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35 /*! \libinternal \file
37 * \brief This file makes declarations used for storing bitfields
38 * describing each atom so that other modules can efficiently process
44 #ifndef GMX_MDTYPES_ATOMINFO_H
45 #define GMX_MDTYPES_ATOMINFO_H
52 /*! \brief Constants whose bit describes a property of an atom in
53 * AtomInfoWithinMoleculeBlock.atomInfo.
55 * No bit should exceed 1 << 63, so that it fits into a 64-bit
58 * Since the tpx format support max 256 energy groups, we do the same
59 * here, reserving bits 0-7 for the energy-group ID.
62 static constexpr int64_t sc_atomInfo_FreeEnergyPerturbation = 1 << 15;
63 static constexpr int64_t sc_atomInfo_HasPerturbedChargeIn14Interaction = 1 << 16;
64 static constexpr int64_t sc_atomInfo_Exclusion = 1 << 17;
65 static constexpr int64_t sc_atomInfo_Constraint = 1 << 20;
66 static constexpr int64_t sc_atomInfo_Settle = 1 << 21;
67 static constexpr int64_t sc_atomInfo_BondCommunication = 1 << 22;
68 static constexpr int64_t sc_atomInfo_HasVdw = 1 << 23;
69 static constexpr int64_t sc_atomInfo_HasCharge = 1 << 24;
71 //! The first 8 bits are reserved for energy-group ID
72 static constexpr int64_t sc_atomInfo_EnergyGroupIdMask = 0b11111111;
74 /*! \brief Contains information about each atom in a molecule block of
75 * the global topology. */
76 struct AtomInfoWithinMoleculeBlock
78 //! Index within the system of the first atom in the molecule block
79 int indexOfFirstAtomInMoleculeBlock = 0;
80 //! Index within the system of the last atom in the molecule block
81 int indexOfLastAtomInMoleculeBlock = 0;
82 /*! \brief Atom info for each atom in the block.
84 * The typical case is that all atoms are identical for each
85 * molecule of the block, and if so this vector has size equal to
86 * the number of atoms in the molecule.
88 * An example of an atypical case is QM/MM, where multiple
89 * molecules might be present and different molecules have
90 * different atoms within any one QM group or region. Now there are
91 * multiple kinds of molecules with the same connectivity, so we simply
92 * write out the atom info for the entire molecule block. Then the
93 * size equals the product of the number of atoms in the
94 * molecule and the number of molecules.
96 * The vector needs to be indexed accordingly.
98 std::vector<int64_t> atomInfo;