include/types/genborn.h

   1 /*
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  34
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #ifdef __cplusplus
  40 extern "C" {
  41 #endif
  42
  43 typedef struct
  44 {
  45         int nbonds;
  46         int bond[10];
  47         real length[10];
  48 } genborn_bonds_t;
  49
  50 typedef struct gbtmpnbls *gbtmpnbls_t;
  51
  52 /* Struct to hold all the information for GB */
  53 typedef struct
  54 {
  55         int nr;                   /* number of atoms, length of arrays below */
  56         int n12;                  /* number of 1-2 (bond) interactions       */
  57         int n13;                  /* number of 1-3 (angle) terms             */
  58         int n14;                  /* number of 1-4 (torsion) terms           */
  59         int nlocal;               /* Length of local arrays (with DD)        */
  60
  61         /* Arrays below that end with _globalindex are used for setting up initial values of
  62          * all gb parameters and values. They all have length natoms, which for DD is the
  63          * global atom number.
  64          * Values are then taken from these arrays to local copies, that have names without
  65          * _globalindex, in the routine make_local_gb(), which is called once for single
  66          * node runs, and for DD at every call to dd_partition_system
  67          */
  68
  69         real  *gpol;              /* Atomic polarisation energies */
  70         real  *gpol_globalindex;  /*  */
  71         real  *gpol_still_work;   /* Work array for Still model */
  72         real  *gpol_hct_work;     /* Work array for HCT/OBC models */
  73         real  *bRad;              /* Atomic Born radii */
  74         real  *vsolv;             /* Atomic solvation volumes */
  75         real  *vsolv_globalindex; /*  */
  76         real  *gb_radius;          /* Radius info, copied from atomtypes */
  77         real  *gb_radius_globalindex;
  78
  79         int  *use;                 /* Array that till if this atom does GB */
  80         int  *use_globalindex;     /* Global array for parallelization */
  81
  82         real es;                  /* Solvation energy and derivatives */
  83         real *asurf;              /* Atomic surface area */
  84         rvec *dasurf;             /* Surface area derivatives */
  85         real as;                  /* Total surface area */
  86
  87         real *drobc;              /* Parameters for OBC chain rule calculation */
  88         real *param;              /* Precomputed factor rai*atype->S_hct for HCT/OBC */
  89         real *param_globalindex;  /*  */
  90
  91         real *log_table;          /* Table for logarithm lookup */
  92
  93         real obc_alpha;           /* OBC parameters */
  94         real obc_beta;            /* OBC parameters */
  95         real obc_gamma;           /* OBC parameters */
  96         real gb_doffset;          /* Dielectric offset for Still/HCT/OBC */
  97         real gb_epsilon_solvent;  /*   */
  98         real epsilon_r;           /* Used for inner dielectric */
  99
 100         real *work;               /* Used for parallel summation and in the chain rule, length natoms         */
 101         real *buf;                /* Used for parallel summation and in the chain rule, length natoms         */
 102         real *dd_work;            /* Used for domain decomposition parallel runs, length natoms              */
 103         int  *count;              /* Used for setting up the special gb nblist, length natoms                 */
 104         gbtmpnbls_t nblist_work;  /* Used for setting up the special gb nblist, dim natoms*nblist_work_nalloc */
 105         int  nblist_work_nalloc;  /* Length of second dimension of nblist_work                                */
 106 }
 107 gmx_genborn_t;
 108
 109 #ifdef __cplusplus
 110 }
 111 #endif
 112