src/gromacs/gmxana/sfactor.h

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