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/forcefieldparameters.h"
  48 #include "gromacs/topology/idef.h"
  49 #include "gromacs/topology/symtab.h"
  50 #include "gromacs/utility/enumerationhelpers.h"
  51 #include "gromacs/utility/unique_cptr.h"
  52
  53 enum class SimulationAtomGroupType : int
  54 {
  55     TemperatureCoupling,
  56     EnergyOutput,
  57     Acceleration,
  58     Freeze,
  59     User1,
  60     User2,
  61     MassCenterVelocityRemoval,
  62     CompressedPositionOutput,
  63     OrientationRestraintsFit,
  64     QuantumMechanics,
  65     Count
  66 };
  67
  68 //! Short strings used for describing atom groups in log and energy files
  69 const char *shortName(SimulationAtomGroupType type);
  70
  71 //const char *shortName(int type); // if necessary
  72
  73 /*! \brief Molecules type data: atoms, interactions and exclusions */
  74 struct gmx_moltype_t
  75 {
  76     gmx_moltype_t();
  77
  78     ~gmx_moltype_t();
  79
  80     /*! \brief Deleted copy assignment operator to avoid (not) freeing pointers */
  81     gmx_moltype_t &operator=(const gmx_moltype_t &) = delete;
  82
  83     /*! \brief Default copy constructor */
  84     gmx_moltype_t(const gmx_moltype_t &) = default;
  85
  86     char              **name;   /**< Name of the molecule type            */
  87     t_atoms             atoms;  /**< The atoms in this molecule           */
  88     InteractionLists    ilist;  /**< Interaction list with local indices  */
  89     t_block             cgs;    /**< The charge groups                    */
  90     t_blocka            excls;  /**< The exclusions                       */
  91 };
  92
  93 /*! \brief Block of molecules of the same type, used in gmx_mtop_t */
  94 struct gmx_molblock_t
  95 {
  96     int                    type = -1; /**< The molecule type index in mtop.moltype  */
  97     int                    nmol = 0;  /**< The number of molecules in this block    */
  98     std::vector<gmx::RVec> posres_xA; /**< Position restraint coordinates for top A */
  99     std::vector<gmx::RVec> posres_xB; /**< Position restraint coordinates for top B */
 100 };
 101
 102 /*! \brief Indices for a gmx_molblock_t, derived from other gmx_mtop_t contents */
 103 struct MoleculeBlockIndices
 104 {
 105     int     numAtomsPerMolecule; /**< Number of atoms in a molecule in the block */
 106     int     globalAtomStart;     /**< Global atom index of the first atom in the block */
 107     int     globalAtomEnd;       /**< Global atom index + 1 of the last atom in the block */
 108     int     globalResidueStart;  /**< Global residue index of the first residue in the block */
 109     int     residueNumberStart;  /**< Residue numbers start from this value if the number of residues per molecule is <= maxres_renum */
 110     int     moleculeIndexStart;  /**< Global molecule indexing starts from this value */
 111 };
 112
 113 /*! \brief Contains the simulation atom groups.
 114  *
 115  * Organized as containers for the different
 116  * SimulationAtomGroupTypes
 117  */
 118 struct SimulationGroups
 119 {
 120     //! Groups of particles
 121     gmx::EnumerationArray<SimulationAtomGroupType, AtomGroupIndices>                     groups;
 122     //! Names of groups, stored as pointer to the entries in the symbol table.
 123     std::vector<char **>                                                                 groupNames;
 124     //! Group numbers for the different SimulationAtomGroupType groups.
 125     gmx::EnumerationArray < SimulationAtomGroupType, std::vector < unsigned char>> groupNumbers;
 126
 127     /*! \brief
 128      * Number of group numbers for a single SimulationGroup.
 129      *
 130      * \param[in] group Integer value for the group type.
 131      */
 132     int numberOfGroupNumbers(SimulationAtomGroupType group) const { return gmx::ssize(groupNumbers[group]); }
 133 };
 134
 135 /*! \brief
 136  * Returns group number of an input group for a given atom.
 137  *
 138  * Returns the group \p type for \p atom in \p group, or 0 if the
 139  * entries for all atoms in the group are 0 and the pointer is thus null.
 140  *
 141  * \param[in] group Group to check.
 142  * \param[in] type  Type of group to check.
 143  * \param[in] atom  Atom to check if it has an entry.
 144  */
 145 int getGroupType (const SimulationGroups &group, SimulationAtomGroupType type, int atom);
 146
 147 /* The global, complete system topology struct, based on molecule types.
 148  * This structure should contain no data that is O(natoms) in memory.
 149  *
 150  * TODO: Find a solution for ensuring that the derived data is in sync
 151  *       with the primary data, possibly by converting to a class.
 152  */
 153 struct gmx_mtop_t //NOLINT(clang-analyzer-optin.performance.Padding)
 154 {
 155     gmx_mtop_t();
 156
 157     ~gmx_mtop_t();
 158
 159     //! Name of the topology.
 160     char                            **name = nullptr;
 161     //! Force field parameters used.
 162     gmx_ffparams_t                    ffparams;
 163     //! Vector of different molecule types.
 164     std::vector<gmx_moltype_t>        moltype;
 165     //! Vector of different molecule blocks.
 166     std::vector<gmx_molblock_t>       molblock;
 167     //! Are there intermolecular interactions?
 168     bool                              bIntermolecularInteractions = false;
 169     /* \brief
 170      * List of intermolecular interactions using system wide
 171      * atom indices, either NULL or size F_NRE
 172      */
 173     std::unique_ptr<InteractionLists>        intermolecular_ilist = nullptr;
 174     //! Number of global atoms.
 175     int                                      natoms = 0;
 176     //! Parameter for residue numbering.
 177     int                                      maxres_renum = 0;
 178     //! The maximum residue number in moltype
 179     int                                      maxresnr = -1;
 180     //! Atomtype properties
 181     t_atomtypes                              atomtypes;
 182     //! Groups of atoms for different purposes
 183     SimulationGroups                         groups;
 184     //! The symbol table
 185     t_symtab                                 symtab;
 186     //! Tells whether we have valid molecule indices
 187     bool                                     haveMoleculeIndices = false;
 188     /*! \brief List of global atom indices of atoms between which
 189      * non-bonded interactions must be excluded.
 190      */
 191     std::vector<int>                  intermolecularExclusionGroup;
 192
 193     /* Derived data  below */
 194     //! Indices for each molblock entry for fast lookup of atom properties
 195     std::vector<MoleculeBlockIndices> moleculeBlockIndices;
 196 };
 197
 198 /*! \brief
 199  * The fully written out topology for a domain over its lifetime
 200  *
 201  * Also used in some analysis code.
 202  */
 203 struct gmx_localtop_t
 204 {
 205     //! Constructor used for normal operation, manages own resources.
 206     gmx_localtop_t();
 207
 208     ~gmx_localtop_t();
 209
 210     //! The interaction function definition
 211     t_idef        idef;
 212     //! Atomtype properties
 213     t_atomtypes   atomtypes;
 214     //! The exclusions
 215     t_blocka      excls;
 216     //! Flag for domain decomposition so we don't free already freed memory.
 217     bool          useInDomainDecomp_ = false;
 218 };
 219
 220 /* The old topology struct, completely written out, used in analysis tools */
 221 typedef struct t_topology
 222 {
 223     char          **name;                        /* Name of the topology                 */
 224     t_idef          idef;                        /* The interaction function definition  */
 225     t_atoms         atoms;                       /* The atoms                            */
 226     t_atomtypes     atomtypes;                   /* Atomtype properties                  */
 227     t_block         cgs;                         /* The charge groups                    */
 228     t_block         mols;                        /* The molecules                        */
 229     gmx_bool        bIntermolecularInteractions; /* Inter.mol. int. ?   */
 230     t_blocka        excls;                       /* The exclusions                       */
 231     t_symtab        symtab;                      /* The symbol table                     */
 232 } t_topology;
 233
 234 void init_top(t_topology *top);
 235 void done_top(t_topology *top);
 236 // Frees both t_topology and gmx_mtop_t when the former has been created from
 237 // the latter.
 238 void done_top_mtop(t_topology *top, gmx_mtop_t *mtop);
 239
 240 bool gmx_mtop_has_masses(const gmx_mtop_t *mtop);
 241 bool gmx_mtop_has_charges(const gmx_mtop_t *mtop);
 242 bool gmx_mtop_has_perturbed_charges(const gmx_mtop_t &mtop);
 243 bool gmx_mtop_has_atomtypes(const gmx_mtop_t *mtop);
 244 bool gmx_mtop_has_pdbinfo(const gmx_mtop_t *mtop);
 245
 246 void pr_mtop(FILE *fp, int indent, const char *title, const gmx_mtop_t *mtop,
 247              gmx_bool bShowNumbers, gmx_bool bShowParameters);
 248 void pr_top(FILE *fp, int indent, const char *title, const t_topology *top,
 249             gmx_bool bShowNumbers, gmx_bool bShowParameters);
 250
 251 /*! \brief Compare two mtop topologies.
 252  *
 253  * \param[in] fp File pointer to write to.
 254  * \param[in] mtop1 First topology to compare.
 255  * \param[in] mtop2 Second topology to compare.
 256  * \param[in] relativeTolerance Relative tolerance for comparison.
 257  * \param[in] absoluteTolerance Absolute tolerance for comparison.
 258  */
 259 void compareMtop(FILE *fp, const gmx_mtop_t &mtop1, const gmx_mtop_t &mtop2, real relativeTolerance, real absoluteTolerance);
 260
 261 /*! \brief Check perturbation parameters in topology.
 262  *
 263  * \param[in] fp File pointer to write to.
 264  * \param[in] mtop1 Topology to check perturbation parameters in.
 265  * \param[in] relativeTolerance Relative tolerance for comparison.
 266  * \param[in] absoluteTolerance Absolute tolerance for comparison.
 267  */
 268 void compareMtopAB(FILE *fp, const gmx_mtop_t &mtop1, real relativeTolerance, real absoluteTolerance);
 269
 270 /*! \brief Compare groups.
 271  *
 272  * \param[in] fp File pointer to write to.
 273  * \param[in] g0 First group for comparison.
 274  * \param[in] g1 Second group for comparison.
 275  * \param[in] natoms0 Number of atoms for first group.
 276  * \param[in] natoms1 Number of atoms for second group.
 277  */
 278 void compareAtomGroups(FILE *fp, const SimulationGroups &g0, const SimulationGroups &g1,
 279                        int natoms0, int natoms1);
 280
 281 //! Typedef for gmx_localtop in analysis tools.
 282 using ExpandedTopologyPtr = std::unique_ptr<gmx_localtop_t>;
 283
 284 void copy_moltype(const gmx_moltype_t *src, gmx_moltype_t *dst);
 285
 286 #endif