src/gromacs/topology/topology.h

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  37 #ifndef GMX_TOPOLOGY_TOPOLOGY_H
  38 #define GMX_TOPOLOGY_TOPOLOGY_H
  39
  40 #include <cstdio>
  41
  42 #include "gromacs/math/vectypes.h"
  43 #include "gromacs/topology/atoms.h"
  44 #include "gromacs/topology/block.h"
  45 #include "gromacs/topology/idef.h"
  46 #include "gromacs/topology/symtab.h"
  47
  48 #ifdef __cplusplus
  49 extern "C" {
  50 #endif
  51
  52 enum {
  53     egcTC,    egcENER,   egcACC, egcFREEZE,
  54     egcUser1, egcUser2,  egcVCM, egcCompressedX,
  55     egcORFIT, egcQMMM,
  56     egcNR
  57 };
  58 /* Names corresponding to groups */
  59 extern const char *gtypes[egcNR+1];
  60
  61 typedef struct gmx_moltype_t
  62 {
  63     char          **name;         /* Name of the molecule type            */
  64     t_atoms         atoms;        /* The atoms in this molecule           */
  65     t_ilist         ilist[F_NRE]; /* Interaction list with local indices  */
  66     t_block         cgs;          /* The charge groups                    */
  67     t_blocka        excls;        /* The exclusions                       */
  68 } gmx_moltype_t;
  69
  70 typedef struct gmx_molblock_t
  71 {
  72     int            type;        /* The molcule type index in mtop.moltype */
  73     int            nmol;        /* The number of molecules in this block  */
  74     int            natoms_mol;  /* The number of atoms in one molecule    */
  75     int            nposres_xA;  /* The number of posres coords for top A  */
  76     rvec          *posres_xA;   /* The posres coords for top A            */
  77     int            nposres_xB;  /* The number of posres coords for top B  */
  78     rvec          *posres_xB;   /* The posres coords for top B            */
  79 } gmx_molblock_t;
  80
  81 typedef struct gmx_groups_t
  82 {
  83     t_grps            grps[egcNR];  /* Groups of things                     */
  84     int               ngrpname;     /* Number of groupnames                 */
  85     char           ***grpname;      /* Names of the groups                  */
  86     int               ngrpnr[egcNR];
  87     unsigned char    *grpnr[egcNR]; /* Group numbers or NULL                */
  88 } gmx_groups_t;
  89
  90 /* This macro gives the group number of group type egc for atom i.
  91  * This macro is useful, since the grpnr pointers are NULL
  92  * for group types that have all entries 0.
  93  */
  94 #define ggrpnr(groups, egc, i) ((groups)->grpnr[egc] ? (groups)->grpnr[egc][i] : 0)
  95
  96 /* The global, complete system topology struct, based on molecule types.
  97    This structure should contain no data that is O(natoms) in memory. */
  98 typedef struct gmx_mtop_t
  99 {
 100     char           **name;      /* Name of the topology                 */
 101     gmx_ffparams_t   ffparams;
 102     int              nmoltype;
 103     gmx_moltype_t   *moltype;
 104     int              nmolblock;
 105     gmx_molblock_t  *molblock;
 106     gmx_bool         bIntermolecularInteractions; /* Are there intermolecular
 107                                                    * interactions?            */
 108     t_ilist         *intermolecular_ilist;        /* List of intermolecular interactions
 109                                                    * using system wide atom indices,
 110                                                    * either NULL or size F_NRE           */
 111     int              natoms;
 112     int              maxres_renum;                /* Parameter for residue numbering      */
 113     int              maxresnr;                    /* The maximum residue number in moltype */
 114     t_atomtypes      atomtypes;                   /* Atomtype properties                  */
 115     t_block          mols;                        /* The molecules                        */
 116     gmx_groups_t     groups;
 117     t_symtab         symtab;                      /* The symbol table                     */
 118 } gmx_mtop_t;
 119
 120 /* The mdrun node-local topology struct, completely written out */
 121 typedef struct gmx_localtop_t
 122 {
 123     t_idef        idef;         /* The interaction function definition  */
 124     t_atomtypes   atomtypes;    /* Atomtype properties                  */
 125     t_block       cgs;          /* The charge groups                    */
 126     t_blocka      excls;        /* The exclusions                       */
 127 } gmx_localtop_t;
 128
 129 /* The old topology struct, completely written out, used in analysis tools */
 130 typedef struct t_topology
 131 {
 132     char          **name;                        /* Name of the topology                 */
 133     t_idef          idef;                        /* The interaction function definition  */
 134     t_atoms         atoms;                       /* The atoms                            */
 135     t_atomtypes     atomtypes;                   /* Atomtype properties                  */
 136     t_block         cgs;                         /* The charge groups                    */
 137     t_block         mols;                        /* The molecules                        */
 138     gmx_bool        bIntermolecularInteractions; /* Inter.mol. int. ?   */
 139     t_blocka        excls;                       /* The exclusions                       */
 140     t_symtab        symtab;                      /* The symbol table                     */
 141 } t_topology;
 142
 143 void init_mtop(gmx_mtop_t *mtop);
 144 void init_top(t_topology *top);
 145 void done_moltype(gmx_moltype_t *molt);
 146 void done_molblock(gmx_molblock_t *molb);
 147 void done_mtop(gmx_mtop_t *mtop, gmx_bool bDoneSymtab);
 148 void done_top(t_topology *top);
 149
 150 t_atoms *mtop2atoms(gmx_mtop_t *mtop);
 151 /* generate a t_atoms struct for the system from gmx_mtop_t */
 152
 153 void pr_mtop(FILE *fp, int indent, const char *title, const gmx_mtop_t *mtop,
 154              gmx_bool bShowNumbers);
 155 void pr_top(FILE *fp, int indent, const char *title, const t_topology *top, gmx_bool bShowNumbers);
 156
 157 #ifdef __cplusplus
 158 }
 159 #endif
 160
 161 #endif