src/gromacs/gmxana/nsfactor.h

   1 /*
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  35
  36 #ifndef _nsfactor_h
  37 #define _nsfactor_h
  38
  39 #include "gromacs/legacyheaders/index.h"
  40 #include "gromacs/legacyheaders/oenv.h"
  41 #include "gromacs/legacyheaders/types/simple.h"
  42 #include "gromacs/legacyheaders/types/topology.h"
  43
  44 #ifdef __cplusplus
  45 extern "C" {
  46 #endif
  47
  48 typedef struct gmx_neutron_atomic_structurefactors_t {
  49     int       nratoms;
  50     int      *p;       /* proton number */
  51     int      *n;       /* neuton number */
  52     double   *slength; /* scattering length in fm */
  53     char    **atomnm;  /* atom symbol */
  54 } gmx_neutron_atomic_structurefactors_t;
  55
  56 typedef struct gmx_sans_t {
  57     t_topology *top;     /* topology */
  58     double     *slength; /* scattering length for this topology */
  59 } gmx_sans_t;
  60
  61 typedef struct gmx_radial_distribution_histogram_t {
  62     int     grn;      /* number of bins */
  63     double  binwidth; /* bin size */
  64     double *r;        /* Distances */
  65     double *gr;       /* Probability */
  66 } gmx_radial_distribution_histogram_t;
  67
  68 typedef struct gmx_static_structurefactor_t {
  69     int      qn;    /* number of items */
  70     double  *s;     /* scattering */
  71     double  *q;     /* q vectors */
  72     double   qstep; /* q increment */
  73 } gmx_static_structurefactor_t;
  74
  75 void check_binwidth(real binwidth);
  76
  77 void check_mcover(real mcover);
  78
  79 void normalize_probability(int n, double *a);
  80
  81 gmx_neutron_atomic_structurefactors_t *gmx_neutronstructurefactors_init(const char *datfn);
  82
  83 gmx_sans_t *gmx_sans_init(t_topology *top, gmx_neutron_atomic_structurefactors_t *gnsf);
  84
  85 gmx_radial_distribution_histogram_t *calc_radial_distribution_histogram  (gmx_sans_t  *gsans,
  86                                                                           rvec        *x,
  87                                                                           matrix       box,
  88                                                                           atom_id     *index,
  89                                                                           int          isize,
  90                                                                           double       binwidth,
  91                                                                           gmx_bool     bMC,
  92                                                                           gmx_bool     bNORM,
  93                                                                           real         mcover,
  94                                                                           unsigned int seed);
  95
  96 gmx_static_structurefactor_t *convert_histogram_to_intensity_curve (gmx_radial_distribution_histogram_t *pr, double start_q, double end_q, double q_step);
  97
  98
  99 #ifdef __cplusplus
 100 }
 101 #endif
 102 #endif