defn.h

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/*
 * Copyright (C) 2004-2006 by David J. Hardy.  All rights reserved.
 */

#ifndef DEFN_H
#define DEFN_H

#ifdef __cplusplus
extern "C" {
#endif

  /*
   * cells for geometric hashing, implement as cursor link list
   *
   * parameterize shell thickness and neighborlist length
   * keep only half-shell of neighbors, including self
   */

  /* maximum shell thickness */
#define FORCE_SHELLMAX  3

  /* number of neighbors */
#define FORCE_NBRLISTLEN \
  ( (2*FORCE_SHELLMAX + 1)*(2*FORCE_SHELLMAX + 1)*(2*FORCE_SHELLMAX + 1) )

  typedef struct ForceCell_t {
    int32 head;         /* index of first atom/hgroup in this cell */
    int32 cnt;          /* count number of atoms/hgroups in this cell */
    int32 nnbrs;        /* number of neighbor cells in list */

    int32 nbr[FORCE_NBRLISTLEN/2 + 1];
    /* up to half-shell of neighbor cells, include self */

    char offset[FORCE_NBRLISTLEN/2 + 1];
    /* index into offset table for periodic image neighbor cells */
  } ForceCell;


  typedef struct ForcePairlist_t {
    int32 *index;       /* array of atom indices giving interactions */
    char *offset;       /* index into table of periodic image offsets */
    int32 len;          /* used length of array */
    int32 max;          /* maximum array elements allocated */
  } ForcePairlist;


  typedef struct ForceVdwparam_t {
    double a;
    double b;
    double a14;
    double b14;
    double rmin2;
  } ForceVdwparam;


  /* constants for safe extension of Buckingham */
  typedef struct ForceBucksafe_t {
    double a;
    double b;
    double rinner2;
  } ForceBucksafe;


  enum ForceBoundary_t {
    FORCE_NONPERIODIC = 0x000,  
    FORCE_X_PERIODIC  = 0x001,  
    FORCE_Y_PERIODIC  = 0x002,  
    FORCE_Z_PERIODIC  = 0x004,  
    FORCE_PERIODIC = (FORCE_X_PERIODIC | FORCE_Y_PERIODIC | FORCE_Z_PERIODIC)
  };


  enum ForceIndex_t {
    FORCE_INDEX_ASET  = 0x001,  
    FORCE_INDEX_BSET  = 0x002,  
    FORCE_INDEX_BOND  = 0x004,  
    FORCE_INDEX_ANGLE = 0x008,  
    FORCE_INDEX_DIHED = 0x010,  
    FORCE_INDEX_IMPR  = 0x020,  
    FORCE_INDEX_BRES  = 0x040,  
    FORCE_INDEX_TOTAL = 0x080   
  };


  enum ForceVirial_t {
    FORCE_VIRIAL_XX = 0,  
    FORCE_VIRIAL_XY,      
    FORCE_VIRIAL_XZ,      
    FORCE_VIRIAL_YX,      
    FORCE_VIRIAL_YY,      
    FORCE_VIRIAL_YZ,      
    FORCE_VIRIAL_ZX,      
    FORCE_VIRIAL_ZY,      
    FORCE_VIRIAL_ZZ       
  };


  struct Force_t {
    ForceParam *param;        
    ForceSelect *select;      
    ForceDomain *domain;      
    /* needed to support efficient atom selection */
    int32 *idmap;             
    int32 *mapnb;             
    int32 *atom_bond_sel;     
    int32 *atom_angle_sel;    
    int32 *atom_dihed_sel;    
    int32 *atom_impr_sel;     
    int32 *abset_sel;         
    int32 *total_sel;         
    int32 atom_bond_sel_len;  
    int32 atom_angle_sel_len; 
    int32 atom_dihed_sel_len; 
    int32 atom_impr_sel_len;  
    int32 abset_sel_len;      
    int32 total_sel_len;      
    int32 is_alloc_sel;       
    /* alternate buffer space */
    double u_buffer;          
    double *e_buffer;         
    MD_Dvec *f_buffer;        
    /* arrays for transformed positions and periodic image wrapping */
    MD_Dvec *trpos;           
    MD_Dvec *poswrap;         
    /* constants derived from ForceParam object */
    double elec_const;        
    double elec_cutoff2;      
    double inv_elec_cutoff2;  
    double ewald_grad_coef;   
    double vdw_cutoff2;       
    double switch_dist2;      
    double inv_denom_switch;  
    ForceVdwparam *vdwparam;  
    ForceBucksafe *bucksafe;  
    /* define domain for system */
    MD_Dvec v1, v2, v3;       
    double lv1, lv2, lv3;     
    MD_Dvec nv1, nv2, nv3;    
    MD_Dvec center;           
    MD_Dvec lowerc;           
    MD_Dvec ta1, ta2, ta3;    
    MD_Dvec offset_table[27]; 
    double volume;            
    int32 is_periodic;        
    int32 is_orthogonal;      
    /* algorithmically motivated parameters */
    double domain_len_frac;   
    int32 max_steps;          
    int32 cnt_steps;          
    int32 is_domain_update;   
    /* compute min/max for scaled coordinates */
    int32 is_minmax;
    MD_Dvec smin, smax;

    /* using a lattice fixed in space */
    int32 is_fixed_lattice;   
    int32 k1, k2, k3;         
    MD_Dvec dv1, dv2, dv3;    
    MD_Dvec tb1, tb2, tb3;    
    /* for geometric hashing to grid cells */
    double ucellsize;         /* grid cell length along u vector */
    double vcellsize;         /* grid cell length along v vector */
    double wcellsize;         /* grid cell length along w vector */
    double inv_ucellsize;     /* 1/ucellsize */
    double inv_vcellsize;     /* 1/vcellsize */
    double inv_wcellsize;     /* 1/wcellsize */

    MD_Dvec lowcell;   
    MD_Dvec delta;     
    MD_Dvec gscale;    
    ForceCell *cell;   /* array of grid cells */
    int32 maxcells;    /* maximum allocation for optimal resizing */
    int32 ncells;      /* number of cells in array: nucells*nvcells*nwcells */
    int32 nucells;     /* number of cells in u direction */
    int32 nvcells;     /* number of cells in v direction */
    int32 nwcells;     /* number of cells in w direction */

    int32 *next;       /* array of next atoms/hgroups for cursor link list */

    /* for using pairlists */
    double outer_cutoff2;
    double delta_dis2;
    MD_Dvec *pos_init;
    MD_Dvec *wrap_save;
    ForcePairlist *pairlist;
    int32 pairlist_set_id;
    int32 need_pairlist_regen;

    /* for nonbonded pairwise interaction exclusions */
    int32 **excl_list;        
    int32 **scaled14_list;    
    /* helper arrays for building exclusion lists */
    int32 **exclx;     
    int32 **excl12;    
    int32 **excl13;    
    int32 **excl14;    
    int32 **scaled14;  
    int32 *lenx;       
    int32 *len12;      
    int32 *len13;      
    int32 *accum;      
    int32 *dest;       
    /* for boundary restraints */
    int32 is_bres_term1;  
    int32 is_bres_term2;  
    double sq_minradius;  
    double minlength;     
  };


#ifdef __cplusplus
}
#endif

#endif /* DEFN_H */

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