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 {
  46     int     nratoms;
  47     int*    p;       /* proton number */
  48     int*    n;       /* neuton number */
  49     double* slength; /* scattering length in fm */
  50     char**  atomnm;  /* atom symbol */
  51 } gmx_neutron_atomic_structurefactors_t;
  52
  53 typedef struct gmx_sans_t
  54 {
  55     const t_topology* top;     /* topology */
  56     double*           slength; /* scattering length for this topology */
  57 } gmx_sans_t;
  58
  59 typedef struct gmx_radial_distribution_histogram_t
  60 {
  61     int     grn;      /* number of bins */
  62     double  binwidth; /* bin size */
  63     double* r;        /* Distances */
  64     double* gr;       /* Probability */
  65 } gmx_radial_distribution_histogram_t;
  66
  67 typedef struct gmx_static_structurefactor_t
  68 {
  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(const 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                                                                         const int*   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,
  97                                                                    double start_q,
  98                                                                    double end_q,
  99                                                                    double q_step);
 100
 101
 102 #endif