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 enum {
  49     egcTC,    egcENER,   egcACC, egcFREEZE,
  50     egcUser1, egcUser2,  egcVCM, egcCompressedX,
  51     egcORFIT, egcQMMM,
  52     egcNR
  53 };
  54 /* Names corresponding to groups */
  55 extern const char *gtypes[egcNR+1];
  56
  57 typedef struct gmx_moltype_t
  58 {
  59     char          **name;         /* Name of the molecule type            */
  60     t_atoms         atoms;        /* The atoms in this molecule           */
  61     t_ilist         ilist[F_NRE]; /* Interaction list with local indices  */
  62     t_block         cgs;          /* The charge groups                    */
  63     t_blocka        excls;        /* The exclusions                       */
  64 } gmx_moltype_t;
  65
  66 /*! \brief Block of molecules of the same type, used in gmx_mtop_t */
  67 typedef struct gmx_molblock_t
  68 {
  69     int     type;               /**< The molecule type index in mtop.moltype  */
  70     int     nmol;               /**< The number of molecules in this block    */
  71     int     nposres_xA;         /**< The number of posres coords for top A    */
  72     rvec   *posres_xA;          /**< Position restraint coordinates for top A */
  73     int     nposres_xB;         /**< The number of posres coords for top B    */
  74     rvec   *posres_xB;          /**< Position restraint coordinates for top B */
  75
  76     /* Convenience information, derived from other gmx_mtop_t contents     */
  77     int     natoms_mol;         /**< The number of atoms in one molecule      */
  78     int     globalAtomStart;    /**< Global atom index of the first atom in the block */
  79     int     globalAtomEnd;      /**< Global atom index + 1 of the last atom in the block */
  80     int     globalResidueStart; /**< Global residue index of the first residue in the block */
  81     int     residueNumberStart; /**< Residue numbers start from this value if the number of residues per molecule is <= maxres_renum */
  82 } gmx_molblock_t;
  83
  84 typedef struct gmx_groups_t
  85 {
  86     t_grps            grps[egcNR];  /* Groups of things                     */
  87     int               ngrpname;     /* Number of groupnames                 */
  88     char           ***grpname;      /* Names of the groups                  */
  89     int               ngrpnr[egcNR];
  90     unsigned char    *grpnr[egcNR]; /* Group numbers or NULL                */
  91 } gmx_groups_t;
  92
  93 /* This macro gives the group number of group type egc for atom i.
  94  * This macro is useful, since the grpnr pointers are NULL
  95  * for group types that have all entries 0.
  96  */
  97 #define ggrpnr(groups, egc, i) ((groups)->grpnr[egc] ? (groups)->grpnr[egc][i] : 0)
  98
  99 /* The global, complete system topology struct, based on molecule types.
 100    This structure should contain no data that is O(natoms) in memory. */
 101 typedef struct gmx_mtop_t
 102 {
 103     char           **name;      /* Name of the topology                 */
 104     gmx_ffparams_t   ffparams;
 105     int              nmoltype;
 106     gmx_moltype_t   *moltype;
 107     int              nmolblock;
 108     gmx_molblock_t  *molblock;
 109     gmx_bool         bIntermolecularInteractions; /* Are there intermolecular
 110                                                    * interactions?            */
 111     t_ilist         *intermolecular_ilist;        /* List of intermolecular interactions
 112                                                    * using system wide atom indices,
 113                                                    * either NULL or size F_NRE           */
 114     int              natoms;
 115     int              maxres_renum;                /* Parameter for residue numbering      */
 116     int              maxresnr;                    /* The maximum residue number in moltype */
 117     t_atomtypes      atomtypes;                   /* Atomtype properties                  */
 118     t_block          mols;                        /* The molecules                        */
 119     gmx_groups_t     groups;
 120     t_symtab         symtab;                      /* The symbol table                     */
 121 } gmx_mtop_t;
 122
 123 /* The mdrun node-local topology struct, completely written out */
 124 typedef struct gmx_localtop_t
 125 {
 126     t_idef        idef;         /* The interaction function definition  */
 127     t_atomtypes   atomtypes;    /* Atomtype properties                  */
 128     t_block       cgs;          /* The charge groups                    */
 129     t_blocka      excls;        /* The exclusions                       */
 130 } gmx_localtop_t;
 131
 132 /* The old topology struct, completely written out, used in analysis tools */
 133 typedef struct t_topology
 134 {
 135     char          **name;                        /* Name of the topology                 */
 136     t_idef          idef;                        /* The interaction function definition  */
 137     t_atoms         atoms;                       /* The atoms                            */
 138     t_atomtypes     atomtypes;                   /* Atomtype properties                  */
 139     t_block         cgs;                         /* The charge groups                    */
 140     t_block         mols;                        /* The molecules                        */
 141     gmx_bool        bIntermolecularInteractions; /* Inter.mol. int. ?   */
 142     t_blocka        excls;                       /* The exclusions                       */
 143     t_symtab        symtab;                      /* The symbol table                     */
 144 } t_topology;
 145
 146 void init_mtop(gmx_mtop_t *mtop);
 147 void init_top(t_topology *top);
 148 void done_moltype(gmx_moltype_t *molt);
 149 void done_molblock(gmx_molblock_t *molb);
 150 void done_gmx_groups_t(gmx_groups_t *g);
 151 void done_mtop(gmx_mtop_t *mtop);
 152 void done_top(t_topology *top);
 153 // Frees both t_topology and gmx_mtop_t when the former has been created from
 154 // the latter.
 155 void done_top_mtop(t_topology *top, gmx_mtop_t *mtop);
 156
 157 bool gmx_mtop_has_masses(const gmx_mtop_t *mtop);
 158 bool gmx_mtop_has_charges(const gmx_mtop_t *mtop);
 159 bool gmx_mtop_has_atomtypes(const gmx_mtop_t *mtop);
 160 bool gmx_mtop_has_pdbinfo(const gmx_mtop_t *mtop);
 161
 162 void pr_mtop(FILE *fp, int indent, const char *title, const gmx_mtop_t *mtop,
 163              gmx_bool bShowNumbers, gmx_bool bShowParameters);
 164 void pr_top(FILE *fp, int indent, const char *title, const t_topology *top,
 165             gmx_bool bShowNumbers, gmx_bool bShowParameters);
 166
 167 void cmp_top(FILE *fp, const t_topology *t1, const t_topology *t2, real ftol, real abstol);
 168 void cmp_groups(FILE *fp, const gmx_groups_t *g0, const gmx_groups_t *g1,
 169                 int natoms0, int natoms1);
 170
 171 #endif