1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
|
/*******************************************************************************
*
* McXtrace, X-ray tracing package
* Copyright, All rights reserved
* DTU Physics, Kgs. Lyngby, Denmark
* Synchrotron SOLEIL, Saint-Aubin, France
*
* Component: Saxs_spheres
*
* %Identification
* Written by: E. B. Knudsen, P. Willendrup, K. Lefmann, L. Arleth
* Date: 28.10.2010
* Origin: DTU Fysik
* Release: McXtrace 1.1
*
* Sample for Small Angle X-ray Scattering - hard spheres in thin solution, mono disperse.
*
* %Description
* Sample for use in a SAXS instrument, models hard, monodisperse spheres in thin solution.
* The shape of the sample may be a filled box with dimensions
* xwidth, yheight, zdepth, a cylinder with dimensions radius and yheight,
* a filled sphere with radius R.
*
* Example: Saxs_spheres(R = 20, Phi = 1e-3, Delta_rho = 0.6, sigma_abs = 50, xwidth=0.01, yheight=0.01, zdepth=0.005)
*
* %Parameters
*
* INPUT PARAMETERS
*
* R: [AA] Radius of scattering hard spheres
* Phi: [1] Particle volume fraction
* Delta_rho: [fm/AA^3] Excess scattering length density
* radius: [m] Outer radius of sample in (x,z) plane for cylinder/sphere
* xwidth: [m] Horiz. dimension of sample, as a width
* yheight: [m] Vert . dimension of sample, as a height for cylinder/box
* zdepth: [m] Depth of sample
* target_index: [1] Relative index of component to focus at, e.g. next is +1
* focus_xw: [m] Horiz. dimension of a rectangular area
* focus_yh: [m] Vert. dimension of a rectangular area
* focus_aw: [deg] Horiz. angular dimension of a rectangular area
* focus_ah: [deg] Vert. angular dimension of a rectangular area
* focus_r: [m] Detector (disk-shaped) radius
*
* Optional parameters:
* target_x: [m] Position of target to focus at, along X
* target_y: [m] Position of target to focus at, along Y
* target_z: [m] Position of target to focus at, along Z
* mu_c: [5] Column of the datafile which contains absorption coefficients.
* sphere_mtrl: [str] Material datafile from which to find absorption. If none is given absorption is neglected.
*
* %End
*******************************************************************************/
DEFINE COMPONENT Saxs_spheres
SETTING PARAMETERS (string sphere_mtrl="", R=100, Phi=1e-3, Delta_rho=0.6,
xwidth=0, yheight=0, zdepth=0, radius=0,
target_x = 0, target_y = 0, target_z = 6, int target_index=0,
focus_xw=0, focus_yh=0, focus_aw=0, focus_ah=0, focus_r=0, mu_c=0)
/* X-ray parameters: (x,y,z,kx,ky,kz,phi,t,Ex,Ey,Ez,p) */
DECLARE
%{
double my_s_pre;
int shape;
int Z;
double At;
double rho;
t_Table T;
int mu_ci;/*which column holds absorption mus*/
int abs_data;
%}
INITIALIZE
%{
shape=-1; /* -1:no shape, 0:cyl, 1:box, 2:sphere */
if (xwidth && yheight && zdepth) shape=1; /* box */
else if (radius > 0 && yheight) shape=0; /* cylinder */
else if (radius > 0 && !yheight) shape=2; /* sphere */
if (shape < 0)
exit(fprintf(stderr,"Saxs_spheres: %s: sample has invalid dimensions.\n"
"ERROR Please check parameter values.\n", NAME_CURRENT_COMP));
/* now compute target coords if a component index is supplied */
if (!target_index && !target_x && !target_y && !target_z) target_index=1;
if (target_index)
{
Coords ToTarget;
ToTarget = coords_sub(POS_A_COMP_INDEX(INDEX_CURRENT_COMP+target_index),POS_A_CURRENT_COMP);
ToTarget = rot_apply(ROT_A_CURRENT_COMP, ToTarget);
coords_get(ToTarget, &target_x, &target_y, &target_z);
}
if (!(target_x || target_y || target_z)) {
printf("Saxs_spheres: %s: The target is not defined. Using direct beam (Z-axis).\n",
NAME_CURRENT_COMP);
target_z=1;
}
/*check for existance of a sphere material datafile. If none is given absorption will be neglected.*/
if (sphere_mtrl && strlen(sphere_mtrl) && strcmp(sphere_mtrl,"NULL")){
int status;
if ( sphere_mtrl && (status=Table_Read(&(T),sphere_mtrl,0))==-1){
fprintf(stderr,"Error(%s): Could not parse file \"%s\"\n",NAME_CURRENT_COMP,sphere_mtrl);
exit(-1);
}
char **header_parsed;
header_parsed=Table_ParseHeader(T.header,"Z","A[r]","rho","Z/A","sigma[a]",NULL);
if(header_parsed[2]){rho=strtod(header_parsed[2],NULL);}
if(header_parsed[0]){Z=strtod(header_parsed[0],NULL);}
if(header_parsed[1]){At=strtod(header_parsed[1],NULL);}
/*which columns holds the mus*/
if (mu_c){
mu_ci=mu_c;
}else{
/*not given so take a guess*/
mu_ci=5;
if (T.columns==3) mu_ci=1;
}
abs_data=1;
}else{
abs_data=0;
}
my_s_pre = Phi * 4*PI*R*R*R/3 * Delta_rho*Delta_rho;
%}
TRACE
%{
double l0, l1, v, l_full, l, l_1, dt, dl, d_phi, theta, my_a_v;
double aim_x=0, aim_y=0, aim_z=1, axis_x, axis_y, axis_z;
double arg, tmp_vx, tmp_vy, tmp_vz, vout_x, vout_y, vout_z;
double f, solid_angle, kx_i, ky_i, kz_i, k, q, qx, qy, qz;
char intersect=0;
/* Intersection particle trajectory / sample (sample surface) */
if (shape == 0)
intersect = cylinder_intersect(&l0, &l1, x, y, z, kx, ky, kz, radius, yheight);
else if (shape == 1)
intersect = box_intersect(&l0, &l1, x, y, z, kx, ky, kz, xwidth, yheight, zdepth);
else if (shape == 2)
intersect = sphere_intersect(&l0, &l1, x, y, z, kx, ky, kz, radius);
if(intersect)
{
if(l0 < 0){
fprintf(stderr,"photon already inside sample %s - absorbing\n",NAME_CURRENT_COMP);
ABSORB;
}
/* Xray enters at l=l0. */
k = sqrt(kx*kx + ky*ky + kz*kz);
l_full = (l1 - l0); /* Length of full path through sample */
dl = rand01()*(l1 - l0) + l0; /* Time of scattering */
PROP_DL(dl); /* Point of scattering */
l = (dl-l0); /* Penetration in sample */
kx_i=kx;
ky_i=ky;
kz_i=kz;
if ((target_x || target_y || target_z)) {
aim_x = target_x-x; /* Vector pointing at target (anal./det.) */
aim_y = target_y-y;
aim_z = target_z-z;
}
if(focus_aw && focus_ah) {
randvec_target_rect_angular(&kx, &ky, &kz, &solid_angle,
aim_x, aim_y, aim_z, focus_aw, focus_ah, ROT_A_CURRENT_COMP);
} else if(focus_xw && focus_yh) {
randvec_target_rect(&kx, &ky, &kz, &solid_angle,
aim_x, aim_y, aim_z, focus_xw, focus_yh, ROT_A_CURRENT_COMP);
} else {
randvec_target_circle(&kx, &ky, &kz, &solid_angle, aim_x, aim_y, aim_z, focus_r);
}
NORM(kx, ky, kz);
kx *= k;
ky *= k;
kz *= k;
qx = (kx_i-kx);
qy = (ky_i-ky);
qz = (kz_i-kz);
q = sqrt(qx*qx+qy*qy+qz*qz);
f = 3 * (sin(q*R) - q*R*cos(q*R))/(q*R*q*R*q*R);
/*calculate absorption*/
if(abs_data){
my_a_v=Table_Value(T,k*K2E,mu_ci);
}else{
my_a_v=0;
}
p *= l_full*solid_angle/(4*PI)*my_s_pre*f*f*exp(-my_a_v*(l+l1));
SCATTER;
}
%}
MCDISPLAY
%{
if (shape == 0) { /* cylinder */
circle("xz", 0, yheight/2.0, 0, radius);
circle("xz", 0, -yheight/2.0, 0, radius);
line(-radius, -yheight/2.0, 0, -radius, +yheight/2.0, 0);
line(+radius, -yheight/2.0, 0, +radius, +yheight/2.0, 0);
line(0, -yheight/2.0, -radius, 0, +yheight/2.0, -radius);
line(0, -yheight/2.0, +radius, 0, +yheight/2.0, +radius);
}
else if (shape == 1) { /* box */
box(0,0,0,xwidth,yheight,zdepth,0, 0, 1, 0);
}
else if (shape == 2) { /* sphere */
circle("xy", 0, 0.0, 0, radius);
circle("xz", 0, 0.0, 0, radius);
circle("yz", 0, 0.0, 0, radius);
}
%}
END
|
