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38 * This file declares functions for setting up a benchmark system
40 * \author Berk Hess <hess@kth.se>
41 * \ingroup module_nbnxm
44 #ifndef GMX_NBNXN_BENCH_SYSTEM_H
45 #define GMX_NBNXN_BENCH_SYSTEM_H
49 #include "gromacs/math/vectypes.h"
50 #include "gromacs/mdtypes/forcerec.h"
51 #include "gromacs/topology/block.h"
52 #include "gromacs/utility/smalloc.h"
57 //! Description of the system used for benchmarking.
58 struct BenchmarkSystem
60 /*! \brief Constructor
62 * Generates a benchmark system of size \p multiplicationFactor
63 * times the base size by stacking cubic boxes of 1000 water molecules
64 * with 3000 atoms total.
66 * \param[in] multiplicationFactor Should be a power of 2, is checked
68 BenchmarkSystem(int multiplicationFactor);
70 //! Number of different atom types in test system.
72 //! Storage for parameters for short range interactions.
73 std::vector<real> nonbondedParameters;
74 //! Storage for atom type parameters.
75 std::vector<int> atomTypes;
76 //! Storage for atom partial charges.
77 std::vector<real> charges;
78 //! Atom info where all atoms are marked to have Van der Waals interactions
79 std::vector<int> atomInfoAllVdw;
80 //! Atom info where only oxygen atoms are marked to have Van der Waals interactions
81 std::vector<int> atomInfoOxygenVdw;
82 //! Information about exclusions.
84 //! Storage for atom positions.
85 std::vector<gmx::RVec> coordinates;
86 //! System simulation box.
88 //! Forcerec with only the entries used in the benchmark set