#ifndef LMP_MANIFOLD_THYLAKOID_H
#define LMP_MANIFOLD_THYLAKOID_H

#include "manifold.h"
#include <vector>
#include <stdio.h>

#include "manifold_thylakoid_shared.h"

namespace LAMMPS_NS {

namespace user_manifold {


  class manifold_thylakoid : public manifold {
   public:
    enum { NPARAMS = 3 };
    manifold_thylakoid( LAMMPS *lmp, int, char ** );
    virtual ~manifold_thylakoid();

    virtual double g( const double *x );
    virtual void   n( const double *x, double *n );

    static const char* type(){ return "thylakoid"; }
    virtual const char *id(){ return type(); }
    static int expected_argc(){ return NPARAMS; }
    virtual int nparams(){ return NPARAMS; }


    virtual void post_param_init();
    virtual void checkup(); // Some diagnostics...
   private:
    void init_domains();

    thyla_part *get_thyla_part( const double *x, int *err_flag, std::size_t *idx = NULL );
    int is_in_domain( thyla_part *p, const double *x );
    void check_overlap();
    std::vector<thyla_part*> parts;

    thyla_part *make_plane_part (double a, double b, double c,
                                 const std::vector<double> &pt);
    thyla_part *make_cyl_part   (double a, double b, double c,
                                 const std::vector<double> &pt, double R);
    thyla_part *make_sphere_part(const std::vector<double> &pt, double R);
    thyla_part *make_cyl_to_plane_part(double X0, double R0, double R, double s,
                                       const std::vector<double> &pt );


    void set_domain( thyla_part *p, const std::vector<double> &lo,
                     const std::vector<double> &hi );

    void print_part_data( FILE *fp_doms, FILE *fp_coms );

    // Coefficients for the thylakoid model. At the moment it is just
    // a cylinder, we slowly expand it.
    double pad;  // Padding to make sure periodic images are mapped back properly.
    double LB, lT, lB, wB, LT;

    // Domain size:
    double x0, y0, z0;
    double x1, y1, z1;
    double Lx, Ly, Lz;
  };



} // namespace LAMMPS_NS

}

#endif // LMP_MANIFOLD_THYLAKOID_H
