src/gromacs/gmxana/nsfactor.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
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   8  *
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  11  * as published by the Free Software Foundation; either version 2.1
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  35
  36 #ifndef _nsfactor_h
  37 #define _nsfactor_h
  38
  39 #include "index.h"
  40 #include "types/simple.h"
  41 #include "oenv.h"
  42
  43 #ifdef __cplusplus
  44 extern "C" {
  45 #endif
  46
  47 typedef struct gmx_neutron_atomic_structurefactors_t {
  48     int       nratoms;
  49     int      *p;       /* proton number */
  50     int      *n;       /* neuton number */
  51     double   *slength; /* scattering length in fm */
  52     char    **atomnm;  /* atom symbol */
  53 } gmx_neutron_atomic_structurefactors_t;
  54
  55 typedef struct gmx_sans_t {
  56     t_topology *top;     /* topology */
  57     double     *slength; /* scattering length for this topology */
  58 } gmx_sans_t;
  59
  60 typedef struct gmx_radial_distribution_histogram_t {
  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     int      qn;    /* number of items */
  69     double  *s;     /* scattering */
  70     double  *q;     /* q vectors */
  71     double   qstep; /* q increment */
  72 } gmx_static_structurefactor_t;
  73
  74 void check_binwidth(real binwidth);
  75
  76 void check_mcover(real mcover);
  77
  78 void normalize_probability(int n, double *a);
  79
  80 gmx_neutron_atomic_structurefactors_t *gmx_neutronstructurefactors_init(const char *datfn);
  81
  82 gmx_sans_t *gmx_sans_init(t_topology *top, gmx_neutron_atomic_structurefactors_t *gnsf);
  83
  84 gmx_radial_distribution_histogram_t *calc_radial_distribution_histogram  (gmx_sans_t  *gsans,
  85                                                                           rvec        *x,
  86                                                                           matrix       box,
  87                                                                           atom_id     *index,
  88                                                                           int          isize,
  89                                                                           double       binwidth,
  90                                                                           gmx_bool     bMC,
  91                                                                           gmx_bool     bNORM,
  92                                                                           real         mcover,
  93                                                                           unsigned int seed);
  94
  95 gmx_static_structurefactor_t *convert_histogram_to_intensity_curve (gmx_radial_distribution_histogram_t *pr, double start_q, double end_q, double q_step);
  96
  97
  98 #ifdef __cplusplus
  99 }
 100 #endif
 101 #endif