Ticket 1156: rename dnn to lattice spacing for paracrystalline models

sasmodels/convert.py

@@ -168,9 +168,16 @@ def _hand_convert(name, oldpars, version=(3, 1, 2)):
     if version == (3, 1, 2):
         oldpars = _hand_convert_3_1_2_to_4_1(name, oldpars)
     if version < (4, 2, 0):
+        oldpars = _hand_convert_4_1_to_4_2(name, oldpars)
         oldpars = _rename_magnetic_pars(oldpars)
     return oldpars
 
+def _hand_convert_4_1_to_4_2(name, oldpars):
+    if name in ('bcc_paracrystal', 'fcc_paracrystal', 'sc_paracrystal'):
+        oldpars['lattice_spacing'] = oldpars.pop('dnn')
+        oldpars['lattice_distortion'] = oldpars.pop('d_factor')
+    return oldpars
+
 def _rename_magnetic_pars(pars):
     """
     Change from M0:par to par_M0, etc.

sasmodels/models/bcc_paracrystal.c

@@ -1,5 +1,5 @@
 static double
-bcc_Zq(double qa, double qb, double qc, double dnn, double d_factor)
+bcc_Zq(double qa, double qb, double qc, double lattice_spacing, double lattice_distortion)
 {
     // Equations from Matsuoka 26-27-28, multiplied by |q|
     const double a1 = (-qa + qb + qc)/2.0;
@@ -16,12 +16,12 @@ bcc_Zq(double qa, double qb, double qc, double dnn, double d_factor)
     // Rewriting denominator
     //         => exp(a)^2 - 2 cos(d ak) exp(a) + 1)
     //         => (exp(a) - 2 cos(d ak)) * exp(a) + 1
-    const double arg = -0.5*square(dnn*d_factor)*(a1*a1 + a2*a2 + a3*a3);
+    const double arg = -0.5*square(lattice_spacing*lattice_distortion)*(a1*a1 + a2*a2 + a3*a3);
     const double exp_arg = exp(arg);
     const double Zq = -cube(expm1(2.0*arg))
-        / ( ((exp_arg - 2.0*cos(dnn*a1))*exp_arg + 1.0)
-          * ((exp_arg - 2.0*cos(dnn*a2))*exp_arg + 1.0)
-          * ((exp_arg - 2.0*cos(dnn*a3))*exp_arg + 1.0));
+        / ( ((exp_arg - 2.0*cos(lattice_spacing*a1))*exp_arg + 1.0)
+          * ((exp_arg - 2.0*cos(lattice_spacing*a2))*exp_arg + 1.0)
+          * ((exp_arg - 2.0*cos(lattice_spacing*a3))*exp_arg + 1.0));
 
 #elif 0
     // ** Alternate form, which perhaps is more approachable
@@ -35,19 +35,19 @@ bcc_Zq(double qa, double qb, double qc, double dnn, double d_factor)
     // One more step leads to the form in sasview 3.x for 2d models
     //            = tanh(-a) / [1 - cos(d a_k)/cosh(-a)]
     //
-    const double arg = 0.5*square(dnn*d_factor)*(a1*a1 + a2*a2 + a3*a3);
+    const double arg = 0.5*square(lattice_spacing*lattice_distortion)*(a1*a1 + a2*a2 + a3*a3);
     const double sinh_qd = sinh(arg);
     const double cosh_qd = cosh(arg);
-    const double Zq = sinh_qd/(cosh_qd - cos(dnn*a1))
-                    * sinh_qd/(cosh_qd - cos(dnn*a2))
-                    * sinh_qd/(cosh_qd - cos(dnn*a3));
+    const double Zq = sinh_qd/(cosh_qd - cos(lattice_spacing*a1))
+                    * sinh_qd/(cosh_qd - cos(lattice_spacing*a2))
+                    * sinh_qd/(cosh_qd - cos(lattice_spacing*a3));
 #else
-    const double arg = 0.5*square(dnn*d_factor)*(a1*a1 + a2*a2 + a3*a3);
+    const double arg = 0.5*square(lattice_spacing*lattice_distortion)*(a1*a1 + a2*a2 + a3*a3);
     const double tanh_qd = tanh(arg);
     const double cosh_qd = cosh(arg);
-    const double Zq = tanh_qd/(1.0 - cos(dnn*a1)/cosh_qd)
-                    * tanh_qd/(1.0 - cos(dnn*a2)/cosh_qd)
-                    * tanh_qd/(1.0 - cos(dnn*a3)/cosh_qd);
+    const double Zq = tanh_qd/(1.0 - cos(lattice_spacing*a1)/cosh_qd)
+                    * tanh_qd/(1.0 - cos(lattice_spacing*a2)/cosh_qd)
+                    * tanh_qd/(1.0 - cos(lattice_spacing*a3)/cosh_qd);
 #endif
 
     return Zq;
@@ -56,9 +56,9 @@ bcc_Zq(double qa, double qb, double qc, double dnn, double d_factor)
 
 // occupied volume fraction calculated from lattice symmetry and sphere radius
 static double
-bcc_volume_fraction(double radius, double dnn)
+bcc_volume_fraction(double radius, double lattice_spacing)
 {
-    return 2.0*sphere_volume(sqrt(0.75)*radius/dnn);
+    return 2.0*sphere_volume(radius/lattice_spacing);
 }
 
 static double
@@ -68,8 +68,8 @@ form_volume(double radius)
 }
 
 
-static double Iq(double q, double dnn,
-    double d_factor, double radius,
+static double Iq(double q, double lattice_spacing,
+    double lattice_distortion, double radius,
     double sld, double solvent_sld)
 {
     // translate a point in [-1,1] to a point in [0, 2 pi]
@@ -93,7 +93,7 @@ static double Iq(double q, double dnn,
             SINCOS(phi, sin_phi, cos_phi);
             const double qa = qab*cos_phi;
             const double qb = qab*sin_phi;
-            const double form = bcc_Zq(qa, qb, qc, dnn, d_factor);
+            const double form = bcc_Zq(qa, qb, qc, lattice_spacing, lattice_distortion);
             inner_sum += GAUSS_W[j] * form;
         }
         inner_sum *= phi_m;  // sum(f(x)dx) = sum(f(x)) dx
@@ -102,16 +102,16 @@ static double Iq(double q, double dnn,
     outer_sum *= theta_m;
     const double Zq = outer_sum/(4.0*M_PI);
     const double Pq = sphere_form(q, radius, sld, solvent_sld);
-    return bcc_volume_fraction(radius, dnn) * Pq * Zq;
+    return bcc_volume_fraction(radius, lattice_spacing) * Pq * Zq;
 }
 
 
 static double Iqabc(double qa, double qb, double qc,
-    double dnn, double d_factor, double radius,
+    double lattice_spacing, double lattice_distortion, double radius,
     double sld, double solvent_sld)
 {
     const double q = sqrt(qa*qa + qb*qb + qc*qc);
-    const double Zq = bcc_Zq(qa, qb, qc, dnn, d_factor);
+    const double Zq = bcc_Zq(qa, qb, qc, lattice_spacing, lattice_distortion);
     const double Pq = sphere_form(q, radius, sld, solvent_sld);
-    return bcc_volume_fraction(radius, dnn) * Pq * Zq;
+    return bcc_volume_fraction(radius, lattice_spacing) * Pq * Zq;
 }

sasmodels/models/bcc_paracrystal.py

@@ -33,7 +33,7 @@
 
 .. math::
 
-    V_\text{lattice} = \frac{16\pi}{3} \frac{R^3}{\left(D\sqrt{2}\right)^3}
+    V_\text{lattice} = \frac{8\pi}{3} \frac{R^3}{\left(2D/\sqrt{3}\right)^3}
 
 
 The distortion factor (one standard deviation) of the paracrystal is included
@@ -104,7 +104,7 @@
 
 * **Author:** NIST IGOR/DANSE **Date:** pre 2010
 * **Last Modified by:** Paul Butler **Date:** September 29, 2016
-* **Last Reviewed by:** Richard Heenan **Date:** March 21, 2016
+* **Last Reviewed by:** Paul Butler **Date:** September 16, 2018
 """
 
 import numpy as np
@@ -126,8 +126,8 @@
 
 # pylint: disable=bad-whitespace, line-too-long
 #             ["name", "units", default, [lower, upper], "type","description" ],
-parameters = [["dnn",         "Ang",       220,    [-inf, inf], "",            "Nearest neighbour distance"],
-              ["d_factor",    "",            0.06, [-inf, inf], "",            "Paracrystal distortion factor"],
+parameters = [["lattice_spacing",         "Ang",       220,    [-inf, inf], "",            "Lattice spacing"],
+              ["lattice_distortion",    "",            0.06, [-inf, inf], "",            "Paracrystal distortion factor"],
               ["radius",      "Ang",        40,    [0, inf],    "volume",      "Particle radius"],
               ["sld",         "1e-6/Ang^2",  4,    [-inf, inf], "sld",         "Particle scattering length density"],
               ["sld_solvent", "1e-6/Ang^2",  1,    [-inf, inf], "sld",         "Solvent scattering length density"],
@@ -149,13 +149,13 @@ def random():
     # useful between 0.01 and 0.7.  Use an exponential distribution
     # in this range 'cuz its easy.
     radius = 10**np.random.uniform(1.3, 4)
-    d_factor = 10**np.random.uniform(-2, -0.7)  # sigma_d in 0.01-0.7
-    dnn_fraction = np.random.beta(a=10, b=1)
-    dnn = radius*4/np.sqrt(3)/dnn_fraction
+    lattice_distortion = 10**np.random.uniform(-2, -0.7)  # sigma_d in 0.01-0.7
+    lattice_spacing_fraction = np.random.beta(a=10, b=1)
+    lattice_spacing = radius*4/np.sqrt(3)/lattice_spacing_fraction
     pars = dict(
         #sld=1, sld_solvent=0, scale=1, background=1e-32,
-        dnn=dnn,
-        d_factor=d_factor,
+        lattice_spacing=lattice_spacing,
+        lattice_distortion=lattice_distortion,
         radius=radius,
     )
     return pars

sasmodels/models/fcc_paracrystal.c

@@ -1,5 +1,5 @@
 static double
-fcc_Zq(double qa, double qb, double qc, double dnn, double d_factor)
+fcc_Zq(double qa, double qb, double qc, double lattice_spacing, double lattice_distortion)
 {
     // Equations from Matsuoka 17-18-19, multiplied by |q|
     const double a1 = ( qa + qb)/2.0;
@@ -15,22 +15,22 @@ fcc_Zq(double qa, double qb, double qc, double dnn, double d_factor)
     // Rewriting denominator
     //         => exp(a)^2 - 2 cos(d ak) exp(a) + 1)
     //         => (exp(a) - 2 cos(d ak)) * exp(a) + 1
-    const double arg = -0.5*square(dnn*d_factor)*(a1*a1 + a2*a2 + a3*a3);
+    const double arg = -0.5*square(lattice_spacing*lattice_distortion)*(a1*a1 + a2*a2 + a3*a3);
     const double exp_arg = exp(arg);
     const double Zq = -cube(expm1(2.0*arg))
-        / ( ((exp_arg - 2.0*cos(dnn*a1))*exp_arg + 1.0)
-          * ((exp_arg - 2.0*cos(dnn*a2))*exp_arg + 1.0)
-          * ((exp_arg - 2.0*cos(dnn*a3))*exp_arg + 1.0));
+        / ( ((exp_arg - 2.0*cos(lattice_spacing*a1))*exp_arg + 1.0)
+          * ((exp_arg - 2.0*cos(lattice_spacing*a2))*exp_arg + 1.0)
+          * ((exp_arg - 2.0*cos(lattice_spacing*a3))*exp_arg + 1.0));
 
     return Zq;
 }
 
 
 // occupied volume fraction calculated from lattice symmetry and sphere radius
 static double
-fcc_volume_fraction(double radius, double dnn)
+fcc_volume_fraction(double radius, double lattice_spacing)
 {
-    return 4.0*sphere_volume(M_SQRT1_2*radius/dnn);
+    return 4.0*sphere_volume(radius/lattice_spacing);
 }
 
 static double
@@ -40,8 +40,8 @@ form_volume(double radius)
 }
 
 
-static double Iq(double q, double dnn,
-  double d_factor, double radius,
+static double Iq(double q, double lattice_spacing,
+  double lattice_distortion, double radius,
   double sld, double solvent_sld)
 {
     // translate a point in [-1,1] to a point in [0, 2 pi]
@@ -65,7 +65,7 @@ static double Iq(double q, double dnn,
             SINCOS(phi, sin_phi, cos_phi);
             const double qa = qab*cos_phi;
             const double qb = qab*sin_phi;
-            const double form = fcc_Zq(qa, qb, qc, dnn, d_factor);
+            const double form = fcc_Zq(qa, qb, qc, lattice_spacing, lattice_distortion);
             inner_sum += GAUSS_W[j] * form;
         }
         inner_sum *= phi_m;  // sum(f(x)dx) = sum(f(x)) dx
@@ -75,15 +75,15 @@ static double Iq(double q, double dnn,
     const double Zq = outer_sum/(4.0*M_PI);
     const double Pq = sphere_form(q, radius, sld, solvent_sld);
 
-    return fcc_volume_fraction(radius, dnn) * Pq * Zq;
+    return fcc_volume_fraction(radius, lattice_spacing) * Pq * Zq;
 }
 
 static double Iqabc(double qa, double qb, double qc,
-    double dnn, double d_factor, double radius,
+    double lattice_spacing, double lattice_distortion, double radius,
     double sld, double solvent_sld)
 {
     const double q = sqrt(qa*qa + qb*qb + qc*qc);
     const double Pq = sphere_form(q, radius, sld, solvent_sld);
-    const double Zq = fcc_Zq(qa, qb, qc, dnn, d_factor);
-    return fcc_volume_fraction(radius, dnn) * Pq * Zq;
-}
+    const double Zq = fcc_Zq(qa, qb, qc, lattice_spacing, lattice_distortion);
+    return fcc_volume_fraction(radius, lattice_spacing) * Pq * Zq;
+}

sasmodels/models/fcc_paracrystal.py

@@ -99,11 +99,11 @@
    (Corrections to FCC and BCC lattice structure calculation)
 
 Authorship and Verification
----------------------------
+----------------------------
 
 * **Author:** NIST IGOR/DANSE **Date:** pre 2010
 * **Last Modified by:** Paul Butler **Date:** September 29, 2016
-* **Last Reviewed by:** Richard Heenan **Date:** March 21, 2016
+* **Last Modified by:** Paul Butler **Date:** September 16, 2018
 """
 
 import numpy as np
@@ -122,8 +122,8 @@
 
 # pylint: disable=bad-whitespace, line-too-long
 #             ["name", "units", default, [lower, upper], "type","description"],
-parameters = [["dnn", "Ang", 220, [-inf, inf], "", "Nearest neighbour distance"],
-              ["d_factor", "", 0.06, [-inf, inf], "", "Paracrystal distortion factor"],
+parameters = [["lattice_spacing", "Ang", 220, [-inf, inf], "", "Lattice spacing"],
+              ["lattice_distortion", "", 0.06, [-inf, inf], "", "Paracrystal distortion factor"],
               ["radius", "Ang", 40, [0, inf], "volume", "Particle radius"],
               ["sld", "1e-6/Ang^2", 4, [-inf, inf], "sld", "Particle scattering length density"],
               ["sld_solvent", "1e-6/Ang^2", 1, [-inf, inf], "sld", "Solvent scattering length density"],
@@ -139,13 +139,13 @@ def random():
     """Return a random parameter set for the model."""
     # copied from bcc_paracrystal
     radius = 10**np.random.uniform(1.3, 4)
-    d_factor = 10**np.random.uniform(-2, -0.7)  # sigma_d in 0.01-0.7
-    dnn_fraction = np.random.beta(a=10, b=1)
-    dnn = radius*4/np.sqrt(2)/dnn_fraction
+    lattice_distortion = 10**np.random.uniform(-2, -0.7)  # sigma_d in 0.01-0.7
+    lattice_spacing_fraction = np.random.beta(a=10, b=1)
+    lattice_spacing = radius*4/np.sqrt(2)/lattice_spacing_fraction
     pars = dict(
         #sld=1, sld_solvent=0, scale=1, background=1e-32,
-        dnn=dnn,
-        d_factor=d_factor,
+        latice_spacing=lattice_spacing,
+        lattice_distortion=d_factor,
         radius=radius,
     )
     return pars

sasmodels/models/sc_paracrystal.c

@@ -1,5 +1,5 @@
 static double
-sc_Zq(double qa, double qb, double qc, double dnn, double d_factor)
+sc_Zq(double qa, double qb, double qc, double lattice_spacing, double lattice_distortion)
 {
     // Equations from Matsuoka 9-10-11, multiplied by |q|
     const double a1 = qa;
@@ -15,21 +15,21 @@ sc_Zq(double qa, double qb, double qc, double dnn, double d_factor)
     // Rewriting denominator
     //         => exp(a)^2 - 2 cos(d ak) exp(a) + 1)
     //         => (exp(a) - 2 cos(d ak)) * exp(a) + 1
-    const double arg = -0.5*square(dnn*d_factor)*(a1*a1 + a2*a2 + a3*a3);
+    const double arg = -0.5*square(lattice_spacing*lattice_distortion)*(a1*a1 + a2*a2 + a3*a3);
     const double exp_arg = exp(arg);
     const double Zq = -cube(expm1(2.0*arg))
-        / ( ((exp_arg - 2.0*cos(dnn*a1))*exp_arg + 1.0)
-          * ((exp_arg - 2.0*cos(dnn*a2))*exp_arg + 1.0)
-          * ((exp_arg - 2.0*cos(dnn*a3))*exp_arg + 1.0));
+        / ( ((exp_arg - 2.0*cos(lattice_spacing*a1))*exp_arg + 1.0)
+          * ((exp_arg - 2.0*cos(lattice_spacing*a2))*exp_arg + 1.0)
+          * ((exp_arg - 2.0*cos(lattice_spacing*a3))*exp_arg + 1.0));
 
     return Zq;
 }
 
 // occupied volume fraction calculated from lattice symmetry and sphere radius
 static double
-sc_volume_fraction(double radius, double dnn)
+sc_volume_fraction(double radius, double lattice_spacing)
 {
-    return sphere_volume(radius/dnn);
+    return sphere_volume(radius/lattice_spacing);
 }
 
 static double
@@ -40,8 +40,8 @@ form_volume(double radius)
 
 
 static double
-Iq(double q, double dnn,
-    double d_factor, double radius,
+Iq(double q, double lattice_spacing,
+    double lattice_distortion, double radius,
     double sld, double solvent_sld)
 {
     // translate a point in [-1,1] to a point in [0, 2 pi]
@@ -66,7 +66,7 @@ Iq(double q, double dnn,
             SINCOS(phi, sin_phi, cos_phi);
             const double qa = qab*cos_phi;
             const double qb = qab*sin_phi;
-            const double form = sc_Zq(qa, qb, qc, dnn, d_factor);
+            const double form = sc_Zq(qa, qb, qc, lattice_spacing, lattice_distortion);
             inner_sum += GAUSS_W[j] * form;
         }
         inner_sum *= phi_m;  // sum(f(x)dx) = sum(f(x)) dx
@@ -76,16 +76,16 @@ Iq(double q, double dnn,
     const double Zq = outer_sum/M_PI_2;
     const double Pq = sphere_form(q, radius, sld, solvent_sld);
 
-    return sc_volume_fraction(radius, dnn) * Pq * Zq;
+    return sc_volume_fraction(radius, lattice_spacing) * Pq * Zq;
 }
 
 static double
 Iqabc(double qa, double qb, double qc,
-    double dnn, double d_factor, double radius,
+    double lattice_spacing, double lattice_distortion, double radius,
     double sld, double solvent_sld)
 {
     const double q = sqrt(qa*qa + qb*qb + qc*qc);
     const double Pq = sphere_form(q, radius, sld, solvent_sld);
-    const double Zq = sc_Zq(qa, qb, qc, dnn, d_factor);
-    return sc_volume_fraction(radius, dnn) * Pq * Zq;
-}
+    const double Zq = sc_Zq(qa, qb, qc, lattice_spacing, lattice_distortion);
+    return sc_volume_fraction(radius, lattice_spacing) * Pq * Zq;
+}