include/types/topology.h

   1 /*
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  38
  39 #include "atoms.h"
  40 #include "idef.h"
  41 #include "block.h"
  42 #include "simple.h"
  43 #include "symtab.h"
  44
  45 #ifdef __cplusplus
  46 extern "C" {
  47 #endif
  48
  49 enum {
  50     egcTC,    egcENER,   egcACC, egcFREEZE,
  51     egcUser1, egcUser2,  egcVCM, egcXTC,
  52     egcORFIT, egcQMMM,
  53     egcNR
  54 };
  55
  56 typedef struct {
  57     char          **name;       /* Name of the molecule type            */
  58     t_atoms         atoms;      /* The atoms                            */
  59     t_ilist         ilist[F_NRE];
  60     t_block         cgs;        /* The charge groups                    */
  61     t_blocka        excls;      /* The exclusions                       */
  62 } gmx_moltype_t;
  63
  64 typedef struct {
  65     int            type;        /* The molcule type index in mtop.moltype */
  66     int            nmol;        /* The number of molecules in this block  */
  67     int            natoms_mol;  /* The number of atoms in one molecule    */
  68     int            nposres_xA;  /* The number of posres coords for top A  */
  69     rvec          *posres_xA;   /* The posres coords for top A            */
  70     int            nposres_xB;  /* The number of posres coords for top B  */
  71     rvec          *posres_xB;   /* The posres coords for top B            */
  72 } gmx_molblock_t;
  73
  74 typedef struct {
  75     t_grps            grps[egcNR];  /* Groups of things                     */
  76     int               ngrpname;     /* Number of groupnames                 */
  77     char           ***grpname;      /* Names of the groups                  */
  78     int               ngrpnr[egcNR];
  79     unsigned char    *grpnr[egcNR]; /* Group numbers or NULL                */
  80 } gmx_groups_t;
  81
  82 /* This macro gives the group number of group type egc for atom i.
  83  * This macro is useful, since the grpnr pointers are NULL
  84  * for group types that have all entries 0.
  85  */
  86 #define ggrpnr(groups, egc, i) ((groups)->grpnr[egc] ? (groups)->grpnr[egc][i] : 0)
  87
  88 /* The global, complete system topology struct, based on molecule types.
  89    This structure should contain no data that is O(natoms) in memory. */
  90 typedef struct {
  91     char           **name;      /* Name of the topology                 */
  92     gmx_ffparams_t   ffparams;
  93     int              nmoltype;
  94     gmx_moltype_t   *moltype;
  95     int              nmolblock;
  96     gmx_molblock_t  *molblock;
  97     int              natoms;
  98     int              maxres_renum; /* Parameter for residue numbering      */
  99     int              maxresnr;     /* The maximum residue number in moltype */
 100     t_atomtypes      atomtypes;    /* Atomtype properties                  */
 101     t_block          mols;         /* The molecules                        */
 102     gmx_groups_t     groups;
 103     t_symtab         symtab;       /* The symbol table                     */
 104 } gmx_mtop_t;
 105
 106 /* The mdrun node-local topology struct, completely written out */
 107 typedef struct {
 108     t_idef        idef;         /* The interaction function definition  */
 109     t_atomtypes   atomtypes;    /* Atomtype properties                  */
 110     t_block       cgs;          /* The charge groups                    */
 111     t_blocka      excls;        /* The exclusions                       */
 112 } gmx_localtop_t;
 113
 114 /* The old topology struct, completely written out, used in analysis tools */
 115 typedef struct {
 116     char          **name;       /* Name of the topology                 */
 117     t_idef          idef;       /* The interaction function definition  */
 118     t_atoms         atoms;      /* The atoms                            */
 119     t_atomtypes     atomtypes;  /* Atomtype properties                  */
 120     t_block         cgs;        /* The charge groups                    */
 121     t_block         mols;       /* The molecules                        */
 122     t_blocka        excls;      /* The exclusions                       */
 123     t_symtab        symtab;     /* The symbol table                     */
 124 } t_topology;
 125
 126 #ifdef __cplusplus
 127 }
 128 #endif