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) 2013,2014,2015,2016,2018 by the GROMACS development team.
   7  * Copyright (c) 2019,2020, by the GROMACS development team, led by
   8  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   9  * and including many others, as listed in the AUTHORS file in the
  10  * top-level source directory and at http://www.gromacs.org.
  11  *
  12  * GROMACS is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU Lesser General Public License
  14  * as published by the Free Software Foundation; either version 2.1
  15  * of the License, or (at your option) any later version.
  16  *
  17  * GROMACS is distributed in the hope that it will be useful,
  18  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  19  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  20  * Lesser General Public License for more details.
  21  *
  22  * You should have received a copy of the GNU Lesser General Public
  23  * License along with GROMACS; if not, see
  24  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  25  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  26  *
  27  * If you want to redistribute modifications to GROMACS, please
  28  * consider that scientific software is very special. Version
  29  * control is crucial - bugs must be traceable. We will be happy to
  30  * consider code for inclusion in the official distribution, but
  31  * derived work must not be called official GROMACS. Details are found
  32  * in the README & COPYING files - if they are missing, get the
  33  * official version at http://www.gromacs.org.
  34  *
  35  * To help us fund GROMACS development, we humbly ask that you cite
  36  * the research papers on the package. Check out http://www.gromacs.org.
  37  */
  38 #ifndef GMX_GMXANA_SFACTOR_H
  39 #define GMX_GMXANA_SFACTOR_H
  40
  41 #include "gromacs/math/gmxcomplex.h"
  42 #include "gromacs/math/vectypes.h"
  43 #include "gromacs/utility/basedefinitions.h"
  44
  45 struct gmx_output_env_t;
  46 struct t_topology;
  47 struct t_trxframe;
  48
  49 typedef struct gmx_structurefactors gmx_structurefactors_t;
  50
  51 typedef struct structure_factor structure_factor_t;
  52
  53 typedef struct reduced_atom reduced_atom_t;
  54
  55 int* create_indexed_atom_type(reduced_atom_t* atm, int size);
  56
  57 void compute_structure_factor(structure_factor_t* sft,
  58                               matrix              box,
  59                               reduced_atom_t*     red,
  60                               int                 isize,
  61                               real                start_q,
  62                               real                end_q,
  63                               int                 group,
  64                               real**              sf_table);
  65
  66 gmx_structurefactors_t* gmx_structurefactors_init(const char* datfn);
  67
  68 void gmx_structurefactors_done(gmx_structurefactors_t* gsf);
  69
  70 int gmx_structurefactors_get_sf(gmx_structurefactors_t* gsf, int elem, real a[4], real b[4], real* c);
  71
  72 real** gmx_structurefactors_table(gmx_structurefactors_t* gsf, real momentum, real ref_k, real lambda, int n_angles);
  73
  74 void save_data(structure_factor_t* sft, const char* file, int ngrps, real start_q, real end_q, const gmx_output_env_t* oenv);
  75
  76 double CMSF(gmx_structurefactors_t* gsf, int type, int nh, double lambda, double sin_theta);
  77
  78 int return_atom_type(const char* name, gmx_structurefactors_t* gsf);
  79
  80 void rearrange_atoms(reduced_atom_t*         positions,
  81                      struct t_trxframe*      fr,
  82                      const int*              index,
  83                      int                     isize,
  84                      const t_topology*       top,
  85                      gmx_bool                flag,
  86                      gmx_structurefactors_t* gsf);
  87
  88 int do_scattering_intensity(const char*             fnTPS,
  89                             const char*             fnNDX,
  90                             const char*             fnXVG,
  91                             const char*             fnTRX,
  92                             const char*             fnDAT,
  93                             real                    start_q,
  94                             real                    end_q,
  95                             real                    energy,
  96                             int                     ng,
  97                             const gmx_output_env_t* oenv);
  98
  99 t_complex*** rc_tensor_allocation(int x, int y, int z);
 100
 101 real** compute_scattering_factor_table(gmx_structurefactors_t* gsf, structure_factor_t* sft);
 102
 103 #endif