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35 #ifndef GMX_MDLIB_MDSETUP_H
36 #define GMX_MDLIB_MDSETUP_H
38 struct bonded_threading_t
;
39 struct gmx_localtop_t
;
53 /*! \brief Sets atom data for several MD algorithms
55 * Most MD algorithms require two different setup calls:
56 * one for initialization and parameter setting and one for atom data setup.
57 * This routine sets the atom data for the (locally available) atoms.
58 * This is called at the start of serial runs and during domain decomposition.
60 * \param[in] cr Communication record
61 * \param[in] ir Input parameter record
62 * \param[in] top_global The global topology
63 * \param[in,out] top The local topology
64 * \param[in,out] fr The force calculation parameter/data record
65 * \param[out] graph The molecular graph, can be NULL
66 * \param[out] mdAtoms The MD atom data
67 * \param[in,out] vsite The virtual site data, can be NULL
68 * \param[in,out] shellfc The shell/flexible-constraint data, can be NULL
70 void mdAlgorithmsSetupAtomData(const t_commrec
*cr
,
72 const gmx_mtop_t
*top_global
,
76 gmx::MDAtoms
*mdAtoms
,
78 gmx_shellfc_t
*shellfc
);
80 /*! \brief Clean up after MD algorithms.
82 * \param[out] bt Manages the bonded threading.
83 * \param[out] top The local topology
85 void mdAlgorithmsTearDownAtomData(bonded_threading_t
*bt
,