Push 6.0.0 docs to website

.buildinfo

@@ -1,4 +1,4 @@
-# Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: fa31d87f544e0cbe6f06c2f39ff5004a
-tags: 645f666f9bcd5a90fca523b33c5a78b7
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: a137ee188497ae683b66cd14ad059f9c
+tags: 645f666f9bcd5a90fca523b33c5a78b7

_downloads/10ed3c9920239a3d8107e1c3ff35d64d/lorentz.c

@@ -0,0 +1,5 @@
+double Iq(double q, double cor_length)
+{
+    double denominator = 1 + (q*cor_length)*(q*cor_length);
+    return 1/denominator;
+}

_downloads/1272b58c6cfe69d71694997b04d09bc5/dab.py

@@ -69,12 +69,7 @@
     ["cor_length", "Ang", 50.0, [0, inf], "", "correlation length"],
     ]
 
-Iq = """
-    double numerator   = cube(cor_length);
-    double denominator = square(1 + square(q*cor_length));
-
-    return numerator / denominator ;
-    """
+source = ["dab.c"]
 
 def random():
     """Return a random parameter set for the model."""

_downloads/1832f7c185470f78530c83e15f9057c9/guinier.c

@@ -0,0 +1,6 @@
+double Iq(double q, double rg)
+{
+    double exponent = fabs(rg)*rg*q*q/3.0;
+    double value = exp(-exponent);
+    return value;
+}

_downloads/2ab21f89819806abac82ca16c56c7451/gaussian_peak.py

@@ -51,10 +51,7 @@
                "Peak width (standard deviation)"],
              ]
 
-Iq = """
-    double scaled_dq = (q - peak_pos)/sigma;
-    return exp(-0.5*scaled_dq*scaled_dq); //sqrt(2*M_PI*sigma*sigma);
-    """
+source = ["gaussian_peak.c"]  
 
 def random():
     """Return a random parameter set for the model."""

_downloads/2b3ff85a3673159026796a2738bfe110/guinier.py

@@ -73,11 +73,8 @@
 #             ["name", "units", default, [lower, upper], "type","description"],
 parameters = [["rg", "Ang", 60.0, [-inf, inf], "", "Radius of Gyration"]]
 
-Iq = """
-    double exponent = fabs(rg)*rg*q*q/3.0;
-    double value = exp(-exponent);
-    return value;
-"""
+source = ["guinier.c"] 
+
 
 def random():
     """Return a random parameter set for the model."""

_downloads/431f2192e6effdcf6fde7c0ce58fa153/stickyhardsphere.c

@@ -0,0 +1,67 @@
+double Iq(double q, double radius_effective, double volfraction, double perturb, double stickiness)
+{
+    double onemineps,eta;
+    double sig,aa,etam1,etam1sq,qa,qb,qc,radic;
+    double lam,lam2,test,mu,alpha,beta;
+    double kk,k2,k3,ds,dc,aq1,aq2,aq3,aq,bq1,bq2,bq3,bq,sq;
+
+    onemineps = 1.0-perturb;
+    eta = volfraction/onemineps/onemineps/onemineps;
+
+    sig = 2.0 * radius_effective;
+    aa = sig/onemineps;
+    etam1 = 1.0 - eta;
+    etam1sq=etam1*etam1;
+    //C
+    //C  SOLVE QUADRATIC FOR LAMBDA
+    //C
+    qa = eta/6.0;
+    qb = stickiness + eta/etam1;
+    qc = (1.0 + eta/2.0)/etam1sq;
+    radic = qb*qb - 2.0*qa*qc;
+    if(radic<0) {
+        //if(x>0.01 && x<0.015)
+        //    Print "Lambda unphysical - both roots imaginary"
+        //endif
+        return(-1.0);
+    }
+    //C   KEEP THE SMALLER ROOT, THE LARGER ONE IS UNPHYSICAL
+    radic = sqrt(radic);
+    lam = (qb-radic)/qa;
+    lam2 = (qb+radic)/qa;
+    if(lam2<lam) {
+        lam = lam2;
+    }
+    test = 1.0 + 2.0*eta;
+    mu = lam*eta*etam1;
+    if(mu>test) {
+        //if(x>0.01 && x<0.015)
+        // Print "Lambda unphysical mu>test"
+        //endif
+        return(-1.0);
+    }
+    alpha = (1.0 + 2.0*eta - mu)/etam1sq;
+    beta = (mu - 3.0*eta)/(2.0*etam1sq);
+    //C
+    //C   CALCULATE THE STRUCTURE FACTOR
+    //C
+    kk = q*aa;
+    k2 = kk*kk;
+    k3 = kk*k2;
+    SINCOS(kk,ds,dc);
+    //ds = sin(kk);
+    //dc = cos(kk);
+    aq1 = ((ds - kk*dc)*alpha)/k3;
+    aq2 = (beta*(1.0-dc))/k2;
+    aq3 = (lam*ds)/(12.0*kk);
+    aq = 1.0 + 12.0*eta*(aq1+aq2-aq3);
+    //
+    bq1 = alpha*(0.5/kk - ds/k2 + (1.0 - dc)/k3);
+    bq2 = beta*(1.0/kk - ds/k2);
+    bq3 = (lam/12.0)*((1.0 - dc)/kk);
+    bq = 12.0*eta*(bq1+bq2-bq3);
+    //
+    sq = 1.0/(aq*aq +bq*bq);
+
+    return(sq);
+}

_downloads/4a33d5085b9d749a6a7666774e071974/hardsphere.py

@@ -87,91 +87,7 @@
                "volume fraction of hard spheres"],
              ]
 
-Iq = r"""
-      double D,A,B,G,X,X2,X4,S,C,FF,HARDSPH;
-      // these are c compiler instructions, can also put normal code inside the "if else" structure
-      #if FLOAT_SIZE > 4
-      // double precision
-      // orig had 0.2, don't call the variable cutoff as PAK already has one called that!
-      // Must use UPPERCASE name please.
-      // 0.05 better, 0.1 OK
-      #define CUTOFFHS 0.05
-      #else
-      // 0.1 bad, 0.2 OK, 0.3 good, 0.4 better, 0.8 no good
-      #define CUTOFFHS 0.4
-      #endif
-
-      if(fabs(radius_effective) < 1.E-12) {
-               HARDSPH=1.0;
-//printf("HS1 %g: %g\n",q,HARDSPH);
-               return(HARDSPH);
-      }
-      // removing use of pow(xxx,2) and rearranging the calcs
-      // of A, B & G cut ~40% off execution time ( 0.5 to 0.3 msec)
-      X = 1.0/( 1.0 -volfraction);
-      D= X*X;
-      A= (1.+2.*volfraction)*D;
-      A *=A;
-      X=fabs(q*radius_effective*2.0);
-
-      if(X < 5.E-06) {
-                 HARDSPH=1./A;
-//printf("HS2 %g: %g\n",q,HARDSPH);
-                 return(HARDSPH);
-      }
-      X2 =X*X;
-      B = (1.0 +0.5*volfraction)*D;
-      B *= B;
-      B *= -6.*volfraction;
-      G=0.5*volfraction*A;
-
-      if(X < CUTOFFHS) {
-      // RKH Feb 2016, use Taylor series expansion for small X
-      // else no obvious way to rearrange the equations to avoid
-      // needing a very high number of significant figures.
-      // Series expansion found using Mathematica software. Numerical test
-      // in .xls showed terms to X^2 are sufficient
-      // for 5 or 6 significant figures, but I put the X^4 one in anyway
-            //FF = 8*A +6*B + 4*G - (0.8*A +2.0*B/3.0 +0.5*G)*X2 +(A/35. +B/40. +G/50.)*X4;
-            // refactoring the polynomial makes it very slightly faster (0.5 not 0.6 msec)
-            //FF = 8*A +6*B + 4*G + ( -0.8*A -2.0*B/3.0 -0.5*G +(A/35. +B/40. +G/50.)*X2)*X2;
-
-            FF = 8.0*A +6.0*B + 4.0*G + ( -0.8*A -B/1.5 -0.5*G +(A/35. +0.0125*B +0.02*G)*X2)*X2;
-
-            // combining the terms makes things worse at smallest Q in single precision
-            //FF = (8-0.8*X2)*A +(3.0-X2/3.)*2*B + (4+0.5*X2)*G +(A/35. +B/40. +G/50.)*X4;
-            // note that G = -volfraction*A/2, combining this makes no further difference at smallest Q
-            //FF = (8 +2.*volfraction + ( volfraction/4. -0.8 +(volfraction/100. -1./35.)*X2 )*X2 )*A  + (3.0 -X2/3. +X4/40.)*2.*B;
-            HARDSPH= 1./(1. + volfraction*FF );
-//printf("HS3 %g: %g\n",q,HARDSPH);
-            return(HARDSPH);
-      }
-      X4=X2*X2;
-      SINCOS(X,S,C);
-
-// RKH Feb 2016, use version FISH code as is better than original sasview one
-// at small Q in single precision, and more than twice as fast in double.
-      //FF=A*(S-X*C)/X + B*(2.*X*S -(X2-2.)*C -2.)/X2 + G*( (4.*X2*X -24.*X)*S -(X4 -12.*X2 +24.)*C +24. )/X4;
-      // refactoring the polynomial here & above makes it slightly faster
-
-      FF=  (( G*( (4.*X2 -24.)*X*S -(X4 -12.*X2 +24.)*C +24. )/X2 + B*(2.*X*S -(X2-2.)*C -2.) )/X + A*(S-X*C))/X ;
-      HARDSPH= 1./(1. + 24.*volfraction*FF/X2 );
-
-      // changing /X and /X2 to *MX1 and *MX2, no significantg difference?
-      //MX=1.0/X;
-      //MX2=MX*MX;
-      //FF=  (( G*( (4.*X2 -24.)*X*S -(X4 -12.*X2 +24.)*C +24. )*MX2 + B*(2.*X*S -(X2-2.)*C -2.) )*MX + A*(S-X*C)) ;
-      //HARDSPH= 1./(1. + 24.*volfraction*FF*MX2*MX );
-
-// grouping the terms, was about same as sasmodels for single precision issues
-//     FF=A*(S/X-C) + B*(2.*S/X - C +2.0*(C-1.0)/X2) + G*( (4./X -24./X3)*S -(1.0 -12./X2 +24./X4)*C +24./X4 );
-//     HARDSPH= 1./(1. + 24.*volfraction*FF/X2 );
-// remove 1/X2 from final line, take more powers of X inside the brackets, stil bad
-//      FF=A*(S/X3-C/X2) + B*(2.*S/X3 - C/X2 +2.0*(C-1.0)/X4) + G*( (4./X -24./X3)*S -(1.0 -12./X2 +24./X4)*C +24./X4 )/X2;
-//      HARDSPH= 1./(1. + 24.*volfraction*FF );
-//printf("HS4 %g: %g\n",q,HARDSPH);
-      return(HARDSPH);
-   """
+source = ["hardsphere.c"]
 
 def random():
     """Return a random parameter set for the model."""
@@ -186,7 +102,7 @@ def random():
 # assuming double precision sasview is correct
 tests = [
     [{'scale': 1.0, 'background' : 0.0, 'radius_effective' : 50.0,
-      'volfraction' : 0.2, 'radius_effective_pd' : 0},
+      'volfraction' : 0.2},
      [0.001, 0.1], [0.209128, 0.930587]],
 ]
 # ADDED by: RKH  ON: 16Mar2016  using equations from FISH as better than

_downloads/57e047d7d856212490d4cb0b056f7a2a/stickyhardsphere.py

@@ -120,6 +120,14 @@
      "stickiness, epsilon"],
     ]
 
+source = ["stickyhardsphere.c"]    
+
+# No volume normalization despite having a volume parameter
+# This should perhaps be volume normalized?
+form_volume = """
+    return 1.0;
+    """
+
 def random():
     """Return a random parameter set for the model."""
     pars = dict(
@@ -131,78 +139,7 @@ def random():
     )
     return pars
 
-# No volume normalization despite having a volume parameter
-# This should perhaps be volume normalized?
-form_volume = """
-    return 1.0;
-    """
 
-Iq = """
-    double onemineps,eta;
-    double sig,aa,etam1,etam1sq,qa,qb,qc,radic;
-    double lam,lam2,test,mu,alpha,beta;
-    double kk,k2,k3,ds,dc,aq1,aq2,aq3,aq,bq1,bq2,bq3,bq,sq;
-
-    onemineps = 1.0-perturb;
-    eta = volfraction/onemineps/onemineps/onemineps;
-
-    sig = 2.0 * radius_effective;
-    aa = sig/onemineps;
-    etam1 = 1.0 - eta;
-    etam1sq=etam1*etam1;
-    //C
-    //C  SOLVE QUADRATIC FOR LAMBDA
-    //C
-    qa = eta/6.0;
-    qb = stickiness + eta/etam1;
-    qc = (1.0 + eta/2.0)/etam1sq;
-    radic = qb*qb - 2.0*qa*qc;
-    if(radic<0) {
-        //if(x>0.01 && x<0.015)
-        //    Print "Lambda unphysical - both roots imaginary"
-        //endif
-        return(-1.0);
-    }
-    //C   KEEP THE SMALLER ROOT, THE LARGER ONE IS UNPHYSICAL
-    radic = sqrt(radic);
-    lam = (qb-radic)/qa;
-    lam2 = (qb+radic)/qa;
-    if(lam2<lam) {
-        lam = lam2;
-    }
-    test = 1.0 + 2.0*eta;
-    mu = lam*eta*etam1;
-    if(mu>test) {
-        //if(x>0.01 && x<0.015)
-        // Print "Lambda unphysical mu>test"
-        //endif
-        return(-1.0);
-    }
-    alpha = (1.0 + 2.0*eta - mu)/etam1sq;
-    beta = (mu - 3.0*eta)/(2.0*etam1sq);
-    //C
-    //C   CALCULATE THE STRUCTURE FACTOR
-    //C
-    kk = q*aa;
-    k2 = kk*kk;
-    k3 = kk*k2;
-    SINCOS(kk,ds,dc);
-    //ds = sin(kk);
-    //dc = cos(kk);
-    aq1 = ((ds - kk*dc)*alpha)/k3;
-    aq2 = (beta*(1.0-dc))/k2;
-    aq3 = (lam*ds)/(12.0*kk);
-    aq = 1.0 + 12.0*eta*(aq1+aq2-aq3);
-    //
-    bq1 = alpha*(0.5/kk - ds/k2 + (1.0 - dc)/k3);
-    bq2 = beta*(1.0/kk - ds/k2);
-    bq3 = (lam/12.0)*((1.0 - dc)/kk);
-    bq = 12.0*eta*(bq1+bq2-bq3);
-    //
-    sq = 1.0/(aq*aq +bq*bq);
-
-    return(sq);
-"""
 
 #
 tests = [

_downloads/651a5546e8d4a3cd3674d51ad8b97dd3/lamellar_hg.py

@@ -29,7 +29,7 @@
 and $\Delta\rho_T$ is tail contrast (*sld* $-$ *sld_solvent*).
 
 The total thickness of the lamellar sheet is
-a_H + \delta_T + \delta_T + \delta_H$. Note that in a non aqueous solvent
+$a_H + \delta_T + \delta_T + \delta_H$. Note that in a non aqueous solvent
 the chemical "head" group may be the "Tail region" and vice-versa.
 
 The 2D scattering intensity is calculated in the same way as 1D, where
@@ -86,23 +86,7 @@
     return 1.0;
     """
 
-Iq = """
-    const double qsq = q*q;
-    const double drh = sld_head - sld_solvent;
-    const double drt = sld - sld_solvent;    //correction 13FEB06 by L.Porcar
-    const double qT = q*length_tail;
-    double Pq, inten;
-    Pq = drh*(sin(q*(length_head+length_tail))-sin(qT)) + drt*sin(qT);
-    Pq *= Pq;
-    Pq *= 4.0/(qsq);
-
-    inten = 2.0e-4*M_PI*Pq/qsq;
-
-    // normalize by the bilayer thickness
-    inten /= 2.0*(length_head+length_tail);
-
-    return inten;
-    """
+source = ["lamellar_hg.c"]
 
 def random():
     """Return a random parameter set for the model."""