include/types/genborn.h

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  38
  39
  40 #ifdef __cplusplus
  41 extern "C" {
  42 #endif
  43
  44 #include "simple.h"
  45
  46 typedef struct
  47 {
  48     int  nbonds;
  49     int  bond[10];
  50     real length[10];
  51 } genborn_bonds_t;
  52
  53 typedef struct gbtmpnbls *gbtmpnbls_t;
  54
  55 /* Struct to hold all the information for GB */
  56 typedef struct
  57 {
  58     int nr;                   /* number of atoms, length of arrays below */
  59     int n12;                  /* number of 1-2 (bond) interactions       */
  60     int n13;                  /* number of 1-3 (angle) terms             */
  61     int n14;                  /* number of 1-4 (torsion) terms           */
  62     int nalloc;               /* Allocation of local arrays (with DD)    */
  63
  64
  65     /* Arrays below that end with _globalindex are used for setting up initial values of
  66      * all gb parameters and values. They all have length natoms, which for DD is the
  67      * global atom number.
  68      * Values are then taken from these arrays to local copies, that have names without
  69      * _globalindex, in the routine make_local_gb(), which is called once for single
  70      * node runs, and for DD at every call to dd_partition_system
  71      */
  72
  73     real       *gpol;              /* Atomic polarisation energies */
  74     real       *gpol_globalindex;  /*  */
  75     real       *gpol_still_work;   /* Work array for Still model */
  76     real       *gpol_hct_work;     /* Work array for HCT/OBC models */
  77     real       *bRad;              /* Atomic Born radii */
  78     real       *vsolv;             /* Atomic solvation volumes */
  79     real       *vsolv_globalindex; /*  */
  80     real       *gb_radius;         /* Radius info, copied from atomtypes */
  81     real       *gb_radius_globalindex;
  82
  83     int        *use;                /* Array that till if this atom does GB */
  84     int        *use_globalindex;    /* Global array for parallelization */
  85
  86     real        es;                 /* Solvation energy and derivatives */
  87     real       *asurf;              /* Atomic surface area */
  88     rvec       *dasurf;             /* Surface area derivatives */
  89     real        as;                 /* Total surface area */
  90
  91     real       *drobc;              /* Parameters for OBC chain rule calculation */
  92     real       *param;              /* Precomputed factor rai*atype->S_hct for HCT/OBC */
  93     real       *param_globalindex;  /*  */
  94
  95     real       *log_table;          /* Table for logarithm lookup */
  96
  97     real        obc_alpha;          /* OBC parameters */
  98     real        obc_beta;           /* OBC parameters */
  99     real        obc_gamma;          /* OBC parameters */
 100     real        gb_doffset;         /* Dielectric offset for Still/HCT/OBC */
 101     real        gb_epsilon_solvent; /*   */
 102     real        epsilon_r;          /* Used for inner dielectric */
 103
 104     real        sa_surface_tension; /* Surface tension for non-polar solvation */
 105
 106     real       *work;               /* Used for parallel summation and in the chain rule, length natoms         */
 107     real       *buf;                /* Used for parallel summation and in the chain rule, length natoms         */
 108     int        *count;              /* Used for setting up the special gb nblist, length natoms                 */
 109     gbtmpnbls_t nblist_work;        /* Used for setting up the special gb nblist, dim natoms*nblist_work_nalloc */
 110     int         nblist_work_nalloc; /* Length of second dimension of nblist_work                                */
 111 }
 112 gmx_genborn_t;
 113
 114 #ifdef __cplusplus
 115 }
 116 #endif