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#ifndef _sfactor_h
#define _sfactor_h

#include "visibility.h"
#include "index.h"
#include "types/simple.h"
#include "gmxcomplex.h"
#include "oenv.h"



#ifdef __cplusplus
extern "C" {
#endif


typedef struct gmx_structurefactors gmx_structurefactors_t;

typedef struct structure_factor structure_factor_t;

typedef struct reduced_atom reduced_atom_t;

int * create_indexed_atom_type (reduced_atom_t * atm, int size);

void compute_structure_factor (structure_factor_t * sft, matrix box,
                               reduced_atom_t * red, int isize, real start_q,
                               real end_q, int group, real **sf_table);

gmx_structurefactors_t *gmx_structurefactors_init(const char *datfn);

void gmx_structurefactors_done(gmx_structurefactors_t *gsf);

int gmx_structurefactors_get_sf(gmx_structurefactors_t *gsf, int elem, real a[4], real b[4], real *c);

real **gmx_structurefactors_table(gmx_structurefactors_t *gsf, real momentum, real ref_k,
                                  real lambda, int n_angles);

void save_data (structure_factor_t * sft, const char *file, int ngrps,
                real start_q, real end_q, const output_env_t oenv);

double CMSF (gmx_structurefactors_t *gsf, int type, int nh, double lambda, double sin_theta);

int return_atom_type (const char *name, gmx_structurefactors_t *gsf);

void rearrange_atoms (reduced_atom_t * positions, t_trxframe *fr, atom_id * index,
                      int isize, t_topology * top, gmx_bool flag, gmx_structurefactors_t *gsf);

GMX_LIBGMX_EXPORT
int do_scattering_intensity (const char* fnTPS, const char* fnNDX,
                             const char* fnXVG, const char *fnTRX,
                             const char* fnDAT,
                             real start_q, real end_q,
                             real energy, int ng, const output_env_t oenv);

t_complex *** rc_tensor_allocation(int x, int y, int z);

real **compute_scattering_factor_table (gmx_structurefactors_t *gsf, structure_factor_t * sft, int *nsftable);

#ifdef __cplusplus
}
#endif
#endif
