/*****************************************************************************
* McXtrace, X-ray tracing package
*         Copyright, All rights reserved
*         DTU Physics, Kgs. Lyngby, Denmark
*         Synchrotron SOLEIL, Saint-Aubin, France
*
* Component: PowderN
*
* %Identification
* Written by: P. Willendrup, L. Chapon, K. Lefmann, A.B.Abrahamsen, N.B.Christensen, E.M.Lauridsen.
* Date: 4.2.98
* Origin: McXtrace release 1.2
* Modified by: KL, KN 20.03.98   (rewrite)
* Modified by: KL,    28.09.01   (two lines)
* Modified by: KL,    22.05.03   (background)
* Modified by: KL, PW 01.05.05   (N lines)
* Modified by: PW, LC 04.10.05   (Merge with Chapon Powder_multi)
* Modified by: PW, KL 05.06.07   (Concentricity)
* Modified by: EF,    17.10.08   (added any shape sample geometry)
* Modified by: EK,    28.10.10   (for X-ray use)
* Modified by: EK,               (Added options for incoherent scattering)
* Modified by: EF, June 2023     (can now read CIF files)
*
* General powder sample (N lines, single scattering, incoherent scattering)
*
* %Description
* General powder sample with
*         many scattering vectors
*         possibility for intrinsic line broadening
*         incoherent background ratio is computed from material datafile.
*         No multiple scattering. No secondary extinction.
*
* Based on Powder1/Powder2/Single_crystal.
* Geometry is a powder filled cylinder, sphere, box or any shape from an OFF file.
* Incoherent scattering is only provided here to account for a background.
* The efficient is highly improved when restricting the vertical scattering
*   range on the Debye-Scherrer cone (with 'd_phi' and 'focus_flip').
* The unit cell volume Vc may also be computed when giving the density,
*   the atomic/molecular weight and the number of atoms per unit cell.
*
* <b>Sample shape:</b>
* Sample shape may be a cylinder, a sphere, a box or any other shape.
*   box/plate:       xwidth x yheight x zdepth (thickness=0)
*   hollow box/plate:xwidth x yheight x zdepth and thickness>0
*   cylinder:        radius x yheight (thickness=0)
*   hollow cylinder: radius x yheight and thickness>0
*   sphere:          radius (yheight=0 thickness=0)
*   hollow sphere:   radius and thickness>0 (yheight=0)
*   any shape:       geometry=OFF_file
*
*   The complex geometry option handles any closed non-convex polyhedra.
*   It computes the intersection points of the xray with the object
*   transparently, so that it can be used like a regular sample object.
*   It supports the PLY, OFF and NOFF file format but not COFF (colored faces).
*   Such files may be generated from XYZ data using:
*   qhull < coordinates.xyz Qx Qv Tv o > geomview.off
*   or
*     powercrust coordinates.xyz
*   and viewed with geomview or java -jar jroff.jar (see below).
*   The default size of the object depends of the OFF file data, but its
*   bounding box may be resized using xwidth,yheight and zdepth.
*
* If you use this component and produce valuable scientific results, please
* cite authors with references bellow (in <a href="#links">Links</a>).
*
* Example: PowderN(reflections = "c60.lau", d_phi = 15 , radius = 0.01,
*   yheight = 0.05, Vc = 1076.89, delta_d_d=0, DW=1)
*
* <b>Powder definition file format</b>
* Powder structure is specified with an ascii data file 'reflections'.
* The powder data are free-text column based files.
* The reflection list should be ordered by decreasing d-spacing values.
*       ... d ... F2
* Lines begining by '#' are read as comments (ignored) but they may contain
* the following keywords (in the header):
*   #Vc           <value of unit cell volume Vc [Angs^3]>
*   #Debye_Waller <value of Debye-Waller factor DW>
*   #delta_d_d/d    <value of delta_d_d/d width for all lines>
* These values are not read if entered as component parameters (Vc=...)
*
* The signification of the columns in the numerical block may be
* set using the 'format' parameter, by defining signification of the
* columns as a vector of indexes in the order
*   format={j,d,F2,DW,delta_d_d/d,1/2d,q,F}
* Signification of the symbols is given below. Indices start at 1.
* Indices with zero means that the column are not present, so that:
*   Crystallographica={ 4,5,7,0,0,0,0,0 }
*   Fullprof         ={ 4,0,8,0,0,5,0,0 }
*   Lazy             ={17,6,0,0,0,0,0,13}
*
* At last, the format may be overridden by direct definition of the
* column indexes in the file itself by using the following keywords
* in the header (e.g. '#column_j 4'):
*   #column_j     <index of the multiplicity 'j' column>
*   #column_d     <index of the d-spacing 'd' column [Angs]>
*   #column_F2    <index of the squared str. factor '|F|^2' column [b]>
*   #column_F     <index of the structure factor norm '|F|' column>
*   #column_DW    <index of the Debye-Waller factor 'DW' column>
*   #column_Dd    <index of the relative line width delta_d_d/d broadening 'Dd' column>
*   #column_inv2d <index of the 1/2d=sin(theta)/lambda 'inv2d' column>
*   #column_q     <index of the scattering wavevector 'q' column [Angs-1]>
*
* Last, CIF, FullProf and ShelX files can be read, and converted to F2(hkl) lists
* if 'cif2hkl' is installed. The CIF2HKL env variable can be used to point to a
* proper executable, else the McCode, then the system installed versions are used.
*
* <b>Concentricity</b>
*
* PowderN assumes 'concentric' shape, i.e. can contain other components inside its
* optional inner hollow. Example, Sample in Al cryostat:
*
*
* COMPONENT Cryo = PowderN(reflections="Al.laz", radius = 0.01, thickness = 0.001,
*                          concentric = 1, p_interact=0.1)
* AT (0,0,0) RELATIVE Somewhere
*
* COMPONENT Sample = some_other_component(with geometry FULLY enclosed in the hollow)
* AT (0,0,0) RELATIVE Somewhere
*
* COMPONENT Cryo2 = COPY(Cryo)(concentric = 0)
* AT (0,0,0) RELATIVE Somewhere
*
*
* (The second instance of the cryostat component can also be written out completely
*  using PowderN(...). In both cases, this second instance needs concentric = 0.)
* The concentric arrangment can not be used with OFF geometry specification.
*
* This sample component can advantageously benefit from the SPLIT feature, e.g.
* SPLIT COMPONENT pow = PowderN(...)
*
* %Parameters
* INPUT PARAMETERS
* radius: [m]          Outer radius of sample in (x,z) plane.
* xwidth: [m]          Horiz. dimension of sample, as a width.
* yheight: [m]         Height of sample y direction.
* zdepth: [m]          Depth of box sample.
* thickness: [m]       Thickness of hollow sample. Negative value extends the hollow volume outside of the box/cylinder.
* reflections: [str]   Input file for reflections (LAZ LAU CIF, FullProf, ShelX). Use only incoherent scattering if NULL or "".
*
* Optional parameters:
* d_phi: [deg]      Angle corresponding to the vertical angular range to focus to, e.g. detector height. 0 for no focusing.
* d_omega: [deg]       Horizontal focus range (only for incoherent scattering), 0 for no focusing.
* tth_sign: [1]        Sign of the scattering angle. If 0, the sign is chosen randomly (left and right). ONLY functional in combination with d_phi and ONLY applies to bragg lines.
* focus_flip:   [1] Controls the sense of d_phi. If 0 d_phi is measured against the xz-plane. If !=0 d_phi is measured against zy-plane.
* tth_sign: [1]     Sign of the scattering angle. If 0, the sign is chosen randomly (left and right).
* pack: [1]         Packing factor
* delta_d_d: [AA]   Global relative Delta_d/d spreading when the 'w' column is not available. Use 0 if ideal.
* format:  [{}]     Name of the format, or list of column indexes (see Description). N.b. no quotes!
* p_inc:   [1]      Fraction of incoherently scattered rays.
* p_transmit: [1]   Fraction of transmitted (only attenuated) rays.
* p_interact: [1]   Fraction of events interacting with sample, e.g. 1-p_transmit-p_inc.
* concentric: [1]   Indicate that this component has a hollow geometry and may contain other components. It should then be duplicated after the inside part (only for box, cylinder, sphere).
* geometry:   [str] Name of an Object File Format (OFF) or PLY file for complex geometry. The OFF/PLY file may be generated from XYZ coordinates using qhull/powercrust.
* barns:   [1]      Flag to indicate if |F|^2 from 'reflections' is in barns or fm^2, (barns=1 for laz, barns=0 for lau type files).
* Vc:      [AA^3]   Volume of unit cell=nb atoms per cell/density of atoms.
* DW:      [1]      Global Debye-Waller factor when the 'DW' column is not available. Use 1 if included in F2.
* weight:  [g/mol]  Atomic/molecular weight of material.
* density: [g/cm^3] Density of material. rho=density/weight/1e24*N_A.
* nb_atoms:[1]      Number of sub-unit per unit cell, that is ratio of sigma for chemical formula to sigma per unit cell.
* material: [Be.txt] File where the material parameters for the absorption may be found. Format is similar to what may be found off the NIST website. 
* mat_format: [{}]  Format of the asorption parameter file.
* target_index: [1]    Relative index of component to focus incoherent scattering at, e.g. next is +1
*
* CALCULATED PARAMETERS:
* line_info: [struct]     Internal structure containing many members/info
* line_info.type: [char]  Interaction type of event 't'=Transmit, 'i'=Incoherent, 'c'=Coherent
* line_info.dq: [Angs^-1] Wavevector transfer of last coherent scattering event.
*
* %Link
* See also: Single_crystal
* %Link
* See <a href="http://icsd.ill.fr">ICSD</a> Inorganic Crystal Structure Database
* <a href="http://www.webelements.com/">Web Elements</a>
* %Link
* <a href="http://www.ill.eu/sites/fullprof/index.html">Fullprof</a> powder refinement
* %Link
* <a href="http://www.crystallographica.com/">Crystallographica</a> software (free license)
* %Link
* <a href="http://www.geomview.org">Geomview and Object File Format (OFF)</a>
* %Link
* Java version of Geomview (display only) <a href="http://www.holmes3d.net/graphics/roffview/">jroff.jar</a>
* %Link
* <a href="http://qhull.org">qhull</a>
* %Link
* <a href="http://www.cs.ucdavis.edu/~amenta/powercrust.html">powercrust</a>
* %Link
* cif2hkl https://gitlab.com/soleil-data-treatment/soleil-software-projects/cif2hkl
* %Link
* material datafile obtained from http://physics.nist.gov/cgi-bin/ffast/ffast.pl
*
* %End
*****************************************************************************/
DEFINE COMPONENT PowderN

SETTING PARAMETERS (
  string reflections="NULL", string material="NULL", string geometry="NULL",
  vector format={0,0,0,0,0,0,0,0}, vector mat_format={0,0,0,0,0},
  radius=0, yheight=0, xwidth=0, zdepth=0, thickness=0,
  pack=1, Vc=0, delta_d_d=0, p_inc=0.1, p_transmit=0.1,
  DW=0, nb_atoms=1, d_omega=0, d_phi=0, tth_sign=0, p_interact=0,
  concentric=0, density=0, weight=0, barns=1, focus_flip=0, int target_index=0)

/* X-ray parameters: (x,y,z,kx,ky,kz,phi,t,Ex,Ey,Ez,p) */
SHARE
%{
/* used for reading data table from file */
%include "read_table-lib"
%include "interoff-lib"
/* Declare structures and functions only once in each instrument. */
#ifndef POWDERN_DECL
#define POWDERN_DECL
  // single reflection data
  struct line_data
    {
      double F2;                  /* Value of structure factor */
      double q;                   /* Qvector */
      int j;                      /* Multiplicity */
      double DWfactor;            /* Debye-Waller factor */
      double w;                   /* Intrinsic line width */
    };
  // absorption data
  struct abs_data
  {
    double E;       /*energy (in keV)*/
    double k;       /*wavenumber corresponding to E*/
    double sigma_a; /*absorption cross section for energy E*/
    double mu;      /*absoprtion coefficient for the energy E*/
    double cohinc;  /*coherent +incoherent scattering coefficient*/
  };
  // component data
  struct line_info_struct
  {
      struct line_data *list;     /* Reflection array */
      int  count;                  /* Number of reflections */
      double Dd;
      double DWfactor;
      double V_0;
      double rho;
      double at_weight;
      double at_nb;
      double sigma_a;
      double sigma_i;
      char   compname[256];
      double flag_barns;
      int    shape; /* 0 cylinder, 1 box, 2 sphere, 3 OFF file */
      int    column_order[8]; /* column signification */
      int    flag_warning;
      double dq;    /* wavevector transfer [Angs-1] */
      double Epsilon; /* global strain in ppm */
      double XsectionFactor;
      double my_s_k2_sum;
      double my_a;
      double my_inc;
      double lfree; // store mean free path for the last event;
      double *w,*q, *my_s_k2;
      double radius_i,xwidth_i,yheight_i,zdepth_i;
      double k; /* last velocity (cached) */
      double Nq;
      int    nb_reuses, nb_refl, nb_refl_count;
      double k_min, k_max;
      double xs_Nq[CHAR_BUF_LENGTH];
      double xs_sum[CHAR_BUF_LENGTH];
      unsigned int photon_passed;
      long   xs_compute, xs_reuse, xs_calls;
      t_Table mat_table;
      int mat_column_order[5]; /*column signification for the coeff. in material data file*/
  };

  off_struct offdata;
  
  // shared functions **********************************************************
  
  // sign = PN_list_compare(a,b) 
  //   used for qsort, to sort reflections
  // input:  a,b: two 'line_data' reflection pointers.
  // output: -1,0,1 for a<b, a=b, a>b
  int PN_list_compare (void const *a, void const *b)
  {
     struct line_data const *pa = a;
     struct line_data const *pb = b;
     double s = pa->q - pb->q;

     if (!s) return 0;
     else    return (s < 0 ? -1 : 1);
  } /* PN_list_compare */
  
#ifndef CIF2HKL
#define CIF2HKL
  // hkl_filename = cif2hkl(file, options)
  //   used to convert CIF/CFL/INS file into F2(hkl)
  //   the CIF2HKL env var can point to a cif2hkl executable
  //   else the McCode binary is attempted, then the system.
  char *cif2hkl(const char *infile, const char *options) {
    char cmd[1024];
    int  ret = 0;
    int  found = 0;
    char *OUTFILE;
    
    // get filename extension
    const char *ext = strrchr(infile, '.');
    if(!ext || ext == infile) return infile;
    else ext++;
    
    // return input when no extension or not a CIF/FullProf/ShelX file
    if ( strcasecmp(ext, "cif") 
      && strcasecmp(ext, "pcr")
      && strcasecmp(ext, "cfl")
      && strcasecmp(ext, "shx")
      && strcasecmp(ext, "ins")
      && strcasecmp(ext, "res")) return infile;
      
    OUTFILE = malloc(1024);
    if (!OUTFILE) return infile;
    
    strncpy(OUTFILE, tmpnam(NULL), 1024); // create an output temporary file name
    
    // try in order the CIF2HKL env var, then the system cif2hkl, then the McCode one
    if (!found && getenv("CIF2HKL")) {
      snprintf(cmd,  1024, "%s -o %s %s %s",
        getenv("CIF2HKL"),
        OUTFILE, options, infile);
      ret = system(cmd);
      if (ret != -1 && ret != 127) found = 1;
    }
    if (!found) {
      // try with cif2hkl command from the system PATH
      snprintf(cmd,  1024, "%s -o %s %s %s",
        "cif2hkl", OUTFILE, options, infile);
      ret = system(cmd);
      if (ret != -1 && ret != 127) found = 1;
    }
    if (!found) {
      // As a last resort, attempt with cif2hkl from $MCXTRACE/bin
      snprintf(cmd,  1024, "%s%c%s%c%s -o %s %s %s",
        getenv(FLAVOR_UPPER) ? getenv(FLAVOR_UPPER) : MCXTRACE,
        MC_PATHSEP_C, "bin", MC_PATHSEP_C, "cif2hkl",
        OUTFILE, options, infile);
      ret = system(cmd);
    }
    // ret = -1:  child process could not be created
    // ret = 127: shell could not be executed in the child process     
    if (ret == -1 || ret == 127) {
      free(OUTFILE);
      return(NULL);
    }
      
    // test if the result file has been created
    FILE *file = Open_File(OUTFILE,"r", NULL);
    if (!file) return(NULL);     
    MPI_MASTER(
    printf("%s: INFO: Converting %s into F2(HKL) list %s\n", 
      __FILE__, infile, OUTFILE);
    printf ("%s\n",cmd);
    );
    fflush(NULL);
    return(OUTFILE);
  } // cif2hkl
#endif

  // count = read_line_data(filename, &info)
  //   read the given file to store F2(HKL) reflections and metadata.
  int read_line_data(char *SC_file, struct line_info_struct *info)
  {
    struct line_data *list = NULL;
    int    size = 0;
    t_Table sTable; /* sample data table structure from SC_file */
    int    i=0;
    int    mult_count  =0;
    char   flag=0;
    double q_count=0, j_count=0, F2_count=0;
    char **parsing;
    int    list_count=0;
    double sum_F2=0;
    char  *filename=NULL;

    if (!SC_file || !strlen(SC_file) || !strcmp(SC_file, "NULL")) {
      MPI_MASTER(
      printf("PowderN: %s: Using incoherent elastic scattering only.\n",
          info->compname);
      );
      info->count = 0;
      return(0);
    }
    filename = cif2hkl(SC_file, "--mode XRA");
    long retval = Table_Read(&sTable, filename, 1); /* read 1st block data from SC_file into sTable*/
    if (retval<0) {
      fprintf(stderr,"PowderN: Could not open file %s - exiting!\n", filename);
      exit(-1);
    }

    /* parsing of header */
    parsing = Table_ParseHeader(sTable.header,
      "Vc","V_0",
      "column_j",
      "column_d",
      "column_F2",
      "column_DW",
      "column_Dd",
      "column_inv2d", "column_1/2d", "column_sintheta/lambda",
      "column_q", /* 10 */
      "DW", "Debye_Waller",
      "delta_d/d",
      "column_F ",
      "V_rho",
      "density",
      "weight",
      "nb_atoms","multiplicity",
      NULL);

    if (parsing) {
      if (parsing[0] && !info->V_0)     info->V_0    =atof(parsing[0]);
      if (parsing[1] && !info->V_0)     info->V_0    =atof(parsing[1]);
      if (parsing[2])                   info->column_order[0]=atoi(parsing[2]);
      if (parsing[3])                   info->column_order[1]=atoi(parsing[3]);
      if (parsing[4])                   info->column_order[2]=atoi(parsing[4]);
      if (parsing[5])                   info->column_order[3]=atoi(parsing[5]);
      if (parsing[6])                  info->column_order[4]=atoi(parsing[6]);
      if (parsing[7])                  info->column_order[5]=atoi(parsing[7]);
      if (parsing[8])                  info->column_order[5]=atoi(parsing[8]);
      if (parsing[9])                  info->column_order[5]=atoi(parsing[9]);
      if (parsing[10])                  info->column_order[6]=atoi(parsing[10]);
      if (parsing[11] && info->DWfactor<=0)    info->DWfactor=atof(parsing[11]);
      if (parsing[12] && info->DWfactor<=0)    info->DWfactor=atof(parsing[12]);
      if (parsing[13] && info->Dd <0)          info->Dd      =atof(parsing[13]);
      if (parsing[14])                  info->column_order[7]=atoi(parsing[14]);
      if (parsing[15] && !info->V_0)    info->V_0    =1/atof(parsing[15]);
      if (parsing[16] && !info->rho)    info->rho    =atof(parsing[16]);
      if (parsing[17] && !info->at_weight)     info->at_weight    =atof(parsing[17]);
      if (parsing[18] && info->at_nb <= 1)  info->at_nb    =atof(parsing[18]);
      if (parsing[19] && info->at_nb <= 1)  info->at_nb    =atof(parsing[19]);
      for (i=0; i<=19; i++) if (parsing[i]) free(parsing[i]);
      free(parsing);
    }

    if (!sTable.rows)
      exit(fprintf(stderr, "PowderN: %s: Error: The number of rows in %s "
       "should be at least %d\n", info->compname, SC_file, 1));
    else
      size = sTable.rows;

    MPI_MASTER(
    Table_Info(sTable);
    printf("PowderN: %s: Reading %d rows from %s\n",
          info->compname, size, SC_file);
    );

    if (info->column_order[0] == 4 && info->flag_barns !=0)
    MPI_MASTER(
      printf("PowderN: %s: Powder file probably of type Crystallographica/Fullprof (lau)\n"
           "WARNING: but F2 unit is set to barns=1 (barns). Intensity might be 100 times too high.\n",
           info->compname);
    );
    if (info->column_order[0] == 17 && info->flag_barns == 0)
    MPI_MASTER(
      printf("PowderN: %s: Powder file probably of type Lazy Pulver (laz)\n"
           "WARNING: but F2 unit is set to barns=0 (fm^2). Intensity might be 100 times too low.\n",
           info->compname);
    );
    /* allocate line_data array */
    list = (struct line_data*)malloc(size*sizeof(struct line_data));

    for (i=0; i<size; i++)
    {
      /*      printf("Reading in line %i\n",i);*/
      double j=0, d=0, w=0, q=0, DWfactor=0, F2=0;
      int index;

      if (info->Dd >= 0)      w         = info->Dd;
      if (info->DWfactor > 0) DWfactor  = info->DWfactor;

      /* get data from table using columns {j d F2 DW Dd inv2d q F} */
      /* column indexes start at 1, thus need to substract 1 */
      if (info->column_order[0] >0)
        j = Table_Index(sTable, i, info->column_order[0]-1);
      if (info->column_order[1] >0)
        d = Table_Index(sTable, i, info->column_order[1]-1);
      if (info->column_order[2] >0)
        F2 = Table_Index(sTable, i, info->column_order[2]-1);
      if (info->column_order[3] >0)
        DWfactor = Table_Index(sTable, i, info->column_order[3]-1);
      if (info->column_order[4] >0)
        w = Table_Index(sTable, i, info->column_order[4]-1);
      if (info->column_order[5] >0 && !(info->column_order[1] >0)) // Only use if d not read already
        { d = Table_Index(sTable, i, info->column_order[5]-1);
          d = (d > 0? 1/d/2 : 0); }
      if (info->column_order[6] >0 && !(info->column_order[1] >0)) // Only use if d not read already  
        { q = Table_Index(sTable, i, info->column_order[6]-1);
          d = (q > 0 ? 2*PI/q : 0); }
      if (info->column_order[7] >0  && !F2)
        { F2 = Table_Index(sTable, i, info->column_order[7]-1); F2 *= F2; }

      /* assign and check values */
      j        = (j > 0 ? j : 0);
      q        = (d > 0 ? 2*PI/d : 0); /* this is q */
      DWfactor = (DWfactor > 0 ? DWfactor : 1);
      w        = (w>0 ? w : 0); /* this is q and d relative spreading */
      F2       = (F2 >= 0 ? F2 : 0);
      if (j == 0 || q == 0) {
        MPI_MASTER(
        printf("PowderN: %s: line %i has invalid definition\n"
               "         (mult=0 or q=0 or d=0)\n", info->compname, i);
        );
        continue;
      }
      list[list_count].j = j;
      list[list_count].q = q;
      list[list_count].DWfactor = DWfactor;
      list[list_count].w = w;
      list[list_count].F2= F2;
      sum_F2 += F2;

      /* adjust multiplicity if j-column + multiple d-spacing lines */
      /* if  d = previous d, increase line duplication index */
      if (!q_count)      q_count  = q;
      if (!j_count)      j_count  = j;
      if (!F2_count)     F2_count = F2;
      if (fabs(q_count-q) < 0.0001*fabs(q)
       && fabs(F2_count-F2) < 0.0001*fabs(F2) && j_count == j) {
       mult_count++; flag=0; }
      else flag=1;
      if (i == size-1) flag=1;
      /* else if d != previous d : just passed equivalent lines */
      if (flag) {
        if (i == size-1) list_count++;
      /*   if duplication index == previous multiplicity */
      /*      set back multiplicity of previous lines to 1 */
        if ((mult_count && list_count>0)
            && (mult_count == list[list_count-1].j
                || ((list_count < size) && (i == size - 1)
                    && (mult_count == list[list_count].j))) ) {
          MPI_MASTER(
          printf("PowderN: %s: Set multiplicity to 1 for lines [%i:%i]\n"
                  "         (d-spacing %g is duplicated %i times)\n",
            info->compname, list_count-mult_count, list_count-1, list[list_count-1].q, mult_count);
          );
          for (index=list_count-mult_count; index<list_count; list[index++].j = 1);
          mult_count = 1;
          q_count   = q;
          j_count   = j;
          F2_count  = F2;
        }
        if (i == size-1) list_count--;
        flag=0;
      }
      list_count++;
    } /* end for */

    Table_Free(&sTable);
    
    if (!sum_F2) {
      MPI_MASTER(
      fprintf(stderr, "PowderN: %s: ERROR: all %i structure factors in file '%s' are null. Check the reflection list.\n",
        info->compname, list_count, SC_file);
      );
      return(0);
    }

    /* sort the list with increasing q */
    qsort(list, list_count, sizeof(struct line_data),  PN_list_compare);

    MPI_MASTER(
    printf("PowderN: %s: Read %i reflections from file '%s'\n",
      info->compname, list_count, SC_file);
    );
    // remove temporary F2(hkl) file when giving CFL/CIF/ShelX file
    if (filename && filename != SC_file)
      unlink(filename);

    info->list  = list;
    info->count = list_count;

    return(list_count);
  } /* read_line_data */


/* calc_xsect: computes the number of possible reflections (return value), and the total xsection 'sum' */
/* this routine looks for a pre-computed value in the Nq and sum cache tables               */
/* when found, the earch starts from the corresponding lower element in the table           */
#pragma acc routine
int calc_xsect(double k, double *q, double *my_s_k2, int count, double *sum,
  struct line_info_struct *line_info) {
  int    Nq = 0, line=0, line0=0;
  *sum=0;

  /* check if a line_info element has been recorded already - not on OpenACC */
  #ifndef OPENACC
  if (k >= line_info->k_min && k <= line_info->k_max && line_info->photon_passed >= CHAR_BUF_LENGTH) {
    line = (int)floor(k - line_info->k_min)*CHAR_BUF_LENGTH/(line_info->k_max - line_info->k_min);
    Nq    = line_info->xs_Nq[line];
    *sum  = line_info->xs_sum[line];
    if (!Nq && *sum == 0) {
      /* not yet set: we compute the sum up to the corresponding wavevector in the table cache */
      double line_k = line_info->k_min + line*(line_info->k_max - line_info->k_min)/CHAR_BUF_LENGTH;
      for(line0=0; line0<count; line0++) {
        if (q[line0] <= 2*line_k) { /* q < 2*kf: restrict structural range */
          *sum += my_s_k2[line0];
          if (Nq < line0+1) Nq=line0+1; /* determine maximum line index which can scatter */
        } else break;
      }
      line_info->xs_Nq[line] = Nq;
      line_info->xs_sum[line]= *sum;
      line_info->xs_compute++;
    } else line_info->xs_reuse++;
    line0 = Nq;
  }

  line_info->xs_calls++;
  #endif

  for(line=line0; line<count; line++) {
    if (q[line] <= 2*k) { /* q < 2*kf: restrict structural range */
      *sum += my_s_k2[line];
      if (Nq < line+1) Nq=line+1; /* determine maximum line index which can scatter */
    } else break;
  }

  return(Nq);
} /* calc_xsect */

#pragma acc routine
int calc_abs_xsect(double k, double *abs, struct line_info_struct *line_info){
    /* compute the absorption cross section.
     * amounts to a table lookup in material data_file by energy*/
    double e=k*K2E;
    *abs=Table_Value((line_info->mat_table), e, line_info->mat_column_order[1]);
    *abs*=100*line_info->rho;
    return 0;
}

#pragma acc routine
int calc_inc_xsect(double k, double *inc, struct line_info_struct *line_info){
    /*TODO choose one of these bits*/

    /* compute the incoherent cross section.
     * amounts to a table lookup in material data_file by energy
     * In time this should be improved to actually handle Compton scattering.*/
    double e=k*K2E;

    double correction;
    int i=2;
    /* To find the inc. scattering column in material datafiles,
     * Find the first non-zero column index (btw. 2..4).*/
    for (i=2;i<5;i++){
        if (line_info->mat_column_order[i]) break;
    }

    switch (i){
        case 2:
            /*inc is explicitly in column i - no correction term.*/
            correction=0;
            break;
        case 3:
            /*inc is given as inc+ćoh in column i*/
            correction=line_info->my_s_k2_sum/(k*k);
            break;
        case 4:
            /*inc is given as total attenuation = inc+coh+abs in column i*/
            correction=line_info->my_s_k2_sum/(k*k) + line_info->my_a;
            break;
        case 5:
            /*means no non-zero index has been found - set xsect to 0*/
            *inc=0;
            return 1;
    }

    *inc=Table_Value((line_info->mat_table), e, line_info->mat_column_order[i]-1)-correction;
    if (*inc<0){
        *inc=0;
    }
    *inc*=100*line_info->rho;/*scale by rho and 100 to get in units m^-1*/
    return 0;
}

#endif /* !POWDERN_DECL */

%}

DECLARE
%{
  struct line_info_struct line_info;
  double *columns;
  double *mat_columns;
  off_struct offdata;
  double tgt_x;
  double tgt_y;
  double tgt_z;
%}

INITIALIZE
%{
  /* We ought to clean up the columns variable as format is now a proper vector/array */
  columns = format;
  mat_columns =  mat_format;
  int i=0;
  struct line_data *L;
  line_info.Dd       = delta_d_d;
  line_info.DWfactor = DW;
  line_info.V_0      = Vc;
  line_info.rho      = density;
  line_info.at_weight= weight;
  line_info.at_nb    = nb_atoms;
  line_info.flag_barns=barns;
  line_info.shape    = 0;
  line_info.flag_warning=0;
  line_info.radius_i =line_info.xwidth_i=line_info.yheight_i=line_info.zdepth_i=0;
  line_info.k  = 0;
  line_info.Nq = 0;
  line_info.k_min = FLT_MAX; line_info.k_max = 0;
  line_info.photon_passed=0;
  line_info.nb_reuses = line_info.nb_refl = line_info.nb_refl_count = 0;
  line_info.xs_compute= line_info.xs_reuse= line_info.xs_calls =0;
  for (i=0; i< 8; i++) {
    line_info.column_order[i] = (int)columns[i];
  }
  for (i=0; i< 4;  i++) {
    line_info.mat_column_order[i] = (int)mat_columns[i];
  }
  strncpy(line_info.compname, NAME_CURRENT_COMP, 256);

  line_info.shape=-1; /* -1:no shape, 0:cyl, 1:box, 2:sphere, 3:any-shape  */
  if (geometry && strlen(geometry) && strcmp(geometry, "NULL") && strcmp(geometry, "0")) {
    #ifndef USE_OFF
    fprintf(stderr,"PowderN: %s: Error: You are attempting to use an OFF geometry without -DUSE_OFF. You will need to recompile with that define set!\n", NAME_CURRENT_COMP);
    exit(-1);
    #else
    if (off_init(geometry, xwidth, yheight, zdepth, 0, &offdata)) {
      line_info.shape=3; thickness=0; concentric=0;
    }
    #endif
  }
  else if (xwidth && yheight && zdepth)  line_info.shape=1; /* box */
  else if (radius > 0 && yheight)        line_info.shape=0; /* cylinder */
  else if (radius > 0 && !yheight)       line_info.shape=2; /* sphere */

  if (line_info.shape < 0)
    exit(fprintf(stderr,"PowderN: %s: sample has invalid dimensions.\n"
                        "ERROR    Please check parameter values (xwidth, yheight, zdepth, radius).\n", NAME_CURRENT_COMP));
  if (thickness) {
    if (radius && (radius < fabs(thickness))) {
      MPI_MASTER(
      printf("PowderN: %s: hollow sample thickness is larger than its volume (sphere/cylinder).\n"
             "WARNING  Please check parameter values. Using bulk sample (thickness=0).\n", NAME_CURRENT_COMP);
      );
      thickness=0;
    }
    else if (!radius && (xwidth < 2*fabs(thickness) || yheight < 2*fabs(thickness) || zdepth < 2*fabs(thickness))) {
      MPI_MASTER(
      printf("PowderN: %s: hollow sample thickness is larger than its volume (box).\n"
             "WARNING  Please check parameter values.\n", NAME_CURRENT_COMP);
      );
    }
  }

  if (concentric && thickness==0) {
    MPI_MASTER(
    printf("PowderN: %s:Can not use concentric mode\n"
           "WARNING     on non hollow shape. Ignoring.\n",
           NAME_CURRENT_COMP);
    );
    concentric=0;
  }

  if (thickness>0) {
    if (radius>thickness) {
      line_info.radius_i=radius-thickness;
    } else {
      if (xwidth>2*thickness)  line_info.xwidth_i =xwidth -2*thickness;
      if (yheight>2*thickness) line_info.yheight_i=yheight-2*thickness;
      if (zdepth>2*thickness)  line_info.zdepth_i =zdepth -2*thickness;
    }
  } else if (thickness<0) {
    thickness = fabs(thickness);
    if (radius) {
      line_info.radius_i=radius;
      radius=line_info.radius_i+thickness;
    } else {
      line_info.xwidth_i =xwidth;
      line_info.yheight_i=yheight;
      line_info.zdepth_i =zdepth;
      xwidth   =xwidth +2*thickness;
      yheight  =yheight+2*thickness;
      zdepth   =zdepth +2*thickness;
    }
  }

  if (!line_info.yheight_i) {
    line_info.yheight_i = yheight;
  }

  if (!p_interact){
    fprintf(stderr,"PowderN: %s: WARNING: p_interact=0, adjusting to 0.01, to avoid algorithm instability\n",NAME_CURRENT_COMP);
    p_interact=1e-2;
  }
  if (!p_inc){
    fprintf(stderr,"PowderN: %s: WARNING: p_inc=0, adjusting to 0.01, to avoid algorithm instability\n",NAME_CURRENT_COMP);
    p_inc     =1e-2;
  }
  if (!p_transmit){
    fprintf(stderr,"PowderN: %s: WARNING: p_transmit=0, adjusting to 0.01, to avoid algorithm instability\n",NAME_CURRENT_COMP);
    p_transmit=1e-2;
  }
  double p_sum=p_interact+p_inc+p_transmit;
  p_interact = p_interact / p_sum;
  p_inc      = p_inc      / p_sum;
  p_transmit = p_transmit / p_sum;

  if (concentric) {
    MPI_MASTER(
    printf("PowderN: %s: Concentric mode - remember to include the 'opposite' copy of this component !\n"
           "WARNING  The equivalent, 'opposite' comp should have concentric=0\n", NAME_CURRENT_COMP);
    );
    if (p_transmit < 0.1) {
      MPI_MASTER(
      printf("PowderN: %s: Concentric mode and p_transmit<0.1 !\n"
        "WARNING  Consider increasing p_transmit as few particles will reach the inner hollow.\n", NAME_CURRENT_COMP);
      );
    }
  }

  if (reflections && strlen(reflections) && strcmp(reflections, "NULL") && strcmp(reflections, "0")) {
    i = read_line_data(reflections, &line_info);
    if (i == 0)
      exit(fprintf(stderr,"PowderN: %s: reflection file %s is not valid.\n"
                          "ERROR    Please check file format.\n", NAME_CURRENT_COMP, reflections));
  }

  /* compute the scattering unit density from material weight and density */
  /* the weight of the scattering element is the chemical formula molecular weight
   * times the nb of chemical formulae in the scattering element (nb_atoms) */
  if (!line_info.V_0 && line_info.at_nb > 0
    && line_info.at_weight > 0 && line_info.rho > 0) {
    /* molar volume [cm^3/mol] = weight [g/mol] / density [g/cm^3] */
    /* atom density per Angs^3 = [mol/cm^3] * N_Avogadro *(1e-8)^3 */
    line_info.V_0 = line_info.at_nb
      /(line_info.rho/line_info.at_weight/1e24*6.02214199e23);
  }

  /* the scattering unit cross sections are the chemical formula onces
   * times the nb of chemical formulae in the scattering element */
  if (line_info.at_nb > 0) {
    line_info.sigma_a *= line_info.at_nb; line_info.sigma_i *= line_info.at_nb;
  }

  if (line_info.sigma_a<0) line_info.sigma_a=0;
  if (line_info.sigma_i<0) line_info.sigma_i=0;

  if (line_info.V_0 <= 0)
  MPI_MASTER(
    printf("PowderN: %s: density/unit cell volume is NULL (Vc). Unactivating component.\n", NAME_CURRENT_COMP);
  );

  if (line_info.V_0 > 0 && p_inc && (!line_info.sigma_i || !(strlen(material) && strcmp(material,"NULL"))) ) {
  MPI_MASTER(
    printf("PowderN: %s: WARNING: You have requested statistics for incoherent scattering but not set a material datafile (\'%s\') nor defined sigma_inc!\n", NAME_CURRENT_COMP, material);
  );
  }

  if (line_info.flag_barns) { /* Factor 100 to convert from barns to fm^2 */
    line_info.XsectionFactor = 100;
  } else {
    line_info.XsectionFactor = 1;
  }

  if (line_info.V_0 > 0 && i) {
    L = line_info.list;

    line_info.q = malloc(line_info.count*sizeof(double));
    line_info.w = malloc(line_info.count*sizeof(double));
    line_info.my_s_k2 = malloc(line_info.count*sizeof(double));
    if (!line_info.q || !line_info.w || !line_info.my_s_k2)
      exit(fprintf(stderr,"PowderN: %s: ERROR allocating memory (init)\n", NAME_CURRENT_COMP));
    for(i=0; i<line_info.count; i++)
    {
      line_info.my_s_k2[i] = 4*PI*PI*PI* 1.0 *(L[i].DWfactor ? L[i].DWfactor : 1)
                 /(line_info.V_0*line_info.V_0)
                 *(L[i].j * L[i].F2 / L[i].q)*line_info.XsectionFactor;
      line_info.q[i] = L[i].q;
      line_info.w[i] = L[i].w;
    }
  }

  if (material && strlen(material) && strcmp(material, "NULL")) {
    int status;
    char **parsing;
    if( (status=Table_Read(&(line_info.mat_table),material,0))==-1){
       fprintf(stderr,"PowderN: %s Error reading material data from file %s.\n",NAME_CURRENT_COMP,material);
    }
    parsing=Table_ParseHeader(line_info.mat_table.header,
       "column_e","column_abs","column_inc","column_cohinc","column_tot",NULL);

    if (parsing){
      int i;
      for (i=0;i<5;i++){
        if (parsing[i]) line_info.mat_column_order[i]=atoi(parsing[i]);
      }
    }
  }

%}

TRACE
%{
  double l0, l1, l2, l3, k, k1,l_full, l, l_1, dl, alpha0, alpha, theta, my_s, my_s_n, sg;
  double solid_angle, photontype, ptype;
  double arg, tmp_kx, tmp_ky, tmp_kz, kout_x, kout_y, kout_z, nx, ny, nz, pmul=1;
  int    line;
  char   intersect=0;
  char   intersecti=0;
  
  // Variables calculated within thread for thread purpose only 
  char type = '\0';
  int itype = 0;
  double d_phi_thread = d_phi;
  // These ones are injected back to struct at the end of TRACE in non-OpenACC case
  int nb_reuses = line_info.nb_reuses;
  int nb_refl = line_info.nb_refl;
  int nb_refl_count = line_info.nb_refl_count;
  double kcache = line_info.k; 
  double Nq = line_info.Nq;
  double k_min = line_info.k_min;
  double k_max = line_info.k_max;
  double lfree = line_info.lfree;
  unsigned int photon_passed = line_info.photon_passed;
  long   xs_compute = line_info.xs_compute;
  long   xs_reuse   = line_info.xs_reuse;
  long   xs_calls   = line_info.xs_calls;
  int    flag_warning = line_info.flag_warning;
  double dq = line_info.dq;

  double my_s_k2_sum = line_info.my_s_k2_sum;
  double my_a = line_info.my_a;
  double my_inc = line_info.my_inc;

  #ifdef USE_OFF
  #ifdef OPENACC
  off_struct thread_offdata = offdata;
  #else
  #define thread_offdata offdata
  #endif
  #endif
  
  if (line_info.V_0 > 0 && (line_info.count || line_info.my_inc)) {
    if (line_info.shape == 1) {
      intersect  = box_intersect(&l0, &l3, x, y, z, kx, ky, kz, xwidth, yheight, zdepth);
      intersecti = box_intersect(&l1, &l2, x, y, z, kx, ky, kz, line_info.xwidth_i, line_info.yheight_i, line_info.zdepth_i);
    } else if (line_info.shape == 0) {
      intersect  = cylinder_intersect(&l0, &l3, x, y, z, kx, ky, kz, radius, yheight);
      intersecti = cylinder_intersect(&l1, &l2, x, y, z, kx, ky, kz, line_info.radius_i, line_info.yheight_i);
    } else if (line_info.shape == 2) {
      intersect  = sphere_intersect  (&l0, &l3, x,y,z, kx,ky,kz, radius);
      intersecti = sphere_intersect  (&l1, &l2, x,y,z, kx,ky,kz, line_info.radius_i);
    }
    #ifdef USE_OFF
      else if (line_info.shape == 3) {
      intersect  = off_x_intersect  (&l0, &l3, NULL, NULL, x,y,z, kx,ky,kz, thread_offdata);
      intersecti = 0;
    }
    #endif
  }

  if(intersect && l3 >0) {

    if (concentric) {
      /* Set up for concentric case */
      /* 'Remove' the backside of this comp */
      if (!intersecti) {
        l1 = (l3 + l0) /2;
      }
      l2 = l1;
      l3 = l1;
      dl = -1.0*rand01(); /* In case of scattering we will scatter on 'forward' part of sample */
    } else {
      if (!intersecti) {
        l1 = (l3 + l0) /2;
        l2 = l1;
      }
      dl = randpm1(); /* Possibility to scatter at all points in line of sight */
    }

    /* X-ray enters at t=l0. */
    if(l0 < 0) l0=0; /* already in sample */
    if(l1 < 0) l1=0; /* already in inner hollow */
    if(l2 < 0) l2=0; /* already past inner hollow */
    k = sqrt(kx*kx + ky*ky + kz*kz);
    l_full =l3 - l2 + l1 - l0;

    if (line_info.photon_passed < CHAR_BUF_LENGTH) {
      if (k < line_info.k_min) line_info.k_min = k;
      if (k > line_info.k_max) line_info.k_max = k;
      photon_passed++;
    }

    /* Calculate total scattering cross section at relevant wavevector.
       Reuse calculation if possible (i.e if photon is identical ot preceeding one and not GPU.*/
    #ifndef OPENACC
    if ( fabs(k - line_info.k) < 1e-15) {
        line_info.nb_reuses++;
	my_s_k2_sum=line_info.my_s_k2_sum;
	my_inc=line_info.my_inc;
	my_a=line_info.my_a;
    } else {
    #endif
        Nq = calc_xsect(k, line_info.q, line_info.my_s_k2, line_info.count, &my_s_k2_sum, &line_info);
        calc_abs_xsect(k, &my_a, &line_info);
        calc_inc_xsect(k, &my_inc, &line_info);
	if(pack!=1){
	  /*apply packing factor correction*/
	  my_a *= pack;
	  my_inc *= pack;
	  my_s_k2_sum *=pack;
	}
    #ifndef OPENACC
        line_info.my_s_k2_sum=my_s_k2_sum;
        line_info.my_inc=my_inc;
        line_info.my_a=my_a;
	line_info.Nq = Nq;
	line_info.k  = k;
        line_info.nb_refl += line_info.Nq;
        line_info.nb_refl_count++;
    }
    #endif

    if (l3 < 0) {
      l3=0; /* Already past sample?! */
      if (flag_warning < 100)
      printf("PowderN: %s: Warning: xray has already passed us? (Skipped).\n"
             "         In concentric geometry, this may be caused by a missing concentric=0 option in 2nd enclosing instance.\n", NAME_CURRENT_COMP);
      flag_warning++;
    } else {
      if (dl<0) { /* Calculate scattering point position */
        dl = fabs(dl)*(l1 - l0); /* 'Forward' part */
      } else {
        dl = dl * (l3 - l2) + (l2-l0) ; /* Possibly also 'backside' part */
      }

      my_s=my_s_k2_sum/(k*k)+my_inc;
      /* Total attenuation from scattering*/

      ptype = rand01();
      /* How to handle this one? Transmit (1) / Incoherent (2) / Coherent (3) ? */
      if (ptype < p_transmit) {
        photontype = 1;
        l = l_full; /* Passing through, full length */
        PROP_DL(l3);
      } else if (ptype >= p_transmit && ptype < (p_transmit + p_inc)) {
        photontype = 2;
        l = dl;       /* Penetration in sample */
        PROP_DL(dl+l0); /* Point of scattering */
        SCATTER;
      } else if (ptype >= p_transmit + p_inc) {
        photontype = 3;
        l=dl;
        PROP_DL(dl+l0); /* Point of scattering */
        SCATTER;
      } else {
        exit(fprintf(stderr,"PowderN %s: DEAD - this shouldn't happen!\n", NAME_CURRENT_COMP));
      }

      if (photontype == 3) { /* Make coherent scattering event */
        if (line_info.count > 0) {
          /* choose line */
          if (Nq > 1) line=floor(Nq*rand01());  /* Select between Nq powder lines */
          else line = 0;
          if (line_info.w[line])
            arg = line_info.q[line]*(1+line_info.w[line]*randnorm())/(2.0*k);
          else
            arg = line_info.q[line]/(2.0*k);
          my_s_n = pack*line_info.my_s_k2[line]/(k*k);
          if(fabs(arg) > 1)
            ABSORB;                   /* No bragg scattering possible*/
	  if (tth_sign == 0) {
		  sg = randpm1();
		  if (sg > 0) sg = 1; else sg=-1;
	  }
          else  {
	   sg = tth_sign/fabs(tth_sign);
          }
          theta = asin(arg);          /* Bragg scattering law */



          /* Choose point on Debye-Scherrer cone */
          if (d_phi_thread)
          { /* relate height of detector to the height on DS cone */
            arg = sin(d_phi_thread*DEG2RAD/2)/sin(2*theta);
            /* If full Debye-Scherrer cone is within d_phi, don't focus */
            if (arg < -1 || arg > 1) d_phi_thread = 0;
            /* Otherwise, determine alpha to rotate from scattering plane
               into d_phi focusing area*/
            else alpha = 2*asin(arg);
          }
          if (d_phi_thread) {
            /* Focusing */
            alpha = fabs(alpha);
	    alpha0 = 0.5*randpm1()*alpha;
            if(focus_flip){
                alpha0+=M_PI_2;
            }
          }
          else
            alpha0 = M_PI*randpm1();

          /* now find a nearly vertical rotation axis:
           * Either
           *  (k along Z) x (X axis) -> nearly Y axis
           * Or
           *  (k along X) x (Z axis) -> nearly Y axis
           */
		   
  /* update originating from McStas, added by JS, 1/7/2017
    If a target is defined, try to define vertical axis as a normal to the plane 
	defined by the incident particle velocity and target position. 
	Check that k is not ~ parallel to the target direction.
  */
			double knorm=0.0;
			if (target_index) {
				vec_prod(tmp_kx, tmp_ky, tmp_kz, kx,ky,kz, tgt_x, tgt_y, tgt_z);
				knorm = sqrt(tmp_kx*tmp_kx+tmp_ky*tmp_ky+tmp_kz*tmp_kz)/k;
			}
			// no target or direction is nearly parallel to k:
			if (knorm<0.01) {
				if (fabs(kx/k) < fabs(kz/k)) {
					nx = 1; ny = 0; nz = 0;
				} else {
					nx = 0; ny = 0; nz = 1;
				}
          			vec_prod(tmp_kx,tmp_ky,tmp_kz, kx,ky,kz, nx,ny,nz);
          		}

          /* k_out = rotate 'k' by 2*theta around tmp_k: Bragg angle */
          rotate(kout_x,kout_y,kout_z, kx,ky,kz, 2*sg*theta, tmp_kx,tmp_ky,tmp_kz);

          /* tmp_k = rotate k_out by alpha0 around 'k' (Debye-Scherrer cone) */
          rotate(tmp_kx,tmp_ky,tmp_kz, kout_x,kout_y,kout_z, alpha0, kx, ky, kz);
          kx = tmp_kx;
          ky = tmp_ky;
          kz = tmp_kz;
          
          /*weight the outgoing signal according to polarization*/
          if (Ex!=0 || Ey!=0 || Ez!=0){
              double EE=sqrt(Ex*Ex+Ey*Ey+Ez*Ez);
              double s=scalar_prod(kx,ky,kz,Ex,Ey,Ez)/k/EE;
              p*=(1-s)*(1-s);
          }else{
              /*unpolarized light in - means an effective reduction according to only theta*/
              p*=(1+cos(theta)*cos(theta))*0.5;
          }

          /* Since now scattered and new direction given, calculate path to exit */
          if (line_info.shape == 1) {
            intersect  = box_intersect(&l0, &l3, x, y, z, kx, ky, kz, xwidth, yheight, zdepth);
            intersecti = box_intersect(&l1, &l2, x, y, z, kx, ky, kz, line_info.xwidth_i, line_info.yheight_i, line_info.zdepth_i);
          } else if (line_info.shape == 0) {
            intersect  = cylinder_intersect(&l0, &l3, x, y, z, kx, ky, kz, radius, yheight);
            intersecti = cylinder_intersect(&l1, &l2, x, y, z, kx, ky, kz, line_info.radius_i, line_info.yheight_i);
          } else if (line_info.shape == 2) {
            intersect  = sphere_intersect  (&l0, &l3, x,y,z, kx,ky,kz, radius);
            intersecti = sphere_intersect  (&l1, &l2, x,y,z, kx,ky,kz, line_info.radius_i);
          } else if (line_info.shape == 3) {
            intersect  = off_x_intersect  (&l0, &l3, NULL, NULL, x,y,z, kx,ky,kz, offdata);
            intersecti = 0;
          }

          if (!intersect) {
            /* Strange error: did not hit cylinder */
            if (flag_warning < 100)
              printf("PowderN: %s: WARNING: Did not hit sample from inside (coh). ABSORB.\n", NAME_CURRENT_COMP);
            flag_warning++;
            ABSORB;
          }

          if (!intersecti) {
            l1 = (l3 + l0) /2;
            l2 = l1;
          }

          if (concentric && intersecti) {
            /* In case of concentricity, 'remove' backward wall of sample */
            l2 = l1;
            l3 = l1;
          }

          if(l0 < 0) l0=0; /* already in sample */
          if(l1 < 0) l1=0; /* already in inner hollow */
          if(l2 < 0) l2=0; /* already past inner hollow */


          l_1 = l3 - l2 + l1 - l0; /* Length to exit */

          pmul  *= Nq*l_full*my_s_n*exp(-(my_a+my_s)*(l+l_1))/(1-(p_inc+p_transmit));
          /* Correction in case of d_phi focusing - BUT only when d_phi != 0 */
	  if (d_phi_thread) {
	    pmul *= alpha/PI;
	    if (tth_sign) pmul *=0.5;
	  }

          type = 'c';
          itype = 1;
	  dq = line_info.q[line];
        } /* else transmit <-- No powder lines in file */
      }  /* Coherent scattering event */
      else if (photontype == 2) {  /* Make incoherent scattering event */
        /*should be replaced by Compton scattering and/or TDS*/
        if (d_omega && d_phi_thread) {
			randvec_target_rect_angular(&kx, &ky, &kz, &solid_angle,
			  tgt_x, tgt_y, tgt_z, d_omega*DEG2RAD, d_phi_thread*DEG2RAD, ROT_A_CURRENT_COMP);
		} else if (d_phi_thread) {
			randvec_target_rect_angular(&kx, &ky, &kz, &solid_angle,
                                      tgt_x, tgt_y, tgt_z,
                                      2*PI, d_phi_thread*DEG2RAD, ROT_A_CURRENT_COMP);
        } else {
          randvec_target_circle(&kx, &ky, &kz,
                                &solid_angle, 0, 0, 1, 0);
        }
        k1 = sqrt(kx*kx+ky*ky+kz*kz);
        kx *= k/k1;
        ky *= k/k1;
        kz *= k/k1;

        /* Since now scattered and new direction given, calculate path to exit */
        if (line_info.shape == 1) {
          intersect  = box_intersect(&l0, &l3, x, y, z, kx, ky, kz, xwidth, yheight, zdepth);
          intersecti = box_intersect(&l1, &l2, x, y, z, kx, ky, kz, line_info.xwidth_i, line_info.yheight_i, line_info.zdepth_i);
        } else if (line_info.shape == 0) {
          intersect  = cylinder_intersect(&l0, &l3, x, y, z, kx, ky, kz, radius, yheight);
          intersecti = cylinder_intersect(&l1, &l2, x, y, z, kx, ky, kz, line_info.radius_i, line_info.yheight_i);
        } else if (line_info.shape == 2) {
          intersect  = sphere_intersect  (&l0, &l3, x,y,z, kx,ky,kz, radius);
          intersecti = sphere_intersect  (&l1, &l2, x,y,z, kx,ky,kz, line_info.radius_i);
        }
	#ifdef USE_OFF
	  else if (line_info.shape == 3) {
          intersect  = off_x_intersect  (&l0, &l3, NULL, NULL, x,y,z, kx,ky,kz, thread_offdata);
          intersecti = 0;
        }
	#endif

        if (!intersect) {
          /* Strange error: did not hit cylinder */
          if (flag_warning < 100)
            printf("PowderN: %s: WARNING: Did not hit sample from inside (inc). ABSORB.\n", NAME_CURRENT_COMP);
          flag_warning++;
          ABSORB;
        }

        if (!intersecti) {
          l1 = (l3 + l0) /2;
          l2 = l1;
        }

        if (concentric && intersecti) {
          /* In case of concentricity, 'remove' backward wall of sample */
          l2 = l1;
          l3 = l1;
        }

        if(l0 < 0) l0=0; /* already in sample */
        if(l1 < 0) l1=0; /* already in inner hollow */
        if(l2 < 0) l2=0; /* already past inner hollow */


        l_1 = (l3 - l2 + l1 - l0); /* Length to exit */

        pmul *= l_full*my_inc*exp(-(my_a+my_s)*(l+l_1))/(p_inc);
        pmul *= solid_angle/(4*PI);

        type = 'i';
	itype = 2;

      }  /* Incoherent scattering event */
      else if (photontype == 1) {
        /* Make transmitted (absorption-corrected) event */
        /* No coordinate changes here, simply change xray weight */
        pmul *= exp(-(my_a+my_s)*(l))/(p_transmit);

        type = 't';
	itype = 3;
      }
      p *= pmul;
    } /* Photon leaving since it has passed already */
  } /* else transmit non interacting xrays */

  // Inject these back to component struct in non-OpenACC case
  #ifndef OPENACC
  line_info.nb_reuses=nb_reuses;
  line_info.nb_refl=nb_refl;
  line_info.nb_refl_count=nb_refl_count;
  line_info.k=kcache;
  line_info.Nq=Nq;
  line_info.k_min=k_min;
  line_info.k_max=k_max;
  line_info.lfree=lfree;
  line_info.xs_compute=xs_compute;
  line_info.xs_reuse=xs_reuse;
  line_info.xs_calls=xs_calls;
  line_info.dq=dq;
  line_info.photon_passed = photon_passed;
  #endif
  // These should be updated in any case
  #pragma acc atomic write
  line_info.flag_warning += flag_warning;
%}

FINALLY
%{
  free(line_info.list);
  free(line_info.q);
  free(line_info.w);
  free(line_info.my_s_k2);

  MPI_MASTER(
  if (line_info.flag_warning)
    printf("PowderN: %s: Error messages were repeated %i times with absorbed xrays.\n",
      NAME_CURRENT_COMP, line_info.flag_warning);

  /* in case this instance is used in a SPLIT, we can recommend the
     optimal iteration value */
  if (line_info.nb_refl_count) {
    double split_iterations = (double)line_info.nb_reuses/line_info.nb_refl_count + 1;
    double split_optimal    = (double)line_info.nb_refl/line_info.nb_refl_count;
    if (split_optimal > split_iterations + 5)
      printf("PowderN: %s: Info: you may highly improve the computation efficiency by using\n"
        "    SPLIT %i COMPONENT %s=PowderN(...)\n"
        "  in the instrument description %s.\n",
        NAME_CURRENT_COMP, (int)split_optimal, NAME_CURRENT_COMP, instrument_source);
  }
  );

%}

MCDISPLAY
%{
  if (line_info.V_0) {

    if (line_info.shape == 0) { /* cyl */
      circle("xz", 0,  yheight/2.0, 0, radius);
      circle("xz", 0, -yheight/2.0, 0, radius);
      line(-radius, -yheight/2.0, 0, -radius, +yheight/2.0, 0);
      line(+radius, -yheight/2.0, 0, +radius, +yheight/2.0, 0);
      line(0, -yheight/2.0, -radius, 0, +yheight/2.0, -radius);
      line(0, -yheight/2.0, +radius, 0, +yheight/2.0, +radius);
      if (thickness) {
        double radius_i=radius-thickness;
        circle("xz", 0,  yheight/2.0, 0, radius_i);
        circle("xz", 0, -yheight/2.0, 0, radius_i);
        line(-radius_i, -yheight/2.0, 0, -radius_i, +yheight/2.0, 0);
        line(+radius_i, -yheight/2.0, 0, +radius_i, +yheight/2.0, 0);
        line(0, -yheight/2.0, -radius_i, 0, +yheight/2.0, -radius_i);
        line(0, -yheight/2.0, +radius_i, 0, +yheight/2.0, +radius_i);
      }
    } else if (line_info.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);
      if (line_info.zdepth_i) {
        xmin = -0.5*line_info.xwidth_i;
        xmax =  0.5*line_info.xwidth_i;
        ymin = -0.5*line_info.yheight_i;
        ymax =  0.5*line_info.yheight_i;
        zmin = -0.5*line_info.zdepth_i;
        zmax =  0.5*line_info.zdepth_i;
        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);
      }
    } if (line_info.shape == 2) { /* sphere */
      if (line_info.radius_i) {
        circle("xy",0,0,0,line_info.radius_i);
        circle("xz",0,0,0,line_info.radius_i);
        circle("yz",0,0,0,line_info.radius_i);
      }
      circle("xy",0,0,0,radius);
      circle("xz",0,0,0,radius);
      circle("yz",0,0,0,radius);
    } else if (line_info.shape == 3) {	/* OFF file */
      off_display(offdata);
    }
  }
%}
END
