Commit 1a0a92ed authored by Heller, William T.'s avatar Heller, William T.
Browse files

Merge branch 'polydis_probs' into 'master' 

Polydis probs

See merge request !23
parents ad3ca778 5a8218ed

documentation/models_and_parameters.yaml

+0 −51
Original line number Diff line number Diff line
@@ -231,10 +231,6 @@ core_multi_shell: 
        linear: [-0.56, 8.00]

    sld10:

        linear: [-0.56, 8.00]

    Structure_Factor: 

        name: hardsphere

        volfraction:

            linear: [0.0, 0.50]

   

core_shell_bicelle_elliptical:

    name: core_shell_bicelle_elliptical
@@ -358,10 +354,6 @@ core_shell_ellipsoid: 
        linear: [0.1, 10.0] 

        polydispersity:

            SchulzDispersion: [0.0, 0.40]

    Structure_Factor: 

        name: hardsphere

        volfraction:

            linear: [0.0, 0.50]



core_shell_parallelepiped:

    name: core_shell_parallelepiped
@@ -426,10 +418,6 @@ core_shell_sphere: 
        log: [0.0, 2.0] 

        polydispersity:

            SchulzDispersion: [0.0, 0.40]

    Structure_Factor: 

        name: hardsphere

        volfraction:

            linear: [0.0, 0.50]



correlation_length:

    name: correlation_length
@@ -498,10 +486,6 @@ ellipsoid: 
        log: [1.0, 3.0] 

        polydispersity:

            SchulzDispersion: [0.0, 0.40]

    Structure_Factor: 

        name: hardsphere

        volfraction:

            linear: [0.0, 0.50]



elliptical_cylinder:

    name: elliptical_cylinder
@@ -668,10 +652,6 @@ fuzzy_sphere: 
    fuzziness: 

        linear: [0.25, 2.0] 

        coupled: [radius]

    Structure_Factor: 

        name: hardsphere

        volfraction: 

            linear: [0.0, 0.50]



gaussian_peak:

    name: gaussian_peak
@@ -1044,10 +1024,6 @@ multilayer_vesicle: 
            SchulzDispersion: [0.0, 0.40]

    n_shells: 

        integer: [1, 25]

    Structure_Factor: 

        name: hardsphere

        volfraction:

            linear: [0.0, 0.50]



onion:

    name: onion
@@ -1240,13 +1216,6 @@ poly_gauss_coil: 
        log: [1.0, 2.8]

    polydispersity: 

        linear: [1.0, 2.0]

    Structure_Factor: 

        name: hardsphere

        volfraction:

            linear: [0.0, 0.50] 

        radius_effective: 

            linear: [1.0, 1.5] 

            coupled: [rg]

        

polymer_excl_volume:

    name: polymer_excl_volume
@@ -1259,10 +1228,6 @@ polymer_excl_volume: 
        log: [1.0, 3.0]

    porod_exp: 

        linear: [1.0, 4.0]

    Structure_Factor: 

        name: hardsphere

        volfraction:

            linear: [0.0, 0.50]



polymer_micelle:

    name: polymer_micelle
@@ -1370,10 +1335,6 @@ raspberry: 
    penetration:

        linear: [0.0, 1.0] 

        coupled: [radius_sm]

    Structure_Factor: 

        name: hardsphere

        volfraction: 

            linear: [ 0.0, 0.50]



rectangular_prism:

    name: rectangular_prism
@@ -1435,10 +1396,6 @@ sphere: 
        log: [1.0, 3.5] 

        polydispersity:

            SchulzDispersion: [0.0, 0.40]

    Structure_Factor: 

        name: hardsphere

        volfraction: 

            linear: [0.0, 0.50]



spherical_sld:

    name: spherical_sld
@@ -1677,10 +1634,6 @@ triaxial_ellipsoid: 
        log: [1.0, 4.0] 

        polydispersity: 

            SchulzDispersion: [0.0, 0.40]

    Structure_Factor: 

        name: hardsphere

        volfraction: 

            linear: [0.0, 0.50]



teubner_strey:

    name: teubner_strey
@@ -1825,8 +1778,4 @@ vesicle: 
        log: [1.0, 2.0] 

        polydispersity:

            SchulzDispersion: [0.0, 0.40]

    Structure_Factor: 

        name: hardsphere

        volfraction:

            linear: [0.0, 0.50]

documentation/structure_factor_examples.yaml

0 → 100644
+108 −0
Original line number Diff line number Diff line 
# this is an example of using the hard sphere structure factor

sphere:

    name: sphere

    Category: shape-sphere

    scale:

        fixed: [1.0]

    background: 

        fixed: [0.001]

    sld: 

        linear: [-0.56, 8.00]

    sld_solvent: 

        linear: [-0.56, 6.38]

    radius: 

        log: [1.0, 3.5] 

        polydispersity:

            SchulzDispersion: [0.0, 0.40]

    Structure_Factor: 

        name: hardsphere

        radius_effective:

            log: [1.0, 3.5]

        volfraction: 

            linear: [0.0, 0.50]



# this is an example of using the sticky hard sphere structure factor

sphere:

    name: sphere

    Category: shape-sphere

    scale:

        fixed: [1.0]

    background: 

        fixed: [0.001]

    sld: 

        linear: [-0.56, 8.00]

    sld_solvent: 

        linear: [-0.56, 6.38]

    radius: 

        log: [1.0, 3.5] 

        polydispersity:

            SchulzDispersion: [0.0, 0.40]

    Structure_Factor: 

        name: stickyhardsphere

        radius_effective:

            log: [1.0, 3.5]

        volfraction: 

            linear: [0.0, 0.50]

        perturb:

            linear: [0.01, 0.1]

        stickiness:

            linear: [0.0, 1.0]



# this is an example of using the square well structure factor

sphere:

    name: sphere

    Category: shape-sphere

    scale:

        fixed: [1.0]

    background: 

        fixed: [0.001]

    sld: 

        linear: [-0.56, 8.00]

    sld_solvent: 

        linear: [-0.56, 6.38]

    radius: 

        log: [1.0, 3.5] 

        polydispersity:

            SchulzDispersion: [0.0, 0.40]

    Structure_Factor: 

        name: squarewell

        radius_effective:

            log: [1.0, 3.5]

        volfraction: 

            linear: [0.0, 0.50]

        welldepth:

            linear: [0.01, 0.1]

        wellwidth:

            linear: [1.0, 2.0]



# this is an example of using the Hayter-Penfold charged sphere structure factor

sphere:

    name: sphere

    Category: shape-sphere

    scale:

        fixed: [1.0]

    background: 

        fixed: [0.001]

    sld: 

        linear: [-0.56, 8.00]

    sld_solvent: 

        linear: [-0.56, 6.38]

    radius: 

        log: [1.0, 3.5] 

        polydispersity:

            SchulzDispersion: [0.0, 0.40]

    Structure_Factor: 

        name: hayter_msa

        radius_effective:

            log: [1.0, 3.5]

        volfraction: 

            linear: [0.0, 0.50]

        charge:

            linear: [0.0, 20.0]

        temperature:

            linear: [273.15, 373.15]

        concentration_salt:

            linear: [0.0, 5.0]

        dielectconst:

            linear: [0.0, 100.0]

            
 No newline at end of file

examples/test_polysphere.yaml

0 → 100644
+31 −0
Original line number Diff line number Diff line 
file: 

    name: sphere_nz_unc.txt

    qmin: 0.01

    qmax: 0.30

    

output_files: test_sphere_nz



sa_parameters: 

    temperatures: 100

    temperature_rate: 0.90

    parameter_rate: 0.95

    iterations: 1000

    models_to_generate: 5



model:

    name: sphere

    category: shape-sphere

    scale:

        fixed: [1.00]

    background: 

        linear: [0.000, 0.10]

    sld: 

        linear: [5.0, 6.0]

    sld_solvent: 

        linear: [3.5, 4.5]

    radius: 

        linear: [50.0, 300.0]

        polydispersity: 

            SchulzDispersion: [0.0, 0.40]

sas_temper/sas_temper_engine.py

+1 −1
Original line number Diff line number Diff line
@@ -453,7 +453,7 @@ def est_uncerts(d, f, modconf, best_model): 
            

            tmp = copy.deepcopy(loc)

            tmp.params[i].polydispersity.val = loc.params[i].polydispersity.val + eps.params[i].polydispersity.val

            if tmp.params[i].polydispsersity.val >= modconf.params[i].polydispersity.max:

            if tmp.params[i].polydispersity.val >= modconf.params[i].polydispersity.max:

                tmp.params[i].polydispersity.val = loc.params[i].polydispersity.val - eps.params[i].polydispersity.val

                

            stepped.append(tmp)

tests/test_polysphere.yaml

0 → 100644
+31 −0
Original line number Diff line number Diff line 
file: 

    name: sphere_nz_unc.txt

    qmin: 0.01

    qmax: 0.30

    

output_files: test_sphere_nz



sa_parameters: 

    temperatures: 100

    temperature_rate: 0.90

    parameter_rate: 0.95

    iterations: 1000

    models_to_generate: 5



model:

    name: sphere

    category: shape-sphere

    scale:

        fixed: [1.00]

    background: 

        linear: [0.000, 0.10]

    sld: 

        linear: [5.0, 6.0]

    sld_solvent: 

        linear: [3.5, 4.5]

    radius: 

        linear: [50.0, 300.0]

        polydispersity: 

            SchulzDispersion: [0.0, 0.40]