added custom model files for rascal1 example

examples/rascal1_example/Model_IIb.m

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+function [output,sub_rough] = Model_IIb(params,bulk_in,bulk_out,contrast)
+%MODEL_1  RASCAL 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 m-file 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
+
+
+Roughness = params(1);
+APM = params(2);
+thickHead = params(3);
+theta = params(4);
+% vTail = params(4);
+% vHead = params(5);
+
+%Make a flag to say which deuteration this is calculating
+%[subs head tail]
+deut = [0 0 1;
+        1 0 1;
+        0 1 0;
+        1 1 0;
+        0 1 1;
+        1 1 1;
+        1 0 0];
+
+
+%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
+bd = 0.6671e-4;     %Deuterium
+
+%Work out the total scattering length in each fragment....
+%Define scattering lengths..
+%Hydrogenated version....
+COO = (4*bo) + (2*bc);
+GLYC = (3*bc) + (5*bh);
+CH3 = (2*bc) + (6*bh);             
+PO4 = (1*bp) + (4*bo);
+CH2 = (1*bc) + (2*bh);
+CHOL = (5*bc) + (12*bh) + (1*bn);
+H2O = (2*bh) + (1*bo);
+
+%..and deuterated...
+dGLYC = (3*bc) + (5*bd);
+dCH3 = (2*bc) + (6*bd); 
+dCH2 = (1*bc) + (2*bd);
+dCHOL = (5*bc) + (12*bd) + (1*bn);
+D2O = (2*bd) + (1*bo);
+
+%And also volumes....
+vCH3 = 52.7;
+vCH2 = 28.1;
+vCOO = 39.0;
+vGLYC = 68.8;
+vPO4 = 53.7;
+vCHOL = 120.4;
+vWAT = 30.4;
+
+vHead = vCHOL + vPO4 + vGLYC + 2*vCOO;
+vTail = 2*(16*vCH2)+ 2*(vCH3);
+
+%Make the SLD's first...
+thisMask = deut(contrast,:);
+
+switch thisMask(1)  
+    case 0
+        thisWater = (H2O * 0.9249) + (D2O * 0.0871);
+    case 1
+        thisWater = D2O;
+end
+
+%Calculate mole fraction of D2O from the bulk SLD..
+d2o_molfr = (1/D2O-H2O)*((bulk_out(contrast)/0.036182336306)-H2O);
+thisWater = (d2o_molfr * D2O) + ((1-d2o_molfr)*H2O);
+
+
+switch thisMask(2)
+    case 0
+        thisHead = CHOL + PO4 + GLYC + COO;
+    case 1
+        thisHead = dCHOL + PO4 + GLYC + COO;
+end
+
+switch thisMask(3);
+    case 0
+        thisTail = (32*CH2) + CH3;
+    case 1
+        thisTail = (32*dCH2) + dCH3;
+end
+
+noWat = ((thickHead*APM)-vHead)/vWAT;
+thisHead = thisHead + noWat*thisWater;
+vHead = vHead + noWat*vWAT;
+
+
+sldHead = thisHead/vHead;
+%thickHead = vHead/APM;
+
+sldTail = thisTail/vTail;
+%thickTail = vTail/APM;
+
+thickTail = (1.5 + 16*1.265)*cosd(theta);
+
+output = [thickTail sldTail Roughness;
+          thickHead sldHead Roughness;];
+
+
+sub_rough = Roughness;
+
+
+
+
+
+

examples/rascal1_example/Model_IIb.py

@@ -0,0 +1,84 @@
+from math import cos, radians
+
+
+def Model_IIb(params, bulk_in, bulk_out, contrast):
+    # converted from matlab file Model_IIb.m
+
+    Roughness, APM, thickHead, theta = params
+
+    # Make a flag to say which deuteration this is calculating
+    # [subs head tail]
+    deut = [[0, 0, 1], [1, 0, 1], [0, 1, 0], [1, 1, 0], [0, 1, 1], [1, 1, 1], [1, 0, 0]]
+
+    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
+    bd = 0.6671e-4  # Deuterium
+
+    # Work out the total scattering length in each fragment
+    # for hydrogenated:
+    COO = (4 * bo) + (2 * bc)
+    GLYC = (3 * bc) + (5 * bh)
+    CH3 = (2 * bc) + (6 * bh)
+    PO4 = (1 * bp) + (4 * bo)
+    CH2 = (1 * bc) + (2 * bh)
+    CHOL = (5 * bc) + (12 * bh) + (1 * bn)
+    H2O = (2 * bh) + (1 * bo)
+
+    # for deuterated:
+    dCH3 = (2 * bc) + (6 * bd)
+    dCH2 = (1 * bc) + (2 * bd)
+    dCHOL = (5 * bc) + (12 * bd) + (1 * bn)
+    D2O = (2 * bd) + (1 * bo)
+
+    # for volumes:
+    vCH3 = 52.7
+    vCH2 = 28.1
+    vCOO = 39.0
+    vGLYC = 68.8
+    vPO4 = 53.7
+    vCHOL = 120.4
+    vWAT = 30.4
+
+    vHead = vCHOL + vPO4 + vGLYC + 2 * vCOO
+    vTail = 2 * (16 * vCH2) + 2 * (vCH3)
+
+    # make SLDs
+    thisMask = deut[contrast]
+
+    if thisMask[0] == 0:
+        thisWater = (H2O * 0.9249) + (D2O * 0.0871)
+    else:
+        thisWater = D2O
+
+    # Calculate mole fraction of D2O from the bulk SLD
+    d2o_molfr = (1 / D2O - H2O) * ((bulk_out[contrast] / 0.036182336306) - H2O)
+    thisWater = (d2o_molfr * D2O) + ((1 - d2o_molfr) * H2O)
+
+    if thisMask[1] == 0:
+        thisHead = CHOL + PO4 + GLYC + COO
+    else:
+        thisHead = dCHOL + PO4 + GLYC + COO
+
+    if thisMask[2] == 0:
+        thisTail = (32 * CH2) + CH3
+    else:
+        thisTail = (32 * dCH2) + dCH3
+
+    noWat = ((thickHead * APM) - vHead) / vWAT
+    thisHead = thisHead + noWat * thisWater
+    vHead = vHead + noWat * vWAT
+
+    sldHead = thisHead / vHead
+
+    sldTail = thisTail / vTail
+
+    thickTail = (1.5 + 16 * 1.265) * cos(radians(theta))
+
+    output = [[thickTail, sldTail, Roughness], [thickHead, sldHead, Roughness]]
+
+    sub_rough = Roughness
+
+    return output, sub_rough