src/gromacs/mdlib/genborn.h

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  37 #ifndef GMX_MDLIB_GENBORN_H
  38 #define GMX_MDLIB_GENBORN_H
  39
  40 #include "gromacs/math/vectypes.h"
  41
  42 struct gmx_genborn_t;
  43 struct gmx_enerdata_t;
  44 struct gmx_localtop_t;
  45 struct gmx_mtop_t;
  46 struct t_commrec;
  47 struct t_forcerec;
  48 struct t_graph;
  49 struct t_idef;
  50 struct t_inputrec;
  51 struct t_mdatoms;
  52 struct t_nblist;
  53 struct t_nrnb;
  54 struct t_pbc;
  55
  56 typedef struct
  57 {
  58     int  nbonds;
  59     int  bond[10];
  60     real length[10];
  61 } genborn_bonds_t;
  62
  63 typedef struct gbtmpnbls *gbtmpnbls_t;
  64
  65 /* Struct to hold all the information for GB */
  66 typedef struct gmx_genborn_t
  67 {
  68     int nr;                   /* number of atoms, length of arrays below */
  69     int n12;                  /* number of 1-2 (bond) interactions       */
  70     int n13;                  /* number of 1-3 (angle) terms             */
  71     int n14;                  /* number of 1-4 (torsion) terms           */
  72     int nalloc;               /* Allocation of local arrays (with DD)    */
  73
  74
  75     /* Arrays below that end with _globalindex are used for setting up initial values of
  76      * all gb parameters and values. They all have length natoms, which for DD is the
  77      * global atom number.
  78      * Values are then taken from these arrays to local copies, that have names without
  79      * _globalindex, in the routine make_local_gb(), which is called once for single
  80      * node runs, and for DD at every call to dd_partition_system
  81      */
  82
  83     real       *gpol;              /* Atomic polarisation energies */
  84     real       *gpol_globalindex;  /*  */
  85     real       *gpol_still_work;   /* Work array for Still model */
  86     real       *gpol_hct_work;     /* Work array for HCT/OBC models */
  87     real       *bRad;              /* Atomic Born radii */
  88     real       *vsolv;             /* Atomic solvation volumes */
  89     real       *vsolv_globalindex; /*  */
  90     real       *gb_radius;         /* Radius info, copied from atomtypes */
  91     real       *gb_radius_globalindex;
  92
  93     int        *use;                /* Array that till if this atom does GB */
  94     int        *use_globalindex;    /* Global array for parallelization */
  95
  96     real        es;                 /* Solvation energy and derivatives */
  97     real       *asurf;              /* Atomic surface area */
  98     rvec       *dasurf;             /* Surface area derivatives */
  99     real        as;                 /* Total surface area */
 100
 101     real       *drobc;              /* Parameters for OBC chain rule calculation */
 102     real       *param;              /* Precomputed factor rai*atype->S_hct for HCT/OBC */
 103     real       *param_globalindex;  /*  */
 104
 105     real       *log_table;          /* Table for logarithm lookup */
 106
 107     real        obc_alpha;          /* OBC parameters */
 108     real        obc_beta;           /* OBC parameters */
 109     real        obc_gamma;          /* OBC parameters */
 110     real        gb_doffset;         /* Dielectric offset for Still/HCT/OBC */
 111     real        gb_epsilon_solvent; /*   */
 112     real        epsilon_r;          /* Used for inner dielectric */
 113
 114     real        sa_surface_tension; /* Surface tension for non-polar solvation */
 115
 116     real       *work;               /* Used for parallel summation and in the chain rule, length natoms         */
 117     real       *buf;                /* Used for parallel summation and in the chain rule, length natoms         */
 118     int        *count;              /* Used for setting up the special gb nblist, length natoms                 */
 119     gbtmpnbls_t nblist_work;        /* Used for setting up the special gb nblist, dim natoms*nblist_work_nalloc */
 120     int         nblist_work_nalloc; /* Length of second dimension of nblist_work                                */
 121 }
 122 gmx_genborn_t;
 123 /* Still parameters - make sure to edit in genborn_sse.c too if you change these! */
 124 #define STILL_P1  0.073*0.1              /* length        */
 125 #define STILL_P2  0.921*0.1*CAL2JOULE    /* energy*length */
 126 #define STILL_P3  6.211*0.1*CAL2JOULE    /* energy*length */
 127 #define STILL_P4  15.236*0.1*CAL2JOULE
 128 #define STILL_P5  1.254
 129
 130 #define STILL_P5INV (1.0/STILL_P5)
 131 #define STILL_PIP5  (M_PI*STILL_P5)
 132
 133
 134 /* Initialise GB stuff */
 135 int init_gb(struct gmx_genborn_t **p_born,
 136             struct t_forcerec *fr, const struct t_inputrec *ir,
 137             const gmx_mtop_t *mtop, int gb_algorithm);
 138
 139
 140 /* Born radii calculations, both with and without SSE acceleration */
 141 int calc_gb_rad(struct t_commrec *cr, struct t_forcerec *fr, struct t_inputrec *ir, gmx_localtop_t *top, rvec x[], t_nblist *nl, struct gmx_genborn_t *born, t_mdatoms *md, t_nrnb     *nrnb);
 142
 143
 144
 145 /* Bonded GB interactions */
 146 real gb_bonds_tab(rvec x[], rvec f[], rvec fshift[], real *charge, real *p_gbtabscale,
 147                   real *invsqrta, real *dvda, real *GBtab, t_idef *idef, real epsilon_r,
 148                   real gb_epsilon_solvent, real facel, const struct t_pbc *pbc,
 149                   const struct t_graph *graph);
 150
 151
 152
 153
 154 /* Functions for calculating adjustments due to ie chain rule terms */
 155 void
 156 calc_gb_forces(struct t_commrec *cr, t_mdatoms *md, struct gmx_genborn_t *born, gmx_localtop_t *top,
 157                rvec x[], rvec f[], struct t_forcerec *fr, t_idef *idef, int gb_algorithm, int sa_algorithm, t_nrnb *nrnb,
 158                const struct t_pbc *pbc, const struct t_graph *graph, struct gmx_enerdata_t *enerd);
 159
 160
 161 int
 162 make_gb_nblist(struct t_commrec *cr, int gb_algorithm,
 163                rvec x[], matrix box,
 164                struct t_forcerec *fr, t_idef *idef, struct t_graph *graph, struct gmx_genborn_t *born);
 165
 166 void
 167 make_local_gb(const struct t_commrec *cr, struct gmx_genborn_t *born, int gb_algorithm);
 168
 169 #endif