[7ef3589] | 1 | double form_volume(double radius); |
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| 2 | |
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| 3 | double Iq(double q, |
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[4a82d4d] | 4 | int n_shells, double thick_inter_0, int func_inter_0, double sld_core_0, double sld_solv, |
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| 5 | double sld_flat_1, double sld_flat_2, double sld_flat_3, double sld_flat_4, double sld_flat_5, |
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| 6 | double sld_flat_6, double sld_flat_7, double sld_flat_8, double sld_flat_9, double sld_flat_10, |
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| 7 | double thick_inter_1, double thick_inter_2, double thick_inter_3, double thick_inter_4, double thick_inter_5, |
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| 8 | double thick_inter_6, double thick_inter_7, double thick_inter_8, double thick_inter_9, double thick_inter_10, |
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| 9 | double thick_flat_1, double thick_flat_2, double thick_flat_3, double thick_flat_4, double thick_flat_5, |
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| 10 | double thick_flat_6, double thick_flat_7, double thick_flat_8, double thick_flat_9, double thick_flat_10, |
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| 11 | int func_inter_1, int func_inter_2, int func_inter_3, int func_inter_4, int func_inter_5, |
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| 12 | int func_inter_6, int func_inter_7, int func_inter_8, int func_inter_9, int func_inter_10, |
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| 13 | double nu_inter_1, double nu_inter_2,double nu_inter_3, double nu_inter_4, double nu_inter_5, |
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| 14 | double nu_inter_6, double nu_inter_7, double nu_inter_8, double nu_inter_9, double nu_inter_10, |
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| 15 | int npts_inter, double nu_inter_0, double rad_core_0); |
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[7ef3589] | 16 | |
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| 17 | double Iqxy(double qx, double qy, |
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[4a82d4d] | 18 | int n_shells, double thick_inter_0, int func_inter_0, double sld_core_0, double sld_solv, |
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| 19 | double sld_flat_1, double sld_flat_2, double sld_flat_3, double sld_flat_4, double sld_flat_5, |
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| 20 | double sld_flat_6, double sld_flat_7, double sld_flat_8, double sld_flat_9, double sld_flat_10, |
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| 21 | double thick_inter_1, double thick_inter_2, double thick_inter_3, double thick_inter_4, double thick_inter_5, |
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| 22 | double thick_inter_6, double thick_inter_7, double thick_inter_8, double thick_inter_9, double thick_inter_10, |
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| 23 | double thick_flat_1, double thick_flat_2, double thick_flat_3, double thick_flat_4, double thick_flat_5, |
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| 24 | double thick_flat_6, double thick_flat_7, double thick_flat_8, double thick_flat_9, double thick_flat_10, |
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| 25 | int func_inter_1, int func_inter_2, int func_inter_3, int func_inter_4, int func_inter_5, |
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| 26 | int func_inter_6, int func_inter_7, int func_inter_8, int func_inter_9, int func_inter_10, |
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| 27 | double nu_inter_1, double nu_inter_2,double nu_inter_3, double nu_inter_4, double nu_inter_5, |
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| 28 | double nu_inter_6, double nu_inter_7, double nu_inter_8, double nu_inter_9, double nu_inter_10, |
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| 29 | int npts_inter, double nu_inter_0, double rad_core_0); |
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[7ef3589] | 30 | |
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| 31 | //TODO: Check what is for volume for this model |
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| 32 | |
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| 33 | double form_volume(double radius) |
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| 34 | { |
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| 35 | //This is normalized for each shell. It is spehere but for each shell |
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| 36 | double vol = 4.0*M_PI/3.0*pow(radius,3); |
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| 37 | return vol; |
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| 38 | } |
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| 39 | |
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| 40 | |
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| 41 | static double sphere_sld_kernel(double dp[], double q) { |
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| 42 | int n = dp[0]; |
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| 43 | int i,j,k; |
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| 44 | |
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| 45 | double scale = dp[1]; |
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| 46 | double thick_inter_core = dp[2]; |
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| 47 | double sld_core = dp[4]; |
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| 48 | double sld_solv = dp[5]; |
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| 49 | double background = dp[6]; |
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| 50 | double npts = dp[57]; //number of sub_layers in each interface |
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| 51 | double nsl=npts;//21.0; //nsl = Num_sub_layer: MUST ODD number in double //no other number works now |
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| 52 | int n_s; |
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| 53 | |
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| 54 | double sld_i,sld_f,dz,bes,fun,f,vol,qr,r,contr,f2; |
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| 55 | double sign,slope=0.0; |
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| 56 | double pi; |
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| 57 | |
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| 58 | //int* fun_type; |
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| 59 | //double* sld; |
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| 60 | //double* thick_inter; |
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| 61 | //double* thick; |
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| 62 | //double* fun_coef; |
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| 63 | |
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| 64 | double total_thick=0.0; |
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| 65 | |
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| 66 | //fun_type = (int*)malloc((n+2)*sizeof(int)); |
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| 67 | //sld = (double*)malloc((n+2)*sizeof(double)); |
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| 68 | //thick_inter = (double*)malloc((n+2)*sizeof(double)); |
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| 69 | //thick = (double*)malloc((n+2)*sizeof(double)); |
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| 70 | //fun_coef = (double*)malloc((n+2)*sizeof(double)); |
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| 71 | |
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| 72 | //TODO: Solution to avoid mallocs but probablyu can be done better |
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| 73 | int fun_type[12]; |
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| 74 | double sld[12]; |
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| 75 | double thick_inter[12]; |
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| 76 | double thick[12]; |
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| 77 | double fun_coef[12]; |
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| 78 | |
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| 79 | fun_type[0] = dp[3]; |
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| 80 | fun_coef[0] = fabs(dp[58]); |
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| 81 | for (i =1; i<=n; i++){ |
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| 82 | sld[i] = dp[i+6]; |
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| 83 | thick_inter[i]= dp[i+16]; |
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| 84 | thick[i] = dp[i+26]; |
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| 85 | fun_type[i] = dp[i+36]; |
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| 86 | fun_coef[i] = fabs(dp[i+46]); |
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| 87 | total_thick += thick[i] + thick_inter[i]; |
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| 88 | } |
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| 89 | sld[0] = sld_core; |
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| 90 | sld[n+1] = sld_solv; |
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| 91 | thick[0] = dp[59]; |
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| 92 | thick[n+1] = total_thick/5.0; |
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| 93 | thick_inter[0] = thick_inter_core; |
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| 94 | thick_inter[n+1] = 0.0; |
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| 95 | fun_coef[n+1] = 0.0; |
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| 96 | |
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| 97 | pi = 4.0*atan(1.0); |
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| 98 | f = 0.0; |
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| 99 | r = 0.0; |
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| 100 | vol = 0.0; |
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| 101 | //vol_pre = 0.0; |
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| 102 | //vol_sub = 0.0; |
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| 103 | sld_f = sld_core; |
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| 104 | |
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| 105 | //floor_nsl = floor(nsl/2.0); |
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| 106 | |
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| 107 | dz = 0.0; |
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| 108 | // iteration for # of shells + core + solvent |
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| 109 | for (i=0;i<=n+1; i++){ |
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| 110 | //iteration for N sub-layers |
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| 111 | //if (fabs(thick[i]) <= 1e-24){ |
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| 112 | // continue; |
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| 113 | //} |
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| 114 | // iteration for flat and interface |
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| 115 | for (j=0;j<2;j++){ |
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| 116 | // iteration for sub_shells in the interface |
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| 117 | // starts from #1 sub-layer |
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| 118 | for (n_s=1;n_s<=nsl; n_s++){ |
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| 119 | // for solvent, it doesn't have an interface |
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| 120 | if (i==n+1 && j==1) |
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| 121 | break; |
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| 122 | // for flat layers |
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| 123 | if (j==0){ |
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| 124 | dz = thick[i]; |
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| 125 | sld_i = sld[i]; |
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| 126 | slope = 0.0; |
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| 127 | } |
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| 128 | // for interfacial sub_shells |
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| 129 | else{ |
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| 130 | dz = thick_inter[i]/nsl; |
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| 131 | // find sld_i at the outer boundary of sub-layer #n_s |
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| 132 | sld_i = intersldfunc(fun_type[i],nsl, n_s, fun_coef[i], sld[i], sld[i+1]); |
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| 133 | // calculate slope |
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| 134 | slope= (sld_i -sld_f)/dz; |
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| 135 | } |
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| 136 | contr = sld_f-slope*r; |
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| 137 | // iteration for the left and right boundary of the shells(or sub_shells) |
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| 138 | for (k=0; k<2; k++){ |
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| 139 | // At r=0, the contribution to I is zero, so skip it. |
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| 140 | if ( i == 0 && j == 0 && k == 0){ |
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| 141 | continue; |
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| 142 | } |
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| 143 | // On the top of slovent there is no interface; skip it. |
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| 144 | if (i == n+1 && k == 1){ |
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| 145 | continue; |
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| 146 | } |
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| 147 | // At the right side (outer) boundary |
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| 148 | if ( k == 1){ |
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| 149 | sign = 1.0; |
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| 150 | r += dz; |
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| 151 | } |
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| 152 | // At the left side (inner) boundary |
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| 153 | else{ |
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| 154 | sign = -1.0; |
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| 155 | } |
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| 156 | qr = q * r; |
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| 157 | fun = 0.0; |
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| 158 | if(qr == 0.0){ |
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| 159 | // sigular point |
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| 160 | bes = sign * 1.0; |
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| 161 | } |
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| 162 | else{ |
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| 163 | // for flat sub-layer |
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| 164 | bes = sign * 3.0 * (sin(qr) - qr * cos(qr)) / (qr * qr * qr); |
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| 165 | // with linear slope |
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| 166 | if (fabs(slope) > 0.0 ){ |
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| 167 | fun = sign * 3.0 * r * (2.0*qr*sin(qr)-((qr*qr)-2.0)*cos(qr))/(qr * qr * qr * qr); |
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| 168 | } |
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| 169 | } |
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| 170 | // update total volume |
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| 171 | vol = 4.0 * pi / 3.0 * r * r * r; |
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| 172 | // we won't do the following volume correction for now. |
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| 173 | // substrate empty area of volume |
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| 174 | //if (k == 1 && fabs(sld_in[i]-sld_solv) < 1e-04*fabs(sld_solv) && fun_type[i]==0){ |
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| 175 | // vol_sub += (vol_pre - vol); |
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| 176 | //} |
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| 177 | f += vol * (bes * contr + fun * slope); |
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| 178 | } |
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| 179 | // remember this sld as sld_f |
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| 180 | sld_f =sld_i; |
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| 181 | // no sub-layer iteration (n_s loop) for the flat layer |
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| 182 | if (j==0) |
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| 183 | break; |
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| 184 | } |
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| 185 | } |
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| 186 | } |
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| 187 | //vol += vol_sub; |
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| 188 | f2 = f * f / vol * 1.0e8; |
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| 189 | f2 *= scale; |
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| 190 | f2 += background; |
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| 191 | //free(fun_type); |
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| 192 | //free(sld); |
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| 193 | //free(thick_inter); |
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| 194 | //free(thick); |
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| 195 | //free(fun_coef); |
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| 196 | |
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| 197 | return (f2); |
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| 198 | } |
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| 199 | |
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| 200 | |
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| 201 | /** |
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| 202 | * Function to evaluate 1D SphereSLD function |
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| 203 | * @param q: q-value |
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| 204 | * @return: function value |
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| 205 | */ |
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| 206 | double Iq(double q, |
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[4a82d4d] | 207 | int n_shells, double thick_inter_0, int func_inter_0, double sld_core_0, double sld_solv, |
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| 208 | double sld_flat_1, double sld_flat_2, double sld_flat_3, double sld_flat_4, double sld_flat_5, |
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| 209 | double sld_flat_6, double sld_flat_7, double sld_flat_8, double sld_flat_9, double sld_flat_10, |
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| 210 | double thick_inter_1, double thick_inter_2, double thick_inter_3, double thick_inter_4, double thick_inter_5, |
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| 211 | double thick_inter_6, double thick_inter_7, double thick_inter_8, double thick_inter_9, double thick_inter_10, |
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| 212 | double thick_flat_1, double thick_flat_2, double thick_flat_3, double thick_flat_4, double thick_flat_5, |
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| 213 | double thick_flat_6, double thick_flat_7, double thick_flat_8, double thick_flat_9, double thick_flat_10, |
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| 214 | int func_inter_1, int func_inter_2, int func_inter_3, int func_inter_4, int func_inter_5, |
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| 215 | int func_inter_6, int func_inter_7, int func_inter_8, int func_inter_9, int func_inter_10, |
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| 216 | double nu_inter_1, double nu_inter_2,double nu_inter_3, double nu_inter_4, double nu_inter_5, |
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| 217 | double nu_inter_6, double nu_inter_7, double nu_inter_8, double nu_inter_9, double nu_inter_10, |
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| 218 | int npts_inter, double nu_inter_0, double rad_core_0) { |
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| 219 | |
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| 220 | //printf("Number of points %d\n",npts_inter); |
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[7ef3589] | 221 | double intensity; |
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| 222 | //TODO: Remove this container at later stage. It is only kept to minimize stupid errors now |
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| 223 | double dp[60]; |
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| 224 | dp[0] = n_shells; |
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| 225 | //This is scale will also have to be removed at some stage |
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| 226 | dp[1] = 1.0; |
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| 227 | dp[2] = thick_inter_0; |
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| 228 | dp[3] = func_inter_0; |
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| 229 | dp[4] = sld_core_0; |
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| 230 | dp[5] = sld_solv; |
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| 231 | dp[6] = 0.0; |
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| 232 | |
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| 233 | dp[7] = sld_flat_1; |
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| 234 | dp[8] = sld_flat_2; |
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| 235 | dp[9] = sld_flat_3; |
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| 236 | dp[10] = sld_flat_4; |
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| 237 | dp[11] = sld_flat_5; |
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| 238 | dp[12] = sld_flat_6; |
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| 239 | dp[13] = sld_flat_7; |
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| 240 | dp[14] = sld_flat_8; |
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| 241 | dp[15] = sld_flat_9; |
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| 242 | dp[16] = sld_flat_10; |
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| 243 | |
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| 244 | dp[17] = thick_inter_1; |
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| 245 | dp[18] = thick_inter_2; |
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| 246 | dp[19] = thick_inter_3; |
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| 247 | dp[20] = thick_inter_4; |
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| 248 | dp[21] = thick_inter_5; |
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| 249 | dp[22] = thick_inter_6; |
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| 250 | dp[23] = thick_inter_7; |
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| 251 | dp[24] = thick_inter_8; |
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| 252 | dp[25] = thick_inter_9; |
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| 253 | dp[26] = thick_inter_10; |
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| 254 | |
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| 255 | dp[27] = thick_flat_1; |
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| 256 | dp[28] = thick_flat_2; |
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| 257 | dp[29] = thick_flat_3; |
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| 258 | dp[30] = thick_flat_4; |
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| 259 | dp[31] = thick_flat_5; |
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| 260 | dp[32] = thick_flat_6; |
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| 261 | dp[33] = thick_flat_7; |
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| 262 | dp[34] = thick_flat_8; |
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| 263 | dp[35] = thick_flat_9; |
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| 264 | dp[36] = thick_flat_10; |
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| 265 | |
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| 266 | dp[37] = func_inter_1; |
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| 267 | dp[38] = func_inter_2; |
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| 268 | dp[39] = func_inter_3; |
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| 269 | dp[40] = func_inter_4; |
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| 270 | dp[41] = func_inter_5; |
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| 271 | dp[42] = func_inter_6; |
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| 272 | dp[43] = func_inter_7; |
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| 273 | dp[44] = func_inter_8; |
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| 274 | dp[45] = func_inter_9; |
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| 275 | dp[46] = func_inter_10; |
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| 276 | |
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| 277 | dp[47] = nu_inter_1; |
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| 278 | dp[48] = nu_inter_2; |
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| 279 | dp[49] = nu_inter_3; |
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| 280 | dp[50] = nu_inter_4; |
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| 281 | dp[51] = nu_inter_5; |
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| 282 | dp[52] = nu_inter_6; |
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| 283 | dp[53] = nu_inter_7; |
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| 284 | dp[54] = nu_inter_8; |
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| 285 | dp[55] = nu_inter_9; |
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| 286 | dp[56] = nu_inter_10; |
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| 287 | |
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| 288 | dp[57] = npts_inter; |
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| 289 | dp[58] = nu_inter_0; |
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| 290 | dp[59] = rad_core_0; |
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| 291 | |
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| 292 | intensity = sphere_sld_kernel(dp,q); |
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[4a82d4d] | 293 | //printf("%10d\n",intensity); |
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[7ef3589] | 294 | return intensity; |
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| 295 | } |
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| 296 | |
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| 297 | /** |
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| 298 | * Function to evaluate 2D SphereSLD function |
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| 299 | * @param q_x: value of Q along x |
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| 300 | * @param q_y: value of Q along y |
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| 301 | * @return: function value |
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| 302 | */ |
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| 303 | double Iqxy(double qx, double qy, |
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[4a82d4d] | 304 | int n_shells, double thick_inter_0, int func_inter_0, double sld_core_0, double sld_solv, |
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| 305 | double sld_flat_1, double sld_flat_2, double sld_flat_3, double sld_flat_4, double sld_flat_5, |
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| 306 | double sld_flat_6, double sld_flat_7, double sld_flat_8, double sld_flat_9, double sld_flat_10, |
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| 307 | double thick_inter_1, double thick_inter_2, double thick_inter_3, double thick_inter_4, double thick_inter_5, |
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| 308 | double thick_inter_6, double thick_inter_7, double thick_inter_8, double thick_inter_9, double thick_inter_10, |
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| 309 | double thick_flat_1, double thick_flat_2, double thick_flat_3, double thick_flat_4, double thick_flat_5, |
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| 310 | double thick_flat_6, double thick_flat_7, double thick_flat_8, double thick_flat_9, double thick_flat_10, |
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| 311 | int func_inter_1, int func_inter_2, int func_inter_3, int func_inter_4, int func_inter_5, |
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| 312 | int func_inter_6, int func_inter_7, int func_inter_8, int func_inter_9, int func_inter_10, |
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| 313 | double nu_inter_1, double nu_inter_2,double nu_inter_3, double nu_inter_4, double nu_inter_5, |
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| 314 | double nu_inter_6, double nu_inter_7, double nu_inter_8, double nu_inter_9, double nu_inter_10, |
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| 315 | int npts_inter, double nu_inter_0, double rad_core_0) { |
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[7ef3589] | 316 | |
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| 317 | double q = sqrt(qx*qx + qy*qy); |
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[4a82d4d] | 318 | return Iq(q, n_shells, thick_inter_0, func_inter_0, sld_core_0, sld_solv, |
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| 319 | sld_flat_1, sld_flat_2, sld_flat_3, sld_flat_4, sld_flat_5, |
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| 320 | sld_flat_6, sld_flat_7, sld_flat_8, sld_flat_9, sld_flat_10, |
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| 321 | thick_inter_1, thick_inter_2, thick_inter_3, thick_inter_4, thick_inter_5, |
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| 322 | thick_inter_6, thick_inter_7, thick_inter_8, thick_inter_9, thick_inter_10, |
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| 323 | thick_flat_1, thick_flat_2, thick_flat_3, thick_flat_4, thick_flat_5, |
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| 324 | thick_flat_6, thick_flat_7, thick_flat_8, thick_flat_9, thick_flat_10, |
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| 325 | func_inter_1, func_inter_2, func_inter_3, func_inter_4, func_inter_5, |
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| 326 | func_inter_6, func_inter_7, func_inter_8, func_inter_9, func_inter_10, |
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| 327 | nu_inter_1, nu_inter_2, nu_inter_3, nu_inter_4, nu_inter_5, |
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| 328 | nu_inter_6, nu_inter_7, nu_inter_8, nu_inter_9, nu_inter_10, |
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| 329 | npts_inter, nu_inter_0, rad_core_0); |
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[7ef3589] | 330 | |
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| 331 | } |
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| 332 | |
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