ratapi 0.0.0.dev16__cp315-cp315-win_amd64.whl

ratapi/examples/normal_reflectivity/DSPC_custom_XY.py

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+"""An example of analysing a Custom XY model."""
+
+import pathlib
+
+import numpy as np
+
+import ratapi as RAT
+
+
+def DSPC_custom_XY():
+    r"""Calculate a Custom XY Example for Supported DSPC layer.
+
+    In this example, we model the same data (DSPC supported bilayer) as the Custom Layers example, but this time we will
+    use continuous distributions of the volume fractions of each component to build up the SLD profiles (as described in
+    Shekhar et al, J. Appl. Phys., 110, 102216 (2011).)
+
+    In this type of model, each 'layer' in the sample is described by a roughened Heaviside step function (really, just
+    two error functions back to back). So, in our case, we will need an oxide, a (possible) intervening water layer, and
+    then the bilayer itself.
+
+    We can define our lipid in terms of an Area per Molecule, almost in its entirety, if we recognise that where the
+    volume is known, the thickness of the layer is simply given by the layer volume / APM:
+
+    .. math:: d_{\textrm{layer}} =\frac{V_{\textrm{layer}} }{{\textrm{APM}}_{\textrm{layer}}}.
+
+    We can then define the Volume Fraction of this layer with a roughened Heaviside of length dlayer and a height of 1.
+    Then, the total volume occupied will be given by the sum of the volume fractions across the interface. Of course,
+    this does not permit any hydration, so to deal with this, we can simply scale the (full occupation) Heaviside
+    functions by relevant coverage parameters. When this is correctly done, we can obtain the remaining water
+    distribution as:
+
+    .. math:: {\textrm{VF}}_{\textrm{wat}} =1-\\sum_n {\textrm{VF}}_n
+
+    where VFn is the Volume Fraction of the n'th layer.
+    """
+    # Start by making the class and setting it to a custom XY type:
+    problem = RAT.Project(name="Orso lipid example - custom XY", model="custom xy", geometry="substrate/liquid")
+
+    # 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=10.0, value=15.0, max=30.0, fit=True)
+    problem.parameters.append(name="Oxide Hydration", min=0.1, value=0.2, max=0.4, fit=True)
+    problem.parameters.append(name="Water Thickness", min=0.0, value=5.0, max=20.0, fit=True)
+    problem.parameters.append(name="Lipid APM", min=40.0, value=50.0, max=90.0, fit=True)
+    problem.parameters.append(name="Lipid Coverage", min=0.9, value=1.0, max=1.0, fit=True)
+    problem.parameters.append(name="Bilayer Roughness", min=3.0, value=5.0, max=8.0, 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, value=6.1e-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_XY_DSPC.py",
+        language="python",
+        path=pathlib.Path(__file__).parent,
+    )
+
+    # 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=0.0, value=1.0e-7, max=1.0e-5, fit=True)
+    problem.background_parameters.append(name="Background parameter H2O", min=0.0, 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)
+
+    # Also, we are going to use the data resolution
+    problem.resolutions.append(name="Data Resolution", type="data")
+
+    # Now add the three contrasts
+    problem.contrasts.append(
+        name="Bilayer / D2O",
+        background="Background D2O",
+        resolution="Data Resolution",
+        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="Data Resolution",
+        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="Data Resolution",
+        scalefactor="Scalefactor 1",
+        bulk_out="SLD H2O",
+        bulk_in="Silicon",
+        data="Bilayer / H2O",
+        model=["DSPC Model"],
+    )
+
+    controls = RAT.Controls()
+    problem, results = RAT.run(problem, controls)
+
+    return problem, results
+
+
+if __name__ == "__main__":
+    problem, results = DSPC_custom_XY()
+    RAT.plotting.plot_ref_sld(problem, results, True)

ratapi/examples/normal_reflectivity/DSPC_custom_layers.py

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+"""Example of using custom layers to model a DSPC supported bilayer."""
+
+import pathlib
+
+import numpy as np
+
+import ratapi as RAT
+
+
+def DSPC_custom_layers():
+    """Calculate a Custom Layers example for a supported DSPC layer."""
+    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=0.0, 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, data_range=[0.013, 0.37])
+    problem.data.append(name="Bilayer / SMW", data=SMW_data, data_range=[0.013, 0.32996])
+    problem.data.append(name="Bilayer / H2O", data=H2O_data, data_range=[0.013, 0.33048])
+
+    # Add the custom file to the project
+    problem.custom_files.append(
+        name="DSPC Model",
+        filename="custom_bilayer_DSPC.py",
+        language="python",
+        path=pathlib.Path(__file__).parent,
+    )
+
+    # Also, add the relevant background parameters - one each for each contrast:
+    problem.background_parameters.set_fields(
+        0,
+        name="Background parameter D2O",
+        min=1.0e-10,
+        max=1.0e-5,
+        value=1.0e-07,
+        fit=True,
+    )
+
+    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)
+
+    # Also, we are going to use the data resolution
+    problem.resolutions.append(name="Data Resolution", type="data")
+
+    # Now add the three contrasts
+    problem.contrasts.append(
+        name="Bilayer / D2O",
+        background="Background D2O",
+        resolution="Data Resolution",
+        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="Data Resolution",
+        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="Data Resolution",
+        scalefactor="Scalefactor 1",
+        bulk_out="SLD H2O",
+        bulk_in="Silicon",
+        data="Bilayer / H2O",
+        model=["DSPC Model"],
+    )
+
+    controls = RAT.Controls()
+    problem, results = RAT.run(problem, controls)
+
+    return problem, results
+
+
+if __name__ == "__main__":
+    problem, results = DSPC_custom_layers()
+    RAT.plotting.plot_ref_sld(problem, results, True)

ratapi/examples/normal_reflectivity/DSPC_data_background.py

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+"""A standard layers example with a data background."""
+
+import pathlib
+
+import numpy as np
+
+import ratapi as RAT
+
+
+def DSPC_data_background():
+    """Calculate a Standard Layers fit of a DSPC floating bilayer with a data background."""
+    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)