MLayer Models

This package can load models from other reflectometry fitting software. In this example we load an mlayer .staj file and fit the parameters within it.

The staj file can be used directly from the graphical interactor or it can be previewed from the command line:

$ refl1d De2_VATR.staj --preview

This shows the model plot:

(Source code, png, hires.png, pdf)

../../_images/readme-11.png

and the available model parameters:

.probe
  .back_absorption = Parameter(1, name='back_absorption')
  .background = Parameter(1e-10, name='background')
  .intensity = Parameter(1, name='intensity')
  .theta_offset = Parameter(0, name='theta_offset')
.sample
  .layers
    [0]
      .interface = Parameter(4.24661e-11, name='B3 interface')
      .material
        .irho = Parameter(3.00904e-05, name='B3 irho')
        .rho = Parameter(5.69228, name='B3 rho')
      .thickness = Parameter(90, name='B3 thickness')
    [1]
      .interface = Parameter(4.24661e-11, name='B2 interface')
      .material
        .irho = Parameter(1.39368e-05, name='B2 irho')
        .rho = Parameter(5.86948, name='B2 rho')
      .thickness = Parameter(64.0154, name='B2 thickness')
    [2]
      .interface = Parameter(83.7958, name='B1 interface')
      .material
        .irho = Parameter(6.93684e-05, name='B1 irho')
        .rho = Parameter(0.340309, name='B1 rho')
      .thickness = Parameter(316.991, name='B1 thickness')
    [3]
      .interface = Parameter(33.2095, name='M2 interface')
      .material
        .irho = Parameter(6.93684e-05, name='M2 irho')
        .rho = Parameter(1.73106, name='M2 rho')
      .thickness = Parameter(1052.77, name='M2 thickness')
    [4]
      .interface = Parameter(20.6753, name='M1 interface')
      .material
        .irho = Parameter(0.00137419, name='M1 irho')
        .rho = Parameter(4.02059, name='M1 rho')
      .thickness = Parameter(567.547, name='M1 thickness')
    [5]
      .interface = Parameter(4.24661e-11, name='V interface')
      .material
        .irho = Parameter(0, name='V irho')
        .rho = Parameter(0, name='V rho')
      .thickness = Parameter(0, name='V thickness')
  .thickness = stack thickness:2091.32

[chisq=2.16242, nllf=408.697]

Note that the parameters are reversed from the order in mlayer, so layer 0 is the substrate rather than the incident medium. The graphical interactor, refl1d_gui, allows you to adjust parameters and fit ranges before starting the fit, but you can also do so from a script, as shown in De2_VATR.py:

from refl1d.names import *
from refl1d.stajconvert import load_mlayer

# Load neutron model and data from staj file
# Layer names are ordered from substrate to surface, and defaults to
# the names in the original staj file.
# Model name defaults to the data file name
layers=["sappire","MgO","MgHx1","MgHx2","Pd","air"]
M = load_mlayer("De2_VATR.staj",layers=layers,name="n6hd2")

# Set thickness/roughness fitting parameters to +/- 20 %
# Set SLD to +/- 5% for all but the incident medium and the substrate.
for L in M.sample[1:-1]:
    L.thickness.pmp(20)
    L.interface.pmp(20)
    L.material.rho.pmp(5)

# Let the substrate SLD vary by 2%
M.sample[0].material.rho.pmp(2)
M.sample[0].interface.range(0,20)
M.sample[1].interface.range(0,20)

problem = FitProblem(M)
problem.name = "Desorption 2"

Staj file constraints are ignored, but you can get similar functionality by setting parameters to equal expressions of other parameters. You can even constrain one staj file to share parameters with another by setting, for example:

M1 = load_mlayer("De1_VATR.staj")
M2 = load_mlayer("De2_VATR.staj")
M1.sample[3].thickness = M2.sample[3].thickness
problem = MultiFitProblem([M1,M2])

Dura, J. A. et al. Porous Mg formation upon dehydrogenation of MgH2 thin films. Journal of Applied Physics 109, 093501–093501–7 (2011).