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added data and function background examples and example test
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@alexhroom
alexhroom committed Dec 11, 2024
1 parent a82b036 commit f609b7e
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6 changes: 5 additions & 1 deletion RATapi/examples/__init__.py
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from RATapi.examples.absorption.absorption import absorption
from RATapi.examples.convert_rascal_project import convert_rascal
from RATapi.examples.convert_rascal_project.convert_rascal import convert_rascal
from RATapi.examples.domains.domains_custom_layers import domains_custom_layers
from RATapi.examples.domains.domains_custom_XY import domains_custom_XY
from RATapi.examples.domains.domains_standard_layers import domains_standard_layers
from RATapi.examples.non_polarised.DSPC_custom_layers import DSPC_custom_layers
from RATapi.examples.non_polarised.DSPC_custom_XY import DSPC_custom_XY
from RATapi.examples.non_polarised.DSPC_data_background import DSPC_data_background
from RATapi.examples.non_polarised.DSPC_function_background import DSPC_function_background
from RATapi.examples.non_polarised.DSPC_standard_layers import DSPC_standard_layers

__all__ = [
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"DSPC_custom_layers",
"DSPC_custom_XY",
"DSPC_standard_layers",
"DSPC_data_background",
"DSPC_function_background",
"convert_rascal",
]
82 changes: 82 additions & 0 deletions RATapi/examples/data/d2o_background_data.dat
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0.011403 1.90034798968076e-06 -9.65035874608547e-07
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0.033357 1.91881656322323e-06 8.87192534478923e-07
0.035025 1.69716945696631e-06 1.80981995646851e-07
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0.59342 2.31356104763158e-06 7.347220470815e-07
218 changes: 218 additions & 0 deletions RATapi/examples/non_polarised/DSPC_data_background.py
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import pathlib

import numpy as np

import RATapi as RAT


def DSPC_data_background():
"""Standard Layers fit of a DSPC floating bilayer"""
problem = RAT.Project(name="original_dspc_bilayer", model="standard layers", geometry="substrate/liquid")

# Set up the relevant parameters
problem.parameters.append(name="Oxide Thickness", min=5.0, value=19.54, max=60.0, fit=True)
problem.parameters.append(name="Oxide SLD", min=3.39e-06, value=3.39e-06, max=3.41e-06, fit=False)
problem.parameters.append(name="SAM Tails Thickness", min=15.0, value=22.66, max=35.0, fit=True)
problem.parameters.append(name="SAM Tails SLD", min=-5e-07, value=-4.01e-07, max=-3e-07, fit=False)
problem.parameters.append(name="SAM Tails Hydration", min=1.0, value=5.252, max=50.0, fit=True)
problem.parameters.append(name="SAM Roughness", min=1.0, value=5.64, max=15.0, fit=True)
problem.parameters.append(name="CW Thickness", min=10.0, value=17.12, max=28.0, fit=True)
problem.parameters.append(name="CW SLD", min=0.0, value=0.0, max=1e-09, fit=False)

problem.parameters.append(
name="SAM Heads Thickness",
min=5.0,
value=8.56,
max=17.0,
fit=True,
prior_type="gaussian",
mu=10.0,
sigma=2.0,
)
problem.parameters.append(name="SAM Heads SLD", min=1.0e-07, value=1.75e-06, max=2.0e-06, fit=False)
problem.parameters.append(
name="SAM Heads Hydration",
min=10.0,
value=45.45,
max=50.0,
fit=True,
prior_type="gaussian",
mu=30.0,
sigma=3.0,
)
problem.parameters.append(
name="Bilayer Heads Thickness",
min=7.0,
value=10.7,
max=17.0,
fit=True,
prior_type="gaussian",
mu=10.0,
sigma=2.0,
)
problem.parameters.append(name="Bilayer Heads SLD", min=5.0e-07, value=1.47e-06, max=1.5e-06, fit=False)
problem.parameters.append(name="Bilayer Roughness", min=2.0, value=6.014, max=15.0, fit=True)
problem.parameters.append(name="Bilayer Tails Thickness", min=14.0, value=17.82, max=22.0, fit=True)
problem.parameters.append(name="Bilayer Tails SLD", min=-5.0e-07, value=-4.61e-07, max=0.0, fit=False)
problem.parameters.append(name="Bilayer Tails Hydration", min=10.0, value=17.64, max=50.0, fit=True)
problem.parameters.append(name="Bilayer Heads Hydration", min=10.0, value=36.15, max=50.0, fit=True)
problem.parameters.append(name="CW Hydration", min=99.9, value=100.0, max=100.0, fit=False)
problem.parameters.append(name="Oxide Hydration", min=0.0, value=23.61, max=60.0, fit=True)

problem.parameters.set_fields(0, max=10)

# Group these into layers
problem.layers.append(
name="Oxide",
thickness="Oxide Thickness",
SLD="Oxide SLD",
roughness="Substrate Roughness",
hydration="Oxide Hydration",
hydrate_with="bulk out",
)

problem.layers.append(
name="SAM Tails",
thickness="SAM Tails Thickness",
SLD="SAM Tails SLD",
roughness="SAM Roughness",
hydration="SAM Tails Hydration",
hydrate_with="bulk out",
)

problem.layers.append(
name="SAM Heads",
thickness="SAM Heads Thickness",
SLD="SAM Heads SLD",
roughness="SAM Roughness",
hydration="SAM Heads Hydration",
hydrate_with="bulk out",
)

problem.layers.append(
name="Central Water",
thickness="CW Thickness",
SLD="CW SLD",
roughness="Bilayer Roughness",
hydration="CW Hydration",
hydrate_with="bulk out",
)

problem.layers.append(
name="Bilayer Heads",
thickness="Bilayer Heads Thickness",
SLD="Bilayer Heads SLD",
roughness="Bilayer Roughness",
hydration="Bilayer Heads Hydration",
hydrate_with="bulk out",
)

problem.layers.append(
name="Bilayer Tails",
thickness="Bilayer Tails Thickness",
SLD="Bilayer Tails SLD",
roughness="Bilayer Roughness",
hydration="Bilayer Tails Hydration",
hydrate_with="bulk out",
)

# Make the bulk SLDs
del problem.bulk_in[0]
problem.bulk_in.append(name="Silicon", min=2.0e-06, value=2.073e-06, max=2.1e-06, fit=False)

del problem.bulk_out[0]
problem.bulk_out.append(name="D2O", min=5.50e-06, value=5.98e-06, max=6.4e-06, fit=True)
problem.bulk_out.append(name="SMW", min=1.0e-06, value=2.21e-06, max=4.99e-06, fit=True)

# Set the scalefactors - use one for each contrast
del problem.scalefactors[0]
problem.scalefactors.append(name="Scalefactor 1", min=0.05, value=0.10, max=0.2, fit=False)
problem.scalefactors.append(name="Scalefactor 2", min=0.05, value=0.15, max=0.2, fit=False)

# Now deal with the backgrounds
# SMW has a constant background
del problem.backgrounds[0]
del problem.background_parameters[0]
problem.background_parameters.append(
name="Background parameter SMW",
min=1.0e-10,
value=3.38e-06,
max=4.99e-06,
fit=True,
)
problem.backgrounds.append(name="SMW Background", type="constant", source="Background parameter SMW")

data_path = pathlib.Path(__file__).parents[1] / "data"

# load in background data for D2O
d2o_background = np.loadtxt(data_path / "d2o_background_data.dat")
problem.data.append(name="D2O Background Data", data=d2o_background)

# add background parameter for the offset
problem.background_parameters.append(
name="D2O Data Offset",
min=-1e-8,
value=0,
max=1e-8,
fit=True,
)

# add the background with data and offset
problem.backgrounds.append(
name="D2O Data Background",
type="data",
source="D2O Background Data",
value_1="D2O Data Offset",
)

# Now add the data
d2o_dat = np.loadtxt(data_path / "DSPC_D2O.dat", delimiter=",")
problem.data.append(name="dspc_bil_D2O", data=d2o_dat)

smw_dat = np.loadtxt(data_path / "DSPC_SMW.dat", delimiter=",")
problem.data.append(name="dspc_bil_smw", data=smw_dat)

# Set the model
stack = [
"Oxide",
"SAM Tails",
"SAM Heads",
"Central Water",
"Bilayer Heads",
"Bilayer Tails",
"Bilayer Tails",
"Bilayer Heads",
]

# Then make the two contrasts
problem.contrasts.append(
name="D2O",
bulk_in="Silicon",
bulk_out="D2O",
background="D2O Data Background",
resolution="Resolution 1",
scalefactor="Scalefactor 1",
data="dspc_bil_D2O",
model=stack,
)

problem.contrasts.append(
name="SMW",
bulk_in="Silicon",
bulk_out="SMW",
background="SMW Background",
resolution="Resolution 1",
scalefactor="Scalefactor 2",
data="dspc_bil_smw",
model=stack,
)

controls = RAT.Controls()
problem, results = RAT.run(problem, controls)

return problem, results


if __name__ == "__main__":
problem, results = DSPC_data_background()
RAT.plotting.plot_ref_sld(problem, results, True)
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