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Copy pathvolume_thiol_bilayer.py
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144 lines (113 loc) · 4.71 KB
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"""Custom layer model file for the absorption example."""
def volume_thiol_bilayer(params, bulk_in, bulk_out, contrast):
"""VolumeThiolBilayer RAT Custom Layer Model File.
This file accepts 3 vectors containing the values for params, bulk in and bulk out.
The final parameter is an index of the contrast being calculated
The function should output a matrix of layer values, in the form...
Output = [thick 1, SLD 1, Rough 1, Percent Hydration 1, Hydrate how 1
....
thick n, SLD n, Rough n, Percent Hydration n, Hydration how n]
The "hydrate how" parameter decides if the layer is hydrated with Bulk out or Bulk in phases.
Set to 1 for Bulk out, zero for Bulk in.
Alternatively, leave out hydration and just return...
Output = [thick 1, SLD 1, Rough 1,
....
thick n, SLD n, Rough n]
The second output parameter should be the substrate roughness.
"""
# Note - The first contrast number is 1 (not 0) so be careful if you use
# this variable for array indexing.
subRough = params[0]
alloyThick = params[1]
alloySLDUp = params[2]
alloyISLDUp = params[3]
alloySLDDown = params[4]
alloyISLDDown = params[5]
alloyRough = params[6]
goldThick = params[7]
goldRough = params[8]
goldSLD = params[9]
goldISLD = params[10]
thiolAPM = params[11]
thiolHeadHydr = params[12]
thiolCoverage = params[13]
cwThick = params[14]
bilayerAPM = params[15]
bilHeadHydr = params[16]
bilayerRough = params[17]
bilayerCoverage = params[18]
# Make the metal layers
gold = [goldThick, goldSLD, goldISLD, goldRough]
alloyUp = [alloyThick, alloySLDUp, alloyISLDUp, alloyRough]
alloyDown = [alloyThick, alloySLDDown, alloyISLDDown, alloyRough]
# Neutron b's..
# define all the neutron b's.
bc = 0.6646e-4 # Carbon
bo = 0.5843e-4 # Oxygen
bh = -0.3739e-4 # Hydrogen
bp = 0.513e-4 # Phosphorus
bn = 0.936e-4 # Nitrogen
# Work out the total scattering length in each fragment
# Define scattering lengths
# Hydrogenated version
COO = (2 * bo) + (bc)
GLYC = (3 * bc) + (5 * bh)
CH3 = (1 * bc) + (3 * bh)
PO4 = (1 * bp) + (4 * bo)
CH2 = (1 * bc) + (2 * bh)
CH = (1 * bc) + (1 * bh)
CHOL = (5 * bc) + (12 * bh) + (1 * bn)
# And also volumes
vCH3 = 52.7 # CH3 volume in the paper appears to be for 2 * CH3's
vCH2 = 28.1
vCOO = 39.0
vGLYC = 68.8
vPO4 = 53.7
vCHOL = 120.4
vCHCH = 42.14
vHead = vCHOL + vPO4 + vGLYC + 2 * vCOO
vTail = (28 * vCH2) + (1 * vCHCH) + (2 * vCH3) # Tail volume
# Calculate sum_b's for other fragments
sumbHead = CHOL + PO4 + GLYC + 2 * COO
sumbTail = (28 * CH2) + (2 * CH) + 2 * CH3
# Calculate SLDs and Thickness
sldHead = sumbHead / vHead
thickHead = vHead / thiolAPM
sldTail = sumbTail / vTail
thickTail = vTail / thiolAPM
# Correct head SLD based on hydration
thiolHeadHydr = thiolHeadHydr / 100
sldHead = sldHead * (1 - thiolHeadHydr) + (thiolHeadHydr * bulk_out[contrast - 1])
# Now correct both the SLDs for the coverage parameter
sldTail = (thiolCoverage * sldTail) + ((1 - thiolCoverage) * bulk_out[contrast - 1])
sldHead = (thiolCoverage * sldHead) + ((1 - thiolCoverage) * bulk_out[contrast - 1])
SAMTAILS = [thickTail, sldTail, 0, goldRough]
SAMHEAD = [thickHead, sldHead, 0, goldRough]
# Now do the same for the bilayer
vHead = vCHOL + vPO4 + vGLYC + 2 * vCOO
vTail = 28 * vCH2 # Tail volume
vMe = 2 * vCH3
sumbHead = CHOL + PO4 + GLYC + 2 * COO
sumbTail = 28 * CH2
sumbMe = 2 * CH3
sldHead = sumbHead / vHead
thickHead = vHead / bilayerAPM
bilHeadHydr = bilHeadHydr / 100
sldHead = sldHead * (1 - bilHeadHydr) + (bilHeadHydr * bulk_out[contrast - 1])
sldTail = sumbTail / vTail
thickTail = vTail / bilayerAPM
sldMe = sumbMe / vMe
thickMe = vMe / bilayerAPM
sldTail = (bilayerCoverage * sldTail) + ((1 - bilayerCoverage) * bulk_out[contrast - 1])
sldHead = (bilayerCoverage * sldHead) + ((1 - bilayerCoverage) * bulk_out[contrast - 1])
sldMe = (bilayerCoverage * sldMe) + ((1 - bilayerCoverage) * bulk_out[contrast - 1])
BILTAILS = [thickTail, sldTail, 0, bilayerRough]
BILHEAD = [thickHead, sldHead, 0, bilayerRough]
BILME = [thickMe, sldMe, 0, bilayerRough]
BILAYER = [BILHEAD, BILTAILS, BILME, BILME, BILTAILS, BILHEAD]
CW = [cwThick, bulk_out[contrast - 1], 0, bilayerRough]
if contrast == 2 or contrast == 4:
output = [alloyUp, gold, SAMTAILS, SAMHEAD, CW, *BILAYER]
elif contrast == 1 or contrast == 3:
output = [alloyDown, gold, SAMTAILS, SAMHEAD, CW, *BILAYER]
return output, subRough