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128 lines (105 loc) · 4.78 KB
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import pathlib
import numpy as np
import RATapi as RAT
def make_example_problem():
"""Custom Layers example for Supported DSPC layer.
Example of using custom layers to model a DSPC supported bilayer.
"""
problem = RAT.Project(name="Orso lipid example - custom layers", model="custom layers", geometry="substrate/liquid")
# First we need to set up a parameters group. We will be using a pre-prepared custom model file, so we need to add
# the relevant parameters we are going to need to define the model (note that Substrate Roughness always exists as
# parameter 1).
problem.parameters.append(name="Oxide Thickness", min=5.0, value=20.0, max=60.0, fit=True)
problem.parameters.append(name="Oxide Hydration", min=0.0, value=0.2, max=0.5, fit=True)
problem.parameters.append(name="Lipid APM", min=45.0, value=55.0, max=65.0, fit=True)
problem.parameters.append(name="Head Hydration", min=00.0, value=0.2, max=0.5, fit=True)
problem.parameters.append(name="Bilayer Hydration", min=0.0, value=0.1, max=0.2, fit=True)
problem.parameters.append(name="Bilayer Roughness", min=2.0, value=4.0, max=8.0, fit=True)
problem.parameters.append(name="Water Thickness", min=0.0, value=2.0, max=10.0, fit=True)
problem.parameters.set_fields(0, min=1.0, max=10.0)
# Need to add the relevant Bulk SLDs.
# Change the bulk in from air to silicon, and add two additional water contrasts:
problem.bulk_in.set_fields(0, name="Silicon", min=2.07e-6, value=2.073e-6, max=2.08e-6, fit=False)
problem.bulk_out.append(name="SLD SMW", min=1.0e-6, value=2.073e-6, max=3.0e-6, fit=True)
problem.bulk_out.append(name="SLD H2O", min=-0.6e-6, value=-0.56e-6, max=-0.3e-6, fit=True)
problem.bulk_out.set_fields(0, min=5.0e-6, fit=True)
# Now add the datafiles. We have three datasets we need to consider - the bilayer against D2O, Silicon Matched Water
# and H2O. Load these datafiles in and put them in the data block
# Read in the datafiles
data_path = pathlib.Path(__file__).parents[1] / "data"
D2O_data = np.loadtxt(data_path / "c_PLP0016596.dat", delimiter=",")
SMW_data = np.loadtxt(data_path / "c_PLP0016601.dat", delimiter=",")
H2O_data = np.loadtxt(data_path / "c_PLP0016607.dat", delimiter=",")
# Add the data to the project - note this data has a resolution 4th column
problem.data.append(name="Bilayer / D2O", data=D2O_data)
problem.data.append(name="Bilayer / SMW", data=SMW_data)
problem.data.append(name="Bilayer / H2O", data=H2O_data)
# Add the custom file to the project
problem.custom_files.append(
name="DSPC Model",
filename="custom_bilayer.py",
language="python",
path=pathlib.Path(__file__).parent.resolve(),
)
# Also, add the relevant background parameters - one each for each contrast:
problem.background_parameters.set_fields(
0,
name="Background parameter D2O",
fit=True,
min=1.0e-10,
max=1.0e-5,
value=1.0e-07,
)
problem.background_parameters.append(
name="Background parameter SMW",
min=1.0e-10,
value=1.0e-7,
max=1.0e-5,
fit=True,
)
problem.background_parameters.append(
name="Background parameter H2O",
min=1.0e-10,
value=1.0e-7,
max=1.0e-5,
fit=True,
)
# And add the two new constant backgrounds
problem.backgrounds.append(name="Background SMW", type="constant", value_1="Background parameter SMW")
problem.backgrounds.append(name="Background H2O", type="constant", value_1="Background parameter H2O")
# And edit the other one
problem.backgrounds.set_fields(0, name="Background D2O", value_1="Background parameter D2O")
# Finally modify some of the other parameters to be more suitable values for a solid / liquid experiment
problem.scalefactors.set_fields(0, value=1.0, min=0.5, max=2.0, fit=True)
# Now add the three contrasts
problem.contrasts.append(
name="Bilayer / D2O",
background="Background D2O",
resolution="Resolution 1",
scalefactor="Scalefactor 1",
bulk_out="SLD D2O",
bulk_in="Silicon",
data="Bilayer / D2O",
model=["DSPC Model"],
)
problem.contrasts.append(
name="Bilayer / SMW",
background="Background SMW",
resolution="Resolution 1",
scalefactor="Scalefactor 1",
bulk_out="SLD SMW",
bulk_in="Silicon",
data="Bilayer / SMW",
model=["DSPC Model"],
)
problem.contrasts.append(
name="Bilayer / H2O",
background="Background H2O",
resolution="Resolution 1",
scalefactor="Scalefactor 1",
bulk_out="SLD H2O",
bulk_in="Silicon",
data="Bilayer / H2O",
model=["DSPC Model"],
)
return problem