src/gromacs/topology/topology.h

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  38 #ifndef GMX_TOPOLOGY_TOPOLOGY_H
  39 #define GMX_TOPOLOGY_TOPOLOGY_H
  40
  41 #include <cstdio>
  42
  43 #include <vector>
  44
  45 #include "gromacs/math/vectypes.h"
  46 #include "gromacs/topology/atoms.h"
  47 #include "gromacs/topology/block.h"
  48 #include "gromacs/topology/forcefieldparameters.h"
  49 #include "gromacs/topology/idef.h"
  50 #include "gromacs/topology/symtab.h"
  51 #include "gromacs/utility/enumerationhelpers.h"
  52 #include "gromacs/utility/listoflists.h"
  53 #include "gromacs/utility/unique_cptr.h"
  54
  55 enum class SimulationAtomGroupType : int
  56 {
  57     TemperatureCoupling,
  58     EnergyOutput,
  59     Acceleration,
  60     Freeze,
  61     User1,
  62     User2,
  63     MassCenterVelocityRemoval,
  64     CompressedPositionOutput,
  65     OrientationRestraintsFit,
  66     QuantumMechanics,
  67     Count
  68 };
  69
  70 //! Short strings used for describing atom groups in log and energy files
  71 const char* shortName(SimulationAtomGroupType type);
  72
  73 // const char *shortName(int type); // if necessary
  74
  75 /*! \brief Molecules type data: atoms, interactions and exclusions */
  76 struct gmx_moltype_t
  77 {
  78     gmx_moltype_t();
  79
  80     ~gmx_moltype_t();
  81
  82     /*! \brief Deleted copy assignment operator to avoid (not) freeing pointers */
  83     gmx_moltype_t& operator=(const gmx_moltype_t&) = delete;
  84
  85     /*! \brief Default copy constructor */
  86     gmx_moltype_t(const gmx_moltype_t&) = default;
  87
  88     char**                name;  /**< Name of the molecule type            */
  89     t_atoms               atoms; /**< The atoms in this molecule           */
  90     InteractionLists      ilist; /**< Interaction list with local indices  */
  91     gmx::ListOfLists<int> excls; /**< The exclusions                       */
  92 };
  93
  94 /*! \brief Block of molecules of the same type, used in gmx_mtop_t */
  95 struct gmx_molblock_t
  96 {
  97     int                    type = -1; /**< The molecule type index in mtop.moltype  */
  98     int                    nmol = 0;  /**< The number of molecules in this block    */
  99     std::vector<gmx::RVec> posres_xA; /**< Position restraint coordinates for top A */
 100     std::vector<gmx::RVec> posres_xB; /**< Position restraint coordinates for top B */
 101 };
 102
 103 /*! \brief Indices for a gmx_molblock_t, derived from other gmx_mtop_t contents */
 104 struct MoleculeBlockIndices
 105 {
 106     int numAtomsPerMolecule; /**< Number of atoms in a molecule in the block */
 107     int globalAtomStart;     /**< Global atom index of the first atom in the block */
 108     int globalAtomEnd;       /**< Global atom index + 1 of the last atom in the block */
 109     int globalResidueStart;  /**< Global residue index of the first residue in the block */
 110     int residueNumberStart; /**< Residue numbers start from this value if the number of residues per molecule is <= maxres_renum */
 111     int moleculeIndexStart; /**< Global molecule indexing starts from this value */
 112 };
 113
 114 /*! \brief Contains the simulation atom groups.
 115  *
 116  * Organized as containers for the different
 117  * SimulationAtomGroupTypes
 118  */
 119 struct SimulationGroups
 120 {
 121     // TODO: collect groups and groupNumbers in a struct for each group type
 122     //! Group numbers for each of the different SimulationAtomGroupType groups.
 123     gmx::EnumerationArray<SimulationAtomGroupType, AtomGroupIndices> groups;
 124     //! Names of groups, stored as pointer to the entries in the symbol table.
 125     std::vector<char**> groupNames;
 126     //! Indices into groups for each atom for each of the different SimulationAtomGroupType groups.
 127     gmx::EnumerationArray<SimulationAtomGroupType, std::vector<unsigned char>> groupNumbers;
 128
 129     /*! \brief
 130      * Number of atoms for which group numbers are stored for a single SimulationGroup.
 131      *
 132      * \param[in] group  The group type.
 133      */
 134     int numberOfGroupNumbers(SimulationAtomGroupType group) const
 135     {
 136         return static_cast<int>(groupNumbers[group].size());
 137     }
 138 };
 139
 140 /*! \brief
 141  * Returns group number of an input group for a given atom.
 142  *
 143  * Returns the group \p type for \p atom in \p group, or 0 if the
 144  * entries for all atoms in the group are 0 and the pointer is thus null.
 145  *
 146  * \param[in] group Group to check.
 147  * \param[in] type  Type of group to check.
 148  * \param[in] atom  Atom to check if it has an entry.
 149  */
 150 int getGroupType(const SimulationGroups& group, SimulationAtomGroupType type, int atom);
 151
 152 /* The global, complete system topology struct, based on molecule types.
 153  * This structure should contain no data that is O(natoms) in memory.
 154  *
 155  * TODO: Find a solution for ensuring that the derived data is in sync
 156  *       with the primary data, possibly by converting to a class.
 157  */
 158 struct gmx_mtop_t //NOLINT(clang-analyzer-optin.performance.Padding)
 159 {
 160     gmx_mtop_t();
 161
 162     ~gmx_mtop_t();
 163
 164     //! Name of the topology.
 165     char** name = nullptr;
 166     //! Force field parameters used.
 167     gmx_ffparams_t ffparams;
 168     //! Vector of different molecule types.
 169     std::vector<gmx_moltype_t> moltype;
 170     //! Vector of different molecule blocks.
 171     std::vector<gmx_molblock_t> molblock;
 172     //! Are there intermolecular interactions?
 173     bool bIntermolecularInteractions = false;
 174     /* \brief
 175      * List of intermolecular interactions using system wide
 176      * atom indices, either NULL or size F_NRE
 177      */
 178     std::unique_ptr<InteractionLists> intermolecular_ilist = nullptr;
 179     //! Number of global atoms.
 180     int natoms = 0;
 181     //! Atomtype properties
 182     t_atomtypes atomtypes;
 183     //! Groups of atoms for different purposes
 184     SimulationGroups groups;
 185     //! The legacy symbol table
 186     t_symtab symtab;
 187     //! Tells whether we have valid molecule indices
 188     bool haveMoleculeIndices = false;
 189     /*! \brief List of global atom indices of atoms between which
 190      * non-bonded interactions must be excluded.
 191      */
 192     std::vector<int> intermolecularExclusionGroup;
 193
 194     //! Maximum number of residues in molecule to trigger renumbering of residues
 195     int maxResiduesPerMoleculeToTriggerRenumber() const
 196     {
 197         return maxResiduesPerMoleculeToTriggerRenumber_;
 198     }
 199     //! Maximum residue number that is not renumbered.
 200     int maxResNumberNotRenumbered() const { return maxResNumberNotRenumbered_; }
 201     /*! \brief Finalize this data structure.
 202      *
 203      * Should be called after generating or reading mtop, to set some compute
 204      * intesive variables to avoid N^2 operations later on.
 205      *
 206      * \todo Move into a builder class, once available.
 207      */
 208     void finalize();
 209
 210     /* Derived data below */
 211     //! Indices for each molblock entry for fast lookup of atom properties
 212     std::vector<MoleculeBlockIndices> moleculeBlockIndices;
 213
 214 private:
 215     //! Build the molblock indices
 216     void buildMolblockIndices();
 217     //! Maximum number of residues in molecule to trigger renumbering of residues
 218     int maxResiduesPerMoleculeToTriggerRenumber_ = 0;
 219     //! The maximum residue number in moltype that is not renumbered
 220     int maxResNumberNotRenumbered_ = -1;
 221 };
 222
 223 /*! \brief
 224  * The fully written out topology for a domain over its lifetime
 225  *
 226  * Also used in some analysis code.
 227  */
 228 struct gmx_localtop_t
 229 {
 230     //! Constructor used for normal operation, manages own resources.
 231     gmx_localtop_t(const gmx_ffparams_t& ffparams);
 232
 233     //! The interaction function definition
 234     InteractionDefinitions idef;
 235     //! The exclusions
 236     gmx::ListOfLists<int> excls;
 237 };
 238
 239 /* The old topology struct, completely written out, used in analysis tools */
 240 typedef struct t_topology
 241 {
 242     char**      name;                        /* Name of the topology                 */
 243     t_idef      idef;                        /* The interaction function definition  */
 244     t_atoms     atoms;                       /* The atoms                            */
 245     t_atomtypes atomtypes;                   /* Atomtype properties                  */
 246     t_block     mols;                        /* The molecules                        */
 247     gmx_bool    bIntermolecularInteractions; /* Inter.mol. int. ?   */
 248     /* Note that the exclusions are not stored in t_topology */
 249     t_symtab symtab; /* The symbol table                     */
 250 } t_topology;
 251
 252 void init_top(t_topology* top);
 253 void done_top(t_topology* top);
 254 // Frees both t_topology and gmx_mtop_t when the former has been created from
 255 // the latter.
 256 void done_top_mtop(t_topology* top, gmx_mtop_t* mtop);
 257
 258 bool gmx_mtop_has_masses(const gmx_mtop_t* mtop);
 259 bool gmx_mtop_has_charges(const gmx_mtop_t* mtop);
 260 bool gmx_mtop_has_perturbed_charges(const gmx_mtop_t& mtop);
 261 bool gmx_mtop_has_atomtypes(const gmx_mtop_t* mtop);
 262 bool gmx_mtop_has_pdbinfo(const gmx_mtop_t* mtop);
 263
 264 void pr_mtop(FILE* fp, int indent, const char* title, const gmx_mtop_t* mtop, gmx_bool bShowNumbers, gmx_bool bShowParameters);
 265 void pr_top(FILE* fp, int indent, const char* title, const t_topology* top, gmx_bool bShowNumbers, gmx_bool bShowParameters);
 266
 267 /*! \brief Compare two mtop topologies.
 268  *
 269  * \param[in] fp File pointer to write to.
 270  * \param[in] mtop1 First topology to compare.
 271  * \param[in] mtop2 Second topology to compare.
 272  * \param[in] relativeTolerance Relative tolerance for comparison.
 273  * \param[in] absoluteTolerance Absolute tolerance for comparison.
 274  */
 275 void compareMtop(FILE* fp, const gmx_mtop_t& mtop1, const gmx_mtop_t& mtop2, real relativeTolerance, real absoluteTolerance);
 276
 277 /*! \brief Check perturbation parameters in topology.
 278  *
 279  * \param[in] fp File pointer to write to.
 280  * \param[in] mtop1 Topology to check perturbation parameters in.
 281  * \param[in] relativeTolerance Relative tolerance for comparison.
 282  * \param[in] absoluteTolerance Absolute tolerance for comparison.
 283  */
 284 void compareMtopAB(FILE* fp, const gmx_mtop_t& mtop1, real relativeTolerance, real absoluteTolerance);
 285
 286 /*! \brief Compare groups.
 287  *
 288  * \param[in] fp File pointer to write to.
 289  * \param[in] g0 First group for comparison.
 290  * \param[in] g1 Second group for comparison.
 291  * \param[in] natoms0 Number of atoms for first group.
 292  * \param[in] natoms1 Number of atoms for second group.
 293  */
 294 void compareAtomGroups(FILE* fp, const SimulationGroups& g0, const SimulationGroups& g1, int natoms0, int natoms1);
 295
 296 //! Typedef for gmx_localtop in analysis tools.
 297 using ExpandedTopologyPtr = std::unique_ptr<gmx_localtop_t>;
 298
 299 void copy_moltype(const gmx_moltype_t* src, gmx_moltype_t* dst);
 300
 301 #endif