/*******************************************************************************
*
* McXtrace, X-ray tracing package
*         Copyright, All rights reserved
*         DTU Physics, Kgs. Lyngby, Denmark
*         Synchrotron SOLEIL, Saint-Aubin, France
*
* Component: SasView_mass_fractal
*
* %Identification
* Written by: Jose Robledo
* Based on sasmodels from SasView
* Origin: FZJ / DTU / ESS DMSC
*
*
* SasView mass_fractal model component as sample description.
*
* %Description
*
* SasView_mass_fractal component, generated from mass_fractal.c in sasmodels.
*
* Example: 
*  SasView_mass_fractal(radius, fractal_dim_mass, cutoff_length, 
*     model_scale=1.0, model_abs=0.0, xwidth=0.01, yheight=0.01, zdepth=0.005, R=0, 
*     int target_index=1, target_x=0, target_y=0, target_z=1,
*     focus_xw=0.5, focus_yh=0.5, focus_aw=0, focus_ah=0, focus_r=0, 
*     pd_radius=0.0, pd_cutoff_length=0.0)
*
* %Parameters
* INPUT PARAMETERS:
* radius: [Ang] ([0.0, inf]) Particle radius.
* fractal_dim_mass: [] ([1.0, 6.0]) Mass fractal dimension.
* cutoff_length: [Ang] ([0.0, inf]) Cut-off length.
* Optional parameters:
* model_abs: [ ] Absorption cross section density at 2200 m/s.
* model_scale: [ ] Global scale factor for scattering kernel. For systems without inter-particle interference, the form factors can be related to the scattering intensity by the particle volume fraction.
* xwidth: [m] ([-inf, inf]) Horiz. dimension of sample, as a width.
* yheight: [m] ([-inf, inf]) vert . dimension of sample, as a height for cylinder/box
* zdepth: [m] ([-inf, inf]) depth of sample
* R: [m] Outer radius of sample in (x,z) plane for cylinder/sphere.
* target_x: [m] relative focus target position.
* target_y: [m] relative focus target position.
* target_z: [m] relative focus target position.
* target_index: [ ] Relative index of component to focus at, e.g. next is +1.
* focus_xw: [m] horiz. dimension of a rectangular area.
* focus_yh: [m], vert. dimension of a rectangular area.
* focus_aw: [deg], horiz. angular dimension of a rectangular area.
* focus_ah: [deg], vert. angular dimension of a rectangular area.
* focus_r: [m] case of circular focusing, focusing radius.
* pd_radius: [] (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable.
* pd_cutoff_length: [] (0,inf) defined as (dx/x), where x is de mean value and dx the standard devition of the variable
*
* %Link
* %End
*******************************************************************************/
DEFINE COMPONENT SasView_mass_fractal

SETTING PARAMETERS (
        radius=10.0,
        fractal_dim_mass=1.9,
        cutoff_length=100.0,
        model_scale=1.0,
        model_abs=0.0,
        xwidth=0.01,
        yheight=0.01,
        zdepth=0.005,
        R=0,
        target_x=0,
        target_y=0,
        target_z=1,
        int target_index=1,
        focus_xw=0.5,
        focus_yh=0.5,
        focus_aw=0,
        focus_ah=0,
        focus_r=0,
        pd_radius=0.0,
        pd_cutoff_length=0.0)


SHARE %{
%include "sas_kernel_header.c"

/* BEGIN Required header for SASmodel mass_fractal */
#define HAS_Iq

#ifndef SAS_HAVE_sas_3j1x_x
#define SAS_HAVE_sas_3j1x_x

#line 1 "sas_3j1x_x"
/**
* Spherical Bessel function 3*j1(x)/x
*
* Used for low q to avoid cancellation error.
* Note that the values differ from sasview ~ 5e-12 rather than 5e-14, but
* in this case it is likely cancellation errors in the original expression
* using double precision that are the source.
*/
double sas_3j1x_x(double q);

// The choice of the number of terms in the series and the cutoff value for
// switching between series and direct calculation depends on the numeric
// precision.
//
// Point where direct calculation reaches machine precision:
//
//   single machine precision eps 3e-8 at qr=1.1 **
//   double machine precision eps 4e-16 at qr=1.1
//
// Point where Taylor series reaches machine precision (eps), where taylor
// series matches direct calculation (cross) and the error at that point:
//
//   prec   n eps  cross  error
//   single 3 0.28  0.4   6.2e-7
//   single 4 0.68  0.7   2.3e-7
//   single 5 1.18  1.2   7.5e-8
//   double 3 0.01  0.03  2.3e-13
//   double 4 0.06  0.1   3.1e-14
//   double 5 0.16  0.2   5.0e-15
//
// ** Note: relative error on single precision starts increase on the direct
// method at qr=1.1, rising from 3e-8 to 5e-5 by qr=1e3.  This should be
// safe for the sans range, with objects of 100 nm supported to a q of 0.1
// while maintaining 5 digits of precision.  For usans/sesans, the objects
// are larger but the q is smaller, so again it should be fine.
//
// See explore/sph_j1c.py for code to explore these ranges.

// Use 4th order series
#if FLOAT_SIZE>4
#define SPH_J1C_CUTOFF 0.1
#else
#define SPH_J1C_CUTOFF 0.7
#endif
#pragma acc routine seq
double sas_3j1x_x(double q)
{
    // 2017-05-18 PAK - support negative q
    if (fabs(q) < SPH_J1C_CUTOFF) {
        const double q2 = q*q;
        return (1.0 + q2*(-3./30. + q2*(3./840. + q2*(-3./45360.))));// + q2*(3./3991680.)))));
    } else {
        double sin_q, cos_q;
        SINCOS(q, sin_q, cos_q);
        return 3.0*(sin_q/q - cos_q)/(q*q);
    }
}


#endif // SAS_HAVE_sas_3j1x_x


#ifndef SAS_HAVE_sas_gamma
#define SAS_HAVE_sas_gamma

#line 1 "sas_gamma"
/*
The wrapper for gamma function from OpenCL and standard libraries
The OpenCL gamma function fails miserably on values lower than 1.0
while works fine on larger values.
We use gamma definition Gamma(t + 1) = t * Gamma(t) to compute
to function for values lower than 1.0. Namely Gamma(t) = 1/t * Gamma(t + 1)
For t < 0, we use Gamma(t) = pi / ( Gamma(1 - t) * sin(pi * t) )
*/

#if defined(NEED_TGAMMA)
#pragma acc routine seq
static double cephes_stirf(double x)
{
	const double MAXSTIR=143.01608;
	const double SQTPI=2.50662827463100050242E0;
	double y, w, v;

	w = 1.0 / x;

	w = ((((
		7.87311395793093628397E-4*w
		- 2.29549961613378126380E-4)*w
		- 2.68132617805781232825E-3)*w
		+ 3.47222221605458667310E-3)*w
		+ 8.33333333333482257126E-2)*w
		+ 1.0;
	y = exp(x);
	if (x > MAXSTIR)
	{ /* Avoid overflow in pow() */
		v = pow(x, 0.5 * x - 0.25);
		y = v * (v / y);
	}
	else
	{
		y = pow(x, x - 0.5) / y;
	}
	y = SQTPI * y * w;
	return(y);
}

#pragma acc routine seq
static double tgamma(double x) {
	double p, q, z;
	int sgngam;
	int i;

	sgngam = 1;
	if (isnan(x))
		return(x);
	q = fabs(x);

	if (q > 33.0)
	{
		if (x < 0.0)
		{
			p = floor(q);
			if (p == q)
			{
				return (NAN);
			}
			i = p;
			if ((i & 1) == 0)
				sgngam = -1;
			z = q - p;
			if (z > 0.5)
			{
				p += 1.0;
				z = q - p;
			}
			z = q * sin(M_PI * z);
			if (z == 0.0)
			{
				return(NAN);
			}
			z = fabs(z);
			z = M_PI / (z * cephes_stirf(q));
		}
		else
		{
			z = cephes_stirf(x);
		}
		return(sgngam * z);
	}

	z = 1.0;
	while (x >= 3.0)
	{
		x -= 1.0;
		z *= x;
	}

	while (x < 0.0)
	{
		if (x > -1.E-9)
			goto small;
		z /= x;
		x += 1.0;
	}

	while (x < 2.0)
	{
		if (x < 1.e-9)
			goto small;
		z /= x;
		x += 1.0;
	}

	if (x == 2.0)
		return(z);

	x -= 2.0;
	p = (((((
		+1.60119522476751861407E-4*x
		+ 1.19135147006586384913E-3)*x
		+ 1.04213797561761569935E-2)*x
		+ 4.76367800457137231464E-2)*x
		+ 2.07448227648435975150E-1)*x
		+ 4.94214826801497100753E-1)*x
		+ 9.99999999999999996796E-1;
	q = ((((((
		-2.31581873324120129819E-5*x
		+ 5.39605580493303397842E-4)*x
		- 4.45641913851797240494E-3)*x
		+ 1.18139785222060435552E-2)*x
		+ 3.58236398605498653373E-2)*x
		- 2.34591795718243348568E-1)*x
		+ 7.14304917030273074085E-2)*x
		+ 1.00000000000000000320E0;
	return(z * p / q);

small:
	if (x == 0.0)
	{
		return (NAN);
	}
	else
		return(z / ((1.0 + 0.5772156649015329 * x) * x));
}
#endif // NEED_TGAMMA

#pragma acc routine seq
inline double sas_gamma(double x)
{
    // Note: the builtin tgamma can give slow and unreliable results for x<1.
    // The following transform extends it to zero and to negative values.
    // It should return NaN for zero and negative integers but doesn't.
    // The accuracy is okay but not wonderful for negative numbers, maybe
    // one or two digits lost in the calculation. If higher accuracy is
    // needed, you could test the following loop:
    //    double norm = 1.;
    //    while (x<1.) { norm*=x; x+=1.; }
    //    return tgamma(x)/norm;
    return (x<0. ? M_PI/tgamma(1.-x)/sin(M_PI*x) : tgamma(x+1)/x);
}


#endif // SAS_HAVE_sas_gamma


#ifndef SAS_HAVE_mass_fractal
#define SAS_HAVE_mass_fractal

#line 1 "mass_fractal"
static double
Iq_mass_fractal(double q, double radius, double fractal_dim_mass, double cutoff_length)
{
    //calculate P(q)
    const double pq = square(sas_3j1x_x(q*radius));

    //calculate S(q)
    // S(q) = gamma(D-1) sin((D-1)atan(q c))/q c^(D-1) (1+(q c)^2)^(-(D-1)/2)
    // lim D->1 [gamma(D-1) sin((D-1) a)] = a
    // lim q->0 [sin((D-1) atan(q c))/q] = (D-1) c
    // lim q,D->0,1 [gamma(D-1) sin((D-1)atan(q c))/q] = c
    double sq;
    if (q > 0. && fractal_dim_mass > 1.) {
        const double Dm1 = fractal_dim_mass - 1.0;
        const double t1 = sas_gamma(Dm1)*sin(Dm1*atan(q*cutoff_length));
        const double t2 = pow(cutoff_length, Dm1);
        const double t3 = pow(1.0 + square(q*cutoff_length), -0.5*Dm1);
        sq = t1 * t2 * t3 / q;
    } else if (q > 0.) {
        sq = atan(q*cutoff_length)/q;
    } else if (fractal_dim_mass > 1.) {
        const double D = fractal_dim_mass;
        sq = pow(cutoff_length, D) * sas_gamma(D);
    } else {
        sq = cutoff_length;
    }

    return pq * sq;
}


#endif // SAS_HAVE_mass_fractal



/* END Required header for SASmodel mass_fractal */
%}
    DECLARE
%{
  double shape;
  double my_a_k;
%}

INITIALIZE
%{
shape=-1;  /* -1:no shape, 0:cyl, 1:box, 2:sphere  */
if (xwidth && yheight && zdepth)
    shape=1;
  else if (R > 0 && yheight)
    shape=0;
  else if (R > 0 && !yheight)
    shape=2;
  if (shape < 0)
    exit(fprintf(stderr, "SasView_model: %s: sample has invalid dimensions.\n"
                         "ERROR     Please check parameter values.\n", NAME_CURRENT_COMP));

  /* now compute target coords if a component index is supplied */
  if (!target_index && !target_x && !target_y && !target_z) target_index=1;
  if (target_index)
  {
    Coords ToTarget;
    ToTarget = coords_sub(POS_A_COMP_INDEX(INDEX_CURRENT_COMP+target_index),POS_A_CURRENT_COMP);
    ToTarget = rot_apply(ROT_A_CURRENT_COMP, ToTarget);
    coords_get(ToTarget, &target_x, &target_y, &target_z);
  }

  if (!(target_x || target_y || target_z)) {
    printf("SasView_model: %s: The target is not defined. Using direct beam (Z-axis).\n",
      NAME_CURRENT_COMP);
    target_z=1;
  }

  /*TODO fix absorption*/
  my_a_k = model_abs; /* assume absorption is given in 1/m */

%}


TRACE
%{
  double l0, l1, k, l_full, l, dl, d_Phi;
  double aim_x=0, aim_y=0, aim_z=1, axis_x, axis_y, axis_z;
  double f, solid_angle, kx_i, ky_i, kz_i, q, qx, qy, qz;
  char intersect=0;

  /* Intersection photon trajectory / sample (sample surface) */
  if (shape == 0){
    intersect = cylinder_intersect(&l0, &l1, x, y, z, kx, ky, kz, R, yheight);}
  else if (shape == 1){
    intersect = box_intersect(&l0, &l1, x, y, z, kx, ky, kz, xwidth, yheight, zdepth);}
  else if (shape == 2){
    intersect = sphere_intersect(&l0, &l1, x, y, z, kx, ky, kz, R);}
  if(intersect)
  {
    if(l0 < 0)
      ABSORB;

    /* Photon enters at l0. */
    k = sqrt(kx*kx + ky*ky + kz*kz);
    l_full = (l1 - l0);          /* Length of full path through sample */
    dl = rand01()*(l1 - l0) + l0;    /* Point of scattering */
    PROP_DL(dl);                     /* Point of scattering */
    l = (dl-l0);                   /* Penetration in sample */

    kx_i=kx;
    ky_i=ky;
    kz_i=kz;
    if ((target_x || target_y || target_z)) {
      aim_x = target_x-x;            /* Vector pointing at target (anal./det.) */
      aim_y = target_y-y;
      aim_z = target_z-z;
    }
    if(focus_aw && focus_ah) {
      randvec_target_rect_angular(&kx, &ky, &kz, &solid_angle,
        aim_x, aim_y, aim_z, focus_aw, focus_ah, ROT_A_CURRENT_COMP);
    } else if(focus_xw && focus_yh) {
      randvec_target_rect(&kx, &ky, &kz, &solid_angle,
        aim_x, aim_y, aim_z, focus_xw, focus_yh, ROT_A_CURRENT_COMP);
    } else {
      randvec_target_circle(&kx, &ky, &kz, &solid_angle, aim_x, aim_y, aim_z, focus_r);
    }
    NORM(kx, ky, kz);
    kx *= k;
    ky *= k;
    kz *= k;
    qx = (kx_i-kx);
    qy = (ky_i-ky);
    qz = (kz_i-kz);
    q = sqrt(qx*qx+qy*qy+qz*qz);
    
    double trace_radius=radius;
    double trace_cutoff_length=cutoff_length;
    if ( pd_radius!=0.0 || pd_cutoff_length!=0.0 ){
    trace_radius = (randnorm()*pd_radius+1.0)*radius;
    trace_cutoff_length = (randnorm()*pd_cutoff_length+1.0)*cutoff_length;
    }

        


    // Sample dependent. Retrieved from SasView./////////////////////
    float Iq_out;
    Iq_out = 1;

    Iq_out = Iq_mass_fractal(q, trace_radius, fractal_dim_mass, trace_cutoff_length);


    float vol;
    vol = 1;

    // Scale by 1.0E2 [SasView: 1/cm  ->   McXtrace: 1/m]
    Iq_out = model_scale*Iq_out / vol * 1.0E2;

    
    p *= l_full*solid_angle/(4*PI)*Iq_out*exp(-my_a_k*(l+l1));


    SCATTER;
  }
%}

MCDISPLAY
%{

  if (shape == 0) {	/* cylinder */
    circle("xz", 0,  yheight/2.0, 0, R);
    circle("xz", 0, -yheight/2.0, 0, R);
    line(-R, -yheight/2.0, 0, -R, +yheight/2.0, 0);
    line(+R, -yheight/2.0, 0, +R, +yheight/2.0, 0);
    line(0, -yheight/2.0, -R, 0, +yheight/2.0, -R);
    line(0, -yheight/2.0, +R, 0, +yheight/2.0, +R);
  }
  else if (shape == 1) { 	/* box */
    double xmin = -0.5*xwidth;
    double xmax =  0.5*xwidth;
    double ymin = -0.5*yheight;
    double ymax =  0.5*yheight;
    double zmin = -0.5*zdepth;
    double zmax =  0.5*zdepth;
    multiline(5, xmin, ymin, zmin,
                 xmax, ymin, zmin,
                 xmax, ymax, zmin,
                 xmin, ymax, zmin,
                 xmin, ymin, zmin);
    multiline(5, xmin, ymin, zmax,
                 xmax, ymin, zmax,
                 xmax, ymax, zmax,
                 xmin, ymax, zmax,
                 xmin, ymin, zmax);
    line(xmin, ymin, zmin, xmin, ymin, zmax);
    line(xmax, ymin, zmin, xmax, ymin, zmax);
    line(xmin, ymax, zmin, xmin, ymax, zmax);
    line(xmax, ymax, zmin, xmax, ymax, zmax);
  }
  else if (shape == 2) {	/* sphere */
    circle("xy", 0,  0.0, 0, R);
    circle("xz", 0,  0.0, 0, R);
    circle("yz", 0,  0.0, 0, R);
  }
%}
END

