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//custom_bilayer.cpp

#include <vector>

#if defined(_WIN32) || defined(_WIN64)

#define LIB_EXPORT __declspec(dllexport)

#else

#define LIB_EXPORT

#endif

// We user extern "C" decorator to avoid name mangling

extern "C" {

LIB_EXPORT void custom_bilayer(std::vector<double>& params, std::vector<double>& bulkIn, std::vector<double>& bulkOut, int contrast, std::vector<double>& output, double* outputSize, double* rough)

{

// Note - The first contrast number is 1 (not 0) so be careful if you use

// this variable for array indexing.

double subRough = params[0];

double oxideThick = params[1];

double oxideHydration = params[2];

double lipidAPM = params[3];

double headHydration = params[4];

double bilayerHydration = params[5];

double bilayerRough = params[6];

double waterThick = params[7];

// We have a constant SLD for the oxide

double oxideSLD = 3.41e-6;

// Now make the lipid layers

// Use known lipid volume and compositions

// to make the layers

// define all the neutron b's

double bc = 0.6646e-4; //Carbon

double bo = 0.5843e-4; //Oxygen

double bh = -0.3739e-4; //Hydrogen

double bp = 0.513e-4; //Phosphorus

double bn = 0.936e-4; //Nitrogen

double bd = 0.6671e-4; //Deuterium

// Now make the lipid groups

double COO = (4*bo) + (2*bc);

double GLYC = (3*bc) + (5*bh);

double CH3 = (2*bc) + (6*bh);

double PO4 = (1*bp) + (4*bo);

double CH2 = (1*bc) + (2*bh);

double CHOL = (5*bc) + (12*bh) + (1*bn);

// Group these into heads and tails:

double Head = CHOL + PO4 + GLYC + COO;

double Tails = (34*CH2) + (2*CH3);

// We need volumes for each.

// Use literature values:

double vHead = 319;

double vTail = 782;

// we use the volumes to calculate the SLDs

double SLDhead = Head / vHead;

double SLDtail = Tails / vTail;

// We calculate the layer thickness from

// the volumes and the APM

double headThick = vHead / lipidAPM;

double tailThick = vTail / lipidAPM;

// Manually deal with hydration for layers in

// this example.

double oxSLD = (oxideHydration * bulkOut[contrast-1]) + ((1 - oxideHydration) * oxideSLD);

double headSLD = (headHydration * bulkOut[contrast-1]) + ((1 - headHydration) * SLDhead);

double tailSLD = (bilayerHydration * bulkOut[contrast-1]) + ((1 - bilayerHydration) * SLDtail);

// Make the layers

// oxide...

output.push_back(oxideThick);

output.push_back(oxSLD);

output.push_back(subRough);

// Water...

output.push_back(waterThick);

output.push_back(bulkOut[contrast-1]);