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Adds examples (#36)
* Adds validation and changes "ClassList.set_fields" functionality * Adds domains examples * Adds non polarised examples * Adds absorption example * Adds example for custom functions in different languages * Updates cells in "make_input.py" * Adds "function_name" field to customFile model * Adds wrappers for custom functions * Fixes bug when adding data in "inputs.py" * Adds run and plot lines to examples * Adds python custom functions * Fixes data resolution bug * Applies updates to submodule * Adds tests for custom function wrappers * Adds "check_indices" routine to "make_inputs.py" * Tidies up examples * Fixes bug in data model. * Moves example data into shared directoy and resolves paths in examples * Allows custom file model to accept pathlib.Path objects * Addresses review comments * Reintroduces "model_post_init" for "CustomFile" model * Removes warning from custom file validator * Adds additional "__init__.py" for test data
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‎RAT/classlist.py‎

Lines changed: 3 additions & 2 deletions
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@@ -218,8 +218,9 @@ def extend(self, other: Sequence[object]) -> None:
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def set_fields(self, index: int, **kwargs) -> None:
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"""Assign the values of an existing object's attributes using keyword arguments."""
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self._validate_name_field(kwargs)
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for key, value in kwargs.items():
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setattr(self.data[index], key, value)
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class_handle = self.data[index].__class__
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new_fields = {**self.data[index].__dict__, **kwargs}
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self.data[index] = class_handle(**new_fields)
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def get_names(self) -> list[str]:
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"""Return a list of the values of the name_field attribute of each class object in the list.

‎RAT/examples/__init__.py‎

Whitespace-only changes.

‎RAT/examples/absorption/__init__.py‎

Whitespace-only changes.

‎RAT/examples/absorption/absorption.py‎

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"""Custom layers model including absorption"""
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import numpy as np
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import os
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import pathlib
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import RAT
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import RAT.utils.plotting
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problem = RAT.Project(name="Absorption example", calculation="non polarised", model="custom layers",
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geometry="substrate/liquid", absorption=True)
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# Add the required parameters (substrate roughness is already there by default)
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problem.parameters.append(name="Alloy Thickness", min=100.0, value=135.6, max=200.0, fit=True)
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problem.parameters.append(name="Alloy SLD up", min=6.0e-6, value=9.87e-6, max=1.2e-5, fit=True)
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problem.parameters.append(name="Alloy SLD imaginary up", min=1.0e-9, value=4.87e-8, max=1.0e-7, fit=True)
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problem.parameters.append(name="Alloy SLD down", min=6.0e-6, value=7.05e-6, max=1.3e-5, fit=True)
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problem.parameters.append(name="Alloy SLD imaginary down", min=1.0e-9, value=4.87e-8, max=1.0e-7, fit=True)
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problem.parameters.append(name="Alloy Roughness", min=2.0, value=5.71, max=10.0, fit=True)
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problem.parameters.append(name="Gold Thickness", min=100.0, value=154.7, max=200.0, fit=True)
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problem.parameters.append(name="Gold Roughness", min=0.1, value=5.42, max=10.0, fit=True)
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problem.parameters.append(name="Gold SLD", min=4.0e-6, value=4.49e-6, max=5.0e-6, fit=True)
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problem.parameters.append(name="Gold SLD imaginary", min=1.0e-9, value=4.20e-8, max=1.0e-7, fit=True)
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problem.parameters.append(name="Thiol APM", min=40.0, value=56.27, max=100.0, fit=True)
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problem.parameters.append(name="Thiol Head Hydration", min=20.0, value=30.0, max=50.0, fit=True)
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problem.parameters.append(name="Thiol Coverage", min=0.5, value=0.9, max=1.0, fit=True)
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problem.parameters.append(name="CW Thickness", min=1.0, value=12.87, max=25.0, fit=True)
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problem.parameters.append(name="Bilayer APM", min=48.0, value=65.86, max=90.0, fit=True)
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problem.parameters.append(name="Bilayer Head Hydration", min=20.0, value=30.0, max=50.0, fit=True)
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problem.parameters.append(name="Bilayer Roughness", min=1.0, value=3.87, max=10.0, fit=True)
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problem.parameters.append(name="Bilayer Coverage", min=0.5, value=0.94, max=1.0, fit=True)
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# Change the existing Bulk In parameter to be Silicon
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problem.bulk_in.set_fields(0, name="Silicon", min=2.0e-6, value=2.073e-6, max=2.1e-6)
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# We need 2 bulk outs - D2O and H2O
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problem.bulk_out.set_fields(0, name="D2O", min=5.8e-06, value=6.21e-06, max=6.35e-06, fit=True)
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problem.bulk_out.append(name="H2O", min=-5.6e-07, value=-3.15e-07, max=0.0, fit=True)
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# Use a different scalefactor for each dataset
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del problem.scalefactors[0]
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problem.scalefactors.append(name="Scalefactor 1", min=0.5, value=1, max=1.5, fit=True)
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problem.scalefactors.append(name="Scalefactor 2", min=0.5, value=1, max=1.5, fit=True)
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problem.scalefactors.append(name="Scalefactor 3", min=0.5, value=1, max=1.5, fit=True)
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problem.scalefactors.append(name="Scalefactor 4", min=0.5, value=1, max=1.5, fit=True)
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# Similarly, use an individual background for each dataset
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del problem.backgrounds[0]
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del problem.background_parameters[0]
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problem.background_parameters.append(name="Background parameter 1", min=5.0e-08, value=7.88e-06, max=9.0e-05, fit=True)
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problem.background_parameters.append(name="Background parameter 2", min=1.0e-08, value=5.46e-06, max=9.0e-05, fit=True)
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problem.background_parameters.append(name="Background parameter 3", min=1.0e-06, value=9.01e-06, max=9.0e-05, fit=True)
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problem.background_parameters.append(name="Background parameter 4", min=1.0e-06, value=5.61e-06, max=9.0e-05, fit=True)
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problem.backgrounds.append(name="Background 1", type="constant", value_1="Background parameter 1")
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problem.backgrounds.append(name="Background 2", type="constant", value_1="Background parameter 2")
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problem.backgrounds.append(name="Background 3", type="constant", value_1="Background parameter 3")
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problem.backgrounds.append(name="Background 4", type="constant", value_1="Background parameter 4")
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# Make the resolution fittable
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problem.resolution_parameters.set_fields(0, fit=True)
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# Now add the data we need
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data_path = os.path.join(pathlib.Path(__file__).parents[1].resolve(), "data")
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data_1 = np.loadtxt(os.path.join(data_path, "D2O_spin_down.dat"))
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problem.data.append(name="D2O_dn", data=data_1)
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data_2 = np.loadtxt(os.path.join(data_path, "D2O_spin_up.dat"))
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problem.data.append(name="D2O_up", data=data_2)
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data_3 = np.loadtxt(os.path.join(data_path, "H2O_spin_down.dat"))
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problem.data.append(name="H2O_dn", data=data_3)
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data_4 = np.loadtxt(os.path.join(data_path, "H2O_spin_up.dat"))
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problem.data.append(name="H2O_up", data=data_4)
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# Add the custom file
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problem.custom_files.append(name="DPPC absorption", filename="volume_thiol_bilayer.py", language="python",
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path=pathlib.Path(__file__).parent.resolve())
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# Finally add the contrasts
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problem.contrasts.append(name="D2O Down", data="D2O_dn", background="Background 1", bulk_in="Silicon",
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bulk_out="D2O", scalefactor="Scalefactor 1", resolution="Resolution 1", resample=True,
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model=["DPPC absorption"])
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problem.contrasts.append(name="D2O Up", data="D2O_up", background="Background 2", bulk_in="Silicon",
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bulk_out="D2O", scalefactor="Scalefactor 2", resolution="Resolution 1", resample=True,
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model=["DPPC absorption"])
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problem.contrasts.append(name="H2O Down", data="H2O_dn", background="Background 3", bulk_in="Silicon",
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bulk_out="H2O", scalefactor="Scalefactor 3", resolution="Resolution 1", resample=True,
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model=["DPPC absorption"])
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problem.contrasts.append(name="H2O Up", data="H2O_up", background="Background 4", bulk_in="Silicon",
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bulk_out="H2O", scalefactor="Scalefactor 4", resolution="Resolution 1", resample=True,
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model=["DPPC absorption"])
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# Now make a controls block
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controls = RAT.set_controls(parallel="contrasts", resampleParams=[0.9, 150.0])
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# Run the code and plot the results
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problem, results = RAT.run(problem, controls)
107+
RAT.utils.plotting.plot_ref_sld(problem, results, True)

‎RAT/examples/absorption/volume_thiol_bilayer.py‎

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def volume_thiol_bilayer(params, bulk_in, bulk_out, contrast):
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"""
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volumeThiolBilayer RAT Custom Layer Model File.
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This file accepts 3 vectors containing the values for params, bulk in and bulk out.
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The final parameter is an index of the contrast being calculated
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The function should output a matrix of layer values, in the form...
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Output = [thick 1, SLD 1, Rough 1, Percent Hydration 1, Hydrate how 1
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....
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thick n, SLD n, Rough n, Percent Hydration n, Hydration how n]
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The "hydrate how" parameter decides if the layer is hydrated with Bulk out or Bulk in phases.
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Set to 1 for Bulk out, zero for Bulk in.
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Alternatively, leave out hydration and just return...
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Output = [thick 1, SLD 1, Rough 1,
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....
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thick n, SLD n, Rough n]
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The second output parameter should be the substrate roughness.
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"""
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subRough = params[0]
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alloyThick = params[1]
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alloySLDUp = params[2]
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alloyISLDUp = params[3]
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alloySLDDown = params[4]
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alloyISLDDown = params[5]
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alloyRough = params[6]
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goldThick = params[7]
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goldRough = params[8]
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goldSLD = params[9]
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goldISLD = params[10]
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thiolAPM = params[11]
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thiolHeadHydr = params[12]
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thiolCoverage = params[13]
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cwThick = params[14]
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bilayerAPM = params[15]
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bilHeadHydr = params[16]
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bilayerRough = params[17]
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bilayerCoverage = params[18]
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# Make the metal layers
45+
gold = [goldThick, goldSLD, goldISLD, goldRough]
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alloyUp = [alloyThick, alloySLDUp, alloyISLDUp, alloyRough]
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alloyDown = [alloyThick, alloySLDDown, alloyISLDDown, alloyRough]
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# Neutron b's..
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# define all the neutron b's.
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bc = 0.6646e-4 # Carbon
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bo = 0.5843e-4 # Oxygen
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bh = -0.3739e-4 # Hydrogen
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bp = 0.513e-4 # Phosphorus
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bn = 0.936e-4 # Nitrogen
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bd = 0.6671e-4 # Deuterium
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# Work out the total scattering length in each fragment
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# Define scattering lengths
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# Hydrogenated version
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COO = (2*bo) + (bc)
62+
GLYC = (3*bc) + (5*bh)
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CH3 = (1*bc) + (3*bh)
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PO4 = (1*bp) + (4*bo)
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CH2 = (1*bc) + (2*bh)
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CH = (1*bc) + (1*bh)
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CHOL = (5*bc) + (12*bh) + (1*bn)
68+
H2O = (2*bh) + (1*bo)
69+
D2O = (2*bd) + (1*bo)
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71+
# And also volumes
72+
vCH3 = 52.7 # CH3 volume in the paper appears to be for 2 * CH3's
73+
vCH2 = 28.1
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vCOO = 39.0
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vGLYC = 68.8
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vPO4 = 53.7
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vCHOL = 120.4
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vWAT = 30.4
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vCHCH = 42.14
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81+
vHead = vCHOL + vPO4 + vGLYC + 2*vCOO
82+
vTail = (28*vCH2) + (1*vCHCH) + (2*vCH3) # Tail volume
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# Calculate sum_b's for other fragments
85+
sumbHead = CHOL + PO4 + GLYC + 2*COO
86+
sumbTail = (28*CH2) + (2*CH) + 2*CH3
87+
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# Calculate SLDs and Thickness
89+
sldHead = sumbHead/vHead
90+
thickHead = vHead/thiolAPM
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sldTail = sumbTail/vTail
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thickTail = vTail/thiolAPM
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# Correct head SLD based on hydration
96+
thiolHeadHydr = thiolHeadHydr/100
97+
sldHead = (sldHead * (1 - thiolHeadHydr) + (thiolHeadHydr * bulk_out[contrast]))
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# Now correct both the SLDs for the coverage parameter
100+
sldTail = (thiolCoverage*sldTail) + ((1-thiolCoverage) * bulk_out[contrast])
101+
sldHead = (thiolCoverage*sldHead) + ((1-thiolCoverage) * bulk_out[contrast])
102+
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SAMTAILS = [thickTail, sldTail, 0, goldRough]
104+
SAMHEAD = [thickHead, sldHead, 0, goldRough]
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# Now do the same for the bilayer
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vHead = vCHOL + vPO4 + vGLYC + 2*vCOO
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vTail = (28*vCH2) # Tail volume
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vMe = (2*vCH3)
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sumbHead = CHOL + PO4 + GLYC + 2*COO
112+
sumbTail = (28*CH2)
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sumbMe = 2*CH3
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sldHead = sumbHead/vHead
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thickHead = vHead/bilayerAPM
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bilHeadHydr = bilHeadHydr / 100
118+
sldHead = (sldHead * (1 - bilHeadHydr) + (bilHeadHydr * bulk_out[contrast]))
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sldTail = sumbTail/vTail
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thickTail = vTail/bilayerAPM
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sldMe = sumbMe/vMe
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thickMe = vMe/bilayerAPM
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sldTail = (bilayerCoverage * sldTail) + ((1-bilayerCoverage) * bulk_out[contrast])
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sldHead = (bilayerCoverage * sldHead) + ((1-bilayerCoverage) * bulk_out[contrast])
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sldMe = (bilayerCoverage * sldMe) + ((1-bilayerCoverage) * bulk_out[contrast])
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BILTAILS = [thickTail, sldTail, 0, bilayerRough]
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BILHEAD = [thickHead, sldHead, 0, bilayerRough]
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BILME = [thickMe, sldMe, 0, bilayerRough]
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BILAYER = [BILHEAD, BILTAILS, BILME, BILME, BILTAILS, BILHEAD]
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CW = [cwThick, bulk_out[contrast], 0, bilayerRough]
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if contrast == 1 or contrast == 3:
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output = [alloyUp, gold, SAMTAILS, SAMHEAD, CW, *BILAYER]
140+
else:
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output = [alloyDown, gold, SAMTAILS, SAMHEAD, CW, *BILAYER]
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return output, subRough

‎RAT/examples/data/D2O_spin_down.dat‎

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0.01218 1.015359223955 0.0231718818417596
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0.012545 0.919431439253596 0.0193509380578665
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0.012922 0.924921688167335 0.0183337262959345
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0.013309 0.892889622419078 0.01658695139614
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0.013709 0.88564788305433 0.0151834012597258
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0.01412 0.954057058169692 0.0152655865808885
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0.014544 0.801205833810502 0.0128764862406952
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0.01498 0.57206372730641 0.00977028529084846
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0.015429 0.507292263127758 0.00840850146518913
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0.015892 0.441240863619522 0.0072616120448651
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0.016369 0.411263430900333 0.00703930748762168
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0.01686 0.398699855165213 0.00667722051938428
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0.017366 0.369396072619489 0.00590757519620061
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0.017887 0.333584829398094 0.00529590083869447
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0.018423 0.300131361783826 0.00480817811310586
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0.018976 0.254862070126983 0.00436222169827209
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0.019545 0.218629795547172 0.0038320590117552
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0.020132 0.183303580450672 0.00337229276836539
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0.020736 0.158391997035939 0.00306386203644447
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0.021358 0.128249520024251 0.00266512849877059
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0.021998 0.0956717976354879 0.0021819192293442
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0.022658 0.0688201017211762 0.00176311091650106
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0.023338 0.0481760921553437 0.00145639799252248
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0.024038 0.0328252888275119 0.00118309811714777
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0.024759 0.0183323789955876 0.000868570851156994
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0.025502 0.0106467041665263 0.000644514803462562
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0.026267 0.00788878035636094 0.000551382666981037
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0.027055 0.0069025565024083 0.0005165549530129
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0.027867 0.00807841288019132 0.000666341069082825
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0.028703 0.0104166526322881 0.000419481963016605
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0.029564 0.0134376368351915 0.000465997507494358
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0.030451 0.0158250530499512 0.000492135134224797
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0.031365 0.018520664219071 0.000528646973626596
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0.032305 0.0188403112263801 0.000530903701707703
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0.033275 0.0189720098352925 0.000529859543938832
36+
0.034273 0.0167957829499141 0.000677826804540402
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0.035301 0.0143561588467109 0.000448314190440904
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0.03636 0.0120825895112668 0.000385361581730607
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0.037451 0.00911010812085284 0.000338273434605409
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0.038574 0.0064407693084981 0.000272228771598909
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0.039732 0.00380747078042373 0.000191909461416686
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0.040924 0.00219977095894102 0.000139024554548823
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0.042151 0.00106749974738118 9.30715079659133e-05
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0.043416 0.000526289198019469 6.53777493347705e-05
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0.044718 0.000538684361211223 6.36026811276904e-05
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0.04606 0.000666071609013439 6.89514635050019e-05
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0.047442 0.00096513860352319 8.1892283337263e-05
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0.048865 0.00123628279834282 9.06632085957762e-05
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0.050331 0.000932500252618815 7.56441779783758e-05
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76+
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0.12583 0.000162551786857085 1.40661524470343e-05
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