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
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  35
  36 #ifndef _nsfactor_h
  37 #define _nsfactor_h
  38
  39 #include "gromacs/legacyheaders/oenv.h"
  40 #include "gromacs/legacyheaders/types/simple.h"
  41
  42 #ifdef __cplusplus
  43 extern "C" {
  44 #endif
  45
  46 struct t_topology;
  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     struct 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(struct 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