include/genborn.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  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  10  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  11  * Copyright (c) 2001-2008, The GROMACS development team,
  12  * check out http://www.gromacs.org for more information.
  13
  14  * This program is free software; you can redistribute it and/or
  15  * modify it under the terms of the GNU General Public License
  16  * as published by the Free Software Foundation; either version 2
  17  * of the License, or (at your option) any later version.
  18  *
  19  * If you want to redistribute modifications, please consider that
  20  * scientific software is very special. Version control is crucial -
  21  * bugs must be traceable. We will be happy to consider code for
  22  * inclusion in the official distribution, but derived work must not
  23  * be called official GROMACS. Details are found in the README & COPYING
  24  * files - if they are missing, get the official version at www.gromacs.org.
  25  *
  26  * To help us fund GROMACS development, we humbly ask that you cite
  27  * the papers on the package - you can find them in the top README file.
  28  *
  29  * For more info, check our website at http://www.gromacs.org
  30  *
  31  * And Hey:
  32  * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
  33  */
  34
  35
  36 #ifndef _genborn_h
  37 #define _genborn_h
  38
  39 #include "typedefs.h"
  40 #include "types/commrec.h"
  41 #include "grompp.h"
  42
  43 #ifdef __cplusplus
  44 extern "C" {
  45 #endif
  46
  47 /* Still parameters - make sure to edit in genborn_sse.c too if you change these! */
  48 #define STILL_P1  0.073*0.1              /* length        */
  49 #define STILL_P2  0.921*0.1*CAL2JOULE    /* energy*length */
  50 #define STILL_P3  6.211*0.1*CAL2JOULE    /* energy*length */
  51 #define STILL_P4  15.236*0.1*CAL2JOULE
  52 #define STILL_P5  1.254
  53
  54 #define STILL_P5INV (1.0/STILL_P5)
  55 #define STILL_PIP5  (M_PI*STILL_P5)
  56
  57
  58 /* Initialise GB stuff */
  59 int init_gb(gmx_genborn_t **p_born,
  60             const t_commrec *cr, t_forcerec *fr, const t_inputrec *ir,
  61             const gmx_mtop_t *mtop, real rgbradii, int gb_algorithm);
  62
  63
  64 /* Born radii calculations, both with and without SSE acceleration */
  65 int calc_gb_rad(t_commrec *cr, t_forcerec *fr, t_inputrec *ir,gmx_localtop_t *top,
  66                                 const t_atomtypes *atype, rvec x[], t_nblist *nl, gmx_genborn_t *born,t_mdatoms *md, t_nrnb     *nrnb);
  67
  68
  69
  70 /* Bonded GB interactions */
  71 real gb_bonds_tab(rvec x[], rvec f[], rvec fshift[], real *charge, real *p_gbtabscale,
  72                                   real *invsqrta, real *dvda, real *GBtab, t_idef *idef, real epsilon_r,
  73                                   real gb_epsilon_solvent, real facel, const t_pbc *pbc, const t_graph *graph);
  74
  75
  76
  77 void gb_pd_send(t_commrec *cr, real *send_data, int nr);
  78
  79
  80 /* Functions for setting up the F_GB12,13,14 lists in grompp */
  81 int
  82 init_gb_plist(t_params *p_list);
  83
  84 int
  85 convert_gb_params(gmx_ffparams_t *ffparams, t_functype ftype, t_params *gb_plist, t_ilist *il);
  86
  87
  88
  89 /* Functions for calculating adjustments due to ie chain rule terms */
  90 void
  91 calc_gb_forces(t_commrec *cr, t_mdatoms *md, gmx_genborn_t *born, gmx_localtop_t *top, const t_atomtypes *atype,
  92                            rvec x[], rvec f[], t_forcerec *fr,t_idef *idef,int gb_algorithm, int sa_algorithm, t_nrnb *nrnb, gmx_bool bRad,
  93                            const t_pbc *pbc, const t_graph *graph, gmx_enerdata_t *enerd);
  94
  95
  96 int
  97 make_gb_nblist(t_commrec *cr, int gb_algorithm, real gbcut,
  98                rvec x[], matrix box,
  99                t_forcerec *fr, t_idef *idef, t_graph *graph, gmx_genborn_t *born);
 100
 101 void
 102 make_local_gb(const t_commrec *cr, gmx_genborn_t *born, int gb_algorithm);
 103
 104 #ifdef __cplusplus
 105 }
 106 #endif
 107
 108 #endif /* _genborn_h */
 109