src/gromacs/swap/swapcoords.h

   1 /*
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  36 /*! \libinternal
  37  * \defgroup module_swap "Computational Electrophysiology" position swapping (swap)
  38  * \ingroup group_mdrun
  39  * \brief
  40  * Implements the "Computational Electrophysiology" protocol.
  41  *
  42  * \author Carsten Kutzner <ckutzne@gwdg.de>
  43  */
  44 /*! \libinternal \file
  45  * \brief
  46  * The "Computational Electrophysiology" protocol for ion/water position swapping.
  47  *
  48  * \author Carsten Kutzner <ckutzne@gwdg.de>
  49  * \inlibraryapi
  50  * \ingroup module_swap
  51  */
  52 #ifndef GMX_SWAP_SWAPCOORDS_H
  53 #define GMX_SWAP_SWAPCOORDS_H
  54
  55 #include "gromacs/legacyheaders/typedefs.h"
  56 #include "gromacs/legacyheaders/types/commrec.h"
  57 #include "gromacs/timing/wallcycle.h"
  58
  59 #ifdef __cplusplus
  60 extern "C" {
  61 #endif
  62
  63
  64 /*! \brief Initialize ion / water position swapping ("Computational Electrophysiology").
  65  *
  66  * This routine does the memory allocation for various helper arrays, opens
  67  * the output file, sets up swap data checkpoint writing, etc.
  68  *
  69  * \param[in] fplog         General output file, normally md.log.
  70  * \param[in] bVerbose      Should we be quiet or verbose?
  71  * \param[in] ir            Structure containing MD input parameters, among those
  72  *                          also the structure needed for position swapping.
  73  * \param[in] fn            Output file name for swap data.
  74  * \param[in] mtop          Molecular topology.
  75  * \param[in] x             The initial positions of all particles.
  76  * \param[in] box           The simulation box.
  77  * \param[in] swapstate     Swap-related data that is read from or written to checkpoint.
  78  * \param[in] cr            Pointer to MPI communication data.
  79  * \param[in] oenv          Needed to open the swap output XVGR file.
  80  * \param[in] Flags         Flags passed over from main, used to determine
  81  *                          whether we are doing a rerun, appending, etc.
  82  */
  83 extern void init_swapcoords(
  84         FILE              *fplog,
  85         gmx_bool           bVerbose,
  86         t_inputrec        *ir,
  87         const char        *fn,
  88         gmx_mtop_t        *mtop,
  89         rvec               x[],
  90         matrix             box,
  91         swapstate_t       *swapstate,
  92         t_commrec         *cr,
  93         const output_env_t oenv,
  94         unsigned long      Flags);
  95
  96
  97 /*! \brief Make a selection of the home atoms for the swap groups. These are
  98  * the ions, the water, and the channels. This routine should be called at every
  99  * domain decomposition.
 100  *
 101  * \param[in] dd            Structure containing domain decomposition data.
 102  * \param[in] si_pub        Pointer to the swap data structure.
 103  */
 104 extern void dd_make_local_swap_groups(gmx_domdec_t *dd, t_swapcoords *si_pub);
 105
 106
 107 /*! \brief "Computational Electrophysiology" main routine within MD loop.
 108  *
 109  * \param[in] cr       Pointer to MPI communication data.
 110  * \param[in] step     The number of the MD time step.
 111  * \param[in] t        The time.
 112  * \param[in] ir       Structure containing MD input parameters, among those
 113  *                     also the structure needed for position swapping.
 114  * \param[in] wcycle   Count wallcycles of swap routines for diagnostic output.
 115  * \param[in] x        Positions of home particles this node owns.
 116  * \param[in] box      The simulation box.
 117  * \param[in] mtop     Molecular topology.
 118  * \param[in] bVerbose Should we be quiet or verbose?
 119  * \param[in] bRerun   Are we doing a rerun?
 120  *
 121  * \returns Whether at least one pair of molecules was swapped.
 122  */
 123 extern gmx_bool do_swapcoords(
 124         t_commrec        *cr,
 125         gmx_int64_t       step,
 126         double            t,
 127         t_inputrec       *ir,
 128         gmx_wallcycle_t   wcycle,
 129         rvec              x[],
 130         matrix            box,
 131         gmx_mtop_t       *mtop,
 132         gmx_bool          bVerbose,
 133         gmx_bool          bRerun);
 134
 135
 136 #ifdef __cplusplus
 137 }
 138 #endif
 139
 140 #endif