include/sfactor.h

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  38
  39 #ifndef _sfactor_h
  40 #define _sfactor_h
  41
  42 #include "visibility.h"
  43 #include "index.h"
  44 #include "types/simple.h"
  45 #include "gmxcomplex.h"
  46 #include "oenv.h"
  47
  48
  49
  50 #ifdef __cplusplus
  51 extern "C" {
  52 #endif
  53
  54
  55 typedef struct gmx_structurefactors gmx_structurefactors_t;
  56
  57 typedef struct structure_factor structure_factor_t;
  58
  59 typedef struct reduced_atom reduced_atom_t;
  60
  61 int * create_indexed_atom_type (reduced_atom_t * atm, int size);
  62
  63 void compute_structure_factor (structure_factor_t * sft, matrix box,
  64                                reduced_atom_t * red, int isize, real start_q,
  65                                real end_q, int group, real **sf_table);
  66
  67 gmx_structurefactors_t *gmx_structurefactors_init(const char *datfn);
  68
  69 void gmx_structurefactors_done(gmx_structurefactors_t *gsf);
  70
  71 int gmx_structurefactors_get_sf(gmx_structurefactors_t *gsf, int elem, real a[4], real b[4], real *c);
  72
  73 real **gmx_structurefactors_table(gmx_structurefactors_t *gsf, real momentum, real ref_k,
  74                                   real lambda, int n_angles);
  75
  76 void save_data (structure_factor_t * sft, const char *file, int ngrps,
  77                 real start_q, real end_q, const output_env_t oenv);
  78
  79 double CMSF (gmx_structurefactors_t *gsf, int type, int nh, double lambda, double sin_theta);
  80
  81 int return_atom_type (const char *name, gmx_structurefactors_t *gsf);
  82
  83 void rearrange_atoms (reduced_atom_t * positions, t_trxframe *fr, atom_id * index,
  84                       int isize, t_topology * top, gmx_bool flag, gmx_structurefactors_t *gsf);
  85
  86 GMX_LIBGMX_EXPORT
  87 int do_scattering_intensity (const char* fnTPS, const char* fnNDX,
  88                              const char* fnXVG, const char *fnTRX,
  89                              const char* fnDAT,
  90                              real start_q, real end_q,
  91                              real energy, int ng, const output_env_t oenv);
  92
  93 t_complex *** rc_tensor_allocation(int x, int y, int z);
  94
  95 real **compute_scattering_factor_table (gmx_structurefactors_t *gsf, structure_factor_t * sft, int *nsftable);
  96
  97 #ifdef __cplusplus
  98 }
  99 #endif
 100 #endif