import numpy as np\n",
"\n",
"\n",
"def custom_bilayer_DSPC(params, bulk_in, bulk_out, contrast):\n",
" """CUSTOMBILAYER RAT Custom Layer Model File.\n",
"\n",
" This file accepts 3 vectors containing the values for params, bulk in and bulk out.\n",
" The final parameter is an index of the contrast being calculated.\n",
"\n",
" The function should output a matrix of layer values, in the form...\n",
"\n",
" Output = [thick 1, SLD 1, Rough 1, Percent Hydration 1, Hydrate how 1\n",
" ....\n",
" thick n, SLD n, Rough n, Percent Hydration n, Hydration how n]\n",
"\n",
" The "hydrate how" parameter decides if the layer is hydrated with Bulk out or Bulk in phases.\n",
" Set to 1 for Bulk out, zero for Bulk in.\n",
" Alternatively, leave out hydration and just return...\n",
"\n",
" Output = [thick 1, SLD 1, Rough 1,\n",
" ....\n",
" thick n, SLD n, Rough n]\n",
"\n",
" The second output parameter should be the substrate roughness.\n",
" """\n",
" sub_rough = params[0]\n",
" oxide_thick = params[1]\n",
" oxide_hydration = params[2]\n",
" lipidAPM = params[3]\n",
" headHydration = params[4]\n",
" bilayerHydration = params[5]\n",
" bilayerRough = params[6]\n",
" waterThick = params[7]\n",
"\n",
" # We have a constant SLD for the bilayer\n",
" oxide_SLD = 3.41e-6\n",
"\n",
" # Now make the lipid layers\n",
" # Use known lipid volume and compositions to make the layers\n",
"\n",
" # define all the neutron b's.\n",
" bc = 0.6646e-4 # Carbon\n",
" bo = 0.5843e-4 # Oxygen\n",
" bh = -0.3739e-4 # Hydrogen\n",
" bp = 0.513e-4 # Phosphorus\n",
" bn = 0.936e-4 # Nitrogen\n",
"\n",
" # Now make the lipid groups\n",
" COO = (4 * bo) + (2 * bc)\n",
" GLYC = (3 * bc) + (5 * bh)\n",
" CH3 = (2 * bc) + (6 * bh)\n",
" PO4 = (1 * bp) + (4 * bo)\n",
" CH2 = (1 * bc) + (2 * bh)\n",
" CHOL = (5 * bc) + (12 * bh) + (1 * bn)\n",
"\n",
" # Group these into heads and tails:\n",
" Head = CHOL + PO4 + GLYC + COO\n",
" Tails = (34 * CH2) + (2 * CH3)\n",
"\n",
" # We need volumes for each. Use literature values:\n",
" vHead = 319\n",
" vTail = 782\n",
"\n",
" # We use the volumes to calculate the SLDs\n",
" SLDhead = Head / vHead\n",
" SLDtail = Tails / vTail\n",
"\n",
" # We calculate the layer thickness' from the volumes and the APM\n",
" headThick = vHead / lipidAPM\n",
" tailThick = vTail / lipidAPM\n",
"\n",
" # Manually deal with hydration for layers in this example.\n",
" oxSLD = (oxide_hydration * bulk_out[contrast]) + ((1 - oxide_hydration) * oxide_SLD)\n",
" headSLD = (headHydration * bulk_out[contrast]) + ((1 - headHydration) * SLDhead)\n",
" tailSLD = (bilayerHydration * bulk_out[contrast]) + ((1 - bilayerHydration) * SLDtail)\n",
"\n",
" # Make the layers\n",
" oxide = [oxide_thick, oxSLD, sub_rough]\n",
" water = [waterThick, bulk_out[contrast], bilayerRough]\n",
" head = [headThick, headSLD, bilayerRough]\n",
" tail = [tailThick, tailSLD, bilayerRough]\n",
"\n",
" output = np.array([oxide, water, head, tail, tail, head])\n",
"\n",
" return output, sub_rough\n",
"