include/sfactor.h

   1 /*
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   9  *                        VERSION 3.2.0
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  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
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  35
  36 #ifndef _sfactor_h
  37 #define _sfactor_h
  38
  39
  40 #include "index.h"
  41 #include "types/simple.h"
  42 #include "gmxcomplex.h"
  43 #include "oenv.h"
  44
  45
  46
  47 #ifdef __cplusplus
  48 extern "C" {
  49 #endif
  50
  51
  52 typedef struct gmx_structurefactors gmx_structurefactors_t;
  53
  54 typedef struct structure_factor structure_factor_t;
  55
  56 typedef struct reduced_atom reduced_atom_t;
  57
  58 int * create_indexed_atom_type (reduced_atom_t * atm, int size);
  59
  60 void compute_structure_factor (structure_factor_t * sft, matrix box,
  61                                reduced_atom_t * red, int isize, real start_q,
  62                                real end_q, int group,real **sf_table);
  63
  64 gmx_structurefactors_t *gmx_structurefactors_init(const char *datfn);
  65
  66 void gmx_structurefactors_done(gmx_structurefactors_t *gsf);
  67
  68 int gmx_structurefactors_get_sf(gmx_structurefactors_t *gsf, int elem, real a[4], real b[4], real *c);
  69
  70 real **gmx_structurefactors_table(gmx_structurefactors_t *gsf,real momentum, real ref_k,
  71         real lambda, int n_angles);
  72
  73 void save_data (structure_factor_t * sft, const char *file, int ngrps,
  74                 real start_q, real end_q, const output_env_t oenv);
  75
  76 double CMSF (gmx_structurefactors_t *gsf,int type,int nh,double lambda, double sin_theta);
  77
  78 int return_atom_type (const char *name,gmx_structurefactors_t *gsf);
  79
  80 void rearrange_atoms (reduced_atom_t * positions, t_trxframe *fr, atom_id * index,
  81                       int isize, t_topology * top, gmx_bool flag,gmx_structurefactors_t *gsf);
  82
  83 int do_scattering_intensity (const char* fnTPS, const char* fnNDX,
  84                              const char* fnXVG, const char *fnTRX,
  85                              const char* fnDAT,
  86                              real start_q,real end_q,
  87                              real energy,int ng,const output_env_t oenv);
  88
  89 t_complex *** rc_tensor_allocation(int x, int y, int z);
  90
  91 real **compute_scattering_factor_table (gmx_structurefactors_t *gsf,structure_factor_t * sft,int *nsftable);
  92
  93 #ifdef __cplusplus
  94 }
  95 #endif
  96 #endif