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DrPaulSharpDrPaulSharp
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Tidies up standard layers example (#91)
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‎RATapi/examples/non_polarised/DSPC_standard_layers.py‎

Lines changed: 20 additions & 178 deletions
Original file line numberDiff line numberDiff line change
@@ -7,95 +7,18 @@
77

88
def DSPC_standard_layers():
99
"""Standard Layers fit of a DSPC floating bilayer"""
10-
problem = RAT.Project(
11-
name="original_dspc_bilayer",
12-
calculation="non polarised",
13-
model="standard layers",
14-
geometry="substrate/liquid",
15-
absorption=False,
16-
)
10+
problem = RAT.Project(name="original_dspc_bilayer", model="standard layers", geometry="substrate/liquid")
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1812
# Set up the relevant parameters
19-
problem.parameters.append(
20-
name="Oxide Thickness",
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min=5.0,
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value=19.54,
23-
max=60.0,
24-
fit=True,
25-
prior_type="uniform",
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mu=0.0,
27-
sigma=np.inf,
28-
)
29-
problem.parameters.append(
30-
name="Oxide SLD",
31-
min=3.39e-06,
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value=3.39e-06,
33-
max=3.41e-06,
34-
fit=False,
35-
prior_type="uniform",
36-
mu=0.0,
37-
sigma=np.inf,
38-
)
39-
problem.parameters.append(
40-
name="SAM Tails Thickness",
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min=15.0,
42-
value=22.66,
43-
max=35.0,
44-
fit=True,
45-
prior_type="uniform",
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mu=0.0,
47-
sigma=np.inf,
48-
)
49-
problem.parameters.append(
50-
name="SAM Tails SLD",
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min=-5e-07,
52-
value=-4.01e-07,
53-
max=-3e-07,
54-
fit=False,
55-
prior_type="uniform",
56-
mu=0.0,
57-
sigma=np.inf,
58-
)
59-
problem.parameters.append(
60-
name="SAM Tails Hydration",
61-
min=1.0,
62-
value=5.252,
63-
max=50.0,
64-
fit=True,
65-
prior_type="uniform",
66-
mu=0.0,
67-
sigma=np.inf,
68-
)
69-
problem.parameters.append(
70-
name="SAM Roughness",
71-
min=1.0,
72-
value=5.64,
73-
max=15.0,
74-
fit=True,
75-
prior_type="uniform",
76-
mu=0.0,
77-
sigma=np.inf,
78-
)
79-
problem.parameters.append(
80-
name="CW Thickness",
81-
min=10.0,
82-
value=17.12,
83-
max=28.0,
84-
fit=True,
85-
prior_type="uniform",
86-
mu=0.0,
87-
sigma=np.inf,
88-
)
89-
problem.parameters.append(
90-
name="CW SLD",
91-
min=0.0,
92-
value=0.0,
93-
max=1e-09,
94-
fit=False,
95-
prior_type="uniform",
96-
mu=0.0,
97-
sigma=np.inf,
98-
)
13+
problem.parameters.append(name="Oxide Thickness", min=5.0, value=19.54, max=60.0, fit=True)
14+
problem.parameters.append(name="Oxide SLD", min=3.39e-06, value=3.39e-06, max=3.41e-06, fit=False)
15+
problem.parameters.append(name="SAM Tails Thickness", min=15.0, value=22.66, max=35.0, fit=True)
16+
problem.parameters.append(name="SAM Tails SLD", min=-5e-07, value=-4.01e-07, max=-3e-07, fit=False)
17+
problem.parameters.append(name="SAM Tails Hydration", min=1.0, value=5.252, max=50.0, fit=True)
18+
problem.parameters.append(name="SAM Roughness", min=1.0, value=5.64, max=15.0, fit=True)
19+
problem.parameters.append(name="CW Thickness", min=10.0, value=17.12, max=28.0, fit=True)
20+
problem.parameters.append(name="CW SLD", min=0.0, value=0.0, max=1e-09, fit=False)
21+
9922
problem.parameters.append(
10023
name="SAM Heads Thickness",
10124
min=5.0,
@@ -106,23 +29,14 @@ def DSPC_standard_layers():
10629
mu=10.0,
10730
sigma=2.0,
10831
)
109-
problem.parameters.append(
110-
name="SAM Heads SLD",
111-
min=1.0e-07,
112-
value=1.75e-06,
113-
max=2.0e-06,
114-
fit=False,
115-
prior_type="uniform",
116-
mu=0.0,
117-
sigma=np.inf,
118-
)
32+
problem.parameters.append(name="SAM Heads SLD", min=1.0e-07, value=1.75e-06, max=2.0e-06, fit=False)
11933
problem.parameters.append(
12034
name="SAM Heads Hydration",
12135
min=10.0,
12236
value=45.45,
12337
max=50.0,
12438
fit=True,
125-
prior_type="uniform",
39+
prior_type="gaussian",
12640
mu=30.0,
12741
sigma=3.0,
12842
)
@@ -136,86 +50,14 @@ def DSPC_standard_layers():
13650
mu=10.0,
13751
sigma=2.0,
13852
)
139-
problem.parameters.append(
140-
name="Bilayer Heads SLD",
141-
min=5.0e-07,
142-
value=1.47e-06,
143-
max=1.5e-06,
144-
fit=False,
145-
prior_type="uniform",
146-
mu=0.0,
147-
sigma=np.inf,
148-
)
149-
problem.parameters.append(
150-
name="Bilayer Roughness",
151-
min=2.0,
152-
value=6.014,
153-
max=15.0,
154-
fit=True,
155-
prior_type="uniform",
156-
mu=0.0,
157-
sigma=np.inf,
158-
)
159-
problem.parameters.append(
160-
name="Bilayer Tails Thickness",
161-
min=14.0,
162-
value=17.82,
163-
max=22.0,
164-
fit=True,
165-
prior_type="uniform",
166-
mu=0.0,
167-
sigma=np.inf,
168-
)
169-
problem.parameters.append(
170-
name="Bilayer Tails SLD",
171-
min=-5.0e-07,
172-
value=-4.61e-07,
173-
max=0.0,
174-
fit=False,
175-
prior_type="uniform",
176-
mu=0.0,
177-
sigma=np.inf,
178-
)
179-
problem.parameters.append(
180-
name="Bilayer Tails Hydration",
181-
min=10.0,
182-
value=17.64,
183-
max=50.0,
184-
fit=True,
185-
prior_type="uniform",
186-
mu=0.0,
187-
sigma=np.inf,
188-
)
189-
problem.parameters.append(
190-
name="Bilayer Heads Hydration",
191-
min=10.0,
192-
value=36.15,
193-
max=50.0,
194-
fit=True,
195-
prior_type="gaussian",
196-
mu=30.0,
197-
sigma=3.0,
198-
)
199-
problem.parameters.append(
200-
name="CW Hydration",
201-
min=99.9,
202-
value=100.0,
203-
max=100.0,
204-
fit=False,
205-
prior_type="uniform",
206-
mu=0.0,
207-
sigma=np.inf,
208-
)
209-
problem.parameters.append(
210-
name="Oxide Hydration",
211-
min=0.0,
212-
value=23.61,
213-
max=60.0,
214-
fit=True,
215-
prior_type="uniform",
216-
mu=0.0,
217-
sigma=np.inf,
218-
)
53+
problem.parameters.append(name="Bilayer Heads SLD", min=5.0e-07, value=1.47e-06, max=1.5e-06, fit=False)
54+
problem.parameters.append(name="Bilayer Roughness", min=2.0, value=6.014, max=15.0, fit=True)
55+
problem.parameters.append(name="Bilayer Tails Thickness", min=14.0, value=17.82, max=22.0, fit=True)
56+
problem.parameters.append(name="Bilayer Tails SLD", min=-5.0e-07, value=-4.61e-07, max=0.0, fit=False)
57+
problem.parameters.append(name="Bilayer Tails Hydration", min=10.0, value=17.64, max=50.0, fit=True)
58+
problem.parameters.append(name="Bilayer Heads Hydration", min=10.0, value=36.15, max=50.0, fit=True)
59+
problem.parameters.append(name="CW Hydration", min=99.9, value=100.0, max=100.0, fit=False)
60+
problem.parameters.append(name="Oxide Hydration", min=0.0, value=23.61, max=60.0, fit=True)
21961

22062
problem.parameters.set_fields(0, max=10)
22163

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