Changeset eb97b11 in sasmodels

Timestamp:

Apr 18, 2016 8:22:12 AM (9 years ago)

Author:

wojciech

Branches:

master, core_shell_microgels, costrafo411, magnetic_model, release_v0.94, release_v0.95, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests

Children:

4605bf10

Parents:

f2f67a6

Message:

Profile function clean-up

Location:

sasmodels/models

Files:

• lib/librefl.c (added)
• spherical_sld.c (modified) (6 diffs)
• spherical_sld.py (modified) (1 diff)

sasmodels/models/spherical_sld.c

@@ -5 +5 @@
     int n_shells);
 
-double Iq(double q,
+static double Iq(double q,
     int n_shells,
     double thick_inter[],
@@ -17 +17 @@
     double core_radius);
 
-double Iqxy(double qx, double qy,
+static double Iqxy(double qx, double qy,
     int n_shells,
     double thick_inter[],
@@ -56 +56 @@
   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 +63 @@
   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 +162 @@
             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);
             }
           }
@@ -285 +273 @@
 
     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, thick_inter[], func_inter[], sld_core, sld_solvent,
+    sld_flat[], thick_flat[],nu_inter[], npts_inter, core_radius)
+
+}
+

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"],
               ["radius_core",      "Ang",            50.0,   [0, inf],       "", "intern layer thickness"],
               ["sld_core",         "1e-6/Ang^2",     2.07,   [-inf, inf],    "", "sld function flat"],
+              ["sld_solvent",      "1e-6/Ang^2",     1.0,    [-inf, inf],    "", "sld function solvent"],
               ["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"],
+              ["nu_inter[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"],
               ]
 # 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.
+    """
+
+    #total_radius = 1.25*(sum(thickness[:n_shells]) + core_radius + 1)
+    #dr = total_radius/400  # 400 points for a smooth plot
+
+    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
+    # put sld of solvent
+    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