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 <vector>
  43
  44 #include "gromacs/math/vectypes.h"
  45 #include "gromacs/topology/atoms.h"
  46 #include "gromacs/topology/block.h"
  47 #include "gromacs/topology/idef.h"
  48 #include "gromacs/topology/symtab.h"
  49
  50 enum {
  51     egcTC,    egcENER,   egcACC, egcFREEZE,
  52     egcUser1, egcUser2,  egcVCM, egcCompressedX,
  53     egcORFIT, egcQMMM,
  54     egcNR
  55 };
  56 /* Names corresponding to groups */
  57 extern const char *gtypes[egcNR+1];
  58
  59 /*! \brief Molecules type data: atoms, interactions and exclusions */
  60 struct gmx_moltype_t
  61 {
  62     /*! \brief Constructor */
  63     gmx_moltype_t();
  64
  65     /*! \brief Destructor */
  66     ~gmx_moltype_t();
  67
  68     /*! \brief Deleted copy assignment operator to avoid (not) freeing pointers */
  69     gmx_moltype_t &operator=(const gmx_moltype_t &) = delete;
  70
  71     /*! \brief Default copy constructor */
  72     gmx_moltype_t(const gmx_moltype_t &) = default;
  73
  74     char          **name;         /**< Name of the molecule type            */
  75     t_atoms         atoms;        /**< The atoms in this molecule           */
  76     t_ilist         ilist[F_NRE]; /**< Interaction list with local indices  */
  77     t_block         cgs;          /**< The charge groups                    */
  78     t_blocka        excls;        /**< The exclusions                       */
  79 };
  80
  81 /*! \brief Block of molecules of the same type, used in gmx_mtop_t */
  82 struct gmx_molblock_t
  83 {
  84     /*! \brief Constructor */
  85     gmx_molblock_t();
  86
  87     /*! \brief Destructor */
  88     ~gmx_molblock_t();
  89
  90     /*! \brief Default copy assignment operator.
  91      *
  92      * NOTE: Does not free the old pointers.
  93      */
  94     gmx_molblock_t &operator=(const gmx_molblock_t &) = default;
  95
  96     /*! \brief Default copy constructor */
  97     gmx_molblock_t(const gmx_molblock_t &) = default;
  98
  99     int     type;               /**< The molecule type index in mtop.moltype  */
 100     int     nmol;               /**< The number of molecules in this block    */
 101     int     nposres_xA;         /**< The number of posres coords for top A    */
 102     rvec   *posres_xA;          /**< Position restraint coordinates for top A */
 103     int     nposres_xB;         /**< The number of posres coords for top B    */
 104     rvec   *posres_xB;          /**< Position restraint coordinates for top B */
 105
 106     /* Convenience information, derived from other gmx_mtop_t contents     */
 107     int     natoms_mol;         /**< The number of atoms in one molecule      */
 108     int     globalAtomStart;    /**< Global atom index of the first atom in the block */
 109     int     globalAtomEnd;      /**< Global atom index + 1 of the last atom in the block */
 110     int     globalResidueStart; /**< Global residue index of the first residue in the block */
 111     int     residueNumberStart; /**< Residue numbers start from this value if the number of residues per molecule is <= maxres_renum */
 112     int     moleculeIndexStart; /**< Global molecule indexing starts from this value */
 113 };
 114
 115 typedef struct gmx_groups_t
 116 {
 117     t_grps            grps[egcNR];  /* Groups of things                     */
 118     int               ngrpname;     /* Number of groupnames                 */
 119     char           ***grpname;      /* Names of the groups                  */
 120     int               ngrpnr[egcNR];
 121     unsigned char    *grpnr[egcNR]; /* Group numbers or NULL                */
 122 } gmx_groups_t;
 123
 124 /* This macro gives the group number of group type egc for atom i.
 125  * This macro is useful, since the grpnr pointers are NULL
 126  * for group types that have all entries 0.
 127  */
 128 #define ggrpnr(groups, egc, i) ((groups)->grpnr[egc] ? (groups)->grpnr[egc][i] : 0)
 129
 130 /* The global, complete system topology struct, based on molecule types.
 131    This structure should contain no data that is O(natoms) in memory. */
 132 struct gmx_mtop_t
 133 {
 134     /* Constructor */
 135     gmx_mtop_t();
 136
 137     /* Destructor */
 138     ~gmx_mtop_t();
 139
 140     char                      **name; /* Name of the topology                 */
 141     gmx_ffparams_t              ffparams;
 142     std::vector<gmx_moltype_t>  moltype;
 143     std::vector<gmx_molblock_t> molblock;
 144     gmx_bool                    bIntermolecularInteractions; /* Are there intermolecular
 145                                                               * interactions?            */
 146     t_ilist                    *intermolecular_ilist;        /* List of intermolecular interactions
 147                                                               * using system wide atom indices,
 148                                                               * either NULL or size F_NRE           */
 149     int              natoms;
 150     int              maxres_renum;                           /* Parameter for residue numbering      */
 151     int              maxresnr;                               /* The maximum residue number in moltype */
 152     t_atomtypes      atomtypes;                              /* Atomtype properties                  */
 153     gmx_groups_t     groups;
 154     t_symtab         symtab;                                 /* The symbol table                     */
 155     bool             haveMoleculeIndices;                    /* Tells whether we have valid molecule indices */
 156 };
 157
 158 /* The mdrun node-local topology struct, completely written out */
 159 typedef struct gmx_localtop_t
 160 {
 161     t_idef        idef;         /* The interaction function definition  */
 162     t_atomtypes   atomtypes;    /* Atomtype properties                  */
 163     t_block       cgs;          /* The charge groups                    */
 164     t_blocka      excls;        /* The exclusions                       */
 165 } gmx_localtop_t;
 166
 167 /* The old topology struct, completely written out, used in analysis tools */
 168 typedef struct t_topology
 169 {
 170     char          **name;                        /* Name of the topology                 */
 171     t_idef          idef;                        /* The interaction function definition  */
 172     t_atoms         atoms;                       /* The atoms                            */
 173     t_atomtypes     atomtypes;                   /* Atomtype properties                  */
 174     t_block         cgs;                         /* The charge groups                    */
 175     t_block         mols;                        /* The molecules                        */
 176     gmx_bool        bIntermolecularInteractions; /* Inter.mol. int. ?   */
 177     t_blocka        excls;                       /* The exclusions                       */
 178     t_symtab        symtab;                      /* The symbol table                     */
 179 } t_topology;
 180
 181 void init_mtop(gmx_mtop_t *mtop);
 182 void init_top(t_topology *top);
 183 void done_gmx_groups_t(gmx_groups_t *g);
 184 void done_top(t_topology *top);
 185 // Frees both t_topology and gmx_mtop_t when the former has been created from
 186 // the latter.
 187 void done_top_mtop(t_topology *top, gmx_mtop_t *mtop);
 188
 189 bool gmx_mtop_has_masses(const gmx_mtop_t *mtop);
 190 bool gmx_mtop_has_charges(const gmx_mtop_t *mtop);
 191 bool gmx_mtop_has_atomtypes(const gmx_mtop_t *mtop);
 192 bool gmx_mtop_has_pdbinfo(const gmx_mtop_t *mtop);
 193
 194 void pr_mtop(FILE *fp, int indent, const char *title, const gmx_mtop_t *mtop,
 195              gmx_bool bShowNumbers, gmx_bool bShowParameters);
 196 void pr_top(FILE *fp, int indent, const char *title, const t_topology *top,
 197             gmx_bool bShowNumbers, gmx_bool bShowParameters);
 198
 199 void cmp_top(FILE *fp, const t_topology *t1, const t_topology *t2, real ftol, real abstol);
 200 void cmp_groups(FILE *fp, const gmx_groups_t *g0, const gmx_groups_t *g1,
 201                 int natoms0, int natoms1);
 202
 203 #endif