src/gromacs/gmxana/nsfactor.h

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  35
  36 #ifndef GMX_GMXANA_NSFACTOR_H
  37 #define GMX_GMXANA_NSFACTOR_H
  38
  39 #include "gromacs/math/vectypes.h"
  40 #include "gromacs/utility/basedefinitions.h"
  41
  42 struct t_topology;
  43
  44 typedef struct gmx_neutron_atomic_structurefactors_t {
  45     int       nratoms;
  46     int      *p;       /* proton number */
  47     int      *n;       /* neuton number */
  48     double   *slength; /* scattering length in fm */
  49     char    **atomnm;  /* atom symbol */
  50 } gmx_neutron_atomic_structurefactors_t;
  51
  52 typedef struct gmx_sans_t {
  53     const t_topology *top;     /* topology */
  54     double           *slength; /* scattering length for this topology */
  55 } gmx_sans_t;
  56
  57 typedef struct gmx_radial_distribution_histogram_t {
  58     int     grn;      /* number of bins */
  59     double  binwidth; /* bin size */
  60     double *r;        /* Distances */
  61     double *gr;       /* Probability */
  62 } gmx_radial_distribution_histogram_t;
  63
  64 typedef struct gmx_static_structurefactor_t {
  65     int      qn;    /* number of items */
  66     double  *s;     /* scattering */
  67     double  *q;     /* q vectors */
  68     double   qstep; /* q increment */
  69 } gmx_static_structurefactor_t;
  70
  71 void check_binwidth(real binwidth);
  72
  73 void check_mcover(real mcover);
  74
  75 void normalize_probability(int n, double *a);
  76
  77 gmx_neutron_atomic_structurefactors_t *gmx_neutronstructurefactors_init(const char *datfn);
  78
  79 gmx_sans_t *gmx_sans_init(const t_topology *top, gmx_neutron_atomic_structurefactors_t *gnsf);
  80
  81 gmx_radial_distribution_histogram_t *calc_radial_distribution_histogram  (gmx_sans_t        *gsans,
  82                                                                           rvec              *x,
  83                                                                           matrix             box,
  84                                                                           const int         *index,
  85                                                                           int                isize,
  86                                                                           double             binwidth,
  87                                                                           gmx_bool           bMC,
  88                                                                           gmx_bool           bNORM,
  89                                                                           real               mcover,
  90                                                                           unsigned int       seed);
  91
  92 gmx_static_structurefactor_t *convert_histogram_to_intensity_curve (gmx_radial_distribution_histogram_t *pr, double start_q, double end_q, double q_step);
  93
  94
  95 #endif