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     //! Groups of particles
 122     gmx::EnumerationArray<SimulationAtomGroupType, AtomGroupIndices> groups;
 123     //! Names of groups, stored as pointer to the entries in the symbol table.
 124     std::vector<char**> groupNames;
 125     //! Group numbers for the different SimulationAtomGroupType groups.
 126     gmx::EnumerationArray<SimulationAtomGroupType, std::vector<unsigned char>> groupNumbers;
 127
 128     /*! \brief
 129      * Number of group numbers for a single SimulationGroup.
 130      *
 131      * \param[in] group Integer value for the group type.
 132      */
 133     int numberOfGroupNumbers(SimulationAtomGroupType group) const
 134     {
 135         return static_cast<int>(groupNumbers[group].size());
 136     }
 137 };
 138
 139 /*! \brief
 140  * Returns group number of an input group for a given atom.
 141  *
 142  * Returns the group \p type for \p atom in \p group, or 0 if the
 143  * entries for all atoms in the group are 0 and the pointer is thus null.
 144  *
 145  * \param[in] group Group to check.
 146  * \param[in] type  Type of group to check.
 147  * \param[in] atom  Atom to check if it has an entry.
 148  */
 149 int getGroupType(const SimulationGroups& group, SimulationAtomGroupType type, int atom);
 150
 151 /* The global, complete system topology struct, based on molecule types.
 152  * This structure should contain no data that is O(natoms) in memory.
 153  *
 154  * TODO: Find a solution for ensuring that the derived data is in sync
 155  *       with the primary data, possibly by converting to a class.
 156  */
 157 struct gmx_mtop_t //NOLINT(clang-analyzer-optin.performance.Padding)
 158 {
 159     gmx_mtop_t();
 160
 161     ~gmx_mtop_t();
 162
 163     //! Name of the topology.
 164     char** name = nullptr;
 165     //! Force field parameters used.
 166     gmx_ffparams_t ffparams;
 167     //! Vector of different molecule types.
 168     std::vector<gmx_moltype_t> moltype;
 169     //! Vector of different molecule blocks.
 170     std::vector<gmx_molblock_t> molblock;
 171     //! Are there intermolecular interactions?
 172     bool bIntermolecularInteractions = false;
 173     /* \brief
 174      * List of intermolecular interactions using system wide
 175      * atom indices, either NULL or size F_NRE
 176      */
 177     std::unique_ptr<InteractionLists> intermolecular_ilist = nullptr;
 178     //! Number of global atoms.
 179     int natoms = 0;
 180     //! Parameter for residue numbering.
 181     int maxres_renum = 0;
 182     //! The maximum residue number in moltype
 183     int maxresnr = -1;
 184     //! Atomtype properties
 185     t_atomtypes atomtypes;
 186     //! Groups of atoms for different purposes
 187     SimulationGroups groups;
 188     //! The legacy symbol table
 189     t_symtab symtab;
 190     //! Tells whether we have valid molecule indices
 191     bool haveMoleculeIndices = false;
 192     /*! \brief List of global atom indices of atoms between which
 193      * non-bonded interactions must be excluded.
 194      */
 195     std::vector<int> intermolecularExclusionGroup;
 196
 197     /* Derived data  below */
 198     //! Indices for each molblock entry for fast lookup of atom properties
 199     std::vector<MoleculeBlockIndices> moleculeBlockIndices;
 200 };
 201
 202 /*! \brief
 203  * The fully written out topology for a domain over its lifetime
 204  *
 205  * Also used in some analysis code.
 206  */
 207 struct gmx_localtop_t
 208 {
 209     //! Constructor used for normal operation, manages own resources.
 210     gmx_localtop_t(const gmx_ffparams_t& ffparams);
 211
 212     //! The interaction function definition
 213     InteractionDefinitions idef;
 214     //! The exclusions
 215     gmx::ListOfLists<int> excls;
 216 };
 217
 218 /* The old topology struct, completely written out, used in analysis tools */
 219 typedef struct t_topology
 220 {
 221     char**      name;                        /* Name of the topology                 */
 222     t_idef      idef;                        /* The interaction function definition  */
 223     t_atoms     atoms;                       /* The atoms                            */
 224     t_atomtypes atomtypes;                   /* Atomtype properties                  */
 225     t_block     mols;                        /* The molecules                        */
 226     gmx_bool    bIntermolecularInteractions; /* Inter.mol. int. ?   */
 227     /* Note that the exclusions are not stored in t_topology */
 228     t_symtab symtab; /* The symbol table                     */
 229 } t_topology;
 230
 231 void init_top(t_topology* top);
 232 void done_top(t_topology* top);
 233 // Frees both t_topology and gmx_mtop_t when the former has been created from
 234 // the latter.
 235 void done_top_mtop(t_topology* top, gmx_mtop_t* mtop);
 236
 237 bool gmx_mtop_has_masses(const gmx_mtop_t* mtop);
 238 bool gmx_mtop_has_charges(const gmx_mtop_t* mtop);
 239 bool gmx_mtop_has_perturbed_charges(const gmx_mtop_t& mtop);
 240 bool gmx_mtop_has_atomtypes(const gmx_mtop_t* mtop);
 241 bool gmx_mtop_has_pdbinfo(const gmx_mtop_t* mtop);
 242
 243 void pr_mtop(FILE* fp, int indent, const char* title, const gmx_mtop_t* mtop, gmx_bool bShowNumbers, gmx_bool bShowParameters);
 244 void pr_top(FILE* fp, int indent, const char* title, const t_topology* top, gmx_bool bShowNumbers, gmx_bool bShowParameters);
 245
 246 /*! \brief Compare two mtop topologies.
 247  *
 248  * \param[in] fp File pointer to write to.
 249  * \param[in] mtop1 First topology to compare.
 250  * \param[in] mtop2 Second topology to compare.
 251  * \param[in] relativeTolerance Relative tolerance for comparison.
 252  * \param[in] absoluteTolerance Absolute tolerance for comparison.
 253  */
 254 void compareMtop(FILE* fp, const gmx_mtop_t& mtop1, const gmx_mtop_t& mtop2, real relativeTolerance, real absoluteTolerance);
 255
 256 /*! \brief Check perturbation parameters in topology.
 257  *
 258  * \param[in] fp File pointer to write to.
 259  * \param[in] mtop1 Topology to check perturbation parameters in.
 260  * \param[in] relativeTolerance Relative tolerance for comparison.
 261  * \param[in] absoluteTolerance Absolute tolerance for comparison.
 262  */
 263 void compareMtopAB(FILE* fp, const gmx_mtop_t& mtop1, real relativeTolerance, real absoluteTolerance);
 264
 265 /*! \brief Compare groups.
 266  *
 267  * \param[in] fp File pointer to write to.
 268  * \param[in] g0 First group for comparison.
 269  * \param[in] g1 Second group for comparison.
 270  * \param[in] natoms0 Number of atoms for first group.
 271  * \param[in] natoms1 Number of atoms for second group.
 272  */
 273 void compareAtomGroups(FILE* fp, const SimulationGroups& g0, const SimulationGroups& g1, int natoms0, int natoms1);
 274
 275 //! Typedef for gmx_localtop in analysis tools.
 276 using ExpandedTopologyPtr = std::unique_ptr<gmx_localtop_t>;
 277
 278 void copy_moltype(const gmx_moltype_t* src, gmx_moltype_t* dst);
 279
 280 #endif