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DrPaulSharpDrPaulSharp
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Makes examples importable (#51)
* Makes examples importable * Adds examples to init for ease of importing * Adds examples to top-level __init__ file
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‎RATapi/__init__.py‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,9 @@
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import RATapi.examples as examples
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from RATapi import events, models
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from RATapi.classlist import ClassList
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from RATapi.controls import Controls
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from RATapi.project import Project
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from RATapi.run import run
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from RATapi.utils import plotting
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__all__ = ["models", "events", "ClassList", "Controls", "Project", "run", "plotting"]
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__all__ = ["examples", "models", "events", "ClassList", "Controls", "Project", "run", "plotting"]

‎RATapi/examples/__init__.py‎

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from RATapi.examples.absorption.absorption import absorption
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from RATapi.examples.domains.domains_custom_layers import domains_custom_layers
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from RATapi.examples.domains.domains_custom_XY import domains_custom_XY
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from RATapi.examples.domains.domains_standard_layers import domains_standard_layers
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from RATapi.examples.non_polarised.DSPC_custom_layers import DSPC_custom_layers
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from RATapi.examples.non_polarised.DSPC_custom_XY import DSPC_custom_XY
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from RATapi.examples.non_polarised.DSPC_standard_layers import DSPC_standard_layers
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__all__ = [
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"absorption",
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"domains_custom_layers",
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"domains_custom_XY",
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"domains_standard_layers",
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"DSPC_custom_layers",
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"DSPC_custom_XY",
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"DSPC_standard_layers",
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]

‎RATapi/examples/absorption/absorption.py‎

Lines changed: 154 additions & 141 deletions
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@@ -1,148 +1,161 @@
1-
"""Custom layers model including absorption"""
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31
import os
42
import pathlib
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64
import numpy as np
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import RATapi as RAT
97

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problem = RAT.Project(
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name="Absorption example",
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calculation="non polarised",
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model="custom layers",
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geometry="substrate/liquid",
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absorption=True,
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)
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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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77-
data_2 = np.loadtxt(os.path.join(data_path, "D2O_spin_up.dat"))
78-
problem.data.append(name="D2O_up", data=data_2)
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80-
data_3 = np.loadtxt(os.path.join(data_path, "H2O_spin_down.dat"))
81-
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"))
84-
problem.data.append(name="H2O_up", data=data_4)
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# Add the custom file
87-
problem.custom_files.append(
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name="DPPC absorption",
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filename="volume_thiol_bilayer.py",
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language="python",
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path=pathlib.Path(__file__).parent.resolve(),
92-
)
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# Finally add the contrasts
95-
problem.contrasts.append(
96-
name="D2O Down",
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data="D2O_dn",
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background="Background 1",
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bulk_in="Silicon",
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bulk_out="D2O",
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scalefactor="Scalefactor 1",
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resolution="Resolution 1",
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resample=True,
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model=["DPPC absorption"],
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)
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problem.contrasts.append(
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name="D2O Up",
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data="D2O_up",
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background="Background 2",
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bulk_in="Silicon",
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bulk_out="D2O",
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scalefactor="Scalefactor 2",
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resolution="Resolution 1",
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resample=True,
116-
model=["DPPC absorption"],
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)
118-
119-
problem.contrasts.append(
120-
name="H2O Down",
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data="H2O_dn",
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background="Background 3",
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bulk_in="Silicon",
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bulk_out="H2O",
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scalefactor="Scalefactor 3",
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resolution="Resolution 1",
127-
resample=True,
128-
model=["DPPC absorption"],
129-
)
130-
131-
problem.contrasts.append(
132-
name="H2O Up",
133-
data="H2O_up",
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background="Background 4",
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bulk_in="Silicon",
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bulk_out="H2O",
137-
scalefactor="Scalefactor 4",
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resolution="Resolution 1",
139-
resample=True,
140-
model=["DPPC absorption"],
141-
)
142-
143-
# Now make a controls block
144-
controls = RAT.Controls(parallel="contrasts", resampleParams=[0.9, 150.0])
145-
146-
# Run the code and plot the results
147-
problem, results = RAT.run(problem, controls)
148-
RAT.plotting.plot_ref_sld(problem, results, True)
8+
9+
def absorption():
10+
"""Custom layers model including absorption"""
11+
problem = RAT.Project(
12+
name="Absorption example",
13+
calculation="non polarised",
14+
model="custom layers",
15+
geometry="substrate/liquid",
16+
absorption=True,
17+
)
18+
19+
# Add the required parameters (substrate roughness is already there by default)
20+
problem.parameters.append(name="Alloy Thickness", min=100.0, value=135.6, max=200.0, fit=True)
21+
problem.parameters.append(name="Alloy SLD up", min=6.0e-6, value=9.87e-6, max=1.2e-5, fit=True)
22+
problem.parameters.append(name="Alloy SLD imaginary up", min=1.0e-9, value=4.87e-8, max=1.0e-7, fit=True)
23+
problem.parameters.append(name="Alloy SLD down", min=6.0e-6, value=7.05e-6, max=1.3e-5, fit=True)
24+
problem.parameters.append(name="Alloy SLD imaginary down", min=1.0e-9, value=4.87e-8, max=1.0e-7, fit=True)
25+
problem.parameters.append(name="Alloy Roughness", min=2.0, value=5.71, max=10.0, fit=True)
26+
problem.parameters.append(name="Gold Thickness", min=100.0, value=154.7, max=200.0, fit=True)
27+
problem.parameters.append(name="Gold Roughness", min=0.1, value=5.42, max=10.0, fit=True)
28+
problem.parameters.append(name="Gold SLD", min=4.0e-6, value=4.49e-6, max=5.0e-6, fit=True)
29+
problem.parameters.append(name="Gold SLD imaginary", min=1.0e-9, value=4.20e-8, max=1.0e-7, fit=True)
30+
31+
problem.parameters.append(name="Thiol APM", min=40.0, value=56.27, max=100.0, fit=True)
32+
problem.parameters.append(name="Thiol Head Hydration", min=20.0, value=30.0, max=50.0, fit=True)
33+
problem.parameters.append(name="Thiol Coverage", min=0.5, value=0.9, max=1.0, fit=True)
34+
35+
problem.parameters.append(name="CW Thickness", min=1.0, value=12.87, max=25.0, fit=True)
36+
problem.parameters.append(name="Bilayer APM", min=48.0, value=65.86, max=90.0, fit=True)
37+
problem.parameters.append(name="Bilayer Head Hydration", min=20.0, value=30.0, max=50.0, fit=True)
38+
problem.parameters.append(name="Bilayer Roughness", min=1.0, value=3.87, max=10.0, fit=True)
39+
problem.parameters.append(name="Bilayer Coverage", min=0.5, value=0.94, max=1.0, fit=True)
40+
41+
# Change the existing Bulk In parameter to be Silicon
42+
problem.bulk_in.set_fields(0, name="Silicon", min=2.0e-6, value=2.073e-6, max=2.1e-6)
43+
44+
# We need 2 bulk outs - D2O and H2O
45+
problem.bulk_out.set_fields(0, name="D2O", min=5.8e-06, value=6.21e-06, max=6.35e-06, fit=True)
46+
problem.bulk_out.append(name="H2O", min=-5.6e-07, value=-3.15e-07, max=0.0, fit=True)
47+
48+
# Use a different scalefactor for each dataset
49+
del problem.scalefactors[0]
50+
problem.scalefactors.append(name="Scalefactor 1", min=0.5, value=1, max=1.5, fit=True)
51+
problem.scalefactors.append(name="Scalefactor 2", min=0.5, value=1, max=1.5, fit=True)
52+
problem.scalefactors.append(name="Scalefactor 3", min=0.5, value=1, max=1.5, fit=True)
53+
problem.scalefactors.append(name="Scalefactor 4", min=0.5, value=1, max=1.5, fit=True)
54+
55+
# Similarly, use an individual background for each dataset
56+
del problem.backgrounds[0]
57+
del problem.background_parameters[0]
58+
59+
problem.background_parameters.append(
60+
name="Background parameter 1", min=5.0e-08, value=7.88e-06, max=9.0e-05, fit=True
61+
)
62+
problem.background_parameters.append(
63+
name="Background parameter 2", min=1.0e-08, value=5.46e-06, max=9.0e-05, fit=True
64+
)
65+
problem.background_parameters.append(
66+
name="Background parameter 3", min=1.0e-06, value=9.01e-06, max=9.0e-05, fit=True
67+
)
68+
problem.background_parameters.append(
69+
name="Background parameter 4", min=1.0e-06, value=5.61e-06, max=9.0e-05, fit=True
70+
)
71+
72+
problem.backgrounds.append(name="Background 1", type="constant", value_1="Background parameter 1")
73+
problem.backgrounds.append(name="Background 2", type="constant", value_1="Background parameter 2")
74+
problem.backgrounds.append(name="Background 3", type="constant", value_1="Background parameter 3")
75+
problem.backgrounds.append(name="Background 4", type="constant", value_1="Background parameter 4")
76+
77+
# Make the resolution fittable
78+
problem.resolution_parameters.set_fields(0, fit=True)
79+
80+
# Now add the data we need
81+
data_path = os.path.join(pathlib.Path(__file__).parents[1].resolve(), "data")
82+
83+
data_1 = np.loadtxt(os.path.join(data_path, "D2O_spin_down.dat"))
84+
problem.data.append(name="D2O_dn", data=data_1)
85+
86+
data_2 = np.loadtxt(os.path.join(data_path, "D2O_spin_up.dat"))
87+
problem.data.append(name="D2O_up", data=data_2)
88+
89+
data_3 = np.loadtxt(os.path.join(data_path, "H2O_spin_down.dat"))
90+
problem.data.append(name="H2O_dn", data=data_3)
91+
92+
data_4 = np.loadtxt(os.path.join(data_path, "H2O_spin_up.dat"))
93+
problem.data.append(name="H2O_up", data=data_4)
94+
95+
# Add the custom file
96+
problem.custom_files.append(
97+
name="DPPC absorption",
98+
filename="volume_thiol_bilayer.py",
99+
language="python",
100+
path=pathlib.Path(__file__).parent.resolve(),
101+
)
102+
103+
# Finally add the contrasts
104+
problem.contrasts.append(
105+
name="D2O Down",
106+
data="D2O_dn",
107+
background="Background 1",
108+
bulk_in="Silicon",
109+
bulk_out="D2O",
110+
scalefactor="Scalefactor 1",
111+
resolution="Resolution 1",
112+
resample=True,
113+
model=["DPPC absorption"],
114+
)
115+
116+
problem.contrasts.append(
117+
name="D2O Up",
118+
data="D2O_up",
119+
background="Background 2",
120+
bulk_in="Silicon",
121+
bulk_out="D2O",
122+
scalefactor="Scalefactor 2",
123+
resolution="Resolution 1",
124+
resample=True,
125+
model=["DPPC absorption"],
126+
)
127+
128+
problem.contrasts.append(
129+
name="H2O Down",
130+
data="H2O_dn",
131+
background="Background 3",
132+
bulk_in="Silicon",
133+
bulk_out="H2O",
134+
scalefactor="Scalefactor 3",
135+
resolution="Resolution 1",
136+
resample=True,
137+
model=["DPPC absorption"],
138+
)
139+
140+
problem.contrasts.append(
141+
name="H2O Up",
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data="H2O_up",
143+
background="Background 4",
144+
bulk_in="Silicon",
145+
bulk_out="H2O",
146+
scalefactor="Scalefactor 4",
147+
resolution="Resolution 1",
148+
resample=True,
149+
model=["DPPC absorption"],
150+
)
151+
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# Now make a controls block and run the code
153+
controls = RAT.Controls(parallel="contrasts", resampleParams=[0.9, 150.0])
154+
problem, results = RAT.run(problem, controls)
155+
156+
return problem, results
157+
158+
159+
if __name__ == "__main__":
160+
problem, results = absorption()
161+
RAT.plotting.plot_ref_sld(problem, results, True)

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