Index: sansmodels/src/sans/models/libigor/libCylinder.c
===================================================================
--- sansmodels/src/sans/models/libigor/libCylinder.c	(revision 34c2649bfe75da15bbebf2ffea0e086db7ad6320)
+++ sansmodels/src/sans/models/libigor/libCylinder.c	(revision 5f0dcab5458a4b59903104d524321c74b70f291c)
@@ -8,4 +8,404 @@
 #include "GaussWeights.h"
 #include "libCylinder.h"
+
+/////////functions for WRC implementation of flexible cylinders
+static double
+gammaln(double xx)
+{
+  double x,y,tmp,ser;
+  static double cof[6]={76.18009172947146,-86.50532032941677,
+    24.01409824083091,-1.231739572450155,
+    0.1208650973866179e-2,-0.5395239384953e-5};
+  int j;
+
+  y=x=xx;
+  tmp=x+5.5;
+  tmp -= (x+0.5)*log(tmp);
+  ser=1.000000000190015;
+  for (j=0;j<=5;j++) ser += cof[j]/++y;
+  return -tmp+log(2.5066282746310005*ser/x);
+}
+/////////functions for WRC implementation of flexible cylinders
+
+//
+static double
+AlphaSquare(double x)
+{
+    double yy;
+    yy = pow( (1.0 + (x/3.12)*(x/3.12) + (x/8.67)*(x/8.67)*(x/8.67)),(0.176/3.0) );
+
+    return (yy);
+}
+
+//
+static double
+Rgsquarezero(double q, double L, double b)
+{
+    double yy;
+    yy = (L*b/6.0) * (1.0 - 1.5*(b/L) + 1.5*pow((b/L),2) - 0.75*pow((b/L),3)*(1.0 - exp(-2.0*(L/b))));
+
+    return (yy);
+}
+
+//
+static double
+Rgsquareshort(double q, double L, double b)
+{
+    double yy;
+    yy = AlphaSquare(L/b) * Rgsquarezero(q,L,b);
+
+    return (yy);
+}
+
+//
+static double
+Rgsquare(double q, double L, double b)
+{
+    double yy;
+    yy = AlphaSquare(L/b)*L*b/6.0;
+
+    return (yy);
+}
+
+// ?? funciton is not used - but should the log actually be log10???
+static double
+miu(double x)
+{
+    double yy;
+    yy = (1.0/8.0)*(9.0*x - 2.0 + 2.0*log(1.0 + x)/x)*exp(1.0/2.565*(1.0/x + (1.0 - 1.0/(x*x))*log(1.0 + x)));
+
+    return (yy);
+}
+
+//WR named this w (too generic)
+static double
+w_WR(double x)
+{
+    double yy;
+    yy = 0.5*(1 + tanh((x - 1.523)/0.1477));
+
+    return (yy);
+}
+
+//
+static double
+u1(double q, double L, double b)
+{
+    double yy;
+
+    yy = Rgsquareshort(q,L,b)*q*q;
+
+    return (yy);
+}
+
+// was named u
+static double
+u_WR(double q, double L, double b)
+{
+    double yy;
+    yy = Rgsquare(q,L,b)*q*q;
+    return (yy);
+}
+
+
+//
+static double
+Sdebye1(double q, double L, double b)
+{
+    double yy;
+    yy = 2.0*(exp(-u1(q,L,b)) + u1(q,L,b) -1.0)/( pow((u1(q,L,b)),2.0) );
+
+    return (yy);
+}
+
+
+//
+static double
+Sdebye(double q, double L, double b)
+{
+    double yy;
+    yy = 2.0*(exp(-u_WR(q,L,b)) + u_WR(q,L,b) -1.0)/(pow((u_WR(q,L,b)),2));
+
+    return (yy);
+}
+
+//
+static double
+Sexv(double q, double L, double b)
+{
+    double yy,C1,C2,C3,miu,Rg2;
+    C1=1.22;
+    C2=0.4288;
+    C3=-1.651;
+    miu = 0.585;
+
+    Rg2 = Rgsquare(q,L,b);
+
+    yy = (1.0 - w_WR(q*sqrt(Rg2)))*Sdebye(q,L,b) + w_WR(q*sqrt(Rg2))*(C1*pow((q*sqrt(Rg2)),(-1.0/miu)) +  C2*pow((q*sqrt(Rg2)),(-2.0/miu)) +    C3*pow((q*sqrt(Rg2)),(-3.0/miu)));
+
+    return (yy);
+}
+
+// this must be WR modified version
+static double
+Sexvnew(double q, double L, double b)
+{
+    double yy,C1,C2,C3,miu;
+    double del=1.05,C_star2,Rg2;
+
+    C1=1.22;
+    C2=0.4288;
+    C3=-1.651;
+    miu = 0.585;
+
+    //calculating the derivative to decide on the corection (cutoff) term?
+    // I have modified this from WRs original code
+
+    if( (Sexv(q*del,L,b)-Sexv(q,L,b))/(q*del - q) >= 0.0 ) {
+        C_star2 = 0.0;
+    } else {
+        C_star2 = 1.0;
+    }
+
+    Rg2 = Rgsquare(q,L,b);
+
+  yy = (1.0 - w_WR(q*sqrt(Rg2)))*Sdebye(q,L,b) + C_star2*w_WR(q*sqrt(Rg2))*(C1*pow((q*sqrt(Rg2)),(-1.0/miu)) + C2*pow((q*sqrt(Rg2)),(-2.0/miu)) + C3*pow((q*sqrt(Rg2)),(-3.0/miu)));
+
+    return (yy);
+}
+
+// these are the messy ones
+static double
+a2short(double q, double L, double b, double p1short, double p2short, double q0)
+{
+    double yy,Rg2_sh;
+    double t1,E,Rg2_sh2,Et1,Emt1,q02,q0p;
+    double pi;
+
+    E = 2.718281828459045091;
+  pi = 4.0*atan(1.0);
+    Rg2_sh = Rgsquareshort(q,L,b);
+    Rg2_sh2 = Rg2_sh*Rg2_sh;
+    t1 = ((q0*q0*Rg2_sh)/(b*b));
+    Et1 = pow(E,t1);
+    Emt1 =pow(E,-t1);
+    q02 = q0*q0;
+    q0p = pow(q0,(-4.0 + p2short) );
+
+    //E is the number e
+    yy = ((-(1.0/(L*((p1short - p2short))*Rg2_sh2)*((b*Emt1*q0p*((8.0*b*b*b*L - 8.0*b*b*b*Et1*L - 2.0*b*b*b*L*p1short + 2.0*b*b*b*Et1*L*p1short + 4.0*b*L*q02*Rg2_sh + 4.0*b*Et1*L*q02*Rg2_sh - 2.0*b*Et1*L*p1short*q02*Rg2_sh - Et1*pi*q02*q0*Rg2_sh2 + Et1*p1short*pi*q02*q0*Rg2_sh2)))))));
+
+    return (yy);
+}
+
+//
+static double
+a1short(double q, double L, double b, double p1short, double p2short, double q0)
+{
+    double yy,Rg2_sh;
+    double t1,E,Rg2_sh2,Et1,Emt1,q02,q0p,b3;
+  double pi;
+
+    E = 2.718281828459045091;
+  pi = 4.0*atan(1.0);
+    Rg2_sh = Rgsquareshort(q,L,b);
+    Rg2_sh2 = Rg2_sh*Rg2_sh;
+    b3 = b*b*b;
+    t1 = ((q0*q0*Rg2_sh)/(b*b));
+    Et1 = pow(E,t1);
+    Emt1 =pow(E,-t1);
+    q02 = q0*q0;
+    q0p = pow(q0,(-4.0 + p1short) );
+
+    yy = ((1.0/(L*((p1short - p2short))*Rg2_sh2)*((b*Emt1*q0p*((8.0*b3*L - 8.0*b3*Et1*L - 2.0*b3*L*p2short + 2.0*b3*Et1*L*p2short + 4.0*b*L*q02*Rg2_sh + 4.0*b*Et1*L*q02*Rg2_sh - 2.0*b*Et1*L*p2short*q02*Rg2_sh - Et1*pi*q02*q0*Rg2_sh2 + Et1*p2short*pi*q02*q0*Rg2_sh2))))));
+
+    return(yy);
+}
+
+
+//need to define this on my own
+static double
+sech_WR(double x)
+{
+  return(1/cosh(x));
+}
+
+// this one will be lots of trouble
+static double
+a2long(double q, double L, double b, double p1, double p2, double q0)
+{
+    double yy,C1,C2,C3,C4,C5,miu,C,Rg2;
+    double t1,t2,t3,t4,t5,t6,t7,t8,t9,t10,pi;
+    double E,b2,b3,b4,q02,q03,q04,q05,Rg22;
+
+    pi = 4.0*atan(1.0);
+    E = 2.718281828459045091;
+    if( L/b > 10.0) {
+        C = 3.06/pow((L/b),0.44);
+    } else {
+        C = 1.0;
+    }
+
+    C1 = 1.22;
+    C2 = 0.4288;
+    C3 = -1.651;
+    C4 = 1.523;
+    C5 = 0.1477;
+    miu = 0.585;
+
+    Rg2 = Rgsquare(q,L,b);
+    Rg22 = Rg2*Rg2;
+    b2 = b*b;
+    b3 = b*b*b;
+    b4 = b3*b;
+    q02 = q0*q0;
+    q03 = q0*q0*q0;
+    q04 = q03*q0;
+    q05 = q04*q0;
+
+    t1 = (1.0/(b* p1*pow(q0,((-1.0) - p1 - p2)) - b*p2*pow(q0,((-1.0) - p1 - p2)) ));
+
+    t2 = (b*C*(((-1.0*((14.0*b3)/(15.0*q03*Rg2))) + (14.0*b3*pow(E,(-((q02*Rg2)/b2))))/(15.0*q03*Rg2) + (2.0*pow(E,(-((q02*Rg2)/b2)))*q0*((11.0/15.0 + (7*b2)/(15.0*q02*Rg2)))*Rg2)/b)))/L;
+
+    t3 = (sqrt(Rg2)*((C3*pow((((sqrt(Rg2)*q0)/b)),((-3.0)/miu)) + C2*pow((((sqrt(Rg2)*q0)/b)),((-2.0)/miu)) + C1*pow((((sqrt(Rg2)*q0)/b)),((-1.0)/miu))))*pow(sech_WR(((-C4) + (sqrt(Rg2)*q0)/b)/C5),2.0))/(2.0*C5);
+
+    t4 = (b4*sqrt(Rg2)*(((-1.0) + pow(E,(-((q02*Rg2)/b2))) + (q02*Rg2)/b2))*pow(sech_WR(((-C4) + (sqrt(Rg2)*q0)/b)/C5),2))/(C5*q04*Rg22);
+
+    t5 = (2.0*b4*(((2.0*q0*Rg2)/b - (2.0*pow(E,(-((q02*Rg2)/b2)))*q0*Rg2)/b))*((1.0 + 1.0/2.0*(((-1.0) - tanh(((-C4) + (sqrt(Rg2)*q0)/b)/C5))))))/(q04*Rg22);
+
+    t6 = (8.0*b4*b*(((-1.0) + pow(E,(-((q02*Rg2)/b2))) + (q02*Rg2)/b2))*((1.0 + 1.0/2.0*(((-1) - tanh(((-C4) + (sqrt(Rg2)*q0)/b)/C5))))))/(q05*Rg22);
+
+    t7 = (((-((3.0*C3*sqrt(Rg2)*pow((((sqrt(Rg2)*q0)/b)),((-1.0) - 3.0/miu)))/miu)) - (2.0*C2*sqrt(Rg2)*pow((((sqrt(Rg2)*q0)/b)),((-1.0) - 2.0/miu)))/miu - (C1*sqrt(Rg2)*pow((((sqrt(Rg2)*q0)/b)),((-1.0) - 1.0/miu)))/miu));
+
+    t8 = ((1.0 + tanh(((-C4) + (sqrt(Rg2)*q0)/b)/C5)));
+
+    t9 = (b*C*((4.0/15.0 - pow(E,(-((q02*Rg2)/b2)))*((11.0/15.0 + (7.0*b2)/(15*q02*Rg2))) + (7.0*b2)/(15.0*q02*Rg2))))/L;
+
+    t10 = (2.0*b4*(((-1) + pow(E,(-((q02*Rg2)/b2))) + (q02*Rg2)/b2))*((1.0 + 1.0/2.0*(((-1) - tanh(((-C4) + (sqrt(Rg2)*q0)/b)/C5))))))/(q04*Rg22);
+
+
+    yy = ((-1.0*(t1* ((-pow(q0,-p1)*(((b2*pi)/(L*q02) + t2 + t3 - t4 + t5 - t6 + 1.0/2.0*t7*t8)) - b*p1*pow(q0,((-1.0) - p1))*(((-((b*pi)/(L*q0))) + t9 + t10 + 1.0/2.0*((C3*pow((((sqrt(Rg2)*q0)/b)),((-3.0)/miu)) + C2*pow((((sqrt(Rg2)*q0)/b)),((-2.0)/miu)) + C1*pow((((sqrt(Rg2)*q0)/b)),((-1.0)/miu))))*((1.0 + tanh(((-C4) + (sqrt(Rg2)*q0)/b)/C5))))))))));
+
+    return (yy);
+}
+//
+static double
+a1long(double q, double L, double b, double p1, double p2, double q0)
+{
+    double yy,C,C1,C2,C3,C4,C5,miu,Rg2;
+    double t1,t2,t3,t4,t5,t6,t7,t8,t9,t10,t11,t12,t13,t14,t15;
+    double E,pi;
+    double b2,b3,b4,q02,q03,q04,q05,Rg22;
+
+    pi = 4.0*atan(1.0);
+    E = 2.718281828459045091;
+
+    if( L/b > 10.0) {
+        C = 3.06/pow((L/b),0.44);
+    } else {
+        C = 1.0;
+    }
+
+    C1 = 1.22;
+    C2 = 0.4288;
+    C3 = -1.651;
+    C4 = 1.523;
+    C5 = 0.1477;
+    miu = 0.585;
+
+    Rg2 = Rgsquare(q,L,b);
+    Rg22 = Rg2*Rg2;
+    b2 = b*b;
+    b3 = b*b*b;
+    b4 = b3*b;
+    q02 = q0*q0;
+    q03 = q0*q0*q0;
+    q04 = q03*q0;
+    q05 = q04*q0;
+
+    t1 = (b*C*((4.0/15.0 - pow(E,(-((q02*Rg2)/b2)))*((11.0/15.0 + (7.0*b2)/(15.0*q02*Rg2))) + (7.0*b2)/(15.0*q02*Rg2))));
+
+    t2 = (2.0*b4*(((-1.0) + pow(E,(-((q02*Rg2)/b2))) + (q02*Rg2)/b2))*((1.0 + 1.0/2.0*(((-1.0) - tanh(((-C4) + (sqrt(Rg2)*q0)/b)/C5))))));
+
+    t3 = ((C3*pow((((sqrt(Rg2)*q0)/b)),((-3.0)/miu)) + C2*pow((((sqrt(Rg2)*q0)/b)),((-2.0)/miu)) + C1*pow((((sqrt(Rg2)*q0)/b)),((-1.0)/miu))));
+
+    t4 = ((1.0 + tanh(((-C4) + (sqrt(Rg2)*q0)/b)/C5)));
+
+    t5 = (1.0/(b*p1*pow(q0,((-1.0) - p1 - p2)) - b*p2*pow(q0,((-1.0) - p1 - p2))));
+
+    t6 = (b*C*(((-((14.0*b3)/(15.0*q03*Rg2))) + (14.0*b3*pow(E,(-((q02*Rg2)/b2))))/(15.0*q03*Rg2) + (2.0*pow(E,(-((q02*Rg2)/b2)))*q0*((11.0/15.0 + (7.0*b2)/(15.0*q02*Rg2)))*Rg2)/b)));
+
+    t7 = (sqrt(Rg2)*((C3*pow((((sqrt(Rg2)*q0)/b)),((-3.0)/miu)) + C2*pow((((sqrt(Rg2)*q0)/b)),((-2.0)/miu)) + C1*pow((((sqrt(Rg2)*q0)/b)),((-1.0)/miu))))*pow(sech_WR(((-C4) + (sqrt(Rg2)*q0)/b)/C5),2));
+
+    t8 = (b4*sqrt(Rg2)*(((-1.0) + pow(E,(-((q02*Rg2)/b2))) + (q02*Rg2)/b2))*pow(sech_WR(((-C4) + (sqrt(Rg2)*q0)/b)/C5),2));
+
+    t9 = (2.0*b4*(((2.0*q0*Rg2)/b - (2.0*pow(E,(-((q02*Rg2)/b2)))*q0*Rg2)/b))*((1.0 + 1.0/2.0*(((-1.0) - tanh(((-C4) + (sqrt(Rg2)*q0)/b)/C5))))));
+
+    t10 = (8.0*b4*b*(((-1.0) + pow(E,(-((q02*Rg2)/b2))) + (q02*Rg2)/b2))*((1.0 + 1.0/2.0*(((-1.0) - tanh(((-C4) + (sqrt(Rg2)*q0)/b)/C5))))));
+
+    t11 = (((-((3.0*C3*sqrt(Rg2)*pow((((sqrt(Rg2)*q0)/b)),((-1.0) - 3.0/miu)))/miu)) - (2.0*C2*sqrt(Rg2)*pow((((sqrt(Rg2)*q0)/b)),((-1.0) - 2.0/miu)))/miu - (C1*sqrt(Rg2)*pow((((sqrt(Rg2)*q0)/b)),((-1.0) - 1.0/miu)))/miu));
+
+    t12 = ((1.0 + tanh(((-C4) + (sqrt(Rg2)*q0)/b)/C5)));
+
+    t13 = (b*C*((4.0/15.0 - pow(E,(-((q02*Rg2)/b2)))*((11.0/15.0 + (7.0*b2)/(15.0*q02* Rg2))) + (7.0*b2)/(15.0*q02*Rg2))));
+
+    t14 = (2.0*b4*(((-1.0) + pow(E,(-((q02*Rg2)/b2))) + (q02*Rg2)/b2))*((1.0 + 1.0/2.0*(((-1.0) - tanh(((-C4) + (sqrt(Rg2)*q0)/b)/C5))))));
+
+    t15 = ((C3*pow((((sqrt(Rg2)*q0)/b)),((-3.0)/miu)) + C2*pow((((sqrt(Rg2)*q0)/b)),((-2.0)/miu)) + C1*pow((((sqrt(Rg2)*q0)/b)),((-1.0)/miu))));
+
+
+    yy = (pow(q0,p1)*(((-((b*pi)/(L*q0))) +t1/L +t2/(q04*Rg22) + 1.0/2.0*t3*t4)) + (t5*((pow(q0,(p1 - p2))*(((-pow(q0,(-p1)))*(((b2*pi)/(L*q02) +t6/L +t7/(2.0*C5) -t8/(C5*q04*Rg22) +t9/(q04*Rg22) -t10/(q05*Rg22) + 1.0/2.0*t11*t12)) - b*p1*pow(q0,((-1.0) - p1))*(((-((b*pi)/(L*q0))) +t13/L +t14/(q04*Rg22) + 1.0/2.0*t15*((1.0 + tanh(((-C4) + (sqrt(Rg2)*q0)/b)/C5)))))))))));
+
+    return (yy);
+}
+
+
+static double
+Sk_WR(double q, double L, double b)
+{
+  //
+  double p1,p2,p1short,p2short,q0;
+  double C,ans,q0short,Sexvmodify,pi;
+
+  pi = 4.0*atan(1.0);
+
+  p1 = 4.12;
+  p2 = 4.42;
+  p1short = 5.36;
+  p2short = 5.62;
+  q0 = 3.1;
+  //
+  q0short = fmax(1.9/sqrt(Rgsquareshort(q,L,b)),3.0);
+
+  //
+  if(L/b > 10.0) {
+    C = 3.06/pow((L/b),0.44);
+  } else {
+    C = 1.0;
+  }
+  //
+
+  if( L > 4*b ) { // Longer Chains
+    if (q*b <= 3.1) {   //Modified by Yun on Oct. 15,
+      Sexvmodify = Sexvnew(q, L, b);
+      ans = Sexvmodify + C * (4.0/15.0 + 7.0/(15.0*u_WR(q,L,b)) - (11.0/15.0 + 7.0/(15.0*u_WR(q,L,b)))*exp(-u_WR(q,L,b)))*(b/L);
+    } else { //q(i)*b > 3.1
+      ans = a1long(q, L, b, p1, p2, q0)/(pow((q*b),p1)) + a2long(q, L, b, p1, p2, q0)/(pow((q*b),p2)) + pi/(q*L);
+    }
+  } else { //L <= 4*b Shorter Chains
+    if (q*b <= fmax(1.9/sqrt(Rgsquareshort(q,L,b)),3.0) ) {
+      if (q*b<=0.01) {
+        ans = 1.0 - Rgsquareshort(q,L,b)*(q*q)/3.0;
+      } else {
+        ans = Sdebye1(q,L,b);
+      }
+    } else {  //q*b > max(1.9/sqrt(Rgsquareshort(q(i),L,b)),3)
+      ans = a1short(q,L,b,p1short,p2short,q0short)/(pow((q*b),p1short)) + a2short(q,L,b,p1short,p2short,q0short)/(pow((q*b),p2short)) + pi/(q*L);
+    }
+  }
+
+  return(ans);
+  //return(a2long(q, L, b, p1, p2, q0));
+}
 
 /*	CylinderForm  :  calculates the form factor of a cylinder at the give x-value p->x
@@ -20,4 +420,5 @@
 CylinderForm(double dp[], double q)
 {
+
 	int i;
 	double Pi;
