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     int                    type = -1; /**< The molecule type index in mtop.moltype  */
  85     int                    nmol = 0;  /**< The number of molecules in this block    */
  86     std::vector<gmx::RVec> posres_xA; /**< Position restraint coordinates for top A */
  87     std::vector<gmx::RVec> posres_xB; /**< Position restraint coordinates for top B */
  88 };
  89
  90 /*! \brief Indices for a gmx_molblock_t, derived from other gmx_mtop_t contents */
  91 struct MoleculeBlockIndices
  92 {
  93     int     numAtomsPerMolecule; /**< Number of atoms in a molecule in the block */
  94     int     globalAtomStart;     /**< Global atom index of the first atom in the block */
  95     int     globalAtomEnd;       /**< Global atom index + 1 of the last atom in the block */
  96     int     globalResidueStart;  /**< Global residue index of the first residue in the block */
  97     int     residueNumberStart;  /**< Residue numbers start from this value if the number of residues per molecule is <= maxres_renum */
  98     int     moleculeIndexStart;  /**< Global molecule indexing starts from this value */
  99 };
 100
 101 typedef struct gmx_groups_t
 102 {
 103     t_grps            grps[egcNR];  /* Groups of things                     */
 104     int               ngrpname;     /* Number of groupnames                 */
 105     char           ***grpname;      /* Names of the groups                  */
 106     int               ngrpnr[egcNR];
 107     unsigned char    *grpnr[egcNR]; /* Group numbers or NULL                */
 108 } gmx_groups_t;
 109
 110 /* This macro gives the group number of group type egc for atom i.
 111  * This macro is useful, since the grpnr pointers are NULL
 112  * for group types that have all entries 0.
 113  */
 114 #define ggrpnr(groups, egc, i) ((groups)->grpnr[egc] ? (groups)->grpnr[egc][i] : 0)
 115
 116 /* The global, complete system topology struct, based on molecule types.
 117  * This structure should contain no data that is O(natoms) in memory.
 118  *
 119  * TODO: Find a solution for ensuring that the derived data is in sync
 120  *       with the primary data, possibly by converting to a class.
 121  */
 122 struct gmx_mtop_t
 123 {
 124     /* Constructor */
 125     gmx_mtop_t();
 126
 127     /* Destructor */
 128     ~gmx_mtop_t();
 129
 130     char                      **name; /* Name of the topology                 */
 131     gmx_ffparams_t              ffparams;
 132     std::vector<gmx_moltype_t>  moltype;
 133     std::vector<gmx_molblock_t> molblock;
 134     gmx_bool                    bIntermolecularInteractions; /* Are there intermolecular
 135                                                               * interactions?            */
 136     t_ilist                    *intermolecular_ilist;        /* List of intermolecular interactions
 137                                                               * using system wide atom indices,
 138                                                               * either NULL or size F_NRE           */
 139     int              natoms;
 140     int              maxres_renum;                           /* Parameter for residue numbering      */
 141     int              maxresnr;                               /* The maximum residue number in moltype */
 142     t_atomtypes      atomtypes;                              /* Atomtype properties                  */
 143     gmx_groups_t     groups;                                 /* Groups of atoms for different purposes */
 144     t_symtab         symtab;                                 /* The symbol table                     */
 145     bool             haveMoleculeIndices;                    /* Tells whether we have valid molecule indices */
 146
 147     /* Derived data */
 148     std::vector<MoleculeBlockIndices> moleculeBlockIndices;  /* Indices for each molblock entry for fast lookup of atom properties */
 149 };
 150
 151 /* The mdrun node-local topology struct, completely written out */
 152 typedef struct gmx_localtop_t
 153 {
 154     t_idef        idef;         /* The interaction function definition  */
 155     t_atomtypes   atomtypes;    /* Atomtype properties                  */
 156     t_block       cgs;          /* The charge groups                    */
 157     t_blocka      excls;        /* The exclusions                       */
 158 } gmx_localtop_t;
 159
 160 /* The old topology struct, completely written out, used in analysis tools */
 161 typedef struct t_topology
 162 {
 163     char          **name;                        /* Name of the topology                 */
 164     t_idef          idef;                        /* The interaction function definition  */
 165     t_atoms         atoms;                       /* The atoms                            */
 166     t_atomtypes     atomtypes;                   /* Atomtype properties                  */
 167     t_block         cgs;                         /* The charge groups                    */
 168     t_block         mols;                        /* The molecules                        */
 169     gmx_bool        bIntermolecularInteractions; /* Inter.mol. int. ?   */
 170     t_blocka        excls;                       /* The exclusions                       */
 171     t_symtab        symtab;                      /* The symbol table                     */
 172 } t_topology;
 173
 174 void init_mtop(gmx_mtop_t *mtop);
 175 void init_top(t_topology *top);
 176 void done_gmx_groups_t(gmx_groups_t *g);
 177 void done_top(t_topology *top);
 178 // Frees both t_topology and gmx_mtop_t when the former has been created from
 179 // the latter.
 180 void done_top_mtop(t_topology *top, gmx_mtop_t *mtop);
 181
 182 bool gmx_mtop_has_masses(const gmx_mtop_t *mtop);
 183 bool gmx_mtop_has_charges(const gmx_mtop_t *mtop);
 184 bool gmx_mtop_has_atomtypes(const gmx_mtop_t *mtop);
 185 bool gmx_mtop_has_pdbinfo(const gmx_mtop_t *mtop);
 186
 187 void pr_mtop(FILE *fp, int indent, const char *title, const gmx_mtop_t *mtop,
 188              gmx_bool bShowNumbers, gmx_bool bShowParameters);
 189 void pr_top(FILE *fp, int indent, const char *title, const t_topology *top,
 190             gmx_bool bShowNumbers, gmx_bool bShowParameters);
 191
 192 void cmp_top(FILE *fp, const t_topology *t1, const t_topology *t2, real ftol, real abstol);
 193 void cmp_groups(FILE *fp, const gmx_groups_t *g0, const gmx_groups_t *g1,
 194                 int natoms0, int natoms1);
 195
 196 #endif