Add module for combining SasView models with reflectivity data

molgroups/refl1d_interface/__init__.py

@@ -2,6 +2,10 @@
                                                    MolgroupsMixedExperiment,
                                                    make_samples)
 
+from molgroups.refl1d_interface.sas import (SASReflectivityModel,
+                                          SASReflectivityExperiment,
+                                          SASReflectivityMolgroupsExperiment)
+
 from molgroups.refl1d_interface.layers import (MolgroupsStack,
                                                MolgroupsLayer)
 

molgroups/refl1d_interface/examples/tiox_dopc/tiox_dopc_sas.py

@@ -0,0 +1,158 @@
+"""Example script using molgroups Refl1D interface objects"""
+
+import numpy as np
+from refl1d.names import Parameter, SLD, Slab, FitProblem, load4
+from refl1d.probe.resolution import divergence
+from molgroups import components as cmp
+from molgroups.refl1d_interface import (SolidSupportedBilayer,
+                                        MolgroupsLayer,
+                                        MolgroupsStack,
+                                        MolgroupsExperiment)
+
+from molgroups.refl1d_interface import SASReflectivityMolgroupsExperiment, SASReflectivityModel
+
+## === Probes/data files ===
+probe_d2o = load4('ch061_d2o_ph7.refl', back_reflectivity=True, name='D2O')
+probe_h2o = load4('ch060_h2o_ph7.refl', back_reflectivity=True, name='H2O')
+
+# Probe parameters
+probes = [probe_d2o, probe_h2o]
+
+# Probe parameters
+intensity = Parameter(name='intensity', value=0.8).range(0.65, 1.0)
+sample_broadening = Parameter(name='sample broadening', value=0.0).range(-0.003, 0.02)
+theta_offset = Parameter(name='theta offset', value=0.0).range(-0.02, 0.02)
+
+# apply background and intensity to all probes
+for probe in probes:
+    probe.background.limits = (-np.inf, np.inf)
+    probe.background.range(-1e-6, 1e-5)
+    probe.intensity = intensity
+
+    # if probes support these
+    probe.sample_broadening = sample_broadening
+    probe.theta_offset = theta_offset
+
+## === Structural parameters ===
+
+vf_bilayer = Parameter(name='volume fraction bilayer', value=0.9).range(0.0, 1.0)
+l_lipid1 = Parameter(name='inner acyl chain thickness', value=10.0).range(8, 30)
+l_lipid2 = Parameter(name='outer acyl chain thickness', value=10.0).range(8, 18)
+l_submembrane = Parameter(name='submembrane thickness', value=10.0).range(0, 50)
+sigma = Parameter(name='bilayer roughness', value=5).range(0.5, 9)
+global_rough = Parameter(name ='substrate roughness', value=5).range(2, 9)
+tiox_rough = Parameter(name='titanium oxide roughness', value=4).range(2, 9)
+d_oxide = Parameter(name='silicon oxide layer thickness', value=10).range(5, 30)
+d_tiox =  Parameter(name='titanium oxide layer thickness', value=110).range(100, 200)
+
+## === Materials ===
+
+# Material definitions
+d2o = SLD(name='d2o', rho=6.3000, irho=0.0000)
+h2o = SLD(name='h2o', rho=-0.56, irho=0.0000)
+tiox = SLD(name='tiox', rho=2.1630, irho=0.0000)
+siox = SLD(name='siox', rho=4.1000, irho=0.0000)
+silicon = SLD(name='silicon', rho=2.0690, irho=0.0000)
+
+# Material SLD parameters
+d2o.rho.range(5.3000, 6.36)
+h2o.rho.range(-0.56, 0.6)
+tiox.rho.range(1.2, 3.2)
+siox.rho.range(2.8, 4.8)
+
+## === Molecular groups ===
+
+# overlap between substrate and molgroups layer
+overlap = 30.0
+
+# thickness of molgroups layer
+thickness = 200.0
+
+# define lipids and number fractions
+DOPC = cmp.Lipid(name='DOPC', headgroup=cmp.pc, tails=2 * [cmp.oleoyl], methyls=[cmp.methyl])
+lipidlist = [DOPC]
+lipid_nf = [1.0]
+
+def bilayer(substrate, contrast):
+
+    blm = SolidSupportedBilayer(name='bilayer',
+                        overlap=overlap,
+                        lipids=lipidlist,
+                        inner_lipid_nf=lipid_nf,
+                        outer_lipid_nf=lipid_nf,
+                        rho_substrate=tiox.rho,
+                        l_siox=0.0,
+                        vf_bilayer=vf_bilayer,
+                        l_lipid1=l_lipid1,
+                        l_lipid2=l_lipid2,
+                        l_submembrane=l_submembrane,
+                        substrate_rough=tiox_rough,
+                        sigma=sigma)
+
+    mollayer = MolgroupsLayer(base_group=blm,
+                            thickness=thickness,
+                            contrast=contrast,
+                            name='bilayer layer ' + contrast.name)
+
+    return MolgroupsStack(substrate=substrate,
+                        molgroups_layer=mollayer,
+                        name=mollayer.name)
+
+## == Sample layer stack ==
+
+layer_silicon = Slab(material=silicon, thickness=0.0000, interface=global_rough)
+layer_siox = Slab(material=siox, thickness=d_oxide, interface=global_rough)
+layer_tiox = Slab(material=tiox, thickness=d_tiox - overlap, interface=0.00)
+
+substrate = layer_silicon | layer_siox | layer_tiox
+
+# Use the bilayer definition function to generate the bilayer SLD profile, passing in the relevant parameters.
+sample_d2o, sample_h2o = [bilayer(substrate, contrast) for contrast in [d2o, h2o]]
+
+## === Problem definition ===
+## step = True corresponds to a calculation of the reflectivity from an actual profile
+## with microslabbed interfaces.  When step = False, the Nevot-Croce
+## approximation is used to account for roughness.  This approximation speeds up
+## the calculation tremendously, and is reasonably accurate as long as the
+## roughness is much less than the layer thickness
+step = False
+STEPSIZE=0.5
+
+# calculate full transverse divergence (2 * FWHM) for MAGIK reflectometer
+S1_transverse = 150.0
+S2_transverse = 25.0
+L2 = 330.0
+L1 = 1403.0 + 330.0
+dTl = 2 * np.ones_like(probe_d2o.Q) * divergence(0, (S1_transverse, S2_transverse), (L1, L2))
+
+bilayer_thickness = Parameter(name='SANS bilayer thickness', value=40.0).range(20.0, 80.0)
+bilayer_spacing = Parameter(name='SANS bilayer spacing', value=20.0).range(5.0, 50.0)
+bilayer_sld = Parameter(name='SANS bilayer sld', value=0.4).range(-0.5, 0.5)
+volume_fraction_bilayer = Parameter(name='SANS volume fraction', value=0.00001).range(0.0, 0.0001)
+n_bilayers =  Parameter(name='SANS number of bilayers', value=4).range(1, 20)
+
+sans_parameters = {'scale': 1.0,
+                    'background': 0.0,
+                    'sld': bilayer_sld,
+                    'thick_shell': bilayer_thickness,
+                    'thick_solvent': bilayer_spacing,
+                    'radius': 100.0,
+                    'volfraction': volume_fraction_bilayer,
+                    'n_shells': n_bilayers * 2 - 1
+                    }
+
+sasmodel_d = SASReflectivityModel(sas_model_name='multilayer_vesicle',
+                                dtheta_l=dTl,
+                                parameters=sans_parameters | {'sld_solvent': d2o.rho})
+
+sasmodel_h = SASReflectivityModel(sas_model_name='multilayer_vesicle',
+                                dtheta_l=dTl,
+                                parameters=sans_parameters | {'sld_solvent': h2o.rho})
+
+
+model_d2o = SASReflectivityMolgroupsExperiment(sas_model=sasmodel_d, sample=sample_d2o, probe=probe_d2o, dz=STEPSIZE, step_interfaces = step)
+model_h2o = SASReflectivityMolgroupsExperiment(sas_model=sasmodel_h, sample=sample_h2o, probe=probe_h2o, dz=STEPSIZE, step_interfaces = step)
+
+problem = FitProblem([model_d2o, model_h2o])
+
+problem.name = "tiox_dopc_d2o_h2o"