From 7244d54035091528c369ba4ab2c1d38c9868c4d3 Mon Sep 17 00:00:00 2001 From: Paul Sharp <44529197+DrPaulSharp@users.noreply.github.com> Date: Tue, 12 Nov 2024 09:52:51 +0000 Subject: [PATCH] Tidies up standard layers example --- .../non_polarised/DSPC_standard_layers.py | 198 ++---------------- 1 file changed, 20 insertions(+), 178 deletions(-) diff --git a/RATapi/examples/non_polarised/DSPC_standard_layers.py b/RATapi/examples/non_polarised/DSPC_standard_layers.py index f583a1b3..8ae59fdd 100644 --- a/RATapi/examples/non_polarised/DSPC_standard_layers.py +++ b/RATapi/examples/non_polarised/DSPC_standard_layers.py @@ -7,95 +7,18 @@ def DSPC_standard_layers(): """Standard Layers fit of a DSPC floating bilayer""" - problem = RAT.Project( - name="original_dspc_bilayer", - calculation="non polarised", - model="standard layers", - geometry="substrate/liquid", - absorption=False, - ) + 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, - prior_type="uniform", - mu=0.0, - sigma=np.inf, - ) - problem.parameters.append( - name="Oxide SLD", - min=3.39e-06, - value=3.39e-06, - max=3.41e-06, - fit=False, - prior_type="uniform", - mu=0.0, - sigma=np.inf, - ) - problem.parameters.append( - name="SAM Tails Thickness", - min=15.0, - value=22.66, - max=35.0, - fit=True, - prior_type="uniform", - mu=0.0, - sigma=np.inf, - ) - problem.parameters.append( - name="SAM Tails SLD", - min=-5e-07, - value=-4.01e-07, - max=-3e-07, - fit=False, - prior_type="uniform", - mu=0.0, - sigma=np.inf, - ) - problem.parameters.append( - name="SAM Tails Hydration", - min=1.0, - value=5.252, - max=50.0, - fit=True, - prior_type="uniform", - mu=0.0, - sigma=np.inf, - ) - problem.parameters.append( - name="SAM Roughness", - min=1.0, - value=5.64, - max=15.0, - fit=True, - prior_type="uniform", - mu=0.0, - sigma=np.inf, - ) - problem.parameters.append( - name="CW Thickness", - min=10.0, - value=17.12, - max=28.0, - fit=True, - prior_type="uniform", - mu=0.0, - sigma=np.inf, - ) - problem.parameters.append( - name="CW SLD", - min=0.0, - value=0.0, - max=1e-09, - fit=False, - prior_type="uniform", - mu=0.0, - sigma=np.inf, - ) + 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, @@ -106,23 +29,14 @@ def DSPC_standard_layers(): 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, - prior_type="uniform", - mu=0.0, - sigma=np.inf, - ) + 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="uniform", + prior_type="gaussian", mu=30.0, sigma=3.0, ) @@ -136,86 +50,14 @@ def DSPC_standard_layers(): 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, - prior_type="uniform", - mu=0.0, - sigma=np.inf, - ) - problem.parameters.append( - name="Bilayer Roughness", - min=2.0, - value=6.014, - max=15.0, - fit=True, - prior_type="uniform", - mu=0.0, - sigma=np.inf, - ) - problem.parameters.append( - name="Bilayer Tails Thickness", - min=14.0, - value=17.82, - max=22.0, - fit=True, - prior_type="uniform", - mu=0.0, - sigma=np.inf, - ) - problem.parameters.append( - name="Bilayer Tails SLD", - min=-5.0e-07, - value=-4.61e-07, - max=0.0, - fit=False, - prior_type="uniform", - mu=0.0, - sigma=np.inf, - ) - problem.parameters.append( - name="Bilayer Tails Hydration", - min=10.0, - value=17.64, - max=50.0, - fit=True, - prior_type="uniform", - mu=0.0, - sigma=np.inf, - ) - problem.parameters.append( - name="Bilayer Heads Hydration", - min=10.0, - value=36.15, - max=50.0, - fit=True, - prior_type="gaussian", - mu=30.0, - sigma=3.0, - ) - problem.parameters.append( - name="CW Hydration", - min=99.9, - value=100.0, - max=100.0, - fit=False, - prior_type="uniform", - mu=0.0, - sigma=np.inf, - ) - problem.parameters.append( - name="Oxide Hydration", - min=0.0, - value=23.61, - max=60.0, - fit=True, - prior_type="uniform", - mu=0.0, - sigma=np.inf, - ) + 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)