src/gromacs/mdlib/mdsetup.h

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  35 #ifndef GMX_MDLIB_MDSETUP_H
  36 #define GMX_MDLIB_MDSETUP_H
  37
  38 struct bonded_threading_t;
  39 struct gmx_localtop_t;
  40 struct gmx_mtop_t;
  41 struct gmx_shellfc_t;
  42 struct gmx_vsite_t;
  43 struct t_commrec;
  44 struct t_forcerec;
  45 struct t_graph;
  46 struct t_inputrec;
  47
  48 namespace gmx
  49 {
  50 class MDAtoms;
  51 }
  52
  53 /*! \brief Sets atom data for several MD algorithms
  54  *
  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.
  59  *
  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
  69  */
  70 void mdAlgorithmsSetupAtomData(const t_commrec   *cr,
  71                                const t_inputrec  *ir,
  72                                const gmx_mtop_t  *top_global,
  73                                gmx_localtop_t    *top,
  74                                t_forcerec        *fr,
  75                                t_graph          **graph,
  76                                gmx::MDAtoms      *mdAtoms,
  77                                gmx_vsite_t       *vsite,
  78                                gmx_shellfc_t     *shellfc);
  79
  80 /*! \brief Clean up after MD algorithms.
  81  *
  82  * \param[out] bt            Manages the bonded threading.
  83  * \param[out] top           The local topology
  84  */
  85 void mdAlgorithmsTearDownAtomData(bonded_threading_t *bt,
  86                                   gmx_localtop_t     *top);
  87
  88 #endif