include/genborn.h

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