function 88 :return: Calculated intensity 89 """ 90 72 91 inten = (porod_scale / q ** porod_exp + lorentz_scale 73 92 / (1.0 + (abs(q - peak_pos) * lorentz_length) ** lorentz_exp)) … … 76 95 77 96 def Iqxy(qx, qy, *args): 97 """ 98 :param qx: Input q_x-value 99 :param qy: Input q_y-value 100 :param args: Remaining arguments 101 :return: 2D-Intensity 102 """ 78 103 return Iq(sqrt(qx ** 2 + qy ** 2), *args) 104 79 105 Iqxy.vectorized = True # Iqxy accepts an array of qx, qy values 80 81 106 82 107 demo = dict(scale=1, background=0, -
sasmodels/models/capped_cylinder.py
reb69cce rdcdf29d 125 125 """ 126 126 category = "shape:cylinder" 127 # pylint: disable=bad-whitespace, line-too-long 128 # ["name", "units", default, [lower, upper], "type", "description"], 129 parameters = [["sld", "1e-6/Ang^2", 4, [-inf, inf], "", "Cylinder scattering length density"], 130 ["solvent_sld", "1e-6/Ang^2", 1, [-inf, inf], "", "Solvent scattering length density"], 131 ["radius", "Ang", 20, [0, inf], "volume", "Cylinder radius"], 127 132 128 # ["name", "units", default, [lower, upper], "type", "description"],129 parameters = [["sld", "1e-6/Ang^2", 4, [-inf, inf], "",130 "Cylinder scattering length density"],131 ["solvent_sld", "1e-6/Ang^2", 1, [-inf, inf], "",132 "Solvent scattering length density"],133 ["radius", "Ang", 20, [0, inf], "volume", "Cylinder radius"],134 133 # TODO: use an expression for cap radius with fixed bounds. 135 134 # The current form requires cap radius R bigger than cylinder radius r. … … 141 140 # in the capped cylinder, and zero for no bar in the barbell model. In 142 141 # both models, one would be a pill. 143 ["cap_radius", "Ang", 20, [0, inf],"volume", "Cap radius"],144 ["length", "Ang", 400, [0, inf],"volume", "Cylinder length"],145 ["theta", "degrees", 60, [-inf, inf], "orientation", "In plane angle"],146 ["phi", "degrees", 60, [-inf, inf], "orientation", "Out of plane angle"],142 ["cap_radius", "Ang", 20, [0, inf], "volume", "Cap radius"], 143 ["length", "Ang", 400, [0, inf], "volume", "Cylinder length"], 144 ["theta", "degrees", 60, [-inf, inf], "orientation", "In plane angle"], 145 ["phi", "degrees", 60, [-inf, inf], "orientation", "Out of plane angle"], 147 146 ] 147 # pylint: enable=bad-whitespace, line-too-long 148 148 149 149 source = ["lib/J1.c", "lib/gauss76.c", "capped_cylinder.c"] … … 159 159 phi_pd=15, phi_pd_n=1) 160 160 oldname = 'CappedCylinderModel' 161 oldpars = dict(sld='sld_capcyl', solvent_sld='sld_solv', 162 length='len_cyl', radius='rad_cyl', cap_radius='rad_cap') 161 oldpars = dict(sld='sld_capcyl', 162 solvent_sld='sld_solv', 163 length='len_cyl', 164 radius='rad_cyl', 165 cap_radius='rad_cap')
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