include/sfactor.h

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * Gromacs Runs On Most of All Computer Systems
  34  */
  35
  36 #ifndef _sfactor_h
  37 #define _sfactor_h
  38
  39
  40 #ifdef HAVE_CONFIG_H
  41 #include <config.h>
  42 #endif
  43
  44 #include "index.h"
  45 #include "types/simple.h"
  46 #include "gmxcomplex.h"
  47 #include "oenv.h"
  48
  49
  50
  51 #ifdef __cplusplus
  52 extern "C" {
  53 #endif
  54
  55
  56 typedef struct gmx_structurefactors gmx_structurefactors_t;
  57
  58 typedef struct structure_factor structure_factor_t;
  59
  60 typedef struct reduced_atom reduced_atom_t;
  61
  62 extern int * create_indexed_atom_type (reduced_atom_t * atm, int size);
  63
  64 extern void compute_structure_factor (structure_factor_t * sft, matrix box,
  65                                reduced_atom_t * red, int isize, real start_q,
  66                                real end_q, int group,real **sf_table);
  67
  68 extern gmx_structurefactors_t *gmx_structurefactors_init(const char *datfn);
  69
  70 extern void gmx_structurefactors_done(gmx_structurefactors_t *gsf);
  71
  72 extern int gmx_structurefactors_get_sf(gmx_structurefactors_t *gsf, int elem, real a[4], real b[4], real *c);
  73
  74 extern real **gmx_structurefactors_table(gmx_structurefactors_t *gsf,real momentum, real ref_k,
  75         real lambda, int n_angles);
  76
  77 extern void save_data (structure_factor_t * sft, const char *file, int ngrps,
  78                 real start_q, real end_q, const output_env_t oenv);
  79
  80 extern double CMSF (gmx_structurefactors_t *gsf,int type,int nh,double lambda, double sin_theta);
  81
  82 extern int return_atom_type (const char *name,gmx_structurefactors_t *gsf);
  83
  84 extern void rearrange_atoms (reduced_atom_t * positions, t_trxframe *fr, atom_id * index,
  85                       int isize, t_topology * top, bool flag,gmx_structurefactors_t *gsf);
  86
  87 extern int do_scattering_intensity (const char* fnTPS, const char* fnNDX,
  88                              const char* fnXVG, const char *fnTRX,
  89                              const char* fnDAT,
  90                              real start_q,real end_q,
  91                              real energy,int ng,const output_env_t oenv);
  92
  93 extern t_complex *** rc_tensor_allocation(int x, int y, int z);
  94
  95 extern real **compute_scattering_factor_table (gmx_structurefactors_t *gsf,structure_factor_t * sft,int *nsftable);
  96
  97 #ifdef __cplusplus
  98 }
  99 #endif
 100 #endif