Changes in / [38a9b07:a7c2cfe] in sasmodels

Location:

sasmodels/models

Files:

• lib/librefl.c (added)
• spherical_sld.c (modified) (8 diffs)
• spherical_sld.py (modified) (2 diffs)

sasmodels/models/spherical_sld.c

@@ -1 @@
-//Headers
-static double form_volume(double thick_inter[],
-    double thick_flat_[],
-    double core_radius,
-    int n_shells);
-
-double Iq(double q,
+static double form_volume(
     int n_shells,
-    double thick_inter[],
-    double func_inter[],
-    double sld_core,
-    double sld_solvent,
-    double sld_flat[],
+    double radius_core,
     double thick_flat[],
-    double nu_inter[],
-    int npts_inter,
-    double core_radius);
-
-double Iqxy(double qx, double qy,
-    int n_shells,
-    double thick_inter[],
-    double func_inter[],
-    double sld_core,
-    double sld_solvent,
-    double sld_flat[],
-    double thick_flat[],
-    double nu_inter[],
-    int npts_inter,
-    double core_radius);
-
-//Main code
-static double form_volume(double thick_inter[],
-    double thick_flat_[],
-    double core_radius,
-    int n)
+    double thick_inter[])
 {
     double radius = 0.0;
     int i;
-    double r = core_radius;
-    for (i=0; i < n; i++) {
+    double r = radius_core;
+    for (i=0; i < n_shells; i++) {
         r += thick_inter[i];
         r += thick_flat[i];
@@ -56 +26 @@
   double background = dp[6];
   double npts = dp[57]; //number of sub_layers in each interface
-  double nsl=npts;//21.0; //nsl = Num_sub_layer:  MUST ODD number in double //no other number works now
+  double nsl=npts;//21.0; //nsl = Num_sub_layer:  must be ODD double number
   int n_s;
 
@@ -63 +33 @@
   double pi;
 
-  //int* fun_type;
-  //double* sld;
-  //double* thick_inter;
-  //double* thick;
-  //double* fun_coef;
-
   double total_thick=0.0;
 
-  //fun_type = (int*)malloc((n+2)*sizeof(int));
-  //sld = (double*)malloc((n+2)*sizeof(double));
-  //thick_inter = (double*)malloc((n+2)*sizeof(double));
-  //thick = (double*)malloc((n+2)*sizeof(double));
-  //fun_coef = (double*)malloc((n+2)*sizeof(double));
-
-  //TODO: Solution to avoid mallocs but probablyu can be done better
   int fun_type[12];
   double sld[12];
@@ -175 +132 @@
             if (fabs(slope) > 0.0 ){
               //fun = sign * 3.0 * r * (2.0*qr*sin(qr)-((qr*qr)-2.0)*cos(qr))/(qr * qr * qr * qr);
-              fun = sign * r * sph_j1c(qr)  +  sign * 3.0 * sin(qr)/(qr * qr * q ) + sign * 6.0 * cos(qr)/(qr * qr * qr * q);
+              fun = sign * r * sph_j1c(qr) + sign * 3.0 * sin(qr)/(qr * qr * q )
+                + sign * 6.0 * cos(qr)/(qr * qr * qr * q);
             }
           }
@@ -203 +161 @@
     }
   }
-  //vol += vol_sub;
   f2 = f * f / vol;
-  //f2 *= scale;
-  //f2 += background;
-  //free(fun_type);
-  //free(sld);
-  //free(thick_inter);
-  //free(thick);
-  //free(fun_coef);
 
   return (f2);
@@ -222 +172 @@
  * @return: function value
  */
-double Iq(double q,
+static double Iq(double q,
     int n_shells,
-    double thick_inter[],
-    double func_inter[],
+    int npts_inter,
+    double radius_core,
     double sld_core,
     double sld_solvent,
     double sld_flat[],
     double thick_flat[],
-    double nu_inter[],
-    int npts_inter,
-    double core_radius
-    ) {
+    double func_inter[],
+    double thick_inter[],
+    double nu_inter[] ) {
 
     //printf("Number of points %d\n",npts_inter);
     double intensity;
-    //TODO: Remove this container at later stage. It is only kept to minimize stupid errors now
+    //TODO: Remove this container at later stage.
     double dp[60];
     dp[0] = n_shells;
     //This is scale will also have to be removed at some stage
     dp[1] = 1.0;
-    dp[2] = thick_inter_0;
-    dp[3] = func_inter_0;
+    dp[2] = thick_inter[0];
+    dp[3] = func_inter[0];
     dp[4] = sld_core;
     dp[5] = sld_solvent;
     dp[6] = 0.0;
 
-    for (i=0; i<n; i++){
+    for (int i=1; i<n_shells; i++){
         dp[i+7] = sld_flat[i];
         dp[i+17] = thick_inter[i];
@@ -257 +206 @@
 
     dp[57] = npts_inter;
-    dp[58] = nu_inter_0;
-    dp[59] = rad_core_0;
+    dp[58] = nu_inter[0];
+    dp[59] = radius_core;
 
     intensity = 1.0e-4*sphere_sld_kernel(dp,q);
@@ -271 +220 @@
  * @return: function value
  */
-double Iqxy(double qx, double qy,
+
+/*static double Iqxy(double qx, double qy,
     int n_shells,
-    double thick_inter[],
-    double func_inter[],
+    int npts_inter,
+    double radius_core
     double sld_core,
     double sld_solvent,
     double sld_flat[],
     double thick_flat[],
+    double func_inter[],
+    double thick_inter[],
     double nu_inter[],
-    int npts_inter,
-    double core_radius
     ) {
 
     double q = sqrt(qx*qx + qy*qy);
-    return Iq(q, n_shells, thick_inter_0, func_inter_0, core0_sld, solvent_sld,
-    flat1_sld, flat2_sld, flat3_sld, flat4_sld, flat5_sld,
-    flat6_sld, flat7_sld, flat8_sld, flat9_sld, flat10_sld,
-    thick_inter_1, thick_inter_2, thick_inter_3, thick_inter_4, thick_inter_5,
-    thick_inter_6, thick_inter_7, thick_inter_8, thick_inter_9, thick_inter_10,
-    thick_flat_1, thick_flat_2, thick_flat_3, thick_flat_4, thick_flat_5,
-    thick_flat_6, thick_flat_7, thick_flat_8, thick_flat_9, thick_flat_10,
-    func_inter_1, func_inter_2, func_inter_3, func_inter_4, func_inter_5,
-    func_inter_6, func_inter_7, func_inter_8, func_inter_9, func_inter_10,
-    nu_inter_1, nu_inter_2, nu_inter_3, nu_inter_4, nu_inter_5,
-    nu_inter_6, nu_inter_7, nu_inter_8, nu_inter_9, nu_inter_10,
-    npts_inter, nu_inter_0, rad_core_0);
-
-    //TODO: Check if evalute rphi is not needed?
-
-}
-
+    return Iq(q, n_shells, npts_inter, radius_core, sld_core, sld_solvent,
+    sld_flat[], thick_flat[], func_inter[], thick_inter[], nu_inter[])
+}*/
+

sasmodels/models/spherical_sld.py

@@ -170 +170 @@
 # pylint: disable=bad-whitespace, line-too-long
 #            ["name", "units", default, [lower, upper], "type", "description"],
-parameters = [["n",                "",               1,      [0, 9],         "", "number of shells"],
+parameters = [["n_shells",                "",               1,      [0, 9],         "", "number of shells"],
+              ["npts_inter",       "",               35,     [0, 35],        "", "number of points in each sublayer Must be odd number"],
               ["radius_core",      "Ang",            50.0,   [0, inf],       "", "intern layer thickness"],
               ["sld_core",         "1e-6/Ang^2",     2.07,   [-inf, inf],    "", "sld function flat"],
-              ["sld_flat[n]",      "1e-6/Ang^2",     4.06,   [-inf, inf],    "", "sld function flat"],
-              ["thick_flat[n]",    "Ang",            100.0,  [0, inf],       "", "flat layer_thickness"],
-              ["func_inter[n]",    "",               0,      [0, 4],         "", "Erf:0, RPower:1, LPower:2, RExp:3, LExp:4"],
-              ["thick_inter[n]",   "Ang",            50.0,   [0, inf],       "", "intern layer thickness"],
-              ["inter_nu[n]",      "",               2.5,    [-inf, inf],    "", "steepness parameter"],
-              ["npts_inter",       "",               35,     [0, 35],        "", "number of points in each sublayer Must be odd number"],
               ["sld_solvent",      "1e-6/Ang^2",     1.0,    [-inf, inf],    "", "sld function solvent"],
+              ["sld_flat[n_shells]",      "1e-6/Ang^2",     4.06,   [-inf, inf],    "", "sld function flat"],
+              ["thick_flat[n_shells]",    "Ang",            100.0,  [0, inf],       "", "flat layer_thickness"],
+              ["func_inter[n_shells]",    "",               0,      [0, 4],         "", "Erf:0, RPower:1, LPower:2, RExp:3, LExp:4"],
+              ["thick_inter[n_shells]",   "Ang",            50.0,   [0, inf],       "", "intern layer thickness"],
+              ["nu_inter[n_shells]",      "",               2.5,    [-inf, inf],    "", "steepness parameter"],
               ]
 # pylint: enable=bad-whitespace, line-too-long
-#source = ["lib/librefl.c",  "lib/sph_j1c.c", "spherical_sld.c"]
-
-def Iq(q, *args, **kw):
-    return q
-
-def Iqxy(qx, *args, **kw):
-    return qx
+source = ["lib/librefl.c",  "lib/sph_j1c.c", "spherical_sld.c"]
+
+#def Iq(q, *args, **kw):
+#    return q
+
+#def Iqxy(qx, *args, **kw):
+#    return qx
+
+def profile(n_shells, radius_core,  sld_core,  sld_solvent, sld_flat,
+            thick_flat, func_inter, thick_inter, nu_inter, npts_inter):
+    """
+    Returns shape profile with x=radius, y=SLD.
+    """
+
+    z = []
+    beta = []
+    z0 = 0
+    # two sld points for core
+    z.append(0)
+    beta.append(sld_core)
+    z.append(radius_core)
+    beta.append(sld_core)
+    z0 += radius_core
+
+    for i in range(1, n_shells+2):
+        dz = thick_inter[i-1]/npts_inter
+        # j=0 for interface, j=1 for flat layer
+        for j in range(0, 2):
+            # interation for sub-layers
+            for n_s in range(0, npts_inter+1):
+                if j == 1:
+                    if i == n_shells+1:
+                        break
+                    # shift half sub thickness for the first point
+                    z0 -= dz#/2.0
+                    z.append(z0)
+                    #z0 -= dz/2.0
+                    z0 += thick_flat[i]
+                    sld_i = sld_flat[i]
+                    beta.append(sld_flat[i])
+                    dz = 0
+                else:
+                    nu = nu_inter[i-1]
+                    # decide which sld is which, sld_r or sld_l
+                    if i == 1:
+                        sld_l = sld_core
+                    else:
+                        sld_l = sld_flat[i-1]
+                    if i == n_shells+1:
+                        sld_r = sld_solvent
+                    else:
+                        sld_r = sld_flat[i]
+                    # get function type
+                    func_idx = func_inter[i-1]
+                    # calculate the sld
+                    sld_i = intersldfunc(func_idx, npts_inter, n_s, nu,
+                                            sld_l, sld_r)
+                # append to the list
+                z.append(z0)
+                beta.append(sld_i)
+                z0 += dz
+                if j == 1:
+                    break
+    z.append(z0)
+    beta.append(sld_solvent)
+    z_ext = z0/5.0
+    z.append(z0+z_ext)
+    beta.append(sld_solvent)
+    # return sld profile (r, beta)
+    return np.asarray(z), np.asarray(beta)*1e-6
+
+def ER(core_radius, n, thickness):
+    return np.sum(thickness[:n[0]], axis=0) + core_radius
+
+def VR(core_radius, n, thickness):
+    return 1.0, 1.0
 
 
@@ -194 +263 @@
     n=4,
     scale=1.0,
-    solvent_sld=1.0,
+    sld_solvent=1.0,
     background=0.0,
     npts_inter=35.0,