Changeset eb97b11 in sasmodels for sasmodels/models/spherical_sld.py

Timestamp:

Apr 18, 2016 8:22:12 AM (8 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

File:

• sasmodels/models/spherical_sld.py (modified) (1 diff)

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