Introduce SimulatorBuilder
[gromacs.git] / src / gromacs / gmxana / nsfactor.h
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36 #ifndef GMX_GMXANA_NSFACTOR_H
37 #define GMX_GMXANA_NSFACTOR_H
39 #include "gromacs/math/vectypes.h"
40 #include "gromacs/utility/basedefinitions.h"
42 struct t_topology;
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;
52 typedef struct gmx_sans_t {
53 const t_topology *top; /* topology */
54 double *slength; /* scattering length for this topology */
55 } gmx_sans_t;
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;
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;
71 void check_binwidth(real binwidth);
73 void check_mcover(real mcover);
75 void normalize_probability(int n, double *a);
77 gmx_neutron_atomic_structurefactors_t *gmx_neutronstructurefactors_init(const char *datfn);
79 gmx_sans_t *gmx_sans_init(const t_topology *top, gmx_neutron_atomic_structurefactors_t *gnsf);
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);
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);
95 #endif