src/gromacs/gmxana/sfactor.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  37 #ifndef GMX_GMXANA_SFACTOR_H
  38 #define GMX_GMXANA_SFACTOR_H
  39
  40 #include "gromacs/math/gmxcomplex.h"
  41 #include "gromacs/math/vectypes.h"
  42 #include "gromacs/utility/basedefinitions.h"
  43
  44 struct gmx_output_env_t;
  45 struct t_topology;
  46 struct t_trxframe;
  47
  48 typedef struct gmx_structurefactors gmx_structurefactors_t;
  49
  50 typedef struct structure_factor structure_factor_t;
  51
  52 typedef struct reduced_atom reduced_atom_t;
  53
  54 int * create_indexed_atom_type (reduced_atom_t * atm, int size);
  55
  56 void compute_structure_factor (structure_factor_t * sft, matrix box,
  57                                reduced_atom_t * red, int isize, real start_q,
  58                                real end_q, int group, real **sf_table);
  59
  60 gmx_structurefactors_t *gmx_structurefactors_init(const char *datfn);
  61
  62 void gmx_structurefactors_done(gmx_structurefactors_t *gsf);
  63
  64 int gmx_structurefactors_get_sf(gmx_structurefactors_t *gsf, int elem, real a[4], real b[4], real *c);
  65
  66 real **gmx_structurefactors_table(gmx_structurefactors_t *gsf, real momentum, real ref_k,
  67                                   real lambda, int n_angles);
  68
  69 void save_data (structure_factor_t * sft, const char *file, int ngrps,
  70                 real start_q, real end_q, const gmx_output_env_t *oenv);
  71
  72 double CMSF (gmx_structurefactors_t *gsf, int type, int nh, double lambda, double sin_theta);
  73
  74 int return_atom_type (const char *name, gmx_structurefactors_t *gsf);
  75
  76 void rearrange_atoms (reduced_atom_t * positions, struct t_trxframe *fr, int * index,
  77                       int isize, const t_topology * top, gmx_bool flag, gmx_structurefactors_t *gsf);
  78
  79 int do_scattering_intensity (const char* fnTPS, const char* fnNDX,
  80                              const char* fnXVG, const char *fnTRX,
  81                              const char* fnDAT,
  82                              real start_q, real end_q,
  83                              real energy, int ng, const gmx_output_env_t *oenv);
  84
  85 t_complex *** rc_tensor_allocation(int x, int y, int z);
  86
  87 real **compute_scattering_factor_table (gmx_structurefactors_t *gsf, structure_factor_t * sft);
  88
  89 #endif