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"""A custom example problem for the languages benchmark."""

import pathlib

import numpy as np

import ratapi as RAT

def make_example_problem():

"""Generate a 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,

)

# Also, add the relevant background parameters - one each for each contrast:

problem.background_parameters.set_fields(

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", source="Background parameter SMW")

problem.backgrounds.append(name="Background H2O", type="constant", source="Background parameter H2O")

# And edit the other one

problem.backgrounds.set_fields(0, name="Background D2O", source="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

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