src/gromacs/legacyheaders/types/topology.h

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  37 #ifndef GMX_LEGACYHEADERS_TOPOLOGY_H
  38 #define GMX_LEGACYHEADERS_TOPOLOGY_H
  39
  40 #include "atoms.h"
  41 #include "idef.h"
  42 #include "block.h"
  43 #include "simple.h"
  44 #include "../../topology/symtab.h"
  45
  46 #ifdef __cplusplus
  47 extern "C" {
  48 #endif
  49
  50 enum {
  51     egcTC,    egcENER,   egcACC, egcFREEZE,
  52     egcUser1, egcUser2,  egcVCM, egcCompressedX,
  53     egcORFIT, egcQMMM,
  54     egcNR
  55 };
  56
  57 typedef struct {
  58     char          **name;       /* Name of the molecule type            */
  59     t_atoms         atoms;      /* The atoms                            */
  60     t_ilist         ilist[F_NRE];
  61     t_block         cgs;        /* The charge groups                    */
  62     t_blocka        excls;      /* The exclusions                       */
  63 } gmx_moltype_t;
  64
  65 typedef struct {
  66     int            type;        /* The molcule type index in mtop.moltype */
  67     int            nmol;        /* The number of molecules in this block  */
  68     int            natoms_mol;  /* The number of atoms in one molecule    */
  69     int            nposres_xA;  /* The number of posres coords for top A  */
  70     rvec          *posres_xA;   /* The posres coords for top A            */
  71     int            nposres_xB;  /* The number of posres coords for top B  */
  72     rvec          *posres_xB;   /* The posres coords for top B            */
  73 } gmx_molblock_t;
  74
  75 typedef struct {
  76     t_grps            grps[egcNR];  /* Groups of things                     */
  77     int               ngrpname;     /* Number of groupnames                 */
  78     char           ***grpname;      /* Names of the groups                  */
  79     int               ngrpnr[egcNR];
  80     unsigned char    *grpnr[egcNR]; /* Group numbers or NULL                */
  81 } gmx_groups_t;
  82
  83 /* This macro gives the group number of group type egc for atom i.
  84  * This macro is useful, since the grpnr pointers are NULL
  85  * for group types that have all entries 0.
  86  */
  87 #define ggrpnr(groups, egc, i) ((groups)->grpnr[egc] ? (groups)->grpnr[egc][i] : 0)
  88
  89 /* The global, complete system topology struct, based on molecule types.
  90    This structure should contain no data that is O(natoms) in memory. */
  91 typedef struct {
  92     char           **name;      /* Name of the topology                 */
  93     gmx_ffparams_t   ffparams;
  94     int              nmoltype;
  95     gmx_moltype_t   *moltype;
  96     int              nmolblock;
  97     gmx_molblock_t  *molblock;
  98     int              natoms;
  99     int              maxres_renum; /* Parameter for residue numbering      */
 100     int              maxresnr;     /* The maximum residue number in moltype */
 101     t_atomtypes      atomtypes;    /* Atomtype properties                  */
 102     t_block          mols;         /* The molecules                        */
 103     gmx_groups_t     groups;
 104     t_symtab         symtab;       /* The symbol table                     */
 105 } gmx_mtop_t;
 106
 107 /* The mdrun node-local topology struct, completely written out */
 108 typedef struct {
 109     t_idef        idef;         /* The interaction function definition  */
 110     t_atomtypes   atomtypes;    /* Atomtype properties                  */
 111     t_block       cgs;          /* The charge groups                    */
 112     t_blocka      excls;        /* The exclusions                       */
 113 } gmx_localtop_t;
 114
 115 /* The old topology struct, completely written out, used in analysis tools */
 116 typedef struct {
 117     char          **name;       /* Name of the topology                 */
 118     t_idef          idef;       /* The interaction function definition  */
 119     t_atoms         atoms;      /* The atoms                            */
 120     t_atomtypes     atomtypes;  /* Atomtype properties                  */
 121     t_block         cgs;        /* The charge groups                    */
 122     t_block         mols;       /* The molecules                        */
 123     t_blocka        excls;      /* The exclusions                       */
 124     t_symtab        symtab;     /* The symbol table                     */
 125 } t_topology;
 126
 127 #ifdef __cplusplus
 128 }
 129 #endif
 130
 131 #endif