include/genborn.h

   1 /*
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  34
  35
  36 #ifndef _genborn_h
  37 #define _genborn_h
  38
  39 #include "typedefs.h"
  40 #include "grompp.h"
  41
  42 #ifdef HAVE_CONFIG_H
  43 #include <config.h>
  44 #endif
  45
  46 #ifdef __cplusplus
  47 extern "C" {
  48 #endif
  49
  50 /* Still parameters - make sure to edit in genborn_sse.c too if you change these! */
  51 #define STILL_P1  0.073*0.1              /* length        */
  52 #define STILL_P2  0.921*0.1*CAL2JOULE    /* energy*length */
  53 #define STILL_P3  6.211*0.1*CAL2JOULE    /* energy*length */
  54 #define STILL_P4  15.236*0.1*CAL2JOULE
  55 #define STILL_P5  1.254
  56
  57 #define STILL_P5INV (1.0/STILL_P5)
  58 #define STILL_PIP5  (M_PI*STILL_P5)
  59
  60
  61 /* Initialise GB stuff */
  62 int init_gb(gmx_genborn_t **p_born,
  63             const t_commrec *cr, t_forcerec *fr, const t_inputrec *ir,
  64             const gmx_mtop_t *mtop, real rgbradii, int gb_algorithm);
  65
  66
  67 /* Born radii calculations, both with and without SSE acceleration */
  68 int calc_gb_rad(t_commrec *cr, t_forcerec *fr, t_inputrec *ir,gmx_localtop_t *top,
  69                                 const t_atomtypes *atype, rvec x[], t_nblist *nl, gmx_genborn_t *born,t_mdatoms *md, t_nrnb     *nrnb);
  70
  71
  72
  73 /* Bonded GB interactions */
  74 real gb_bonds_tab(rvec x[], rvec f[], rvec fshift[], real *charge, real *p_gbtabscale,
  75                                   real *invsqrta, real *dvda, real *GBtab, t_idef *idef, real epsilon_r,
  76                                   real gb_epsilon_solvent, real facel, const t_pbc *pbc, const t_graph *graph);
  77
  78
  79
  80 void gb_pd_send(t_commrec *cr, real *send_data, int nr);
  81
  82
  83 /* Functions for setting up the F_GB12,13,14 lists in grompp */
  84 int
  85 init_gb_plist(t_params *p_list);
  86
  87 int
  88 convert_gb_params(gmx_ffparams_t *ffparams, t_functype ftype, t_params *gb_plist, t_ilist *il);
  89
  90
  91
  92 /* Functions for calculating adjustments due to ie chain rule terms */
  93 real
  94 calc_gb_forces(t_commrec *cr, t_mdatoms *md, gmx_genborn_t *born, gmx_localtop_t *top, const t_atomtypes *atype,
  95                            rvec x[], rvec f[], t_forcerec *fr,t_idef *idef,int gb_algorithm, t_nrnb *nrnb, bool bRad,
  96                            const t_pbc *pbc, const t_graph *graph);
  97
  98
  99 int
 100 make_gb_nblist(t_commrec *cr, int gb_algorithm, real gbcut,
 101                rvec x[], matrix box,
 102                t_forcerec *fr, t_idef *idef, t_graph *graph, gmx_genborn_t *born);
 103
 104 void
 105 make_local_gb(const t_commrec *cr, gmx_genborn_t *born, int gb_algorithm);
 106
 107 #ifdef __cplusplus
 108 }
 109 #endif
 110
 111 #endif /* _genborn_h */
 112