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 #include "gromacs/utility/unique_cptr.h"
  50
  51 enum
  52 {
  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 /*! \brief Molecules type data: atoms, interactions and exclusions */
  62 struct gmx_moltype_t
  63 {
  64     gmx_moltype_t();
  65
  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     InteractionList ilist[F_NRE]; /**< Interaction list with local indices  */
  77     t_block         cgs;          /**< The charge groups                    */
  78     t_blocka        excls;        /**< The exclusions                       */
  79
  80     /* TODO: Change ilist to InteractionLists */
  81 };
  82
  83 /*! \brief Block of molecules of the same type, used in gmx_mtop_t */
  84 struct gmx_molblock_t
  85 {
  86     int                    type = -1; /**< The molecule type index in mtop.moltype  */
  87     int                    nmol = 0;  /**< The number of molecules in this block    */
  88     std::vector<gmx::RVec> posres_xA; /**< Position restraint coordinates for top A */
  89     std::vector<gmx::RVec> posres_xB; /**< Position restraint coordinates for top B */
  90 };
  91
  92 /*! \brief Indices for a gmx_molblock_t, derived from other gmx_mtop_t contents */
  93 struct MoleculeBlockIndices
  94 {
  95     int     numAtomsPerMolecule; /**< Number of atoms in a molecule in the block */
  96     int     globalAtomStart;     /**< Global atom index of the first atom in the block */
  97     int     globalAtomEnd;       /**< Global atom index + 1 of the last atom in the block */
  98     int     globalResidueStart;  /**< Global residue index of the first residue in the block */
  99     int     residueNumberStart;  /**< Residue numbers start from this value if the number of residues per molecule is <= maxres_renum */
 100     int     moleculeIndexStart;  /**< Global molecule indexing starts from this value */
 101 };
 102
 103 typedef struct gmx_groups_t
 104 {
 105     t_grps            grps[egcNR];  /* Groups of things                     */
 106     int               ngrpname;     /* Number of groupnames                 */
 107     char           ***grpname;      /* Names of the groups                  */
 108     int               ngrpnr[egcNR];
 109     unsigned char    *grpnr[egcNR]; /* Group numbers or NULL                */
 110 } gmx_groups_t;
 111
 112 /*! \brief
 113  * Returns group number of an input group for a given atom.
 114  *
 115  * Returns the group \p type for \p atom in \p group, or 0 if the
 116  * entries for all atoms in the group are 0 and the pointer is thus null.
 117  *
 118  * \param[in] group Group to check.
 119  * \param[in] type  Type of group to check.
 120  * \param[in] atom  Atom to check if it has an entry.
 121  */
 122 int getGroupType (const gmx_groups_t *group, int type, int atom);
 123
 124 /* The global, complete system topology struct, based on molecule types.
 125  * This structure should contain no data that is O(natoms) in memory.
 126  *
 127  * TODO: Find a solution for ensuring that the derived data is in sync
 128  *       with the primary data, possibly by converting to a class.
 129  */
 130 struct gmx_mtop_t //NOLINT(clang-analyzer-optin.performance.Padding)
 131 {
 132     gmx_mtop_t();
 133
 134     ~gmx_mtop_t();
 135
 136     char                            **name; /* Name of the topology                 */
 137     gmx_ffparams_t                    ffparams;
 138     std::vector<gmx_moltype_t>        moltype;
 139     std::vector<gmx_molblock_t>       molblock;
 140     gmx_bool                          bIntermolecularInteractions; /* Are there intermolecular
 141                                                                     * interactions?            */
 142     std::unique_ptr<InteractionLists> intermolecular_ilist;        /* List of intermolecular interactions
 143                                                                     * using system wide atom indices,
 144                                                                     * either NULL or size F_NRE           */
 145     int              natoms;
 146     int              maxres_renum;                                 /* Parameter for residue numbering      */
 147     int              maxresnr;                                     /* The maximum residue number in moltype */
 148     t_atomtypes      atomtypes;                                    /* Atomtype properties                  */
 149     gmx_groups_t     groups;                                       /* Groups of atoms for different purposes */
 150     t_symtab         symtab;                                       /* The symbol table                     */
 151     bool             haveMoleculeIndices;                          /* Tells whether we have valid molecule indices */
 152
 153     /* Derived data */
 154     std::vector<MoleculeBlockIndices> moleculeBlockIndices;  /* Indices for each molblock entry for fast lookup of atom properties */
 155 };
 156
 157 /* The mdrun node-local topology struct, completely written out */
 158 typedef struct gmx_localtop_t
 159 {
 160     t_idef        idef;         /* The interaction function definition  */
 161     t_atomtypes   atomtypes;    /* Atomtype properties                  */
 162     t_block       cgs;          /* The charge groups                    */
 163     t_blocka      excls;        /* The exclusions                       */
 164 } gmx_localtop_t;
 165
 166 /* The old topology struct, completely written out, used in analysis tools */
 167 typedef struct t_topology
 168 {
 169     char          **name;                        /* Name of the topology                 */
 170     t_idef          idef;                        /* The interaction function definition  */
 171     t_atoms         atoms;                       /* The atoms                            */
 172     t_atomtypes     atomtypes;                   /* Atomtype properties                  */
 173     t_block         cgs;                         /* The charge groups                    */
 174     t_block         mols;                        /* The molecules                        */
 175     gmx_bool        bIntermolecularInteractions; /* Inter.mol. int. ?   */
 176     t_blocka        excls;                       /* The exclusions                       */
 177     t_symtab        symtab;                      /* The symbol table                     */
 178 } t_topology;
 179
 180 void init_mtop(gmx_mtop_t *mtop);
 181 void init_top(t_topology *top);
 182 void done_gmx_groups_t(gmx_groups_t *g);
 183 void done_top(t_topology *top);
 184 // Frees both t_topology and gmx_mtop_t when the former has been created from
 185 // the latter.
 186 void done_top_mtop(t_topology *top, gmx_mtop_t *mtop);
 187 void done_localtop(gmx_localtop_t *top);
 188 void done_and_sfree_localtop(gmx_localtop_t *top);
 189
 190 bool gmx_mtop_has_masses(const gmx_mtop_t *mtop);
 191 bool gmx_mtop_has_charges(const gmx_mtop_t *mtop);
 192 bool gmx_mtop_has_perturbed_charges(const gmx_mtop_t &mtop);
 193 bool gmx_mtop_has_atomtypes(const gmx_mtop_t *mtop);
 194 bool gmx_mtop_has_pdbinfo(const gmx_mtop_t *mtop);
 195
 196 void pr_mtop(FILE *fp, int indent, const char *title, const gmx_mtop_t *mtop,
 197              gmx_bool bShowNumbers, gmx_bool bShowParameters);
 198 void pr_top(FILE *fp, int indent, const char *title, const t_topology *top,
 199             gmx_bool bShowNumbers, gmx_bool bShowParameters);
 200
 201 void cmp_top(FILE *fp, const t_topology *t1, const t_topology *t2, real ftol, real abstol);
 202 void cmp_groups(FILE *fp, const gmx_groups_t *g0, const gmx_groups_t *g1,
 203                 int natoms0, int natoms1);
 204
 205 //! Deleter for gmx_localtop_t, needed until it has a proper destructor.
 206 using ExpandedTopologyPtr = gmx::unique_cptr<gmx_localtop_t, done_and_sfree_localtop>;
 207
 208 #endif